@article {pmid40273425,
year = {2025},
author = {Bonacolta, AM and Weiler, BA and Grimes, CJ and Trznadel, M and Vermeij, MJA and Keeling, PJ and Del Campo, J},
title = {Fireworms are a reservoir and potential vector for coral-infecting apicomplexans.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf078},
pmid = {40273425},
issn = {1751-7370},
abstract = {Corals (Cnidaria; Anthozoa) play critical roles as habitat-forming species with a wide range, from warm shallow-water tropical coral reefs to cold-water ecosystems. They also represent a complex ecosystem as intricate holobionts made up of microbes from all domains of the Tree of Life that can play significant roles in host health and fitness. The corallicolids are a clade of apicomplexans that infect a wide variety of anthozoans worldwide and can influence the thermal tolerance of habitat-forming corals. Despite their potentially important impacts on reef ecosystems, much of the basic biology and ecology of corallicolids remains unclear. Apicomplexans often have a closed life cycle, with minimal environmental exposure and sometimes multiple hosts. Corallicolids have only been documented in anthozoan hosts, with no known secondary/reservoir hosts or vectors. Here, we show that abundant corallicolid sequences are recovered from bearded fireworms (Hermodice carunculata) in tropical reef habitats off Curaçao and that they are distinct from corallicolids infecting the corals on which the fireworms were feeding at the time of their collection. These data are consistent with a fireworm-specific corallicolid infection, not merely a byproduct of the worms feeding on infected corals. Furthermore, we suggest that H. carunculata is potentially a vector moving corallicolids among coral hosts through its feces. These findings not only expand our understanding of the ecological interactions within coral reef ecosystems but also highlight the potential role of host-associated parasites in shaping the resilience of reef habitats.},
}

@article {pmid40269580,
year = {2025},
author = {Ahrar, M and Glenn, L and Held, M and Jackson, A and Kus, K and Hurst, GDD and Chrostek, E},
title = {Development of Antisense Tools to Study Bodo saltans and Its Intracellular Symbiont.},
journal = {MicrobiologyOpen},
volume = {14},
number = {2},
pages = {e70018},
doi = {10.1002/mbo3.70018},
pmid = {40269580},
issn = {2045-8827},
support = {//This study was funded by Gordon and Betty Moore Foundation's Symbiosis in Aquatic Systems Initiative, Grant ID: #9357 (10.37807/GBMF9357), awarded to G.H., E.C., and A.J./ ; },
mesh = {*Symbiosis/genetics ; Animals ; *Kinetoplastida/microbiology/genetics/physiology ; *RNA, Antisense/genetics ; },
abstract = {Obligate symbioses are common in nature and present a particular challenge for functional genetic analysis. In many cases, the host is a non-model species with poor tools for genetic manipulation, and the symbiont cannot be cultured or its gene expression manipulated to investigate function. Here, we investigated the potential for using antisense inhibition to analyze host and symbiont gene function within an obligate aquatic symbiosis. We focused on the kinetoplastid host Bodo saltans and its bacterial symbiont, Candidatus Bodocaedibacter vickermanii, a member of Rickettsiales. We conclude that antisense inhibition is not feasible in the Bodo saltans and its symbiont, as the holobiont feeds on the antisense molecules-and increases in numbers-upon treatment with the antisense construct. Although our approach has proven unsuccessful, we have developed an array of protocols that can be used to study the biology of this microeukaryote and its microbial associates.},
}

*Symbiosis/genetics
Animals
*Kinetoplastida/microbiology/genetics/physiology
*RNA, Antisense/genetics

@article {pmid40268344,
year = {2025},
author = {Förster, F and Sauzéat, L and Ferrier-Pagès, C and Reynaud, S and Sheldrake, TE},
title = {Redox-sensitive δ65Cu isotopic fractionation in the tissue of the scleractinian coral Stylophora pistillata: A biomarker of holobiont photophysiology following volcanic ash exposure.},
journal = {Metallomics : integrated biometal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/mtomcs/mfaf011},
pmid = {40268344},
issn = {1756-591X},
abstract = {Volcanic ash is a significant source of micronutrients including iron (Fe), copper (Cu), and zinc (Zn) in oligotrophic tropical waters. These bioactive metals enhance primary productivity, influencing local and global biogeochemical cycles. This study e10xplores how volcanic ash exposure affects trace metal uptake and photophysiological response, and how redox-sensitive metal stable isotope measurements in the tissues of the scleractinian coral Stylophora pistillata can provide crucial information on coral health. Controlled coral culture experiments were conducted in which coral nubbins were exposed to varying intensity and duration of volcanic ash. Throughout the experiment, coral symbionts showed enhanced photosynthetic performance irrespective of intensity or duration of ash exposure. Stable isotopes, such as δ[65]Cu and δ56Fe, in the coral tissue are marked by systematic variations, not associated with intensity or duration of ash exposure. Instead, we suggest biologically modulated redox-sensitive fractionation associated with ash exposure, linked to the coral host's oxidative stress state. This is evidenced by significant correlations between δ[65]Cu in coral hosts and photophysiology, with lighter Cu isotope ratios associated with higher photosynthetic performances. Hence, we propose that δ65Cu, and more generally redox-sensitive isotopic ratios (i.e. δ56Fe), in coral hosts serve as an indicator of the physiological state of symbiotic corals.},
}

@article {pmid40266833,
year = {2025},
author = {Huang, YH and Wang, M and Chang, XP and Ke, YL and Li, ZQ},
title = {Comparison Between Worker and Soldier Transcriptomes of Termite Neotermes binovatus Reveals Caste Specialization of Host-Flagellate Symbiotic System.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030325},
pmid = {40266833},
issn = {2075-4450},
support = {2023A1515011424//Natural Science Foundation of Guangdong Province of China/ ; },
abstract = {Termites are eusocial insects with functionally specialized workers and soldiers, both sharing the same genotype. Additionally, lower termites host flagellates in their hindguts that assist in wood digestion. However, worker-biased and soldier-biased gene expression patterns of the host-flagellate symbiotic system remain underexplored in most taxonomic groups. In this study, we sequenced high-depth transcriptomes from the workers and soldiers of a lower termite, Neotermes binovatus (Kalotermitidae), to investigate the differentially expressed termite transcripts, flagellate transcript abundance, and co-expression patterns of the host-flagellate transcript pairs in both castes. The worker-biased transcripts were enriched in functions related to cuticle development, nervous system regulation, pheromone biosynthesis, and metabolism, whereas the soldier-biased transcripts were predominantly involved in muscle development and kinesis, body morphogenesis, protein modification, and aggression. Flagellate transcripts from the orders Cristamonadida, Trichomonadida, Tritrichomonadida, and Oxymonadida were identified in both workers and soldiers, with the abundance of most flagellate transcripts tending to be higher in workers than in soldiers. Furthermore, we observed a much larger number of strong co-expression correlations between the termite and flagellate transcripts in workers than in soldiers, suggesting the possibility that soldiers depend more on food processed by worker holobionts than on their own symbiotic system. This research provides insights into the functional specialization of the host-flagellate symbiotic system in the worker and soldier castes of termites, supporting the workers' roles in nest maintenance, preliminary food processing, and communication, while emphasizing the defensive role of soldiers. Additionally, it offers new perspectives on the potential termite-flagellate interactions and underscores the need for whole-genome data of termite flagellates in further studies.},
}

@article {pmid40266732,
year = {2025},
author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX},
title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030269},
pmid = {40266732},
issn = {2075-4450},
support = {Hermes 57545//Universidad Nacional de Colombia/ ; },
abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.},
}

@article {pmid40261735,
year = {2025},
author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD},
title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baae112},
pmid = {40261735},
issn = {1758-0463},
mesh = {Animals ; *Chickens/microbiology ; *Microbiota ; *Salmon/microbiology ; *Databases, Genetic ; *Host Microbial Interactions ; Metadata ; *Gastrointestinal Microbiome ; },
abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.},
}

Animals
*Chickens/microbiology
*Microbiota
*Salmon/microbiology
*Databases, Genetic
*Host Microbial Interactions
Metadata
*Gastrointestinal Microbiome

@article {pmid40256745,
year = {2025},
author = {Ruiz-Toquica, J and Franco Herrera, A and Medina, M},
title = {Endozoicomonas dominance and Vibrionaceae stability underpin resilience in urban coral Madracis auretenra.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19226},
pmid = {40256745},
issn = {2167-8359},
mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; Colombia ; Ecosystem ; Seasons ; },
abstract = {Coral resilience varies across species, with some exhibiting remarkable stability and adaptability, often mediated by their associated microbiomes. Given the species-specific nature of coral-microbiome interactions, investigating the microbiomes of urban-adapted corals provides critical insights into the health, dynamics, and functioning of coral holobionts. In this study, we examined the microbiome of Madracis auretenra, a Caribbean coral from Santa Marta, Colombia, across contrasting environmental conditions. Over two years, we compared the microbiomes of healthy and stressed coral colonies from two distinct reef habitats-urban and protected-using 16S rRNA gene sequencing (V4 region) to assess microbial diversity. Our findings revealed microbial richness and diversity were primarily influenced by seasonal and local factors rather than host-specific traits such as interaction with algae, health status, or microhabitat. These variations were not substantial enough to disrupt the overall microbial community structure, which remained stable across temporal and spatial scales. Dominant taxa included Endozoicomonas, along with Vibrionaceae and Rhodobacteraceae, which form dense ecological interaction networks. Notably, nutrient and oxygen levels emerged as key drivers of microbiome fluctuations, yet Vibrionaceae populations exhibited exceptional temporal stability. These findings highlight the presence of a well-structured and resilient coral microbiome with minimal seasonal variability, even in urban-influenced environments. We propose that the dominance of Endozoicomonas and the stability of Vibrionaceae populations play a pivotal role in maintaining microbiome balance, ultimately contributing to the ecological resilience of M. auretenra in dynamic reef habitats.},
}

Animals
*Anthozoa/microbiology/physiology
*Microbiota
RNA, Ribosomal, 16S/genetics
Coral Reefs
Colombia
Ecosystem
Seasons

@article {pmid40252635,
year = {2025},
author = {Taylor, H and Uhlig, HH and Powrie, F},
title = {Autoimmunity in inflammatory bowel disease: a holobiont perspective.},
journal = {Current opinion in immunology},
volume = {94},
number = {},
pages = {102557},
doi = {10.1016/j.coi.2025.102557},
pmid = {40252635},
issn = {1879-0372},
abstract = {Adaptive immunity towards self-antigens (autoimmunity) and intestinal commensal microbiota is a key feature of inflammatory bowel disease (IBD). Considering mucosal adaptive immunity from a holobiont perspective, where the host and its microbiome form a single physiological unit, emphasises the challenge of avoiding damaging responses to self-antigen and symbiotic microbial communities in the gut while protecting against potential pathogens. Intestinal tolerance mechanisms prevent maladaptive T and B cell responses to microbial, environmental, and self-antigens, which drive inflammation. We discuss the spectrum of antimicrobial and autoantibody responses and highlight mechanisms by which common IBD-associated adaptive immune responses contribute to disease.},
}

@article {pmid40251276,
year = {2025},
author = {Al-Kaisy, R and Bhatt, S and Duchêne, DA},
title = {Distinct evolutionary regimes across domains of the Plasmodium falciparum CSP gene.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13507},
pmid = {40251276},
issn = {2045-2322},
support = {NNF23OC0084647//Novo Nordisk Fonden/ ; NNF20OC0059309//Novo Nordisk Fonden/ ; DNRF160//Danish National Research Foundation/ ; G-22-63345//The Eric and Wendy Schmidt Fund/ ; NIHR200908//UK National Institute for Health Research/ ; },
mesh = {*Plasmodium falciparum/genetics ; *Protozoan Proteins/genetics/chemistry ; *Evolution, Molecular ; Phylogeny ; Malaria, Falciparum/parasitology ; Humans ; Protein Domains ; },
abstract = {Malaria disease caused by parasites of genus Plasmodium places an enormous disease burden across tropical regions of the world. The circumsporozoite protein (CSP) of Plasmodium has several key functions in binding and accessing host cells, with functions subdivided across multiple protein regions. While its key roles during infection make the gene a primary target for malaria vaccine development, the evolutionary dynamics that could affect the forecasting of useful strains remain poorly understood. We tested whether the gene undergoes multiple DNA substitution processes and whether these are divided across gene regions using a phylogenetic mixture model, and a global sample of CSP sequences specific to P. falciparum. These analyses reveal evolutionary processes unique to the central repeat region and the C-terminus. The central repeat region is dominated by synonymous substitutions (putatively neutral) and heavy C-T substitution bias, while the C-terminus undergoes mostly non-synonymous changes. These evolutionary processes are not strongly geographically restricted, and lineages from Africa and Asia where the parasite is most abundant appear to drive evolution across all CSP gene regions. We propose that insights about DNA substitution processes can help forecast the variants of importance to vaccine development, aided by state-of-the-art evolutionary modelling.},
}

*Plasmodium falciparum/genetics
*Protozoan Proteins/genetics/chemistry
*Evolution, Molecular
Phylogeny
Malaria, Falciparum/parasitology
Humans
Protein Domains

@article {pmid40247696,
year = {2025},
author = {Tortorelli, G and Rosset, SL and Sullivan, CES and Woo, S and Johnston, EC and Walker, NS and Hancock, JR and Caruso, C and Varela, AC and Hughes, K and Martin, C and Quinn, RA and Drury, C},
title = {Heat-induced Stress Modulates Cell Surface Glycans and Membrane Lipids of Coral Symbionts.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf073},
pmid = {40247696},
issn = {1751-7370},
abstract = {The susceptibility of corals to environmental stress is determined by complex interactions between host genetic variation and the Symbiodiniaceae family community. We exposed genotypes of Montipora capitata hosting primarily Cladocopium or Durusdinium symbionts to ambient conditions and an eight-day heat stress. Symbionts' cell surface glycan composition differed between genera and was significantly affected by temperature and oxidative stress. The metabolic profile of coral holobionts was primarily shaped by symbionts identity, but was also strongly responsive to oxidative stress. At peak temperature stress, betaine lipids in Cladocopium were remodeled to more closely resemble the abundance and saturation state of Durusdinium symbionts, which paralleled a larger metabolic shift in Cladocopium. Exploring how Symbiodiniaceae members regulate stress and host-symbiont affinity helps identify the traits contributing to coral resilience under climate change.},
}

@article {pmid40216077,
year = {2025},
author = {Armengaud, J and Cardon, T and Cristobal, S and Matallana-Surget, S and Bertile, F},
title = {Novel model organisms and proteomics for a better biological understanding.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105441},
doi = {10.1016/j.jprot.2025.105441},
pmid = {40216077},
issn = {1876-7737},
abstract = {The concept of « model organisms » is being revisited in the light of the latest advances in multi-omics technologies that can now capture the full range of molecular events that occur over time, regardless of the organism studied. Classic, well-studied models, such as Escherichia coli, Saccharomyces cerevisiae, to name a few, have long been valuable for hypothesis testing, reproducibility, and sharing common platforms among researchers. However, they are not suitable for all types of research. The complexity of unanswered questions in biology demands more elaborated systems, particularly to study plant and animal biodiversity, microbial ecosystems and their interactions with their hosts if any. More integrated systems, known as « holobionts », are emerging to describe and unify host organisms and associated microorganisms, providing an overview of all their possible interactions and trajectories. Comparative evolutionary proteomics offers interesting prospects for extrapolating knowledge from a few selected model organisms to others. This approach enables a deeper characterization of the diversity of proteins and proteoforms across the three branches of the tree of life, i.e. Bacteria, Archaea, and Eukarya. It also provides a powerful means to address remaining biological questions, such as identifying the key molecular players in organisms when they are confronted to environmental challenges, like anthropogenic toxicants, pathogens, dietary shifts or climate stressors, and proposing long-term sustainable solutions. SIGNIFICANCE: In this commentary, we reevaluated the concept of "model organisms" in light of advancements in multi-omics technologies. Traditional models have proven invaluable for hypothesis testing, reproducibility, and fostering shared research frameworks. However, we discussed that they are not universally applicable. To address complexities such as biodiversity and understand microbial ecosystems and their host interactions, integrated systems like "holobionts," which encompass host organisms and their associated microbes, are gaining prominence. Comparative evolutionary proteomics further enhances our understanding by enabling detailed exploration of protein diversity across organisms. This approach also facilitates the identification of critical molecular players in organisms facing environmental challenges, such as pollutants, pathogens, dietary changes, or climate stress, and contributes to developing sustainable long-term solutions.},
}

@article {pmid40215444,
year = {2025},
author = {Kerwin, AH and Ohdera, A and Bier, J and Goodman, D and Mammone, M and Sharp, V and Echeandía, A and Medina, M},
title = {Cassiopea xamachana microbiome across anatomy, development, and geography.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0319944},
doi = {10.1371/journal.pone.0319944},
pmid = {40215444},
issn = {1932-6203},
mesh = {Animals ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Larva/microbiology ; *Hydrozoa/microbiology/growth & development/anatomy & histology ; Female ; Phylogeny ; Symbiosis ; Male ; Geography ; },
abstract = {The upside-down jellyfish holobiont, Cassiopea xamachana, is a useful model system for tri-partite interactions between the cnidarian host, the photosymbiont, and the bacterial microbiome. While the interaction between the host and photosymbiont has been well studied, less is understood of the associated bacterial community. To date, the bacterial microbiome of wild C. xamachana has remained largely uncharacterized. Thus, wild medusae (n=6) and larvae (n=3) were collected from two sites in the Florida Keys. Bacterial community composition was characterized via amplicon sequencing of the 16S rRNA gene V4 region. The medusa bacterial community was dominated by members of the Alphaproteobacteria and Gammaproteobacteria, while Planctomycetota, Actinomycetota, Bacteroidota, and Bacillota were also present, among others. Community composition was consistent between locations and across medusa structures (oral arm, bell, and gonad). The larval bacterial community clustered apart from the medusa community in beta diversity analysis and was characterized by the presence of several Pseudomonadota taxa that were not present in the medusa, including the Alteromonas, Pseudoalteromonas, and Thalassobius genera. A bacterial isolate library encompassing much of the amplicon sequencing diversity was also developed and tested via metabolic assays in a separate culture-dependent analysis of isolates from medusa bells, oral arms, and laplets. Most characteristics were not correlated with host sex or medusa structure, but gelatinase production was more common in laplet isolates, while lactose fermentation was more common in female oral arm isolates. The Endozoicomonas genus was dominant in both amplicon sequencing and in our isolate library, and was equally prevalent across all medusa structures and in both sexes. Understanding the bacterial component of the C. xamachana holobiont will allow us to further develop this important model cnidarian holobiont.},
}

Animals
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Larva/microbiology
*Hydrozoa/microbiology/growth & development/anatomy & histology
Female
Phylogeny
Symbiosis
Male
Geography

@article {pmid40208324,
year = {2025},
author = {Mazzella, V and Zahn, G and Dell'Anno, A and Pons, LN},
title = {Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {25},
pmid = {40208324},
issn = {1432-184X},
support = {C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; },
mesh = {Animals ; *Porifera/microbiology ; *Fungi/classification/genetics/isolation & purification ; Mediterranean Sea ; *Mycobiome ; *Seawater/microbiology ; Phylogeny ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Ecosystem ; },
abstract = {Marine sponges are widespread, sessile, filter-feeding animals, known for living in association with complex prokaryotic communities structured by host species. Though marine fungi are ubiquitous across marine environments, little is known about sponge-associated fungal communities (mycobiome). Indeed, aside from a few studies based on the isolation of fungal strains for biotechnological purposes, little information is available to understand the diversity and structure of sponge mycobiome. Here, a metabarcoding approach based on the ITS1 marker was applied to examine the structure and composition of fungal communities associated with four Mediterranean sponges. The species: Petrosia ficiformis, Chondrosia reniformis, Crambe crambe, and Chondrilla nucula were analyzed along with the surrounding seawater, revealing Aspergillus (1-56%), Cladosporium (1-75%), Malassezia (1-38.5%), and Pennicillium (1.5-36%) as the most represented fungal genera. Our data showed high intra-specific variability and no clear core mycobiome within each of the sponge species host, suggesting stochastic and perhaps transient community membership. This study sheds light on one of the most abundant yet least understood components of the marine ecosystem. Unraveling the dynamics of fungal interactions within sponge holobionts is essential to advance our understanding of their ecological roles and functions. By addressing the enigmatic nature of sponge-associated fungi, this research opens new avenues for exploring their contributions to marine ecosystems and resolving the many unanswered questions in this field.},
}

Animals
*Porifera/microbiology
*Fungi/classification/genetics/isolation & purification
Mediterranean Sea
*Mycobiome
*Seawater/microbiology
Phylogeny
Biodiversity
DNA Barcoding, Taxonomic
DNA, Fungal/genetics
Ecosystem

@article {pmid40205751,
year = {2025},
author = {Dho, M and Montagna, M and Liu, C and Magoga, G and Forni, G and Alma, A and Gonella, E},
title = {Multilocus sequence typing of the invasive pest Halyomorpha halys (Hemiptera: Pentatomidae) and associated endosymbiont reveals unexplored diversity.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70034},
pmid = {40205751},
issn = {1744-7917},
abstract = {Halyomorpha halys is an invasive pest affecting a wide range of crops in many regions of the world. Rapid and cost-effective methods to reconstruct its invasion routes are crucial for implementing strategies to prevent further spread. The mitochondrial markers COI and COII and the pseudogene ΔybgF of the primary symbiont "Candidatus Pantoea carbekii" have been analyzed to track the spread of H. halys. However, these markers do not provide sufficient resolution to fully elucidate invasion routes. Here, H. halys individuals from native and invasive populations were analyzed to identify new DNA markers and evaluate their effectiveness in a multilocus sequence typing (MLST) framework. Three new nuclear markers for H. halys (Hh_KsPi, Hh_UP1, Hh_D3PDh) and three new markers for P. carbekii (Pc_TamA, Pc_SucA, Pc_SurA) were identified. Hh_D3PDh was the most informative marker for H. halys, describing two more haplotypes than COI. By integrating Hh_D3PDh with mitochondrial markers, 30 distinct haplotypes were identified, with each of the populations studied exhibiting multiple haplotypes. Pc_SucA was the most informative symbiont marker, and when all P. carbekii markers were combined, symbiont diversity was greatly increased. The low network specialization between the novel nuclear markers and both mitochondrial and symbiont markers underlined the higher power of nuclear markers. Interestingly, perfect network specialization between H. halys COI and symbiont markers was found in populations from invaded areas, suggesting that some holobiont variants may contribute to enhanced invasive ability. A MLST workflow is proposed as a new tool for population genetics analysis and reconstruction of H. halys invasion.},
}

@article {pmid40194944,
year = {2025},
author = {Wilson, I and Perry, T and Eisenhofer, R and Rismiller, P and Shaw, M and Grutzner, F},
title = {Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus).},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf036},
pmid = {40194944},
issn = {1574-6941},
abstract = {Monotreme and marsupial development is characterised by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich environment. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation, but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiota (n = 22) during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Metataxonomic profiling using 16S rRNA gene sequencing revealed that pseudo-pouch microbial communities undergo dramatic changes during lactation, with significant differences in taxonomic composition compared with samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. Furthermore, captivity was not found to have a significant effect on pseudo-pouch microbiota. This study pioneers pouch microbiota research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programs in the future.},
}

@article {pmid39508584,
year = {2024},
author = {Thomas, F and Asselin, K and MacDonald, N and Brazier, L and Meliani, J and Ujvari, B and Dujon, AM},
title = {Oncogenic processes: a neglected parameter in the evolutionary ecology of animals.},
journal = {Comptes rendus biologies},
volume = {347},
number = {},
pages = {137-157},
doi = {10.5802/crbiol.159},
pmid = {39508584},
issn = {1768-3238},
abstract = {Cancer is a biological process that emerged at the end of the Precambrian era with the rise of multicellular organisms. Traditionally, cancer has been viewed primarily as a disease relevant to human and domesticated animal health, attracting attention mainly from oncologists. In recent years, however, the community of ecologists and evolutionary biologists has recognized the pivotal role of cancer-related issues in the evolutionary paths of various species, influencing multiple facets of their biology. It has become evident that overlooking these issues is untenable for a comprehensive understanding of species evolution and ecosystem functioning. In this article, we highlight some significant advancements in this field, also underscoring the pressing need to consider reciprocal interactions not only between cancer cells and their hosts but also with all entities comprising the holobiont. This reflection gains particular relevance as ecosystems face increasing pollution from mutagenic substances, resulting in a resurgence of cancer cases in wildlife.},
}

@article {pmid40175359,
year = {2025},
author = {Sipos, A and Kerekes, É and Szeőcs, D and Szarvas, F and Schwarcz, S and Tóth, E and Ujlaki, G and Mikó, E and Bai, P},
title = {Ursodeoxycholic acid prompts glycolytic dominance, reductive stress and epithelial-to-mesenchymal transition in ovarian cancer cells through NRF2 activation.},
journal = {Cell death discovery},
volume = {11},
number = {1},
pages = {134},
pmid = {40175359},
issn = {2058-7716},
support = {K142141//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; FK146 852//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; FK 128 387//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; },
abstract = {Numerous secreted bacterial metabolites were identified with bioactivity in various neoplasias, including ovarian cancer. One such metabolite is ursodeoxycholic acid (UDCA), a secondary bile acid that has widespread beneficial effects in neoplasias. Hereby, we assessed the bioactivity of UDCA in cell models of ovarian cancer, by applying UDCA in concentrations corresponding to the serum reference concentrations of UDCA (300 nM). UDCA induced epithelial-to-mesenchymal transition (EMT), increased the flux of glycolysis and reduced the naturally occurring oxidative stress in ovarian cancer cells. These changes were dependent on the activation of NRF2. The tumoral overexpression of UDCA-induced genes in humans correlated with worse survival. These results point out that bacterial metabolites may have opposite effects in different neoplasias and raise the possibility that UDCA-containing remedies on the long run may support cancer progression in ovarian cancer patients.},
}

@article {pmid40171541,
year = {2025},
author = {Robert, C and Alves Monteiro, HJ and Le Moan, A and Tanguy, A and Laugen, AT and Hemmer-Hansen, J and Strand, Å and De Wit, P},
title = {Fine Scale Patterns of Population Structure and Connectivity in Scandinavian Flat Oysters in Scandinavia (Ostrea edulis L.).},
journal = {Evolutionary applications},
volume = {18},
number = {4},
pages = {e70096},
pmid = {40171541},
issn = {1752-4571},
abstract = {Stocks of the European flat oyster, Ostrea edulis, have collapsed due to overfishing, habitat destruction, and pathogen outbreaks across most of their distribution range. Nonetheless, as a result of lower exploitation pressure and the absence of pathogens in the most northern part of the range, a large part of the remaining wild population can be found in relatively high densities in Scandinavia, a region in Northern Europe. However, despite recent studies focusing on flat oyster population structure along the European coast, little is known about the population structure of oysters in the Skagerrak marginal sea in Scandinavia, and how it is related to neighbouring regions. This study, therefore, aimed to investigate the population structure of flat oysters in Scandinavia, with a special emphasis on the Skagerrak. We gathered low-coverage whole-genome sequencing data from oysters in Sweden, Norway, and Denmark, the three countries that border the Skagerrak. Genetic diversity appeared to be homogeneously distributed over the sampled area in the Skagerrak, while samples collected from the east coast of Denmark and from a location with known historical farming activity on the Norwegian West Coast were genetically distinct from Skagerrak samples. A genetic barrier analysis indicated barriers to gene flow in the Baltic Sea transition zone and on the west coast of Norway. Overall, our results suggest that flat oysters from the Swedish Skagerrak coasts form a single panmictic population that is distinct from neighbouring seas, potentially allowing for regional management of stocks and restoration translocations in the area. However, the genetic composition of donor and recipient stocks should be assessed on a case-by-case basis, genetic diversity effects of hatchery practices should be monitored, and biosecurity measures need to be considered prior to any movement of stock.},
}

@article {pmid40165613,
year = {2025},
author = {Fialas, PC and Santini, L and Russo, D and Amorim, F and Rebelo, H and Novella-Fernandez, R and Marques, F and Domer, A and Vella, A and Martinoli, A and Figurek, A and Tsoar, A and Sandor, A and Ibanez, C and Korine, C and Kerbiriou, C and Voigt, C and Mifsud, C and Jére, C and Ridha, D and Preatoni, D and Hamidović, D and Tidenberg, EM and Çoraman, E and Mathews, F and Lison, F and Joanna, F and Petersons, G and Loumassine, H and Garin, I and Csősz, I and Liira, J and Juste, J and Julien, JF and van der Kooij, J and Darija, J and Aihartza, J and Eldegard, K and Phelps, K and Olival, KJ and Marina, K and Ancillotto, L and Grzegorz, L and Barti, L and Salazar, LC and Bosso, L and Rodrigues, L and Hamel, L and Uhrin, M and Mas, M and Cerekovic, N and Toshkova, N and Roche, N and Kalda, O and Aizpurua, O and Georgiakakis, P and Kanuch, P and Presetnik, P and Bilgin, R and McKay, RA and Dina, R and Goran, R and Ireneusz, R and Sørås, R and Robert, S and Aulagnier, S and Kramer-Schadt, S and Gazaryan, S and Bücs, SL and Yorulmaz, T and Stjernberg, T and Liukko, UM and Nistreanu, V and Vintulis, V and Radchuk, V and Puig-Montserrat, X and Bas, Y and Zagmajster, M and Zegarek, M and Vida, Z and Razgour, O},
title = {Changes in community composition and functional diversity of European bats under climate change.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {e70025},
doi = {10.1111/cobi.70025},
pmid = {40165613},
issn = {1523-1739},
support = {//Natural Environment Research Council/ ; //NE/M018660/1, NE/S007504/1/ ; //COST ACTION CA18107 'Climate change and bats: from science to conservation - ClimBats' (https://climbats.eu/)/ ; },
abstract = {Climate change is predicted to drive geographical range shifts that will result in changes in species diversity and functional composition and have potential repercussions for ecosystem functioning. However, the effect of these changes on species composition and functional diversity (FD) remains unclear, especially for mammals, specifically bats. We used species distribution models and a comprehensive ecological and morphometrical trait database to estimate how projected future climate and land-use changes could influence the distribution, composition, and FD of the European bat community. Future bat assemblages were predicted to undergo substantial shifts in geographic range and trait structure. Range suitability decreased substantially in southern Europe and increased in northern latitudes. Our findings highlight the potential for climate change to drive shifts in bat FD, which has implications for ecosystem function and resilience at a continental scale. It is important to incorporate FD in conservation strategies. These efforts should target species with key functional traits predicted to be lost and areas expected to experience losses in FD. Conservation strategies should include habitat and roost protection, enhancing landscape connectivity, and international monitoring to preserve bat populations and their ecosystem services.},
}

@article {pmid40159998,
year = {2025},
author = {Iglesias-Carrasco, M and Torres, J and Cruz-Dubon, A and Candolin, U and Wong, BBM and Velo-Antón, G},
title = {Global impacts of exotic eucalypt plantations on wildlife.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.70022},
pmid = {40159998},
issn = {1469-185X},
support = {PID2022-137901NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; DOC_00453//Junta de Andalucia/ ; },
abstract = {The establishment of exotic tree plantations poses a pervasive threat to wildlife across the globe. Among the most important tree species used for forestry purposes worldwide are members of the genus Eucalyptus, which have now been established in at least 107 countries outside of their native range. When introduced into non-native areas, eucalypt plantations are associated with myriad novel challenges for native fauna, and have often been associated with reductions in the biodiversity of local communities. However, similar to other anthropogenic habitats, eucalypt plantations can also create novel opportunities for species that can allow them to survive and thrive in these novel environments. In this review, we use eucalypt plantations as a case study for understanding the ecological and evolutionary responses of wildlife to anthropogenic habitat loss and change. We begin by summarising the main avenues of research addressing the study of wildlife responses at the individual, community, and ecosystem levels, and highlight critical research gaps. We also consider the characteristics of different types of eucalypt plantations and how such attributes are linked with the ability of animals to respond appropriately to the establishment of plantations, and summarise important considerations for the conservation of animal communities in these human-altered habitats.},
}

@article {pmid40154760,
year = {2025},
author = {Sutcliffe, EI and Irvine, A and Rooney, J and Smith, D and Northcote, HM and McKenzie, D and Bakshi, S and Nisbet, AJ and Price, D and Graham, R and Morphew, R and Atkinson, L and Mousley, A and Cantacessi, C},
title = {Antimicrobial peptides in nematode secretions - Unveiling biotechnological opportunities for therapeutics and beyond.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108572},
doi = {10.1016/j.biotechadv.2025.108572},
pmid = {40154760},
issn = {1873-1899},
abstract = {Gastrointestinal (GI) parasitic nematodes threaten food security and affect human health and animal welfare globally. Current anthelmintics for use in humans and livestock are challenged by continuous re-infections and the emergence and spread of multidrug resistance, underscoring an urgent need to identify novel control targets for therapeutic exploitation. Recent evidence has highlighted the occurrence of complex interplay between GI parasitic nematodes of humans and livestock and the resident host gut microbiota. Antimicrobial peptides (AMPs) found within nematode biofluids have emerged as potential effectors of these interactions. This review delves into the occurrence, structure, and function of nematode AMPs, highlighting their potential as targets for drug discovery and development. We argue that an integrated approach combining advanced analytical techniques, scalable production methods, and innovative experimental models is needed to unlock the full potential of nematode AMPs and pave the way for the discovery and development of sustainable parasite control strategies.},
}

@article {pmid40151579,
year = {2025},
author = {de Breuyn, M and Ostendarp, M and El-Khaled, YC and Garcias-Bonet, N and Carvalho, S and Wild, C and Peixoto, RS},
title = {Probiotics prevent mortality of thermal-sensitive corals exposed to short-term heat stress.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf039},
pmid = {40151579},
issn = {2730-6151},
abstract = {The use of coral probiotics, i.e. beneficial microorganisms for corals (BMCs), is a novel approach to enhancing coral health under heat stress. While BMCs mitigate coral bleaching and mortality during prolonged heat stress conditions, their effectiveness in mitigating short-term acute heat stress remains understudied. This study investigates the effects of BMCs on two Red Sea hard coral species, Acropora cf. hemprichii and Pocillopora verrucosa, during short-term heat stress. Twelve coral fragments per species were allocated to each treatment across two temperature regimes (26°C and 32°C) for 48 hours, with half receiving BMC inoculation and half serving as controls. Results show BMC supplementation significantly prevented mortality in Acropora cf. hemprichii at 32°C, contrasting with a 100% mortality observed in the control group. Specifically, probiotic-inoculated Acropora cf. hemprichii at 32°C exhibited preserved primary production, a 12-13 fold increase in algal cell densities, 4-5 times higher FV/Fm ratios, and 4-5 and 2-3 times higher chlorophyll a and c2 concentrations, respectively, compared to their untreated conspecifics. All P. verrucosa colonies survived the 32°C exposure without tissue loss or reduced holobiont function in both control and BMC treatments. These findings underscore the rapid effects of BMC inoculation, initiated just 2 hours prior to acute heat stress, in protecting heat-sensitive Acropora cf. hemprichii against mortality and adverse photo-physiological changes, with beneficial effects visible within 2 days. Recognizing the critical timeframe for beneficial effects is paramount for management strategies to address heat-sensitive corals on natural reefs, such as implementing probiotic interventions before anticipated marine heatwaves.},
}

@article {pmid40143859,
year = {2025},
author = {Abou Jaoudé, R and Luziatelli, F and Ficca, AG and Ruzzi, M},
title = {Soil microbiome transplantation to enhance the drought response of Salvia officinalis L.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1553922},
pmid = {40143859},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil microbiome transplantation is a promising technique for enhancing plant holobiont response to abiotic and biotic stresses. However, the rapid assessment of microbiome-plant functional integration in short-term experiments remains a challenge.

METHODS: This study investigates the potential of three evergreen sclerophyll species, Pistacia lentiscus (PL), Rosmarinus officinalis (RO), and Juniperus phoenicea (JP), to serve as a reservoir for microbial communities able to confer enhanced tolerance to drought in Salvia officinalis cultivated under water shortage, by analyzing biomass production, plant phenotype, plant ecophysiological responses, and leaf metabolome.

RESULTS: Our results showed that the inoculation with the three rhizomicrobiomes did not enhance total plant biomass, while it significantly influenced plant architecture, ecophysiology, and metabolic responses. The inoculation with the JP rhizomicrobiome led to a significant increase in root biomass, resulting in smaller leaves and a higher leaf number. These morphological changes suggest improved water acquisition and thermoregulation strategies. Furthermore, distinct stomatal conductance patterns were observed in plants inoculated with microbiomes from PJ and PL, indicating altered responses to drought stress. The metabolome analysis demonstrated that rhizomicrobiome transplantation significantly influenced the leaf metabolome of S. officinalis. All three rhizomicrobiomes promoted the accumulation of phenolic compounds, terpenoids, and alkaloids, known to play crucial roles in plant defense and stress response. Five molecules (genkwanin, beta-ionone, sumatrol, beta-peltatin-A-methyl ester, and cinnamoyl-beta-D-glucoside) were commonly accumulated in leaves of inoculated sage, independently of the microbiome. Furthermore, unique metabolic alterations were observed depending on the specific inoculated rhizomicrobiome, highlighting the specialized nature of plant-microbe interactions and the possible use of these specific molecules as biomarkers to monitor the recruitment of beneficial microorganisms.

DISCUSSION: This study provides compelling evidence that microbiome transplantation can induce phenotypic and metabolic changes in recipient plants, potentially enhancing their resilience to water scarcity. Our findings emphasize the importance of considering multiple factors, including biomass, physiology, and metabolomics, when evaluating the effectiveness of microbiome engineering for improving plant stress tolerance.},
}

@article {pmid40139064,
year = {2025},
author = {Yang, H and Yuan, D and Zhou, Z and Zhao, H},
title = {Nitrate enrichment exacerbates microbiome and metabolism disturbances of the coral holobiont under heat stress.},
journal = {Marine environmental research},
volume = {208},
number = {},
pages = {107098},
doi = {10.1016/j.marenvres.2025.107098},
pmid = {40139064},
issn = {1879-0291},
abstract = {Coral reef ecosystems are facing severe deterioration due to escalating global temperatures and human-induced activities. Combined nitrate and heat stress can exacerbate coral bleaching, however, the underlying mechanism is still unclear. In the present study, we assessed the bleaching status of Acropora hyacinthus, a reef-building coral species, under high temperature and nitrate stress conditions using chemostat cultivation. We observed nitrate enrichment (9 μM) induced a significant reduction in photosystem efficiency (Fv/Fm) of Symbiodiniaceae and an increased thermal bleaching of corals under high temperature (30 °C). Nitrate exposure promoted the proliferation of Enterobacteriaceae and Vibrionaceae, which are bacterial families, potentially augmenting the coral's susceptibility to disease while exerting negligible effects on the fungal community. Alterations were observed in the metabolic pathways of both the coral hosts and Symbiodiniaceae, including down-regulated folate biosynthesis and inflammatory mediator regulation of TRP channels. Our findings indicate that nitrate enrichment under heat stress disrupts the metabolism of coral holobionts through altering bacterial communities, ultimately leading to increased coral bleaching.},
}

@article {pmid40132032,
year = {2025},
author = {Ostendarp, M and de Breuyn, M and El-Khaled, YC and Garcias-Bonet, N and Carvalho, S and Peixoto, RS and Wild, C},
title = {Temperature-dependent responses of the hard corals Acropora sp. and Pocillopora verrucosa to molecular hydrogen.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0308894},
doi = {10.1371/journal.pone.0308894},
pmid = {40132032},
issn = {1932-6203},
mesh = {*Anthozoa/physiology ; Animals ; *Hydrogen/metabolism ; *Photosynthesis ; *Temperature ; Coral Reefs ; Seawater/chemistry ; Electron Transport ; Indian Ocean ; },
abstract = {Coral reefs are increasingly threatened by mass bleaching events due to global ocean warming. Novel management strategies are urgently needed to support coral survival until global efforts can mitigate ocean warming. Given the strong antioxidant, anti-inflammatory and anti-apoptotic properties of molecular hydrogen, our study explores its potential to alleviate the negative effects of heat stress on corals. We investigated the ecophysiological responses of two common hard corals (Acropora sp. and Pocillopora verrucosa) from the Central Red Sea under ambient (26 °C) and elevated seawater temperatures (32 °C), with and without hydrogen addition (~ 150 µ M H2) over 48 h. Our results showed that at 32 °C without hydrogen addition, P. verrucosa exhibited high temperature tolerance, whereas Acropora sp. showed significant reductions in photosynthetic efficiency and maximum electron transport rate compared to the ambient condition (26 °C). The addition of hydrogen at 32 °C increased the maximum electron transport rate of Acropora sp. by 28%, maintaining it at levels compared to those at 26 °C. In contrast, the addition of hydrogen at 26 °C caused a significant decrease in the photophysiology of both Acropora sp. and P. verrucosa. This suggests that the short-term response of the coral holobiont to molecular hydrogen is temperature-dependent, potentially benefiting the coral holobiont under heat stress, while impairing the photophysiology under ambient temperatures. Our findings therefore provide the foundation for future long-term studies uncovering the mechanisms behind molecular hydrogen, potentially informing the development of new management strategies to enhance coral resilience to ocean warming.},
}

*Anthozoa/physiology
Animals
*Hydrogen/metabolism
*Photosynthesis
*Temperature
Coral Reefs
Seawater/chemistry
Electron Transport
Indian Ocean

@article {pmid40130423,
year = {2025},
author = {Silver, LW and Farquharson, KA and Peel, E and Gilbert, MTP and Belov, K and Morales, HE and Hogg, CJ},
title = {Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17746},
doi = {10.1111/mec.17746},
pmid = {40130423},
issn = {1365-294X},
support = {CE200100012//Australian Research Council/ ; },
abstract = {Loss of genetic diversity threatens a species' adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a critically endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016, and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary (N = 19) and historical (N = 16) resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples were also observed. A temporal reduction in the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridisation and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred in this species in order to prevent extinction.},
}

@article {pmid40123705,
year = {2025},
author = {Hasnain, SE and Ahmed, N},
title = {Rethinking Conservation in the Anthropocene-The Case of Holobionts.},
journal = {Disease biology, genetics, and socioecology},
volume = {1},
number = {1},
pages = {},
pmid = {40123705},
}

@article {pmid40116496,
year = {2025},
author = {Baa-Puyoulet, P and Gerlin, L and Parisot, N and Peignier, S and Renoz, F and Calevro, F and Charles, H},
title = {ArtSymbioCyc, a metabolic network database collection dedicated to arthropod symbioses: a case study, the tripartite cooperation in Sipha maydis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0014025},
doi = {10.1128/msystems.00140-25},
pmid = {40116496},
issn = {2379-5077},
abstract = {Most arthropods live in close association with bacteria. The genomes of associated partners have co-evolved, creating situations of interdependence that are complex to decipher despite the availability of their complete sequences. We developed ArtSymbioCyc, a metabolism-oriented database collection gathering genomic resources for arthropods and their associated bacteria. ArtSymbioCyc uses the powerful tools of the BioCyc community to produce high-quality annotations and to analyze and compare metabolic networks on a genome-wide scale. We used ArtSymbioCyc to study the case of the tripartite symbiosis of the cereal aphid Sipha maydis focusing on amino acid and vitamin metabolisms, as these compounds are known to be important in this strictly phloemophagous insect. We showed that the metabolic pathways of the insect host and its two obligate bacterial associates are interdependent and specialized in the exploitation of Poaceae phloem, particularly for the biosynthesis of sulfur-containing amino acids and most vitamins. This demonstrates that ArtSymbioCyc does not only reveal the individual metabolic capacities of each partner and their respective contributions to the holobiont they constitute but also allows to predict the essential inputs that must come from host nutrition.IMPORTANCEThe evolution has driven the emergence of complex arthropod-microbe symbiotic systems, whose metabolic integration is difficult to unravel. With its user-friendly interface, ArtSymbioCyc (https://artsymbiocyc.cycadsys.org) eases and speeds up the analysis of metabolic networks by enabling precise inference of compound exchanges between associated partners and helps unveil the adaptive potential of arthropods in contexts such as conservation or agricultural control.},
}

@article {pmid40113967,
year = {2025},
author = {Mannaa, M and Park, AR and Kim, JC and Seo, YS},
title = {Microbial allies recruited by Bacillus subtilis JCK-1398 to defend pine trees against pinewood nematode.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9670},
pmid = {40113967},
issn = {2045-2322},
mesh = {Animals ; *Pinus/parasitology/microbiology ; *Plant Diseases/parasitology/microbiology/prevention & control ; *Bacillus subtilis/physiology ; Rhizosphere ; Microbiota ; Nematoda/microbiology/physiology ; Soil Microbiology ; Disease Resistance ; Pantoea/physiology/genetics ; },
abstract = {Pine wilt disease (PWD) is a devastating disease caused by the pinewood nematode (Bursaphelenchus xylophilus). Its substantial ecological disruption harms global forestry and poses serious economic challenges. Although previous research has demonstrated that Bacillus subtilis JCK-1398 has the potential to induce systemic resistance in pine trees, the ecological mechanisms underlying its biocontrol efficacy remain underexplored. This study investigated how JCK-1398 treatment influences rhizosphere- and nematode-associated microbial communities to mitigate PWD. Metabarcoding analyses revealed that JCK-1398 treatment increased the abundance of beneficial microbial taxa (e.g., Nocardioides and Mesorhizobium) in the rhizosphere microbiome. Concurrently, nematode-associated microbial communities became dominated by Pantoea, a genus with known nematicidal properties. Isolation and characterization of Pantoea dispersa BC11 confirmed that it significantly limits nematode viability. These findings highlight the multifaceted defense that JCK-1398 offers, not only inducing systemic resistance, but also orchestrating beneficial microbiome dynamics. This study emphasizes the potential of manipulating a microbial holobiont for eco-friendly and sustainable disease management. The ability of JCK-1398 to recruit and enhance microbial allies offers a novel framework for developing biocontrol agents, with implications for managing PWD and other plant-pathogen systems.},
}

Animals
*Pinus/parasitology/microbiology
*Plant Diseases/parasitology/microbiology/prevention & control
*Bacillus subtilis/physiology
Rhizosphere
Microbiota
Nematoda/microbiology/physiology
Soil Microbiology
Disease Resistance
Pantoea/physiology/genetics

@article {pmid40111689,
year = {2025},
author = {Mattos, MCO and Vivacqua, A and Carneiro, VMA and Grisi, DC and Guimarães, MDCM},
title = {Interaction of the Systemic Inflammatory State, Inflammatory Mediators, and the Oral Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {121-132},
pmid = {40111689},
issn = {0065-2598},
mesh = {Humans ; *Microbiota/immunology ; *Mouth/microbiology/immunology ; *Inflammation Mediators/metabolism ; *Inflammation/microbiology/immunology ; *Periodontitis/microbiology/immunology ; Dysbiosis/microbiology/immunology ; Animals ; },
abstract = {Humans are biological units that host numerous microbial symbionts and their genomes, which together form a superorganism or holobiont. Changes in the balance of the oral ecosystem can have consequences for both general and oral health, such as cavities, gingivitis, and periodontitis. Periodontitis is initiated by a synergistic and dysbiotic microbial community that causes local inflammation and destruction of the tooth's supporting tissues, potentially leading to systemic inflammation. This inflammation caused by periodontal disease has been associated with various systemic alterations, and the immune system is largely responsible for the body's exacerbated response, which can induce and exacerbate chronic conditions. Studies indicate that subgingival microorganisms found in periodontitis reach the bloodstream and are distributed throughout the body and, therefore, can be found in distant tissues and organs. Among all diseases associated with periodontal disease, diabetes mellitus presents the strongest and most elucidated link, and its bidirectional relationship has already been demonstrated. Chronic hyperglycemia favors the worsening of periodontal parameters, while the aggravation of periodontal parameters can promote an increase in glycemic indexes. Other systemic diseases have been related to periodontitis, such as Alzheimer's, chronic kidney disease, atherosclerosis, and respiratory diseases. The importance of periodontal control may suggest a reduction in the chances of developing chronic inflammatory diseases because these two alterations often share inflammatory pathways and, for this reason, may influence each other.},
}

Humans
*Microbiota/immunology
*Mouth/microbiology/immunology
*Inflammation Mediators/metabolism
*Inflammation/microbiology/immunology
*Periodontitis/microbiology/immunology
Dysbiosis/microbiology/immunology
Animals

@article {pmid40108459,
year = {2025},
author = {Duchêne, DA and Chowdhury, AA and Yang, J and Iglesias-Carrasco, M and Stiller, J and Feng, S and Bhatt, S and Gilbert, MTP and Zhang, G and Tobias, JA and Ho, SYW},
title = {Drivers of avian genomic change revealed by evolutionary rate decomposition.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40108459},
issn = {1476-4687},
abstract = {Modern birds have diversified into a striking array of forms, behaviours and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change[1-4], but disentangling the drivers of rate variation at the whole-genome scale has been difficult. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds[5,6], we find that genome-wide mutation rates across lineages are predominantly explained by clutch size and generation length, whereas rate variation across genes is driven by the content of guanine and cytosine. Here, to find the subsets of genes and lineages that dominate evolutionary rate variation in birds, we estimated the influence of individual lineages on decomposed axes of gene-specific evolutionary rates. We find that most of the rate variation occurs along recent branches of the tree, associated with present-day families of birds. Additional tests on axes of rate variation show rapid changes in microchromosomes immediately after the Cretaceous-Palaeogene transition. These apparent pulses of evolution are consistent with major changes in the genetic machineries for meiosis, heart performance, and RNA splicing, surveillance and translation, and correlate with the ecological diversity reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolution, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage and niche expansion in the early Palaeogene period.},
}

@article {pmid40092220,
year = {2025},
author = {Bhatia, A and Sharma, D and Mehta, J and Kumarasamy, V and Begum, MY and Siddiqua, A and Sekar, M and Subramaniyan, V and Wong, LS and Mat Rani, NNI},
title = {Probiotics and Synbiotics: Applications, Benefits, and Mechanisms for the Improvement of Human and Ecological Health.},
journal = {Journal of multidisciplinary healthcare},
volume = {18},
number = {},
pages = {1493-1510},
pmid = {40092220},
issn = {1178-2390},
abstract = {This review explores the multifaceted roles and applications of probiotics, emphasizing their significance in maintaining and enhancing host health through microbial interactions. It includes the concept of holobionts and the symbiotic relationships between hosts and their microbiomes, illustrating how various microbiota can enhance immunity, support growth, and prevent diseases. It delves into the customization of probiotics using molecular and genomic techniques, focusing Enterococcus, Bifidobacterium, and Lactobacillus species. Furthermore, it discusses the symbiotic effects of symbiotics which aids in enhancing the survivability and beneficial effects of probiotics. The role beneficial microbes in gut is emphasized, noting its impact on preventing diseases and maintaining a stable microbial community. The potential therapeutic value of probiotics includes the ability to treat gastrointestinal diseases, as well as to strengthen the immune system and reduce the number of free radicals that are present in the body. Additionally, it explores secondary metabolites produced by bacteria in the gut, such as bacteriocins and exopolysaccharides, and their effect on the health of human, particularly in the gastrointestinal tract. The review concludes by addressing the use of probiotics in traditional medicine and their potential in novel therapeutic applications, including the treatment of endangered wildlife species and various human ailments.},
}

@article {pmid40081757,
year = {2025},
author = {Armengaud, J},
title = {The dawn of the revolution that will allow us to precisely describe how microbiomes function.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105430},
doi = {10.1016/j.jprot.2025.105430},
pmid = {40081757},
issn = {1876-7737},
abstract = {The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins. Indeed, proteins - through their roles as catalytic units, structural components, and signaling molecules - are the main drivers of biological processes. Metagenomics has significantly expanded what we know about the genetic material present in microbiota, revealing their functional potential; metabolomics delivers an overall snapshot of the metabolites produced by the community. But metaproteomics offers a complementary approach to explore microbiome and holobiont functionality by focusing on the active proteins and functional pathways from each taxon. Significant recent advances in high-resolution tandem mass spectrometry have greatly expanded the catalog of peptide sequences accessible in each sample, creating the conditions for unprecedented taxonomical profiling, while also providing more accurate biomass quantification, more detailed protein characterization, and a greater capacity to monitor abundance and distinguish host biomarkers. By integrating artificial intelligence into the metaproteomics pipeline, extended datasets can now be efficiently mined to gain a more comprehensive functional view of complex biological systems, paving the way for next-generation metaproteomics. In this perspective, I discuss the transformative potential of this methodology. We are on the cusp of a remarkable omic revolution that promises to uncover the intricate workings of microbiomes by producing a vast array of new knowledge with multiple applications. SIGNIFICANCE: Metaproteomics provides a powerful lens to investigate microbiome and holobiont functionality by identifying and quantifying active proteins and functional pathways within each taxon. Recent breakthroughs in high-resolution tandem mass spectrometry have dramatically expanded the repertoire of peptide sequences detectable per sample. This progress enables unprecedented taxonomic resolution for microbial identification, more precise biomass quantification, comprehensive protein characterization, abundance monitoring, and the unique identification of host biomarkers. In this commentary, I delve into the distinctive features that make metaproteomics a transformative tool. I discuss the recent advancements in tandem mass spectrometry and argue that the primary challenge in analyzing complex samples is shifting from data acquisition to data interpretation. With the integration of artificial intelligence, I believe next-generation metaproteomics is poised to become the next Big Thing in microbiome research, unlocking profound insights into microbial functionality and ecosystem dynamics.},
}

@article {pmid40077904,
year = {2025},
author = {Brunet, M and Le Duff, N and Barbeyron, T and Thomas, F},
title = {Year-Round Quantification, Structure and Dynamics of Epibacterial Communities From Diverse Macroalgae Reveal a Persistent Core Microbiota and Strong Host Specificities.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70077},
doi = {10.1111/1758-2229.70077},
pmid = {40077904},
issn = {1758-2229},
support = {ANR-10-BTBR-04//Agence Nationale de la Recherche/ ; ANR-18-CE02-0001-01//Agence Nationale de la Recherche/ ; },
mesh = {*Seaweed/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Seasons ; Phylogeny ; Host Specificity ; Ulva/microbiology ; Phaeophyceae/microbiology ; DNA, Bacterial/genetics ; Ecosystem ; Biodiversity ; Rhodophyta/microbiology ; },
abstract = {Macroalgae-bacteria interactions play pivotal ecological roles in coastal ecosystems. Previous characterisation of surface microbiota from various macroalgae evidenced fluctuations based on host tissues, physicochemical and environmental parameters. However, the dynamics and degree of similarity of epibacterial communities colonising phylogenetically distant algae from the same habitat are still elusive. We conducted a year-long monthly epimicrobiota sampling on five algal species inhabiting an English Channel rocky shore: Laminaria digitata, Ascophyllum nodosum, Fucus serratus (brown algae), Palmaria palmata (red alga) and Ulva sp. (green alga). To go beyond relative compositional data and estimate absolute variations in taxa abundance, we combined qPCR measurements of 16S rRNA gene copies with amplicon metabarcoding. A core microbiome composed of 10 genera was consistently found year-round on all algae. Notably, the abundant genus Granulosicoccus stood out for being the only one present in all samples and displayed an important microdiversity. Algal host emerged as the primary driver of epibacterial community composition, before seasonality, and bacterial taxa specifically associated with one or several algae were identified. Moreover, the impact of seasons on the epimicrobiota varied depending on algal tissues. Overall, this study provides an extensive characterisation of the microbiota of intertidal macroalgae and enhances our understanding of algal-bacteria holobionts.},
}

*Seaweed/microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Seasons
Phylogeny
Host Specificity
Ulva/microbiology
Phaeophyceae/microbiology
DNA, Bacterial/genetics
Ecosystem
Biodiversity
Rhodophyta/microbiology

@article {pmid40071145,
year = {2025},
author = {Prioux, C and Ferrier-Pagès, C and Del Campo, J and Guillou, L and Estaque, T and Allemand, D and Tignat-Perrier, R},
title = {Unraveling the impact of marine heatwaves on the Eukaryome of the emblematic Mediterranean red coral Corallium rubrum.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf035},
doi = {10.1093/ismeco/ycaf035},
pmid = {40071145},
issn = {2730-6151},
abstract = {Global warming is intensifying heatwaves worldwide, leading to more frequent and severe temperature extremes. This study investigates the impact of the unprecedented 2022 Mediterranean heatwaves on the coral eukaryome, which has received little attention despite its known importance to coral holobiont functioning. Fifty-six colonies of the iconic red coral Corallium rubrum from the Mediterranean Sea were collected at different sites, depths, and health states. The microeukaryotic communities were analyzed using an 18S rRNA gene metabarcoding approach. Primers were designed to reduce amplification of the 18S rRNA gene sequences of the red coral while being universal for amplification of microeukaryotes. Our results showed that the red coral eukaryome was dominated by Dino-Group I, Licnophoridae, and Labyrinthulomycetes in the control sites that were not affected by the heat waves. In the heat-affected colonies, the composition of the coral eukaryome changed, with the relative abundances of Ephelotidae, Exobasidiomycetes, Corallicolidae, Labyrinthulomycetes, and/or the epibionts Phaeophyceae increasing depending on the intensity of heat stress experienced by the colonies. It was thus possible to link colony health to changes in the eukaryome. Finally, we illustrated putative interactions (competition, predator-prey relationship, and parasitism) occurring within C. rubrum eukaryome that could explain the compositional changes observed in the microeukaryotic communities under heat stress. Our findings improve our understanding of the ecological effects of heatwaves on marine ecosystems.},
}

@article {pmid40060185,
year = {2025},
author = {Khattak, AA and Huang, Y and Afzal, M and Wang, X},
title = {MHZ3: a key regulator of ethylene signaling in rice.},
journal = {aBIOTECH},
volume = {6},
number = {1},
pages = {133-138},
pmid = {40060185},
issn = {2662-1738},
abstract = {The plant hormone ethylene regulates plant growth, development, and stress responses. Recent studies on early signaling events following ethylene perception in rice (Oryza sativa) have identified MAO HU ZI 3 (MHZ3) as a stabilizer of the ethylene receptors ETHYLENE RESPONSE SENSOR 2 (OsERS2) and ETHYLENE RECEPTOR 2 (OsETR2). MHZ3 ensures the interaction of these receptors with CONSTITUTIVE TRIPLE RESPONSE 2 (OsCTR2), thereby maintaining OsCTR2 activity. Ethylene treatment disrupts the interactions within the MHZ3/receptors/OsCTR2 protein complex, leading to decreased OsCTR2 phosphorylation and the initiation of downstream signaling. Recent studies have established MHZ3 as the primary regulator and switch for OsCTR2 phosphorylation. In this review, we explore the role of MHZ3 in regulating ethylene signaling and highlight its effects on plant growth, development, and stress responses at the plant holobiont level.},
}

@article {pmid40057976,
year = {2025},
author = {Nikitashina, V and Bartels, B and Mansour, JS and LeKieffre, C and Decelle, J and Hertweck, C and Not, F and Pohnert, G},
title = {Metabolic interdependence and rewiring in Radiolaria-microalgae Photosymbioses.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf047},
pmid = {40057976},
issn = {1751-7370},
abstract = {Marine planktonic Radiolaria harboring symbiotic microalgae are ubiquitous in the oceans and abundant in oligotrophic areas. In these low-nutrient environments, they are among the most important primary producers. Systematic studies of radiolarian biology are limited because Radiolaria are non-culturable and prone to damage during sampling. To obtain insight into the mechanistic basis of radiolarian photosymbiosis we address here the metabolic contributions of the partners to the performance of the holobiont. Therefore, we describe the metabolic inventory of two highly abundant photosymbiotic Radiolaria - colony-forming Collodaria and single-celled Acantharia and compare their metabolomes to metabolomes of respective free-living algae. Most of the metabolites detected in the symbiosis are not present in the free-living algae, suggesting a significant transformation of symbionts' metabolites by the host. The metabolites identified in both the holobiont and the free-living algae encompass molecules of primary metabolism and a number of osmolytes, including dimethylsulfoniopropionate. Mass spectrometry imaging revealed the presence of dimethylsulfoniopropionate in both the symbionts and host cells, indicating that the algae provide osmolytic protection to the host. Furthermore, our findings suggest a possible dependence of Collodaria on symbiotic vitamin B3. Distinctive differences in phospholipid composition between free-living and symbiotic stages indicate that the algal cell membrane may undergo rearrangement in the symbiosis. Our results demonstrate a strong interdependence and rewiring of the algal metabolism underlying Radiolaria-microalgae photosymbioses.},
}

@article {pmid40057975,
year = {2025},
author = {Adomako, MO and Wu, J and Yu, FH},
title = {Ecological and evolutionary responses of earthworm holobionts to environmental changes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf044},
pmid = {40057975},
issn = {1751-7370},
abstract = {Global environmental change substantially affects soil detritivores, including earthworms, impacting host-microbiota interactions and altering key soil biogeochemical processes such as litter decomposition. As microbial communities are inherently capable of rapid evolution, responses of earthworms and associated microbiota (i.e., earthworm holobionts) to global environmental change may likely involve the interplay of ecological and evolutionary processes and feedbacks. Although species-level responses of earthworms to global environmental change are well-studied, the potential ecological and evolutionary responses of earthworm holobionts to environmental change remain unexplored. Here, we provide a conceptual framework to elaborate on the complex network of earthworm host-microbiota interactions that modify their traits in response to global environmental change, jointly shaping their ecology and evolution. Based on literature, we synthesize evidence of global environmental change impacts on earthworm host-microbiota and discuss evidence of their ecological and evolutionary responses to environmental change. Lastly, we highlight the agro- and eco-system level consequences of environmental change-mediated shift in earthworm host-microbiota functions. Soil legacies of environmental change have cascading detrimental impacts on the abundance, diversity, and functional dynamics of earthworm host-microbiota interactions in agriculture and ecosystems. The primary mechanisms driving such responses of earthworm hosts and associated microbial communities to environmental change include altered litter quality and host dietary preferences, competitive interactions and exclusion, habitat homogenization, and a shift in soil physicochemical and biological processes. Therefore, advancing knowledge of the intricate animal-microorganism interactions is crucial for belowground biodiversity management in a changing global environment.},
}

@article {pmid40054249,
year = {2025},
author = {Walling, LK and Gamache, MH and González-Pech, RA and Harwood, VJ and Ibrahim-Hashim, A and Jung, JH and Lewis, DB and Margres, MJ and McMinds, R and Rasheed, K and Reis, F and van Riemsdijk, I and Santiago-Alarcon, D and Sarmiento, C and Whelan, CJ and Zalamea, PC and Parkinson, JE and Richards, CL},
title = {Incorporating microbiome analyses can enhance conservation of threatened species and ecosystem functions.},
journal = {The Science of the total environment},
volume = {970},
number = {},
pages = {178826},
doi = {10.1016/j.scitotenv.2025.178826},
pmid = {40054249},
issn = {1879-1026},
abstract = {Conservation genomics is a rapidly growing subdiscipline of conservation biology that uses genome-wide information to inform management of biodiversity at all levels. Such efforts typically focus on species or systems of conservation interest, but rarely consider associated microbes. At least three major approaches have been used to study how microorganisms broadly contribute to conservation areas: (1) diversity surveys map out microbial species distribution patterns in a variety of hosts, natural environments or regions; (2) functional surveys associate microbial communities with factors of interest, such as host health, symbiotic interactions, environmental characteristics, ecosystem processes, and biological invasions; and (3) manipulative experiments examine the response of changes to microbial communities or determine the functional roles of specific microbes within hosts or communities by adding, removing, or genetically modifying microbes. In practice, multiple approaches are often applied simultaneously. The results from all three conservation genomics approaches can be used to help design practical interventions and improve management actions, some of which we highlight below. However, experimental manipulations allow for more robust causal inferences and should be the ultimate goal of future work. Here we discuss how further integration of microbial research of a host's microbiome and of free living microbes into conservation biology will be an essential advancement for conservation of charismatic organisms and ecosystem functions in light of ongoing global environmental change.},
}

@article {pmid40054578,
year = {2025},
author = {Zeng, Y and Lu, X and Wang, M and Chen, R and Li, Q and Zhu, J and Su, Z and Lin, F},
title = {Endophyte Acrocalymma vagum establishes the holobiont with rice to attract beneficial microorganisms and promote disease resistance.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.03.008},
pmid = {40054578},
issn = {2090-1224},
abstract = {INTRODUCTION: Endophytic fungi are essential microorganisms in promoting plant health. However, the mechanism of endophytic fungi regulating root microbiota to enhance crop production and resistance remains unclear.

OBJECTIVES: We aimed i) to explore the microbial alteration driven by endophytic Acrocalymma vagum in developing crop yield and rice resistance; ii) to reveal the mechanism of root-released compound stimulated by A. vagum in recruiting benefit microbes.

METHODS: The microbiome was applied in a culture-dependent and culture-independent method to study the microbial communities of the A. vagum-rice holobiont using 16S rRNA and ITS gene metabarcoding. Non-target metabolome identified distinct metabolites responsible for community variations. Label-free proteomic analyses investigated the association between primary genes related to the holobiont formation. CRISPR/Cas9 technique and homologous recombination replacement were used to characterize the functions of putative genes.

RESULTS: A. vagum enhanced cultivated rice yield by 5.73 ± 1.76 % and induced 83.24 ± 9.86 % control efficiency against rice blast. We discovered that A. vagum simplified rice microbial structure based on co-occurrence networks, by lowering the proportion of potentially pathogenic predominant Burkholderia and driving rice to recruit beneficial Lactobacillus, Sarocladium and Nigrospora to promote rice growth with the increases of 44.41 ± 5.10 % shoot height and 70.21 ± 9.57 % shoot biomass. Moreover, the holobiont released coumaric and trans-ferulic acids to attract beneficial microbes. 206 rice proteins were notably up-regulated in the holobiont, particularly the OsPrxs. CRISPR/Cas9-edited mutants of OsPRX70 and OsPRX95 reduced the promotion effect of A. vagum on rice growth. Furthermore, the pathways of 39 overexpressed proteins in A. vagum were enriched in invading the host and inducing resistance. The knockouts of AvGH3, AvGH7, AvMFS1, and AvCBA transformed A. vagum role from endophyte to pathogen.

CONCLUSIONS: The A. vagum-rice holobiont releases recruitment signals and improves the rice community structure. We provide ecological and molecular evidence to confirm the mutualism of endophyte-plant-promoting growth and disease resistance.},
}

@article {pmid40054197,
year = {2025},
author = {Jiang, S and He, L and Cao, L and Sun, R and Dai, Z and Liang, YQ and Ren, L and Sun, S and Li, C},
title = {Unraveling individual and combined toxicity of microplastics and tetracycline at environment-related concentrations to coral holobionts.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137823},
doi = {10.1016/j.jhazmat.2025.137823},
pmid = {40054197},
issn = {1873-3336},
abstract = {Coral holobionts constitute the foundational organisms of coral reef ecosystems. As an emerging pollutant, the projected accumulated levels of microplastics (MPs) are expected to continue increasing. Meanwhile, due to their properties, MPs can absorb multiple other marine pollutants, such as antibiotics (ATs). However, the co-toxicity mechanism of MPs and ATs to coral holobionts remains to be explored. Here, using Zoanthus sociatus as a model organism, we investigate the individual and combined toxicity of MPs and tetracycline (TC) at environment-related concentrations to coral holobionts. Microbiomics indicate that MPs and TC increase coral holobionts bacterial species richness while concurrently reducing the microbial community structure stability. The key metabolites and enzyme activity results demonstrated that the impacts of MPs and TC on corals encompassed antioxidant capacity, detoxification capability, immune function, and lipid metabolism. Transcriptomics shows that MPs and TC disrupt coral-algae relationships mainly through host nutrition limitation and inhibition of symbiotic algae carbon/nitrogen metabolism, respectively. A synergistic effect between MPs and TC has also been observed. In contrast, coral holobionts have shown adaptability through activating coral-symbiodiniaceae-bacteria interactions, mainly including: 1) enhancing the abundance of BMCs (beneficial microorganisms for corals); 2) enhancing host lipid accumulation; 3) immunoregulation; 4) symbiotic regulation. Overall, our findings provide new insights into the co-toxicity of MPs and TC, and highlight those MPs and TC at current environment concentration and predicted for most oceans in the coming decades, can ultimately cause coral bleaching.},
}

@article {pmid40048537,
year = {2025},
author = {Kistler, L and de Oliveira Freitas, F and Gutaker, RM and Maezumi, SY and Ramos-Madrigal, J and Simon, MF and Mendoza F, JM and Drovetski, SV and Loiselle, H and de Oliveira, EJ and Vieira, EA and Carvalho, LJCB and Ellis Perez, M and Lin, AT and Liu, HL and Miller, R and Przelomska, NAS and Ratan, A and Wales, N and Wann, K and Zhang, S and García, M and Valenzuela, D and Rothhammer, F and Santoro, CM and Domic, AI and Capriles, JM and Allaby, RG},
title = {Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation.},
journal = {Science (New York, N.Y.)},
volume = {387},
number = {6738},
pages = {eadq0018},
doi = {10.1126/science.adq0018},
pmid = {40048537},
issn = {1095-9203},
mesh = {*Manihot/genetics ; *Genome, Plant ; *Genetic Variation ; *Crops, Agricultural/genetics ; Brazil ; Domestication ; Heterozygote ; Gene Pool ; },
abstract = {Manioc-also called cassava and yuca-is among the world's most important crops, originating in South America in the early Holocene. Domestication for its starchy roots involved a near-total shift from sexual to clonal propagation, and almost all manioc worldwide is now grown from stem cuttings. In this work, we analyze 573 new and published genomes, focusing on traditional varieties from the Americas and wild relatives from herbaria, to reveal the effects of this shift to clonality. We observe kinship over large distances, maintenance of high genetic diversity, intergenerational heterozygosity enrichment, and genomic mosaics of identity-by-descent haploblocks that connect all manioc worldwide. Interviews with Indigenous traditional farmers in the Brazilian Cerrado illuminate how traditional management strategies for sustaining, diversifying, and sharing the gene pool have shaped manioc diversity.},
}

*Manihot/genetics
*Genome, Plant
*Genetic Variation
*Crops, Agricultural/genetics
Brazil
Domestication
Heterozygote
Gene Pool

@article {pmid40038092,
year = {2025},
author = {Million, WC and Voolstra, CR and Perna, G and Puntin, G and Rowe, K and Ziegler, M},
title = {Resolving Symbiodiniaceae Diversity Across Coral Microhabitats and Reef Niches.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70065},
doi = {10.1111/1462-2920.70065},
pmid = {40038092},
issn = {1462-2920},
support = {//German Academic Exchange Service/ ; 469364832//Deutsche Forschungsgemeinschaft/ ; SPP 2299/441832482//Deutsche Forschungsgemeinschaft/ ; //King Abdullah University of Science and Technology/ ; },
mesh = {Animals ; *Coral Reefs ; *Anthozoa ; *Dinoflagellida/classification/genetics/physiology ; *Ecosystem ; *Symbiosis ; *Biodiversity ; Seawater/microbiology ; Phylogeny ; Indian Ocean ; },
abstract = {Dinoflagellates of the family Symbiodiniaceae are important symbionts of diverse marine animals and they also occupy different environmental niches on coral reefs. The link between diversity at ecosystem-scale to microhabitats of Symbiodiniaceae within the coral holobiont is largely unknown. Using ITS2-amplicon sequencing, we compared Symbiodiniaceae communities across four environments (seawater, near-reef vs. distant sediments and turf algae) and two coral microhabitats (tissue, mucus) on a coral reef in the Red Sea. We found that coral and environmental habitats were both dominated by the genera Symbiodinium, Cladocopium and Durusdinium, but environmental habitats additionally harboured Fugacium, Gerakladium and Halluxium. Each environmental habitat harboured a distinct Symbiodiniaceae community. Nonetheless, 17 ITS2 sequences were shared among coral and environmental habitats and were also part of nearly half of the ITS2 type profiles in coral-based communities. Tissues and mucus of 49 coral colonies from 17 genera had largely identical Symbiodiniaceae communities. Together with the large difference between environmental Symbiodiniaceae communities and those in the coral tissue and mucus, our results indicate a clear barrier between host-associated and environmental Symbiodiniaceae communities marked by only few shared complete type profiles. Monitoring coral colonies after mucus sampling confirmed its suitability for long-term monitoring of coral-associated Symbiodiniaceae communities.},
}

Animals
*Coral Reefs
*Anthozoa
*Dinoflagellida/classification/genetics/physiology
*Ecosystem
*Symbiosis
*Biodiversity
Seawater/microbiology
Phylogeny
Indian Ocean

@article {pmid40037084,
year = {2025},
author = {Zhang, J and Liu, C and Ling, J and Zhou, W and Wang, Y and Cheng, H and Huang, X and Yang, Q and Zhang, W and Liang, T and Zhang, Y and Dong, J},
title = {Revealing the potential of biochar for heavy metal polluted seagrass remediation from microbial perspective.},
journal = {Ecotoxicology and environmental safety},
volume = {292},
number = {},
pages = {117991},
doi = {10.1016/j.ecoenv.2025.117991},
pmid = {40037084},
issn = {1090-2414},
abstract = {Seagrass meadows are under threat due to climate change and human activities, including heavy metal contamination, which can accumulate in seagrass tissues and harm their health and productivity. Despite extensive research, effective remediation strategies are lacking. This study investigated biochar's potential as a remediation agent for seagrass meadows affected by heavy metal pollution. Heavy metal pollution was simulated by adding copper (Cu) and chromium (Cd) to seagrass Thalassia hemprichii, and the remediation effects of biochar were evaluated by monitoring seagrass physiology, root-associated microbial communities, and heavy metal concentrations. Seagrasses can accumulate heavy metals, which adversely affect their health and alter microbial communities. Seagrasses may resist heavy metal stress by releasing dissolved organic carbon (DOC) and recruiting beneficial bacteria. Biochar reduced heavy metal bioavailability and restored seagrass ecosystem health, as evidenced by restored microbial community dynamics. This study highlights biochar's promising role in seagrass meadow restoration impacted by heavy metal pollution.},
}

@article {pmid40034670,
year = {2025},
author = {Adair, MG and Tolley, KA and van Vuuren, BJ and da Silva, JM},
title = {Anthropogenic reverberations on the gut microbiome of dwarf chameleons (Bradypodion).},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18811},
pmid = {40034670},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *RNA, Ribosomal, 16S/genetics ; *Lizards/microbiology ; Feces/microbiology ; Ecosystem ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Exploration of the microbiome has been referred to as a final frontier in biological research. This is due to its precedence for generating insights on the holistic functioning of organismal biology by exploring the interactions between hosts and their associated symbiotic organisms. The microbiomes of many vertebrate groups still require exploration to advance current knowledge and fill previous knowledge gaps. This study generated initial descriptions of the bacterial microbiomes of three species of dwarf chameleon (Bradypodion) from the 16S rRNA gene region targeting the V3 and V4 hypervariable regions. This led to the successful identification of 1,073 and 4,502 independent amplicon sequence variants from buccal swab and faecal material samples, respectively. This newly acquired information is intended as a baseline for future work incorporating holobiont information. The diversity of microbial taxa suggests that the total dwarf chameleon microbiome is similar to other squamates investigated to date, as well as chelonians (Testudines). Microbial frequency differences were noted in comparison to crocodilians (Archosauria) and mammalian groups. Furthermore, this study aimed to examine the influence of habitat transformation on the composition of the microbiome in dwarf chameleons as each of the study species occupy both urban and natural habitats. Given that most urban habitats are highly transformed, the expectation was that microbial assemblages of the gastro-intestinal tracts of all three Bradypodion species would show significant differences between populations (i.e., natural, or urban). It was found, however, that the level of effect was contingent on species: B. melanocephalum populations showed noticeable microbiome differences between urban and natural populations; B. thamnobates showed variations in microbial community dispersions between populations; and B. setaroi showed no significant microbiome differences based on diversity metrics although some frequency differences, in microbiome composition, were observed between populations. We suggest that the magnitude of difference between the habitats occupied by the populations is a factor, given the apparent disparity between the natural and urban habitats for B. melanocephalum as compared to the other two species.},
}

Animals
*Gastrointestinal Microbiome/genetics/physiology
*RNA, Ribosomal, 16S/genetics
*Lizards/microbiology
Feces/microbiology
Ecosystem
Bacteria/genetics/classification/isolation & purification

@article {pmid39952679,
year = {2025},
author = {Lobo, D and Morales, HE and Van Oosterhout, C and López-Bao, JV and Silva, P and Llaneza, L and Pacheco, C and Castro, D and Hernández-Alonso, G and Pacheco, G and Archer, J and Gilbert, MTP and Ferrand, N and Godinho, R},
title = {Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279093.124},
pmid = {39952679},
issn = {1549-5469},
abstract = {Understanding how large carnivores respond to increasingly human-dominated landscapes will determine their future adaptive potential. The Iberian wolf (Canis lupus signatus), a gray wolf subspecies endemic to the Iberian Peninsula (Portugal and Spain), has uniquely persisted in human-dominated landscapes, unlike many other wolf populations that faced widespread extinction across Europe during the twentieth century. In this study, we conducted a comprehensive genome-wide analysis of 145 historical and contemporary Iberian wolf samples to investigate whether hybridization with domestic dogs resulted in genetic introgression. We identified a dog-derived block on Chromosome 2 in Iberian wolves, displaying signatures consistent with introgression and high nucleotide similarity among introgressed individuals. Additionally, our estimates place the average timing of introgression between 6100 and 3000 years ago, with low sequence divergence to dogs from the Iberian Peninsula suggesting a single local origin for the hybridization event. Using forward genetic simulations, we show that the introgressed haplotype is most likely being maintained in Iberian wolves by selection. The introgressed dog variants are located within the MAST4 gene, which has been linked to neurological disorders, including cognitive and motor developmental delays, hinting at a potential role in cognitive behavior in Iberian wolves. This study uncovers a case of putative adaptive introgression from domestic dogs into wolves, offering new insights into wild canids' adaptation to human-dominated landscapes.},
}

@article {pmid40028829,
year = {2025},
author = {Leiva, C and Torda, G and Zhou, C and Pan, Y and Harris, J and Xiang, X and Tan, S and Tian, W and Hume, B and Miller, DJ and Li, Q and Zhang, G and Cooke, I and Rodolfo-Metalpa, R},
title = {Rapid Evolution in Action: Environmental Filtering Supports Coral Adaptation to a Hot, Acidic, and Deoxygenated Extreme Habitat.},
journal = {Global change biology},
volume = {31},
number = {3},
pages = {e70103},
doi = {10.1111/gcb.70103},
pmid = {40028829},
issn = {1365-2486},
support = {DE200101064//Australian Research Council's Discovery Early Career Award/ ; Adaptationofcoralstoclimatechange//French Government's Ministry of Foreign Affairs' Fonds Pacifique scheme/ ; //Flotte Océanographique Française/ ; OIA-1946352//National Science Foundation NSF-EPSCoR/ ; //BGI Australia through the BGI Biodiversity Research Grant/ ; //China National GeneBank/ ; },
mesh = {Animals ; *Anthozoa/physiology/genetics ; New Caledonia ; Symbiosis ; Hot Temperature ; Ecosystem ; Hydrogen-Ion Concentration ; Extreme Environments ; Adaptation, Physiological/genetics ; Climate Change ; Biological Evolution ; Oxygen/metabolism/analysis ; Coral Reefs ; Polymorphism, Single Nucleotide ; Stress, Physiological ; },
abstract = {The semienclosed Bouraké lagoon in New Caledonia is a natural system that enables observation of evolution in action with respect to stress tolerance in marine organisms, a topic directly relevant to understanding the consequences of global climate change. Corals inhabiting the Bouraké lagoon endure extreme conditions of elevated temperature (> 33°C), acidification (7.2 pH units), and deoxygenation (2.28 mg O2 L-1), which fluctuate with the tide due to the lagoon's geomorphology. To investigate the underlying bases of the apparent stress tolerance of these corals, we combined whole genome resequencing of the coral host and ITS2 metabarcoding of the photosymbionts from 90 Acropora tenuis colonies from three localities along the steep environmental gradient from Bouraké to two nearby control reefs. Our results highlight the importance of coral flexibility to associate with different photosymbionts in facilitating stress tolerance of the holobiont; but, perhaps more significantly, strong selective effects were detected at specific loci in the host genome. Fifty-seven genes contained SNPs highly associated with the extreme environment of Bouraké and were enriched in functions related to sphingolipid metabolism. Within these genes, the conserved sensor of noxious stimuli TRPA1 and the ABCC4 transporter stood out due to the high number of environmentally selected SNPs that they contained. Protein 3D structure predictions suggest that a single-point mutation causes the rotation of the main regulatory domain of TRPA1, which may be behind this case of natural selection through environmental filtering. While the corals of the Bouraké lagoon provide a striking example of rapid adaptation to extreme conditions, overall, our results highlight the need to preserve the current standing genetic variation of coral populations to safeguard their adaptive potential to ongoing rapid environmental change.},
}

Animals
*Anthozoa/physiology/genetics
New Caledonia
Symbiosis
Hot Temperature
Ecosystem
Hydrogen-Ion Concentration
Extreme Environments
Adaptation, Physiological/genetics
Climate Change
Biological Evolution
Oxygen/metabolism/analysis
Coral Reefs
Polymorphism, Single Nucleotide
Stress, Physiological

@article {pmid40015318,
year = {2025},
author = {Mudlaff, CM and Weinberger, F and Düsedau, L and Ghotbi, M and Künzel, S and Bonthond, G},
title = {Seasonal Cycles in a Seaweed Holobiont: A Multiyear Time Series Reveals Repetitive Microbial Shifts and Core Taxa.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70062},
doi = {10.1111/1462-2920.70062},
pmid = {40015318},
issn = {1462-2920},
support = {WE2700/5-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Seasons ; *Microbiota ; *Seaweed/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Gracilaria/microbiology ; },
abstract = {Seasonality is an important natural feature that drives cyclic environmental changes. Seaweed holobionts, inhabiting shallow waters such as rocky shores and mud flats, are subject to seasonal changes in particular, but little is known about the influence of seasonality on their microbial communities. In this study, we conducted a three-year time series, sampling at two-month intervals, to assess the seasonality of microbial epibiota in the seaweed holobiont Gracilaria vermiculophylla. Our results reveal pronounced seasonal shifts that are both taxonomic and functional, oscillating between late winter and early summer across consecutive years. While epibiota varied taxonomically between populations, they were functionally similar, indicating that seasonal variability drives functional changes, while spatial variability is more redundant. We also identified seasonal core microbiota that consistently (re)associated with the host at specific times, alongside a permanent core that is present year-round, independent of season or geography. These findings highlight the dynamic yet resilient nature of seaweed holobionts and demonstrate that their epibiota undergo predictable changes. Therewith, this research offers important insights into the temporal dynamics of seaweed-associated microbiota and demonstrates that the relationship between seaweed host and its epibiota is not static but naturally subject to an ongoing seasonal succession process.},
}

*Seasons
*Microbiota
*Seaweed/microbiology
*Bacteria/classification/genetics/isolation & purification
Gracilaria/microbiology

@article {pmid40005803,
year = {2025},
author = {Minerdi, D and Sabbatini, P},
title = {Exploring the Grapevine Microbiome: Insights into the Microbial Ecosystem of Grape Berries.},
journal = {Microorganisms},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/microorganisms13020438},
pmid = {40005803},
issn = {2076-2607},
abstract = {Plant growth, health, and resilience to stress are intricately linked to their associated microbiomes. Grapevine, functioning as a holobiont, forms essential relationships with fungi and bacteria across both its belowground (roots) and aboveground (leaves and berries) compartments. The root microbiome exhibits a stable, site-specific structure, whereas the microbiomes of ephemeral tissues such as leaves and berries, which regenerate annually, display more stochastic assembly patterns across growing seasons. Among these, grape berries represent a critical component in viticulture due to their direct influence on wine quality and flavor complexity. Berries provide a unique ecological niche, hosting diverse microbial communities composed of yeasts, bacteria, and fungi that interact with the grapevine and its surrounding environment. These microorganisms are not only pivotal to berry development but also contribute significantly to the synthesis of secondary metabolites and fermentation processes, ultimately shaping the sensory and organoleptic properties of wine. This review consolidates current knowledge on the grapevine microbiome, with a particular emphasis on the microbial dynamics of grape berries.},
}

@article {pmid40003826,
year = {2025},
author = {Castañeda-Espinosa, A and Duque-Granda, D and Cadavid-Restrepo, G and Murcia, LM and Junca, H and Moreno-Herrera, CX and Vivero-Gómez, RJ},
title = {Study of Bacterial Communities in Water and Different Developmental Stages of Aedes aegypti from Aquatic Breeding Sites in Leticia City, Colombian Amazon Biome.},
journal = {Insects},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/insects16020195},
pmid = {40003826},
issn = {2075-4450},
support = {57545//Universidad Nacional de Colombia/ ; },
abstract = {Aedes aegypti is a key vector in the transmission of arboviral diseases in the Colombian Amazon. This study aimed to characterize microbiota composition using DNA extracted from water in artificial breeding sites, immature stages, and adults of Ae. aegypti in Leticia, Amazonas. Additionally, the physicochemical water variables were correlated with the bacterial communities present. Eight artificial breeding sites were identified, with bucket, plant pot, and tire being the most frequent. The breeding sites exhibited similar physicochemical profiles, with significant temperature and salinity differences (p-value < 0.03). The most representative bacterial genera included Ottowia (82%), Xanthobacter (70.59%), and Rhodocyclaceae (92.78%) in breeding site water; Aquabacterium (61.07%), Dechloromonas (82.85%), and Flectobacillus (58.94%) in immature stages; and Elizabethkingia (70.89%) and Cedecea (39.19%) in males and females of Ae. aegypti. Beta diversity analysis revealed distinct clustering between adults and the water and immature communities (p-value < 0.001). Multivariate analysis showed strong correlations among bacterial communities, breeding sites, and physicochemical variables such as tire and drum cover which exhibited high levels of total dissolved solids, conductivity, and salinity associated with Flectobacillus, Leifsonia, Novosphingobium, Ottowia, and Rhodobacter. Bacterial genera such as Mycobacterium, Escherichia, Salmonella, and Clostridium, present in artificial breeding sites, are associated with public health relevance. This study provides insights into bacterial community dynamics across Ae. aegypti's life cycle and underscores the importance of water physicochemical and biological characteristics for developing new vector control strategies.},
}

@article {pmid39998222,
year = {2025},
author = {Williamson, EM and Hammer, TJ and Hogendoorn, K and Eisenhofer, R},
title = {Blanking on blanks: few insect microbiota studies control for contaminants.},
journal = {mBio},
volume = {},
number = {},
pages = {e0265824},
doi = {10.1128/mbio.02658-24},
pmid = {39998222},
issn = {2150-7511},
abstract = {Research on insect-microbe relationships is booming, with DNA sequencing being the most commonly used method to describe insect microbiota. However, sequencing is vulnerable to contamination, especially when the sample has low microbial biomass. Such low-biomass samples are common across insect taxa, developmental stages, and tissue types. Identifying putative contaminants is essential to distinguish between true microbiota and introduced contaminant DNA. It is therefore important that studies control for contamination, but how often this is done is unknown. To investigate the status quo of contamination control, we undertook a systematic literature review to quantify the prevalence of negative control usage and contamination control across the literature on insect microbiota (specifically bacterial communities) over a 10 year period. Two-thirds of the 243 insect microbiota studies evaluated had not included blanks (negative controls), and only 13.6% of the studies sequenced these blanks and controlled for contamination in their samples. Our findings highlight a major lack of contamination control in the field of insect microbiota research. This result suggests that a number of microbes reported in the literature may be contaminants as opposed to insect-associated microbiota and that more rigorous contamination control is needed to improve research reliability, validity, and reproducibility. Based on our findings, we recommend the previously developed guidelines outlined in the RIDE checklist, with the addition of one more guideline. We refer to this as the RIDES checklist, which stands for Report methodology, Include negative controls, Determine the level of contamination, Explore contamination downstream, and State the amount of off-target amplification.IMPORTANCEOur systematic review reveals a major lack of methodological rigor within the field of research on insect-associated microbiota. The small percentage of studies that control for contamination suggests that an unknown but potentially considerable number of bacteria reported in the literature could be contaminants. The implication of this finding is that true microbiota may be masked or misrepresented, especially in insects with low microbial biomass.},
}

@article {pmid39993925,
year = {2025},
author = {Sajid, S and Xiao, B and Zhang, G and Zhang, Z and Chen, L and Fang, JK and Lu, Y and Cai, L},
title = {Increased sulfate-reducing bacteria can drive microbial dysbiosis in bleached corals.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf043},
pmid = {39993925},
issn = {1365-2672},
abstract = {AIMS: Coral bleaching occurs when coral colonies lose their Symbiodiniaceae partner and turn pale or white. Although this event is generally temperature-induced, there is also the possibility of holobiont microbial infection and dysbiosis. To address this issue, this study was conducted to investigate the diversity and composition of Symbiodiniaceae and bacteria in healthy and bleached colonies of Porites lutea collected from eastern Shenzhen.

METHODS AND RESULTS: Internal transcribed spacer 2 (ITS2) and 16S amplicon sequencing analysis were used to explore the diversity and composition of Symbiodiniaceae and bacteria in healthy and bleached colonies of P. lutea. Bacterial diversity and richness were significantly higher in bleached colonies than in healthy colonies (P < 0.05), whereas the diversity and richness of Symbiodiniaceae showed no significant changes. The bleaching event exerted a more significant impact on Symbiodiniaceae composition, which differed between healthy and bleached colonies (PERMANOVA, F = 8.246, P < 0.05). In terms of composition, Clade C (Cladocopium) was the predominant Symbiodiniaceae, whereas subclade C116 and C2r were significantly less abundant in bleached colonies than in healthy colonies (P < 0.05). The phyla Bacteroidetes, Acidobacteria, and Actinobacteria were significantly more abundant in bleached colonies than in healthy colonies (P < 0.05). The sulfate-reducing bacteria (SRB) Desulfobulbus and Desulfobacter at the genus level and Desulfobacterales and Desulfuromonadales at the order level were significantly more abundant in bleached colonies than in healthy colonies (P < 0.05). The co-occurrence patterns of Symbiodiniaceae and bacteria revealed a negative correlation of Desulfofaba, Desulfovibrio, Desulfarculus, and Desulfobulbus with Endozoicomonas, a very common symbiotic bacterial genus found in corals.

CONCLUSION: Coral bleaching may be associated with significant shifts in microbial communities, including increased SRB abundance, which may disrupt microbial balance and contribute to bleaching.},
}

@article {pmid39985228,
year = {2025},
author = {Song, MJ and Freund, F and Tribble, CM and Toffelmier, E and Miller, C and Bradley Shaffer, H and Li, FW and Rothfels, CJ},
title = {The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e70010},
doi = {10.1002/ajb2.70010},
pmid = {39985228},
issn = {1537-2197},
support = {//California Conservation Genomics Project, with funding provided to the University of California by the State of California, State Budget Act of 2019 [UC Award ID RSI-19-690224]./ ; },
abstract = {PREMISE: Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown.

METHODS: We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction.

RESULTS: Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome.

CONCLUSIONS: These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.},
}

@article {pmid39984283,
year = {2025},
author = {Adouane, E and Hubas, C and Leblanc, C and Lami, R and Prado, S},
title = {Multi-omics analysis of the correlation between surface microbiome and metabolome in Saccharina latissima (Laminariales, Phaeophyceae).},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae160},
pmid = {39984283},
issn = {1574-6941},
abstract = {The microbiome of Saccharina latissima, an important brown macroalgal species in Europe, significantly influences its health, fitness, and pathogens resistance. Yet, comprehensive studies on the diversity and function of microbial communities (bacteria, eukaryotes, and fungi) associated with this species are lacking. Using metabarcoding, we investigated the epimicrobiota of S. latissima and correlated microbial diversity with metabolomic patterns (LC-MS/MS). Specific epibacterial and eukaryotic communities inhabit the S. latissima surface, alongside a core microbiota, while fungal communities show lower and more heterogeneous diversity. Metabolomic analysis revealed a large diversity of mass features, including putatively annotated fatty acids, amino derivatives, amino acids, and naphthofurans. Multiple-factor analysis linked microbial diversity with surface metabolome variations, driven mainly by fungi and bacteria. Two taxa groups were identified: one associated with bacterial consortia and the other with fungal consortia, each correlated with specific metabolites. This study demonstrated a core bacterial and eukaryotic microbiota associated with a core metabolome and highlighted interindividual variations. Annotating the surface metabolome using Natural Products databases suggested numerous metabolites potentially involved in inter-species chemical interactions. Our findings establish a link between microbial community structure and function, identifying two microbial consortia potentially involved in the chemical defense of S. latissima.},
}

@article {pmid39980208,
year = {2025},
author = {Holman, LE and Zampirolo, G and Gyllencreutz, R and Scourse, J and Frøslev, T and Carøe, C and Gopalakrishnan, S and Pedersen, MW and Bohmann, K},
title = {Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14086},
doi = {10.1111/1755-0998.14086},
pmid = {39980208},
issn = {1755-0998},
support = {856488//H2020 European Research Council/ ; },
abstract = {The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.},
}

@article {pmid39974953,
year = {2025},
author = {Cansado-Utrilla, C and Saldaña, MA and Golovko, G and Khanipov, K and Wild, AL and Brettell, LE and Weaver, SC and Heinz, E and Hughes, GL},
title = {Mosquito host background influences microbiome-ZIKV interactions in field and laboratory-reared Aedes aegypti.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.02.636091},
pmid = {39974953},
issn = {2692-8205},
abstract = {UNLABELLED: The mosquito microbiota represents an intricate assemblage of microorganisms, comprising bacteria, fungi, viruses, and protozoa. Factors modulating microbiome abundance and composition include host genetic background, environmental parameters, and pathogen exposure. Conversely, the microbiome profoundly influences pathogen infection of the mosquito host and thus harbours considerable potential to impact the transmission of vector-borne diseases. As such, there is a growing interest in using the microbiome in novel vector-control strategies, including exploiting the natural ability of some microbes to interfere with infection of the vectors by pathogens. However, before novel microbiome-based vector control approaches can move towards translation, a more complete understanding of the interactions between mosquitoes, their microbiome, and the pathogens they transmit, is required to better appreciate how variation in the microbiome of field mosquitoes affects these interactions. To examine the impact of the host background and the associated diversity of microbiomes within distinct hosts, but without artificially manipulating the microbiome, we exposed several laboratory-reared and field-collected Aedes aegypti mosquito lines to Zika virus (ZIKV) and correlated their microbial load and composition to pathogen exposure and viral infection success. We observed significant differences in ZIKV exposure outcomes between the different mosquito lines and their associated microbiomes, and found that ZIKV alteration of the microbiomes was distinct in different lines. We also identified microbial taxa correlating with either ZIKV infection or a lack of infection. In summary, our study provides novel insights into the variability of pathogen interactions within the mosquito holobiont. A more complete understanding of which factors influence the tripartite interactions between Aedes mosquitoes, their microbiome, and arboviral pathogens, will be critical for the development of microbial-based interventions aimed at reducing vector-borne disease burden.

AUTHOR SUMMARY: The mosquito microbiome composition differs within an individual across its development, as well as between individual mosquitoes at the same developmental stage, and between spatially or genomically different mosquito populations. The microbiome is highly relevant for the ability of mosquitoes to transmit pathogens. Furthermore, certain microbes have been shown to influence pathogen infection of the mosquito, while conversely, infection with a pathogen can alter the mosquito microbiome. However, we have a poor understanding how universally conserved these pathogen-related effects observed in a specific host-microbiome combination are in different mosquito populations with their respective microbiomes. To address this, we infected different mosquito lines, either reared in the laboratory or caught in the field and examined the microbiomes after exposure to Zika virus (ZIKV) compared to unchallenged microbiomes. We also examined how the virus infection progressed in different mosquito lines and correlations with further microbiome changes. The observed microbiome responses differed between host lines, potentially due to either different microbiomes associated with the respective hosts. Alternatively, the host may respond differently to the viral infection, which subsequently alters the microbiome in a distinct manner, or a combination of host and microbiome effects may occur. As microbes are being evaluated for novel approaches to control mosquito-borne disease, our findings are highly relevant to contribute to a more complete understanding of host-microbe interactions which will be critical to develop these approaches. Variation of the microbiome of different mosquito lines need to be considered in experimental designs and when interpreting results from specific studies. It is especially relevant for deployment of interventions in the field where microbial variability is known to be higher and where variation is observed between mosquito populations.},
}

@article {pmid39965412,
year = {2025},
author = {Secomandi, E and De Gregorio, MA and Garcia-Perez, P and Vaccari, F and Puglisi, E and Lucini, L},
title = {Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: A multi-omics perspective on root metabolome, root exudation and rhizomicrobiome.},
journal = {Plant physiology and biochemistry : PPB},
volume = {221},
number = {},
pages = {109646},
doi = {10.1016/j.plaphy.2025.109646},
pmid = {39965412},
issn = {1873-2690},
abstract = {Despite the growing evidence on unique and unpredictable impact of stress combination over plants, waterlogging-combined stresses effects are still underexplored. Under those conditions, besides the impairment of plant aerial parts, the root system is particularly vulnerable, leading to consequences on plant survival. Here, we report on the short-term exposure of soil-grown Arabidopsis thaliana L. to waterlogging alone and combined with cold, heat, and salinity to inspect their antagonistic, additive or synergistic effects in the rhizosphere. To this aim, root metabolic changes, exudation profiles, and microbial diversity were investigated using a combination of metabolomics and metagenomics, and their interaction was analysed through multi-omics data integration. In roots, waterlogging strongly affected metabolism compared to other single stresses, causing a down-accumulation of targeted classes of compounds including, phenylpropanoids, sterols, terpenoids, and alkaloids. Additive and synergistic effects were reported in roots under waterlogging combined with heat and cold stresses, respectively. Regarding root exudates, flavonoids, terpenoids, and alkaloids were the main classes of compounds affected. Waterlogging caused a down-accumulation of all classes except for coumarins, and mixed trends were observed in waterlogging-combined stresses, with waterlogging-salinity stresses resulting in an ameliorating effect. Even though microbial communities' alpha- and beta-diversity remained stable, suggesting their resilience under short-term exposure, specific taxa modulation was recorded under each condition. Overall, these results contribute to understanding the hierarchical impact of waterlogging on root metabolism and exudation, influencing rhizosphere interactions. This multi-omics approach advances our understanding of plant stress responses and microbial dynamics, paving the way for future studies on adaptive mechanisms.},
}

@article {pmid39955302,
year = {2025},
author = {Khogali, R and Bastos, A and Getange, D and Bargul, JL and Kalayou, S and Ongeso, N and Verhoeven, JTP and Kabii, J and Ngiela, J and Masiga, D and Villinger, J},
title = {Exploring the microbiomes of camel ticks to infer vector competence: insights from tissue-level symbiont-pathogen relationships.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5574},
pmid = {39955302},
issn = {2045-2322},
support = {101000365/ERC_/European Research Council/International ; 101000365/ERC_/European Research Council/International ; 101000365/ERC_/European Research Council/International ; 101000365/ERC_/European Research Council/International ; 101000365/ERC_/European Research Council/International ; },
mesh = {Animals ; *Camelus/microbiology/parasitology ; *Symbiosis ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Rickettsia/genetics/isolation & purification ; Salivary Glands/microbiology ; Ticks/microbiology ; Coxiella/genetics/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; Saliva/microbiology ; Female ; Kenya ; Phylogeny ; },
abstract = {Ticks are blood-feeding ectoparasites that harbor diverse pathogens and endosymbionts. Their microbial communities vary based on tick species, stage, sex, geographical location, surrounding environment, and tissue type. Understanding tick microbiota at the tissue level is crucial for unraveling how microbiomes are distributed in tick tissues and influence pathogen transmission. We used V1-V2 16 S rRNA gene sequencing to analyze tissue-specific bacterial compositions (hemolymph, saliva, salivary glands, and midgut) of Amblyomma gemma, Rhipicephalus pulchellus, Hyalomma dromedarii, and Hyalomma rufipes ticks collected from camels in Marsabit County, northern Kenya. The V1-V2 region of the 16 S rRNA gene effectively differentiated 43 Rickettsia africae and 16 Rickettsia aeschlimannii tick samples from other rickettsial species, as well as Coxiella endosymbionts from Coxiella burnetii. In contrast, the V3-V4 region sequences of these species could not be clearly distinguished. Coxiella endosymbionts were most common in Am. gemma and Rh. pulchellus, while Francisella endosymbionts predominated in Hyalomma ticks; both were primarily localized in the salivary glands. High abundances of Coxiella endosymbionts, as well as Pseudomonas, were associated with the absence or low abundance of Rickettsia pathogens in both Am. gemma and Rh. pulchellus, suggesting competitive interactions between these microbes. Additionally, Proteus mirabilis, an opportunistic pathogen of the urinary tract in humans, was found predominantly in Hyalomma ticks, except for the salivary glands, which were most abundant with Francisella endosymbionts. Furthermore, we detected the Acinetobacter, Pseudomonas, and Corynebacterium genera in all the tick tissues, supporting the hypothesis that these bacteria might circulate between camel blood and ticks. Saliva and hemolymph generally harbored more extracellular bacteria than the salivary glands and midgut. This study provides a new approach to unravel tick-endosymbiont-pathogen interactions by examining the tissue localization of tick-borne pathogens and symbionts in Am. gemma, Rh. pulchellus, Hy. dromedarii, and Hy. rufipes from camels in northern Kenya. Our findings establish a baseline for developing an understanding of the functional capacities of symbionts and for designing symbiont-based control strategies.},
}

Animals
*Camelus/microbiology/parasitology
*Symbiosis
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
*Rickettsia/genetics/isolation & purification
Salivary Glands/microbiology
Ticks/microbiology
Coxiella/genetics/isolation & purification
Bacteria/genetics/classification/isolation & purification
Saliva/microbiology
Female
Kenya
Phylogeny

@article {pmid39955557,
year = {2025},
author = {Hernández, M and Langa, J and Aizpurua, O and Navarro-Noya, YE and Alberdi, A},
title = {Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {15},
pmid = {39955557},
issn = {2524-4671},
support = {POS_2022_1_0011//Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
abstract = {Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.},
}

@article {pmid39953749,
year = {2025},
author = {Aizpurua, O and Botnen, AB and Eisenhofer, R and Odriozola, I and Santos-Bay, L and Bjørnsen, MB and Gilbert, MTP and Alberdi, A},
title = {Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17695},
doi = {10.1111/mec.17695},
pmid = {39953749},
issn = {1365-294X},
support = {CF20-0460//Carlsbergfondet/ ; 17417//Villum Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
abstract = {Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.},
}

@article {pmid39947860,
year = {2025},
author = {Hu, J and Camerón, H and Rilling, JI and Campos, M and Ruiz-Gil, T and Gonzalez, MA and Gajardo, G and Vergara, K and Guzmán, L and Espinoza-González, O and Fuenzalida, G and Riquelme, C and Ueki, S and Nagai, S and Maruyama, F and Fujiyoshi, S and Yarimizu, K and Perera, IU and Ávila, A and Acuña, JJ and Zhang, Q and Jorquera, MA},
title = {Differentiation of microbial communities in coastal seawater before and during an Akashiwo sanguinea (Dinophyceae) bloom in the urban area of Antofagasta city (northern Chile).},
journal = {Harmful algae},
volume = {142},
number = {},
pages = {102782},
doi = {10.1016/j.hal.2024.102782},
pmid = {39947860},
issn = {1878-1470},
mesh = {Chile ; *Seawater/microbiology ; *Dinoflagellida/genetics/physiology ; *Harmful Algal Bloom ; *Microbiota ; RNA, Ribosomal, 16S/analysis/genetics ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; RNA, Ribosomal, 18S/analysis/genetics ; Cities ; },
abstract = {Harmful algal blooms (HABs) are highly relevant for public health, the economy, the ecosystem, and biodiversity stability in southern Chile (40° to 53°S), where they occur regularly and are frequently monitored. However, HAB events and their associated microbes in northern Chile (17° to 30°S) remain unknown and difficult to track due to a lack of monitoring, particularly in urban areas. We investigated changes in microbial communities in coastal seawater before and during an Akashiwo sanguinea bloom (B) at two sampling points in Antofagasta city (23°38'39S, 70°24'39W). Seawater samples (filtered at 1 and 0.2 μm) were collected during distinct bloom phases (control, prebloom, and in-bloom), and 16S and 18S rDNA gene libraries were constructed and analyzed via the DNA metabarcoding technique. Our findings indicate that species diversity within the 16S rDNA-based community was greater during the prebloom phase than during the control and in-bloom phases. Conversely, species diversity within the 18S rDNA-based community was lower during the in-bloom phase than during the control and prebloom phases. Independent of the sampling points and fractions, principal coordinate analysis (PCoA) revealed distinct differences in both the 16S and 18S rDNA-based communities between the analyzed bloom phases. Our analysis further revealed that the 16S rDNA-based community was dominated by the Flavobacteriaceae and Rhodobacteraceae families, whose abundance decreased and increased, respectively, during the bloom. As anticipated, the structure of the 18S rDNA-based community was predominantly governed by the Gymnodiniaceae family, specifically the Akashiwo genus, during the bloom. The differentiation in microbial communities was more pronounced in taxa with low abundances than in the dominant taxa. Additionally, co-occurrence network analysis revealed predominantly positive relationships within the microbial communities, particularly during the bloom event. Our analysis also identified several bacterial genera as keystone taxa within the microbial communities, notably members of Pseudomonadota and Bacteroidota.},
}

Chile
*Seawater/microbiology
*Dinoflagellida/genetics/physiology
*Harmful Algal Bloom
*Microbiota
RNA, Ribosomal, 16S/analysis/genetics
Bacteria/genetics/classification/isolation & purification
Biodiversity
RNA, Ribosomal, 18S/analysis/genetics
Cities

@article {pmid39930064,
year = {2025},
author = {Eriksen, AMH and Rodríguez, JA and Seersholm, F and Hollund, HI and Gotfredsen, AB and Collins, MJ and Grønnow, B and Pedersen, MW and Gilbert, MTP and Matthiesen, H},
title = {Exploring DNA degradation in situ and in museum storage through genomics and metagenomics.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {210},
pmid = {39930064},
issn = {2399-3642},
abstract = {Understanding the environmental and microbial processes involved in DNA degradation from archaeological remains is a fundamental part of managing bone specimens. We investigated the state of DNA preservation in 33 archaeozoological caribou (Rangifer tarandus) ribs excavated from the same excavation trench at a former Inuit hunting camp in West Greenland, separated by 43 years: 1978 and 2021. Our findings show that DNA is better preserved in the most recently excavated samples, indicating a detrimental effect of museum storage on DNA integrity. Additionally, our data reveals a diverse microbiome in these bones, encoding genes relevant for bone degradation, such as enzymatic families relating to collagenases, peptidases and glycosidases. Microbes associated with bone degradation were present in both new and historical samples, with museum-stored bones showing significantly more DNA damage. Overall, our research sheds light on the nuanced dynamics governing the preservation of genomic material in archaeological contexts, underscoring the vital importance of careful considerations in museum curation practices for the sustainable conservation of invaluable skeletal records in museum repositories and in situ.},
}

@article {pmid39921668,
year = {2025},
author = {Duan, S and Jin, Z and Zhang, L and Declerck, S},
title = {Mechanisms of cooperation in the plants-arbuscular mycorrhizal fungi-bacteria continuum.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf023},
pmid = {39921668},
issn = {1751-7370},
abstract = {In nature, cooperation is an essential way for species, whether they belong to the same kingdom or to different kingdoms, to overcome the scarcity of resources and improve their fitness. Arbuscular mycorrhizal fungi are symbiotic microorganisms whose origin date back 400 million years. They form symbiotic associations with the vast majority of terrestrial plants, helping them to obtain nutrients from the soil in exchange for carbon. At the more complex level, soil bacteria participate in the symbiosis between arbuscular mycorrhizal fungi and plants: they obtain carbon from the exudation of hyphae connected to the roots and compensate for the limited saprophytic capacity of arbuscular mycorrhizal fungi by mineralizing organic compounds. Therefore, plants, arbuscular mycorrhizal fungi and soil bacteria constitute a continuum that may be accompanied by multiple forms of cooperation. In this review, we first analyzed the functional complementarities and differences between plants and arbuscular mycorrhizal fungi in arbuscular mycorrhizal symbiosis. Secondly, we discussed the resource exchange relationship between plants and arbuscular mycorrhizal fungi from the perspective of biological market theory and "surplus carbon" hypothesis. Finally, on the basis of mechanisms for maintaining cooperation, direct and indirect reciprocity in the hyphosphere, induced by the availability of external resource and species fitness, were examined. Exploring these reciprocal cooperations will provide a better understanding of the intricate ecological relationships between plants, arbuscular mycorrhizal fungi and soil bacteria as well as their evolutionary implications.},
}

@article {pmid39915510,
year = {2025},
author = {Rabbani, G and Afiq-Rosli, L and Lee, JN and Waheed, Z and Wainwright, BJ},
title = {Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4459},
pmid = {39915510},
issn = {2045-2322},
mesh = {*Anthozoa/microbiology ; Animals ; Malaysia ; *Microbiota ; *Symbiosis ; Biodiversity ; Bacteria/genetics/classification ; Climate Change ; Coral Reefs ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.},
}

*Anthozoa/microbiology
Animals
Malaysia
*Microbiota
*Symbiosis
Biodiversity
Bacteria/genetics/classification
Climate Change
Coral Reefs
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid39906166,
year = {2025},
author = {Shi, WX and Guo, JJ and Yu, XX and Li, ZX and Weng, BY and Wang, DX and Su, SH and Sun, YF and Tan, JF and Xie, RH},
title = {Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances.},
journal = {Horticulture research},
volume = {12},
number = {2},
pages = {uhae290},
pmid = {39906166},
issn = {2662-6810},
abstract = {Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e. multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.},
}

@article {pmid39899343,
year = {2025},
author = {Narechania, A and Bobo, D and DeSalle, R and Mathema, B and Kreiswirth, B and Planet, PJ},
title = {What do we gain when tolerating loss? The information bottleneck wrings out recombination.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf029},
pmid = {39899343},
issn = {1537-1719},
abstract = {Most microbes have the capacity to acquire genetic material from their environment. Recombination of foreign DNA yields genomes that are, at least in part, incongruent with the vertical history of their species. Dominant approaches for detecting these transfers are phylogenetic, requiring a painstaking series of analyses including alignment and tree reconstruction. But these methods do not scale. Here we propose an unsupervised, alignment-free and tree-free technique based on the sequential information bottleneck (SIB), an optimization procedure designed to extract some portion of relevant information from one random variable conditioned on another. In our case, this joint probability distribution tabulates occurrence counts of k-mers against their genomes of origin with the expectation that recombination will create a strong signal that unifies certain sets of co-occuring k-mers. We conceptualize the technique as a rate-distortion problem, measuring distortion in the relevance information as k-mers are compressed into clusters based on their co-occurrence in the source genomes. The result is fast, model-free, lossy compression of k-mers into learned groups of shared genome sequence, differentiating recombined elements from the vertically inherited core. We show that the technique yields a new recombination measure based purely on information, divorced from any biases and limitations inherent to alignment and phylogeny.},
}

@article {pmid39897778,
year = {2025},
author = {Raethong, N and Chamtim, P and Thananusak, R and Whanmek, K and Santivarangkna, C},
title = {Genome-wide transcriptomics revealed carbon source-mediated gamma-aminobutyric acid (GABA) production in a probiotic, Lactiplantibacillus pentosus 9D3.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41879},
pmid = {39897778},
issn = {2405-8440},
abstract = {GABA-producing probiotics present promising opportunities for developing functional foods. Carbon sources have been identified as a critical influence on GABA production. Therefore, this study investigated the holistic metabolic responses and GABA biosynthesis to various carbon sources of Lactiplantibacillus pentosus 9D3, a proficient GABA producer, using a genome-wide transcriptomic approach. The analysis revealed 414 genes with differential expression responses to altering carbon sources, i.e., glucose, sucrose, and lactose, notably sugar phosphotransferase systems (PTS) (11 genes), indicating carbon source-mediated transcriptional change patterns in L. pentosus 9D3. The integration of transcriptome data with a genome-scale metabolic network (GSMN) revealed that L. pentosus 9D3 displays adaptability by synthesizing GABA as an alternative acid-tolerant mechanism when lactose is used as a carbon source rather than depending on the fatty acid synthesis and the arginine catabolic pathway. The findings of this study offer valuable insights into optimal carbon source utilization and gene expression co-regulation, thereby enhancing the GABA-producing capability of a probiotic and broadening its potential applications in the functional food industry.},
}

@article {pmid39891167,
year = {2025},
author = {Marangon, E and Rädecker, N and Li, JYQ and Terzin, M and Buerger, P and Webster, NS and Bourne, DG and Laffy, PW},
title = {Destabilization of mutualistic interactions shapes the early heat stress response of the coral holobiont.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {31},
pmid = {39891167},
issn = {2049-2618},
mesh = {*Anthozoa/microbiology/physiology ; *Symbiosis ; Animals ; *Heat-Shock Response/physiology ; *Dinoflagellida/physiology/genetics ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; Microbiota/physiology ; Hot Temperature ; Bacteria/classification/genetics/metabolism ; },
abstract = {BACKGROUND: The stability of the symbiotic relationship between coral and their dinoflagellate algae (Symbiodiniaceae) is disrupted by ocean warming. Although the coral thermal response depends on the complex interactions between host, Symbiodiniaceae and prokaryotes, the mechanisms underlying the initial destabilization of these symbioses are poorly understood.

RESULTS: In a 2-month manipulative experiment, we exposed the coral Porites lutea to gradually increasing temperatures corresponding to 0-8 degree heating weeks (DHW) and assessed the response of the coral holobiont using coral and Symbiodiniaceae transcriptomics, microbial 16S rRNA gene sequencing and physiological measurements. From early stages of heat stress (< 1 DHW), the increase in metabolic turnover shifted the holobiont to a net heterotrophic state in which algal-derived nutrients were insufficient to meet host energy demands, resulting in reduced holobiont performance at 1 DHW. We postulate the altered nutrient cycling also affected the coral-associated microbial community, with the relative abundance of Endozoicomonas bacteria declining under increasing heat stress. Integration of holobiont stress responses correlated this decline to an increase in expression of a host ADP-ribosylation factor, suggesting that Symbiodiniaceae and Endozoicomonas may underlie similar endosymbiotic regulatory processes.

CONCLUSIONS: The thermotolerance of coral holobionts therefore is influenced by the nutritional status of its members and their interactions, and this identified metabolic interdependency highlights the importance of applying an integrative approach to guide coral reef conservation efforts. Video Abstract.},
}

*Anthozoa/microbiology/physiology
*Symbiosis
Animals
*Heat-Shock Response/physiology
*Dinoflagellida/physiology/genetics
RNA, Ribosomal, 16S/genetics
Coral Reefs
Microbiota/physiology
Hot Temperature
Bacteria/classification/genetics/metabolism

@article {pmid39884320,
year = {2025},
author = {Thanh Pham, HT and Kuroda, S and Khairina, Y and Morikawa, M},
title = {Reconstruction of a functional duckweed holobiont to reduce nutrient competition with microalgae for high-yield biomass production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132110},
doi = {10.1016/j.biortech.2025.132110},
pmid = {39884320},
issn = {1873-2976},
abstract = {Duckweed has been highlighted as an appropriate biomass for low-carbon industries because of its significantly high production rate and multiple resource value. However, the outbreak of microalgae is a practical issue that decreases duckweed production yield. This study demonstrated that the growth of the duckweed Lemna aequinoctialis from factory wastewater was enhanced by colonization with indigenous plant growth-promoting bacteria (PGPB), whereas the growth of a duckweed competitor microalga, Coelastrella sp. KC10, from the same wastewater was reduced by indigenous microalgal growth-inhibiting bacteria (MGIB). Finally, a quadruple co-culture of a synthetic duckweed holobiont, L. aequinoctialis colonized by both KLaR20 (PGPB) and KLaR16 (MGIB), and Coelastrella sp. KC10 successfully recovered the duckweed production level by 117.5% in frond number and 84.5% in dry weight in the absence of microalgae. This case study demonstrates for the first time that duckweed holobionts can be reconstructed and enforced to antagonize growth competitor microalgae.},
}

@article {pmid39879954,
year = {2025},
author = {Estrada, CSD and Oliveira, OA and Varasteh, T and Avelino-Alves, D and Lima, M and Barelli, V and Campos, LS and Cavalcanti, G and Dias, GM and Tschoeke, D and Thompson, C and Thompson, F},
title = {Short-term negative effects of seawater acidification on the rhodolith holobionts metatranscriptome.},
journal = {The Science of the total environment},
volume = {965},
number = {},
pages = {178614},
doi = {10.1016/j.scitotenv.2025.178614},
pmid = {39879954},
issn = {1879-1026},
abstract = {Rhodolith holobionts are formed by calcareous coralline algae (e.g., Corallinales) and associated microbiomes. The largest rhodolith bank in the South Atlantic is located in the Abrolhos Bank, in southwestern Brazil, covering an area of 22,000 km[2]. Rhodoliths serve as nurseries for marine life. However, ocean acidification threatens them with extinction. The acute effects of high pCO2 levels on rhodolith metatranscriptomes remain unknown. This study investigates the transcriptomic profiles of rhodoliths exposed to short-term (96-h) high pCO2 levels (up to 1638 ppm). Metatranscriptomes were generated for both dead and alive rhodoliths (15.48 million Illumina reads in total). Alive rhodoliths showed an enrichment of gene transcripts related to environmental stress responses and photosynthesis (Cyanobacteria). In contrast, the metatranscriptomes of dead rhodoliths were dominated by heterotrophic (Proteobacteria and Bacteroidetes) metabolism and virulence factors. The rhodolith holobiont metatranscriptomes respond rapidly to short-term acidification (within 1 h), suggesting that these holobionts may have some capacity to cope with acute acidification effects. However, the negative impacts of prolonged ocean acidification on rhodolith health cannot be overlooked. Rhodoliths exposed to low pH (7.5) for 96 h exhibited a completely altered transcriptomic profile compared to controls. This study highlights the plasticity of rhodolith transcriptomes in the face of ocean acidification and climate change.},
}

@article {pmid39879552,
year = {2025},
author = {Tomarovsky, A and Khan, R and Dudchenko, O and Totikov, A and Serdyukova, NA and Weisz, D and Vorobieva, NV and Bulyonkova, T and Abramov, AV and Nie, W and Wang, J and Romanenko, SA and Proskuryakova, AA and Cherkasov, N and Ferguson-Smith, MA and Yang, F and Balanovskaya, E and Gilbert, MTP and Graphodatsky, AS and Aiden, EL and Powell, R and Koepfli, KP and Perelman, PL and Kliver, S},
title = {Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esaf001},
pmid = {39879552},
issn = {1465-7333},
abstract = {The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n=38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long RoHs require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.},
}

@article {pmid39865026,
year = {2024},
author = {Fayoud, H and Belousov, MV and Antonets, KS and Nizhnikov, AA},
title = {Pathogenesis-Associated Bacterial Amyloids: The Network of Interactions.},
journal = {Biochemistry. Biokhimiia},
volume = {89},
number = {12},
pages = {2107-2132},
doi = {10.1134/S0006297924120022},
pmid = {39865026},
issn = {1608-3040},
mesh = {Humans ; *Amyloid/metabolism ; *Bacterial Proteins/metabolism ; Bacteria/metabolism ; Animals ; Biofilms/growth & development ; Amyloidosis/metabolism ; },
abstract = {Amyloids are protein fibrils with a characteristic cross-β structure that is responsible for the unusual resistance of amyloids to various physical and chemical factors, as well as numerous pathogenic and functional consequences of amyloidogenesis. The greatest diversity of functional amyloids was identified in bacteria. The majority of bacterial amyloids are involved in virulence and pathogenesis either via facilitating formation of biofilms and adaptation of bacteria to colonization of a host organism or through direct regulation of toxicity. Recent studies have shown that, beside their commonly known activity, amyloids may be involved in the spatial regulation of proteome by modulating aggregation of other amyloidogenic proteins with multiple functional or pathological effects. Although the studies on the role of microbiome-produced amyloids in the development of amyloidoses in humans and animals have only been started, it is clear that humans as holobionts contain amyloids encoded not only by the host genome, but also by microorganisms that constitute the microbiome. Amyloids acquired from external sources (e.g., food) can interact with holobiont amyloids and modulate the effects of bacterial and host amyloids, thus adding another level of complexity to the holobiont-associated amyloid network. In this review, we described bacterial amyloids directly or indirectly involved in disease pathogenesis in humans and discussed the significance of bacterial amyloids in the three-component network of holobiont-associated amyloids.},
}

Humans
*Amyloid/metabolism
*Bacterial Proteins/metabolism
Bacteria/metabolism
Animals
Biofilms/growth & development
Amyloidosis/metabolism

@article {pmid39864304,
year = {2025},
author = {Labarga, D and Mairata, A and Puelles, M and Wallner, A and Aziz, A and Alícia, P},
title = {Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128073},
doi = {10.1016/j.micres.2025.128073},
pmid = {39864304},
issn = {1618-0623},
abstract = {The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.},
}

@article {pmid39858777,
year = {2024},
author = {Apostolou, K and Radea, C and Meziti, A and Kormas, KA},
title = {Bacterial Diversity Associated with Terrestrial and Aquatic Snails.},
journal = {Microorganisms},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/microorganisms13010008},
pmid = {39858777},
issn = {2076-2607},
abstract = {The introduction of the holobiont concept has triggered scientific interest in depicting the structural and functional diversity of animal microbial symbionts, which has resulted in an unprecedented wealth of such cross-domain biological associations. The steadfast technological progress in nucleic acid-based approaches would cause one to expect that scientific works on the microbial symbionts of animals would be balanced at least for the farmed animals of human interest. For some animals, such as ruminants and a few farmed fish species of financial significance, the scientific wealth of the microbial worlds they host is immense and ever growing. The opposite happens for other animals, such as snails, in both the wild and farmed species. Snails are evolutionary old animals, with complex ecophysiological roles, living in rich microbial habitats such as soil and sediments or water. In order to create a stepping stone for future snail microbiome studies, in this literature review, we combined all the available knowledge to date, as documented in scientific papers, on any microbes associated with healthy and diseased terrestrial and aquatic snail species from natural and farmed populations. We conducted a Boolean search in Scopus, Web of Science, and ScienceDirect until June 2024, identifying 137 papers, of which 60 were used for original data on snail bacterial communities in the gastrointestinal tract, hepatopancreas, and feces. We provide a synthesis on how representative this knowledge is towards depicting the possible snail core microbiota, as well as the steps that need to be taken in the immediate future to increase the in-depth and targeted knowledge of the bacterial component in snail holobionts.},
}

@article {pmid39852521,
year = {2025},
author = {De Domenico, S and Toso, A and De Rinaldis, G and Mammone, M and Fumarola, LM and Piraino, S and Leone, A},
title = {Wild or Reared? Cassiopea andromeda Jellyfish as a Potential Biofactory.},
journal = {Marine drugs},
volume = {23},
number = {1},
pages = {},
doi = {10.3390/md23010019},
pmid = {39852521},
issn = {1660-3397},
support = {No. 774499 - GoJelly_ Research and Innovation Program project//European Union/ ; Practice code AFD9B120, project idea UNISAL119//Apulian Region program "REFIN-Research for Innovation"/ ; n.3138-"National Biodiversity Future Center-NBFC", Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022,NextGenerationEU, Italian National Recovery and Resilience Plan (NRRP)//European Union/ ; },
mesh = {Animals ; *Scyphozoa/chemistry ; *Antioxidants/chemistry/pharmacology ; Mediterranean Sea ; Dinoflagellida/chemistry ; },
abstract = {The zooxanthellate jellyfish Cassiopea andromeda (Forsskål, 1775), a Lessepsian species increasingly common in the western and central Mediterranean Sea, was investigated here to assess its potential as a source of bioactive compounds from medusa specimens both collected in the wild (the harbor of Palermo, NW Sicily) and reared under laboratory-controlled conditions. A standardized extraction protocol was used to analyze the biochemical composition of the two sampled populations in terms of protein, lipid, and pigment contents, as well as for their relative concentrations of dinoflagellate symbionts. The total extracts and their fractions were also biochemically characterized and analyzed for their in vitro antioxidant activity to quantify differences in functional compounds between wild and reared jellyfish. The two populations were similar in terms of extract yield, but with substantial differences in biomass, the number of zooxanthellae, protein and lipid contents, and fatty acid composition. The hydroalcoholic extracts obtained from jellyfish grown under controlled conditions showed greater antioxidant activity due to the presence of a higher content of bioactive compounds compared to wild jellyfish. This study could be the basis for considering the sustainable breeding of this holobiont or other similar organisms as a source of valuable compounds that can be used in the food, nutraceutical, or pharmaceutical sectors.},
}

Animals
*Scyphozoa/chemistry
*Antioxidants/chemistry/pharmacology
Mediterranean Sea
Dinoflagellida/chemistry

@article {pmid39844957,
year = {2025},
author = {Martins, V and Abdallah, C and Teixeira, A and Moreira, C and Nóbrega, M and Lanoue, A and Gerós, H},
title = {Subregional pedoclimatic conditions with contrasted UV-radiation shape host-microbiome and metabolome phenotypes in the grape berry.},
journal = {Food chemistry: X},
volume = {25},
number = {},
pages = {102139},
pmid = {39844957},
issn = {2590-1575},
abstract = {This study used integrative omics to address the response of key elements of the grapevine holobiont to contrasted pedoclimatic conditions found in distinct subregions of Douro Valley (Portugal). A metabolic OPLS-DA model predicted with 100 % accuracy the geographic origin of berries; higher UV radiation, higher temperature and lower precipitation stimulated the accumulation of phenolic acids, flavonols and malvidin conjugates, in detriment of amino acids, organic acids, flavan-3-ols, proanthocyanidins and non-malvidin anthocyanins. Metabarcoding showed a trade-off between bacteria and fungal diversity among subregions, with Pseudomonas, Lactobacillus, Aspergillus and Penicillium acting as intraregional microbial markers. The high phenotypic plasticity of berries and the role of microbes in this process are relevant upon current projections for increased UV radiation and temperature in Southern European viticulture, in a climate change scenario, with predicted impacts on regional wine quality and on the development of adaptation strategies for resilient viticulture.},
}

@article {pmid39844274,
year = {2025},
author = {Camper, BT and Kanes, AS and Laughlin, ZT and Manuel, RT and Bewick, SA},
title = {Transgressive hybrids as hopeful holobionts.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {19},
pmid = {39844274},
issn = {2049-2618},
mesh = {*Hybridization, Genetic ; *Symbiosis ; *Microbiota ; Animals ; Biological Evolution ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Hybridization between evolutionary lineages has profound impacts on the fitness and ecology of hybrid progeny. In extreme cases, the effects of hybridization can transcend ecological timescales by introducing trait novelty upon which evolution can act. Indeed, hybridization can even have macroevolutionary consequences, for example, as a driver of adaptive radiations and evolutionary innovations. Accordingly, hybridization is now recognized as a motor for macrobial evolution. By contrast, there has been substantially less progress made towards understanding the positive eco-evolutionary consequences of hybridization on holobionts. Rather, the emerging paradigm in holobiont literature is that hybridization disrupts symbiosis between a host lineage and its microbiome, leaving hybrids at a fitness deficit. These conclusions, however, have been drawn based on results from predominantly low-fitness hybrid organisms. Studying "dead-end" hybrids all but guarantees finding that hybridization is detrimental. This is the pitfall that Dobzhansky fell into over 80 years ago when he used hybrid sterility and inviability to conclude that hybridization hinders evolution. Goldschmidt, however, argued that rare saltational successes-so-called hopeful monsters-disproportionately drive positive evolutionary outcomes. Goldschmidt's view is now becoming a widely accepted explanation for the prevalence of historical hybridization in extant macrobial lineages. Aligning holobiont research with this broader evolutionary perspective requires recognizing the importance of similar patterns in host-microbiome systems. That is, rare and successful "hopeful holobionts" (i.e., hopeful monsters at the holobiont scale) might be disproportionately responsible for holobiont evolution. If true, then it is these successful systems that we should be studying to assess impacts of hybridization on the macroevolutionary trajectories of host-microbiome symbioses.

RESULTS: In this paper, we explore the effects of hybridization on the gut (cloacal) and skin microbiota in an ecologically successful hybrid lizard, Aspidoscelis neomexicanus. Specifically, we test the hypothesis that hybrid lizards have host-associated (HA) microbiota traits strongly differentiated from their progenitor species. Across numerous hybrid microbiota phenotypes, we find widespread evidence of transgressive segregation. Further, microbiota restructuring broadly correlates with niche restructuring during hybridization. This suggests a relationship between HA microbiota traits and ecological success.

CONCLUSION: Transgressive segregation of HA microbiota traits is not only limited to hybrids at a fitness deficit but also occurs in ecologically successful hybrids. This suggests that hybridization may be a mechanism for generating novel and potentially beneficial holobiont phenotypes. Supporting such a conclusion, the correlations that we find between hybrid microbiota and the hybrid niche indicate that hybridization might change host microbiota in ways that promote a shift or an expansion in host niche space. If true, hybrid microbiota restructuring may underly ecological release from progenitors. This, in turn, could drive evolutionary diversification. Using our system as an example, we elaborate on the evolutionary implications of host hybridization within the context of holobiont theory and then outline the next steps for understanding the role of hybridization in holobiont research. Video Abstract.},
}

*Hybridization, Genetic
*Symbiosis
*Microbiota
Animals
Biological Evolution
Bacteria/genetics/classification

@article {pmid39838803,
year = {2025},
author = {Chan, WY and Sakamoto, R and Doering, T and Narayana, VK and De Souza, DP and McConville, MJ and van Oppen, MJH},
title = {Heat-Evolved Microalgae (Symbiodiniaceae) Are Stable Symbionts and Influence Thermal Tolerance of the Sea Anemone Exaiptasia diaphana.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70011},
doi = {10.1111/1462-2920.70011},
pmid = {39838803},
issn = {1462-2920},
support = {DE240100317//Australian Research Council/ ; FL180100036//Australian Research Council/ ; APP1154540//National Health and Medical Research Council/ ; //Westpac Research Fellowship/ ; },
mesh = {*Sea Anemones/physiology ; *Symbiosis ; Animals ; *Thermotolerance ; *Hot Temperature ; Microalgae/metabolism ; Dinoflagellida/physiology ; },
abstract = {Symbiotic cnidarians, such as sea anemones and corals, rely on their mutualistic microalgal partners (Symbiodiniaceae) for survival. Marine heatwaves can disrupt this partnership, and it has been proposed that introducing experimentally evolved, heat-tolerant algal symbionts could enhance host thermotolerance. To test this hypothesis, the sea anemone Exaiptasia diaphana (a coral model) was inoculated with either the heterologous wild type or heat-evolved algal symbiont, Cladocopium proliferum, and homologous wild-type Breviolum minutum. The novel symbioses persisted for 1.5 years and determined holobiont thermotolerance during a simulated summer heatwave. Anemones hosting SS8, one of the six heat-evolved strains tested, exhibited the highest thermotolerance. Notably, anemones hosting the wild-type C. proliferum (WT10) were the second most thermally tolerant group, whereas anemones hosting the heat-evolved SS5 or SS9 strains were among the most thermosensitive. Elevated temperatures led to an increase in the levels of many amino acids and a decrease in tricarboxylic acid (TCA) metabolites in all anemone hosts, potentially indicating an increase in autophagy and a reduction in energy and storage production. Some consistent differences were observed in changes in metabolite levels between anemone groups in response to elevated temperature, suggesting that the algal symbiont influenced host metabolome and nutritional budget.},
}

*Sea Anemones/physiology
*Symbiosis
Animals
*Thermotolerance
*Hot Temperature
Microalgae/metabolism
Dinoflagellida/physiology

@article {pmid39832281,
year = {2025},
author = {Middelboe, M and Traving, SJ and Castillo, D and Kalatzis, PG and Glud, RN},
title = {Prophage-encoded chitinase gene supports growth of its bacterial host isolated from deep-sea sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf004},
pmid = {39832281},
issn = {1751-7370},
abstract = {Auxiliary metabolic genes encoded by bacteriophages can influence host metabolic function during infection. In temperate phages, auxiliary metabolic genes may increase host fitness when integrated as prophages into the host genome. However, little is known about the contribution of prophage-encoded auxiliary metabolic genes to host metabolic properties. In this study, we examined a temperate bacteriophage, and its piezotolerant Pseudomonas sp. host obtained from sediment samples collected from the Kermadec Trench at ~10 000 m water depth. Both the phage and host were present throughout the sediment profiles from the surface to 30 cm into the sediment, covering large gradients of environmental conditions. The host and phage each carried one chitinase gene, which differed from each other, suggesting that chitin degradation plays a role in their substrate supply. We demonstrated that prophage-encoded chitinase supported host chitin degradation and growth in the presence of chitin. Furthermore, prophage induction dynamics were strongly substrate-dependent, suggesting that the host controls the lysis-lysogeny switch in response to the presence of chitin, thus optimizing the trade-off between the loss of cells from prophage induction and prophage enhancement of host performance. Overall, the results demonstrate prophage-encoded auxiliary metabolic genes as collaborative goods for their hosts and emphasize the potential role of phage-host interactions in benthic biogeochemical cycling, as well as for the capability of deep-sea bacteria to efficiently adapt and thrive at a wide range of environmental conditions.},
}

@article {pmid39827902,
year = {2025},
author = {Brown, TM and Dunn, AM and Quinnell, RJ and Clarke, E and Cunningham, AA and Goodman, SJ},
title = {An interdisciplinary approach to improving conservation outcomes for parasites.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {e14431},
doi = {10.1111/cobi.14431},
pmid = {39827902},
issn = {1523-1739},
support = {//The Leverhulme Trust/ ; },
abstract = {Parasites represent a significant proportion of Earth's biodiversity and play important roles in the ecology and biology of ecosystems and hosts, making them an important target for conservation. Despite increasing calls to prioritize protection for parasites in the academic literature, they remain undervalued and underrepresented in global biodiversity conservation efforts, not least due to the perception that the interests of parasite and host conservation are opposing and the common misconception that parasites are a threat, rather than a benefit, to conservation. We considered whether taking an interdisciplinary approach to parasite conservation research will generate novel insights and solutions concerning why and how parasite conservation should be practiced for the benefit of parasites, their hosts, ecosystems, and people. We argue that 2 of the main barriers to more widespread parasite conservation are the knowledge gap concerning the role of sociocultural factors affecting the willingness to enact parasite conservation and the lack of a consistent and cohesive philosophical basis for parasite conservation. Possible sociocultural barriers to parasite conservation include misconceptions of the risks posed by parasites, taxonomic bias, differences in conservation values, economic constraints, and technical challenges. The use of social science can generate insights into levels of awareness and support for parasite conservation and improve understanding of how human values and attitudes mediate conservation practices concerning parasites. Such knowledge will have a critical role in addressing sociocultural barriers and improving support for parasite conservation. Issues with the current philosophical basis for parasite conservation include contradictory accounts of which parasites merit conservation, insufficient explanation of how different conservation values apply to parasite biodiversity, and the existence of a false antagonism between host and parasite conservation. Greater engagement with philosophical work on environmental ethics and biological unitization will strengthen existing arguments for parasite conservation and will support conservation decision-making processes.},
}

@article {pmid39827366,
year = {2025},
author = {Liu, HJ and Liu, J and Zhai, Z and Dai, M and Tian, F and Wu, Y and Tang, J and Lu, Y and Wang, H and Jackson, D and Yang, X and Qin, F and Xu, M and Fernie, AR and Zhang, Z and Yan, J},
title = {Maize2035: A decadal vision for intelligent maize breeding.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.01.012},
pmid = {39827366},
issn = {1752-9867},
abstract = {Maize, a cornerstone of global food security, has undergone remarkable transformations through breeding, yet it faces mounting challenges in a changing world. In this review, we trace the historical successes of maize breeding which laid the foundation for present opportunities. We examine both the specific and shared breeding goals related to diverse geographies and end-use demands. Achieving these coordinated breeding objectives requires a holistic approach to trait improvement for sustainable agriculture. We discuss cutting-edge solutions, including multi-omics approaches from single-cell analysis to holobionts, smart breeding with advanced technologies and algorithms, and the transformative potential of rational design with synthetic biology. A transition towards a data-driven future is currently underway, with large-scale precision agriculture and autonomous systems poised to revolutionize farming practice. Realizing these futuristic opportunities hinges on collaborative efforts spanning scientific discoveries, technology translations, and socioeconomic considerations in maximizing human and environmental well-being.},
}

@article {pmid39823339,
year = {2025},
author = {van der Loos, LM and Steinhagen, S and Stock, W and Weinberger, F and D'hondt, S and Willems, A and De Clerck, O},
title = {Low functional change despite high taxonomic turnover characterizes the Ulva microbiome across a 2000-km salinity gradient.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadr6070},
doi = {10.1126/sciadv.adr6070},
pmid = {39823339},
issn = {2375-2548},
mesh = {*Ulva/genetics ; *Salinity ; *Microbiota ; Bacteria/genetics/classification/metabolism ; Metagenome ; Metagenomics/methods ; },
abstract = {The green seaweed Ulva relies on associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. However, the functional variation of these bacteria in relation to environmental changes remains unclear. We analyzed 91 Ulva samples across a 2000-kilometer Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, nitrogen, sulfur, and vitamin metabolism. Although the R[2] value for salinity explained 70% of taxonomic variation, it accounted only for 17% of functional variation. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis, which likely contribute to stress mitigation and osmotic homeostasis in response to salinity variations. Our results emphasize the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.},
}

*Ulva/genetics
*Salinity
*Microbiota
Bacteria/genetics/classification/metabolism
Metagenome
Metagenomics/methods

@article {pmid39823335,
year = {2025},
author = {Santoro, EP and Cárdenas, A and Villela, HDM and Vilela, CLS and Ghizelini, AM and Duarte, GAS and Perna, G and Saraiva, JP and Thomas, T and Voolstra, CR and Peixoto, RS},
title = {Inherent differential microbial assemblages and functions associated with corals exhibiting different thermal phenotypes.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq2583},
doi = {10.1126/sciadv.adq2583},
pmid = {39823335},
issn = {2375-2548},
mesh = {*Anthozoa/microbiology/metabolism/physiology ; Animals ; *Microbiota ; *Phenotype ; Symbiosis ; Metagenomics/methods ; Bacteria/metabolism/genetics ; },
abstract = {Certain coral individuals exhibit enhanced resistance to thermal bleaching, yet the specific microbial assemblages and their roles in these phenotypes remain unclear. We compared the microbial communities of thermal bleaching-resistant (TBR) and thermal bleaching-sensitive (TBS) corals using metabarcoding and metagenomics. Our multidomain approach revealed stable distinct microbial compositions between thermal phenotypes. Notably, TBR corals were inherently enriched with microbial eukaryotes, particularly Symbiodiniaceae, linked to photosynthesis, and the biosynthesis of antibiotic and antitumor compounds and glycosylphosphatidylinositol-anchor proteins, crucial for cell wall regulation and metabolite exchange. In contrast, TBS corals were dominated by bacterial metabolic genes related to nitrogen, amino acid, and lipid metabolism. The inherent microbiome differences between TBR and TBS corals, already observed before thermal stress, point to distinct holobiont phenotypes associated to thermal bleaching resistance, offering insights into mechanisms underlying coral response to climate-induced stress.},
}

*Anthozoa/microbiology/metabolism/physiology
Animals
*Microbiota
*Phenotype
Symbiosis
Metagenomics/methods
Bacteria/metabolism/genetics

@article {pmid39822124,
year = {2025},
author = {Doonan, JM and Budde, KB and Kosawang, C and Lobo, A and Verbylaite, R and Brealey, JC and Martin, MD and Pliura, A and Thomas, K and Konrad, H and Seegmüller, S and Liziniewicz, M and Cleary, M and Nemesio-Gorriz, M and Fussi, B and Kirisits, T and Gilbert, MTP and Heuertz, M and Kjær, ED and Nielsen, LR},
title = {Multiple, Single Trait GWAS and Supervised Machine Learning Reveal the Genetic Architecture of Fraxinus excelsior Tolerance to Ash Dieback in Europe.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15361},
pmid = {39822124},
issn = {1365-3040},
support = {//This research was supported by the Independent Research Fund Denmark (DFF|Technology and Production Sciences) under the grant no. 8022-00355B. Field work in Austria was supported by BML DaFNE grant no. 101476 ("Esche in Not-Phase II") funded by the Austrian Federal Ministry of Agriculture, Forestry, Regions and Water Management, the Austrian Chamber of Agriculture, the governments of all Austrian provinces, the Forest Office and Urban Agriculture (MA 49) of the Vienna City Administration and "Österreichischer Forstverein"; as well as by BML DaFNE grant no. 101684 ("Waldfonds" project "AshBack") funded by the Austrian Federal Ministry of Agriculture, Forestry, Regions and Water Management. The establishment of the German trial site "Chiemsee" was supported by the Bavarian Ministry under the projects KLIP1 and ST272. J.C.B. was funded by the European Union's Horizon 2020 Action grant 8177291009 "HoloFood"./ ; },
abstract = {Common ash (Fraxinus excelsior) is under intensive attack from the invasive alien pathogenic fungus Hymenoscyphus fraxineus, causing ash dieback at epidemic levels throughout Europe. Previous studies have found significant genetic variation among genotypes in ash dieback susceptibility and that host phenology, such as autumn yellowing, is correlated with susceptibility of ash trees to H. fraxineus; however, the genomic basis of ash dieback tolerance in F. excelsior requires further investigation. Here, we integrate quantitative genetics based on multiple replicates and genome-wide association analyses with machine learning to reveal the genetic architecture of ash dieback tolerance and of phenological traits in F. excelsior populations in six European countries (Austria, Denmark, Germany, Ireland, Lithuania, Sweden). Based on phenotypic data of 486 F. excelsior replicated genotypes we observed negative genotypic correlations between crown damage caused by ash dieback and intensity of autumn leaf yellowing within multiple sampling sites. Our results suggest that the examined traits are polygenic and using genomic prediction models, with ranked single nucleotide polymorphisms (SNPs) based on GWAS associations as input, a large proportion of the variation was predicted by unlinked SNPs. Based on 100 unlinked SNPs, we can predict 55% of the variation in disease tolerance among genotypes (as phenotyped in genetic trials), increasing to a maximum of 63% when predicted from 9155 SNPs. In autumn leaf yellowing, 52% of variation is predicted by 100 unlinked SNPs, reaching a peak of 72% using 3740 SNPs. Based on feature permutations within genomic prediction models, a total of eight nonsynonymous SNPs linked to ash dieback crown damage and autumn leaf yellowing (three and five SNPs, respectively) were identified, these were located within genes related to plant defence (pattern triggered immunity, pathogen detection) and phenology (regulation of flowering and seed maturation, auxin transport). We did not find an overlap between genes associated with crown damage level and autumn leaf yellowing. Hence, our results shed light on the difference in the genomic basis of ADB tolerance and autumn leaf yellowing despite these two traits being correlated in quantitative genetic analysis. Overall, our methods show the applicability of genomic prediction models when combined with GWAS to reveal the genomic architecture of polygenic disease tolerance enabling the identification of ash dieback tolerant trees for breeding or conservation purposes.},
}

@article {pmid39116436,
year = {2025},
author = {Voolstra, CR and Alderdice, R and Colin, L and Staab, S and Apprill, A and Raina, JB},
title = {Standardized Methods to Assess the Impacts of Thermal Stress on Coral Reef Marine Life.},
journal = {Annual review of marine science},
volume = {17},
number = {1},
pages = {193-226},
doi = {10.1146/annurev-marine-032223-024511},
pmid = {39116436},
issn = {1941-0611},
mesh = {*Coral Reefs ; Animals ; *Climate Change ; *Anthozoa/physiology ; Hot Temperature ; Stress, Physiological ; Oceans and Seas ; Environmental Monitoring/methods ; },
abstract = {The Earth's oceans have absorbed more than 90% of the excess, climate change-induced atmospheric heat. The resulting rise in oceanic temperatures affects all species and can lead to the collapse of marine ecosystems, including coral reefs. Here, we review the range of methods used to measure thermal stress impacts on reef-building corals, highlighting current standardization practices and necessary refinements to fast-track discoveries and improve interstudy comparisons. We also present technological developments that will undoubtedly enhance our ability to record and analyze standardized data. Although we use corals as an example, the methods described are widely employed in marine sciences, and our recommendations therefore apply to all species and ecosystems. Enhancing collaborative data collection efforts, implementing field-wide standardized protocols, and ensuring data availability through dedicated, openly accessible databases will enable large-scale analysis and monitoring of ecosystem changes, improving our predictive capacities and informing active intervention to mitigate climate change effects on marine life.},
}

*Coral Reefs
Animals
*Climate Change
*Anthozoa/physiology
Hot Temperature
Stress, Physiological
Oceans and Seas
Environmental Monitoring/methods

@article {pmid39816161,
year = {2025},
author = {Parreira, BR and Gopalakrishnan, S and Chikhi, L},
title = {Effects of Social Structure on Effective Population Size Change Estimates.},
journal = {Evolutionary applications},
volume = {18},
number = {1},
pages = {e70063},
pmid = {39816161},
issn = {1752-4571},
abstract = {Most methods currently used to infer the "demographic history of species" interpret this expression as a history of population size changes. The detection, quantification, and dating of demographic changes often rely on the assumption that population structure can be neglected. However, most vertebrates are typically organized in populations subdivided into social groups that are usually ignored in the interpretation of genetic data. This could be problematic since an increasing number of studies have shown that population structure can generate spurious signatures of population size change. Here, we simulate microsatellite data from a species subdivided into social groups where reproduction occurs according to different mating systems (monogamy, polygynandry, and polygyny). We estimate the effective population size (N e) and quantify the effect of social structure on estimates of changes in N e. We analyze the simulated data with two widely used methods for demographic inference. The first approach, BOTTLENECK, tests whether the samples are at mutation-drift equilibrium and thus whether a single N e can be estimated. The second approach, msvar, aims at quantifying and dating changes in N e. We find that social structure may lead to signals of departure from mutation-drift equilibrium including signals of expansion and bottlenecks. We also find that expansion signals may be observed under simple stationary Wright-Fisher models with low diversity. Since small populations tend to characterize many endangered species, we stress that methods trying to infer N e should be interpreted with care and validated with simulated data incorporating information about structure. Spurious expansion signals due to social structure can mask critical population size changes. These can obscure true bottleneck events and be particularly problematic in endangered species.},
}

@article {pmid39813343,
year = {2025},
author = {Aichelman, HE and Benson, BE and Gomez-Campo, K and Martinez-Rugerio, MI and Fifer, JE and Tsang, L and Hughes, AM and Bove, CB and Nieves, OC and Pereslete, AM and Stanizzi, D and Kriefall, NG and Baumann, JH and Rippe, JP and Gondola, P and Castillo, KD and Davies, SW},
title = {Cryptic coral diversity is associated with symbioses, physiology, and response to thermal challenge.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadr5237},
doi = {10.1126/sciadv.adr5237},
pmid = {39813343},
issn = {2375-2548},
mesh = {*Symbiosis ; *Anthozoa/physiology ; Animals ; *Coral Reefs ; Climate Change ; Biodiversity ; Temperature ; Phylogeny ; },
abstract = {Coral persistence in the Anthropocene depends on interactions among holobiont partners (coral animals and microbial symbionts) and their environment. Cryptic coral lineages-genetically distinct yet morphologically similar groups-are critically important as they often exhibit functional diversity relevant to thermal tolerance. In addition, environmental parameters such as thermal variability may promote tolerance, but how variability interacts with holobiont partners to shape responses to thermal challenge remains unclear. Here, we identified three cryptic lineages of Siderastrea siderea in Bocas del Toro, Panamá that differ in distributions across inshore and offshore reefs, microbial associations, phenotypic traits of holobiont partners (i.e., phenomes), and skeleton morphologies. A thermal variability experiment failed to increase thermal tolerance, but subsequent thermal challenge and recovery revealed that one lineage maintained elevated energetic reserves, photochemical efficiency, and growth. Last, coral cores highlighted that this lineage also exhibited greater growth historically. Functional variation among cryptic lineages highlights their importance in predicting coral reef responses to climate change.},
}

*Symbiosis
*Anthozoa/physiology
Animals
*Coral Reefs
Climate Change
Biodiversity
Temperature
Phylogeny

@article {pmid39812892,
year = {2025},
author = {Kerlin, JR and Barnas, DM and Silbiger, NJ},
title = {Conspecific interactions between corals mediate the effect of submarine groundwater discharge on coral physiology.},
journal = {Oecologia},
volume = {207},
number = {1},
pages = {21},
pmid = {39812892},
issn = {1432-1939},
support = {1924281//Division of Ocean Sciences/ ; 1637396//Division of Ocean Sciences/ ; },
mesh = {Animals ; *Anthozoa/physiology ; *Symbiosis ; *Groundwater ; Photosynthesis ; Coral Reefs ; Chlorophyll A ; Ecosystem ; },
abstract = {Land-based inputs, such as runoff, rivers, and submarine groundwater, can alter biologic processes on coral reefs. While the abiotic factors associated with land-based inputs have strong effects on corals, corals are also affected by biotic interactions, including other neighboring corals. The biologic responses of corals to changing environmental conditions and their neighbors are likely interactive; however, few studies address both biotic and abiotic interactions in concert. In a manipulative field experiment, we tested how the natural environmental gradient created by submarine groundwater discharge (SGD) affected holobiont and symbiont metabolic rates and endosymbiont physiology of Porites rus. We further tested how the effect of SGD on the coral was mediated by intra and interspecific interactions. SGD is a natural land-sea connection that delivers nutrients, inorganic carbon, and other solutes to coastal ecosystems worldwide. Our results show that a natural gradient of nutrient enrichment and pH variability as a result of acute SGD exposure generally benefited P. rus, increasing gross photosynthesis, respiration, endosymbiont densities, and chlorophyll a content. Conspecifics in direct contact with the a neighboring coral, however, altered the relationship between coral physiology and SGD, lowering the photosynthetic and respiration rates from expected values when the coral had no neighbor. We show that the response of corals to environmental change is dependent on the types of nearby neighbor corals and how neighbors alter the chemical or physical environment around the coral. Our study underscores the importance of considering biotic interactions when predicting the physiologic responses of corals to the environment.},
}

Animals
*Anthozoa/physiology
*Symbiosis
*Groundwater
Photosynthesis
Coral Reefs
Chlorophyll A
Ecosystem

@article {pmid39810029,
year = {2025},
author = {de Freitas Neto, LL and Santos, RFB and da Silva, MA and de Souza Bezerra, R and Saldanha-Corrêa, F and Espósito, BP},
title = {Zinc speciation promotes distinct effects on dinoflagellate growth and coral trypsin-like enzyme activity.},
journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine},
volume = {},
number = {},
pages = {},
pmid = {39810029},
issn = {1572-8773},
support = {2021/07153-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/10894-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 372742/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Zinc is an essential metal to living organisms, including corals and their symbiotic microalgae (Symbiodiniaceae). Both Zn(II) deprivation and overload are capable of leading to dysfunctional metabolism, coral bleaching, and even organism death. The present work investigated the effects of chemically defined Zn species (free Zn, ZnO nanoparticles, and the complexes Zn-histidinate and Zn-EDTA) over the growth of the dinoflagellates Symbiodinium microadriaticum, Breviolum minutum, and Effrenium voratum, and on the trypsin-like proteolytic activity of the hydrocoral Millepora alcicornis. B. minutum was the most sensitive strain to any form of added Zn. For the other strains, the complex [Zn(His)2] better translated metal load into growth. This complex was the only tested compound that did not interfere with the trypsin-like activity of Millepora alcicornis extracts. Also, histidine was able to recover the activity of the enzyme inhibited by zinc. [Zn(His)2] is a potential biocarrier of zinc for microalgae or coral cultivation. These findings suggest that the control of chemical speciation of an essential metal could lead to useful compounds that assist autotrophy, while not affecting heterotrophy, in the coral holobiont.},
}

@article {pmid39799372,
year = {2025},
author = {Perez, V and Boulo, V and De Lorgeril, J and Pham, D and Ansquer, D and Plougoulen, G and Ballan, V and Lam, JS and Romatif, O and Le Luyer, J and Falchetto, C and Basset, C and Flohr, S and Maamaatuaiahutapu, M and Lafille, MA and Lau, C and Saulnier, D and Wabete, N and Callac, N},
title = {Hemolymph microbiota and immune effectors' expressions driven by geographical rearing acclimation of the aquacultured Penaeus stylirostris.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {5},
pmid = {39799372},
issn = {2524-4671},
abstract = {BACKGROUND: In holobiont, microbiota is known to play a central role on the health and immunity of its host. Then, understanding the microbiota, its dynamic according to the environmental conditions and its link to the immunity would help to react to potential dysbiosis of aquacultured species. While the gut microbiota is highly studied, in marine invertebrates the hemolymph microbiota is often set aside even if it remains an important actor of the hemolymph homeostasis. Indeed, the hemolymph harbors the factors involved in the animal homeostasis that interacts with the microbiota, the immunity. In the Southwest Pacific, the high economical valued shrimp Penaeus stylirostris is reared in two contrasted sites, in New Caledonia (NC) and in French Polynesia (FP).

RESULTS: We characterized the active microbiota inhabiting the hemolymph of shrimps while considering its stability during two seasons and at a one-month interval and evidenced an important microbial variability between the shrimps according to the rearing conditions and the sites. We highlighted specific biomarkers along with a common core microbiota composed of 6 ASVs. Putative microbial functions were mostly associated with bacterial competition, infections and metabolism in NC, while they were highly associated with the cell metabolism in FP suggesting a rearing site discrimination. Differential relative expression of immune effectors measured in the hemolymph of two shrimp populations from NC and FP, exhibited higher level of expression in NC compared to FP. In addition, differential relative expression of immune effectors was correlated to bacterial biomarkers based on their geographical location.

CONCLUSIONS: Our data suggest that, in Pacific shrimps, both the microbiota and the expression of the immune effectors could have undergone differential immunostimulation according to the rearing site as well as a geographical adaptative divergence of the shrimps as an holobiont, to their rearing sites. Further, the identification of proxies such as the core microbiota and site biomarkers, could be used to guide future actions to monitor the bacterial microbiota and thus preserve the productions.},
}

@article {pmid39797569,
year = {2025},
author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD},
title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baae112},
pmid = {39797569},
issn = {1758-0463},
mesh = {Animals ; *Chickens/microbiology ; Host Microbial Interactions/genetics ; Salmon/microbiology ; Microbiota ; Databases, Genetic ; Gastrointestinal Microbiome ; },
abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.},
}

Animals
*Chickens/microbiology
Host Microbial Interactions/genetics
Salmon/microbiology
Microbiota
Databases, Genetic
Gastrointestinal Microbiome

@article {pmid39769364,
year = {2024},
author = {Grzyb, T and Szulc, J},
title = {Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
doi = {10.3390/ijms252413601},
pmid = {39769364},
issn = {1422-0067},
mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Phosphorus/metabolism ; Nitrogen/metabolism ; Symbiosis ; Nutrients/metabolism ; },
abstract = {While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.},
}

*Microbiota
*Bacteria/genetics/classification/metabolism
*Plants/microbiology
Biodiversity
Ecosystem
Phosphorus/metabolism
Nitrogen/metabolism
Symbiosis
Nutrients/metabolism

@article {pmid39762949,
year = {2025},
author = {Ferreira, C and Burgsdorf, I and Perez, T and Ramírez, G and Lalzar, M and Huchon, D and Steindler, L},
title = {Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {4},
pmid = {39762949},
issn = {2049-2618},
support = {GBMF9352//Gordon and Betty Moore Foundation/ ; 933/23//Israel Science Foundation/ ; },
abstract = {BACKGROUND: Sponges harbor microbial communities that play crucial roles in host health and ecology. However, the genetic adaptations that enable these symbiotic microorganisms to thrive within the sponge environment are still being elucidated. To understand these genetic adaptations, we conducted a comparative genomics analysis on 350 genomes of Actinobacteriota, a phylum commonly associated with sponges.

RESULTS: Our analysis uncovered several differences between symbiotic and free-living bacteria, including an increased abundance of genes encoding prokaryotic defense systems (PDSs) and eukaryotic-like proteins (ELPs) in symbionts. Furthermore, we identified GPP34 as a novel symbiosis-related gene family, found in two symbiotic Actinobacteriota clades, but not in their closely related free-living relatives. Analyses of a broader set of microbes showed that members of the GPP34 family are also found in sponge symbionts across 16 additional bacterial phyla. While GPP34 proteins were thought to be restricted to eukaryotes, our phylogenetic analysis shows that the GPP34 domain is found in all three domains of life, suggesting its ancient origin. We also show that the GPP34 family includes genes with two main structures: a short form that includes only the GPP34 domain and a long form that encompasses a GPP34 domain coupled with a cytochrome P450 domain, which is exclusive to sponge symbiotic bacteria.

CONCLUSIONS: Given previous studies showing that GPP34 is a phosphatidylinositol-4-phosphate (PI4P)-binding protein in eukaryotes and that other PI4P-binding proteins from bacterial pathogens can interfere with phagolysosome maturation, we propose that symbionts employ GPP34 to modulate phagocytosis to colonize and persist within sponge hosts. Video Abstract.},
}

@article {pmid39750118,
year = {2025},
author = {Butdee, W and Saimee, Y and Suriyachadkun, C and Duangmal, K},
title = {Pseudonocardia spirodelae sp. nov., isolated from duckweed and formal proposal to reclassify Pseudonocardia antarctica as a later heterotypic synonym of Pseudonocardia alni and reclassify Pseudonocardia carboxydivorans as Pseudonocardia alni subsp. carboxydivorans.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {1},
pages = {},
doi = {10.1099/ijsem.0.006608},
pmid = {39750118},
issn = {1466-5034},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Nucleic Acid Hybridization ; *Vitamin K 2/analogs & derivatives/analysis ; *Fatty Acids/chemistry ; *Sequence Analysis, DNA ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *Araceae/microbiology ; Base Composition ; Phospholipids ; },
abstract = {A novel Pseudonocardia strain DW16-2[T], isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8[T] (98.8%), followed by Pseudonocardia tropica YIM 61452[T] (98.7%), Pseudonocardia antarctica DVS 5a1[T] (98.7%) and Pseudonocardia alni DSM 44104[T] (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2[T] and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2[T] were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2[T] contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H4). The cellular fatty acids (>5 %) were iso-C16 : 0, iso-C16 : 1 H, summed feature 3: C16 : 1 ω7c/C16 : 1 ω6c; C16 : 1 ω6c/C16 : 1 ω7c, C17 : 1 ω8c and anteiso-C17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2[T] represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2[T] = TBRC 16418[T] = NBRC 115857[T]) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.},
}

*RNA, Ribosomal, 16S/genetics
*Phylogeny
*Nucleic Acid Hybridization
*Vitamin K 2/analogs & derivatives/analysis
*Fatty Acids/chemistry
*Sequence Analysis, DNA
*DNA, Bacterial/genetics
*Bacterial Typing Techniques
*Araceae/microbiology
Base Composition
Phospholipids

@article {pmid39748821,
year = {2024},
author = {Senizza, B and Araniti, F and Lewin, S and Wende, S and Kolb, S and Lucini, L},
title = {A multi-omics approach to unravel the interaction between heat and drought stress in the Arabidopsis thaliana holobiont.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1484251},
pmid = {39748821},
issn = {1664-462X},
abstract = {The impact of combined heat and drought stress was investigated in Arabidopsis thaliana and compared to individual stresses to reveal additive effects and interactions. A combination of plant metabolomics and root and rhizosphere bacterial metabarcoding were used to unravel effects at the plant holobiont level. Hierarchical cluster analysis of metabolomics signatures pointed out two main clusters, one including heat and combined heat and drought, and the second cluster that included the control and drought treatments. Overall, phenylpropanoids and nitrogen-containing compounds, hormones and amino acids showed the highest discriminant potential. A decrease in alpha-diversity of Bacteria was observed upon stress, with stress-dependent differences in bacterial microbiota composition. The shift in beta-diversity highlighted the pivotal enrichment of Proteobacteria, including Rhizobiales, Enterobacteriales and Azospirillales. The results corroborate the concept of stress interaction, where the combined heat and drought stress is not the mere combination of the single stresses. Intriguingly, multi-omics interpretations evidenced a good correlation between root metabolomics and root bacterial microbiota, indicating an orchestrated modulation of the whole holobiont.},
}

@article {pmid39738126,
year = {2024},
author = {Zhang, S and Song, W and Marinos, G and Waschina, S and Zimmermann, J and Kaleta, C and Thomas, T},
title = {Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10858},
pmid = {39738126},
issn = {2041-1723},
mesh = {*Symbiosis ; *Porifera/microbiology/metabolism ; Animals ; *Microbiota/genetics ; *Metabolic Networks and Pathways/genetics ; Bacteria/metabolism/genetics/classification ; Phylogeny ; Genome ; Genome, Bacterial ; Models, Biological ; Metagenomics/methods ; },
abstract = {Sponges harbour complex microbiomes and as ancient metazoans and important ecosystem players are emerging as powerful models to understand the evolution and ecology of symbiotic interactions. Metagenomic studies have previously described the functional features of sponge symbionts, however, little is known about the metabolic interactions and processes that occur under different environmental conditions. To address this issue, we construct here constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp. Our models define the importance of sponge-derived nutrients for microbiome stability and discover how different organic inputs can result in net heterotrophy or autotrophy of the symbiont community. The analysis further reveals the key role that a newly discovered bacterial taxon has in cross-feeding activities and how it dynamically adjusts with nutrient inputs. Our study reveals insights into the functioning of a sponge microbiome and provides a framework to further explore and define metabolic interactions in holobionts.},
}

*Symbiosis
*Porifera/microbiology/metabolism
Animals
*Microbiota/genetics
*Metabolic Networks and Pathways/genetics
Bacteria/metabolism/genetics/classification
Phylogeny
Genome
Genome, Bacterial
Models, Biological
Metagenomics/methods

@article {pmid39735181,
year = {2024},
author = {Trefault, N},
title = {Editorial: Impact of anthropogenic stressors on marine sponge holobiomes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1533416},
pmid = {39735181},
issn = {1664-302X},
}

@article {pmid39731136,
year = {2024},
author = {Balamurugan, BS and Marimuthu, MMC and Sundaram, VA and Saravanan, B and Chandrababu, P and Chopra, H and Malik, T},
title = {Micro nutrients as immunomodulators in the ageing population: a focus on inflammation and autoimmunity.},
journal = {Immunity & ageing : I & A},
volume = {21},
number = {1},
pages = {88},
pmid = {39731136},
issn = {1742-4933},
abstract = {Immunosenescence, the slow degradation of immune function over time that is a hallmark and driver of aging, makes older people much more likely to be killed by common infections (such as flu) than young adults, but it also contributes greatly to rates of chronic inflammation in later life. Such micro nutrients are crucial for modulating effective immune responses and their deficiencies have been associated with dysfunctional immunity in the elderly. In this review, we specifically focused on the contribution of major micro nutrients (Vitamins A, D and E, Vitamin C; Zinc and Selenium) as immunomodulators in ageing population especially related to inflame-ageing process including autoimmunity. This review will cover these hologenomic interactions, including how micro nutrients can modulate immune cell function and/or cytokine production to benefit their hosts with healthy mucous-associated immunity along with a sustainable immunologic homeostasis. For example, it points out the modulatory effects of vitamin D on both innate and adaptive immunity, with a specific focus on its ability to suppress pro-inflammatory cytokines synthesis while enhancing regulatory T-cell function. In the same context, also zinc is described as important nutrient for thymic function and T-cell differentiation but exhibits immunomodulatory functions by decreasing inflammation. In addition, the review will go over how micro nutrient deficiencies increase systemic chronic low-grade inflammation and, inflammaging as well as actually enhance autoimmune pathologies in old age. It assesses the potential role of additional targeted nutritional supplementation with micro nutrients to counteract these effects, promoting wider immune resilience in older adults. This review collates the current evidence and highlights the role of adequate micro nutrient intake on inflammation and autoimmunity during ageing, providing plausible origins for nutritional interventions to promote healthy immune aging.},
}

@article {pmid39730835,
year = {2024},
author = {Orkin, JD and Kuderna, LFK and Hermosilla-Albala, N and Fontsere, C and Aylward, ML and Janiak, MC and Andriaholinirina, N and Balaresque, P and Blair, ME and Fausser, JL and Gut, IG and Gut, M and Hahn, MW and Harris, RA and Horvath, JE and Keyser, C and Kitchener, AC and Le, MD and Lizano, E and Merker, S and Nadler, T and Perry, GH and Rabarivola, CJ and Rasmussen, L and Raveendran, M and Roos, C and Wu, DD and Zaramody, A and Zhang, G and Zinner, D and Pozzi, L and Rogers, J and Farh, KK and Marques Bonet, T},
title = {Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {39730835},
issn = {2397-334X},
support = {LCF/BQ/PI20/11760004//"la Caixa" Foundation (Caixa Foundation)/ ; DGECR-2023-00272//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; STF 8286//European Molecular Biology Organization (EMBO)/ ; NE/T000341/1//RCUK | Natural Environment Research Council (NERC)/ ; BCS 1926215//National Science Foundation (NSF)/ ; BCS 1926105//National Science Foundation (NSF)/ ; 864203//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; },
abstract = {Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors.},
}

@article {pmid39729906,
year = {2024},
author = {Abdelghany, S and Simancas-Giraldo, SM and Zayed, A and Farag, MA},
title = {How does the coral microbiome mediate its natural host fitness under climate stress conditions? Physiological, molecular, and biochemical mechanisms.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106920},
doi = {10.1016/j.marenvres.2024.106920},
pmid = {39729906},
issn = {1879-0291},
abstract = {Although the symbiotic partnership between corals and algal endosymbionts has been extensively explored, interactions between corals, their algal endosymbionts and microbial associates are still less understood. Screening the response of natural microbial consortiums inside corals can aid in exploiting them as markers for dysbiosis interactions inside the coral holobiont. The coral microbiome includes archaea, bacteria, fungi, and viruses hypothesized to play a pivotal vital role in coral health and tolerance to heat stress condition via different physiological, biochemical, and molecular mechanisms. The dynamic behaviour of microbial associates could denote their potential role in coral adaptation to future climate change, with microbiome shifts occurring independently as a response to thermal stress or as a response to host stress response. Associated adaptations include regulation of coral-algal-microbial interactions, expression of heat shock proteins, microbial composition changes, and accumulation of secondary metabolites to aid in sustaining the coral's overall homeostasis under ocean warming scenarios.},
}