@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.},
}

@article {pmid39715180,
year = {2024},
author = {Bjørnsen, MB and Valerón, NR and Vásquez, DP and Velasco, EM and Hansen, AJ and Hauptmann, AL},
title = {Microbiota in the ptarmigan intestine-An Inuit delicacy and its potential in popular cuisine.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0305317},
doi = {10.1371/journal.pone.0305317},
pmid = {39715180},
issn = {1932-6203},
mesh = {Animals ; *Inuit ; *Intestines/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Humans ; Galliformes/microbiology ; Greenland ; },
abstract = {The consumption of prey intestines and their content, known as gastrophagy, is well-documented among Arctic Indigenous peoples, particularly Inuit. In Greenland, Inuit consume intestines from various animals, including the ptarmigan, a small herbivorous grouse bird. While gastrophagy provides the potential to transfer a large number of intestinal microorganisms from prey to predator, including to the human gut, its microbial implications remain to be investigated. This study addresses this gap by investigating the microbial composition of the Greenlandic rock ptarmigan's gastrointestinal tract by analyzing the crop, stomach, and intestines while also comparing it with the microbiota found in garum, a fermented sauce made from ptarmigan meat and intestines. Through 16S rRNA gene sequencing, we assessed whether garum made from ptarmigan intestines provides access to microbial diversity otherwise only accessible through gastrophagy. Our findings reveal that garum made from ptarmigan intestines displayed distinct flavors and microbial composition similar to that found in the ptarmigan gut and intestines, highlighting the potential role of fermented products in mediating food microbial diversity associated with Indigenous food practices. Furthermore, our study underscores the broader importance of understanding microbial diversity in different food systems, particularly in the context of shifting dietary patterns and concerns about diminishing food microbial diversity. By elucidating the microbial richness gained through gastrophagy this research contributes to a deeper understanding of traditional and Indigenous foodways and their implications for human gut health.},
}

Animals
*Inuit
*Intestines/microbiology
*Gastrointestinal Microbiome
*RNA, Ribosomal, 16S/genetics
Humans
Galliformes/microbiology
Greenland

@article {pmid39710259,
year = {2024},
author = {Callaway, T and Perez, HG and Corcionivoschi, N and Bu, D and Fluharty, FL},
title = {The Holobiont concept in ruminant physiology - more of the same, or something new and meaningful to food quality, food security, and animal health?.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25847},
pmid = {39710259},
issn = {1525-3198},
abstract = {The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as impacted by the microbial communities that colonize and/or co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been "pushed" by the advent of high throughput DNA sequencing and, to a lesser extent, other "omics"-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant "holobiont" is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the "holobiont" approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinalmicrobiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. While the holobiont approach might improve food quality, food security and animal health, these benefits will be most likely achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale, as well as its generation in context with the "forgotten" knowledge of ruminant and human physiology.},
}

@article {pmid39709663,
year = {2024},
author = {Augusto, AM and Pereira, S and Rodrigues, S and Marques, F and Aizpurua, O and Alberdi, A and Jones, G and Razgour, O and Marques, TA and Russo, D and Rebelo, H},
title = {Landscape influences bat suppression of pine processionary moth: Implications for pest management.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123803},
doi = {10.1016/j.jenvman.2024.123803},
pmid = {39709663},
issn = {1095-8630},
abstract = {Bats provide important ecosystem services, particularly in agriculture, yet integrating bat management into conservation plans remains challenging. Some landscape features considerably influence bat presence, diversity, and ecosystem service provision. Understanding the relationship between landscape structure, composition, pest suppression, and ecosystem services is crucial. We modelled areas where bats most effectively suppress pine processionary moths (Thaumetopoea pityocampa), considering landscape characteristics to predict ecosystem services and optimise pest suppression in Serra da Estrela, Portugal. Faecal samples collected during fieldwork were analysed for pine processionary moth presence in bat diets. Lasso regression assessed spatial landscape variables to create an "optimal landscape" for predation. Landscape structure and composition influenced pest suppression differently, with the greatest impact within a 5000-m buffer. "Riparian edge" and "tree cover density" were key habitat structure variables supporting bat navigation and access to hunting areas, while "other forest" and "vineyard/orchard" areas were important composition variables. Optimising landscape composition involves incorporating diverse forest within agroforestry systems to enhance pest suppression by creating habitats reflecting bats' foraging preferences. We recommend strategies focusing on riparian edge conservation, selective canopy reduction, and promoting diverse forest compositions. These strategies aim to create mosaic landscapes balancing land uses, fostering optimal conditions for bat foraging. Our study shows edges provide the highest rates of bats-pine processionary moth interactions. However, caution is needed to avoid excessive fragmentation, which may reduce habitat suitability and increase pest presence before effective bat predation. A balanced approach, focusing on edge creation without over-fragmenting the landscape, is key to promoting sustainable pest management.},
}

@article {pmid39702455,
year = {2024},
author = {García, FC and Osman, EO and Garcias-Bonet, N and Delgadillo-Ordoñez, N and Santoro, EP and Raimundo, I and Villela, HDM and Voolstra, CR and Peixoto, RS},
title = {Seasonal changes in coral thermal threshold suggest species-specific strategies for coping with temperature variations.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1680},
pmid = {39702455},
issn = {2399-3642},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; FCC/1/1973-51-01//King Abdullah University of Science and Technology (KAUST)/ ; URF/1/4723-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
mesh = {*Anthozoa/physiology ; Animals ; *Seasons ; *Temperature ; *Species Specificity ; Acclimatization ; Thermotolerance ; Photosynthesis ; Indian Ocean ; },
abstract = {Coral thermotolerance research has focused on the ability of coral holobionts to maximize withstanding thermal stress exposure. Yet, it's unclear whether thermal thresholds adjust across seasons or remain constant for a given species and location. Here, we assessed the thermal tolerance thresholds over time spanning the annual temperature variation in the Red Sea for Pocillopora verrucosa and Acropora spp. colonies. Utilizing the Coral Bleaching Automated Stress System (CBASS), we conducted standardized acute thermal assays by exposing corals to a range of temperatures (30 to 39 °C) and measuring their photosynthetic efficiency (Fv/Fm). Our results reveal species-specific thermal tolerance patterns. P. verrucosa exhibited significant seasonal changes in their thermal thresholds of around 3 °C, while Acropora spp. remained rather stable, showing changes of around 1 °C between seasons. Our work shows that thermal thresholds can vary with seasonal temperature fluctuations, suggesting that coral species may acclimate to these natural temperature hanges over short periods in a species-specific manner.},
}

*Anthozoa/physiology
Animals
*Seasons
*Temperature
*Species Specificity
Acclimatization
Thermotolerance
Photosynthesis
Indian Ocean

@article {pmid39701859,
year = {2024},
author = {Barnes, CJ and Bahram, M and Nicolaisen, M and Gilbert, MTP and Vestergård, M},
title = {Microbiome selection and evolution within wild and domesticated plants.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.11.011},
pmid = {39701859},
issn = {1878-4380},
abstract = {Microbes are ubiquitously found across plant surfaces and even within their cells, forming the plant microbiome. Many of these microbes contribute to the functioning of the host and consequently affect its fitness. Therefore, in many contexts, including microbiome effects enables a better understanding of the phenotype of the plant rather than considering the genome alone. Changes in the microbiome composition are also associated with changes in the functioning of the host, and there has been considerable focus on how environmental variables regulate plant microbiomes. More recently, studies suggest that the host genome also preconditions the microbiome to the environment of the plant, and the microbiome is therefore subject to evolutionary forces. Here, we outline how plant microbiomes are governed by both environmental variables and evolutionary processes and how they can regulate plant health together.},
}

@article {pmid39691438,
year = {2024},
author = {Armstrong, KC and Lippert, M and Hanson, E and Nestor, V and Cornwell, B and Walker, NS and Golbuu, Y and Palumbi, SR},
title = {Fine-Scale Geographic Variation of Cladocopium in Acropora hyacinthus Across the Palauan Archipelago.},
journal = {Ecology and evolution},
volume = {14},
number = {12},
pages = {e70650},
doi = {10.1002/ece3.70650},
pmid = {39691438},
issn = {2045-7758},
abstract = {Symbiont genotype plays a vital role in the ability of a coral host to tolerate rising ocean temperatures, with some members of the family Symbiodiniaceae possessing more thermal tolerance than others. While existing studies on genetic structure in symbiont populations have focused on broader scales of 10-100 s of km, there is a noticeable gap in understanding the seascape genetics of coral symbionts at finer-yet ecologically and evolutionarily relevant-scales. Here, we mapped short reads from 271 holobiont genome libraries of individual Acropora hyacinthus colonies to protein coding genes from the chloroplast genome to identify patterns of symbiont population genetic structure. Utilizing this low-pass method, we assayed over 13,000 bases from every individual, enabling us to discern genetic variation at a finer geographic scale than previously reported at the population level. We identified five common Cladocopium chloroplast SNP profiles present across Palau, with symbiont structure varying between Northern, mid-lagoon, and Southern regions, and inshore-offshore gradients. Although symbiont populations within reefs typically contained significant genetic diversity, we also observed genetic structure between some nearby reefs. To explore whether coral hosts retain their symbionts post-transplantation, we experimentally moved 79 corals from their native reefs to transplant sites with both different and similar chloroplast SNP profiles. Over 12 months, we observed 12 instances where transplanted corals changed profiles, often transitioning to a profile present in adjacent corals. Symbiont genetic structure between reefs suggests either low dispersal of symbionts or environmental selection against dispersers, both resulting in the potential for significant adaptive differentiation across reef environments. The extent to which local corals and their symbionts are co-adapted to environments on a reef-by-reef scale is currently poorly known. Chloroplast sequences offer an additional tool for monitoring symbiont genetics and coral-symbiont interactions when assisted migration is used in restoration.},
}

@article {pmid39681619,
year = {2024},
author = {Niedzwiedz, S and Schmidt, C and Yang, Y and Burgunter-Delamare, B and Andersen, S and Hildebrandt, L and Pröfrock, D and Thomas, H and Zhang, R and Damsgård, B and Bischof, K},
title = {Run-off impacts on Arctic kelp holobionts have strong implications on ecosystem functioning and bioeconomy.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {30506},
pmid = {39681619},
issn = {2045-2322},
support = {869154//European Union's Horizon 2020 research and innovation programme/ ; 869383//European Union's Horizon 2020 research and innovation programme/ ; 869154//European Union's Horizon 2020 research and innovation programme/ ; 869383//European Union's Horizon 2020 research and innovation programme/ ; 869154//European Union's Horizon 2020 research and innovation programme/ ; 869154//European Union's Horizon 2020 research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 2021YFE0193000//National Key Research and Development Program of China/ ; 2021YFE0193000//National Key Research and Development Program of China/ ; SML2023SP218//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP218//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
mesh = {*Kelp ; Arctic Regions ; *Ecosystem ; *Climate Change ; Food Chain ; },
abstract = {Kelps (Laminariales, Phaeophyceae) are foundation species along Arctic rocky shores, providing the basis for complex ecosystems and supporting a high secondary production. Due to ongoing climate change glacial and terrestrial run-off are currently accelerating, drastically changing physical and chemical water column parameters, e.g., water transparency for photosynthetically active radiation or dissolved concentrations of (harmful) elements. We investigated the performance and functioning of Arctic kelp holobionts in response to run-off gradients, with a focus on the effect of altered element concentrations in the water column. We found that the kelp Saccharina latissima accumulates harmful elements (e.g., cadmium, mercury) originating from coastal run-off. As kelps are at the basis of the food web, this might lead to biomagnification, with potential consequences for high-latitude kelp maricultures. In contrast, the high biosorption potential of kelps might be advantageous in monitoring environmental pollution or potentially extracting dissolved rare earth elements. Further, we found that the relative abundances of several kelp-associated microbial taxa significantly responded to increasing run-off influence, changing the kelps functioning in the ecosystem, e.g., the holobionts nutritional value and elemental cycling. The responses of kelp holobionts to environmental changes imply cascading ecological and economic consequences for Arctic kelp ecosystems in future climate change scenarios.},
}

*Kelp
Arctic Regions
*Ecosystem
*Climate Change
Food Chain

@article {pmid39680902,
year = {2024},
author = {Lipowska, MM and Sadowska, ET and Kohl, KD and Koteja, P},
title = {Experimental Evolution of a Mammalian Holobiont? Genetic and Maternal Effects on the Cecal Microbiome in Bank Voles Selectively Bred for Herbivorous Capability.},
journal = {Ecological and evolutionary physiology},
volume = {97},
number = {5},
pages = {274-291},
doi = {10.1086/732781},
pmid = {39680902},
issn = {2993-7973},
mesh = {Animals ; *Arvicolinae/microbiology/genetics ; *Herbivory ; *Gastrointestinal Microbiome/genetics ; Female ; Cecum/microbiology ; Biological Evolution ; Maternal Inheritance/genetics ; Selective Breeding/genetics ; Male ; Diet/veterinary ; },
abstract = {AbstractMammalian herbivory represents a complex adaptation requiring evolutionary changes across all levels of biological organization, from molecules to morphology to behavior. Explaining the evolution of such complex traits represents a major challenge in biology, as it is simultaneously muddled and enlightened by a growing awareness of the crucial role of symbiotic associations in shaping organismal adaptations. The concept of hologenomic evolution includes the partnered unit of the holobiont, the host with its microbiome, as a selection unit that may undergo adaptation. Here, we test some of the assumptions underlying the concept of hologenomic evolution using a unique experimental evolution model: lines of the bank vole (Myodes [=Clethrionomys] glareolus) selected for increased ability to cope with a low-quality herbivorous diet and unselected control lines. Results from a complex nature-nurture design, in which we combined cross-fostering between the selected and control lines with dietary treatment, showed that the herbivorous voles harbored a cecal microbiome with altered membership and structure and changed abundances of several phyla and genera regardless of the origin of their foster mothers. Although the differences were small, they were statistically significant and partially robust to changes in diet and housing conditions. Microbial characteristics also correlated with selection-related traits at the level of individual variation. Thus, the results support the hypothesis that selection on a host performance trait leads to genetic changes in the host that promote the maintenance of a beneficial microbiome. Such a result is consistent with some of the assumptions underlying the concept of hologenomic evolution.},
}

Animals
*Arvicolinae/microbiology/genetics
*Herbivory
*Gastrointestinal Microbiome/genetics
Female
Cecum/microbiology
Biological Evolution
Maternal Inheritance/genetics
Selective Breeding/genetics
Male
Diet/veterinary

@article {pmid39670091,
year = {2024},
author = {Garzon-Machado, M and Luna-Fontalvo, J and García-Urueña, R},
title = {Disease prevalence and bacterial isolates associated with Acropora palmata in the Colombian Caribbean.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16886},
pmid = {39670091},
issn = {2167-8359},
mesh = {*Anthozoa/microbiology ; Animals ; Colombia/epidemiology ; Caribbean Region/epidemiology ; Prevalence ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; Vibrio/isolation & purification/genetics/pathogenicity ; },
abstract = {The decline in Acropora palmata populations in Colombian reefs has been mainly attributed to diseases outbreaks. The population size structure and prevalence of white pox and white band disease were evaluated in six localities of the Colombian Caribbean. Here, we aimed to isolate enteric bacteria and Vibrios from healthy and diseased coral mucus to relate its presence to the health status of Acropora palmata. The isolated bacteria were identified using molecular analyses with the 16S rRNA gene. Larger colonies had the highest percentage of the prevalence of both diseases. The strains that were identified as Vibrio sp. and Bacillus sp. were common in the healthy and diseased mucus of the holobiont. The Exiguobacterium sp. and Cobetia sp. strains isolated from diseased mucus may indicate maintenance and resilience mechanisms in the coral. Enterococcus sp. and other bacteria of the Enterobacteriaceae family were isolated from some localities, suggesting that probably contamination due to poor treatment of domestic wastewater and contributions from river discharges can affect coral health. The spatial heterogeneity of Colombian coral reefs exhibited variability in the bacteria, wherein environmental alterations can trigger signs of disease.},
}

*Anthozoa/microbiology
Animals
Colombia/epidemiology
Caribbean Region/epidemiology
Prevalence
RNA, Ribosomal, 16S/genetics
Coral Reefs
Vibrio/isolation & purification/genetics/pathogenicity

@article {pmid39658219,
year = {2024},
author = {Juéry, C and Auladell, A and Füssy, Z and Chevalier, F and Yee, DP and Pelletier, E and Corre, E and Allen, AE and Richter, DJ and Decelle, J},
title = {Transportome remodeling of a symbiotic microalga inside a planktonic host.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae239},
pmid = {39658219},
issn = {1751-7370},
abstract = {Metabolic exchange is one of the foundations of symbiotic associations between organisms and is a driving force in evolution. In the ocean, photosymbiosis between heterotrophic hosts and microalgae is powered by photosynthesis and relies on the transfer of organic carbon to the host (e.g. sugars). Yet, the identity of transferred carbohydrates as well as the molecular mechanisms that drive this exchange remain largely unknown, especially in unicellular photosymbioses that are widespread in the open ocean. Combining genomics, single-holobiont transcriptomics, and environmental metatranscriptomics, we revealed the transportome of the marine microalga Phaeocystis in symbiosis within acantharia, with a focus on sugar transporters. At the genomic level, the sugar transportome of Phaeocystis is comparable to non-symbiotic haptophytes. By contrast, we found significant remodeling of the expression of the transportome in symbiotic microalgae compared to the free-living stage. More particularly, 36% of sugar transporter genes were differentially expressed. Several of them, such as GLUTs, TPTs, and aquaporins, with glucose, triose-phosphate sugars, and glycerol as potential substrates, were upregulated at the holobiont and community level. We also showed that algal sugar transporter genes exhibit distinct temporal expression patterns during the day. This reprogrammed transportome indicates that symbiosis has a major impact on sugar fluxes within and outside the algal cell, and highlights the complexity and the dynamics of metabolic exchanges between partners. This study improves our understanding of the molecular players of the metabolic connectivity underlying the ecological success of planktonic photosymbiosis and paves the way for more studies on transporters across photosymbiotic models.},
}

@article {pmid39653763,
year = {2024},
author = {Forrester, JV and McMenamin, PG},
title = {Evolution of the ocular immune system.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {39653763},
issn = {1476-5454},
abstract = {The evolution of the ocular immune system should be viewed within the context of the evolution of the immune system, and indeed organisms, as a whole. Since the earliest time, the most primitive responses of single cell organisms involved molecules such as anti-microbial peptides and behaviours such as phagocytosis. Innate immunity took shape ~2.5 billion years ago while adaptive immunity and antigen specificity appeared with vertebrate evolution ~ 500 million years ago. The invention of the microscope and the germ theory of disease precipitated debate on cellular versus humoral immunity, resolved by the discovery of B and T cells. Most recently, our understanding of the microbiome and consideration of the host existing symbiotically with trillions of microbial genes (the holobiont), suggests that the immune system is a sensor of homoeostasis rather than simply a responder to pathogens. Each tissue type in multicellular organisms, such as vertebrates, has a customised response to immune challenge, with powerful reactions most evident in barrier tissues such as the skin and gut mucosa, while the eye and brain occupy the opposite extreme where responses are attenuated. The experimental background which historically led to the concept of immune privilege is discussed in this review; however, we propose that the ocular immune response should not be viewed as unique but simply an example of how the tissues variably respond in nature, more or less to the same challenge (or danger).},
}

@article {pmid39651872,
year = {2024},
author = {Marques, M and da Silva, DM and Santos, E and Baylina, N and Peixoto, R and Kyrpides, NC and Woyke, T and Whitman, WB and Keller-Costa, T and Costa, R},
title = {Genome sequences of four novel Endozoicomonas strains associated with a tropical octocoral in a long-term aquarium facility.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0083324},
doi = {10.1128/mra.00833-24},
pmid = {39651872},
issn = {2576-098X},
abstract = {We report the genome sequences of four Endozoicomonas sp. strains isolated from the octocoral Litophyton maintained long term at an aquarium facility. Our analysis reveals the coding potential for versatile polysaccharide metabolism; Type II, III, IV, and VI secretion systems; and the biosynthesis of novel ribosomally synthesized and post-translationally modified peptides.},
}

@article {pmid39637852,
year = {2024},
author = {Ramos-Madrigal, J and Fritz, GJ and Schroeder, B and Smith, B and Sánchez-Barreiro, F and Carøe, C and Runge, AKW and Boer, S and McGrath, K and Vieira, FG and Liu, S and da Fonseca, RR and Guo, C and Zhang, G and Petersen, B and Sicheritz-Pontén, T and Gopalakrishnan, S and Gilbert, MTP and Wales, N},
title = {The genomic origin of early maize in eastern North America.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.11.003},
pmid = {39637852},
issn = {1097-4172},
abstract = {Indigenous maize varieties from eastern North America have played an outsized role in breeding programs, yet their early origins are not fully understood. We generated paleogenomic data to reconstruct how maize first reached this region and how it was selected during the process. Genomic ancestry analyses reveal recurrent movements northward from different parts of Mexico, likely culminating in at least two dispersals from the US Southwest across the Great Plains to the Ozarks and beyond. We find that 1,000-year-old Ozark specimens carry a highly differentiated wx1 gene, which is involved in the synthesis of amylose, highlighting repeated selective pressures on the starch metabolic pathway throughout maize's domestication. This population shows a close affinity with the lineage that ultimately became the Northern Flints, a major contributor to modern commercial maize.},
}

@article {pmid39633476,
year = {2024},
author = {Manrique-de-la-Cuba, MF and Parada-Pozo, G and Rodríguez-Marconi, S and López-Rodríguez, MR and Abades, S and Trefault, N},
title = {Evidence of habitat specificity in sponge microbiomes from Antarctica.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {100},
pmid = {39633476},
issn = {2524-6372},
support = {Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; DG_02-22//Instituo Antartico Chileno- INACH/ ; Doctoral fellowship N° 21211164//Agencia Nacional de Investigación e Innovación/ ; },
abstract = {BACKGROUND: Marine sponges and their microbiomes are ecosystem engineers distributed across the globe. However, most research has focused on tropical and temperate sponges, while polar regions like Antarctica have been largely neglected. Despite its harsh conditions and geographical isolation, Antarctica is densely populated by sponges. In this study, we explored the extent of habitat specificity in the diversity, community composition, and microbial co-occurrence within Antarctic sponge microbiomes, in comparison to those from other marine environments. We used massive sequencing of 16S rRNA genes and integrated multiple databases to incorporate Antarctic sponges as a habitat in global microbiome analyses.

RESULTS: Our study revealed significant differences in microbial diversity and community composition between Antarctic and non-Antarctic sponges. We found that most microorganisms present in Antarctic sponges are unique to the South Shetland Islands. Nitrosomonas oligotropha, Candidatus Nitrosopumilus, Polaribacter, SAR116 clade, and Low Salinity Nitrite-Oxidizing Bacteria (LS-NOB) are microbial members characterizing the Antarctic sponge microbiomes. Based on their exclusivity and presence across different sponges worldwide, we identified habitat-specific and habitat-generalist bacteria associated with each habitat. They are particularly abundant and connected within all the Antarctic sponges, suggesting that they may play a crucial role as keystone species within these sponge ecosystems.

CONCLUSIONS: This study provides significant insights into the microbial diversity and community composition of sponges in Antarctica and non-Antarctic ecoregions. Our findings provide evidence for habitat-specific patterns that differentiate the microbiomes of Antarctic sponges from elsewhere, indicating the strong influence of environmental selection and dispersal limitation wrapped into the Antarctic ecoregions to shape more similar microbial communities in distantly related sponges. This study contributes to understanding signatures of microbial community assembly in the Antarctic sponges and has important implications for the ecology and evolution of these unique marine environments.},
}

@article {pmid39631125,
year = {2024},
author = {Zhang, JY and Li, XY and Li, DX and Zhang, ZH and Hu, LQ and Sun, CX and Zhang, XN and Wu, M and Liu, LT},
title = {Endoplasmic reticulum stress in intestinal microecology: A controller of antineoplastic drug-related cardiovascular toxicity.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {181},
number = {},
pages = {117720},
doi = {10.1016/j.biopha.2024.117720},
pmid = {39631125},
issn = {1950-6007},
abstract = {Endoplasmic reticulum (ER) stress is extensively studied as a pivotal role in the pathological processes associated with intestinal microecology. In antineoplastic drug treatments, ER stress is implicated in altering the permeability of the mechanical barrier, depleting the chemical barrier, causing dysbiosis, exacerbating immune responses and inflammation in the immune barrier. Enteric dysbiosis and intestinal dysfunction significantly affect the circulatory system in various heart disorders. In antineoplastic drug-related cardiovascular (CV) toxicity, ER stress constitutes a web of relationships in the host-microbiome symbiotic regulatory loop. Therefore, understanding the holobiont perspective will help de-escalate spatial and temporal restrictions. This review investigates the role of ER stress-mediated gut microecological alterations in antineoplastic treatment-induced CV toxicity.},
}

@article {pmid39620136,
year = {2024},
author = {Ellegaard, MR and Ebenesersdóttir, SS and Moore, KHS and Petersén, A and Vågene, ÅJ and Bieker, VC and Denham, SD and Cavalleri, GL and Gilbert, E and Werge, T and Hansen, TF and Kockum, I and Alfredsson, L and Olsson, T and Hovig, E and Gilbert, MTP and Stefánsson, K and Stenøien, HK and Helgason, A and Martin, MD},
title = {Corroborating written history with ancient DNA: The case of the Well-man described in an Old Norse saga.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111076},
pmid = {39620136},
issn = {2589-0042},
abstract = {The potential of ancient DNA analyses to provide independent sources of information about events in the historical record remains to be demonstrated. Here we apply palaeogenomic analysis to human remains excavated from a medieval well at the ruins of Sverresborg Castle in central Norway. In Sverris Saga, the Old Norse saga of King Sverre Sigurdsson, one passage details a 1197-CE raid on the castle and mentions a dead man thrown into the well. Radiocarbon dating supports that these are that individual's remains. We sequenced the Well-man's nuclear genome to 3.4× and compared it to Scandinavian populations, revealing he was closely related to inhabitants of southern Norway. This was surprising because King Sverre's defeated army was assumed to be recruited from parts of central Norway, whereas the raiders were from the south. The findings also indicate that the unique genetic drift seen in present-day southern Norwegians already existed 800 years ago.},
}

@article {pmid39620087,
year = {2024},
author = {Zhang, X and Xi, T and Wang, Y and Fan, X and Xu, D and Zhang, P and Sun, K and Zhang, Y and Ma, J and Ye, N},
title = {Chemical interactions between kelp Macrocystis pyrifera and symbiotic bacteria under elevated CO2 condition.},
journal = {Marine life science & technology},
volume = {6},
number = {4},
pages = {700-712},
pmid = {39620087},
issn = {2662-1746},
abstract = {UNLABELLED: Kelps are pivotal to temperate coastal ecosystems, providing essential habitat and nutrients for diverse marine life, and significantly enhancing local biodiversity. The impacts of elevated CO2 levels on kelps may induce far-reaching effects throughout the marine food web, with potential consequences for biodiversity and ecosystem functions. This study considers the kelp Macrocystis pyrifera and its symbiotic microorganisms as a holistic functional unit (holobiont) to examine their collective response to heightened CO2 levels. Over a 4 month cultivation from the fertilization of M. pyrifera gametes to the development of juvenile sporophytes, our findings reveal that elevated CO2 levels influence the structure of the M. pyrifera symbiotic microbiome, alter metabolic profiles, and reshape microbe-metabolite interactions using 16S rRNA amplicon sequencing and liquid chromatography coupled to mass spectrometry analysis. Notably, Dinoroseobacter, Sulfitobacter, Methylotenera, Hyphomonas, Milano-WF1B-44 and Methylophaga were selected as microbiome biomarkers, which showed significant increases in comparative abundance with elevated CO2 levels. Stress-response molecules including fatty-acid metabolites, oxylipins, and hormone-like compounds such as methyl jasmonate and prostaglandin F2a emerged as critical metabolomic indicators. We propose that elevated CO2 puts certain stress on the M. pyrifera holobiont, prompting the release of these stress-response molecules. Moreover, these molecules may aid the kelp's adaptation by modulating the microbial community structure, particularly influencing potential pathogenic bacteria, to cope with environmental change. These results will enrich the baseline data related to the chemical interactions between the microbiota and M. pyrifera and provide clues for predicting the resilience of kelps to future climate change.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00259-5.},
}

@article {pmid39615101,
year = {2024},
author = {Huang, W and Huang, Z and Yang, E and Meng, L and Chen, J and Tan, R and Xiao, Z and Zhou, Y and Xu, M and Yu, K},
title = {High- and low-temperature stress responses of Porites lutea from the relatively high-latitude region of the South China Sea.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106858},
doi = {10.1016/j.marenvres.2024.106858},
pmid = {39615101},
issn = {1879-0291},
abstract = {Global climate change has led to more frequent extreme temperature (extreme heat and cold) events, posing a serious threat to coral reef ecosystems. Higher latitudes are considered potential refuges for reef-building corals, but their response to extreme temperature stress in these regions remain unclear. This study, indoor simulated stress experiments ranging on Porites lutea from Weizhou Island in the northern part of the South China Sea, simulating suitable (26 °C) to extreme high (34 °C) and extreme low (12 °C) temperatures. Physiological, biochemical, and transcriptional responses, were analysed. Results showed P. lutea's tentacles contracted, and symbiotic relationships broke down at both high and low temperatures; leading to oxidative stress, and a higher risk of disease. The coral host's response to temperature stress was positively regulated, mainly through apoptosis and metabolic inhibition pathways, whereas Symbiodiniaceae C15 showed no significant response to either high- or low-temperature stress. The coral host played a dominant role in the holobiont's stress response, using similar mechanisms for both high- and low-temperatures with some differences in the details. This study enhances understanding the temperature response mechanisms of the dominant coral species, P. lutea in the relatively high-latitude regions of the South China Sea.},
}

@article {pmid39603001,
year = {2024},
author = {Gao, X and Chen, J and Ma, Y and Zheng, Y and Bu, Y and Yu, X and Yu, K},
title = {Differential physiological and microbial responses of the octocoral Junceella squamata to high-temperature and cadmium stress.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106865},
doi = {10.1016/j.marenvres.2024.106865},
pmid = {39603001},
issn = {1879-0291},
abstract = {Global warming and heavy metals have become the major threat to the growth and reproduction of corals. However, unlike scleractinian corals, in the context of widespread coral degradation worldwide, there are few reports on the response of octocorallia corals to high-temperature stress and heavy metals. In the present study, we conducted indoor simulation experiments using Junceella squamata. We evaluated the physiological response of these corals under high-temperature stress at 33 °C and cadmium (Cd) stress by comparing the composition and diversity of their symbiotic bacteria and analyzing differences in their transcriptome. The results show that high-temperature stress has more severe adverse effects than cadmium stress. High-temperature stress disrupts coral symbiotic relationships, leading to an increase in alpha diversity associated with disease-causing bacteria, which may increase the risk of infection and potentially contribute to coral mortality. Meanwhile, cadmium stress increases the instability of the coral holobiont, potentially disrupting DNA stability and RNA transcriptional regulation. However, an increase in Cd-tolerant bacteria may help corals respond to cadmium stress. This study reveals the effects of harmful substances on coral and highlights the urgent need for action to protect octocorals in the face of environmental stress.},
}

@article {pmid39602985,
year = {2024},
author = {Gao, X and Chen, J and Yu, K and Bu, Y and Wang, L and Yu, X},
title = {Exposure to polypropylene microplastics induces the upregulation of protein digestion-associated genes and microbiome reorganization in the octocoral Junceella squamata.},
journal = {Marine pollution bulletin},
volume = {210},
number = {},
pages = {117331},
doi = {10.1016/j.marpolbul.2024.117331},
pmid = {39602985},
issn = {1879-3363},
abstract = {Microplastics, a new type of pollutants found in coral reefs, have attracted increasing attention. However, most of the current research focuses on the scleractinian corals and few reports on Octocorallia. To reveal the impact of microplastic exposure on Octocorallia, we analyzed the transcriptional response of the coral hosts Junceella squamata along with changes to the diversity and community structure of its symbiotic bacteria following exposure to polystyrene microplastics. These results suggest that the microplastics have adverse impacts on nutrient metabolism and absorption in J. squamata. The symbiotic bacteria of J. squamata exhibited a clear response after exposure to microplastics, which may also reflect an adaptation mechanism of corals, and help to maintain the physiological function of coral symbiotic function under the exposure of microplastics. This study has revealed the impact of microplastic exposure on J. squamata, providing new insights for coral protection against the background of increased microplastics pollution.},
}

@article {pmid39600252,
year = {2024},
author = {Grupstra, CGB and Meyer-Kaiser, KS and Bennett, MJ and Andres, MO and Juszkiewicz, DJ and Fifer, JE and Da-Anoy, JP and Gomez-Campo, K and Martinez-Rugerio, I and Aichelman, HE and Huzar, AK and Hughes, AM and Rivera, HE and Davies, SW},
title = {Holobiont Traits Shape Climate Change Responses in Cryptic Coral Lineages.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17578},
doi = {10.1111/gcb.17578},
pmid = {39600252},
issn = {1365-2486},
support = {2048589//The National Science Foundation's Division of Ocean Sciences/ ; 2048678//The National Science Foundation's Division of Ocean Sciences/ ; },
mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Climate Change ; *Coral Reefs ; *Symbiosis ; Microbiota ; Dinoflagellida/physiology ; },
abstract = {As ocean warming threatens reefs worldwide, identifying corals with adaptations to higher temperatures is critical for conservation. Genetically distinct but morphologically similar (i.e. cryptic) coral populations can be specialized to extreme habitats and thrive under stressful conditions. These corals often associate with locally beneficial microbiota (Symbiodiniaceae photobionts and bacteria), obscuring the main drivers of thermal tolerance. Here, we leverage a holobiont (massive Porites) with high fidelity for C15 photobionts to investigate adaptive variation across classic ("typical" conditions) and extreme reefs characterized by higher temperatures and light attenuation. We uncovered three cryptic lineages that exhibit limited micro-morphological variation; one lineage dominated classic reefs (L1), one had more even distributions (L2), and a third was restricted to extreme reefs (L3). L1 and L2 were more closely related to populations ~4300 km away, suggesting that some lineages are widespread. All corals harbored Cladocopium C15 photobionts; L1 and L2 shared a photobiont pool that differed in composition between reef types, yet L3 mostly harbored unique photobiont strains not found in the other lineages. Assemblages of bacterial partners differed among reef types in lineage-specific ways, suggesting that lineages employ distinct microbiome regulation strategies. Analysis of light-harvesting capacity and thermal tolerance revealed adaptive variation underpinning survival in distinct habitats: L1 had the highest light absorption efficiency and lowest thermal tolerance, suggesting that it is a classic reef specialist. L3 had the lowest light absorption efficiency and the highest thermal tolerance, showing that it is an extreme reef specialist. L2 had intermediate light absorption efficiency and thermal tolerance, suggesting that is a generalist lineage. These findings reveal diverging holobiont strategies to cope with extreme conditions. Resolving coral lineages is key to understanding variation in thermal tolerance among coral populations, can strengthen our understanding of coral evolution and symbiosis, and support global conservation and restoration efforts.},
}

*Anthozoa/microbiology/physiology
Animals
*Climate Change
*Coral Reefs
*Symbiosis
Microbiota
Dinoflagellida/physiology

@article {pmid39593141,
year = {2024},
author = {Steiner, LX and Schmittmann, L and Rahn, T and Lachnit, T and Jahn, MT and Hentschel, U},
title = {Phage-induced disturbance of a marine sponge microbiome.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {97},
pmid = {39593141},
issn = {2524-6372},
support = {CRC1182-TP C04//Deutsche Forschungsgemeinschaft/ ; CRC1182-TP C04//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Bacteriophages are known modulators of community composition and activity in environmental and host-associated microbiomes. However, the impact single phages have on bacterial community dynamics under viral predation, the extent and duration of their effect, are not completely understood. In this study, we combine morphological and genomic characterization of a novel marine phage, isolated from the Baltic sponge Halichondria panicea, and report on first attempts of controlled phage-manipulation of natural sponge-associated microbiomes.

RESULTS: We used culture-based and culture-independent (16S rRNA gene amplicon sequencing) methods to investigate bacterial community composition and dynamics in sponge microbiomes with and without the addition of phages. Upon application of a novel Maribacter specialist phage Panino under controlled conditions, we were able to detect community-wide shifts in the microbiome composition and load after 72 h. While bacterial community composition became more dissimilar over time in the presence of phages, species evenness and richness were maintained. Upon phage exposure, we observed the loss of several low-abundance constituent taxa of the resident microbiota, while other originally underrepresented taxa increased. Virulent phages likely induce community-wide disturbances, evident in changes in the total sponge microbial profile by specific elimination of constituent taxa, which leads to an increase in bacterial abundance of opportunistic taxa, such as the genera Vibrio, Pseudoalteromonas, and Photobacterium.

CONCLUSIONS: Our findings suggest that sponge microbiome diversity and, by extension, its resilience depend on the maintenance of resident bacterial community members, irrespective of their abundance. Phage-induced disturbances can significantly alter community structure by promoting the growth of opportunistic bacteria like Vibrio and shifting the microbiome to a dysbiotic state. These insights highlight the role of bacteriophages in shaping microbiome dynamics and underscore the potential for phage application in managing bacterial community composition in marine host-associated environments.},
}

@article {pmid39590502,
year = {2024},
author = {Schapheer, C and González, LM and Villagra, C},
title = {Microorganism Diversity Found in Blatta orientalis L. (Blattodea: Blattidae) Cuticle and Gut Collected in Urban Environments.},
journal = {Insects},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/insects15110903},
pmid = {39590502},
issn = {2075-4450},
abstract = {Pest cockroaches share urban habitats with us; their prevalence in urban areas prompts concerns regarding their effect on human health, as synanthropic cockroaches often host pathogenic microorganisms. Nonetheless, microbial associates in these insects can also be related to their biology, contributing to their physiological homeostasis and reproductive success. In this article, we present in detail, for the first time, the bacterial community associated with the oriental cockroach Blatta orientalis, one of the world's five most prominent pest cockroaches. We report the composition of the communities of bacteria found over the exoskeleton and inside the gut of this global pest. We collected B. orientalis in Santiago, Chile's capital city, and the urban nucleus in this country. We conducted DNA extractions and metabarcoding analysis. We found diverse bacterial lineages, including mutualist symbiotic strains, and microorganisms considered pathogenic to humans. We also analyzed the metabolic functions of the bacterial communities identified and discussed the role of B. orientalis as a reservoir and vector of pathogens in urban areas. We discuss to what extent the diversity of functions of the microbial community associated with cockroaches may contribute to emergent properties enabling these insects to inhabit human-modified habitats.},
}

@article {pmid39589622,
year = {2024},
author = {Wong, JM and Liu, AC and Lin, HT and Shinzato, C and Yang, SY and Yang, SH},
title = {An Improved RNA Extraction Method for Octocorals and Its Application in Transcriptome Analysis of Dark-Induced Bleaching Octocoral.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {1},
pages = {8},
pmid = {39589622},
issn = {1436-2236},
support = {NSTC 112-2311-B-002 -017//National Science and Technology Council/ ; NTU 112L2033-05//National Taiwan University/ ; },
mesh = {*Anthozoa/genetics/metabolism ; Animals ; *Gene Expression Profiling ; *RNA/isolation & purification/genetics ; *Dinoflagellida/genetics ; *Transcriptome ; Symbiosis ; Coral Reefs ; },
abstract = {Octocorals, vital components of reef ecosystems, inhabit various marine environments across diverse climate zones, spanning from tropical shallows to frigid deep-sea regions. Certain octocoral species, notably Lobophytum and Sinularia, are particularly intriguing due to their production of diverse metabolites, warranting continuous investigation. Although octocorals played the roles in coral ecosystems, the studies are rare in comparison to scleractinian corals, especially in transcriptomic and genomic data. However, RNA extraction was massively interfered by the polysaccharides and secondary metabolites produced from octocoral holobiont. For this purpose, five lysis buffer systems and two extraction processes were examined for the RNA extraction efficiency in octocorals. We found CTAB/10%SDS as a new method for RNA extraction from six different octocoral genera. Furthermore, our new method is enable to extract RNA with good quality for downstream application such as quantitative PCR and RNA sequencing. Finally, comparative transcriptomic analysis between healthy octocorals and those dark-induced bleaching corals in Lobophytum hsiehi revealed extracellular matrix and immunity-related genes may play the important roles in coral-symbiodinium symbiosis. We believe that this study's findings and the developed RNA extraction method will serve as valuable references for future research, particularly in octocorals.},
}

*Anthozoa/genetics/metabolism
Animals
*Gene Expression Profiling
*RNA/isolation & purification/genetics
*Dinoflagellida/genetics
*Transcriptome
Symbiosis
Coral Reefs

@article {pmid39589125,
year = {2024},
author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J},
title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081624},
doi = {10.1128/msphere.00816-24},
pmid = {39589125},
issn = {2379-5042},
abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.

IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.},
}

@article {pmid39580487,
year = {2024},
author = {Rosenberg, E},
title = {Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {134},
pmid = {39580487},
issn = {2055-5008},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Biodiversity ; Colon/microbiology ; },
abstract = {The composition of bacteria in the human colon has been a subject of interest since the beginning of microbiology. With the development of methods for culturing strict anaerobic bacteria under multiple culture conditions, it was shown the gut contained more than 400 bacterial species and different people harbor different abundant species. The term "gut microbiome" in this review refers to bacteria studied in stool samples. Molecular methods for determining the bacterial composition of human gut has revealed more than 3000 species and less than 130 genera, indicating that the diversity of human colonic bacteria is concentrated at the species and strain levels. This review concludes with a discussion of how diversity can lead to unity of individual holobionts, between holobionts, and between populations. One of the reasons for the unity is that different bacterial species can have similar functional genes.},
}

Humans
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Biodiversity
Colon/microbiology

@article {pmid39575186,
year = {2024},
author = {Verma, T and Hendiani, S and Carbajo, C and Andersen, SB and Hammarlund, EU and Burmølle, M and Sand, KK},
title = {Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1449094},
pmid = {39575186},
issn = {1664-302X},
abstract = {Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to common sedimentary minerals and that the transformation frequencies scale with mineral surface properties. Our work highlights that ancient environmental DNA can fuel the evolution of contemporary bacteria. In contrast to heritable stochastic mutations, the processes by which bacteria acquire new genomic material during times of increased stress and needs, indicate a non-random mechanism that may propel evolution in a non-stochastic manner.},
}

@article {pmid39574203,
year = {2024},
author = {Rhimi, S and Jablaoui, A and Hernandez, J and Mariaule, V and Akermi, N and Méric, T and Mkaouar, H and Wysocka, M and Lesner, A and Borgi, MA and Maguin, E and Rhimi, M},
title = {Industrial diet intervention modulates the interplay between gut microbiota and host in semi-stray dogs.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {69},
pmid = {39574203},
issn = {2524-4671},
support = {twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; RestorPro no ANR-23-CE14-0073-01//Agence Nationale de la Recherche/ ; RestorPro no ANR-23-CE14-0073-01//Agence Nationale de la Recherche/ ; RestorPro no ANR-23-CE14-0073-01//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: The gut microbiota and derived metabolites play a key role in regulating host physiology. Diet is identified as a key regulatory factor of the microbiota composition and, potentially, of subsequent functionalities. Demonstrating the role of diet may be complex as most human studies are cross-sectional and dietary intervention is often accompanied by hygienic changes. The objective of the present study was to investigate the impact of an industrial diet on the modulation of the microbiota and targeted functionalities using a canine "natural" model.

RESULTS: We carried out a controlled dietary trial in a cohort of Tunisian semi-stray dogs. We made a transition from a natural diet to an industrial kibble diet and monitored the composition of the fecal microbiota, the concentration of short-chain fatty acids (SCFA) and bile acids (BAs), and protease activities. We demonstrated that dietary change significantly decreased fecal primary bile acids levels and protease activities. Interestingly, correlation analyses demonstrated that variation of specific microbial genera were associated with modulated physiological parameters.

CONCLUSIONS: Our study reveals that an industrial diet induces beneficial changes in microbial composition and functions characterised by increased diversity, synthesis of SCFA and secondary bile acids production, stressing the key role of the diet-microbiota-dog crosstalk.},
}

@article {pmid39574002,
year = {2024},
author = {Pereira, H and Chakarov, N and Caspers, BA and Gilles, M and Jones, W and Mijoro, T and Zefania, S and Székely, T and Krüger, O and Hoffman, JI},
title = {The gut microbiota of three avian species living in sympatry.},
journal = {BMC ecology and evolution},
volume = {24},
number = {1},
pages = {144},
pmid = {39574002},
issn = {2730-7182},
support = {316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Sympatry ; Species Specificity ; Madagascar ; },
abstract = {BACKGROUND: Evolutionary divergence and genetic variation are often linked to differences in microbial community structure and diversity. While environmental factors and diet heavily influence gut microbial communities, host species contributions are harder to quantify. Closely related species living in sympatry provide a unique opportunity to investigate species differences without the confounding effects of habitat and dietary variation. We therefore compared and contrasted the gut microbiota of three sympatric plover species: the widespread Kittlitz's and white-fronted plovers (Anarhynchus pecuarius and A. marginatus) and the endemic and vulnerable Madagascar plover (A. thoracicus).

RESULTS: We found no significant differences in the beta diversity (composition) of the gut microbiota of the three species. However, A. thoracicus exhibited higher intraspecific compositional similarity (i.e. lower pairwise distances) than the other two species; this pattern was especially pronounced among juveniles. By contrast, microbial alpha diversity varied significantly among the species, being highest in A. pecuarius, intermediate in A. marginatus and lowest in A. thoracicus. This pattern was again stronger among juveniles. Geographical distance did not significantly affect the composition of the gut microbiota, but genetic relatedness did.

CONCLUSION: While patterns of microbial diversity varied across species, the lack of compositional differences suggests that habitat and diet likely exert a strong influence on the gut microbiota of plovers. This may be enhanced by their precocial, ground-dwelling nature, which could facilitate the horizontal transmission of microbes from the environment. We hypothesise that gut microbiota diversity in plovers primarily reflects the ecological pool of microbiota, which is subsequently modified by host-specific factors including genetics. The reduced microbial and genetic diversity of the endemic A. thoracicus may hinder its ability to adapt to environmental changes, highlighting the need for increased conservation efforts for this vulnerable species.},
}

Animals
*Gastrointestinal Microbiome/genetics/physiology
*Sympatry
Species Specificity
Madagascar

@article {pmid39570654,
year = {2024},
author = {Yan, C and Zhang, K and Shi, S and Jian, L and Chen, B and Quadri, SR and Tian, X},
title = {Alterisphingorhabdus coralli gen. nov. sp. nov., a novel aerobic anoxygenic phototrophic bacteria isolated from reef-building coral.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006577},
pmid = {39570654},
issn = {1466-5034},
mesh = {*Phylogeny ; *Anthozoa/microbiology ; Animals ; *Fatty Acids ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Ubiquinone ; *Coral Reefs ; Base Composition ; Sphingomonadaceae/genetics/isolation & purification/classification ; Nucleic Acid Hybridization ; Phototrophic Processes ; },
abstract = {The photosynthetic microorganisms within the coral holobiont produce energy and organic compounds through photosynthesis, which are vital for the biocalcification and heat tolerance of coral hosts. However, aerobic anoxygenic phototrophic bacteria (AAPB), which are one of the most important photosynthetic microorganisms, have not been thoroughly investigated in this environment. In this study, a novel AAPB, SCSIO 66989[T], was isolated from the reef-building coral Favia sp. and considered a beneficial microorganism for corals (BMC). The polyphasic taxonomic analysis showed that it had the highest similarities with Parasphingorhabdus litoris DSM 22379[T] (95.9%) and Altererythrobacter ishigakiensis ATCC BAA-2084[T] (95.7%). Phylogenetic analysis showed that it formed an independent clade, distinguishing it from other genera within the family Sphingomonadaceae. The predominant fatty acids were C18 : 1 ω7c and/or C18 : 1 ω6c and C16 : 0. The major respiratory quinone was ubiquinone-10 (Q-10). Sphingolipid, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the diagnostic polar lipids. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between SCSIO 66989[T] and the type strains of P. litoris DSM 22379[T] and A. ishigakiensis ATCC BAA-2084[T] were 69.2-70.0%, 58.6-61.2% and 19.2-19.7%, respectively. These results indicate that strain SCSIO 66989[T] represents a new species of a novel genus in the family Sphingomonadaceae, for which the name Alterisphingorhabdus coralli gen. nov. sp. nov. is proposed.},
}

*Phylogeny
*Anthozoa/microbiology
Animals
*Fatty Acids
*DNA, Bacterial/genetics
*Bacterial Typing Techniques
*RNA, Ribosomal, 16S/genetics
*Sequence Analysis, DNA
*Ubiquinone
*Coral Reefs
Base Composition
Sphingomonadaceae/genetics/isolation & purification/classification
Nucleic Acid Hybridization
Phototrophic Processes

@article {pmid39570026,
year = {2024},
author = {Waterworth, SC and Solomons, GM and Kalinski, J-CJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA},
title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0084524},
doi = {10.1128/msphere.00845-24},
pmid = {39570026},
issn = {2379-5042},
abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, sponge-associated unclassified lineage (SAUL), and Tethybacterales, appear to have broad-host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, having thus far been observed only in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.IMPORTANCESouth African latrunculid sponges are host to co-dominant Tethybacterales and Spirochete symbionts. While the Tethybacterales are broad-host range symbionts, the spirochetes have not been reported as abundant in any other marine sponge except Clathrina clathrus. However, spirochetes are regularly the most dominant populations in marine corals and terrestrial invertebrates where they are predicted to serve as beneficial symbionts. Here, we interrogated eight metagenome-assembled genomes of the latrunculid-associated spirochetes and found that these symbionts are phylogenetically distinct from all invertebrate-associated spirochetes. The symbiosis between the spirochetes and their sponge host appears to have been established relatively recently.},
}

@article {pmid39568770,
year = {2024},
author = {Guéganton, M and Methou, P and Aubé, J and Noël, C and Rouxel, O and Cueff-Gauchard, V and Gayet, N and Durand, L and Pradillon, F and Cambon-Bonavita, MA},
title = {Symbiont Acquisition Strategies in Post-Settlement Stages of Two Co-Occurring Deep-Sea Rimicaris Shrimp.},
journal = {Ecology and evolution},
volume = {14},
number = {11},
pages = {e70369},
pmid = {39568770},
issn = {2045-7758},
abstract = {At deep-sea hydrothermal vents, deprived of light, most living communities are fueled by chemosynthetic microorganisms. These can form symbiotic associations with metazoan hosts, which are then called holobionts. Among these, two endemic co-occurring shrimp of the Mid-Atlantic Ridge (MAR), Rimicaris exoculata and Rimicaris chacei are colonized by dense and diversified chemosynthetic symbiotic communities in their cephalothoracic cavity and their digestive system. Although both shrimp harbor similar communities, they exhibit widely different population densities, distribution patterns at small scale and diet, as well as differences in post-settlement morphological modifications leading to the adult stage. These contrasting biological traits may be linked to their symbiotic development success. Consequently, key questions related to the acquisition of the symbiotic communities and the development of the three symbiotic organs are still open. Here we examined symbiotic development in juveniles of R. exoculata and R. chacei from TAG and Snake Pit using 16S metabarcoding to identify which symbiotic lineages are present at each juvenile stage. In addition, we highlighted the abundance and distribution of microorganisms at each stage using Fluorescence in situ Hybridization (FISH) and Scanning Electron Microscopy (SEM). For the first time, Candidatus Microvillispirillaceae family with Candidatus Rimicarispirillum spp. (midgut tube), Candidatus Foregutplasma rimicarensis and Candidatus BG2-rimicarensis (foregut) were identified in late juvenile stages. However, these lineages were absent in early juvenile stages, which coincides for the midgut tube with our observations of an immature tissue, devoid of microvilli. Conversely, symbiotic lineages from the cephalothoracic cavity were present from the earliest juvenile stages of both species and their overall diversities were similar to those of adults. These results suggest different symbiont acquisition dynamics between the cephalothoracic cavity and the digestive system, which may also involve distinct transmission mechanisms.},
}

@article {pmid39565113,
year = {2024},
author = {Nowak, VV and Hou, P and Owen, JG},
title = {Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0072624},
doi = {10.1128/aem.00726-24},
pmid = {39565113},
issn = {1098-5336},
abstract = {Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.},
}

@article {pmid39558079,
year = {2024},
author = {Sun, Y and Sheng, H and Rädecker, N and Lan, Y and Tong, H and Huang, L and Jiang, L and Diaz-Pulido, G and Zou, B and Zhang, Y and Kao, SJ and Qian, PY and Huang, H},
title = {Symbiodiniaceae algal symbionts of Pocillopora damicornis larvae provide more carbon to their coral host under elevated levels of acidification and temperature.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1528},
pmid = {39558079},
issn = {2399-3642},
support = {42206153//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 41906040//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
abstract = {Climate change destabilizes the symbiosis between corals and Symbiodiniaceae. The effects of ocean acidification and warming on critical aspects of coral survical such as symbiotic interactions (i.e., carbon and nitrogen assimilation and exchange) during the planula larval stage remain understudied. By combining physiological and stable isotope techniques, here we show that photosynthesis and carbon and nitrogen assimilation (H[13]CO3[-] and [15]NH4[+]) in Pocillopora damicornis coral larvae is enhanced under acidification (1000 µatm) and elevated temperature (32 °C). Larvae maintain high survival and settlement rates under these treatment conditions with no observed decline in symbiont densities or signs of bleaching. Acidification and elevated temperature both enhance the net and gross photosynthesis of Symbiodiniaceae. This enhances light respiration and elevates C:N ratios within the holobiont. The increased carbon availability is primarily reflected in the [13]C enrichment of the host, indicating a greater contribution of the algal symbionts to the host metabolism. We propose that this enhanced mutualistic symbiotic nutrient cycling may bolster coral larvae's resistance to future ocean conditions. This research broadens our understanding of the early life stages of corals by emphasizing the significance of symbiotic interactions beyond those of adult corals.},
}

@article {pmid39553893,
year = {2024},
author = {Pfab, F and Detmer, AR and Moeller, HV and Nisbet, RM and Putnam, HM and Cunning, R},
title = {Heat stress and bleaching in corals: a bioenergetic model.},
journal = {Coral reefs (Online)},
volume = {43},
number = {6},
pages = {1627-1645},
pmid = {39553893},
issn = {1432-0975},
abstract = {UNLABELLED: The coral-dinoflagellate endosymbiosis is based on nutrient exchanges that impact holobiont energetics. Of particular concern is the breakdown or dysbiosis of this partnership that is seen in response to elevated temperatures, where loss of symbionts through coral bleaching can lead to starvation and mortality. Here we extend a dynamic bioenergetic model of coral symbioses to explore the mechanisms by which temperature impacts various processes in the symbiosis and to enable simulational analysis of thermal bleaching. Our model tests the effects of two distinct mechanisms for how increased temperature impacts the symbiosis: 1) accelerated metabolic rates due to thermodynamics and 2) damage to the photosynthetic machinery of the symbiont caused by heat stress. Model simulations show that the model can capture key biological responses to different levels of increased temperatures. Moderately increased temperatures increase metabolic rates and slightly decrease photosynthesis. The slightly decreased photosynthesis rates cause the host to receive less carbon and share more nitrogen with the symbiont. This results in temporarily increased symbiont growth and a higher symbiont/host ratio. In contrast, higher temperatures cause a breakdown of the symbiosis due to escalating feedback that involves further reduction in photosynthesis and insufficient energy supply for CO 2 concentration by the host. This leads to the accumulation of excess light energy and the generation of reactive oxygen species, eventually triggering symbiont expulsion and coral bleaching. Importantly, bleaching does not result from accelerated metabolic rates alone; it only occurs as a result of the photodamage mechanism due to its effect on nutrient cycling. Both higher light intensities and higher levels of DIN render corals more susceptible to heat stress. Conversely, heterotrophic feeding can increase the maximal temperature that can be tolerated by the coral. Collectively these results show that a bioenergetics model can capture many observed patterns of heat stress in corals, such as higher metabolic rates and higher symbiont/host ratios at moderately increased temperatures and symbiont expulsion at strongly increased temperatures.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00338-024-02561-1.},
}

@article {pmid39543733,
year = {2024},
author = {Köster, PC and Figueiredo, AM and Maloney, JG and Dashti, A and Bailo, B and Torres, RT and Fonseca, C and Mysterud, A and Habela, MÁ and Rivero-Juarez, A and Vicente, J and Serrano, E and Arnal, MC and de Luco, DF and Armenteros, JA and Balseiro, A and Cardona, GA and Carvalho, J and Hipólito, D and Fernandes, J and Palmeira, JD and Calero-Bernal, R and González-Barrio, D and Santin, M and Carmena, D},
title = {Correction: Blastocystis occurrence and subtype diversity in European wild boar (Sus scrofa) from the Iberian Peninsula.},
journal = {Veterinary research},
volume = {55},
number = {1},
pages = {152},
pmid = {39543733},
issn = {1297-9716},
}

@article {pmid39541453,
year = {2024},
author = {Bordenstein, SR and The Holobiont Biology Network, and , },
title = {The disciplinary matrix of holobiont biology.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6723},
pages = {731-732},
doi = {10.1126/science.ado2152},
pmid = {39541453},
issn = {1095-9203},
mesh = {*Symbiosis ; Biology ; },
abstract = {Uniting life's seen and unseen realms guides a conceptual advance in research.},
}

*Symbiosis
Biology

@article {pmid39539714,
year = {2024},
author = {Hauptmann, AL and Johansen, J and Stæger, FF and Nielsen, DS and Mulvad, G and Hanghøj, K and Rasmussen, S and Hansen, T and Albrechtsen, A},
title = {Gut heavy metal and antibiotic resistome of humans living in the high Arctic.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1493803},
doi = {10.3389/fmicb.2024.1493803},
pmid = {39539714},
issn = {1664-302X},
abstract = {Contaminants, such as heavy metals (HMs), accumulate in the Arctic environment and the food web. The diet of the Indigenous Peoples of North Greenland includes locally sourced foods that are central to their nutritional, cultural, and societal health but these foods also contain high concentrations of heavy metals. While bacteria play an essential role in the metabolism of xenobiotics, there are limited studies on the impact of heavy metals on the human gut microbiome, and it is so far unknown if and how Arctic environmental contaminants impact the gut microbes of humans living in and off the Arctic environment. Using a multiomics approach including amplicon, metagenome, and metatranscriptome sequencing, we identified and assembled a near-complete (NC) genome of a mercury-resistant bacterial strain from the human gut microbiome, which expressed genes known to reduce mercury toxicity. At the overall ecological level studied through α- and β-diversity, there was no significant effect of heavy metals on the gut microbiota. Through the assembly of a high number of NC metagenome-assembled genomes (MAGs) of human gut microbes, we observed an almost complete overlap between heavy metal-resistant strains and antibiotic-resistant strains in which resistance genes were all located on the same genetic elements.},
}

@article {pmid39536868,
year = {2024},
author = {Koll, R and Hauten, E and Theilen, J and Bang, C and Bouchard, M and Thiel, R and Möllmann, C and Woodhouse, JN and Fabrizius, A},
title = {Spatio-temporal plasticity of gill microbiota in estuarine fish.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177505},
doi = {10.1016/j.scitotenv.2024.177505},
pmid = {39536868},
issn = {1879-1026},
abstract = {Coastal marine and estuarine systems are subject to enormous endogenous and exogenous pressures, particularly climate change, while at the same time being highly productive sources and nurseries for fish populations. Interactions between host and microbiome are increasingly recognized for their importance for fish health, with growing evidence indicating that increasing environmental pressures impact host resilience and favor the raise of opportunistic bacterial taxa. The microbial composition of the gill mucus reflects environmental conditions and represents an entry route for pathogens into the fish body. High-throughput sequencing of prokaryotic populations from 250 samples of two fish species with highly different habitat preferences, as well as seasonal and spatial distributions in the Elbe estuary system, allowed us to describe the variation of the microbiota along a salinity gradient and under fluctuating environmental conditions. The analysis of estuarine fish core microbiota in relation to variable bacterial components indicated dysbiotic states under sustained hypoxia and high nutrient loads largely driven by increased prevalence of facultatively aerobic (Acinetobacter) and anaerobic heterotrophs (Shewanella, Aeromonas). By correlating bacterial abundances with environmental and physiological parameters in a co-occurrence network approach, we describe plasticity in microbiota composition, identify potential biomarkers for fish health monitoring and reconstruct movement patterns of the fish. Our results can help to shape future minimal-invasive and cost-effective monitoring programs, and identify factors that need to be controlled in the estuary to promote fish and stock health.},
}

@article {pmid39536370,
year = {2024},
author = {Anthony, CJ and Lock, C and Pérez-Rosales, G and Rouzé, H and Paulino, L and Raymundo, LJ and Bentlage, B},
title = {Symbiodiniaceae phenotypic traits as bioindicators of acclimatization after coral transplantation.},
journal = {Marine pollution bulletin},
volume = {209},
number = {Pt B},
pages = {117250},
doi = {10.1016/j.marpolbul.2024.117250},
pmid = {39536370},
issn = {1879-3363},
abstract = {Coral-dinoflagellate symbiosis underpins coral reef resilience and influences conservation success, given the relationship's role in coral bleaching. Here, we transplanted Guam's dominant staghorn coral, Acropora pulchra, across four coral gardens and monitored their endosymbiotic dinoflagellates (family Symbiodiniaceae) for ∼15 months (May 2021-August 2022). Transplantation and predation resulted in temporary symbiotic destabilization, as signaled by increased cell roughness and decreased cell density. Eventually, the Symbiodiniaceae phenotypic profile mostly converged with the wild population, although cell density and red fluorescing photopigments remained modified. In March, corals paled, which allowed us to evaluate the Symbiodiniaceae assemblage's relationship with host color. Interestingly, cell density was not the most informative when predicting host color. Instead, fluorescence from antioxidant-associated pigments were most informative. We conclude that Symbiodiniaceae phenotypic traits respond differently depending on the condition, supporting their development as acclimatization bioindicators.},
}

@article {pmid39529628,
year = {2024},
author = {López-Rodríguez, MR and Gérikas Ribeiro, C and Rodríguez-Marconi, S and Parada-Pozo, G and Manrique-de-la-Cuba, M and Trefault, N},
title = {Stable dominance of parasitic dinoflagellates in Antarctic sponges.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18365},
pmid = {39529628},
issn = {2167-8359},
mesh = {Antarctic Regions ; *Dinoflagellida/genetics/physiology ; Animals ; *Porifera/parasitology ; Symbiosis ; Seawater/parasitology/microbiology ; Biodiversity ; },
abstract = {BACKGROUND: Marine sponges are dominant components of Antarctic benthos and representative of the high endemism that characterizes this environment. All microbial groups are part of the Antarctic sponge holobionts, but microbial eukaryotes have been studied less, and their symbiotic role still needs to be better understood. Here, we characterize the dynamics of microbial eukaryotes associated with Antarctic sponges, focusing on dinoflagellates over three summer periods to better understand the members, interannual variations, and trophic and lifestyle strategies.

RESULTS: The analysis revealed that dinoflagellates dominate microeukaryotic communities in Antarctic sponges. The results also showed significant differences in the diversity and composition of dinoflagellate communities associated with sponges compared to those in seawater. Antarctic sponges were dominated by a single dinoflagellate family, Syndiniales Dino-Group-I-Clade 1, which was present in high abundance in Antarctic sponges compared to seawater communities. Despite minor differences, the top microeukaryotic amplicon sequence variants (ASVs) showed no significant interannual abundance changes, indicating general temporal stability within the studied sponge species. Our findings highlight the abundance and importance of parasitic groups, particularly the classes Coccidiomorphea, Gregarinomorphea, and Ichthyosporea, with the exclusive dominance of Syndiniales Dino-Group-I-Clade 1 within sponges.

CONCLUSIONS: The present study comprehensively characterizes the microbial eukaryotes associated with Antarctic sponges, showing a remarkable stability of parasitic dinoflagellates in Antarctic sponges. These findings underscore the significant role of parasites in these marine hosts, with implications for population dynamics of the microeukaryome and the holobiont response to a changing ocean.},
}

Antarctic Regions
*Dinoflagellida/genetics/physiology
Animals
*Porifera/parasitology
Symbiosis
Seawater/parasitology/microbiology
Biodiversity