@article {pmid38033807,
year = {2023},
author = {Mauduit, M and Derrien, M and Grenier, M and Greff, S and Molinari, S and Chevaldonné, P and Simmler, C and Pérez, T},
title = {In Situ Capture and Real-Time Enrichment of Marine Chemical Diversity.},
journal = {ACS central science},
volume = {9},
number = {11},
pages = {2084-2095},
doi = {10.1021/acscentsci.3c00661},
pmid = {38033807},
issn = {2374-7943},
abstract = {Analyzing the chemical composition of seawater to understand its influence on ecosystem functions is a long-lasting challenge due to the inherent complexity and dynamic nature of marine environments. Describing the intricate chemistry of seawater requires optimal in situ sampling. Here is presented a novel underwater hand-held solid-phase extraction device, I-SMEL (In Situ Marine moleculELogger), which aims to concentrate diluted molecules from large volumes of seawater in a delimited zone targeting keystone benthic species. Marine benthic holobionts, such as sponges, can impact the chemical composition of their surroundings possibly through the production and release of their specialized metabolites, hence termed exometabolites (EMs). I-SMEL was deployed in a sponge-dominated Mediterranean ecosystem at a 15 m depth. Untargeted MS-based metabolomics was performed on enriched EM extracts and showed (1) the chemical diversity of enriched seawater metabolites and (2) reproducible recovery and enrichment of specialized sponge EMs such as aerothionin, demethylfurospongin-4, and longamide B methyl ester. These EMs constitute the chemical identity of each targeted species: Aplysina cavernicola, Spongia officinalis, and Agelas oroides, respectively. I-SMEL concentrated sponge EMs from 10 L of water in a 10 min sampling time. The present proof of concept with I-SMEL opens new research perspectives in marine chemical ecology and sets the stage for further sustainable efforts in natural product chemistry.},
}

@article {pmid38030702,
year = {2023},
author = {Romanenko, SA and Kliver, SF and Serdyukova, NA and Perelman, PL and Trifonov, VA and Seluanov, A and Gorbunova, V and Azpurua, J and Pereira, JC and Ferguson-Smith, MA and Graphodatsky, AS},
title = {Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {21055},
pmid = {38030702},
issn = {2045-2322},
support = {19-14-00034-П//Russian Science Foundation/ ; },
abstract = {Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.},
}

@article {pmid38023867,
year = {2023},
author = {Cardoni, M and Mercado-Blanco, J},
title = {Confronting stresses affecting olive cultivation from the holobiont perspective.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1261754},
doi = {10.3389/fpls.2023.1261754},
pmid = {38023867},
issn = {1664-462X},
abstract = {The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.},
}

@article {pmid38014935,
year = {2023},
author = {Shimpi, GG and De la Vega, P and Bentlage, B},
title = {Complete genome sequence of Brachybacterium sp. GU-2 (Actinomycetota), isolated from the massive coral Porites lobata.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0085523},
doi = {10.1128/MRA.00855-23},
pmid = {38014935},
issn = {2576-098X},
abstract = {Brachybacterium sp. GU-2 was isolated from the hard coral Porites lobata found in Apra Harbor, Guam, Micronesia. This genome sequence will be beneficial to understand the role of actinomycetes in coral holobionts. The Brachybacterium genome contains several gene clusters for bioactive compounds, including antibiotics.},
}

@article {pmid38000749,
year = {2023},
author = {Lewin, S and Wende, S and Wehrhan, M and Verch, G and Ganugi, P and Sommer, M and Kolb, S},
title = {Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168794},
doi = {10.1016/j.scitotenv.2023.168794},
pmid = {38000749},
issn = {1879-1026},
abstract = {Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.},
}

@article {pmid37996910,
year = {2023},
author = {Li, J and Zou, Y and Li, Q and Zhang, J and Bourne, DG and Lyu, Y and Liu, C and Zhang, S},
title = {A coral-associated actinobacterium mitigates coral bleaching under heat stress.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {83},
pmid = {37996910},
issn = {2524-6372},
support = {42122045//National Natural Science Foundation of China/ ; 41890853//National Natural Science Foundation of China/ ; GJTD-2020-12//K. C. Wong Education Foundation/ ; },
abstract = {BACKGROUND: The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled with 5 (and - 6)-carboxytetramethylrhodamine, succinimidyl ester and the labeled cell suspension directly inoculated onto the coral polyp tissues when nubbins were under thermal stress in a mesocosm experiment. We then visualized the labelled bacterial cells and analyzed the coral physiological, transcriptome and microbiome to elucidate the effect this strain conferred on the coral holobiont under thermal stress.

RESULTS: Subsequent microscopic observations confirmed the presence of the bacterium attached to the coral polyps. Addition of the SCSIO 13291 strain reduced signs of bleaching in the corals subjected to heat stress. At the same time, alterations in gene expression, which were involved in reactive oxygen species and light damage mitigation, attenuated apoptosis and exocytosis in addition to metabolite utilization, were observed in the coral host and Symbiodiniaceae populations. In addition, the coral associated bacterial community altered with a more stable ecological network for samples inoculated with the bacterial strain.

CONCLUSIONS: Our results provide insights into the benefits of a putative actinobacterial probiotic strain that mitigate coral bleaching signs. This study suggests that the inoculation of bacteria can potentially directly benefit the coral holobiont through conferring metabolic activities or through indirect mechanisms of suppling additional nutrient sources.},
}

@article {pmid37993882,
year = {2023},
author = {Rice, ES and Alberdi, A and Alfieri, J and Athrey, G and Balacco, JR and Bardou, P and Blackmon, H and Charles, M and Cheng, HH and Fedrigo, O and Fiddaman, SR and Formenti, G and Frantz, LAF and Gilbert, MTP and Hearn, CJ and Jarvis, ED and Klopp, C and Marcos, S and Mason, AS and Velez-Irizarry, D and Xu, L and Warren, WC},
title = {A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {267},
pmid = {37993882},
issn = {1741-7007},
support = {2020-67015-31574//National Institute of Food and Agriculture/ ; 2022-67015-36218//National Institute of Food and Agriculture/ ; 817729//HORIZON EUROPE Research Infrastructures/ ; },
abstract = {BACKGROUND: The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome.

METHODS: We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines.

RESULTS: We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference.

CONCLUSIONS: We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.},
}

@article {pmid37992160,
year = {2023},
author = {Coffroth, MA and Buccella, LA and Eaton, KM and Lasker, HR and Gooding, AT and Franklin, H},
title = {What makes a winner? Symbiont and host dynamics determine Caribbean octocoral resilience to bleaching.},
journal = {Science advances},
volume = {9},
number = {47},
pages = {eadj6788},
doi = {10.1126/sciadv.adj6788},
pmid = {37992160},
issn = {2375-2548},
abstract = {Unlike reef-building, scleractinian corals, Caribbean soft corals (octocorals) have not suffered marked declines in abundance associated with anthropogenic ocean warming. Both octocorals and reef-building scleractinians depend on a nutritional symbiosis with single-celled algae living within their tissues. In both groups, increased ocean temperatures can induce symbiont loss (bleaching) and coral death. Multiple heat waves from 2014 to 2016 resulted in widespread damage to reef ecosystems and provided an opportunity to examine the bleaching response of three Caribbean octocoral species. Symbiont densities declined during the heat waves but recovered quickly, and colony mortality was low. The dominant symbiont genotypes within a host generally did not change, and all colonies hosted symbiont species in the genus Breviolum. Their association with thermally tolerant symbionts likely contributes to the octocoral holobiont's resistance to mortality and the resilience of their symbiont populations. The resistance and resilience of Caribbean octocorals offer clues for the future of coral reefs.},
}

@article {pmid37991377,
year = {2023},
author = {Šigutová, H and Pyszko, P and Šigut, M and Czajová, K and Kostovčík, M and Kolařík, M and Hařovská, D and Drozd, P},
title = {Concentration-dependent effect of plant secondary metabolites on bacterial and fungal microbiomes in caterpillar guts.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0299423},
doi = {10.1128/spectrum.02994-23},
pmid = {37991377},
issn = {2165-0497},
abstract = {The caterpillar gut is an excellent model system for studying host-microbiome interactions, as it represents an extreme environment for microbial life that usually has low diversity and considerable variability in community composition. Our study design combines feeding caterpillars on a natural and artificial diet with controlled levels of plant secondary metabolites and uses metabarcoding and quantitative PCR to simultaneously profile bacterial and fungal assemblages, which has never been performed. Moreover, we focus on multiple caterpillar species and consider diet breadth. Contrary to many previous studies, our study suggested the functional importance of certain microbial taxa, especially bacteria, and confirmed the previously proposed lower importance of fungi for caterpillar holobiont. Our study revealed the lack of differences between monophagous and polyphagous species in the responses of microbial assemblages to plant secondary metabolites, suggesting the limited role of the microbiome in the plasticity of the herbivore diet.},
}

@article {pmid37979302,
year = {2023},
author = {Chai, G and Li, J and Li, Z},
title = {The interactive effects of ocean acidification and warming on bioeroding sponge Spheciospongia vesparium microbiome indicated by metatranscriptomics.},
journal = {Microbiological research},
volume = {278},
number = {},
pages = {127542},
doi = {10.1016/j.micres.2023.127542},
pmid = {37979302},
issn = {1618-0623},
abstract = {Global climate change will cause coral reefs decline and is expected to increase the reef erosion potential of bioeroding sponges. Microbial symbionts are essential for the overall fitness and survival of sponge holobionts in changing ocean environments. However, we rarely know about the impacts of ocean warming and acidification on bioeroding sponge microbiome. Here, the structural and functional changes of the bioeroding sponge Spheciospongia vesparium microbiome, as well as its recovery potential, were investigated at the RNA level in a laboratory system simulating 32 °C and pH 7.7. Based on metatranscriptome analysis, acidification showed no significant impact, while warming or simultaneous warming and acidification disrupted the sponge microbiome. Warming caused microbial dysbiosis and recruited potentially opportunistic and pathogenic members of Nesiotobacter, Oceanospirillaceae, Deltaproteobacteria, Epsilonproteobacteria, Bacteroidetes and Firmicutes. Moreover, warming disrupted nutrient exchange and molecular interactions in the sponge holobiont, accompanied by stimulation of virulence activity and anaerobic metabolism including denitrification and dissimilatory reduction of nitrate and sulfate to promote sponge necrosis. Particularly, the interaction between acidification and warming alleviated the negative effects of warming and enhanced the Rhodobacteraceae-driven ethylmalonyl-CoA pathway and sulfur-oxidizing multienzyme system. The microbiome could not recover during the experiment period after warming or combined stress was removed. This study suggests that warming or combined warming and acidification will irreversibly destabilize the S. vesparium microbial community structure and function, and provides insight into the molecular mechanisms of the interactive effects of acidification and warming on the sponge microbiome.},
}

@article {pmid37968499,
year = {2023},
author = {Pfister, CA and Cardini, U and Mirasole, A and Montilla, LM and Veseli, I and Gattuso, JP and Teixido, N},
title = {Microbial associates of an endemic Mediterranean seagrass enhance the access of the host and the surrounding seawater to inorganic nitrogen under ocean acidification.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {19996},
pmid = {37968499},
issn = {2045-2322},
abstract = {Seagrasses are important primary producers in oceans worldwide. They live in shallow coastal waters that are experiencing carbon dioxide enrichment and ocean acidification. Posidonia oceanica, an endemic seagrass species that dominates the Mediterranean Sea, achieves high abundances in seawater with relatively low concentrations of dissolved inorganic nitrogen. Here we tested whether microbial metabolisms associated with P. oceanica and surrounding seawater enhance seagrass access to nitrogen. Using stable isotope enrichments of intact seagrass with amino acids, we showed that ammonification by free-living and seagrass-associated microbes produce ammonium that is likely used by seagrass and surrounding particulate organic matter. Metagenomic analysis of the epiphytic biofilm on the blades and rhizomes support the ubiquity of microbial ammonification genes in this system. Further, we leveraged the presence of natural carbon dioxide vents and show that the presence of P. oceanica enhanced the uptake of nitrogen by water column particulate organic matter, increasing carbon fixation by a factor of 8.6-17.4 with the greatest effect at CO2 vent sites. However, microbial ammonification was reduced at lower pH, suggesting that future ocean climate change will compromise this microbial process. Thus, the seagrass holobiont enhances water column productivity, even in the context of ocean acidification.},
}

@article {pmid37964575,
year = {2023},
author = {Giesler, JK and Harder, T and Wohlrab, S},
title = {Microbiome and photoperiod interactively determine thermal sensitivity of polar and temperate diatoms.},
journal = {Biology letters},
volume = {19},
number = {11},
pages = {20230151},
doi = {10.1098/rsbl.2023.0151},
pmid = {37964575},
issn = {1744-957X},
abstract = {The effect of temperature on ectothermic organisms in the context of climate change has long been considered in isolation (i.e. as a single driver). This is challenged by observations demonstrating that temperature-dependent growth is correlated to further factors. However, little is known how the chronobiological history of an organism reflected in its adaptation to re-occurring cyclic patterns in its environment (e.g. annual range of photoperiods in its habitat) and biotic interactions with its microbiome, contribute to shaping its realized niche. To address this, we conducted a full-factorial microcosm multi-stressor experiment with the marine diatoms Thalassiosira gravida (polar) and Thalassiosira rotula (temperate) across multiple levels of temperature (4°C; 9°C; 13.5°C) and photoperiod (4 h; 16 h; 24 h), both in the presence or absence of their microbiomes. While temperature-dependent growth of the temperate diatom was constrained by short and long photoperiods, the polar diatom coped with a 24 h photoperiod up to its thermal optimum (9°C). The algal microbiomes particularly supported host growth at the margins of their respective fundamental niches except for the combination of the warmest temperature tested at 24 h photoperiod. Overall, this study demonstrates that temperature tolerances may have evolved interactively and that the mutualistic effect of the microbiome can only be determined once the multifactorial abiotic niche is defined.},
}

@article {pmid37962344,
year = {2023},
author = {Ramírez-Mendoza, R and Ángeles-Argáiz, R and Lozano Aguirre-Beltrán, LF and Almaraz-Suárez, JJ and Hernández-Oaxaca, D and Ortiz-Lopez, I and Perez-Moreno, J},
title = {Whole-genome sequence of Pseudomonas yamanorum OLsAu1 isolated from the edible wild ectomycorrhizal mushroom Lactarius sp. section Deliciosi.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0084323},
doi = {10.1128/MRA.00843-23},
pmid = {37962344},
issn = {2576-098X},
abstract = {We announce the genome sequencing, assembly, and annotation of the OLsAu1 strain and its taxonomic assignment to Pseudomonas yamanorum. The isolate comes from a wild edible ectomycorrhizal Lactarius sp. mushroom in the Abies forest. There is information regarding the strain's ability to promote plant growth, indicating its potential application in forestry.},
}

@article {pmid37950889,
year = {2023},
author = {Hernández-Alonso, G and Ramos-Madrigal, J and van Grouw, H and Ciucani, MM and Cavill, EL and Sinding, MS and Gopalakrishnan, S and Pacheco, G and Gilbert, MTP},
title = {Redefining the evolutionary history of the rock dove, Columba livia, using whole genome sequences.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad243},
pmid = {37950889},
issn = {1537-1719},
abstract = {The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia, has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognised subspecies and span the species' original geographic distribution. Our dataset includes three specimens from Darwin's collection, and the type specimens of five different taxa. We characterised their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggest gene-flow between the rock dove's sister species C. rupestris and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least one domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.},
}

@article {pmid37941678,
year = {2023},
author = {Li, T and Gao, J},
title = {Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1168760},
pmid = {37941678},
issn = {1664-462X},
abstract = {Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.},
}

@article {pmid37938763,
year = {2022},
author = {Xiang, N and Rädecker, N and Pogoreutz, C and Cárdenas, A and Meibom, A and Wild, C and Gärdes, A and Voolstra, CR},
title = {Presence of algal symbionts affects denitrifying bacterial communities in the sea anemone Aiptasia coral model.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {105},
pmid = {37938763},
issn = {2730-6151},
support = {15902919 FP 029/19//Universität Konstanz (University of Konstanz)/ ; 15902919 FP 029/19//Universität Konstanz (University of Konstanz)/ ; 15902919 FP 029/19//Universität Konstanz (University of Konstanz)/ ; 200021_179092//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {The coral-algal symbiosis is maintained by a constant and limited nitrogen availability in the holobiont. Denitrifiers, i.e., prokaryotes reducing nitrate/nitrite to dinitrogen, could contribute to maintaining the nitrogen limitation in the coral holobiont, however the effect of host and algal identity on their community is still unknown. Using the coral model Aiptasia, we quantified and characterized the denitrifier community in a full-factorial design combining two hosts (CC7 and H2) and two strains of algal symbionts of the family Symbiodiniaceae (SSA01 and SSB01). Strikingly, relative abundance of denitrifiers increased by up to 22-fold in photosymbiotic Aiptasia compared to their aposymbiotic (i.e., algal-depleted) counterparts. In line with this, while the denitrifier community in aposymbiotic Aiptasia was largely dominated by diet-associated Halomonas, we observed an increasing relative abundance of an unclassified bacterium in photosymbiotic CC7, and Ketobacter in photosymbiotic H2, respectively. Pronounced changes in denitrifier communities of Aiptasia with Symbiodinium linucheae strain SSA01 aligned with the higher photosynthetic carbon availability of these holobionts compared to Aiptasia with Breviolum minutum strain SSB01. Our results reveal that the presence of algal symbionts increases abundance and alters community structure of denitrifiers in Aiptasia. Thereby, patterns in denitrifier community likely reflect the nutritional status of aposymbiotic vs. symbiotic holobionts. Such a passive regulation of denitrifiers may contribute to maintaining the nitrogen limitation required for the functioning of the cnidarian-algal symbiosis.},
}

@article {pmid37938762,
year = {2022},
author = {Lesser, MP and Sabrina Pankey, M and Slattery, M and Macartney, KJ and Gochfeld, DJ},
title = {Microbiome diversity and metabolic capacity determines the trophic ecology of the holobiont in Caribbean sponges.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {112},
pmid = {37938762},
issn = {2730-6151},
support = {OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638289//National Science Foundation (NSF)/ ; OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638289//National Science Foundation (NSF)/ ; },
abstract = {Sponges are increasingly recognized as an ecologically important taxon on coral reefs, representing significant biomass and biodiversity where sponges have replaced scleractinian corals. Most sponge species can be divided into two symbiotic states based on symbiont community structure and abundance (i.e., the microbiome), and are characterized as high microbial abundance (HMA) or low microbial abundance (LMA) sponges. Across the Caribbean, sponge species of the HMA or LMA symbiotic states differ in metabolic capacity, as well as their trophic ecology. A metagenetic analysis of symbiont 16 S rRNA and metagenomes showed that HMA sponge microbiomes are more functionally diverse than LMA microbiomes, offer greater metabolic functional capacity and redundancy, and encode for the biosynthesis of secondary metabolites. Stable isotope analyses showed that HMA and LMA sponges primarily consume dissolved organic matter (DOM) derived from external autotrophic sources, or live particulate organic matter (POM) in the form of bacterioplankton, respectively, resulting in a low degree of resource competition between these symbiont states. As many coral reefs have undergone phase shifts from coral- to macroalgal-dominated reefs, the role of DOM, and the potential for future declines in POM due to decreased picoplankton productivity, may result in an increased abundance of chemically defended HMA sponges on tropical coral reefs.},
}

@article {pmid37938252,
year = {2022},
author = {Palladino, G and Caroselli, E and Tavella, T and D'Amico, F and Prada, F and Mancuso, A and Franzellitti, S and Rampelli, S and Candela, M and Goffredo, S and Biagi, E},
title = {Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {65},
pmid = {37938252},
issn = {2730-6151},
abstract = {Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions.},
}

@article {pmid37935117,
year = {2023},
author = {Jamieson, A and Carmagnini, A and Howard-McCombe, J and Doherty, S and Hirons, A and Dimopoulos, E and Lin, AT and Allen, R and Anderson-Whymark, H and Barnett, R and Batey, C and Beglane, F and Bowden, W and Bratten, J and De Cupere, B and Drew, E and Foley, NM and Fowler, T and Fox, A and Geigl, EM and Gotfredsen, AB and Grange, T and Griffiths, D and Groß, D and Haruda, A and Hjermind, J and Knapp, Z and Lebrasseur, O and Librado, P and Lyons, LA and Mainland, I and McDonnell, C and Muñoz-Fuentes, V and Nowak, C and O'Connor, T and Peters, J and Russo, IM and Ryan, H and Sheridan, A and Sinding, MS and Skoglund, P and Swali, P and Symmons, R and Thomas, G and Trolle Jensen, TZ and Kitchener, AC and Senn, H and Lawson, D and Driscoll, C and Murphy, WJ and Beaumont, M and Ottoni, C and Sykes, N and Larson, G and Frantz, L},
title = {Limited historical admixture between European wildcats and domestic cats.},
journal = {Current biology : CB},
volume = {33},
number = {21},
pages = {4751-4760.e14},
doi = {10.1016/j.cub.2023.08.031},
pmid = {37935117},
issn = {1879-0445},
abstract = {Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities.},
}

@article {pmid37933991,
year = {2023},
author = {Isaac, P and Mutusamy, P and Su Yin, L and Jing Wei, Y and Mohd Salleh, F and Abu Bakar, MALb and Parimannan, S and Rajandas, H},
title = {Complete genome sequences of Lactococcus lactis D1_2, a bacterium with antimicrobial properties isolated from peat soil.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0068023},
doi = {10.1128/MRA.00680-23},
pmid = {37933991},
issn = {2576-098X},
abstract = {Lactococcus lactis is a beneficial lactic acid bacterium commonly studied for its probiotic properties and role in dairy production. Here, we present a complete genome of Lactococcus lactis D1_2, isolated from peat swamp forests. To discover the potential antimicrobial properties, the complete genome of the strain was sequenced and analyzed.},
}

@article {pmid37933583,
year = {2023},
author = {Cortazar-Chinarro, M and Richter-Boix, A and Rödin-Mörch, P and Halvarsson, P and Logue, JB and Laurila, A and Höglund, J},
title = {Association between the skin microbiome and MHC class II diversity in an amphibian.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17198},
pmid = {37933583},
issn = {1365-294X},
support = {BS2018-0110//Kungliga Vetenskapsakademin/ ; FO2018-0540//Stiftelsen Lars Hiertas Minne/ ; DO2013-0013//Stiftelsen Oscar och Lili Lamms Minne/ ; //Stilftensen for zoologiska forskning/ ; 146400178//Svenska Forskningsrådet Formas/ ; 621-2013-4503//Swedish research Council/ ; },
abstract = {Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (Rana arvalis) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.},
}

@article {pmid37919016,
year = {2024},
author = {Kothe, CI and Rasmussen, JA and Mak, SST and Gilbert, MTP and Evans, J},
title = {Exploring the microbial diversity of novel misos with metagenomics.},
journal = {Food microbiology},
volume = {117},
number = {},
pages = {104372},
doi = {10.1016/j.fm.2023.104372},
pmid = {37919016},
issn = {1095-9998},
abstract = {Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and kōji (Aspergillus oryzae grown on grains or beans)-has gained attention among chefs for its rich flavour and versatility. Some chefs have even been experimenting with making novel misos with untraditional substrates to create new flavours. Such novel fermented foods also offer new scientific opportunities. To explore the microbial diversity of these new traditional foods, we sampled six misos made by the team at a leading restaurant called Noma in Copenhagen (Denmark), using yellow peas (including a nixtamalised treatment), lupin seeds, Swedish Vreta peas, grey peas, and Gotland lentils as substrates. All misos were made with the same recipe and fermented for 3 months at 28 °C. Samples were collected at the end of fermentation for subsequent shotgun metagenomic sequencing and a genome-resolved metagenomic analysis. The taxonomic profile of the samples revealed the presence of kōji mould (A. oryzae) and Bacillus amyloliquefaciens in all misos. Various species of the genera Latilactobacillus, Lactiplantibacillus, Pediococcus and Staphylococcus were also detected. The Metagenome-Assembled Genomes (MAGs) revealed genomic sequences belonging to 12 different species and functional analyses of these MAGs were performed. Notably, we detected the presence of Exiguobacterium-the first reported instance of the genus in miso-and Average Nucleotide Identity (ANI) analyses suggest a potentially new species. We hope these results will improve the scientific literature on misos and contribute to developing novel fermented plant-based foods.},
}

@article {pmid37916820,
year = {2023},
author = {Howard, RD and Schul, MD and Rodriguez Bravo, LM and Altieri, AH and Meyer, JL},
title = {Shifts in the coral microbiome in response to in situ experimental deoxygenation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0057723},
doi = {10.1128/aem.00577-23},
pmid = {37916820},
issn = {1098-5336},
abstract = {Global climate change impacts marine ecosystems through rising surface temperatures, ocean acidification, and deoxygenation. While the response of the coral holobiont to the first two effects has been relatively well studied, less is known about the response of the coral microbiome to deoxygenation. In this study, we investigated the response of the microbiome to hypoxia in two coral species that differ in their tolerance to hypoxia. We conducted in situ oxygen manipulations on a coral reef in Bahía Almirante on the Caribbean coast of Panama, which has previously experienced documented episodes of hypoxia. Naïve coral colonies (previously unexposed to hypoxia) of Siderastrea siderea and Agaricia lamarcki were transplanted to a reef and either enclosed in chambers that created hypoxic conditions or left at ambient oxygen levels. We collected samples of surface mucus and tissue after 48 hours of exposure and characterized the microbiome by sequencing 16S rRNA genes. We found that the microbiomes of the two coral species were distinct from one another and remained so after exhibiting similar shifts in microbiome composition in response to hypoxia. There was an increase in both abundance and number of taxa of anaerobic microbes after exposure to hypoxia. Some of these taxa may play beneficial roles in the coral holobiont by detoxifying the surrounding environment during hypoxic stress or may represent opportunists exploiting host stress. This work describes the first characterization of the coral microbiome under hypoxia and is an initial step toward identifying potential beneficial bacteria for corals facing this environmental stressor.IMPORTANCEMarine hypoxia is a threat for corals but has remained understudied in tropical regions where coral reefs are abundant. Though microbial symbioses can alleviate the effects of ecological stress, we do not yet understand the taxonomic or functional response of the coral microbiome to hypoxia. In this study, we experimentally lowered oxygen levels around Siderastrea siderea and Agaricia lamarcki colonies in situ to observe changes in the coral microbiome in response to deoxygenation. Our results show that hypoxia triggers a stochastic change of the microbiome overall, with some bacterial families changing deterministically after just 48 hours of exposure. These families represent an increase in anaerobic and opportunistic taxa in the microbiomes of both coral species. Thus, marine deoxygenation destabilizes the coral microbiome and increases bacterial opportunism. This work provides novel and fundamental knowledge of the microbial response in coral during hypoxia and may provide insight into holobiont function during stress.},
}

@article {pmid37914705,
year = {2023},
author = {Rädecker, N and Escrig, S and Spangenberg, JE and Voolstra, CR and Meibom, A},
title = {Coupled carbon and nitrogen cycling regulates the cnidarian-algal symbiosis.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {6948},
pmid = {37914705},
issn = {2041-1723},
support = {205321_212614//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Efficient nutrient recycling underpins the ecological success of cnidarian-algal symbioses in oligotrophic waters. In these symbioses, nitrogen limitation restricts the growth of algal endosymbionts in hospite and stimulates their release of photosynthates to the cnidarian host. However, the mechanisms controlling nitrogen availability and their role in symbiosis regulation remain poorly understood. Here, we studied the metabolic regulation of symbiotic nitrogen cycling in the sea anemone Aiptasia by experimentally altering labile carbon availability in a series of experiments. Combining [13]C and [15]N stable isotope labeling experiments with physiological analyses and NanoSIMS imaging, we show that the competition for environmental ammonium between the host and its algal symbionts is regulated by labile carbon availability. Light regimes optimal for algal photosynthesis increase carbon availability in the holobiont and stimulate nitrogen assimilation in the host metabolism. Consequently, algal symbiont densities are lowest under optimal environmental conditions and increase toward the lower and upper light tolerance limits of the symbiosis. This metabolic regulation promotes efficient carbon recycling in a stable symbiosis across a wide range of environmental conditions. Yet, the dependence on resource competition may favor parasitic interactions, explaining the instability of the cnidarian-algal symbiosis as environmental conditions in the Anthropocene shift towards its tolerance limits.},
}

@article {pmid37905582,
year = {2023},
author = {Radice, VZ and Martinez, A and Paytan, A and Potts, DC and Barshis, DJ},
title = {Complex dynamics of coral gene expression responses to low pH across species.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17186},
pmid = {37905582},
issn = {1365-294X},
support = {9915-16//The National Geographic Explorer grant/ ; //The National Park Foundation Science Fellowship/ ; },
abstract = {Coral capacity to tolerate low pH affects coral community composition and, ultimately, reef ecosystem function. Low pH submarine discharges ('Ojo'; Yucatán, México) represent a natural laboratory to study plasticity and acclimatization to low pH in relation to ocean acidification. A previous >2-year coral transplant experiment to ambient and low pH common garden sites revealed differential survivorship across species and sites, providing a framework to compare mechanistic responses to differential pH exposures. Here, we examined gene expression responses of transplants of three species of reef-building corals (Porites astreoides, Porites porites and Siderastrea siderea) and their algal endosymbiont communities (Symbiodiniaceae) originating from low pH (Ojo) and ambient pH native origins (Lagoon or Reef). Transplant pH environment had the greatest effect on gene expression of Porites astreoides hosts and symbionts and P. porites hosts. Host P. astreoides Ojo natives transplanted to ambient pH showed a similar gene expression profile to Lagoon natives remaining in ambient pH, providing evidence of plasticity in response to ambient pH conditions. Although origin had a larger effect on host S. siderea gene expression due to differences in symbiont genera within Reef and Lagoon/Ojo natives, subtle effects of low pH on all origins demonstrated acclimatization potential. All corals responded to low pH by differentially expressing genes related to pH regulation, ion transport, calcification, cell adhesion and stress/immune response. This study demonstrates that the magnitude of coral gene expression responses to pH varies considerably among populations, species and holobionts, which could differentially affect acclimatization to and impacts of ocean acidification.},
}

@article {pmid37902324,
year = {2023},
author = {Matthews, JL and Bartels, N and Elahee Doomun, SN and Davy, SK and De Souza, DP},
title = {Gas Chromatography-Mass Spectrometry-Based Targeted Metabolomics of Hard Coral Samples.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {200},
pages = {},
doi = {10.3791/65628},
pmid = {37902324},
issn = {1940-087X},
abstract = {Gas chromatography-mass spectrometry (GC-MS)-based approaches have proven to be powerful for elucidating the metabolic basis of the cnidarian-dinoflagellate symbiosis and how coral responds to stress (i.e., during temperature-induced bleaching). Steady-state metabolite profiling of the coral holobiont, which comprises the cnidarian host and its associated microbes (Symbiodiniaceae and other protists, bacteria, archaea, fungi, and viruses), has been successfully applied under ambient and stress conditions to characterize the holistic metabolic status of the coral. However, to answer questions surrounding the symbiotic interactions, it is necessary to analyze the metabolite profiles of the coral host and its algal symbionts independently, which can only be achieved by physical separation and isolation of the tissues, followed by independent extraction and analysis. While the application of metabolomics is relatively new to the coral field, the sustained efforts of research groups have resulted in the development of robust methods for analyzing metabolites in corals, including the separation of the coral host tissue and algal symbionts. This paper presents a step-by-step guide for holobiont separation and the extraction of metabolites for GC-MS analysis, including key optimization steps for consideration. We demonstrate how, once analyzed independently, the combined metabolite profile of the two fractions (coral and Symbiodiniaceae) is similar to the profile of the whole (holobiont), but by separating the tissues, we can also obtain key information about the metabolism of and interactions between the two partners that cannot be obtained from the whole alone.},
}

@article {pmid37876012,
year = {2023},
author = {Yu, J and Jiang, C and Yamano, R and Koike, S and Sakai, Y and Mino, S and Sawabe, T},
title = {Unveiling the early life core microbiome of the sea cucumber Apostichopus japonicus and the unexpected abundance of the growth-promoting Sulfitobacter.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {54},
pmid = {37876012},
issn = {2524-4671},
abstract = {BACKGROUND: Microbiome in early life has long-term effects on the host's immunological and physiological development and its disturbance is known to trigger various diseases in host Deuterostome animals. The sea cucumber Apostichopus japonicus is one of the most valuable marine Deuterostome invertebrates in Asia and a model animal in regeneration studies. To understand factors that impact on host development and holobiont maintenance, host-microbiome association has been actively studied in the last decade. However, we currently lack knowledge of early life core microbiome during its ontogenesis and how it benefits the host's growth.

RESULTS: We analyzed the microbial community in 28 sea cucumber samples from a laboratory breeding system, designed to replicate aquaculture environments, across six developmental stages (fertilized eggs to the juvenile stage) over a three years-period to examine the microbiomes' dynamics and stability. Microbiome shifts occurred during sea cucumber larval ontogenesis in every case. Application of the most sophisticated core microbiome extraction methodology, a hybrid approach with abundance-occupancy core microbiome analyses (top 75% of total reads and > 70% occupation) and core index calculation, first revealed early life core microbiome consisted of Alteromonadaceae and Rhodobacteraceae, as well as a stage core microbiome consisting of pioneer core microbe Pseudoalteromonadaceae in A. japonicus, suggesting a stepwise establishment of microbiome related to ontogenesis and feeding behavior in A. japonicus. More interestingly, four ASVs affiliated to Alteromonadaceae and Rhodobacteraceae were extracted as early life core microbiome. One of the ASV (ASV0007) was affiliated to the Sulfitobactor strain BL28 (Rhodobacteraceae), isolated from blastula larvae in the 2019 raring batch. Unexpectedly, a bioassay revealed the BL28 strain retains a host growth-promoting ability. Further meta-pangenomics approach revealed the BL28 genome reads were abundant in the metagenomic sequence pool, in particular, in that of post-gut development in early life stages of A. japonicus.

CONCLUSION: Repeated rearing efforts of A. japonicus using laboratory aquaculture replicating aquaculture environments and hybrid core microbiome extraction approach first revealed particular ASVs affiliated to Alteromonadaceae and Rhodobacteraceae as the A. japonicus early life core microbiome. Further bioassay revealed the growth promoting ability to the host sea cucumber in one of the core microbes, the Sulfitobactor strain BL28 identified as ASV0007. Genome reads of the BL28 were abundant in post-gut development of A. japonicus, which makes us consider effective probiotic uses of those core microbiome for sea cucumber resource production and conservation. The study also emphasizes the importance of the core microbiome in influencing early life stages in marine invertebrates. Understanding these dynamics could offer pathways to improve growth, immunity, and disease resistance in marine invertebrates.},
}

@article {pmid37872593,
year = {2023},
author = {Zhao, W and Chen, X and Liu, R and Tian, P and Niu, W and Zhang, XH and Liu, J and Wang, X},
title = {Distinct coral environments shape the dynamic of planktonic Vibrio spp.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {77},
pmid = {37872593},
issn = {2524-6372},
support = {42006085//National Natural Science Foundation of China/ ; 2021J05094//Marine S&T Fund of Fujian Province/ ; EPR2023001//Fund of Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources/ Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration/ ; 202312034//Fundamental Research Funds for the Central Universities/ ; 2020005//Scientific Research Foundation of the Third Institute of Oceanography, MNR/ ; },
abstract = {BACKGROUND: Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic microbiome, including bacteria, archaea, viruses and eukaryotic microbes, are referred to coral holobionts. Among them, coral diseases, mainly caused by Vibrio spp., have significantly contributed to the loss of coral cover and diversity. Habitat filtering across the globe has led to a variety structure of marine bacterial communities. Coral species, quantity and characteristics are significant differences between the Xisha Islands and Daya Bay (Guangdong Province). Thus, the Vibrio communities may be distinct between coral rich and poor areas.

RESULTS: Through comparison of Vibrio dynamics between coral-rich (Xisha Islands) and coral-poor (Daya Bay) locations, we uncovered differences in Vibrio abundance, diversity, community composition and assembly mechanisms associated with corals. The higher abundance of Vibrio in coral rich areas may indicate a strong interaction between vibrios and corals. V. campbellii, Paraphotobacterium marinum and V. caribbeanicus were widely distributed in both coral rich and poor areas, likely indicating weak species specificity in the coral-stimulated growth of Vibrio. Random-forest prediction revealed Vibrio species and Photobacterium species as potential microbial indicators in the coral rich and coral poor areas, respectively. Ecological drift rather than selection governed the Vibrio community assembly in the Xisha Islands. Comparatively, homogenizing selection was more important for the Daya Bay community, which may reflect a role of habitat filtration.

CONCLUSION: This study revealed the different distribution pattern and assembly mechanism of Vibrio spp. between coral rich and poor areas, providing the background data for the research of Vibrio community in coral reef areas and may help the protection of coral reef at the biological level. The main reasons for the difference were different number and species of corals, environmental (e.g., temperature) and spatial factors. It reflected the strong interaction between Vibrio and corals, and provided a new perspective for the investigation of Vibrio in coral reef ecosystem.},
}

@article {pmid37860235,
year = {2023},
author = {De-la-Vega-Camarillo, E and Hernández-García, JA and Villa-Tanaca, L and Hernández-Rodríguez, C},
title = {Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1247814},
pmid = {37860235},
issn = {1664-462X},
abstract = {The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: Zea diploperennis, Zea perennis, and Zea mays. In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. Streptomyces, Acinetobacter, Olivibacter, Erwinia, Bacillus, Pseudomonas, Cellvibrio, Achromobacter, Devosia, Lysobacter, Sphingopyxis, Stenotrophomonas, Ochrobactrum, Delftia, Lactobacillus, among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of Z. diploperennis was the highest, while the alpha diversity in Z. mays subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as Agrobacterium, Burkholderia, Erwinia, Lactobacillus, Ochrobactrum, Paenibacillus, Pseudomonas, Sphingomonas, Streptomyces, among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.},
}

@article {pmid37857885,
year = {2023},
author = {Bertile, F and Matallana-Surget, S and Tholey, A and Cristobal, S and Armengaud, J},
title = {Diversifying the concept of model organisms in the age of -omics.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {1062},
pmid = {37857885},
issn = {2399-3642},
abstract = {In today's post-genomic era, it is crucial to rethink the concept of model organisms. While a few historically well-established organisms, e.g. laboratory rodents, have enabled significant scientific breakthroughs, there is now a pressing need for broader inclusion. Indeed, new organisms and models, from complex microbial communities to holobionts, are essential to fully grasp the complexity of biological principles across the breadth of biodiversity. By fostering collaboration between biology, advanced molecular science and omics communities, we can collectively adopt new models, unraveling their molecular functioning, and uncovering fundamental mechanisms. This concerted effort will undoubtedly enhance human health, environmental quality, and biodiversity conservation.},
}

@article {pmid37609337,
year = {2023},
author = {Yee, SW and Ferrández-Peral, L and Alentorn, P and Fontsere, C and Ceylan, M and Koleske, ML and Handin, N and Artegoitia, VM and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, CM and Capra, JA and Artursson, P and Newman, JW and Marques-Bonet, T and Giacomini, KM},
title = {Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37609337},
abstract = {SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.},
}

@article {pmid37790518,
year = {2023},
author = {Yee, SW and Ferrández-Peral, L and Alentorn, P and Fontsere, C and Ceylan, M and Koleske, ML and Handin, N and Artegoitia, VM and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, CM and Capra, JA and Artursson, P and Newman, JW and Marques-Bonet, T and Giacomini, KM},
title = {Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37790518},
abstract = {SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.},
}

@article {pmid37848067,
year = {2023},
author = {Sinotte, VM and Renelies-Hamilton, J and Andreu-Sánchez, S and Vasseur-Cognet, M and Poulsen, M},
title = {Selective enrichment of founding reproductive microbiomes allows extensive vertical transmission in a fungus-farming termite.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2009},
pages = {20231559},
doi = {10.1098/rspb.2023.1559},
pmid = {37848067},
issn = {1471-2954},
abstract = {Mutualistic coevolution can be mediated by vertical transmission of symbionts between host generations. Termites host complex gut bacterial communities with evolutionary histories indicative of mixed-mode transmission. Here, we document that vertical transmission of gut bacterial strains is congruent across parent to offspring colonies in four pedigrees of the fungus-farming termite Macrotermes natalensis. We show that 44% of the offspring colony microbiome, including more than 80 bacterial genera and pedigree-specific strains, are consistently inherited. We go on to demonstrate that this is achieved because colony-founding reproductives are selectively enriched with a set of non-random, environmentally sensitive and termite-specific gut microbes from their colonies of origin. These symbionts transfer to offspring colony workers with high fidelity, after which priority effects appear to influence the composition of the establishing microbiome. Termite reproductives thus secure transmission of complex communities of specific, co-evolved microbes that are critical to their offspring colonies. Extensive yet imperfect inheritance implies that the maturing colony benefits from acquiring environmental microbes to complement combinations of termite, fungus and vertically transmitted microbes; a mode of transmission that is emerging as a prevailing strategy for hosts to assemble complex adaptive microbiomes.},
}

@article {pmid37841893,
year = {2023},
author = {Xiang, X and Vilar Gomez, AA and Blomberg, SP and Yuan, H and Degnan, BM and Degnan, SM},
title = {Potential for host-symbiont communication via neurotransmitters and neuromodulators in an aneural animal, the marine sponge Amphimedon queenslandica.},
journal = {Frontiers in neural circuits},
volume = {17},
number = {},
pages = {1250694},
pmid = {37841893},
issn = {1662-5110},
abstract = {Interkingdom signalling within a holobiont allows host and symbionts to communicate and to regulate each other's physiological and developmental states. Here we show that a suite of signalling molecules that function as neurotransmitters and neuromodulators in most animals with nervous systems, specifically dopamine and trace amines, are produced exclusively by the bacterial symbionts of the demosponge Amphimedon queenslandica. Although sponges do not possess a nervous system, A. queenslandica expresses rhodopsin class G-protein-coupled receptors that are structurally similar to dopamine and trace amine receptors. When sponge larvae, which express these receptors, are exposed to agonists and antagonists of bilaterian dopamine and trace amine receptors, we observe marked changes in larval phototactic swimming behaviour, consistent with the sponge being competent to recognise and respond to symbiont-derived trace amine signals. These results indicate that monoamines synthesised by bacterial symbionts may be able to influence the physiology of the host sponge.},
}

@article {pmid37840369,
year = {2023},
author = {Chrismas, N and Tindall-Jones, B and Jenkins, H and Harley, J and Bird, K and Cunliffe, M},
title = {Metatranscriptomics reveals diversity of symbiotic interaction and mechanisms of carbon exchange in the marine cyanolichen Lichina pygmaea.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19320},
pmid = {37840369},
issn = {1469-8137},
support = {218328/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Lichens are exemplar symbioses based upon carbon exchange between photobionts and their mycobiont hosts. Historically considered a two-way relationship, some lichen symbioses have been shown to contain multiple photobiont partners; however, the way in which these photobiont communities react to environmental change is poorly understood. Lichina pygmaea is a marine cyanolichen that inhabits rocky seashores where it is submerged in seawater during every tidal cycle. Recent work has indicated that L. pygmaea has a complex photobiont community including the cyanobionts Rivularia and Pleurocapsa. We performed rRNA-based metabarcoding and mRNA metatranscriptomics of the L. pygmaea holobiont at high and low tide to investigate community response to immersion in seawater. Carbon exchange in L. pygmaea is a dynamic process, influenced by both tidal cycle and the biology of the individual symbiotic components. The mycobiont and two cyanobiont partners exhibit distinct transcriptional responses to seawater hydration. Sugar-based compatible solutes produced by Rivularia and Pleurocapsa in response to seawater are a potential source of carbon to the mycobiont. We propose that extracellular processing of photobiont-derived polysaccharides is a fundamental step in carbon acquisition by L. pygmaea and is analogous to uptake of plant-derived carbon in ectomycorrhizal symbioses.},
}

@article {pmid37833238,
year = {2023},
author = {Karimi, E and Dittami, SM},
title = {Maintaining beneficial alga-associated bacterial communities under heat stress: Insights from controlled co-culture experiments using antibiotic-resistant bacterial strains.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad130},
pmid = {37833238},
issn = {1574-6941},
abstract = {Brown algae, like many eukaryotes, possess diverse microbial communities. Ectocarpus - a model brown alga- relies on these communities for essential processes, such as growth development. Controlled laboratory systems are needed for functional studies of these algal-bacterial interactions. We selected bacterial strains based on their metabolic networks to provide optimal completion of the algal metabolism, rendered them resistant to two antibiotics, and inoculate them to establish controlled co-cultures with Ectocarpus under continuous antibiotic treatment. We then monitored the stability of the resulting associations under control conditions and heat stress using 16S metabarcoding. Antibiotics strongly reduced bacterial diversity both in terms of taxonomy and predicted metabolic functions. In the inoculated sample, 63-69% of reads corresponded to the inoculated strains, and the communities remained stable during temperature stress. They also partially restored the predicted metabolic functions of the natural community. Overall, the development of antibiotic-resistant helper cultures offers a promising route to fully controlled laboratory experiments with algae and microbiota and thus represents an important step towards generating experimental evidence for specific host-microbe interactions in the systems studied. Further work will be required to achieve full control and progressively expand our repertoire of helper strains including those currently "unculturable".},
}

@article {pmid37810788,
year = {2023},
author = {Ochoa-Sánchez, M and Acuña Gomez, EP and Ramírez-Fenández, L and Eguiarte, LE and Souza, V},
title = {Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15978},
pmid = {37810788},
issn = {2167-8359},
abstract = {Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.},
}

@article {pmid37804485,
year = {2023},
author = {Pearman, WS and Duffy, GA and Liu, XP and Gemmell, NJ and Morales, SE and Fraser, CI},
title = {Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographic distance.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcad151},
pmid = {37804485},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: Contrasting patterns of host and microbiome biogeography can provide insight into the drivers of microbial community assembly. Distance-decay relationships are a classic biogeographic pattern that are shaped by interactions between selective and non-selective processes. Joint biogeography of microbiomes and their hosts are of increasing interest due to the potential for microbiome-facilitated adaptation.

METHODS: In this study we examine the coupled biogeography of the model macroalgae Durvillaea and its microbiome using a combination of Genotyping-by-Sequencing (host) and 16S rRNA amplicon sequencing (microbiome). Alongside these approaches, we employ environmental data to characterize the relationship between the microbiome, the host, and the environment.

KEY RESULTS: We show that although host and microbiome exhibit shared biogeographic structure, these arise from different processes - with host biogeography showing classic signs of geographic distance decay, but the microbiome showing environmental distance decay. Examination of microbial sub communities, defined by abundance, revealed that the abundance of microbes is linked to environmental selection. As microbes become less common, the dominant ecological processes shift away from selective processes and towards neutral processes. Contrary to expectations, we found that ecological drift does not promote structuring of the microbiome.

CONCLUSIONS: Our results suggest that although host macroalgae exhibit a relatively 'typical' biogeographic pattern of declining similarity with increasing geographic distance, the microbiome is more variable, and is primarily shaped by environmental conditions. Our findings suggest that the Baas Becking hypothesis of "everything is everywhere, the environment selects" may be a useful hypothesis to understand biogeography of macroalgal microbiomes. As environmental conditions change in response to anthropogenic influences, the processes structuring the microbiome of macroalgae may shift while those governing the host biogeography are less likely to change. As a result, increasingly decoupled host-microbe biogeography may be observed in response to such human influences.},
}

@article {pmid37799611,
year = {2023},
author = {Buschi, E and Dell'Anno, A and Tangherlini, M and Stefanni, S and Lo Martire, M and Núñez-Pons, L and Avila, C and Corinaldesi, C},
title = {Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1234725},
pmid = {37799611},
issn = {1664-302X},
abstract = {Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.},
}

@article {pmid37789578,
year = {2023},
author = {Embacher, J and Zeilinger, S and Kirchmair, M and Neuhauser, S},
title = {Prokaryote communities associated with different types of tissue formed and substrates inhabited by Serpula lacrymans.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.13191},
pmid = {37789578},
issn = {1758-2229},
support = {Y0801-B16//Austrian Science Fund/ ; 346314//Universität Innsbruck/ ; },
abstract = {The basidiomycete Serpula lacrymans is responsible for major timber devastation in houses. Basidiomycetes are known to harbour a diverse but poorly understood microbial community of bacteria, archaea, yeasts and filamentous fungi. In this study, we used amplicon-sequencing to analyse the abundance and composition of prokaryotic communities associated with fruiting bodies of S. lacrymans and compared them to communities of surrounding material to access the 'background' community structure. Our findings indicate that bacterial genera cluster depended on sample type and that the main driver for microbial diversity is specimen, followed by sample origin. The most abundant bacterial phylum identified in the fruiting bodies was Pseudomonadota, followed by Actinomycetota and Bacteroidota. The prokaryote community of the mycelium was dominated by Actinomycetota, Halobacterota and Pseudomonadota. Actinomycetota was the most abundant phylum in both environment samples (infested timber and underground scree), followed by Bacillota in wood and Pseudomonadota in underground samples. Nocardioides, Pseudomonas, Pseudonochardia, Streptomyces and Rubrobacter spp. were among others found to comprise the core microbiome of S. lacrymans basidiocarps. This research contributes to the understanding of the holobiont S. lacrymans and gives hints to potential bacterial phyla important for its development and lifestyle.},
}

@article {pmid37781006,
year = {2023},
author = {Liu, Y and Ge, W and Dong, C and Shao, Q and Zhang, Z and Zou, X and Hu, H and Han, Y},
title = {The Analysis of Microbial Community Characteristics Revealed that the Pathogens of Leaf Spot of Rosa roxburghii Originated from the Phyllosphere.},
journal = {Indian journal of microbiology},
volume = {63},
number = {3},
pages = {324-336},
pmid = {37781006},
issn = {0046-8991},
abstract = {Members of the plant mycobiota are all associated to varying degrees with the development of plant diseases. Although many reports on the plant mycobiota are well documented, the relationships between mycobiota of Rosa roxburghii and plant diseases are poorly understood. Mutual interactions and extent of the roles of microbial communities associated with R. roxburghii and the source of pathogens are still unclear, and more research is needed on the health benefits of this ecologically important population. Using high-throughput sequencing, we analyzed the mycobiota composition and ecological guilds of the rhizosphere, root, and phyllosphere of healthy and diseased R. roxburghii from the Tianfu R. roxburghii Industrial Park in Panzhou city, Guizhou province. Analysis of community composition showed that the relative abundance of pathogens of leaf spot, including Alternaria, Pestalotiopsis and Neofusicoccum in the phyllosphere of diseased plant (LD), were 1.15%, 0.15% and 0.06%, and the relative abundance of Alternaria and Pestalotiopsis were 0.96% and 0.58% in healthy plant (LH). The alpha diversity indices indicated that fungal diversity was higher in healthy plants compared to diseased plants in each compartment. The alpha diversity index of fungi in the phyllosphere (LH) of healthy R. roxburghii, including Shannon, Chao-1, and Faith-pd indices, was 1.02, 81.50 and 10.42 higher than that of the diseased (LD), respectively. The fungi in the rhizosphere of healthy was 1.03, 59.00 and 5.56 higher than the diseased, respectively. The Shannon index of fungi in the root of healthy was 0.29 higher than that of diseased. Principal Coordinate analysis and ANOSIM results showed that there were significant differences in mycobiota composition between healthy and diseased phyllospheres (P < 0.05), as well as rhizosphere fungal community, while there was no significant difference between healthy and diseased roots (P > 0.05). Linear discriminant analysis effect size revealed that, at different taxonomic levels, there were significantly different taxa between the healthy and diseased plants in each compartment. The ecological guilds differed between healthy and diseased plants according to the FUNGuild analysis. For example, of healthy compared to diseased plants, the percentages of "lichenized-undefined saprotroph" were increased by 2.34%, 0.44%, and 1.54% in the phyllosphere, root, and rhizosphere, respectively. In addition, the plant pathogens existed in each compartment of R. roxburghii, but the percentages of "plant pathogen" were increased by 1.16% in the phyllosphere of diseased compared to healthy plants. Together, the ecological guild and co-occurrence network indicated that the potential pathogens of leaf spot were mainly found in the phyllosphere. This study explained one of pathogen origin of leaf spots of R. roxburghii by the microbial community ecology, which will provide the new insights for identification of plant pathogens.},
}

@article {pmid37775014,
year = {2023},
author = {Xu, M and Lyu, Y and Cheng, K and Zhang, B and Cai, Z and Chen, G and Zhou, J},
title = {Interactions between quorum sensing/quorum quenching and virulence genes may affect coral health by regulating symbiotic bacterial community.},
journal = {Environmental research},
volume = {238},
number = {Pt 2},
pages = {117221},
doi = {10.1016/j.envres.2023.117221},
pmid = {37775014},
issn = {1096-0953},
abstract = {Quorum sensing (QS) and quorum quenching (QQ) are two antagonistic processes that may regulate the composition, function and structure of bacterial community. In coral holobiont, autoinducers signaling mediate the communication pathways between interspecies and intraspecies bacteria, which regulate the expression of the virulence factors that can damage host health. However, under environmental stressors, the interaction between the QS/QQ gene and virulence factors and their role in the bacterial communities and coral bleaching is still not fully clear. To address this question, here, metagenomics method was used to examine the profile of QS/QQ and virulence genes from a deeply sequenced microbial database, obtained from three bleached and non-bleached corals species. The prediction of bacterial genes of bleached samples involved in functional metabolic pathways were remarkably decreased, and the bacterial community structure on bleached samples was significantly different compared to non-bleached samples. The distribution and significant difference in QS/QQ and virulence genes were also carried out. We found that Proteobacteria was dominant bacteria among all samples, and AI-1 system is widespread within this group of bacteria. The identified specific genes consistently exhibited a trend of increased pathogenicity in bleached corals relative to non-bleached corals. The abundance of pathogenicity-associated QS genes, including bapA, pfoA and dgcB genes, were significantly increased in bleached corals and can encode the protein of biofilm formation and the membrane damaging toxins promoting pathogenic adhesion and infection. Similarly, the virulence genes, such as superoxide dismutase (Mn-SOD gene), metalloproteinase (yme1, yydH and zmpB), glycosidases (malE, malF, malG, and malK) and LodAB (lodB) genes significantly increased. Conversely, QQ genes that inhibit QS activity and virulence factors to defense the pathogens, including blpA, lsrK, amiE, aprE and gmuG showed a significant decrease in bleached groups. Furthermore, the significant correlations were found among virulence, QS/QQ genes, and coral associated bacterial community, and the virulence genes interact with key QS/QQ genes, directly or indirectly influence symbiotic bacterial communities homeostasis, thereby impacting coral health. It suggested that the functional and structural divergence in the symbiont bacteria may be partially attribute to the interplay, involving interactions among the host, bacterial communication signal systems, and bacterial virulence factors. In conclusion, these data helped to reveal the characteristic behavior of coral symbiotic bacteria, and facilitated a better understanding of bleaching mechanism from a chemical ecological perspective.},
}

@article {pmid37755006,
year = {2023},
author = {Ševčíková, H and Malysheva, EF and Antonín, V and Borovička, J and Dovana, F and Ferisin, G and Eyssartier, G and Grootmyers, D and Heilmann-Clausen, J and Kalichman, J and Kaygusuz, O and Lebeuf, R and Muñoz González, G and Minnis, AM and Russell, SD and Saar, I and Nielsen, IB and Frøslev, TG and Justo, A},
title = {Holarctic Species in the Pluteus podospileus Clade: Description of Six New Species and Reassessment of Old Names.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {9},
pages = {},
doi = {10.3390/jof9090898},
pmid = {37755006},
issn = {2309-608X},
abstract = {We studied the taxonomy of Pluteus podospileus and similar species using morphological and molecular (nrITS, TEF1-α) data, including a detailed study of the type collections of P. inflatus var. alneus, Pluteus minutissimus f. major, and P. granulatus var. tenellus. Within the P. podospileus complex, we phylogenetically confirmed six species in Europe, five in Asia, and eight in North America. Based on our results, we recognize P. seticeps as a separate species occurring in North America, while P. podospileus is limited to Eurasia. We describe six new species and a new variety: P. absconditus, P. fuscodiscus, P. gausapatus, P. inexpectatus, P. millsii, and P. notabilis and its variety, P. notabilis var. insignis. We elevate Pluteus seticeps var. cystidiosus to species rank as Pluteus cystidiosus. Based on the holotype of P. inflatus var. alneus, collections of P. inflatus identified by Velenovský, and several modern collections, we resurrect the name P. inflatus. Based on molecular analyses of syntypes of Pluteus minutissimus f. major and a holotype of Pluteus granulatus var. tenellus, we synonymize them under P. inflatus. We also increase our knowledge about the morphology and distribution of P. cutefractus.},
}

@article {pmid37752841,
year = {2023},
author = {Lyndby, NH and Murthy, S and Bessette, S and Jakobsen, SL and Meibom, A and Kühl, M},
title = {Non-invasive investigation of the morphology and optical properties of the upside-down jellyfish Cassiopea with optical coherence tomography.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2007},
pages = {20230127},
doi = {10.1098/rspb.2023.0127},
pmid = {37752841},
issn = {1471-2954},
abstract = {The jellyfish Cassiopea largely cover their carbon demand via photosynthates produced by microalgal endosymbionts, but how holobiont morphology and tissue optical properties affect the light microclimate and symbiont photosynthesis in Cassiopea remain unexplored. Here, we use optical coherence tomography (OCT) to study the morphology of Cassiopea medusae at high spatial resolution. We include detailed 3D reconstructions of external micromorphology, and show the spatial distribution of endosymbionts and white granules in the bell tissue. Furthermore, we use OCT data to extract inherent optical properties from light-scattering white granules in Cassiopea, and show that granules enhance local light-availability for symbionts in close proximity. Individual granules had a scattering coefficient of µs = 200-300 cm[-1], and scattering anisotropy factor of g = 0.7, while large tissue-regions filled with white granules had a lower µs = 40-100 cm[-1], and g = 0.8-0.9. We combined OCT information with isotopic labelling experiments to investigate the effect of enhanced light-availability in whitish tissue regions. Endosymbionts located in whitish tissue exhibited significantly higher carbon fixation compared to symbionts in anastomosing tissue (i.e. tissue without light-scattering white granules). Our findings support previous suggestions that white granules in Cassiopea play an important role in the host modulation of the light-microenvironment.},
}

@article {pmid37752514,
year = {2023},
author = {Wang, C and Zheng, X and Kvitt, H and Sheng, H and Sun, D and Niu, G and Tchernov, D and Shi, T},
title = {Lineage-specific symbionts mediate differential coral responses to thermal stress.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {211},
pmid = {37752514},
issn = {2049-2618},
support = {2020YFA0607602//National Key Research and Development Program of China/ ; 2020YFA0607602//National Key Research and Development Program of China/ ; 41976127//National Natural Science Foundation of China/ ; 41976127//National Natural Science Foundation of China/ ; TIO2019017, TIO2020017//Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; SML2020SP004//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) of China/ ; 31661143029//National Natural Science Foundation of China-Israel Science Foundation (NSFC-ISF) Research Program/ ; 31661143029//National Natural Science Foundation of China-Israel Science Foundation (NSFC-ISF) Research Program/ ; },
abstract = {BACKGROUND: Ocean warming is a leading cause of increasing episodes of coral bleaching, the dissociation between coral hosts and their dinoflagellate algal symbionts in the family Symbiodiniaceae. While the diversity and flexibility of Symbiodiniaceae is presumably responsible for variations in coral response to physical stressors such as elevated temperature, there is little data directly comparing physiological performance that accounts for symbiont identity associated with the same coral host species. Here, using Pocillopora damicornis harboring genotypically distinct Symbiodiniaceae strains, we examined the physiological responses of the coral holobiont and the dynamics of symbiont community change under thermal stress in a laboratory-controlled experiment.

RESULTS: We found that P. damicornis dominated with symbionts of metahaplotype D1-D4-D6 in the genus Durusdinium (i.e., PdD holobiont) was more robust to thermal stress than its counterpart with symbionts of metahaplotype C42-C1-C1b-C1c in the genus Cladocopium (i.e., PdC holobiont). Under ambient temperature, however, the thermally sensitive Cladocopium spp. exhibited higher photosynthetic efficiency and translocated more fixed carbon to the host, likely facilitating faster coral growth and calcification. Moreover, we observed a thermally induced increase in Durusdinium proportion in the PdC holobiont; however, this "symbiont shuffling" in the background was overwhelmed by the overall Cladocopium dominance, which coincided with faster coral bleaching and reduced calcification.

CONCLUSIONS: These findings support that lineage-specific symbiont dominance is a driver of distinct coral responses to thermal stress. In addition, we found that "symbiont shuffling" may begin with stress-forced, subtle changes in the rare biosphere to eventually trade off growth for increased resilience. Furthermore, the flexibility in corals' association with thermally tolerant symbiont lineages to adapt or acclimatize to future warming oceans should be viewed with conservative optimism as the current rate of environmental changes may outpace the evolutionary capabilities of corals. Video Abstract.},
}

@article {pmid37752236,
year = {2023},
author = {Roach, TNF and Matsuda, SB and Martin, C and Huckeba, G and Huckeba, J and Kahkejian, V and Santoro, EP and van der Geer, A and Drury, C and Quinn, RA},
title = {Single-polyp metabolomics reveals biochemical structuring of the coral holobiont at multiple scales.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {984},
pmid = {37752236},
issn = {2399-3642},
abstract = {All biology happens in space, and spatial structuring plays an important role in mediating biological processes at all scales from cells to ecosystems. However, the metabolomic structuring of the coral holobiont has yet to be fully explored. Here, we present a method to detect high-quality metabolomic data from individual coral polyps and apply this method to study the patterning of biochemicals across multiple spatial (~1 mm - ~100 m) and organizational scales (polyp to population). The data show a strong signature for individual coral colonies, a weaker signature of branches within colonies, and variation at the polyp level related to the polyps' location along a branch. Mapping metabolites to either the coral or algal components of the holobiont reveals that polyp-level variation along the length of a branch was largely driven by molecules associated with the cnidarian host as opposed to the algal symbiont, predominantly putative sulfur-containing metabolites. This work yields insights on the spatial structuring of biochemicals in the coral holobiont, which is critical for design, analysis, and interpretation of studies on coral reef biochemistry.},
}

@article {pmid37744040,
year = {2023},
author = {Galià-Camps, C and Baños, E and Pascual, M and Carreras, C and Turon, X},
title = {Multidimensional variability of the microbiome of an invasive ascidian species.},
journal = {iScience},
volume = {26},
number = {10},
pages = {107812},
pmid = {37744040},
issn = {2589-0042},
abstract = {Animals, including invasive species, are complex entities consisting of a host and its associated symbionts (holobiont). The interaction between the holobiont components is crucial for the host's survival. However, our understanding of how microbiomes of invasive species change across different tissues, localities, and ontogenetic stages, is limited. In the introduced ascidian Styela plicata, we found that its microbiome is highly distinct and specialized among compartments (tunic, gill, and gut). Smaller but significant differences were also found across harbors, suggesting local adaptation, and between juveniles and adults. Furthermore, we found a correlation between the microbiome and environmental trace element concentrations, especially in adults. Functional analyses showed that adult microbiomes possess specific metabolic pathways that may enhance fitness during the introduction process. These findings highlight the importance of integrated approaches in studying the interplay between animals and microbiomes, as a first step toward understanding how it can affect the species' invasive success.},
}

@article {pmid37746232,
year = {2022},
author = {Flores, GAM and Lopez, RP and Cerrudo, CS and Consolo, VF and Berón, CM},
title = {Culex quinquefasciatus Holobiont: A Fungal Metagenomic Approach.},
journal = {Frontiers in fungal biology},
volume = {3},
number = {},
pages = {918052},
pmid = {37746232},
issn = {2673-6128},
abstract = {Microorganisms associated with mosquitoes have fundamental roles, not only in their nutrition, but also in physiological and immunological processes, and in their adaptation to the environment as well. Studies on mosquito hologenomes have increased significantly during the last years, achieving important advances in the characterization of the "core bacteriome" of some species of health importance. However, the fungal mycobiome has not been exhaustively researched, especially throughout the life cycle of some hematophagous mosquito species. In this work, the diversity and composition of fungal communities in different developmental stages, sexes, and adult nutrition of Culex quinquefasciatus reared on laboratory conditions were characterized, using internal transcribed spacer high throughput amplicon sequencing. Larvae presented a higher fungal richness, while sucrose-fed males and females showed a similar diversity between them. Blood-fed females presented few operational taxonomic units with an even distribution. Results are consistent with the reduction of larval microbiota after molting, observed for the bacterial microbiome in other mosquito species. The filamentous Ascomycota Penicillium polonicum and Cladosporium sp. were present in all stages of the mosquitoes; in addition, the presence of yeasts in the insects or their subsequent colonization associated with their diet is also discussed. These results suggest that some species of fungi could be essential for the nutrition and development of mosquitoes throughout their life cycle.},
}

@article {pmid37731336,
year = {2023},
author = {Aizpurua, O and Dunn, RR and Hansen, LH and Gilbert, MTP and Alberdi, A},
title = {Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/07388551.2023.2254933},
pmid = {37731336},
issn = {1549-7801},
abstract = {Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.},
}

@article {pmid37726938,
year = {2023},
author = {Markussen Bjorbaekmo, MF and Brodie, J and Krabberød, AK and Logares, R and Fuss, J and Fredriksen, S and Wold-Dobbe, A and Shalchian-Tabrizi, K and Bass, D},
title = {18S rDNA gene metabarcoding of microeukaryotes and epi-endophytes in the holobiome of seven species of large brown algae.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.13377},
pmid = {37726938},
issn = {1529-8817},
support = {//Sunniva og Egil Baardseths legat/ ; },
abstract = {Brown algae (Phaeophyceae) are habitat-forming species in coastal ecosystems and include kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology, and whereas the bacterial microbial partners have received considerable attention, the microbial eukaryotes associated with brown algae have hardly been studied. Here, we used broadly targeted "pan-eukaryotic" primers (metabarcoding) to investigate brown algal-associated eukaryotes (the eukaryome). Using this approach, we aimed to investigate the eukaryome of seven large brown algae that are important and common species in coastal ecosystems. We also aimed to assess whether these macroalgae harbor novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome based on taxonomic affiliation and phylogenetic placement. We detected a significant diversity of microeukaryotic and algal lineages associated with the brown algal species investigated. The operational taxonomic units (OTUs) were taxonomically assigned to 10 of the eukaryotic major supergroups, including taxonomic groups known to be associated with seaweeds as epibionts, endobionts, parasites, and commensals. Additionally, we revealed previously unrecorded sequence types, including novel phaeophyte OTUs, particularly in the Fucus spp. samples, that may represent fucoid genomic variants, sequencing artifacts, or undescribed epi-/endophytes. Our results provide baseline data and technical insights that will be useful for more comprehensive seaweed eukaryome studies investigating the evidently lineage-rich and functionally diverse symbionts of brown algae.},
}

@article {pmid37719127,
year = {2023},
author = {Castañeda-Molina, Y and Marulanda-Moreno, SM and Saldamando-Benjumea, C and Junca, H and Moreno-Herrera, CX and Cadavid-Restrepo, G},
title = {Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15916},
pmid = {37719127},
issn = {2167-8359},
abstract = {BACKGROUND: Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.

METHODS: The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.

RESULTS: Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.},
}

@article {pmid37702122,
year = {2023},
author = {Rasmussen, L and Fontsere, C and Soto-Calderón, ID and Guillen, R and Savage, A and Hansen, AJ and Hvilsom, C and Gilbert, MTP},
title = {Assessing the genetic composition of cotton-top tamarins (Saguinus oedipus) before sweeping anthropogenic impact.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17130},
pmid = {37702122},
issn = {1365-294X},
support = {//Alfred Benzon Foundation/ ; 143//Danmarks Grundforskningsfond/ ; //Torben & Alice Frimodts Fund/ ; },
abstract = {During the last century, the critically endangered cotton-top tamarin (Saguinus oedipus) has been threatened by multiple anthropogenic factors that drastically affected their habitat and population size. As the genetic impact of these pressures is largely unknown, this study aimed to establish a genetic baseline with the use of temporal sampling to determine the genetic makeup before detrimental anthropogenic impact. Genomes were resequenced from a combination of historical museum samples and modern wild samples at low-medium coverage, to unravel how the cotton-top tamarin population structure and genomic diversity may have changed during this period. Our data suggest two populations can be differentiated, probably separated historically by the mountain ranges of the Paramillo Massif in Colombia. Although this population structure persists in the current populations, modern samples exhibit genomic signals consistent with recent inbreeding, such as long runs of homozygosity and a reduction in genome-wide heterozygosity especially in the greater northeast population. This loss is likely the consequence of the population reduction following the mass exportation of cotton-top tamarins for biomedical research in the 1960s, coupled with the habitat loss this species continues to experience. However, current populations have not experienced an increase in genetic load. We propose that the historical genetic baseline established in this study can be used to provide insight into alteration in the modern population influenced by a drastic reduction in population size as well as providing background information to be used for future conservation decision-making for the species.},
}

@article {pmid37702036,
year = {2023},
author = {Peng, L and Hoban, J and Joffe, J and Smith, AH and Carpenter, M and Marcelis, T and Patel, V and Lynn-Bell, N and Oliver, KM and Russell, JA},
title = {Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jeb.14216},
pmid = {37702036},
issn = {1420-9101},
support = {1050098//National Science Foundation/ ; 1050128//National Science Foundation/ ; 1754302//National Science Foundation/ ; 1754597//National Science Foundation/ ; },
abstract = {Most insects harbour influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across US populations of the pea aphid, Acyrthosiphon pisum. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping five out of nine previously reported co-infection trends. Field data provide a mixture of evidence for synergistic fitness effects and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. 12 pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts-Serratia symbiotica and Rickettsiella viridis. Applying the expansion network algorithm, through additional use of pea aphid and obligate Buchnera symbiont genomes, Serratia and Rickettsiella emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps, creating a multi-party mutualism within their nutrient-limited, phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of Serratia and Rickettsiella, raises further questions on the origins of mutualisms and host-symbiont interdependencies.},
}

@article {pmid37694134,
year = {2023},
author = {Williams, A and Stephens, TG and Shumaker, A and Bhattacharya, D},
title = {Peeling back the layers of coral holobiont multi-omics data.},
journal = {iScience},
volume = {26},
number = {9},
pages = {107623},
doi = {10.1016/j.isci.2023.107623},
pmid = {37694134},
issn = {2589-0042},
abstract = {The integration of multiple 'omics' datasets is a promising avenue for answering many important and challenging questions in biology, particularly those relating to complex ecological systems. Although multi-omics was developed using data from model organisms with significant prior knowledge and resources, its application to non-model organisms, such as coral holobionts, is less clear-cut. We explore, in the emerging rice coral model Montipora capitata, the intersection of holobiont transcriptomic, proteomic, metabolomic, and microbiome amplicon data and investigate how well they correlate under high temperature treatment. Using a typical thermal stress regime, we show that transcriptomic and proteomic data broadly capture the stress response of the coral, whereas the metabolome and microbiome datasets show patterns that likely reflect stochastic and homeostatic processes associated with each sample. These results provide a framework for interpreting multi-omics data generated from non-model systems, particularly those with complex biotic interactions among microbial partners.},
}

@article {pmid37692426,
year = {2023},
author = {Senizza, B and Araniti, F and Lewin, S and Wende, S and Kolb, S and Lucini, L},
title = {Trichoderma spp.-mediated mitigation of heat, drought, and their combination on the Arabidopsis thaliana holobiont: a metabolomics and metabarcoding approach.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1190304},
doi = {10.3389/fpls.2023.1190304},
pmid = {37692426},
issn = {1664-462X},
abstract = {INTRODUCTION: The use of substances to increase productivity and resource use efficiency is now essential to face the challenge of feeding the rising global population with the less environmental impact on the ecosystems. Trichoderma-based products have been used as biopesticides, to inhibit pathogenic microorganisms, and as biostimulants for crop growth, nutrient uptake promotion, and resistance to abiotic stresses.

METHODS: In this work, plant metabolomics combined with roots and rhizosphere bacterial metabarcoding were exploited to inspect the performance of Trichoderma spp. biostimulants on Arabidopsis thaliana under drought, heat and their combination and its impact on plant holobiont.

RESULTS AND DISCUSSION: An overall modulation of N-containing compounds, phenylpropanoids, terpenes and hormones could be pointed out by metabolomics. Moreover, metabarcoding outlined an impact on alpha and beta-diversity with an abundance of Proteobacteria, Pseudomonadales, Burkholderiales, Enterobacteriales and Azospirillales. A holobiont approach was applied as an integrated analytical strategy to resolve the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria using Arabidopsis thaliana as a model host species.},
}

@article {pmid37670990,
year = {2023},
author = {Pérez-Llano, Y and Yarzábal Rodríguez, LA and Martínez-Romero, E and Dobson, ADW and Gunde-Cimerman, N and Vasconcelos, V and Batista-García, RA},
title = {From friends to foes: fungi could be emerging marine sponge pathogens under global change scenarios.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1213340},
pmid = {37670990},
issn = {1664-302X},
}

@article {pmid37669892,
year = {2023},
author = {Hellal, J and Barthelmebs, L and Bérard, A and Cébron, A and Cheloni, G and Colas, S and Cravo-Laureau, C and De Clerck, C and Gallois, N and Hery, M and Martin-Laurent, F and Martins, J and Morin, S and Palacios, C and Pesce, S and Richaume, A and Vuilleumier, S},
title = {Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad102},
pmid = {37669892},
issn = {1574-6941},
abstract = {Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment and also play key roles in the fate of pollutants through the degradation, transformation and transfer of organic or inorganic compounds. They are thus crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.},
}

@article {pmid37664515,
year = {2023},
author = {Hill, CEL and Abbass, SG and Caporale, G and El-Khaled, YC and Kuhn, L and Schlenzig, T and Wild, C and Tilstra, A},
title = {Physiology of the widespread pulsating soft coral Xenia umbellata is affected by food sources, but not by water flow.},
journal = {Ecology and evolution},
volume = {13},
number = {9},
pages = {e10483},
pmid = {37664515},
issn = {2045-7758},
abstract = {Coral energy and nutrient acquisition strategies are complex and sensitive to environmental conditions such as water flow. While high water flow can enhance feeding in hard corals, knowledge about the effects of water flow on the feeding of soft corals, particularly those pulsating, is still limited. In this study, we thus investigated the effects of feeding and water flow on the physiology of the pulsating soft coral Xenia umbellata. We crossed three feeding treatments: (i) no feeding, (ii) particulate organic matter (POM) in the form of phytoplankton and (iii) dissolved organic carbon (DOC) in the form of glucose, with four water volume exchange rates (200, 350, 500 and 650 L h[-1]) over 15 days. Various ecophysiological parameters were assessed including pulsation rate, growth rate, isotopic and elemental ratios of carbon (C) and nitrogen (N) as well as photo-physiological parameters of the Symbiodiniaceae (cell density, chlorophyll-a and mitotic index). Water flow had no significant effect but feeding had a substantial impact on the physiology of the X. umbellata holobiont. In the absence of food, corals exhibited significantly lower pulsation rates, lower Symbiodiniaceae cell density and lower mitotic indices compared to the fed treatments, yet significantly higher chlorophyll-a per cell and total N content. Differences were also observed between the two feeding treatments, with significantly higher pulsation rates and lower chlorophyll-a per cell in the DOC treatment, but higher C and N content in the POM treatment. Our findings suggest that the X. umbellata holobiont can be viable under different trophic strategies, though favouring mixotrophy. Additionally, the physiology of the X. umbellata may be regulated through its own pulsating behaviour without any positive or negative effects from different water flow. Therefore, this study contributes to our understanding of soft coral ecology, particularly regarding the competitive success and widespread distribution of X. umbellata.},
}

@article {pmid37652999,
year = {2023},
author = {Sun, X and Liu, YC and Tiunov, MP and Gimranov, DO and Zhuang, Y and Han, Y and Driscoll, CA and Pang, Y and Li, C and Pan, Y and Velasco, MS and Gopalakrishnan, S and Yang, RZ and Li, BG and Jin, K and Xu, X and Uphyrkina, O and Huang, Y and Wu, XH and Gilbert, MTP and O'Brien, SJ and Yamaguchi, N and Luo, SJ},
title = {Ancient DNA reveals genetic admixture in China during tiger evolution.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {37652999},
issn = {2397-334X},
support = {NSFC32070598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18-04-00327//Russian Foundation for Basic Research (RFBR)/ ; },
abstract = {The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.},
}

@article {pmid37653089,
year = {2023},
author = {Mannochio-Russo, H and Swift, SOI and Nakayama, KK and Wall, CB and Gentry, EC and Panitchpakdi, M and Caraballo-Rodriguez, AM and Aron, AT and Petras, D and Dorrestein, K and Dorrestein, TK and Williams, TM and Nalley, EM and Altman-Kurosaki, NT and Martinelli, M and Kuwabara, JY and Darcy, JL and Bolzani, VS and Wegley Kelly, L and Mora, C and Yew, JY and Amend, AS and McFall-Ngai, M and Hynson, NA and Dorrestein, PC and Nelson, CE},
title = {Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {896},
pmid = {37653089},
issn = {2399-3642},
support = {OCE-2118618//NSF | Office of the Director (NSF Office of the Director)/ ; 2025669//NSF | Office of the Director (NSF Office of the Director)/ ; 2124922//NSF | Office of the Director (NSF Office of the Director)/ ; OCE-2023298//NSF | Office of the Director (NSF Office of the Director)/ ; P20GM125508//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P20GM125508//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, O'ahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.},
}

@article {pmid37650630,
year = {2023},
author = {Koziol, A and Odriozola, I and Leonard, A and Eisenhofer, R and San José, C and Aizpurua, O and Alberdi, A},
title = {Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors.},
journal = {mBio},
volume = {},
number = {},
pages = {e0160623},
doi = {10.1128/mbio.01606-23},
pmid = {37650630},
issn = {2150-7511},
abstract = {The ability of the gut microbiome has been posited as an additional axis of animals' phenotypic plasticity. However, whether and how such plasticity varies across hosts with different biological features remains unclear. We performed a captivity experiment to compare how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of temperature and dietary disturbances in two mammals: the insectivorous-specialist Crocidura russula and the omnivorous-generalist Apodemus sylvaticus. Combining genome-resolved metagenomics, metabolic pathway distillation and joint species distribution modeling, we observed that, although microbiome alpha diversity of both species remained stable, C. russula exhibited substantially higher variability and directionality of microbial responses than A. sylvaticus. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts. IMPORTANCE In our manuscript, we report the first interspecific comparative study about the plasticity of the gut microbiota. We conducted a captivity experiment that exposed wild-captured mammals to a series of environmental challenges over 45 days. We characterized their gut microbial communities using genome-resolved metagenomics and modeled how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of disturbances in both species. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.},
}

@article {pmid37647612,
year = {2023},
author = {Zhou, K and Zhang, T and Chen, XW and Xu, Y and Zhang, R and Qian, PY},
title = {Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts.},
journal = {Annual review of marine science},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-marine-021623-093133},
pmid = {37647612},
issn = {1941-0611},
abstract = {Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts. Expected final online publication date for the Annual Review of Marine Science, Volume 16 is January 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid37645461,
year = {2023},
author = {Zuzolo, D and Ranauda, MA and Maisto, M and Tartaglia, M and Prigioniero, A and Falzarano, A and Marotta, G and Sciarrillo, R and Guarino, C},
title = {The rootstock shape microbial diversity and functionality in the rhizosphere of Vitis vinifera L. cultivar Falanghina.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1205451},
pmid = {37645461},
issn = {1664-462X},
abstract = {The rhizosphere effect occurring at the root-soil interface has increasingly been shown to play a key role in plant fitness and soil functionality, influencing plants resilience. Here, for the first time, we investigated whether the rootstock genotype on which Vitis vinifera L. cultivar Falanghina is grafted can influence the rhizosphere microbiome. Specifically, we evaluated to which extent the 5BB and 1103P rootstocks are able to shape microbial diversity of rhizosphere environment. Moreover, we explored the potential function of microbial community and its shift under plant genotype influence. We investigated seven vineyards subjected to the same pedo-climatic conditions, similar age, training system and management and collected twelve rhizosphere soil samples for metagenomic analyses and composite soil samples for physical-chemical properties. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the rhizosphere bacterial diversity and composition. Liner discriminant analysis effect size (LEFSe) was conducted for metagenomic biomarker discovery. The functional composition of sampled communities was determined using PICRUSt, which is based on marker gene sequencing profiles. Soil analyses involved the determination of texture, pH, Cation Exchange Capacity (CSC), Organic Carbon (OC), electrical conductivity (EC), calcium (Ca), magnesium (Mg), potassium (K) content, Phosphorous (P), nitrogen (N). The latter revealed that soil features were quite homogenous. The metagenomic data showed that the bacterial alpha-diversity (Observed OTUs) significantly increased in 1103P rhizosphere microbiota. Irrespective of cultivar, Pseudomonadota was the dominant phylum, followed by Actinomycetota > Bacteroidota > Thermoproteota. However, Actinomycetota was the major marker phyla differentiating the rhizosphere microbial communities associated with the different rootstock types. At the genus level, several taxa belonging to Actinomycetota and Alphaproteobacteria classes were enriched in 1103P genotype rhizosphere. Investigating the potential functional profile, we found that most key enzyme-encoding genes involved in N cycling were significantly more abundant in 5BB rootstock rhizosphere soil. However, we found that 1103P rhizosphere was enriched in genes involved in C cycle and Plant Growth Promotion (PGP) functionality. Our results suggest that the different rootstocks not only recruit specific bacterial communities, but also specific functional traits within the same environment.},
}

@article {pmid37638757,
year = {2023},
author = {Chaturvedi, A and Li, X and Dhandapani, V and Marshall, H and Kissane, S and Cuenca-Cambronero, M and Asole, G and Calvet, F and Ruiz-Romero, M and Marangio, P and Guigó, R and Rago, D and Mirbahai, L and Eastwood, N and Colbourne, JK and Zhou, J and Mallon, E and Orsini, L},
title = {The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad685},
pmid = {37638757},
issn = {1362-4962},
support = {NE/N016777/1//NERC/ ; 965406//European Union/ ; 101028700//Marie Skłodowska-Curie/ ; IC160121//Royal Society International Collaboration Award/ ; },
abstract = {Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.},
}

@article {pmid37626434,
year = {2023},
author = {Kelliher, JM and Robinson, AJ and Longley, R and Johnson, LYD and Hanson, BT and Morales, DP and Cailleau, G and Junier, P and Bonito, G and Chain, PSG},
title = {The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {192},
pmid = {37626434},
issn = {2049-2618},
support = {This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; },
abstract = {As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.},
}

@article {pmid37626254,
year = {2023},
author = {Hussain, A and Kumar, SHK and Prathiviraj, R and Kumar, AA and Renjith, K and Kiran, GS and Selvin, J},
title = {The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India.},
journal = {Archives of microbiology},
volume = {205},
number = {9},
pages = {319},
pmid = {37626254},
issn = {1432-072X},
support = {BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {An increase in antibiotic pollution in reef areas will lead to the emergence of antibiotic-resistant bacteria, leading to ecological disturbances in the sensitive coral holobiont. This study provides insights into the genome of antibiotics-resistant Stutzerimonas frequens CAM01, isolated from Favites-associated Symbiodiniaceae of a near-shore polluted reef of Palk Bay, India. The draft genome contains 4.67 Mbp in size with 52 contigs. Further genome analysis revealed the presence of four antibiotic-resistant genes, namely, adeF, rsmA, APH (3")-Ib, and APH (6)-Id that provide resistance by encoding resistance-nodulation-cell division (RND) antibiotic efflux pump and aminoglycoside phosphotransferase. The isolate showed resistance against 73% of the antibiotics tested, concurrent with the predicted AMR genes. Four secondary metabolites, namely Aryl polyene, NRPS-independent-siderophore, terpenes, and ectoine were detected in the isolate, which may play a role in virulence and pathogenicity adaptation in microbes. This study provides key insights into the genome of Stutzerimonas frequens CAM01 and highlights the emergence of antibiotic-resistant bacteria in coral reef ecosystems.},
}

@article {pmid37625782,
year = {2023},
author = {Prabhakaran, P and Nazir, MYM and Thananusak, R and Hamid, AA and Vongsangnak, W and Song, Y},
title = {Uncovering global lipid accumulation routes towards docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1 using integrative proteomic analysis.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {},
number = {},
pages = {159381},
doi = {10.1016/j.bbalip.2023.159381},
pmid = {37625782},
issn = {1879-2618},
abstract = {Aurantiochytrium sp., a marine thraustochytrid possesses a remarkable ability to produce lipid rich in polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (DHA). Although gene regulation underlying lipid biosynthesis has been previously reported, proteomic analysis is still limited. In this study, high DHA accumulating strain Aurantiochytrium sp. SW1 has been used as a study model to elucidate the alteration in proteome profile under different cultivation phases i.e. growth, nitrogen-limitation and lipid accumulation. Of the total of 5146 identified proteins, 852 proteins were differentially expressed proteins (DEPs). The largest number of DEPs (488 proteins) was found to be uniquely expressed between lipid accumulating phase and growth phase. Interestingly, there were up-regulated proteins involved in glycolysis, glycerolipid, carotenoid and glutathione metabolism which were preferable metabolic routes towards lipid accumulation and DHA production as well as cellular oxidative defence. Integrated proteomic and transcriptomic data were also conducted to comprehend the gene and protein regulation underlying the lipid and DHA biosynthesis. A significant up-regulation of acetyl-CoA synthetase was observed which suggests alternative route of acetate metabolism for acetyl-CoA producer. This study presents the holistic routes underlying lipid accumulation and DHA production in Aurantiochytrium sp. SW1 and other relevant thraustochytrid.},
}

@article {pmid37623217,
year = {2023},
author = {Petrushin, IS and Vasilev, IA and Markova, YA},
title = {Drought Tolerance of Legumes: Physiology and the Role of the Microbiome.},
journal = {Current issues in molecular biology},
volume = {45},
number = {8},
pages = {6311-6324},
doi = {10.3390/cimb45080398},
pmid = {37623217},
issn = {1467-3045},
support = {23-26-00204//Russian Science Foundation/ ; },
abstract = {Water scarcity and global warming make drought-tolerant plant species more in-demand than ever. The most drastic damage exerted by drought occurs during the critical growth stages of seed development and reproduction. In the course of their evolution, plants form a variety of drought-tolerance mechanisms, including recruiting beneficial microorganisms. Legumes (one of the three largest groups of higher plants) have unique features and the potential to adapt to abiotic stress. The available literature discusses the genetic (breeding) and physiological aspects of drought tolerance in legumes, neglecting the role of the microbiome. Our review aims to fill this gap: starting with the physiological mechanisms of legume drought adaptation, we describe the symbiotic relationship of the plant host with the microbial community and its role in facing drought. We consider two types of studies related to microbiomes in low-water conditions: comparisons and microbiome engineering (modulation). The first type of research includes diversity shifts and the isolation of microorganisms from the various plant niches to which they belong. The second type focuses on manipulating the plant holobiont through microbiome engineering-a promising biotech strategy to improve the yield and stress-resistance of legumes.},
}

@article {pmid37604380,
year = {2023},
author = {Yu, X and Yu, K and Liao, Z and Chen, B and Qin, Z and Liang, J and Gao, X},
title = {Adaptation strategies of relatively high-latitude marginal reef corals in response to severe temperature fluctuations.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {166439},
doi = {10.1016/j.scitotenv.2023.166439},
pmid = {37604380},
issn = {1879-1026},
abstract = {The large seasonal temperature fluctuations caused by global warming and frequent marine heatwaves pose new challenges to survival of relatively high-latitude marginal reef corals. However, the adaptation strategies of high-latitude marginal corals are not fully understood. We employed integrated approach to investigate the response mechanism of hosts, Symbiodiniaceae, and symbiotic bacteria of marginal reef corals Acropora pruinosa and Pavona decussate in response to large seasonal temperature fluctuations. The coral holobiont maintained a high level of immunity to adapt to seasonal pressure by increasing Symbiodiniaceae energy supply. The symbiotic Symbiodiniaceae of two coral was dominated by C1 subgroup, and was stable across seasons. The α-diversity of symbiotic bacteria P. decussata and A. pruinosa in summer was higher than that in winter. The symbiotic bacterial community of two coral reorganized during different seasons. Scleractinian corals improve adaptability to seasonal stress by increasing energy supply to maintain high levels of immunity, increasing symbiotic bacterial α-diversity, and changing dominant bacteria. This study demonstrates the adaptation strategies of marginal reef corals to seasonal temperature fluctuations and provides novel insights into the study of the adaptation of corals and relatively high-latitude coral refuges in the context of global warming and intensified marine heatwaves.},
}

@article {pmid37601769,
year = {2023},
author = {Mochales-Riaño, G and Fontsere, C and de Manuel, M and Talavera, A and Burriel-Carranza, B and Tejero-Cicuéndez, H and AlGethami, RHM and Shobrak, M and Marques-Bonet, T and Carranza, S},
title = {Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr).},
journal = {iScience},
volume = {26},
number = {9},
pages = {107481},
pmid = {37601769},
issn = {2589-0042},
abstract = {In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.},
}

@article {pmid37601376,
year = {2023},
author = {Caetano-Anollés, G and Claverie, JM and Nasir, A},
title = {A critical analysis of the current state of virus taxonomy.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1240993},
pmid = {37601376},
issn = {1664-302X},
abstract = {Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification.},
}

@article {pmid37587369,
year = {2023},
author = {Gavriilidou, A and Avcı, B and Galani, A and Schorn, MA and Ingham, CJ and Ettema, TJG and Smidt, H and Sipkema, D},
title = {Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {37587369},
issn = {1751-7370},
support = {897121//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 817834//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 679849//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Members of the candidate phylum Dadabacteria, recently reassigned to the phylum Candidatus Desulfobacterota, are cosmopolitan in the marine environment found both free-living and associated with hosts that are mainly marine sponges. Yet, these microorganisms are poorly characterized, with no cultured representatives and an ambiguous phylogenetic position in the tree of life. Here, we performed genome-centric metagenomics to elucidate their phylogenomic placement and predict the metabolism of the sponge-associated members of this lineage. Rank-based phylogenomics revealed several new species and a novel family (Candidatus Spongomicrobiaceae) within a sponge-specific order, named here Candidatus Nemesobacterales. Metabolic reconstruction suggests that Ca. Nemesobacterales are aerobic heterotrophs, capable of synthesizing most amino acids, vitamins and cofactors and degrading complex carbohydrates. We also report functional divergence between sponge- and seawater-associated metagenome-assembled genomes. Niche-specific adaptations to the sponge holobiont were evident from significantly enriched genes involved in defense mechanisms against foreign DNA and environmental stressors, host-symbiont interactions and secondary metabolite production. Fluorescence in situ hybridization gave a first glimpse of the morphology and lifestyle of a member of Ca. Desulfobacterota. Candidatus Nemesobacterales spp. were found both inside sponge cells centred around sponge nuclei and in the mesohyl of the sponge Geodia barretti. This study sheds light on the enigmatic group Ca. Nemesobacterales and their functional characteristics that reflect a symbiotic lifestyle.},
}

@article {pmid37586539,
year = {2023},
author = {He, R and Hu, S and Li, Q and Zhao, D and Wu, QL and Zeng, J},
title = {Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {166229},
doi = {10.1016/j.scitotenv.2023.166229},
pmid = {37586539},
issn = {1879-1026},
abstract = {Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) and roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiomes in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.},
}

@article {pmid37580830,
year = {2023},
author = {Tignat-Perrier, R and van de Water, JAJM and Allemand, D and Ferrier-Pagès, C},
title = {Holobiont responses of mesophotic precious red coral Corallium rubrum to thermal anomalies.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {70},
pmid = {37580830},
issn = {2524-6372},
abstract = {Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with shallow populations of habitat-forming octocorals facing the threat of local extinction. The mesophotic zone, which is less affected by MHWs, may be of ecological importance in conservation strategies for these species. However, our understanding of the response of mesophotic octocoral holobionts to changes in seawater temperature remains limited. To address this knowledge gap, we conducted a study on an iconic Mediterranean octocoral, the red coral Corallium rubrum sampled at 60 m depth and 15 °C. We exposed the colonies to temperatures they occasionally experience (18 °C) and temperatures that could occur at the end of the century if global warming continues (21 °C). We also tested their response to extremely cold and warm temperatures (12 °C and 24 °C). Our results show a high tolerance of C. rubrum to a two-month long exposure to temperatures ranging from 12 to 21 °C as no colony showed signs of tissue loss, reduced feeding ability, stress-induced gene expression, or disruption of host-bacterial symbioses. At 24 °C, however, we measured a sharp decrease in the relative abundance of Spirochaetaceae, which are the predominant bacterial symbionts under healthy conditions, along with a relative increase in Vibrionaceae. Tissue loss and overexpression of the tumor necrosis factor receptor 1 gene were also observed after two weeks of exposure. In light of ongoing global warming, our study helps predict the consequences of MHWs on mesophotic coralligenous reefs and the biodiversity that depends on them.},
}

@article {pmid37570868,
year = {2023},
author = {Ujlaki, G and Kovács, T and Vida, A and Kókai, E and Rauch, B and Schwarcz, S and Mikó, E and Janka, E and Sipos, A and Hegedűs, C and Uray, K and Nagy, P and Bai, P},
title = {Identification of Bacterial Metabolites Modulating Breast Cancer Cell Proliferation and Epithelial-Mesenchymal Transition.},
journal = {Molecules (Basel, Switzerland)},
volume = {28},
number = {15},
pages = {},
pmid = {37570868},
issn = {1420-3049},
support = {K123975//National Research, Development and Innovation Office/ ; K124141//National Research, Development and Innovation Office/ ; FK128387//National Research, Development and Innovation Office/ ; TKP2021-EGA-19//National Research, Development and Innovation Office/ ; TKP2021-EGA-20//National Research, Development and Innovation Office/ ; POST-COVID2021-33//Hungarian Academy of Sciences/ ; },
abstract = {Breast cancer patients are characterized by the oncobiotic transformation of multiple microbiome communities, including the gut microbiome. Oncobiotic transformation of the gut microbiome impairs the production of antineoplastic bacterial metabolites. The goal of this study was to identify bacterial metabolites with antineoplastic properties. We constructed a 30-member bacterial metabolite library and screened the library compounds for effects on cell proliferation and epithelial-mesenchymal transition. The metabolites were applied to 4T1 murine breast cancer cells in concentrations corresponding to the reference serum concentrations. However, yric acid, glycolic acid, d-mannitol, 2,3-butanediol, and trans-ferulic acid exerted cytostatic effects, and 3-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, and vanillic acid exerted hyperproliferative effects. Furthermore, 3-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, 2,3-butanediol, and hydrocinnamic acid inhibited epithelial-to-mesenchymal (EMT) transition. We identified redox sets among the metabolites (d-mannitol-d-mannose, 1-butanol-butyric acid, ethylene glycol-glycolic acid-oxalic acid), wherein only one partner within the set (d-mannitol, butyric acid, glycolic acid) possessed bioactivity in our system, suggesting that changes to the local redox potential may affect the bacterial secretome. Of the nine bioactive metabolites, 2,3-butanediol was the only compound with both cytostatic and anti-EMT properties.},
}

@article {pmid37550887,
year = {2023},
author = {Hernández, M and Hereira-Pacheco, S and Alberdi, A and Díaz DE LA Vega-Pérez, AH and Estrada-Torres, A and Ancona, S and Navarro-Noya, YE},
title = {DNA metabarcoding reveals seasonal changes in diet composition across four arthropod-eating lizard species (Phrynosomatidae: Sceloporus).},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12755},
pmid = {37550887},
issn = {1749-4877},
support = {//Consejo Nacional de Ciencia y Tecnología (CONACyT)/ ; 205945//Infraestructura project/ ; 137748//Ciencia de Frontera project/ ; 883//Cátedras CONACyT project/ ; //Universidad Nacional Autónoma de México (UNAM)/ ; },
abstract = {Diet composition and its ecological drivers are rarely investigated in coexisting closely related species. We used a molecular approach to characterize the seasonal variation in diet composition in four spiny lizard species inhabiting a mountainous ecosystem. DNA metabarcoding revealed that the lizards Sceloporus aeneus, S. bicanthalis, S. grammicus, and S. spinosus mostly consumed arthropods of the orders Hemiptera, Araneae, Hymenoptera, and Coleoptera. The terrestrial lizards S. aeneus and S. bicanthalis mostly predated ants and spiders, whereas the arboreal-saxicolous S. grammicus and saxicolous S. spinosus largely consumed grasshoppers and leafhoppers. The taxonomic and phylogenetic diversity of the prey was higher during the dry season than the rainy season, likely because reduced prey availability in the dry season forced lizards to diversify their diets to meet their nutritional demands. Dietary and phylogenetic composition varied seasonally depending on the species, but only dietary composition varied with altitude. Seasonal dietary turnover was greater in S. spinosus than in S. bicanthalis, suggesting site-specific seasonal variability in prey availability; no other differences among species were observed. S. bicanthalis, which lives at the highest altitude in our study site, displayed interseasonal variation in diet breadth. Dietary differences were correlated with the species' feeding strategies and elevational distribution, which likely contributed to the coexistence of these lizard species in the studied geographic area and beyond.},
}

@article {pmid37549265,
year = {2023},
author = {Hung, TH and So, T and Thammavong, B and Chamchumroon, V and Theilade, I and Phourin, C and Bouamanivong, S and Hartvig, I and Gaisberger, H and Jalonen, R and Boshier, DH and MacKay, JJ},
title = {Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {33},
pages = {e2301603120},
doi = {10.1073/pnas.2301603120},
pmid = {37549265},
issn = {1091-6490},
support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Adaptation, Physiological/genetics ; *Acclimatization/genetics ; Genomics ; Climate Change ; },
abstract = {In the billion-dollar global illegal wildlife trade, rosewoods have been the world's most trafficked wild product since 2005. Dalbergia cochinchinensis and Dalbergia oliveri are the most sought-after rosewoods in the Greater Mekong Subregion. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here, we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic offset to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge of Vietnam suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on hotspots of genomic offset in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change.},
}

*Adaptation, Physiological/genetics
*Acclimatization/genetics
Genomics
Climate Change

@article {pmid37548791,
year = {2023},
author = {Rotini, A and Conte, C and Winters, G and Vasquez, MI and Migliore, L},
title = {Undisturbed Posidonia oceanica meadows maintain the epiphytic bacterial community in different environments.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {37548791},
issn = {1614-7499},
support = {COST-STSM- CA15121-39495//COST Action CA 15121 Mar Cons/ ; },
abstract = {Seagrasses harbour different and rich epiphytic bacterial communities. These microbes may establish intimate and symbiotic relationships with the seagrass plants and change according to host species, environmental conditions, and/or ecophysiological status of their seagrass host. Although Posidonia oceanica is one of the most studied seagrasses in the world, and bacteria associated with seagrasses have been studied for over a decade, P. oceanica's microbiome remains hitherto little explored. Here, we applied 16S rRNA amplicon sequencing to explore the microbiome associated with the leaves of P. oceanica growing in two geomorphologically different meadows (e.g. depth, substrate, and turbidity) within the Limassol Bay (Cyprus). The morphometric (leaf area, meadow density) and biochemical (pigments, total phenols) descriptors highlighted the healthy conditions of both meadows. The leaf-associated bacterial communities showed similar structure and composition in the two sites; core microbiota members were dominated by bacteria belonging to the Thalassospiraceae, Microtrichaceae, Enterobacteriaceae, Saprospiraceae, and Hyphomonadaceae families. This analogy, even under different geomorphological conditions, suggest that in the absence of disturbances, P. oceanica maintains characteristic-associated bacterial communities. This study provides a baseline for the knowledge of the P. oceanica microbiome and further supports its use as a putative seagrass descriptor.},
}

@article {pmid37546572,
year = {2023},
author = {Hernández-Alonso, G and Ramos-Madrigal, J and Sun, X and Scharff-Olsen, CH and Sinding, MS and Martins, NF and Ciucani, MM and Mak, SST and Lanigan, LT and Clausen, CG and Bhak, J and Jeon, S and Kim, C and Eo, KY and Cho, SH and Boldgiv, B and Gantulga, G and Unudbayasgalan, Z and Kosintsev, PA and Stenøien, HK and Gilbert, MTP and Gopalakrishnan, S},
title = {Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing.},
journal = {Ecology and evolution},
volume = {13},
number = {8},
pages = {e10404},
pmid = {37546572},
issn = {2045-7758},
abstract = {The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.},
}

@article {pmid37540022,
year = {2023},
author = {Balasubramaniam, HM and Tze Yan, F and Michelle JiaMin, L and Parimannan, S and Mutusamy, P and Jaya Jothi, S and Rajandas, H},
title = {Genome characterization of Dickeya solani bacteriophage W2B.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0045223},
doi = {10.1128/MRA.00452-23},
pmid = {37540022},
issn = {2576-098X},
abstract = {We have successfully characterized the complete genome sequence of the lytic Dickeya solani bacteriophage W2B, isolated from the Bunus Sewage Treatment Plant. The lytic phage from the Ningirsuvirus family has a 40,385-bp linear double-stranded DNA genome containing 51 coding sequences (CDSs).},
}

@article {pmid37530752,
year = {2023},
author = {Jiménez-Guerrero, I and López-Baena, FJ and Borrero-de Acuña, JM and Pérez-Montaño, F},
title = {Membrane vesicle engineering with "à la carte" bacterial-immunogenic molecules for organism-free plant vaccination.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.14323},
pmid = {37530752},
issn = {1751-7915},
support = {EMERGIA20_00048//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; ProyExcel_00450//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; //European Union NextGenerationEU/PRTR/ ; PID2019-107634RB-I00//Ministerio de Ciencia e Innovación/ ; PID2020-118279R (MCIN/AEI/10.13039/501100011033)//Ministerio de Ciencia e Innovación/ ; PID2021-122395OA-I00 (MCIN/AEI/ 10.13039/501100011)//Ministerio de Ciencia e Innovación/ ; TED2021-130357B-I00 (MCIN/AEI/ 10.13039/5011000110)//Ministerio de Ciencia e Innovación/ ; },
abstract = {The United Nations heralds a world population exponential increase exceeding 9.7 billion by 2050. This poses the challenge of covering the nutritional needs of an overpopulated world by the hand of preserving the environment. Extensive agriculture practices harnessed the employment of fertilizers and pesticides to boost crop productivity and prevent economic and harvest yield losses attributed to plagues and diseases. Unfortunately, the concomitant hazardous effects stemmed from such agriculture techniques are cumbersome, that is, biodiversity loss, soils and waters contaminations, and human and animal poisoning. Hence, the so-called 'green agriculture' research revolves around designing novel biopesticides and plant growth-promoting bio-agents to the end of curbing the detrimental effects. In this field, microbe-plant interactions studies offer multiple possibilities for reshaping the plant holobiont physiology to its benefit. Along these lines, bacterial extracellular membrane vesicles emerge as an appealing molecular tool to capitalize on. These nanoparticles convey a manifold of molecules that mediate intricate bacteria-plant interactions including plant immunomodulation. Herein, we bring into the spotlight bacterial extracellular membrane vesicle engineering to encase immunomodulatory effectors into their cargo for their application as biocontrol agents. The overarching goal is achieving plant priming by deploying its innate immune responses thereby preventing upcoming infections.},
}

@article {pmid37525683,
year = {2023},
author = {Giraud, É and Milon, G},
title = {[Elucidating and characterizing the dynamic biological processes that account for the sustainability of Leishmania populations].},
journal = {Medecine tropicale et sante internationale},
volume = {3},
number = {2},
pages = {},
pmid = {37525683},
issn = {2778-2034},
mesh = {Cricetinae ; Humans ; Mice ; Rats ; Animals ; *Leishmania ; Ecosystem ; *Leishmaniasis ; *Phlebotomus ; *Psychodidae ; Rodentia ; },
abstract = {To attempt resolving this issue accurately, it was necessary to anchor our experimental approaches in the observations and pioneering work of our predecessors, notably Alphonse Laveran, Louis Parrot, Edmond and Étienne Sergent. The latter, among other things, had identified as natural hosts of leishmaniasis, rodent populations with which hematophagous telmophagous sand fly populations cohabited closely.When human populations emerged in these natural ecosystems, after the sedentarization of Homo sapiens, more or less important disturbances would have led to a transition of sand fly hematophagy, from zoophilia, to zoo-anthropophilia and anthropophilia.The creation of infrastructures that allow the breeding and integration into experimental groups of both holobiont sand flies and holobiont laboratory rodents (rats, mice, hamsters, etc.) remains crucial. With such infrastructures, it becomes possible to grasp and characterize the multilateral dynamic processes - mostly clinically silent - that account for the biogenesis of tissue and/or cellular niches protecting populations of Leishmania developmental morphotypes, including those ensuring host-to-host transmission, albeit in small numbers.},
}

Cricetinae
Humans
Mice
Rats
Animals
*Leishmania
Ecosystem
*Leishmaniasis
*Phlebotomus
*Psychodidae
Rodentia

@article {pmid37520373,
year = {2023},
author = {Roy, A and Houot, B and Kushwaha, S and Anderson, P},
title = {Impact of transgenerational host switch on gut bacterial assemblage in generalist pest, Spodoptera littoralis (Lepidoptera: Noctuidae).},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1172601},
pmid = {37520373},
issn = {1664-302X},
abstract = {Diet composition is vital in shaping gut microbial assemblage in many insects. Minimal knowledge is available about the influence of transgenerational diet transition on gut microbial community structure and function in polyphagous pests. This study investigated transgenerational diet-induced changes in Spodoptera littoralis larval gut bacteriome using 16S ribosomal sequencing. Our data revealed that 88% of bacterial populations in the S. littoralis larval gut comprise Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The first diet transition experiment from an artificial diet (F0) to a plant diet (F1), cabbage and cotton, caused an alteration of bacterial communities in the S. littoralis larval gut. The second transgenerational diet switch, where F1 larvae feed on the same plant in the F2 generation, displayed a significant variation suggesting further restructuring of the microbial communities in the Spodoptera larval gut. F1 larvae were also challenged with the plant diet transition at the F2 generation (cabbage to cotton or cotton to cabbage). After feeding on different plant diets, the microbial assemblage of F2 larvae pointed to considerable differences from other F2 larvae that continued on the same diet. Our results showed that S. littoralis larval gut bacteriome responds rapidly and inexplicably to different diet changes. Further experiments must be conducted to determine the developmental and ecological consequences of such changes. Nevertheless, this study improves our perception of the impact of transgenerational diet switches on the resident gut bacteriome in S. littoralis larvae and could facilitate future research to understand the importance of symbiosis in lepidopteran generalists better.},
}

@article {pmid37516623,
year = {2023},
author = {Venegas, L and López, P and Derome, N and Yáñez, JM},
title = {Leveraging microbiome information for animal genetic improvement.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2023.07.004},
pmid = {37516623},
issn = {0168-9525},
abstract = {There is growing evidence that the microbiome influences host phenotypic variation. Incorporating information about the holobiont - the host and its microbiome - into genomic prediction models may accelerate genetic improvements in farmed animal populations. Importantly, these models must account for the indirect effects of the host genome on microbiome-mediated phenotypes.},
}

@article {pmid37511931,
year = {2023},
author = {Costa, DA and Dolbeth, M and Christoffersen, ML and Zúñiga-Upegui, PT and Venâncio, M and de Lucena, RFP},
title = {An Overview of Rhodoliths: Ecological Importance and Conservation Emergency.},
journal = {Life (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {37511931},
issn = {2075-1729},
support = {UIDB/04423/2020 and UIDP/04423/2020; CEECINST/00027/2021/CP2789/CT0001//Fundação para a Ciência e Tecnologia/ ; Finance Code 001; PDSE/Edital nº 47/2017//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; Edital nº 03/2016//Fundação de Apoio à Pesquisa do Estado da Paraíba/ ; },
abstract = {Red calcareous algae create bio-aggregations ecosystems constituted by carbonate calcium, with two main morphotypes: geniculate and non-geniculate structures (rhodoliths may form bio-encrustations on hard substrata or unattached nodules). This study presents a bibliographic review of the order Corallinales (specifically, rhodoliths), highlighting on morphology, ecology, diversity, related organisms, major anthropogenic influences on climate change and current conservation initiatives. These habitats are often widespread geographically and bathymetrically, occurring in the photic zone from the intertidal area to depths of 270 m. Due to its diverse morphology, this group offers a special biogenic environment that is favourable to epiphyte algae and a number of marine invertebrates. They also include holobiont microbiota made up of tiny eukaryotes, bacteria and viruses. The morphology of red calcareous algae and outside environmental conditions are thought to be the key forces regulating faunistic communities in algae reefs. The impacts of climate change, particularly those related to acidification, might substantially jeopardise the survival of the Corallinales. Despite the significance of these ecosystems, there are a number of anthropogenic stresses on them. Since there have been few attempts to conserve them, programs aimed at their conservation and management need to closely monitor their habitats, research the communities they are linked with and assess the effects they have on the environment.},
}

@article {pmid37508443,
year = {2023},
author = {Wuerz, M and Lawson, CA and Oakley, CA and Possell, M and Wilkinson, SP and Grossman, AR and Weis, VM and Suggett, DJ and Davy, SK},
title = {Symbiont Identity Impacts the Microbiome and Volatilome of a Model Cnidarian-Dinoflagellate Symbiosis.},
journal = {Biology},
volume = {12},
number = {7},
pages = {},
pmid = {37508443},
issn = {2079-7737},
support = {DP200100091//Australian Research Council discovery project/ ; 19-VUW-086//Marsden Fund/ ; },
abstract = {The symbiosis between cnidarians and dinoflagellates underpins the success of reef-building corals in otherwise nutrient-poor habitats. Alterations to symbiotic state can perturb metabolic homeostasis and thus alter the release of biogenic volatile organic compounds (BVOCs). While BVOCs can play important roles in metabolic regulation and signalling, how the symbiotic state affects BVOC output remains unexplored. We therefore characterised the suite of BVOCs that comprise the volatilome of the sea anemone Exaiptasia diaphana ('Aiptasia') when aposymbiotic and in symbiosis with either its native dinoflagellate symbiont Breviolum minutum or the non-native symbiont Durusdinium trenchii. In parallel, the bacterial community structure in these different symbiotic states was fully characterised to resolve the holobiont microbiome. Based on rRNA analyses, 147 unique amplicon sequence variants (ASVs) were observed across symbiotic states. Furthermore, the microbiomes were distinct across the different symbiotic states: bacteria in the family Vibrionaceae were the most abundant in aposymbiotic anemones; those in the family Crocinitomicaceae were the most abundant in anemones symbiotic with D. trenchii; and anemones symbiotic with B. minutum had the highest proportion of low-abundance ASVs. Across these different holobionts, 142 BVOCs were detected and classified into 17 groups based on their chemical structure, with BVOCs containing multiple functional groups being the most abundant. Isoprene was detected in higher abundance when anemones hosted their native symbiont, and dimethyl sulphide was detected in higher abundance in the volatilome of both Aiptasia-Symbiodiniaceae combinations relative to aposymbiotic anemones. The volatilomes of aposymbiotic anemones and anemones symbiotic with B. minutum were distinct, while the volatilome of anemones symbiotic with D. trenchii overlapped both of the others. Collectively, our results are consistent with previous reports that D. trenchii produces a metabolically sub-optimal symbiosis with Aiptasia, and add to our understanding of how symbiotic cnidarians, including corals, may respond to climate change should they acquire novel dinoflagellate partners.},
}

@article {pmid37491455,
year = {2023},
author = {von der Dunk, SHA and Hogeweg, P and Snel, B},
title = {Obligate endosymbiosis enables genome expansion during eukaryogenesis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {777},
pmid = {37491455},
issn = {2399-3642},
mesh = {Phylogeny ; *Eukaryotic Cells/metabolism ; *Symbiosis/genetics ; Biological Evolution ; Mitochondria/genetics ; },
abstract = {The endosymbiosis of an alpha-proteobacterium that gave rise to mitochondria was one of the key events in eukaryogenesis. One striking outcome of eukaryogenesis was a much more complex cell with a large genome. Despite the existence of many alternative hypotheses for this and other patterns potentially related to endosymbiosis, a constructive evolutionary model in which these hypotheses can be studied is still lacking. Here, we present a theoretical approach in which we focus on the consequences rather than the causes of mitochondrial endosymbiosis. Using a constructive evolutionary model of cell-cycle regulation, we find that genome expansion and genome size asymmetry arise from emergent host-symbiont cell-cycle coordination. We also find that holobionts with large host and small symbiont genomes perform best on long timescales and mimic the outcome of eukaryogenesis. By designing and studying a constructive evolutionary model of obligate endosymbiosis, we uncovered some of the forces that may drive the patterns observed in nature. Our results provide a theoretical foundation for patterns related to mitochondrial endosymbiosis, such as genome size asymmetry, and reveal evolutionary outcomes that have not been considered so far, such as cell-cycle coordination without direct communication.},
}

Phylogeny
*Eukaryotic Cells/metabolism
*Symbiosis/genetics
Biological Evolution
Mitochondria/genetics

@article {pmid37486074,
year = {2023},
author = {Li, Y and He, X and Lin, Y and Li, YX and Kamenev, GM and Li, J and Qiu, JW and Sun, J},
title = {Reduced chemosymbiont genome in the methane seep thyasirid and the cooperated metabolisms in the holobiont under anaerobic sediment.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13846},
pmid = {37486074},
issn = {1755-0998},
support = {LSKJ202203104//Science and Technology Innovation Project of Laoshan Laboratory/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 202241002//Fundamental Research Funds for the Central Universities/ ; 12101021//General Research Fund of Hong Kong Special Administrative Region/ ; KF2022NO03//Open Fund of CAS and Shandong Province Key Laboratory of Experimental Marine Biology/ ; tsqn202103036//Young Taishan Scholars Program of Shandong Province/ ; },
abstract = {Previous studies have deciphered the genomic basis of host-symbiont metabolic complementarity in vestimentiferans, bathymodioline mussels, vesicomyid clams and Alviniconcha snails, yet little is known about the chemosynthetic symbiosis in Thyasiridae-a family of Bivalvia regarded as an excellent model in chemosymbiosis research due to their wide distribution in both deep-sea and shallow-water habitats. We report the first circular thyasirid symbiont genome, named Candidatus Ruthturnera sp. Tsphm01, with a size of 1.53 Mb, 1521 coding genes and 100% completeness. Compared to its free-living relatives, Ca. Ruthturnera sp. Tsphm01 genome is reduced, lacking components for chemotaxis, citric acid cycle and de novo biosynthesis of small molecules (e.g. amino acids and cofactors), indicating it is likely an obligate intracellular symbiont. Nevertheless, the symbiont retains complete genomic components of sulphur oxidation and assimilation of inorganic carbon, and these systems were highly and actively expressed. Moreover, the symbiont appears well-adapted to anoxic environment, including capable of anaerobic respiration (i.e. reductions of DMSO and nitrate) and possession of a low oxygen-adapted type of cytochrome c oxidase. Analysis of the host transcriptome revealed its metabolic complementarity to the incomplete metabolic pathways of the symbiont and the acquisition of nutrients from the symbiont via phagocytosis and exosome. By providing the first complete genome of reduced size in a thyasirid symbiont, this study enhances our understanding of the diversity of symbiosis that has enabled bivalves to thrive in chemosynthetic habitats. The resources will be widely used in phylogenetic, geographic and evolutionary studies of chemosynthetic bacteria and bivalves.},
}

@article {pmid37485344,
year = {2023},
author = {Sakai, R and Goto-Inoue, N and Yamashita, H and Aimoto, N and Kitai, Y and Maruyama, T},
title = {Smart utilization of betaine lipids in the giant clam Tridacna crocea.},
journal = {iScience},
volume = {26},
number = {7},
pages = {107250},
pmid = {37485344},
issn = {2589-0042},
abstract = {The giant clam Tridacna crocea thrives in poorly nourished coral reef water by forming a holobiont with zooxanthellae and utilizing photosynthetic products of the symbiont. However, detailed metabolic crosstalk between clams and symbionts is elusive. Here, we discovered that the nonphosphorous microalgal betaine lipid DGCC (diacylglycerylcarboxy-hydroxymethylcholine) and its deacylated derivative GCC are present in all tissues and organs, including algae-free sperm and eggs, and are metabolized. Colocalization of DGCC and PC (phosphatidylcholine) evidenced by MS imaging suggested that DGCC functions as a PC substitute. The high content of GCC in digestive diverticula (DD) suggests that the algal DGCC was digested in DD for further utilization. Lipidomics analysis showing the organ-specific distribution pattern of DGCC species suggests active utilization of DGCC as membrane lipids in the clam. Thus, the utilization of zooxanthellal DGCC in animal cells is a unique evolutionary outcome in phosphorous-deficient coral reef waters.},
}

@article {pmid37481685,
year = {2023},
author = {Leiva, C and Pérez-Portela, R and Lemer, S},
title = {Genomic signatures suggesting adaptation to ocean acidification in a coral holobiont from volcanic CO2 seeps.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {769},
pmid = {37481685},
issn = {2399-3642},
mesh = {Animals ; *Carbon Dioxide ; *Anthozoa/genetics ; Ocean Acidification ; Hydrogen-Ion Concentration ; Seawater ; Genomics ; },
abstract = {Ocean acidification, caused by anthropogenic CO2 emissions, is predicted to have major consequences for reef-building corals, jeopardizing the scaffolding of the most biodiverse marine habitats. However, whether corals can adapt to ocean acidification and how remains unclear. We addressed these questions by re-examining transcriptome and genome data of Acropora millepora coral holobionts from volcanic CO2 seeps with end-of-century pH levels. We show that adaptation to ocean acidification is a wholistic process involving the three main compartments of the coral holobiont. We identified 441 coral host candidate adaptive genes involved in calcification, response to acidification, and symbiosis; population genetic differentiation in dinoflagellate photosymbionts; and consistent transcriptional microbiome activity despite microbial community shifts. Coral holobionts from natural analogues to future ocean conditions harbor beneficial genetic variants with far-reaching rapid adaptation potential. In the face of climate change, these populations require immediate conservation strategies as they could become key to coral reef survival.},
}

Animals
*Carbon Dioxide
*Anthozoa/genetics
Ocean Acidification
Hydrogen-Ion Concentration
Seawater
Genomics

@article {pmid37475177,
year = {2023},
author = {Carvalho, J and Morales, HE and Faria, R and Butlin, RK and Sousa, VC},
title = {Integrating Pool-seq uncertainties into demographic inference.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13834},
pmid = {37475177},
issn = {1755-0998},
support = {2020.00275.CEECIND//Fundação para a Ciência e a Tecnologia/ ; CEECINST/00032/2018/CP1523/CT0008//Fundação para a Ciência e a Tecnologia/ ; PD/BD/128350/2017//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-EVL/1614/2021//Fundação para a Ciência e a Tecnologia/ ; UIDB/00329/2020//Fundação para a Ciência e a Tecnologia/ ; 2021.09795.CPCA//Fundação para a Ciência e a Tecnologia/ ; ERC-2015-AdG-693030-BARRIERS//H2020 European Research Council/ ; RGY0081/2020//Human Frontier Science Program/ ; },
abstract = {Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool-seq sources of error. By jointly modelling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole-genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.},
}

@article {pmid37471099,
year = {2023},
author = {Mesny, F and Hacquard, S and Thomma, BP},
title = {Co-evolution within the plant holobiont drives host performance.},
journal = {EMBO reports},
volume = {},
number = {},
pages = {e57455},
doi = {10.15252/embr.202357455},
pmid = {37471099},
issn = {1469-3178},
support = {//Alexander von Humboldt-Stiftung (AvH)/ ; 390686111//Deutsche Forschungsgemeinschaft (DFG)/ ; ME 6064/1-1//Deutsche Forschungsgemeinschaftmeinschaft/ ; 101089198//European Resuscitation Council (ERC)/ ; },
abstract = {Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.},
}

@article {pmid37457347,
year = {2023},
author = {Ferrarezi, JA and Defant, H and de Souza, LF and Azevedo, JL and Hungria, M and Quecine, MC},
title = {Meta-omics integration approach reveals the effect of soil native microbiome diversity in the performance of inoculant Azospirillum brasilense.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1172839},
pmid = {37457347},
issn = {1664-462X},
abstract = {Plant growth promoting bacteria (PGPB) have been used as integrative inputs to minimize the use of chemical fertilizers. However, a holistic comprehension about PGPB-plant-microbiome interactions is still incipient. Furthermore, the interaction among PGPB and the holobiont (host-microbiome association) represent a new frontier to plant breeding programs. We aimed to characterize maize bulk soil and rhizosphere microbiomes in irradiated soil (IS) and a native soil (NS) microbial community gradient (dilution-to-extinction) with Azospirillum brasilense Ab-V5, a PGPB commercial inoculant. Our hypothesis was that plant growth promotion efficiency is a result of PGPB niche occupation and persistence according to the holobiont conditions. The effects of Ab-V5 and NS microbial communities were evaluated in microcosms by a combined approach of microbiomics (species-specific qPCR, 16S rRNA metataxonomics and metagenomics) and plant phenomics (conventional and high-throughput methods). Our results revealed a weak maize growth promoting effect of Ab-V5 inoculation in undiluted NS, contrasting the positive effects of NS dilutions 10[-3], 10[-6], 10[-9] and IS with Ab-V5. Alpha diversity in NS + Ab-V5 soil samples was higher than in all other treatments in a time course of 25 days after sowing (DAS). At 15 DAS, alpha diversity indexes were different between NS and IS, but similar in all NS dilutions in rhizospheric samples. These differences were not persistent at 25 DAS, demonstrating a stabilization process in the rhizobiomes. In NS 10[-3] +Ab-V5 and NS 10[-6] Ab-V5, Ab-V5 persisted in the maize rhizosphere until 15 DAS in higher abundances compared to NS. In NS + Ab-V5, abundance of six taxa were positively correlated with response to (a)biotic stresses in plant-soil interface. Genes involved in bacterial metabolism of riboses and amino acids, and cresol degradation were abundant on NS 10[-3] + Ab-V5, indicating that these pathways can contribute to plant growth promotion and might be a result of Ab-V5 performance as a microbial recruiter of beneficial functions to the plant. Our results demonstrated the effects of holobiont on Ab-V5 performance. The meta-omics integration supported by plant phenomics opens new perspectives to better understanding of inoculants-holobiont interaction and for developing better strategies for optimization in the use of microbial products.},
}

@article {pmid37437771,
year = {2023},
author = {Prosdocimi, F and Cortines, JR and José, MV and Farias, ST},
title = {Decoding viruses: An alternative perspective on their history, origins and role in nature.},
journal = {Bio Systems},
volume = {231},
number = {},
pages = {104960},
doi = {10.1016/j.biosystems.2023.104960},
pmid = {37437771},
issn = {1872-8324},
abstract = {This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.},
}

@article {pmid37423403,
year = {2023},
author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Quintanilla-Carvajal, MX and Díaz, LE and Alzate, JF and Junca, H and Rodríguez Orjuela, JA and Villamil Diaz, LM},
title = {Evaluation of dietary single probiotic isolates and probiotic multistrain consortia in growth performance, gut histology, gut microbiota, immune regulation, and infection resistance of Nile tilapia, Oreochromis niloticus, shows superior monostrain performance.},
journal = {Fish & shellfish immunology},
volume = {140},
number = {},
pages = {108928},
doi = {10.1016/j.fsi.2023.108928},
pmid = {37423403},
issn = {1095-9947},
abstract = {The probiotic potential of a designed bacterial consortia isolated from a competitive exclusion culture originally obtained from the intestinal contents of tilapia juveniles were evaluated on Nile tilapia alevins. The growth performance, intestinal histology, microbiota effects, resistance to Streptococcus agalactiae challenge, and immune response were assessed. In addition, the following treatments were included in a commercial feed: A12+M4+M10 (Lactococcus lactis A12, Priestia megaterium M4, and Priestia sp. M10), M4+M10 (P. megaterium M4, and Priestia sp. M10) and the single bacteria as controls; A12 (L. lactis A12), M4 (P. megaterium M4), M10 (Priestia sp. M10), also a commercial feed without any probiotic addition was included as a control. The results showed that all probiotic treatments improved the growth performance, intestinal histology, and resistance during experimental infection with S. agalactiae in comparison to the control fish. Also, the administration of probiotics resulted in the modulation of genes associated with the innate and adaptive immune systems that were non-dependent on microbial colonization. Surprisingly, L. lactis A12 alone induced benefits in fish compared to the microbial consortia, showing the highest increase in growth rate, survival during experimental infection with S. agalactiae, increased intestinal fold length, and the number of differentially expressed genes. Lastly, we conclude that a competitive exclusion culture is a reliable source of probiotics, and monostrain L. lactis A12 has comparable or even greater probiotic potential than the bacterial consortia.},
}

@article {pmid37415044,
year = {2023},
author = {King, NG and Uribe, R and Moore, PJ and Earp, HS and Gouraguine, A and Hinostroza, D and Perez-Matus, A and Smith, K and Smale, DA},
title = {Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37415044},
issn = {1432-184X},
abstract = {Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.},
}

@article {pmid37404156,
year = {2023},
author = {Hu, S and He, R and He, X and Zeng, J and Zhao, D},
title = {Niche-Specific Restructuring of Bacterial Communities Associated with Submerged Macrophyte under Ammonium Stress.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {7},
pages = {e0071723},
pmid = {37404156},
issn = {1098-5336},
mesh = {*Ammonium Compounds ; Bacteria ; *Microbiota ; Biomass ; Rhizosphere ; *Hydrocharitaceae ; },
abstract = {Submerged macrophytes and their epiphytic microbes form a "holobiont" that plays crucial roles in regulating the biogeochemical cycles of aquatic ecosystems but is sensitive to environmental disturbances such as ammonium loadings. Increasingly more studies suggest that plants may actively seek help from surrounding microbial communities whereby conferring benefits in responding to particular abiotic stresses. However, empirical evidence is scarce regarding how aquatic plants reconstruct their microbiomes as a "cry-for-help" against acute ammonium stress. Here, we investigated the temporal dynamics of the phyllosphere and rhizosphere bacterial communities of Vallisneria natans following ammonium stress and recovery periods. The bacterial community diversity of different plant niches exhibited opposite patterns with ammonium stress, that is, decreasing in the phyllosphere while increasing in the rhizosphere. Furthermore, both phyllosphere and rhizosphere bacterial communities underwent large compositional changes at the end of ammonium stress, significantly enriching of several nitrifiers and denitrifiers. Meanwhile, bacterial legacies wrought by ammonium stress were detected for weeks; some plant growth-promoting and stress-relieving bacteria remained enriched even after stress disappeared. Structural equation model analysis showed that the reshaped bacterial communities in plant niches collectively had a positive effect on maintaining plant biomass. Additionally, we applied an age-prediction model to predict the bacterial community's successional trajectory, and the results revealed a persistent change in bacterial community development under ammonium treatment. Our findings highlight the importance of plant-microbe interactions in mitigating plant stress and fostering a better understanding of the assembly of plant-beneficial microbes under ammonium stress in aquatic ecosystems. IMPORTANCE Increasing anthropogenic input of ammonium is accelerating the decline of submerged macrophytes in aquatic ecosystems. Finding efficient ways to release submerged macrophytes from ammonium stress is crucial to maintain their ecological benefits. Microbial symbioses can alleviate abiotic stress in plants, but harnessing these beneficial interactions requires a detailed understanding of plant microbiome responses to ammonium stress, especially over a continuous time course. Here, we tracked the temporal changes in bacterial communities associated with the phyllosphere and rhizosphere of Vallisneria natans during ammonium stress and recovery periods. Our results showed that severe ammonium stress triggers a plant-driven timely reshaping of the associated bacterial community in a niche-specific strategy. The reassembled bacterial communities could potentially benefit the plant by positively contributing to nitrogen transformation and plant growth promotion. These findings provide empirical evidence regarding the adaptive strategy of aquatic plants whereby they recruit beneficial microbes against ammonium stress.},
}

*Ammonium Compounds
Bacteria
*Microbiota
Biomass
Rhizosphere
*Hydrocharitaceae

@article {pmid37401172,
year = {2023},
author = {Hardoim, CCP and Hardoim, PR and Lôbo-Hajdu, G and Custódio, MR and Thomas, T},
title = {The microbiome of the sponge Aplysina caissara in two sites with different levels of anthropogenic impact.},
journal = {FEMS microbiology letters},
volume = {370},
number = {},
pages = {},
doi = {10.1093/femsle/fnad064},
pmid = {37401172},
issn = {1574-6968},
mesh = {Animals ; *Porifera ; Anthropogenic Effects ; Brazil ; Seawater ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Despite the important roles that marine sponges play in ecosystem functioning and structuring, little is known about how the sponge holobiont responds to local anthropogenic impacts. Here we assess the influence of an impacted environment (Praia Preta) on the microbial community associated with the endemic sponge Aplysina caissara in comparison to a less-impacted area (Praia do Guaecá) from the coast of São Paulo state (Brazil, southwestern Atlantic coast). We hypothesized that the local anthropogenic impacts will change the microbiome of A. caissara and that the community assembly will be driven by a different process (i.e. deterministic versus stochastic) under distinct levels of impact. The microbiome at the amplicon sequence variants level was found to be statistically distinct between sponges from the different sites, and this was also seen for the microbial communities of the surrounding seawater and sediments. Microbial communities of A. caissara from both sites were found to be assembled by deterministic processes, even though the sites presented distinct anthropogenic impacts, showing a pivotal role of the sponge host in selecting its own microbiome. Overall, this study revealed that local anthropogenic impacts altered the microbiome of A. caissara; however, assembly processes are largely determined by the sponge host.},
}

Animals
*Porifera
Anthropogenic Effects
Brazil
Seawater
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid37382454,
year = {2023},
author = {Liu, W and Cui, X and Wang, X and Shen, C and Ji, L and Zhang, M and Wong, MH and Zhang, J and Shan, S},
title = {Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019823},
doi = {10.1128/msystems.00198-23},
pmid = {37382454},
issn = {2379-5077},
abstract = {Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.},
}

@article {pmid37367660,
year = {2023},
author = {Sikorskaya, TV},
title = {Coral Lipidome: Molecular Species of Phospholipids, Glycolipids, Betaine Lipids, and Sphingophosphonolipids.},
journal = {Marine drugs},
volume = {21},
number = {6},
pages = {},
pmid = {37367660},
issn = {1660-3397},
mesh = {Animals ; *Anthozoa/microbiology ; Phospholipids ; Ecosystem ; Lipidomics ; Betaine ; Glycolipids ; Coral Reefs ; Phosphatidylcholines ; *Dinoflagellida ; Phosphatidylglycerols ; Symbiosis ; },
abstract = {Coral reefs are the most biodiversity-rich ecosystems in the world's oceans. Coral establishes complex interactions with various microorganisms that constitute an important part of the coral holobiont. The best-known coral endosymbionts are Symbiodiniaceae dinoflagellates. Each member of the coral microbiome contributes to its total lipidome, which integrates many molecular species. The present study summarizes available information on the molecular species of the plasma membrane lipids of the coral host and its dinoflagellates (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI), ceramideaminoethylphosphonate, and diacylglyceryl-3-O-carboxyhydroxymethylcholine), and the thylakoid membrane lipids of dinoflagellates (phosphatidylglycerol (PG) and glycolipids). Alkyl chains of PC and PE molecular species differ between tropical and cold-water coral species, and features of their acyl chains depend on the coral's taxonomic position. PS and PI structural features are associated with the presence of an exoskeleton in the corals. The dinoflagellate thermosensitivity affects the profiles of PG and glycolipid molecular species, which can be modified by the coral host. Coral microbiome members, such as bacteria and fungi, can also be the source of the alkyl and acyl chains of coral membrane lipids. The lipidomics approach, providing broader and more detailed information about coral lipid composition, opens up new opportunities in the study of biochemistry and ecology of corals.},
}

Animals
*Anthozoa/microbiology
Phospholipids
Ecosystem
Lipidomics
Betaine
Glycolipids
Coral Reefs
Phosphatidylcholines
*Dinoflagellida
Phosphatidylglycerols
Symbiosis