Environmental Microbiome最新文献

{"title":"Regional scale diversity and distribution of soil inhabiting Tetracladium.","authors":"Anna Lazar, Robert I Griffiths, Tim Goodall, Lisa R Norton, Ryan M Mushinski, Gary D Bending","doi":"10.1186/s40793-024-00646-6","DOIUrl":"10.1186/s40793-024-00646-6","url":null,"abstract":"<p><p>The genus Tetracladium has historically been regarded as an aquatic hyphomycete. However, sequencing of terrestrial ecosystems has shown that Tetracladium species might also be terrestrial soil and plant-inhabiting fungi. The diversity of Tetracladium species, their distribution across ecosystems, and the factors that shape community composition remain largely unknown. Using internal transcribed spacer (ITS) amplicon sequencing, we investigated the spatial distribution of Tetracladium in 970 soil samples representing the major ecosystems found across the British landscape. Species of the genus were found in 57% of the samples and across all vegetation types. The Tetracladium sequences we recovered included species common in aquatic ecosystems. However, we found five additional clades that clustered with environmental sequences previously found in terrestrial environments. The community composition of the Tetracladium OTUs was mainly related to vegetation type and soil pH. Strikingly, both taxon richness and overall abundance were highest in arable soils and showed positive relationships with soil pH. T. maxilliforme and a taxon of environmental sequences, Tetracladium group 1, was the biggest group, had the most relative abundance across ecosystems and was found in all vegetation types. Overall, this study provides insights into the community composition patterns of Tetracladium in terrestrial ecosystems and highlights the importance of vegetation characteristics in shaping Tetracladium communities.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"111"},"PeriodicalIF":6.2,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.","authors":"Yuki Amano, Rohan Sachdeva, Daniel Gittins, Karthik Anantharaman, Shufei Lei, Luis E Valentin-Alvarado, Spencer Diamond, Hikari Beppu, Teruki Iwatsuki, Akihito Mochizuki, Kazuya Miyakawa, Eiichi Ishii, Hiroaki Murakami, Alexander L Jaffe, Cindy Castelle, Adi Lavy, Yohey Suzuki, Jillian F Banfield","doi":"10.1186/s40793-024-00649-3","DOIUrl":"10.1186/s40793-024-00649-3","url":null,"abstract":"<p><strong>Background: </strong>Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO₂ and H₂ stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan.</p><p><strong>Results: </strong>We reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO₂ fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO₂-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity.</p><p><strong>Conclusions: </strong>Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"105"},"PeriodicalIF":6.2,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of pepper-maize intercropping on the physicochemical properties, microbial communities, and metabolites of rhizosphere and bulk soils.","authors":"Zeli Chen, Wenzhi Wang, Lu Chen, Peng Zhang, Zhenhuan Liu, Xukun Yang, Jinliang Shao, Yan Ding, Yanhua Mi","doi":"10.1186/s40793-024-00653-7","DOIUrl":"10.1186/s40793-024-00653-7","url":null,"abstract":"<p><strong>Background: </strong>Intercropping increases land use efficiency and farmland ecological diversity. However, little is understood about whether and how soil biota, metabolites, and nutrients change under interspecific competition among plants. Thus, this study aimed to explore the changes in the physicochemical properties, microbial communities, and metabolites of rhizosphere and bulk soils of pepper monocropping and pepper-maize intercropping systems.</p><p><strong>Results: </strong>Intercropping significantly increased the contents of available phosphorus (AP) and available potassium (AK), and decreased the pH value, whereas it had little effect on the total nitrogen (TN) and organic matter (OM) in the rhizosphere and bulk soils, compared with those in monocropping pepper. Moreover, the OM content was higher in rhizosphere soil than in bulk soil. The microbial community structures and metabolite profiles also differed between the two systems. The diversity of bacteria and fungi increased in intercropped pepper. The relative abundances of Actinobacteria, Chloroflexi, Cyanobacteria, and Ascomycota were higher while those of Proteobacteria, Planctomycetes, Mucoromycota, and Basidiomycota were significantly lower in the rhizosphere and bulk soils from the intercropping system than in those from the monocropping system. Linear discriminant analysis revealed that the predominant bacteria and fungi in the rhizosphere soil from the intercropping system belonged to the order Sphingomonadales and genera Nitrospira, Phycicoccus and Auricularia, whereas those in the bulk soil from the intercropping system belonged to the phylum Acidobacteria and genera Calocera, Pseudogymnoascus, and Trichosporon. Intercropping promoted the secretion of flavonoids, alkaloids, and nucleotides and their derivatives in the rhizosphere soil and significantly increased the contents of organoheterocyclic compounds in the bulk soil. Furthermore, the AP and AK contents, and pH value had strong positive correlations with bacteria. In addition, co-occurrence network analysis also showed that asebogenin, trachelanthamidine, 5-methyldeoxycytidine, and soil pH were the key factors mediating root-soil-microbe interactions.</p><p><strong>Conclusion: </strong>Intercropping can alter microbial community structures and soil metabolite composition in rhizosphere and bulk soils, enhancing soil nutrient contents, enriching soil beneficial microbes and secondary metabolites (flavonoids and alkaloids) of intercropped pepper, and provided a scientific basis for sustainable development in the pepper-maize intercropping system.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"108"},"PeriodicalIF":6.2,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Millennial-scale microbiome analysis reveals ancient antimicrobial resistance conserved despite modern selection pressures.","authors":"Sankaranarayanan Gomathinayagam, Swathi Kanagalingam, Srimathi Chandrasekaran, Thirumoorthy Krishnan, Gothandam Kodiveri Muthukaliannan","doi":"10.1186/s40793-024-00652-8","DOIUrl":"10.1186/s40793-024-00652-8","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance presents a formidable challenge, yet its existence predates the introduction of antibiotics. Our study delves into the presence of antimicrobial resistance genes (ARGs) in ancient permafrost microbiomes, comparing them with contemporary soil and pristine environments. Majority of the samples are from regions around Beringia, encompassing parts of Russia and Alaska, with only one sample originating from the Tien Shan Mountain range in Kyrgyzstan.</p><p><strong>Results: </strong>From over 2.3 tera basepairs of raw metagenomic data, retrieved from samples ranging in age from approximately 7,000 years to 1.1 million years, we assembled about 1.3 billion metagenomic contigs and explored the prevalence of ARGs within them. Our findings reveal a diverse array of ARGs in ancient microbiomes, akin to contemporary counterparts. On average, we identified 2 ARGs per rRNA gene in ancient samples. Actinomycetota, Bacillota, and several thermophiles were prominent carriers of ARGs in Chukochi and Kamchatkan samples. Conversely, ancient permafrost from the Tien Shan Mountain range exhibited no Thermophiles or Actinomycetota carrying ARGs. Both ancient and contemporary microbiomes showcased numerous divergent ARGs, majority of which have identity between 40 and 60% to genes in antibiotic resistance gene databases. To study the selection pressure on ARGs, we performed dN/dS analysis specifically on antibiotic inactivation-type ARGs, which exhibited purifying selection compared to contemporary genes.</p><p><strong>Conclusion: </strong>Antibiotic resistance has existed throughout microbial evolution and will likely persist, as microbes have the capacity to develop and retain resistance genes through evolutionary processes. The classes of antimicrobial resistance genes profiled and the function of antibiotic-inactivating enzymes from ancient permafrost microbiomes do not seem to be very different from the genes found in the antibiotic era. Additionally, we retrieved 359 putative complete viruses from ancient microbiomes and none of them harboured any ARGs.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"110"},"PeriodicalIF":6.2,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11657988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evidence of habitat specificity in sponge microbiomes from Antarctica.","authors":"Maria F Manrique-de-la-Cuba, Génesis Parada-Pozo, Susana Rodríguez-Marconi, Marileyxis R López-Rodríguez, Sebastián Abades, Nicole Trefault","doi":"10.1186/s40793-024-00648-4","DOIUrl":"10.1186/s40793-024-00648-4","url":null,"abstract":"<p><strong>Background: </strong>Marine sponges and their microbiomes are ecosystem engineers distributed across the globe. However, most research has focused on tropical and temperate sponges, while polar regions like Antarctica have been largely neglected. Despite its harsh conditions and geographical isolation, Antarctica is densely populated by sponges. In this study, we explored the extent of habitat specificity in the diversity, community composition, and microbial co-occurrence within Antarctic sponge microbiomes, in comparison to those from other marine environments. We used massive sequencing of 16S rRNA genes and integrated multiple databases to incorporate Antarctic sponges as a habitat in global microbiome analyses.</p><p><strong>Results: </strong>Our study revealed significant differences in microbial diversity and community composition between Antarctic and non-Antarctic sponges. We found that most microorganisms present in Antarctic sponges are unique to the South Shetland Islands. Nitrosomonas oligotropha, Candidatus Nitrosopumilus, Polaribacter, SAR116 clade, and Low Salinity Nitrite-Oxidizing Bacteria (LS-NOB) are microbial members characterizing the Antarctic sponge microbiomes. Based on their exclusivity and presence across different sponges worldwide, we identified habitat-specific and habitat-generalist bacteria associated with each habitat. They are particularly abundant and connected within all the Antarctic sponges, suggesting that they may play a crucial role as keystone species within these sponge ecosystems.</p><p><strong>Conclusions: </strong>This study provides significant insights into the microbial diversity and community composition of sponges in Antarctica and non-Antarctic ecoregions. Our findings provide evidence for habitat-specific patterns that differentiate the microbiomes of Antarctic sponges from elsewhere, indicating the strong influence of environmental selection and dispersal limitation wrapped into the Antarctic ecoregions to shape more similar microbial communities in distantly related sponges. This study contributes to understanding signatures of microbial community assembly in the Antarctic sponges and has important implications for the ecology and evolution of these unique marine environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"100"},"PeriodicalIF":6.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11619120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the bacterial diversity and potential of the Avicennia marina ecosystem for enhancing plant resilience to saline conditions.","authors":"Amal Khalaf Alghamdi, Sabiha Parween, Heribert Hirt, Maged M Saad","doi":"10.1186/s40793-024-00642-w","DOIUrl":"10.1186/s40793-024-00642-w","url":null,"abstract":"<p><strong>Background: </strong>Avicennia marina ecosystems are critical for coastal protection, water quality enhancement, and biodiversity support. These unique ecosystems thrive in extreme saline conditions and host a diverse microbiome that significantly contributes to plant resilience and growth. Global food security is increasingly threatened by crop yield losses due to abiotic stresses, including saline soils. Traditional plant breeding for salt tolerance is both costly and time-consuming. This study explores the potential of bacteria from A. marina to enhance plant growth under saline conditions, emphasizing their ecological significance.</p><p><strong>Results: </strong>We analyzed the microbiome of A. marina from the Red Sea coast using high-throughput Illumina sequencing and culture-dependent methods across various compartments (bulk soil, rhizosphere, rhizoplane, roots, and leaves). Our findings revealed distinct compartment-specific microbial communities, with Proteobacteria being the dominant phylum. Functional predictions indicated diverse microbial roles in metal uptake and plant growth promotion (PGP). Remarkably, our culture-dependent methods allowed us to recover 56% of the bacterial diversity present in the microbiome, resulting in the isolation and characterization of 256 bacterial strains. These isolates were screened for PGP traits, including salt and heat tolerance, siderophore production, and pectinase activity. Out of the 77 bacterial isolates tested, 11 demonstrated a significant ability to enhance Arabidopsis growth under salt stress.</p><p><strong>Conclusions: </strong>Our study highlights the ecological significance of mangrove microbiomes and the potential of culture collections in offering innovative solutions for ecological restoration and crop production in saline conditions. The unique collection of mangrove bacteria, particularly from the rhizosphere and endophytes, showcases significant PGP traits and stress tolerance capabilities. These findings emphasize the importance of functional traits, such as salt tolerance, in the recruitment of endophytic bacteria by plants over taxonomic affiliation. The identified bacterial strains hold potential not only for developing biofertilizers to improve crop productivity but also for ecological restoration projects aimed at rehabilitating saline-degraded lands, thereby contributing to overall ecosystem health and sustainability.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"101"},"PeriodicalIF":6.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11619459/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes.","authors":"Etienne Richy, Priscila Thiago Dobbler, Vojtěch Tláskal, Rubén López-Mondéjar, Petr Baldrian, Martina Kyselková","doi":"10.1186/s40793-024-00639-5","DOIUrl":"10.1186/s40793-024-00639-5","url":null,"abstract":"<p><strong>Background: </strong>Deadwood decomposition is an essential ecological process in forest ecosystems, playing a key role in nutrient cycling and carbon sequestration by enriching soils with organic matter. This process is driven by diverse microbial communities encompassing specialized functions in breaking down organic matter, but the specific roles of individual microorganisms in this process are still not fully understood.</p><p><strong>Results: </strong>Here, we characterized the deadwood microbiome in a natural mixed temperate forest in Central Europe using PacBio HiFi long-read sequencing and a genome-resolved transcriptomics approach in order to uncover key microbial contributors to wood decomposition. We obtained high quality assemblies, which allowed attribution of complex microbial functions such as nitrogen fixation to individual microbial taxa and enabled the recovery of metagenome-assembled genomes (MAGs) from both abundant and rare deadwood bacteria. We successfully assembled 69 MAGs (including 14 high-quality and 7 single-contig genomes) from 4 samples, representing most of the abundant bacterial phyla in deadwood. The MAGs exhibited a rich diversity of carbohydrate-active enzymes (CAZymes), with Myxococcota encoding the highest number of CAZymes and the full complement of enzymes required for cellulose decomposition. For the first time we observed active nitrogen fixation by Steroidobacteraceae, as well as hemicellulose degradation and chitin recycling by Patescibacteria. Furthermore, PacBio HiFi sequencing identified over 1000 biosynthetic gene clusters, highlighting a vast potential for secondary metabolite production in deadwood, particularly in Pseudomonadota and Myxococcota.</p><p><strong>Conclusions: </strong>PacBio HiFi long-read sequencing offers comprehensive insights into deadwood decomposition processes by advancing the identification of functional features involving multiple genes. It represents a robust tool for unraveling novel microbial genomes in complex ecosystems and allows the identification of key microorganisms contributing to deadwood decomposition.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"99"},"PeriodicalIF":6.2,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142773853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.","authors":"Alexandre J Paquette, Srijak Bhatnagar, Agasteswar Vadlamani, Timber Gillis, Varada Khot, Breda Novotnik, Hector De la Hoz Siegler, Marc Strous, Jayne E Rattray","doi":"10.1186/s40793-024-00632-y","DOIUrl":"10.1186/s40793-024-00632-y","url":null,"abstract":"<p><strong>Background: </strong>Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.</p><p><strong>Results: </strong>Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.</p><p><strong>Conclusions: </strong>Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"98"},"PeriodicalIF":6.2,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11606062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phage-induced disturbance of a marine sponge microbiome.","authors":"Leon X Steiner, Lara Schmittmann, Tanja Rahn, Tim Lachnit, Martin T Jahn, Ute Hentschel","doi":"10.1186/s40793-024-00637-7","DOIUrl":"10.1186/s40793-024-00637-7","url":null,"abstract":"<p><strong>Background: </strong>Bacteriophages are known modulators of community composition and activity in environmental and host-associated microbiomes. However, the impact single phages have on bacterial community dynamics under viral predation, the extent and duration of their effect, are not completely understood. In this study, we combine morphological and genomic characterization of a novel marine phage, isolated from the Baltic sponge Halichondria panicea, and report on first attempts of controlled phage-manipulation of natural sponge-associated microbiomes.</p><p><strong>Results: </strong>We used culture-based and culture-independent (16S rRNA gene amplicon sequencing) methods to investigate bacterial community composition and dynamics in sponge microbiomes with and without the addition of phages. Upon application of a novel Maribacter specialist phage Panino under controlled conditions, we were able to detect community-wide shifts in the microbiome composition and load after 72 h. While bacterial community composition became more dissimilar over time in the presence of phages, species evenness and richness were maintained. Upon phage exposure, we observed the loss of several low-abundance constituent taxa of the resident microbiota, while other originally underrepresented taxa increased. Virulent phages likely induce community-wide disturbances, evident in changes in the total sponge microbial profile by specific elimination of constituent taxa, which leads to an increase in bacterial abundance of opportunistic taxa, such as the genera Vibrio, Pseudoalteromonas, and Photobacterium.</p><p><strong>Conclusions: </strong>Our findings suggest that sponge microbiome diversity and, by extension, its resilience depend on the maintenance of resident bacterial community members, irrespective of their abundance. Phage-induced disturbances can significantly alter community structure by promoting the growth of opportunistic bacteria like Vibrio and shifting the microbiome to a dysbiotic state. These insights highlight the role of bacteriophages in shaping microbiome dynamics and underscore the potential for phage application in managing bacterial community composition in marine host-associated environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"97"},"PeriodicalIF":6.2,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11590407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142733534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the biosynthesis potential of permafrost microbiomes.","authors":"Aileen Ute Geers, Yannick Buijs, Morten Dencker Schostag, Bo Elberling, Mikkel Bentzon-Tilia","doi":"10.1186/s40793-024-00644-8","DOIUrl":"10.1186/s40793-024-00644-8","url":null,"abstract":"<p><strong>Background: </strong>Permafrost microbiomes are of paramount importance for the biogeochemistry of high latitude soils and while endemic biosynthetic domain sequences involved in secondary metabolism have been found in polar surface soils, the biosynthetic potential of permafrost microbiomes remains unexplored. Moreover, the nature of these ecosystems facilitates the unique opportunity to study the distribution and diversity of biosynthetic genes in relic DNA from ancient microbiomes. To explore the biosynthesis potential in permafrost, we used adenylation (AD) domain sequencing to evaluate non-ribosomal peptide (NRP) production in permafrost cores housing microbiomes separated at kilometer and kiloyear scales.</p><p><strong>Results: </strong>Permafrost microbiomes represented NRP repertoires significantly different from that of temperate soil microbiomes, but as for temperate soils, the estimated domain richness and diversity was strongly correlated to the bacterial taxonomic diversity across locations. Furthermore, we found significant differences in both community composition and AD domain composition across geographical and temporal distances. Overall, the vast majority of biosynthetic domains showed below 90% amino acid similarity to characterized BGCs, confirming the high degree of novelty of NRPs inherent to permafrost microbiomes. Using available metagenomic sequences, we further identified a high biosynthetic diversity beyond NRPs throughout arctic surface soils down to deep and ancient (megayear old) permafrost microbiomes.</p><p><strong>Conclusion: </strong>We have shown that arctic permafrost microbiomes harbor a unique biosynthetic repertoire rich in hitherto undescribed NRPs. This diversity is driven by geographic separation across kilometer scales and by the bacterial taxonomic diversity between microbiomes confined in separate permafrost layers. Hence the permafrost biome represents a unique resource for studying secondary metabolism, and potentially for the discovery of novel drug leads.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"96"},"PeriodicalIF":6.2,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11583570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}