ISME communications最新文献

{"title":"Evaluating agar-plating and dilution-to-extinction isolation methods for generating oak-associated microbial culture collections.","authors":"Alejandra Ordonez, Usman Hussain, Marine C Cambon, Peter N Golyshin, Jim Downie, James E McDonald","doi":"10.1093/ismeco/ycaf019","DOIUrl":"10.1093/ismeco/ycaf019","url":null,"abstract":"<p><p>Microbial isolation methods are crucial for producing comprehensive microbial culture collections that reflect the richness and diversity of natural microbiotas. Few studies have focused on isolation of plant-associated microbiota, with even less focus on forest trees. Here, we tested two isolation methods, (i) agar plating and (ii) dilution-to-extinction, for isolation of microbiota from leaf, stem, and root/rhizosphere tissues of oak trees. Microbial isolates obtained (culture-dependent) and the endogenous oak microbiota of the source tissue samples (culture-independent) were characterized by 16S rRNA gene and ITS community profiling. We found that the type of growth medium, incubation conditions, and sample type inoculated onto agar influenced the number of isolates and taxonomic richness of the isolates obtained. Most bacterial and fungal ASVs obtained from isolation-based approaches were only obtained using one of the two isolation methods, with only 12% of the ASVs detected in both. Moreover, the isolation methods captured microorganisms not detected by culture-independent analysis of the microbiota, suggesting these approaches can complement culture-independent analysis by enriching low-abundant taxa. Our results suggest that dilution-to-extinction and agar-plating approaches captured distinct fractions of the oak microbiota, and that a combination of both isolation methods was required to produce taxonomically richer microbial culture collections.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf019"},"PeriodicalIF":5.1,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Terrestrial-aquatic connectivity structures microbial communities during the formation of thermokarst lakes.","authors":"Martial Leroy, Melanie S Burnett, Isabelle Laurion, Peter M J Douglas, Cynthia M Kallenbach, Jérôme Comte","doi":"10.1093/ismeco/ycaf027","DOIUrl":"10.1093/ismeco/ycaf027","url":null,"abstract":"<p><p>Rising air temperatures and permafrost degradation drive the erosion of palsas (permafrost mounds mainly composed of frozen peat and ice layers) and lead to the formation of thermokarst ponds and lakes, known for their high greenhouse gas (GHG) emissions. This study investigates the impact of permafrost soil erosion during thermokarst lake formation on microbial community structure and its implications for GHG dynamics in a highly degraded permafrost valley (Nunavik, northern Quebec, Canada). Samples were collected from a palsa, an emerging lake connected to the palsa, surrounding peat and soil pore water, and two mature lakes which are older, stratified, and less connected to the palsa. Analysis of total and potentially active microbial communities, based on 16S rRNA gene amplicon sequence variants revealed significant changes in taxonomic and phylogenetic diversity during thermokarst lake formation. We found distinct assembly processes depending on the stage of formation. Firstly stochastics, they became more deterministic as lakes mature. Distinct methanogens/trophs communities in emerging lake led to lower CO₂:CH₄ ratio compared to the surface of mature lakes. Which presented a greater diversity of methanogens and distinct methanotrophic communities, with acetogenic, hydrogenotrophic and methylotrophic methanogens along anaerobic an aerobic methanotrophs. Multivariate analyses revealed that selection processes were primarily driven by concentrations of CH₄, CO₂, and NO₃ ^-. The interplay between the nitrogen and carbon cycles appears to be pivotal in these assemblages, with nitrogen playing key roles on community structure. These findings underscore the significance of terrestrial-aquatic connectivity in shaping microbial communities and GHG emissions in thermokarst lakes.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf027"},"PeriodicalIF":5.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distinct phytoplankton size classes respond differently to biotic and abiotic factors.","authors":"Stefanie Eyring, Ewa Merz, Marta Reyes, Pinelopi Ntetsika, Stuart R Dennis, Peter D F Isles, Sreenath Kyathanahally, Marco Baity-Jesi, Sze-Wing To, Agostino Merico, Francesco Pomati","doi":"10.1093/ismeco/ycae148","DOIUrl":"10.1093/ismeco/ycae148","url":null,"abstract":"<p><p>The interplay between abiotic (resource supply, temperature) and biotic (grazing) factors determines growth and loss processes in phytoplankton through resource competition and trophic interactions, which are mediated by morphological traits like size. Here, we study the relative importance of grazers, water physics, and chemistry on the daily net accumulation rates (ARs) of individual phytoplankton from natural communities, grouped into six size classes from circa 10 to 500 μm. Using a Random Forest modelling approach and 4 years of daily data from a lake, we find that water temperature is generally a pivotal control of all phytoplankton ARs. At the same time, nutrients and light are important for the smallest and the largest classes. Mesozooplankton abundance is a key predictor of the AR for small phytoplankton, with microzooplankton being important for the middle-size range. In our data, large and small phytoplankton have different (seasonal) blooming patterns: small forms are favoured by low temperature and grazing, and high phosphorus levels. Larger forms show positive ARs at high temperatures and low phosphorus (being relatively insensitive to zooplankton grazing). These results help us understand the opportunities and limitations of using size to explain and model phytoplankton responses to biotic and abiotic environmental change.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae148"},"PeriodicalIF":5.1,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Different intestinal ecological niches drive the divergent evolution of probiotics in the gut.","authors":"Zhe Han, Denggao Huang, Xinlei Liu, Wenyao Ma, Weipeng Cui, Shuaiming Jiang, Dongyu Zhen, Jiachao Zhang","doi":"10.1093/ismeco/ycaf023","DOIUrl":"10.1093/ismeco/ycaf023","url":null,"abstract":"<p><p>Previously, we described the divergent evolution of probiotics in the gut, which potentially compromises their health-promoting effects. Here, we employed a spatiotemporal multiomic approach to explore the distribution and evolutionary trends of the probiotic <i>Lactiplantibacillus plantarum</i> HNU082 (Lp082) in specific-pathogen-free and monocolonized mouse models. Initially, after establishing the inherent differences in the gut microbiota between the small and large intestines, we observed that the small intestine served as the main site for Lp082 survival and colonization. Subsequently, we discovered that the small intestine was the sole site where Lp082 exhibited divergent evolution. Moreover, our research indicated that Lp082 had a more substantial impact on the small-intestinal microbiota than on the large-intestinal microbiota. Consequently, we observed a significantly greater number of closely associated species coevolving with Lp082 in the small intestine than in the large intestine. This suggests that Lp082 faced higher selective pressures within the small intestine, potentially leading to the emergence of a greater number of mutants. Our findings will contribute to the differentiated application of probiotics, enhancing their beneficial effects, and offer insights into the targeted domestication of probiotic strains.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf023"},"PeriodicalIF":5.1,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selective enrichment of high-affinity clade II N₂O-reducers in a mixed culture.","authors":"Michele Laureni, Francesc Corbera-Rubio, DaeHyun Daniel Kim, Savanna Browne, Nina Roothans, David G Weissbrodt, Karel Olavaria, Nadieh de Jonge, Sukhwan Yoon, Martin Pabst, Mark C M van Loosdrecht","doi":"10.1093/ismeco/ycaf022","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf022","url":null,"abstract":"<p><p>Microorganisms encoding for the N₂O reductase (NosZ) are the only known biological sink of the potent greenhouse gas N₂O and are central to global N₂O mitigation efforts. Clade II NosZ populations are of particular biotechnological interest as they usually feature high N₂O affinities and often lack other denitrification genes. We focus on the yet-unresolved ecological constraints selecting for different N₂O-reducers strains and controlling the assembly of N₂O-respiring communities. Two planktonic N₂O-respiring mixed cultures were enriched at low dilution rates under limiting and excess dissolved N₂O availability to assess the impact of substrate affinity and N₂O cytotoxicity, respectively. Genome-resolved metaproteomics was used to infer the metabolism of the enriched populations. Under N₂O limitation, clade II N₂O-reducers fully outcompeted clade I affiliates, a scenario previously only theorized based on pure-cultures. All enriched N₂O-reducers encoded and expressed the sole clade II NosZ, while also possessing other denitrification genes. Two <i>Azonexus</i> and <i>Thauera</i> genera affiliates dominated the culture, and we hypothesize their coexistence to be explained by the genome-inferred metabolic exchange of cobalamin intermediates. Under excess N₂O, clade I and II populations coexisted; yet, proteomic evidence suggests that clade II affiliates respired most of the N₂O, <i>de facto</i> outcompeting clade I affiliates. The single dominant N₂O-reducer (genus <i>Azonexus</i>) notably expressed most cobalamin biosynthesis marker genes, likely to contrast the continuous cobalamin inactivation by dissolved cytotoxic N₂O concentrations (400 μM). Ultimately, our results strongly suggest the solids dilution rate to play a pivotal role in controlling the selection among NosZ clades, albeit the conditions selecting for genomes possessing the sole <i>nosZ</i> remain elusive. We furthermore highlight the potential significance of N₂O-cobalamin interactions in shaping the composition of N₂O-respiring microbiomes.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf022"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits.","authors":"Yoshiaki Sato","doi":"10.1093/ismeco/ycaf021","DOIUrl":"10.1093/ismeco/ycaf021","url":null,"abstract":"<p><p>Rumen deoxyribonucleic acid viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen deoxyribonucleic acid virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high vs low carcass weight cattle and high vs low marbling cattle. Viruses associated with <i>Methanobrevibacter</i> were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf021"},"PeriodicalIF":5.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prophage dynamics in gastric and enterohepatic environments: unraveling ecological barriers and adaptive transitions.","authors":"Marta Proença, Luís Tanoeiro, James G Fox, Filipa F Vale","doi":"10.1093/ismeco/ycaf017","DOIUrl":"10.1093/ismeco/ycaf017","url":null,"abstract":"<p><p>Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the <i>Helicobacter</i> genus remain inadequately studied. <i>Helicobacter</i> species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g. <i>Helicobacter pylori</i>) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-<i>pylori Helicobacter</i> genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalog of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. <i>Helicobacter cinaedi</i> stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts-though exceptions, such as the enterohepatic prophages from <i>H. canis</i>, <i>H. equorum</i>, <i>H. jaachi</i>, and the gastric prophage from <i>H. himalayensis</i>-suggesting more complex co-evolutionary dynamics like host jumps, recombination, and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in <i>Helicobacter</i>, emphasizing their role in bacterial adaptation, virulence, and host specificity.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf017"},"PeriodicalIF":5.1,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143470081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Puzzling out the ecological niche construction for nitrogen fixers in a coastal upwelling system.","authors":"Marcos Fontela, Daniel Fernández-Román, Esperanza Broullón, Hanna Farnelid, Ana Fernández-Carrera, Emilio Marañón, Sandra Martínez-García, Tamara Rodríguez-Ramos, Marta M Varela, Beatriz Mouriño-Carballido","doi":"10.1093/ismeco/ycaf018","DOIUrl":"10.1093/ismeco/ycaf018","url":null,"abstract":"<p><p>Diazotrophs are a diverse group of microorganisms that can fertilize the ocean through biological nitrogen fixation (BNF). Due to the high energetic cost of this process, diazotrophy in nitrogen-replete regions remains enigmatic. We use multidisciplinary observations to propose a novel framework for the ecological niche construction of nitrogen fixers in the upwelling region off NW Iberia-one of the most productive coastal regions in Europe-characterized by weak and intermittent wind-driven upwelling and the presence of bays. The main diazotroph detected (UCYN-A2) was more abundant and active during summer and early autumn, coinciding with relatively high temperatures (>16°C), low nitrogen:phosphorus ratios (N:P < 7.2), and a large contribution of ammonium (>75%) to the total dissolved inorganic nitrogen available. Furthermore, nutrient amendment experiments showed that BNF is detectable when phytoplankton biomass and productivity are nitrogen limited. Seasonally recurrent biogeochemical processes driven by hydrography create an ecological niche for nitrogen fixers in this system. During the spring-summer upwelling, nondiazotroph autotrophs consume nitrate and produce organic matter inside the bays. Thereafter, the combined effect of intense remineralization on the shelf and sustained positive circulation within the bays in late summer-early autumn, conveys enhanced ammonium content and excess phosphate into the warm surface layer. The low N:P ratio confers a competitive advantage to diazotrophs since they are not restricted by nitrogen supply. The new nitrogen supply mediated by BNF could extend the productivity period, and may be a key reason why upwelling bays are more productive than upwelled offshore waters.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf018"},"PeriodicalIF":5.1,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamics of bacterial growth, and life-history tradeoffs, explain differences in soil carbon cycling due to land-use.","authors":"Cassandra J Wattenburger, Evangeline Wang, Daniel H Buckley","doi":"10.1093/ismeco/ycaf014","DOIUrl":"10.1093/ismeco/ycaf014","url":null,"abstract":"<p><p>Soil contains a considerable fraction of Earth's organic carbon. Bacterial growth and mortality drive the microbial carbon pump, influencing carbon use efficiency and necromass production, key determinants for organic carbon persistence in soils. However, bacterial growth dynamics in soil are poorly characterized. We used an internal standard approach to normalize 16S ribosomal RNA gene sequencing data allowing us to quantify growth dynamics for 30 days following plant litter input to soil. We show that clustering taxa into three groups optimized variation of bacterial growth parameters in situ. These three clusters differed significantly with respect to their lag time, growth rate, growth duration, and change in abundance due to growth (ΔN_g) and mortality (ΔN_d), matching predictions of Grime's CSR life-history framework. In addition, we show a striking relationship between ΔN_g and ΔN_d, which reveals that growth in soil is tightly coupled to death. This result suggests a fitness paradox whereby some bacteria can optimize fitness in soil by minimizing mortality rather than maximizing growth. We hypothesized that land-use constrains microbial growth dynamics by favoring different life-history strategies and that these constraints control carbon mineralization. We show that life-history groups vary in prevalence with respect to land-use, and that bacterial growth dynamics correlated with carbon mineralization rate and net growth efficiency. Meadow soil supported more bacterial growth, greater mortality, and higher growth efficiency than agricultural soils, pointing toward more efficient conversion of plant litter into microbial necromass, which should promote long-term C stabilization.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf014"},"PeriodicalIF":5.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the influence of microbial necromass on subsurface microbiomes: metabolite utilization and community dynamics.","authors":"Brianna K Finley, Brandon C Enalls, Markus de Raad, Mariam Al Said, Mingfei Chen, Dominique C Joyner, Terry C Hazen, Trent R Northen, Romy Chakraborty","doi":"10.1093/ismeco/ycaf006","DOIUrl":"10.1093/ismeco/ycaf006","url":null,"abstract":"<p><p>The role of microbial necromass (nonliving microbial biomass), a significant component of belowground organic carbon, in nutrient cycling and its impact on the dynamics of microbial communities in subsurface systems remains poorly understood. It is currently unclear whether necromass metabolites from various microbes are different, whether certain groups of metabolites are preferentially utilized over others, or whether different microbial species respond to various necromass metabolites. In this study, we aimed to fill these knowledge gaps by designing enrichments with necromass as the sole nutrient source for subsurface microbial communities. We used the soluble fraction of necromass from bacterial isolates belonging to <i>Arthrobacter</i>, <i>Agrobacterium</i>, and <i>Pseudomonas</i> genera, and our results indicate that metabolite composition of necromass varied slightly across different strains but generally included amino acids, organic acids, and nucleic acid constituents. <i>Arthrobacter</i>-derived necromass appeared more recalcitrant. Necromass metabolites enriched diverse microbial genera, particularly <i>Massilia</i> sp. responded quickly regardless of the necromass source. Despite differences in necromass utilization, microbial community composition converged rapidly over time across the three different necromass amendments. Uracil, xanthine, valine, and phosphate-containing isomers were generally depleted over time, indicating microbial assimilation for maintenance and growth. However, numerous easily assimilable metabolites were not significantly depleted, suggesting efficient necromass recycling and the potential for necromass stabilization in systems. This study highlights the dynamic interactions between microbial necromass metabolites and subsurface microbial communities, revealing both selective utilization and rapid community and necromass convergence regardless of the necromass source.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf006"},"PeriodicalIF":5.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}