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Correction to: Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat. 修正:氧化还原决定了水饱和融化的永久冻土泥炭的温室气体产生动力学和代谢特性。
IF 6.4
ISME communications Pub Date : 2026-07-03 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycaf111
{"title":"Correction to: Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat.","authors":"","doi":"10.1093/ismeco/ycaf111","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf111","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycaf009.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycaf111"},"PeriodicalIF":6.4,"publicationDate":"2026-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13331343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148392627","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}
引用次数: 0
Microbial community shifts in deposits from the 2018 Palu-Donggala tsunami. 2018年帕鲁-东加拉海啸后沉积物中微生物群落的变化。
IF 6.4
ISME communications Pub Date : 2026-07-03 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag114
Wenshu Yap, Adam D Switzer, Jędrzej M Majewski, Winona Wijaya, Ezequiel Santillan, Rachel Y S Guan, Benjamin P Horton, Benazir Benazir, Ella Meilianda, Federico M Lauro
{"title":"Microbial community shifts in deposits from the 2018 Palu-Donggala tsunami.","authors":"Wenshu Yap, Adam D Switzer, Jędrzej M Majewski, Winona Wijaya, Ezequiel Santillan, Rachel Y S Guan, Benjamin P Horton, Benazir Benazir, Ella Meilianda, Federico M Lauro","doi":"10.1093/ismeco/ycag114","DOIUrl":"10.1093/ismeco/ycag114","url":null,"abstract":"<p><p>The 2018 Palu-Donggala earthquake in Indonesia generated a devastating tsunami, despite originating from a strike-slip fault, which typically does not produce significant tsunamis. This tsunami was triggered by a combination of subaerial landslides, liquefaction, and submarine landslides. Here, we present the first application of sedimentary environmental DNA to characterize microbial community changes in deposits from a landslide-triggered tsunami. Sediment samples collected 2 months after the event provide a rare snapshot of the near-immediate microbial response to tsunami disturbance. Microbial assemblages derived from 16S rRNA gene sequencing clearly distinguished tsunami deposits from pre-tsunami samples across three sites in Palu Bay, even where conventional sedimentary evidence was inconclusive. The community composition varied among sites, suggesting site-specific environmental filters, which explain the absence of a universal tsunami microbial signature. Tsunami deposits were associated with microbial communities shaped by strong environmental disturbance linked to saline inundation and geochemical change. Microbial communities in the Palu tsunami deposits provide new insight into early microbial responses to extreme coastal flooding events.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag114"},"PeriodicalIF":6.4,"publicationDate":"2026-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13335651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148439232","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}
引用次数: 0
The larval gut as a mirror: bacterial community composition and functional potential of mayfly larvae reflect site and seasonality differences. 幼虫肠道作为镜子:蜉蝣幼虫的细菌群落组成和功能潜力反映了地点和季节的差异。
IF 6.4
ISME communications Pub Date : 2026-07-03 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag192
Rubén Martínez-Cuesta, Rebecca Hoess, Juergen Geist, Michael Schloter, Stefanie Schulz
{"title":"The larval gut as a mirror: bacterial community composition and functional potential of mayfly larvae reflect site and seasonality differences.","authors":"Rubén Martínez-Cuesta, Rebecca Hoess, Juergen Geist, Michael Schloter, Stefanie Schulz","doi":"10.1093/ismeco/ycag192","DOIUrl":"10.1093/ismeco/ycag192","url":null,"abstract":"<p><p>Land use intensification is a major driver of biodiversity loss across ecosystems, yet its consequences for host-associated microbiomes in freshwater food webs remain poorly understood. In this case study, we used the gut microbiome of mayfly larvae (<i>Ephemera danica</i>) as a sensitive biological interface to assess how site-specific adjacent land use types shape microbial community composition and functions in stream ecosystems. Larvae were sampled in summer and autumn from sites adjacent to forest, extensive grassland, and intensive agriculture along the Otterbach stream (Bavarian Forest, Germany). Combining 16S ribosomal RNA (rRNA) amplicon sequencing with long-read metagenomics, we show that site-specific land use, in interaction with seasonality, significantly restructures larval gut bacterial communities without affecting alpha diversity. Rather than introducing distinct agriculturally derived taxa, agricultural land use acted as a selective environmental filter, enriching bacterial groups with specific functional traits. Taxa enriched in the sites adjacent to agricultural sites harboured genes involved in complex carbon and xenobiotic degradation, short-chain fatty acid production, efflux pumps, and stress response. These functional signatures were further supported by 14 metagenome-assembled genomes linked to these enriched taxa. Together, our results reveal that site in combination with seasonality not only reshaped bacterial community composition without affecting alpha diversity but also triggered shifts in the abundance of genes involved in microbial-host interactions and degradation pathways in <i>E. danica</i> larvae. This study also highlights the larval gut microbiome as a sensitive indicator of environmental change, suggesting that environmental microbial shifts may have cascading consequences for freshwater trophic interactions and ecosystem functioning.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag192"},"PeriodicalIF":6.4,"publicationDate":"2026-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148708642","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}
引用次数: 0
Viral lysis and host reprogramming impact carbohydrate, amino acid, and osmolyte cycling in salt-marsh tidal creek sediments. 病毒裂解和宿主重编程影响碳水化合物、氨基酸和渗透物循环在盐沼潮汐溪沉积物。
IF 6.4
ISME communications Pub Date : 2026-07-01 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag184
Riccardo Frizzo, Silvia Pettenuzzo, Enrico Bortoletto, Irene Gregori, Alessandro Vezzi, Mattia Panin, Sciamila Hemmati, Lorenzo Archetti, Stefano Mammi, Sara Bogialli, Paola Venier
{"title":"Viral lysis and host reprogramming impact carbohydrate, amino acid, and osmolyte cycling in salt-marsh tidal creek sediments.","authors":"Riccardo Frizzo, Silvia Pettenuzzo, Enrico Bortoletto, Irene Gregori, Alessandro Vezzi, Mattia Panin, Sciamila Hemmati, Lorenzo Archetti, Stefano Mammi, Sara Bogialli, Paola Venier","doi":"10.1093/ismeco/ycag184","DOIUrl":"https://doi.org/10.1093/ismeco/ycag184","url":null,"abstract":"<p><p>Salt marshes are highly productive ecosystems where microbial communities drive key transformations of organic matter at rates often exceeding those of oceanic and inland environments. Viruses are recognized as important drivers and regulators of global biogeochemical cycling, yet their diversity, host range, and functional roles in salt marsh ecosystems remain largely unresolved. To address these gaps, we investigated how viral lysis and host reprogramming can affect microbe-mediated organic matter transformations in a salt marsh of the Venice lagoon (Italy). Focusing on tidal creek surface sediments, we reconstructed 311 metagenome-assembled genomes (MAGs), built corresponding genome-scale metabolic models (GEMs) individually constrained with 121 metabolites detected in the sediments, and identified 3537 viral populations (vOTUs) across 10 samples. To assess the impact of viral lysis, we inferred prokaryotic hosts for 243 vOTUs and analysed host metabolism through MAG pathway analysis and GEM flux modelling across 13 bacterial orders, thus highlighting a negative impact on polysaccharide degradation, organic nitrogen mineralization, and organosulphur mineralization/volatilization processes. For host metabolic reprogramming, we characterized a subset of 50 auxiliary viral genes (AVGs) by mapping them to GEM reactions and analysing their stoichiometry, directionality, and pathway context, outlining two dominant strategies: resource scavenging through nucleotide-sugar biosynthesis, amino acid utilization, and sulphate assimilation; functional host maintenance through cofactor biosynthesis, electron transport, and energy production through carbonyl-compound utilization. Our findings provide a mechanistic view of the viral influence on organic matter transformations in salt marsh sediments and confirm viruses as key players in salt marsh biogeochemistry.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag184"},"PeriodicalIF":6.4,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13477221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148762702","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}
引用次数: 0
Resource competition modeling suggests hydrogen peroxide determines competitive outcomes among oligotrophic cyanobacteria. 资源竞争模型表明过氧化氢决定了低营养蓝藻之间的竞争结果。
IF 6.4
ISME communications Pub Date : 2026-07-01 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag188
Donna Katie McCullough, David Talmy
{"title":"Resource competition modeling suggests hydrogen peroxide determines competitive outcomes among oligotrophic cyanobacteria.","authors":"Donna Katie McCullough, David Talmy","doi":"10.1093/ismeco/ycag188","DOIUrl":"10.1093/ismeco/ycag188","url":null,"abstract":"<p><p><i>Prochlorococcus</i> is the most numerically abundant photosynthetic organism in the oligotrophic ocean; yet, it is vulnerable to damage by the reactive oxygen species (ROS) hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>). Detoxifying microbes and abiotic decay are thought to mitigate the most harmful impacts of H<sub>2</sub>O<sub>2</sub>, but the ecological impacts of ROS on ocean microbial community composition are not fully understood. Here, we introduce ROS dynamics within a resource competition model to investigate H<sub>2</sub>O<sub>2</sub> impacts on a community with one catalase negative <i>Prochlorococcus</i> analogue, one catalase positive <i>Synechococcus</i> analogue, and a heterotrophic bacterium. Model parameters defining resource utilization, H<sub>2</sub>O<sub>2</sub> detoxification, and H<sub>2</sub>O<sub>2</sub>-mediated cell death are constrained with data from laboratory experiments. With these ecologically realistic parameter values, we investigate the community composition for a range of ammonium and H<sub>2</sub>O<sub>2</sub> supply rates. In the absence of a heterotrophic bacterium, <i>Synechococcus</i>' modest ability to detoxify H<sub>2</sub>O<sub>2</sub> facilitates the survival of <i>Prochlorococcus</i> under conditions that would otherwise be fatal. However, in the absence of a strong bacterial detoxifier, unrealistically high <i>Synechococcus</i> concentrations (>10<sup>6</sup> mL<sup>-1</sup>) are required for it to coexist with <i>Prochlorococcus</i> on a single limiting nutrient. Coexistence among <i>Prochlorococcus</i> and <i>Synechococcus</i> at ecologically realistic cell densities and H<sub>2</sub>O<sub>2</sub> concentrations is observed when heterotrophic bacteria with high detoxification rates reach cell densities on the order of 10<sup>5</sup> cells mL<sup>-1</sup>. Our analysis suggests that environmentally relevant ROS concentrations have the potential to determine whether <i>Prochlorococcus</i> and <i>Synechococcus</i> coexist on ammonium and points to the importance of ROS supply and degradation for understanding marine cyanobacteria ecology.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag188"},"PeriodicalIF":6.4,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13431279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148671508","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}
引用次数: 0
Unraveling fitness landscapes in plant-associated Bacteroidota. 揭示与植物相关的拟杆菌群的适应性景观。
IF 6.4
ISME communications Pub Date : 2026-07-01 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag186
Marta Torres, Vincent Lombard, Nicolas Terrapon, Adam M Deutschbauer
{"title":"Unraveling fitness landscapes in plant-associated Bacteroidota.","authors":"Marta Torres, Vincent Lombard, Nicolas Terrapon, Adam M Deutschbauer","doi":"10.1093/ismeco/ycag186","DOIUrl":"10.1093/ismeco/ycag186","url":null,"abstract":"<p><p>Members of the bacterial phylum Bacteroidota inhabit diverse ecosystems, yet environmental species remain poorly understood compared to clinically relevant ones. Although Bacteroidota are dominant in crop-associated microbiomes, the mechanisms enabling them to thrive in plant and soil environments remain unclear. A key obstacle in understanding gene fitness in Bacteroidota is the lack of genome-wide functional studies, largely due to their inherent resistance to antibiotics, which hinders genetic manipulation. Here, we applied randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) to measure gene fitness in a plant-associated Bacteroidota, <i>Mucilaginibacter yixingensis</i> YX-36. Our data sheds light on pathways involved in rhizosphere colonization, gliding motility, stress tolerance, and carbon metabolism. Notably, we found that phylum-specific genes such as polysaccharide utilization loci and carbohydrate-active enzymes are needed for fitness in the plant niche. Overall, this work advances our understanding of gene functions in environmental Bacteroidota species and provides a foundation for future research on their roles in plant-microbe interactions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag186"},"PeriodicalIF":6.4,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148681399","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}
引用次数: 0
Microbial degradation of jellyfish detritus promotes phytoplankton growth in coastal marine ecosystems. 水母碎屑的微生物降解促进沿海海洋生态系统中浮游植物的生长。
IF 6.4
ISME communications Pub Date : 2026-07-01 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag185
Tinkara Tinta, Eduard Fadeev, Mauro Celussi, Cecilia Balestra, Katja Klun, Patricija Mozetič, Gerhard J Herndl
{"title":"Microbial degradation of jellyfish detritus promotes phytoplankton growth in coastal marine ecosystems.","authors":"Tinkara Tinta, Eduard Fadeev, Mauro Celussi, Cecilia Balestra, Katja Klun, Patricija Mozetič, Gerhard J Herndl","doi":"10.1093/ismeco/ycag185","DOIUrl":"10.1093/ismeco/ycag185","url":null,"abstract":"<p><p>Gelatinous zooplankton (hereinafter cnidarian <i>Medusozoa</i> and ctenophores or \"jellyfish\") are widespread in marine ecosystems and can form blooms, releasing large amounts of labile, protein-rich organic matter (jelly-OM) upon decay. This material fuels intense bacterial activity, yet its ecological consequences remain poorly understood. We conducted a two-stage microcosm experiment simulating a bloom decay of the invasive ctenophore <i>Mnemiopsis leidyi</i> to examine microbial processing of jelly-OM and its effect on primary production (PP). In the first stage, over the course of 3 days, we observed jelly-OM stimulating rapid growth of opportunistic bacterial community. The community was dominated by <i>Pseudoalteromonadaceae</i>-key degraders of diverse jellyfish, which exhibited enhanced metabolism of amino acids, lipids, and carbohydrates and elevated extracellular enzymatic activities, including leucine aminopeptidase, lipase, chitinase, and alkaline phosphatase. These processes led to marked ammonium accumulation. In the second stage, exposure of a fresh microbial assemblage to residues from jelly-OM degradation resulted in a significant increase of PP and phytoplankton biomass over a period of five days. This was dominated by diatoms and was fueled by accumulated ammonium. Concurrently, the bacterial community shifted toward taxa typically associated with phytoplankton blooms. Together, these results, further supported by <i>in situ</i> observations, reveal a likely coupling between jellyfish decay and phytoplankton growth, suggesting that jellyfish blooms act as transient but powerful nutrient sources capable of triggering ecosystem shifts. As jellyfish are projected to thrive under future ocean conditions, our findings underscore the need to re-evaluate their role in biogeochemical cycles-particularly as overlooked drivers of phytoplankton dynamics.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag185"},"PeriodicalIF":6.4,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13452463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148698332","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}
引用次数: 0
Antibiotic course frequency and recovery strategies alter gut microbial composition and metabolism. 抗生素疗程频率和恢复策略改变肠道微生物组成和代谢。
IF 6.4
ISME communications Pub Date : 2026-06-28 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag145
Kaoutar Abaakil, Zhigang Liu, Mu Wang, Elina Kuznecova, Ming S C Sung, Julian R Marchesi, Michaela A Mausz, Jia V Li
{"title":"Antibiotic course frequency and recovery strategies alter gut microbial composition and metabolism.","authors":"Kaoutar Abaakil, Zhigang Liu, Mu Wang, Elina Kuznecova, Ming S C Sung, Julian R Marchesi, Michaela A Mausz, Jia V Li","doi":"10.1093/ismeco/ycag145","DOIUrl":"10.1093/ismeco/ycag145","url":null,"abstract":"<p><p>Antibiotics profoundly alter the gut microbiome, but how exposure frequencies shape microbial recovery remains unclear. The effectiveness of post-antibiotic interventions, e.g. probiotics or autologous fecal microbiota transplantation, (aFMT) requires further exploration. This study investigated how antibiotic course timing and recovery strategies influence gut microbiome and metabolism in male Wistar rats. A single oral dose of vancomycin-ciprofloxacin (VC) caused rapid urinary and fecal metabolic shifts within 8-12 h and reduced bacterial α-diversity in cecal and colonic contents. When three VC courses were administered at regular (every 3 weeks; VCr) or irregular (1-3 weeks; VCi) intervals, VCr showed greater suppression of fecal α-diversity and stronger disruption of amino acid and host-microbial co-metabolism than VCi. Over the 3-week recovery period, VCr exhibited slower fecal α-diversity restoration; at week 3, β-diversity remained significantly different between groups, and cecal butyrate levels were persistently reduced in VCr. Both groups showed elevated levels of 5-aminovalerate in feces and colon compared with controls, whereas only VCi showed reductions in jejunal and ileal amino acids. Probiotics or aFMT had limited influence on small intestinal alterations, though aFMT accelerated fecal α-diversity recovery, and both interventions promoted partial normalization of fecal amino acids and 5-aminovalerate, without achieving complete restoration. Overall, shorter antibiotic intervals exerted stronger effects on the small intestinal luminal chemical environment, whereas longer intervals led to greater suppression of colonic and fecal microbial metabolism. Probiotics and aFMT supported selective metabolic recovery without fully reversing antibiotics-induced disturbances, highlighting the need for more targeted restoration strategies across gastrointestinal regions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag145"},"PeriodicalIF":6.4,"publicationDate":"2026-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13310174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148347699","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}
引用次数: 0
Metatranscriptomics reveals protistan and viral metabolic reprogramming of sinking particle microbiomes in Oyashio waters. 亚转录组学揭示了在oashhio水域下沉颗粒微生物组的原体和病毒代谢重编程。
IF 6.4
ISME communications Pub Date : 2026-06-27 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag182
Qingwei Yang, Hisashi Endo, Yanhui Yang, Akiko Ebihara, Yosuke Yamada, Hideki Fukuda, Toshi Nagata, Hiroyuki Ogata
{"title":"Metatranscriptomics reveals protistan and viral metabolic reprogramming of sinking particle microbiomes in Oyashio waters.","authors":"Qingwei Yang, Hisashi Endo, Yanhui Yang, Akiko Ebihara, Yosuke Yamada, Hideki Fukuda, Toshi Nagata, Hiroyuki Ogata","doi":"10.1093/ismeco/ycag182","DOIUrl":"10.1093/ismeco/ycag182","url":null,"abstract":"<p><p>Protists and viruses play a crucial role in the biological carbon pump by aggregating and degrading organic carbon. However, the identities of active lineages and their metabolic activities within sinking particles remain poorly characterized. Here, we examined the transcriptional dynamics of protists and viruses in sinking and suspended particles collected by a marine snow catcher in the Oyashio region. We found taxon-specific metabolic variations, with sinking particles showing high abundance of upregulated transcripts from ciliates, dinoflagellates, and viruses, while suspended particles exhibited those from haptophytes and chlorophytes. Diatoms exhibited species-specific responses to particle types: <i>Minidiscus variabilis</i> upregulated more genes in suspended particles, whereas the large chain-forming <i>Thalassiosira rotula</i> overexpressed genes in sinking particles. Gene co-expression network analysis revealed that the diatom <i>Thalassiosira</i> and <i>Chaetoceros</i>, which include chain-forming species, constitute a co-expression module positively correlated with POC and PON fluxes, while modules enriched in small phytoplankton (e.g. <i>Minidiscus</i>, haptophytes, and chlorophytes) were negatively correlated with these fluxes. A module dominated by ciliates, dinoflagellates, and viruses associated with sinking particles was negatively correlated with POC and PON fluxes, implying that their consumption and lysis of the sinking organisms could reduce the vertical export. Consistently, dinoflagellate species such as <i>Karlodinium veneficum</i> and <i>Karenia brevis</i> exhibited enrichment of functional genes involved in carbon degradation pathways. Overall, our findings underscore the importance of specific plankton and viral lineages and their functions in aggregation and degradation processes of sinking particles.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag182"},"PeriodicalIF":6.4,"publicationDate":"2026-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148681397","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}
引用次数: 0
Land use reshapes soil cercozoan functional architecture through soil chemistry and fungal networks. 土地利用通过土壤化学和真菌网络重塑土壤线虫的功能结构。
IF 6.4
ISME communications Pub Date : 2026-06-27 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag181
Yijia Tang, Budiman Minasny, Peipei Xue, Ho Jun Jang, Alex McBratney
{"title":"Land use reshapes soil cercozoan functional architecture through soil chemistry and fungal networks.","authors":"Yijia Tang, Budiman Minasny, Peipei Xue, Ho Jun Jang, Alex McBratney","doi":"10.1093/ismeco/ycag181","DOIUrl":"10.1093/ismeco/ycag181","url":null,"abstract":"<p><p>Soil protists are key regulators of microbial turnover and nutrient fluxes, yet their functional organization across managed landscapes remains poorly resolved. Among them, Cercozoa constitute one of the most abundant and ecologically influential lineages in terrestrial ecosystems. However, we lack a mechanistic framework explaining how protist functional composition reorganizes under land-use change and how abiotic filtering and biotic interactions jointly shape these shifts. Here, we examined cercozoan functional trait structure across cropping, pasture and woodland soils in the lower Namoi Valley, New South Wales, Australia, using 18S rRNA gene amplicon sequencing integrated with a curated trait database. Across land uses, communities were dominated by small, gliding bacterivores and omnivores, indicating strong convergence toward highly motile microbial grazers. Cropping soils exhibited higher functional alpha diversity and stronger coupling between trait composition and soil physicochemical gradients than woodland soils, suggesting intensified environmental filtering under agricultural management. Functional diversity was positively associated with fungal diversity and sodium, and negatively associated with organic carbon and total nitrogen, highlighting coordinated responses to both microbial networks and soil chemistry. Several trait categories showed consistent associations with fungal diversity, indicating that biotic coupling contributes to niche structuring alongside abiotic constraints. Together, these results demonstrate that land use reorganizes soil protist functional architecture through interacting physicochemical and biotic drivers, rather than through wholesale biodiversity loss. Trait-based protist metrics therefore provide a mechanistic lens for understanding soil ecological reassembly and offer a promising avenue for integrating microbial eukaryotes into soil health assessment under global change.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag181"},"PeriodicalIF":6.4,"publicationDate":"2026-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148681327","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}
引用次数: 0
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