FEMS microbiology ecology最新文献_第8页

Unraveling underlying mechanisms and responsible microbes of organic residue-stimulated atmospheric methane uptake in agricultural soils. 揭示有机残留物刺激农业土壤中大气甲烷吸收的潜在机制和负责微生物。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-05-21 DOI: 10.1093/femsec/fiag048

Stijn G van den Bergh, Iris Chardon, Marion Meima-Franke, Gabriel S Rocha, Xiaoyu Cheng, Ciska Raaijmakers, Wietse de Boer, Paul L E Bodelier

{"title":"Unraveling underlying mechanisms and responsible microbes of organic residue-stimulated atmospheric methane uptake in agricultural soils.","authors":"Stijn G van den Bergh, Iris Chardon, Marion Meima-Franke, Gabriel S Rocha, Xiaoyu Cheng, Ciska Raaijmakers, Wietse de Boer, Paul L E Bodelier","doi":"10.1093/femsec/fiag048","DOIUrl":"10.1093/femsec/fiag048","url":null,"abstract":"It has been reported that compost amendment improves atmospheric CH4 uptake of agricultural soils. However, microbes involved as well as the underlying mechanisms responsible for the observed effect remain unclear. Here we identified active methane-oxidizing bacteria (MOB) at (circum-) atmospheric CH4 concentrations in agricultural soils amended with green compost, and investigated three complementary hypotheses: (i) atmospheric CH4 consumption is driven by highly activated, flush-feeding MOB; (ii) stimulation of internal CH4 production which fuels flush-feeding methanotrophic activity; and (iii) increased availability of H2 that can serve as additional energy source for mixotrophic methanotrophy. First, we showed that MOB previously activated by exposure to high CH4 concentrations can subsequently oxidize atmospheric CH4 via the flush-feeding lifestyle. Second, no internal CH4 production in soil was observed following compost amendment, likely due to lack of suitable substrates for methanogenesis. Third, provision of elevated H2 concentrations did not affect the concurrent atmospheric CH4 oxidation. Phospholipid fatty acid-stable isotope probing revealed that four distinct MOB groups were active at (circum-) atmospheric CH4 concentrations in agricultural soils and green compost: Methylocaldum sp., Methylosinus sporium, Methylocystis sp./Methylosinus trichosporium, and USCα. These findings enhance our understanding of methanotroph ecology and can be used to craft more effective strategies of creating \"climate-smart\" soils.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13214991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147835654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater. 鬼岩微生物群：对溶洞和地下水生物地球化学影响的宏基因组研究。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-05-21 DOI: 10.1093/femsec/fiag047

Guillaume Peugnet, Célie Pisapia, Bénédicte Ménez, Maud Watkinson, Léna Lecourt, Nicolas Peugnet, Julien Bouchez, Laurent Bruxelles, Emmanuelle Gérard

{"title":"Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.","authors":"Guillaume Peugnet, Célie Pisapia, Bénédicte Ménez, Maud Watkinson, Léna Lecourt, Nicolas Peugnet, Julien Bouchez, Laurent Bruxelles, Emmanuelle Gérard","doi":"10.1093/femsec/fiag047","DOIUrl":"10.1093/femsec/fiag047","url":null,"abstract":"Microbial communities in the critical zone drive key geochemical processes, but many subsurface habitats remain poorly characterized. Ghost-rock karst systems in particular represent unexplored microbial niches. Here, we provide the first genome-resolved metagenomic comparison of ghost-rock and groundwater microbial communities from the Sterkfontein karst system (South Africa). Ghost-rock and groundwater communities host distinct taxonomic and metabolic assemblages. Groundwater communities are dominated by chemolithotrophs capable of oxidizing sulfur- and nitrogen-bearing compounds, and by heterotrophs degrading refractory, plant-derived organic matter. In contrast, primary producers in ghost-rocks likely rely on atmospheric chemosynthesis via trace gas oxidation, while glycogen metabolism and necromass recycling point to adaptations to oligotrophic and fluctuating hydrological conditions. Groundwater taxa with metal-interacting pathways may initiate bedrock colonization via metal oxidation, whereas ghost-rock communities include potential metal reducers that could drive iron and manganese oxide dissolution and influence trace element mobility. Together, these results underscore ghost-rocks as active microbial and geochemical hot spots within karst systems that may play a non-negligible role on biomineralization/bioweathering processes and on shaping (sub)terrestrial landscapes and global biogeochemical cycles.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13264449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148217208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Temperature at parental generation affects bacterial communities associated with offspring for both host and parasitoid. 亲代温度对寄主和拟寄生物后代相关的细菌群落都有影响。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-05-21 DOI: 10.1093/femsec/fiag046

Camila Souza Beraldo, Diego Castillo Franco, Saskya van Nouhuys, Anne Duplouy

{"title":"Temperature at parental generation affects bacterial communities associated with offspring for both host and parasitoid.","authors":"Camila Souza Beraldo, Diego Castillo Franco, Saskya van Nouhuys, Anne Duplouy","doi":"10.1093/femsec/fiag046","DOIUrl":"10.1093/femsec/fiag046","url":null,"abstract":"The thermal conditions experienced during development can affect host-associated microbial communities. We still know little about whether such effects similarly persist across life stages between different species. In particular, it is unclear if the bacterial communities of closely interacting species, such as hosts and their endoparasitoids, exhibit similar responses to thermal conditions. We reared two generations of the Melitaea cinxia butterfly and its specialised parasitoid wasp, Hyposoter horticola, at three temperatures in the laboratory (26°C, 28°C, and 31°C). We found that the two species harbour different bacterial communities as adults, with the parasitoid exhibiting higher bacterial richness than its host butterfly. When the parental generation of the butterfly was exposed to high temperatures, the F1 generation exhibited increased bacterial richness but a reduced diversity (Shannon index). The opposite effect was observed for its parasitoid, but only for the wasps infected with Wolbachia, which appears sensitive to thermal conditions. Collectively, these results highlight that the bacterial communities of insect hosts and their parasitoids are distinct units, differently susceptible to environmental thermal conditions, particularly to temperatures experienced at the parental generation.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13192552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147812813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Arbuscular mycorrhizal fungi- linked microbial processes in soil nitrogen cycling. 丛枝菌根真菌在土壤氮循环中的相关微生物过程。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-05-21 DOI: 10.1093/femsec/fiag050

Anukool Vaishnav, Jan Jansa

{"title":"Arbuscular mycorrhizal fungi- linked microbial processes in soil nitrogen cycling.","authors":"Anukool Vaishnav, Jan Jansa","doi":"10.1093/femsec/fiag050","DOIUrl":"10.1093/femsec/fiag050","url":null,"abstract":"Arbuscular mycorrhizal fungi (AMF) create an extended plant-soil interface (referred to as mycorrhizal hyphosphere) where specific microbial interactions shape key steps of the nitrogen (N) cycle. Extraradical hyphae of the AMF host diverse microbes that help mineralize organic substrates, regulate ammonium and nitrate transformations, and enhance N retention. These processes allow plants to access both inorganic N and the N released from complex organic compounds. This review synthesizes current evidence for AMF-microbe interactions in relation to mineralization, nitrification, denitrification, and (di)nitrogen fixation. It also highlights unresolved questions, such as when AMF transition from facilitating to competing for N, how they access stabilized organic N pools, and how the carbon: nitrogen: phosphorus (C: N: P) nutrient stoichiometry of the soil environment constrain AMF-mediated N transfer to plants. Furthermore, we discuss how AMF-centered pathways can contribute to more circular N flows in agroecosystems by promoting tighter internal N cycling through microbial immobilization, turnover, and subsequent transfer to plants via AMF hyphae. By integrating spatial, microbial, and stoichiometric perspectives, this review provides a mechanistic framework for understanding AMF-driven N dynamics and their potential role in enhancing N use efficiency in managed and natural systems.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13201079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147874082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Uncovering syntrophic potential from genome-resolved metagenomics of suspended and granular anaerobic digestion sludges. 从悬浮和粒状AD污泥的基因组解析宏基因组揭示合成潜能。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-05-21 DOI: 10.1093/femsec/fiag052

Maaike S Besteman, Emilie Alaux, Anna Doloman, Guillaume Tahon, Thijs J G Ettema, Diana Z Sousa

{"title":"Uncovering syntrophic potential from genome-resolved metagenomics of suspended and granular anaerobic digestion sludges.","authors":"Maaike S Besteman, Emilie Alaux, Anna Doloman, Guillaume Tahon, Thijs J G Ettema, Diana Z Sousa","doi":"10.1093/femsec/fiag052","DOIUrl":"10.1093/femsec/fiag052","url":null,"abstract":"Syntrophic microbial interactions are fundamental to the degradation of organic matter (e.g. fatty acids), playing a central role in natural anoxic ecosystems and engineered systems such as anaerobic digestion (AD). Despite their ecological and biotechnological importance, only a limited number of (obligate) syntrophic fatty-acid oxidizers have been successfully isolated. In this study, microbial communities from suspended and granular sludge samples were characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Network analysis of the 16S rRNA gene amplicon data revealed strong positive associations between methanogens and known syntrophic fatty-acid oxidizers, particularly in granular sludge samples. 743 High-Completion Metagenome Assembled Genomes (HC-MAGs) were recovered. This comprehensive HC-MAGs dataset provides a valuable resource for identifying novel microorganisms with genomic potential for syntrophic oxidation of butyrate, propionate, and acetate. This analysis identified multiple interesting novel targets, including the families DTU052 and CALXsZ01 (class Syntrophomonadia) as potential butyrate oxidizers; the families UBA6807, PHBD01, FEN-1087, and FEN-1099 (class Syntrophia) as potential propionate oxidizers; and genus DTU068 (family Thermacetogeniaceae) together with the family-level lineage 4572-78 (phylum Chloroflexota) as potential acetate oxidizers. These findings highlight granular sludges as a reservoir for previously uncharacterized syntrophic microorganisms. The recovered HC-MAG dataset also provides a framework to further elucidating fatty-acid oxidizing bacterial lineages within complex anaerobic communities.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13248872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147981395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula. 在南极半岛西部夏季-秋季过渡期间，浮游植物动态影响浮游细菌群落结构和代谢。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-05-21 DOI: 10.1093/femsec/fiag053

Mariia Pavlovska, Yevheniia Prekrasna-Kviatkovska, Andrii Zotov, Artem Dzhulai, Evgen Dykyi, Bruno Huettel, Bernhard M Fuchs, Rudolf I Amann, Hanno Teeling, Chandni Sidhu

{"title":"Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula.","authors":"Mariia Pavlovska, Yevheniia Prekrasna-Kviatkovska, Andrii Zotov, Artem Dzhulai, Evgen Dykyi, Bruno Huettel, Bernhard M Fuchs, Rudolf I Amann, Hanno Teeling, Chandni Sidhu","doi":"10.1093/femsec/fiag053","DOIUrl":"10.1093/femsec/fiag053","url":null,"abstract":"Seasonal changes in Antarctic coastal waters trigger pronounced shifts in microbial community composition and function, yet sparse spatial and temporal coverage currently limits our understanding of phytoplankton-bacterioplankton coupling. This study combines metagenomic and metatranscriptomic analyses of marine bacterioplankton with environmental data to address the functional dynamics of planktonic communities off the Western Antarctic Peninsula during the austral summer-autumn transition. Diatoms dominated the phytoplankton community, with generally low biomass and abundance, yet a species-specific succession was observed. The bacterioplankton community structure shifted from dominance of copiotrophic taxa (e.g. Polaribacter) towards oligotrophic lineages (e.g. SAR11) adapted to low-nutrient conditions, accompanied by a decrease in microbial carbohydrate-degradation activity. The capacity to degrade algal-derived polysaccharides varied between community members, with ß-glucan, α-glucan, chitin, and host glycan utilization present in all, and fucose, β-galactan and trehalose degradation restricted to specific taxa. DMSP metabolism also showed taxonomic specificity and was shaped by both physical (ice melt and fluctuations in solar irradiation) and biological factors (phytoplankton succession). Together, these findings reveal a complex, taxon-specific coupling between bacterioplankton and phytoplankton communities in the Western Antarctic Peninsula, linking community structure to likely functional gene expression and highlight how Antarctic bacterioplankton drives carbon and sulfur turnover in a polar marine ecosystem.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13251894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148014092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Conventional and biodegradable microplastics elicit contrasting taxon-level responses in rhizosphere microbiomes of maize and strawberry. 常规微塑料和可生物降解微塑料在玉米和草莓根际微生物群中引起不同分类群水平的响应。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-05-21 DOI: 10.1093/femsec/fiag040

Aileen Jung, Ryan Bartnick, Daniel Churchill Thomas, Eva Lehndorff, Tillmann Lueders

{"title":"Conventional and biodegradable microplastics elicit contrasting taxon-level responses in rhizosphere microbiomes of maize and strawberry.","authors":"Aileen Jung, Ryan Bartnick, Daniel Churchill Thomas, Eva Lehndorff, Tillmann Lueders","doi":"10.1093/femsec/fiag040","DOIUrl":"10.1093/femsec/fiag040","url":null,"abstract":"Microplastics (MP) are relevant contaminants in agroecosystems, influencing soil nutrient dynamics and soil-plant-microbial interactions. As agriculture shifts from conventional to biodegradable plastics, their impacts on different crop rhizosphere microbiomes considering both total (DNA-derived) and transcriptionally active (rRNA-derived) communities have not been clearly elaborated. We hypothesized that microbiome impacts would be distinct across different plants and polymer types. Maize and strawberry plants were cultivated with 1% MP by soil weight, including two conventional polymers (low-density polyethylene-LDPE and polyethylene terephthalate-PET) and one biodegradable polymer (poly(butylene adipate-co-terephthalate)-PBAT). Strawberry plants increased biomass across all MP treatments, accompanied by greater soil nitrate depletion. MP-induced impacts on soil prokaryotic communities were mostly additive to plant effects, as determined by 16S rRNA amplicon sequence profiling. PBAT stimulated Cupriavidus spp. and members of Saccharimonadales, suggesting a selection of potential polymer-degraders and microbial interactions, independent of plant species and root proximity. In contrast, conventional MPs induced a less selective response with compositional shifts across a greater number of taxa. MP-induced changes were more apparent in rRNA- than DNA-derived profiles, suggesting a profound response of putative active taxa. Together, we demonstrate that plant species and MP type jointly modulate rhizosphere microbial community response to MP pollution, with direct implications for soil biogeochemistry, rhizosphere functioning, and crop performance.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13192445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Soil microbial diversity, succession, and greenhouse gas cycling across a Greenlandic glacial chronosequence. 土壤微生物多样性、演替和温室气体循环跨越格陵兰冰川时间序列。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-05-21 DOI: 10.1093/femsec/fiag054

Grace Marsh, Massimo Bourquin, Alanna Leale, Lisa Bröder, Ianina Altshuler

{"title":"Soil microbial diversity, succession, and greenhouse gas cycling across a Greenlandic glacial chronosequence.","authors":"Grace Marsh, Massimo Bourquin, Alanna Leale, Lisa Bröder, Ianina Altshuler","doi":"10.1093/femsec/fiag054","DOIUrl":"10.1093/femsec/fiag054","url":null,"abstract":"Accelerated glacial retreat in Greenland drives increased development of glacial outwash plains. These newly exposed landscapes provide an opportunity to study microbial dynamics during soil development. We explore soil microbial diversity, community assembly, and biogeochemical cycling across the Kiattuut Sermiat glacial chronosequence (southern Greenland) via 16S rRNA gene amplicon analysis paired with microbial abundance, soil physicochemical parameters, and gas flux data. Microbial diversity varied with soil depth, with more acidic topsoils abundant in Cyanobacteriota and Armatimonadota taxa. While aerobic lower soils likely contained relatively more anoxic pore spaces, hosting aerobic nitrifiers such as Nitrospirota, low-oxygen-associated Planctomycetota taxa, and less characterized Gemmatimonadota. Microbial diversity varied across the chronosequence following distance-decay principles, as communities were predominately dispersal limited and shaped by heterogeneous selection, with greater heterogeneous conditions further from the glacier terminus. Soil CO2 fluxes increased with distance from the glacier, following a shift from autotrophic sulfur- and iron-oxidizing taxa towards heterotrophic members. CH4 fluxes demonstrated greater uptake further from the glacier, and CH4-oxidation was associated with the methanotroph Methylocapsa. Considering the climatic relevancy of Greenlandic proglacial environments, we describe the largely unexplored microbial diversity and biogeochemical cycling of greenhouse gases in these developing soils.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13264440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148217188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Incomplete denitrifying bacteria drive N2O fluxes in ancient Siberian permafrost microcosms. 古西伯利亚永久冻土微观环境中不完全反硝化细菌驱动N2O通量

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-04-16 DOI: 10.1093/femsec/fiag034

Yanchen Sun, Xiaofen Wu, Oksana G Zanina, Elizaveta M Rivkina, Karen G Lloyd, Frank E Löffler, Tatiana A Vishnivetskaya

{"title":"Incomplete denitrifying bacteria drive N2O fluxes in ancient Siberian permafrost microcosms.","authors":"Yanchen Sun, Xiaofen Wu, Oksana G Zanina, Elizaveta M Rivkina, Karen G Lloyd, Frank E Löffler, Tatiana A Vishnivetskaya","doi":"10.1093/femsec/fiag034","DOIUrl":"10.1093/femsec/fiag034","url":null,"abstract":"Nitrous oxide (N2O) contributes to stratospheric ozone depletion and global warming. Knowledge about microbial formation and consumption of N2O in old permafrost remains limited. Permafrost samples collected on the East Siberian Sea coast of Russia from a single borehole at depths of 5.4 and 16.9 m, which showed presence of nitrogen substances and nitrogen cycling genes, were used to establish microcosms supplemented with NO3- and N2O to assess denitrification and N2O consumption at 4°C and 20°C. Rapid N2O formation was observed in NO3--supplemented microcosms, but N2O consumption was slow and incomplete over a 1-year incubation in all microcosms. Twenty-three qualified metagenome-assembled genomes (MAGs) harboring genes involved in NO3- and/or N2O reduction were recovered from both NO3-- and N2O-supplemented microcosms. Twenty MAGs represent novel taxa. Four MAGs, two of each from NO3-- and N2O-supplemented microcosms, contained nosZ genes indicating N2O consumption potential, however the complete denitrification (i.e. NO3-→N2) gene sets were not detected in these MAGs. Though, N2O production exceeded N2O consumption in NO3--supplemented microcosms at 4°C. Our microcosm experiments suggest N2O formation surpasses its consumption in newly thawed ∼120 kyr old permafrost, emphasizing the importance of using integrated approaches to assess and predict N turnover in response to permafrost degradation.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13094547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147580511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Longitudinal sampling of New Zealand cockles (Austrovenus stutchburyi) reveals high viral diversity and taxa-specific responses to environmental factors. 新西兰蛤（Austrovenus stutchburyi）的纵向采样揭示了高病毒多样性和分类群对环境因素的特异性反应。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-04-16 DOI: 10.1093/femsec/fiag033

Isa F de Vries, Stephanie J Waller, Rebecca K French, Rebecca M Grimwood, Jemma L Geoghegan

{"title":"Longitudinal sampling of New Zealand cockles (Austrovenus stutchburyi) reveals high viral diversity and taxa-specific responses to environmental factors.","authors":"Isa F de Vries, Stephanie J Waller, Rebecca K French, Rebecca M Grimwood, Jemma L Geoghegan","doi":"10.1093/femsec/fiag033","DOIUrl":"10.1093/femsec/fiag033","url":null,"abstract":"Bivalves bioaccumulate microorganisms and, therefore, serve as effective indicators of microbial activity in intertidal ecosystems. Monitoring bivalve-associated viruses can provide insight into circulating viral communities and their relationship with environmental change. The New Zealand cockle (Austrovenus stutchburyi) is culturally, ecologically, and economically important, yet little is known about the viruses it hosts, how these change over time, or whether cockles act as reservoirs for pathogenic viruses affecting bivalves or humans. We used a metatranscriptomic approach to characterise the cockle RNA virome over 12 months and assess whether environmental parameters influenced viral dynamics. Longitudinal sampling revealed a highly diverse RNA virome spanning 16 viral orders within the kingdom Orthornavirae. Phylogenetic analysis of RNA-dependent RNA polymerase sequences identified 358 viral transcripts representing 213 distinct viral species, of which 199 were likely novel, including several putative new virus families and three orders. No viruses known to be pathogenic to humans or bivalves were detected. While total virome composition showed no strong seasonal patterns, environmental parameters influenced virus abundance within specific viral orders, including the highly abundant Picornavirales, Wolframvirales, Bunyavirales, and Sobelivirales. Overall, New Zealand cockles harbour an exceptionally diverse RNA virome, with environmental drivers acting in a taxon-specific rather than community-wide manner.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13089499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147590896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0