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":"https://doi.org/10.1093/femsec/fiag048","url":null,"abstract":"<p><p>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 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 (PLFA-SIP) 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.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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":"https://doi.org/10.1093/femsec/fiag046","url":null,"abstract":"<p><p>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 specialized parasitoid wasp, Hyposoter horticola, at three temperatures in the laboratory (26, 28, 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.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A systematic review on soil microbial shifts under drought stress: A climate-smart agriculture perspective.","authors":"Ndivhuwo Ramatsitsi, Alen Manyevere","doi":"10.1093/femsec/fiag044","DOIUrl":"https://doi.org/10.1093/femsec/fiag044","url":null,"abstract":"<p><p>Major shifts in temperature and rainfall patterns resulting from climate change are projected to continue increasing intensely over the course of the century. Ecosystems' functionality and well-being of above-ground plant community are all significantly impacted by soil microbes' response to these shifting abiotic stresses. With an emphasis on improving their usefulness in climate-smart agriculture (CSA), we reviewed how soil bacteria and fungi tolerate drought stress and improve plant development under water shortage conditions. This systematic analysis used Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) to elaborate how microbe-based solutions could be incorporated in CSA. A total of 31 articles satisfied the inclusion criteria. The review demonstrated that soil microbial diversity and abundance are considerably altered by drought stress, improve resilience of plants and soil functionality. There was a further observation of high microbial community in the endosphere, and rhizosphere as compared to bulk soil; a clear indication of plants' potential to facilitate soil microbial assemblages. Evidently, plants under drought conditions exude metabolites that stimulate drought-tolerant microbes; that in-turn promote the plants' tolerance to drought. Accordingly, this remarkable synergy between microbes and plants could help forecast how agroecosystems would function in the face of climate change.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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":"https://doi.org/10.1093/femsec/fiag040","url":null,"abstract":"<p><p>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 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 (LDPE, PET) and one biodegradable polymer (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.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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":"<p><p>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.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"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}
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":"<p><p>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.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"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}
Adele Pioppi, Sofia I F Gomes, Mette Nicolaisen, Xinming Xu, Ákos T Kovács
{"title":"Successive cultivation under drought selects for specific microbiome members in the wheat rhizosphere.","authors":"Adele Pioppi, Sofia I F Gomes, Mette Nicolaisen, Xinming Xu, Ákos T Kovács","doi":"10.1093/femsec/fiag037","DOIUrl":"10.1093/femsec/fiag037","url":null,"abstract":"<p><p>Growing knowledge on plant microbiomes demonstrates the contribution of the host plant during microbiome assembly, especially under stress conditions commonly threatening crops. To dissect the influence of a plant on its microbiome, repeated cycling of microbiomes can be utilized to enhance functional properties in the enriched microbial communities. We used such a successive cultivation approach for wheat (Triticum aestivum) microbiome under drought conditions and selected lineages for drought resilience and susceptibility, with and without enriching the starting community with a library of bacterial isolates obtained from wheat. Significant differences in the rhizosphere microbiome between selection regimes were confirmed through 16S rRNA gene amplicon sequencing. Notably, replicate lineages of each selection regime showed convergence to similar microbiomes. Specific genera were abundant depending on the selection regimes; Stenotrophomonas under drought resilience, while Rahnella under drought conditions when the strain library was added initially. Applying Stenotrophomonas or Rahnella as single inoculum did not improve drought resilience in wheat. We hypothesize that complex microbiome dynamics take place during successive cultivation, which underscores the importance of considering complex plant-microbiome systems for studying plant stress resilience. Successive cultivation remains a valuable approach for observing rhizosphere microbiome changes under different conditions.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13114863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147671692","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}
{"title":"Priority effects drive fungal and nematode emergence from insect larvae.","authors":"Amaury Payelleville, Magdalena Warren, Chloe Golde, Devyn Sasai, Benny Pan, Patrick Cleary, Arizbel Gomez, Rubina Shrestha, Jean-Claude Ogier, Sophie Gaudriault, Christine Jacobs-Wagner, Tadashi Fukami","doi":"10.1093/femsec/fiag036","DOIUrl":"10.1093/femsec/fiag036","url":null,"abstract":"<p><p>Priority effects, in which species arrival history influences community assembly, are increasingly recognized to affect host-parasite systems. However, priority effects across disparate groups of parasitic organisms are poorly understood despite the wide range of taxonomic groups involved. In California oak woodland, we investigated how priority effects between two insect-parasitic fungi (Metarhizium and Beauveria) influenced emergence of nematodes from insect larvae. Field and laboratory results indicated that both fungi were common, but priority effects prevented them from co-emerging from the same larva. Metarhizium- and Beauveria-infected insects did not differ in the species composition of emerging nematodes, but larvae without fungal emergence had distinct nematode communities, with Oscheius almost always emerging without fungi. Experiments indicated that none of the commonly found nematodes (Acrobeloides, Mesorhabditis, Oscheius, and Rhabditis) were entomopathogenic, but that Oscheius could exclude Beauveria if it arrived early. This time-dependent exclusion was likely caused by a bacterium that Oscheius nematodes carried (Serratia proteamaculans). Together, these findings suggest that fungi enter insects as primary arrivers, while nematodes come as secondary arrivers to exploit fungus-killed insects, with priority effects influencing both groups. We suggest that this system is a promising natural microcosm for understanding priority effects across disparate groups in host-parasite systems.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13089402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147644727","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}
{"title":"Protein folds and catalytic strategies at the origin of biological CO2 fixation.","authors":"Natalia Mrnjavac","doi":"10.1093/femsec/fiag041","DOIUrl":"10.1093/femsec/fiag041","url":null,"abstract":"<p><p>Biological carbon fixation is the basis of all ecosystems. Out of the seven known pathways organisms use to fix CO2, the acetyl-CoA pathway is assumed to be the most ancient. Its enzymes bear primordial traits, including carbon-metal bonds and an abundance of transition metal clusters. Ancient traits can also be reflected in structural folds adopted by the enzymes and the catalytic strategies they employ. Here I show that the most common catalytic strategies used to accelerate reactions in the acetyl-CoA pathway are cofactor-aided catalysis, electrostatic interactions and general acid/base catalysis. Enzymes of the acetyl-CoA pathway are replete with Rossman folds, TIM barrel folds, and alpha-beta plaits. These topologies evolved before the divergence of bacteria and archaea, along with five other catalytic folds of the acetyl-CoA pathway. Rossmann folds and TIM barrels likely underwent rapid diversification early in the history of life. In contrast, over half of the folds in the pathway are weakly diversified folds that emerged only once in the history of life, at the origin of biological CO2 fixation. Ancient metabolic pathways point to enzymes with conserved structural cores, which uncover topologies and catalytic strategies employed at the onset of metabolism.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Zn-mobilizing bacteria improve shoot biomass and zinc content in wheat.","authors":"Belay Berza, Fassil Assefa, Tesfaye Wubet, Undine Behrendt, Sizhong Yang, Paul Reim, Steffen Kolb","doi":"10.1093/femsec/fiag030","DOIUrl":"10.1093/femsec/fiag030","url":null,"abstract":"<p><p>Enhancing zinc (Zn) content in wheat grains by using Zn-mobilizing rhizosphere bacteria is becoming an eco-friendly and sustainable alternative to conventional approaches such as chemical fertilization. Our study aimed to isolate, screen, and evaluate Zn-mobilizing rhizosphere bacteria to improve its content in wheat biomass. Wheat rhizosphere soils were collected in several wheat planted soils in Ethiopia and Zn-solubilizing bacteria were isolated and screened for their plant beneficial traits. Isolates W8_A, W25_A, and W63_B were selected. Pot experiments were conducted in sterilized river sand supplemented with 0.05% zinc oxide by using these isolates. The experiment consisted of nine treatments in complete randomized design with four replications. Data were means of three independent experiments. W8_A, W25_A, and W63_B exhibited zinc solubilization index > 4.0. Consortium inoculation showed the highest improvements in plant growth. Inoculations improved shoot length and dry weigh on average by 67.4% and 84.2%, respectively compared to the control. On average, 90.2% root and 75.5% shoot Zn content increased compared to the untreated control. Hence, the isolates can be applied for Zn bio-fortification in wheat to combat Zn deficiencies in food grains.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13089531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147671660","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}