Environmental Microbiome最新文献

{"title":"Meloidogyne incognita parasitism is affected by Pseudomonas protegens CHA0 and its effects on tomato-associated microbiota.","authors":"Olivera Topalović, Enoch Narh Kudjordjie, Sanea Sheikh, Gnimavo Bonaventure Kenou, Frederik Bak, Flemming Ekelund, Mette Vestergård","doi":"10.1186/s40793-025-00743-0","DOIUrl":"10.1186/s40793-025-00743-0","url":null,"abstract":"<p><strong>Background: </strong>The multitrophic interactions in plant rhizosphere and endosphere can be beneficial or deleterious for the plant health. The parasitism by root-feeding nematodes is on the negative end of the interaction spectrum, and may be very difficult to control. Biological agents are a promising alternative to the environmentally harmful nematicides; however, their efficiency in natural soil often seems to be low due to their limited establishment and dispersal. Thus, understanding how the introduced biological agents interact with nematodes and the surrounding microbiota is necessary to improve sustainable management of root-feeding nematodes. Here, we conducted two experiments to study the effects of Pseudomonas protegens strain CHA0 (CHA0) on the performance of the root-knot nematode Meloidogyne incognita. In the first experiment, we compared M. incognita performance in natural and sterilized soil in the presence and absence of CHA0. In the second experiment, we studied the composition of microbes in the rhizosphere and endosphere of tomato plants grown in native soil in response to M. incognita and CHA0.</p><p><strong>Results: </strong>We found that nematode performance, especially nematode reproduction, was significantly increased in native soil amended with CHA0. In addition, we found the highest relative abundance of Pseudomonas in tomato endosphere in response to nematode co-inoculations with CHA0, which suggests that root wounding, caused by nematodes, increased the entrance of inoculated and/or native Pseudomonas spp. As many Pseudomonas spp. are plant growth promoting, this may explain that plant growth was highest in this treatment. Furthermore, the rhizosphere of nematode-inoculated plants was enriched with Flavobacterium, Hydrogenophaga and Variovorax, which are genera generally associated with nematode-suppressive soils. On the other hand, other known nematode-suppressive genera such as Bacillus, Lysobacter, Devosia and Rhizobium were depleted in plants where nematodes were co-inoculated with CHA0, which may explain the higher nematode performance when plants were co-inoculated with CHA0.</p><p><strong>Conclusions: </strong>Our findings show that the effect of P. protegens strain CHA0 on M. incognita parasitism is influenced by the multitrophic interactions in the rhizosphere and endosphere of tomato plants. We must understand these interactions thoroughly to optimize sustainable means to mitigate the root-knot nematodes.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"79"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211340/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid and sustained differentiation of disease-suppressive phyllosphere microbiomes in tomato following experimental microbiome selection.","authors":"Hanareia Ehau-Taumaunu, Terrence H Bell, Javad Sadeghi, Kevin L Hockett","doi":"10.1186/s40793-025-00734-1","DOIUrl":"10.1186/s40793-025-00734-1","url":null,"abstract":"<p><strong>Background: </strong>Microbial-based treatments to protect plants against phytopathogens typically focus on soil-borne disease or the aboveground application of one or a few biocontrol microorganisms. However, diverse microbiomes may provide unique benefits to phytoprotection in the phyllosphere, by restricting pathogen access to niche space and/or through multiple forms of direct antagonism. We previously showed that successive experimental passaging of phyllosphere microbiomes along with the phytopathogen Pseudomonas syringae pv. tomato (Pto), which causes bacterial speck in tomato, led to the development of a disease suppressive microbial community. Here, we used amplicon sequencing to assess bacterial and fungal composition at the end of each passage, as well as shotgun metagenomics at key passages based on observed disease-suppressive phenotypes, to assess differences in functional potential between suppressive and non-suppressive communities.</p><p><strong>Results: </strong>Bacterial composition changed and diversity declined quickly due to passaging and remained low, particularly in treatments with Pto present, whereas fungal diversity did not. Pseudomonas and Xanthomonas populations were particularily enriched in disease-suppressive microbiomes compared to conducive microbiomes. The relative abundance of Pseudomonas syringae group gemonosp. 3 (the clade to which the introduced pathogen belongs) in shotgun metagenomic data was similar to what we observed for Pseudomonas ASVs in the 16S rRNA gene dataset. We also observed an increase in the abundance of genes associated with microbial antagonism at Passage 4, corresponding to the highest observed disease severity.</p><p><strong>Conclusions: </strong>Taxonomic richness and evenness were low within samples, with clustering occurring for suppressive or non-suppressive microbiomes. The relative abundance of genes associated with antagonism was higher for disease-suppressive phyllosphere microbiomes. This work is an important step towards understanding the microbe-microbe interactions within disease-suppressive phyllosphere communities.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"77"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics reveals the inhibition of asexual reproduction in the jellyfish Aurelia coerulea polyp by Bacillus pacificus.","authors":"Hao Sun, Xuerui Liu, Manzoor Ahmad, Xiangrui Guo, Zhen Yu, Ye Zhao, Pingping Shen, Yanying Zhang, Zhijun Dong","doi":"10.1186/s40793-025-00740-3","DOIUrl":"10.1186/s40793-025-00740-3","url":null,"abstract":"<p><strong>Background: </strong>Jellyfish blooms pose a serious threat to marine ecosystems and coastal socio-economic activities, requiring urgent development of control technologies to manage harmful jellyfish. Associated bacteria hold considerable importance in the growth and development of marine invertebrates. We isolated Bacillus pacificus SG15 from the seagrass rhizosphere and observed that this strain could inhibit the asexual reproduction of the jellyfish Aurelia coerulea polyp. However, the precise interaction processes underlying this inhibition remain unclear. Therefore, we aimed to elucidate these processes by performing a coculture experiment coupled with analyses utilizing high-throughput sequencing, transcriptomics, metabolomics, and fluorescence in situ hybridization.</p><p><strong>Results: </strong>Our findings indicate that the transcription of genes involved in the absorption of vitamins B5, B11, B12, C and biotin was inhibited with SG15 treatment despite relatively high concentrations of vitamins and their derivatives in the culture medium. SG15 treatment increased the levels of carbohydrate metabolism genes, including those involved in pyruvate metabolism, glycolysis/gluconeogenesis, pentose phosphate pathways, and citrate cycle metabolites. Furthermore, SG15 influenced both endodermal and ectodermal polyp cells.</p><p><strong>Conclusions: </strong>Collectively, our findings helped elucidate the interactions between associated bacteria and polyps and the process by which B. pacificus SG15 inhibits polyp asexual reproduction, providing novel insights into the role of bacteria in the development of marine invertebrates. This study could provide a theoretical framework and empirical evidence for the biological control of jellyfish blooms in the marine aquaculture area, which may help develop strategies aimed at mitigating the impacts of jellyfish blooms on marine ecosystems and coastal communities.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"78"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities.","authors":"Marie C Thomas, Gretel Waugh, Katarina Damjanovic, Inka Vanwonterghem, Nicole S Webster, Andrew P Negri, Heidi M Luter","doi":"10.1186/s40793-025-00741-2","DOIUrl":"10.1186/s40793-025-00741-2","url":null,"abstract":"","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"81"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biochar-based organic substrates enhance tomato growth by promoting specific microbial communities in rooftop farming.","authors":"Miguel de Celis, Laura L de Sosa, Giuseppe Picca, Noelia González-Polo, Cristina Gómez Ruano, Luciano Beneduce, Claudio Zaccone, Marco Panettieri","doi":"10.1186/s40793-025-00744-z","DOIUrl":"10.1186/s40793-025-00744-z","url":null,"abstract":"<p><strong>Background: </strong>Urban agriculture represents an opportunity to alleviate some of the issues related with the increased urbanization and global human population. Productive rooftops offer a promising solution that combines food production and recycling of organic waste, while providing green spaces without consuming urban soils. In addition, harnessing natural resources, including plant-associated microbiomes, is proposed as an effective approach to sustainably improve farm productivity and food quality. However, little attention has been given to the importance of selecting the appropriate organic substrate to enhance plant-microbe interactions and rooftop farming in urban areas. Here, we study the influence of different organic substrates on tomato, and its associated microbial community, in an open-air rooftop farming setup. Specifically, we evaluate combinations of peat with a high quantity (50% of volume) of compost derived from different feedstocks (seaweed biomass or coffee byproducts), and how biochar-blending alters these compositions.</p><p><strong>Results: </strong>We found that substrate properties were mainly defined by the compost feedstocks. Biochar blending had a minor influence on substrate composition, although it enhanced tomato yield. Overall, alternative substrates differed from peat mainly by showing higher phosphorus content, pH, and electric conductivity. Similarly, compost feedstock had a greater impact on microbial communities than biochar blending. Even though alternative substrates presented higher bacterial diversity than peat, the taxonomic composition was similar across alternative substrates, reflecting the functional redundancy of the bacterial communities. In addition, we identified specific microbes associated with each compost feedstock. The abundance of bacteria and fungi associated with composted seaweed biomass was positively associated with tomato yield. Among them, bacterial genera like Acidibacter, Altererythrobacter, Amaricoccus, Luteitalea, Microvirga, Pedomicrobium or Pseudorhodoplanes stood out presenting strong correlations with tomato yield.</p><p><strong>Conclusions: </strong>The studied substrates influenced tomato growth and yield directly via their chemical and physical properties and by influencing microbial community composition. Thus, our results reveal the importance of using the appropriate organic substrate for enhancing the effectiveness of rooftop agriculture while increasing microbial diversity in urban unexploited areas.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"82"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbes with plastic-degrading and pathogenic potentials are present on plastics in the final polishing pond of a wastewater treatment plant.","authors":"Jessica A Wallbank, Fraser Doake, Lloyd Donaldson, Joanne M Kingsbury, Hayden Masterton, Olga Pantos, Dawn A Smith, Beatrix Theobald, Louise Weaver, Gavin Lear","doi":"10.1186/s40793-025-00737-y","DOIUrl":"10.1186/s40793-025-00737-y","url":null,"abstract":"<p><p>We characterised plastisphere microbial communities in the polishing pond of a municipal wastewater treatment plant, applying prokaryotic 16S rRNA gene, eukaryotic 18S rRNA gene and fungal ITS2 region sequencing to identify changes in microbial biofilm community compositions over time. Pondwater and biofilm from linear low-density polyethylene (LLDPE), nylon-6 (PA), polyethylene terephthalate (PET), polylactic acid (PLA), oxo-degradable linear low-density polyethylene (OXO) and glass were sampled after 2, 6, 26 and 52 weeks of constant immersion. Microbial communities in ambient pondwater differed significantly from those forming biofilms on solid substrates. Biofilm age and depth in the water influenced microbial community compositions. However, no substrate-specific microbial communities were found among glass and plastic polymer types, regardless of artificial ageing. All substrates housed taxa associated with microbes previously reported to biodegrade plastics, being most abundant at two and 52 weeks for bacteria and fungi, respectively. Potential pathogens were found on all substrates, also being most abundant at two and 52 weeks for bacteria and eukaryotes, respectively. Our study highlights that the volume of plastics, more than its polymer form, may be most important when considering plastic's potential impacts on terrestrial and aquatic ecosystems, and for public health.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"80"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Warming increases richness and shapes assemblages of eukaryotic parasitic plankton.","authors":"Amruta Rajarajan, Sławek Cerbin, Kingsly C Beng, Michael T Monaghan, Justyna Wolinska","doi":"10.1186/s40793-025-00724-3","DOIUrl":"10.1186/s40793-025-00724-3","url":null,"abstract":"<p><strong>Background: </strong>Anthropogenic activities have led to a global rise in water temperatures, prompting increased interest in how warming affects infectious disease ecology. While most studies have focused on individual host-parasite systems, there is a gap in understanding the impact of warming on multi-host, multi-parasite assemblages in natural ecosystems. To address this gap, we investigated freshwater eukaryotic parasite communities in ten natural lakes near Konin, Poland: five artificially heated and five non-heated \"control\" lakes. Since 1958, the heated lakes have experienced a mean annual temperature increase of 2 °C due to hot water discharge from two adjacent power plants. We collected seasonal environmental DNA (eDNA) samples from surface waters over a two-year period and applied targeted metabarcoding to compare the richness and distribution of eukaryotic parasites across lake types with a focus on protists and fungi.</p><p><strong>Results: </strong>Using literature searches and sequence metadata from GenBank, we identified putative parasites which included Alveolates, Stramenopiles, basal Fungi and Ichthyosporeans as well as their associated hosts. Heated lakes harboured distinct parasite assemblages with higher richness of chytrids and aphelids, suggesting thermal preferences among certain freshwater microeukaryotic parasites. Other groups exhibited clear seasonal trends with richness of oomycetes peaking in spring and summer, and that of Cryptomycota in winter and autumn. A general linear model revealed a marginally positive correlation between chytrid parasite richness and richness of their green algal, diatom, and dinoflagellate hosts. Post-hoc analyses indicated that heated lakes exhibited greater seasonal variation in chytrid parasite richness and a stronger correlation between host and parasite richness than control lakes.</p><p><strong>Conclusion: </strong>These findings demonstrate that warming can induce strong shifts in the richness and assemblages of freshwater microeukaryotic parasites. Using chytrids as a focal group, we additionally demonstrate that warming may amplify seasonal variation in parasite richness and strengthen host-parasite richness relationships.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"76"},"PeriodicalIF":6.2,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contrasting stability of fungal and bacterial communities during long-term decomposition of fungal necromass in Arctic tundra.","authors":"Andrea Moravcová, Florian Barbi, Camelia Algora, Gabriele Tosadori, Petr Macek, Jana Albrechtová, Petr Baldrian, Petr Kohout","doi":"10.1186/s40793-025-00730-5","DOIUrl":"10.1186/s40793-025-00730-5","url":null,"abstract":"<p><p>Decomposition is a crucial process in terrestrial ecosystems, driving nutrient cycling and carbon storage dynamics. Considering the amount of fungal necromass produced in soils annually, its decomposition represents an important nutrient recycling process. Understanding the decomposition dynamics and associated microbial communities of fungal necromass is essential for elucidating ecosystem functioning, especially in environmentally sensitive regions such as the Arctic tundra, which remain under-explored. In a three-year field experiment conducted in the Svalbard archipelago, we investigated the decomposition of two types of fungal necromass with differing biochemical properties. We studied the decomposition rate, changes in chemical composition, and the succession of fungal and bacterial communities associated with the decaying fungal necromass. We discovered that up to 20% of fungal necromass remained even after three years of decomposition, indicating that the decomposition process was incomplete. Our results indicate the crucial role of Pseudogymnoascus in decomposing low-quality, highly melanized necromass with a high C:N ratio in Arctic soils, underscoring its importance in carbon cycling in the Arctic tundra. Notably, we observed dynamic changes in bacterial communities, with increasing richness over time and a shift from copiotrophic to oligotrophic species specializing in decomposing recalcitrant material. Our study indicates the strong potential that fungal necromass can play in carbon sequestration of arctic soils and reveals the distinct dynamics between rather stable fungal and rapidly changing bacterial communities associated with the decomposing fungal necromass in the Arctic tundra. These findings enhance our understanding of microbial succession during decomposition in extreme environments and highlight the potentially differing roles of fungi and bacteria in these processes.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"75"},"PeriodicalIF":6.2,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12180224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative metagenomics indicates metabolic niche differentiation of benthic and planktonic Woeseiaceae.","authors":"Tomeu Viver, Katrin Knittel, Rudolf Amann, Luis H Orellana","doi":"10.1186/s40793-025-00732-3","DOIUrl":"10.1186/s40793-025-00732-3","url":null,"abstract":"<p><strong>Background: </strong>Benthic microbiomes exhibit remarkable temporal stability, contrasting with the dynamic, substrate-driven successions of bacterioplankton. Nonetheless, understanding their role in carbon cycling and interactions between these two microbial communities is limited due to the complexity of benthic microbiomes.</p><p><strong>Results: </strong>Here, we used a long-reads (LRs) metagenomic approach to examine benthic microbiomes and compared them to the microbiomes in the overlaying water column and on particles, sampled at the same site and time off the island Heligoland in the North Sea. Although the diversity is vast in marine sediments, we recovered high quality metagenome assembled genomes (MAGs). Based on taxonomy and metabolic annotation of predicted proteins, benthic microbiomes are distinctly different from pelagic microbiomes. When comparing the 270 MAGs from free living and particle attached microbes from the water column to 115 MAGs from sediments only 2 MAGs affiliated to Acidimicrobiia and Desulfocapsaceae were shared at species level. Although, we recovered MAGs with the same taxonomic annotation in pelagic and benthic microbiomes, their metabolic potentials were different. A prominent example was the family Woeseiaceae that was among the most abundant taxa in the sediments. In benthic Woeseiaceae MAGs, we found polysaccharide utilization loci (PULs), predicted to target laminarin, alginate, and α-glucan. In contrast, pelagic Woeseiaceae MAGs were only recovered in the particle attached but not in the free-living fraction, and lacked PULs. They encoded a significantly more sulfatases and peptidases genes. Additionally, while genes involved in iron acquisition, gene regulation, and iron storage were widespread in Woeseiaceae MAGs, genes linked to dissimilatory iron reduction were mostly restricted to benthic Woeseiaceae, suggesting niche-specific adaptations to sediment redox conditions. Both, benthic and pelagic particle-attached Woeseiaceae MAGs encoded pilus TadA genes, which are essential for adhesion, colonization, and biofilm formation.</p><p><strong>Conclusions: </strong>LR sequencing is currently the most valuable tool for analyzing highly diverse benthic microbiomes. The small overlap of MAGs from water column and sediments indicated a limited bentho-pelagic coupling. The data suggest that Woeseiaceae have habitat-specific metabolic specialization: while benthic Woeseiaceae possess the metabolic capabilities to utilize fresh organic compounds like laminarin derived from algae blooms, and to perform dissimilatory nitrate, nitrite and iron reduction for gain energy, particle attached Woeseiaceae from the water column may be specialized in degrading protein-rich and sulfated organic matter likely reflecting adaptation to the different types of organic matter and redox conditions in sediments vs. the water column.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"74"},"PeriodicalIF":6.2,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Salinization alters microbial methane cycling in freshwater sediments.","authors":"Lorena Selak, Dimitri V Meier, Maja Marinović, Andrea Čačković, Katarina Kajan, Petra Pjevac, Sandi Orlić","doi":"10.1186/s40793-025-00739-w","DOIUrl":"10.1186/s40793-025-00739-w","url":null,"abstract":"<p><p>Climate change-induced salinization poses a global threat to freshwater ecosystems and challenges microbial communities driving crucial biogeochemical processes, particularly methane cycling. This study examined the impact of salinization and the accompanying sulfate concentration increases on microbial community dynamics and methane cycling in coastal freshwater lake sediments. We show that sulfate enrichment in sediment profiles enables the proliferation of distinct sulfate-reducing bacteria (SRB) that reshape microbial niches by competing with methanogens and promoting sulfate-dependent anaerobic oxidation of methane (AOM). Freshwater SRB clusters, which compete with some methanogens for substrates but also degrade organic compounds into methanogenesis precursors, are replaced by the SEEP-SRB groups that form syntrophic relationships with ANME-1 in salinized sediments. As seawater intrudes and reshapes microbial communities, a methane pocket forms that escapes both aerobic and anaerobic oxidation. Underneath this methane pocket, SRB play a key role in enabling sulfate-dependent AOM, facilitating methane consumption at higher sediment depths. While all microorganisms demonstrated some physiological adaptability potential to elevated osmotic stress, SRB exhibited the highest resilience to increased salinity. These findings highlight how salinization-induced geochemical shifts, particularly sulfate enrichment, directly affect microbial community assembly and impact methane cycling in coastal freshwater ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"73"},"PeriodicalIF":6.2,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12172229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}