Environmental Microbiome最新文献

{"title":"Organic fertilizers increase microbial community diversity and stability slowing down the transformation process of nutrient cycling.","authors":"Xueli Chen, Xingzhu Ma, Zhuxiu Liu, Haidong Gu, Hairui Fang, Zongzhuan Shen, Huibo Zhang, Shuming Wan, Weiqun Li, Xiaoyu Hao, Nicholas John Clarke, Junjie Liu","doi":"10.1186/s40793-025-00791-6","DOIUrl":"https://doi.org/10.1186/s40793-025-00791-6","url":null,"abstract":"<p><strong>Background: </strong>Soil microbes play a central role in nutrient recycling in soils: however, the genetic mechanisms governing their responses to long-term fertilization remain poorly understood. While the agronomic benefits of long-term fertilization are well-documented, the genetic mechanisms and ecological processes underlying microbial community responses to different fertilization regimes remain poorly understood, particularly in unique soil systems such as black soils (Mollisols), which are critical for global food security. A deeper insight into how organic and inorganic fertilizers influence microbial assembly, functional potential, and community stability is essential for developing sustainable soil management practices.</p><p><strong>Results: </strong>This study deciphers microbial assembly mechanisms, functional gene dynamics, and community restructuring in black soils subjected to 44 years of chemical fertilizer (CF), manure amendment (M), and integrated chemical fertilizer with manure (CFM) treatments. Results revealed that CF significantly enhances functional gene abundance related to carbon (C) degradation (e.g., starch, cellulose, chitin and lignin) and nitrification, accelerating the conversion of recalcitrant C to labile C pools and ammonium to nitrate. Conversely, M and CFM treatments promote microbial diversity and stability while decelerating nutrient transformation processes. In addition, microbial assembly mechanisms shift from stochastic to deterministic processes with long-term fertilizer application in CF. The structural equation modeling (SEM) indicated that soil chemical properties shape both the diversity and composition of taxonomic and functional gene communities which subsequently regulate microbial -mediated nutrient cycling processes and crop yield.</p><p><strong>Conclusions: </strong>Our findings highlight the trade-offs between microbial functional potential and community stability under contrasting fertilization strategies, emphasizing the need to integrate microbial metrics into sustainable land management frameworks.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"130"},"PeriodicalIF":5.4,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145293728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil.","authors":"Ernest D Osburn, J L Weissman, Michael S Strickland, Mo Bahram, Bram W Stone, Steven G McBride","doi":"10.1186/s40793-025-00790-7","DOIUrl":"https://doi.org/10.1186/s40793-025-00790-7","url":null,"abstract":"<p><strong>Background: </strong>To improve our understanding of microbial systems, it is essential to refine the conceptual frameworks that connect microorganisms to their ecological functions. While trait-based approaches can provide nuanced perspectives on how microorganisms influence ecosystem processes, there is ongoing debate over the link between microbial taxonomic classifications and life history traits. Here, we integrate genomic, metagenomic, amplicon sequencing, and experimental (stable isotope probing) data to investigate the scaling of bacterial growth traits from individual taxa to complex assemblages and to identify specific taxonomic groups of soil bacteria that can be used as indicators of community-scale microbial growth.</p><p><strong>Results: </strong>Our results revealed broadly different distributions of growth rates among bacterial phyla, including significantly different mean and median rates. This, in turn, manifested in strong relationships between relative abundances of some phyla and community-scale growth rates in soil. Specifically, we calculated community weighted mean growth rates using measured growth rates of constituent taxa and found that the fast-growing taxa that had sufficient abundance and ubiquity across samples to contribute to variation in community-average growth were mostly lineages of Proteobacteria (e.g., Sphingomonas). As a result, the relative abundance of phylum Proteobacteria was the single strongest taxonomic predictor of community-average growth, explaining up to ~ 60% of the variation in growth rates across communities. In contrast, Verrucomicrobia were consistent indicators of slower community-average growth. These patterns were especially strong when using taxon-level growth rates measured following carbon and nitrogen additions to soil.</p><p><strong>Conclusions: </strong>Our results demonstrate that phylum relative abundances can be strong indicators of community-level bacterial growth despite the wide variation in growth rates observed within phyla. The stronger phylum-growth relationships for whole assemblages than are apparent for individual taxa are due to relative abundance-weighted trait averaging in complex assemblages, i.e., at the community scale, broad differences in growth traits among phyla become more important than variation within phyla. Overall, our results provide clarity regarding the use of bacterial taxonomic information for inferring traits, demonstrating that high taxonomic ranks can be valid indicators of microbial traits in soil provided that inferences are drawn at the appropriate scale.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"131"},"PeriodicalIF":5.4,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145294069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beyond dikarya: 28S metabarcoding uncovers cryptic fungal lineages across a tidal estuary.","authors":"Madeleine A Thompson, Birch Maxwell Lazo-Murphy, Bruce W Pfirrmann, William H J Strosnider, James L Pinckney, Xuefeng Peng","doi":"10.1186/s40793-025-00786-3","DOIUrl":"10.1186/s40793-025-00786-3","url":null,"abstract":"<p><p>Fungi are key drivers of biogeochemical processes, yet marine fungi remain understudied and under-characterized due to primer biases and database gaps. In this study, we conducted a metabarcoding survey targeting the small and large subunit rRNA genes and the internal transcribed spacer region of fungi (18S, 28S, and ITS2) in the sediment and surface water of salt and brackish marshes in the North Inlet-Winyah Bay estuarine system (Georgetown, South Carolina, USA). The universal 18S/16S primer set (515F-Y and 926R) identified few fungal taxa. The ITS2 primer set (ITS3mix and ITS4) revealed high diversity among Dikarya but failed to capture the full extent of early diverging fungi (EDF). In contrast, the 28S primer set (LR0R and LF402) excelled at identifying EDF lineages, including Chytridiomycota, Mucoromycota, Zoopagomycota, and Blastocladiomycota, many of which dominated the brackish marsh sampling site but were less prevalent in the salt marsh sampling sites. Over half of the fungal OTUs identified by the 28S primer set were from EDF lineages. Copy-normalized 28S qPCR showed that EDF were more abundant in brackish sediments than in the salt marsh. Several putative denitrifying fungi, primarily species from Trichoderma and Purpureocillium, were also detected, suggesting overlooked functional guilds that may contribute to estuarine nitrogen cycling. A FUNGuild analysis found that most lineages were saprotrophic. Overall, our findings show that EDF are key contributors to community differences across salinity gradients and may play more important functional roles in coastal biogeochemistry than is currently understood. The 28S primer set is ideal for marine fungal metabarcoding because it provides comprehensive taxonomic coverage and enables phylogenetic analysis.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"129"},"PeriodicalIF":5.4,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505610/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145245564","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":"New insights into the evolution and metabolism of the bacterial phylum Candidatus Acidulodesulfobacteriota through metagenomics.","authors":"Yanhu Ren, Yue-Hong Wu, Jun Chen, Zhen-Hao Luo, Xue-Wei Xu","doi":"10.1186/s40793-025-00779-2","DOIUrl":"10.1186/s40793-025-00779-2","url":null,"abstract":"<p><p>Candidatus Acidulodesulfobacterales, a formerly proposed bacterial order within the Deltaproteobacteria lineage, represents an ecologically significant group in sulfur-rich environments. Their diversity and functional potential in artificial acid mine drainage (AMD) ecosystems have been well studied; however, their distribution and ecological role in marine hydrothermal sulfides remain poorly understood. Here we integrated publicly available metagenome-assembled genomes (MAGs) with a newly reconstructed MAG from hydrothermal sulfides to perform comprehensive phylogenetic, metabolic, and host-virus interaction analyses. Phylogenomic and 16S rRNA gene analyses indicated that this lineage represents a distinct phylum-level clade, leading us to propose the designation Ca. Acidulodesulfobacteriota. Metabolic reconstructions indicated a versatile lifestyle, encompassing pathways for carbon fixation, nitrogen fixation, sulfur metabolism, iron oxidation, and hydrogen oxidation. Notably, the concatenated DsrAB protein phylogeny and the mixed enzyme types involved in Dsr-dependent dissimilatory sulfur metabolism suggest that Ca. Acidulodesulfobacteriota may represent a transitional lineage in the evolutionary shift from reductive to oxidative Dsr metabolism. Viral auxiliary metabolic genes (AMGs) associated with this phylum were predicted to modulate host metabolic pathways, including folate biosynthesis and sulfur metabolism, highlighting intricate host-virus interactions. These findings advance our understanding of the evolution, metabolic potential, and ecological roles of Ca. Acidulodesulfobacteriota in biogeochemical cycling.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"127"},"PeriodicalIF":5.4,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506266/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145245616","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":"Variations in plant's cry for help evidenced by modifications of rice root microbiota induced by blast or brown spot diseases.","authors":"Léa Jobert, Gabriel Boulard, Nicolas Poncelet, Henri Adreit, Gilles Béna, Lionel Moulin","doi":"10.1186/s40793-025-00787-2","DOIUrl":"10.1186/s40793-025-00787-2","url":null,"abstract":"<p><strong>Background: </strong>Plants can recruit specific microbes to help them defend themselves against phytopathogens in a process known as \"cry for help\". In this study, we investigated whether a plant species modulates its root-associated microbiome differently - i.e. \"cries out differently\" - depending on the diversity of fungal pathogens attacking its leaves. To address this question, we monitored changes in the root microbiome of Oryza sativa cv. Nipponbare following infection with two fungal pathogens: Pyricularia oryzae (leaf blast) and Bipolaris oryzae (brown spot), under controlled conditions and using the same soil.</p><p><strong>Results: </strong>Our results support the \"cry for help\" hypothesis, suggesting that pathogen-induced stress drives the recruitment of beneficial microbes. While the composition of the root-associated microbiota remained globally stable after infection, subtle but significant taxonomic shifts were observed. Alpha diversity was unaffected, but changes in beta diversity occurred in micro-eukaryotic communities one week after brown spot infection and in bacterial communities two weeks after blast infection. Notably, beneficial taxa such as the bacterial genera Lentzea and Streptomyces, as well as the fungi Cladosporium halotolerans and Rhizophagus irregularis, were enriched in the below-ground microbiome of leaf-infected plants. The biocontrol potential of Rhizophagus irregularis was confirmed against blast but not brown spot infection.</p><p><strong>Conclusions: </strong>These results advance our understanding of the \"cry for help\" hypothesis in rice and provide potential candidates for biocontrol. They highlight the complexity of plant-microbe interactions and suggest that rice plants specifically modulate their root microbiome in response to fungal infections, potentially shaping microbial communities to enhance defence strategies.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"128"},"PeriodicalIF":5.4,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145245567","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":"Deciphering the influence of fertilization systems on the Allium ampeloprasum rhizosphere microbial diversity and community structure through a shotgun metagenomics profiling approach.","authors":"Oluwaseun Emmanuel Shittu, Ben Jesuorsemwen Enagbonma, Olubukola Oluranti Babalola","doi":"10.1186/s40793-025-00771-w","DOIUrl":"10.1186/s40793-025-00771-w","url":null,"abstract":"<p><strong>Background: </strong>Chemical fertilizer application in agriculture over the years has been a vital instrument to boost agricultural yields and soil fertility, but has threatened the diversity of the rhizosphere microbiomes in the soil. However, knowledge about the impacts of biofertilizers (BF) as well as chemical fertilizers (CF) on Allium ampeloprasum rhizosphere's microbiomes is still limited. Hence, this study investigated the metagenomic profiling of A. ampeloprasum rhizosphere under different fertilization systems and in bulk soils, to obtain a depiction of their associated microbial diversity and community structure, which will inform best agricultural practices.</p><p><strong>Method: </strong>The entire DNA sample was mined from soil samples taken from an independent uncultivated bulk soil and the rhizosphere of A. ampeloprasum treated with chemical and biofertilizer and subjected to shotgun metagenomics sequencing.</p><p><strong>Results: </strong>The taxonomic analysis of our metagenome unveiled that while all soil samples exhibited similar core microbial phyla, Bacteroidota and Verrucomicrobiota were exclusive to the biofertilizer (G2) plot. Actinobacteria and Pseudomonadota (Proteobacteria) were predominant in the biofertilizer plot (G2), chemical fertilizer (G1), and bulk soil (G3) plots, respectively. Genera such as Dyadobacter, Verrucomicrobium, Streptomyces, and Haliangium were exclusively detected in the biofertilizer plot (G2). Alpha diversity analysis showed that G2 harboured the most diverse microbial community, followed by G3, with the lowest diversity found in the G1 plot, highlighting the importance of biofertilizer in increasing microbial diversity. The observed differences in the microbial diversity and community structure are highly linked to the nature of fertilizer applied and the distinct physicochemical parameters of the three plots. However, redundancy analysis subsequently highlighted total nitrogen and carbon as the key environmental influencers impacting the microbial community structure and composition.</p><p><strong>Conclusion: </strong>This study underscores the potential of biofertilizers in boosting the rhizosphere microbial diversity, improving soil health, and offer a sustainable alternative to chemical fertilizers, thereby supporting long-term agricultural sustainability and resilience in food production systems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"126"},"PeriodicalIF":5.4,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12502447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240193","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":"Multidimensional sampling framework reveals plant-driven effects on microbial spatial heterogeneity and niche differentiation in a natural ecosystem.","authors":"Seong-Jun Chun, Yingshun Cui, Jihoon Kim, Jun-Woo Lee, Kyong-Hee Nam","doi":"10.1186/s40793-025-00793-4","DOIUrl":"10.1186/s40793-025-00793-4","url":null,"abstract":"<p><strong>Background: </strong>The identification of complex spatial patterns of microbial communities in relation to their ecological niches is fundamental to understanding the mechanisms of ecological interactions among diverse organisms. This study introduces a novel three-dimensional (3D) sampling approach to examine the spatial dynamics of microbial populations and niche differentiation influenced by plant-mediated effects in natural ecosystem.</p><p><strong>Results: </strong>Microbial communities across horizontal and vertical dimensions were systematically mapped, and we found that the total microbial diversity, particularly among eukaryotes, increased more than ten-fold compared to that obtained via single-grid sampling, emphasizing the importance of spatial heterogeneity in shaping microbial dynamics. Moreover, the 3D framework enabled us to identify taxa specifically associated with particular plants, offering insights into plant-microbe interactions, pathogen prevalence, and ecological consequences of plant-driven effects on local communities.</p><p><strong>Conclusions: </strong>Collectively, these findings demonstrate that 3D sampling approach provides a reproducible and scalable methodology for investigating microbial spatial heterogeneity, pathogen ecology, and niche differentiation in natural environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"125"},"PeriodicalIF":5.4,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145226098","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":"Viral ecogenomics across oxic and anoxic zones of the Yongle Blue Hole.","authors":"Ming Yang, Hong-Xi Zhang, Ying-Li Zhou, Ramganesh Selvarajan, Pei-Kuan Xu, Zhao-Ming Gao, Yong Wang","doi":"10.1186/s40793-025-00778-3","DOIUrl":"10.1186/s40793-025-00778-3","url":null,"abstract":"<p><strong>Background: </strong>Deep ocean blue holes are characterized by distinct physicochemical gradients and complex biological processes, and Yongle Blue Hole (YBH) in the South China Sea (SCS) is the world's deepest (301 m) underwater cavern with unique environmental characteristics. So far, studies investigated the bacterial community structure with different lifestyles of the YBH; however, our understanding of viruses in the YBH remains limited. Here, we utilized a metagenomic approach to investigate viral communities in both the \"viral fraction\" and \"cellular fraction\" of seawater samples in oxic and anoxic zones within YBH.</p><p><strong>Results: </strong>A total of 1,730 viral operational taxonomic units (vOTUs) were identified, with over 70% affiliated with the classes Caudoviricetes and Megaviricetes, particularly within the families Kyanoviridae, Phycodnaviridae and Mimiviridae. Gene-sharing network analyses indicated that the deeper anoxic layers contain a high proportion of novel viral genera, while the oxic layer's viral genera overlap with those found in the open water samples from SCS. Virus-linked prokaryotic hosts predominantly belong to the phyla Patescibacteria, Desulfobacterota, and Planctomycetota. Notably, the detected putative auxiliary metabolic genes (AMGs) suggest that these viruses may influence photosynthetic and chemosynthetic pathways, as well as methane, nitrogen, and sulfur metabolisms, especially with several high-abundance AMGs potentially involved in prokaryotic assimilatory sulfur reduction.</p><p><strong>Conclusions: </strong>Together, these findings highlight the potential ecological roles and diversity of viral communities within YBH and shedding light on niche-separated viral speciation.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"119"},"PeriodicalIF":5.4,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145193669","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":"Diversity and distribution of the lanthanome in aerobic methane-oxidising bacteria.","authors":"Shamsudeen Umar Dandare, Alexander Allenby, Eleonora Silvano, Peter Nockemann, Yin Chen, Thomas J Smith, Deepak Kumaresan","doi":"10.1186/s40793-025-00776-5","DOIUrl":"10.1186/s40793-025-00776-5","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Lanthanides (Ln) play important and often regulatory roles in the metabolism of methylotrophs, including methanotrophs, particularly through their involvement in methanol oxidation. However, the diversity, distribution, and ecological relevance of Ln-associated proteins (the lanthanome) in aerobic methane-oxidising bacteria (MOB) remain underexplored. This study investigates the lanthanome using genome, plasmid, and proteome data, alongside metatranscriptome data from methane-rich lake sediments.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;We surveyed 179 genomes spanning Proteobacterial, Verrucomicrobial, and Actinobacterial MOBs to examine the distribution of Ln-dependent methanol dehydrogenases (MDHs) and Ln transport proteins. Distinct lineage-specific patterns were observed: XoxF5 was the most widespread MDH variant in Proteobacteria, while XoxF2 was restricted to Verrucomicrobia. Transporter systems also showed distinct patterns, with LanM restricted to Alphaproteobacteria, LanPepSY and LanA confined to Gammaproteobacteria, and LutH-like receptors broadly distributed across all lineages. Homologues of these genes were also detected on plasmids, indicating potential for horizontal gene transfer. In Lake Washington sediment metatranscriptomes, lanthanome transcripts were detected, with Proteobacteria as dominant contributors. Notably, a large fraction of xoxF transcripts were affiliated with non-MOB Methylophilaceae, consistent with known cooperative interactions with MOB. Using Methylosinus trichosporium OB3b as a model, we assessed methane oxidation and proteomic responses to soluble CeCl&lt;sub&gt;3&lt;/sub&gt; and a mixed-lanthanide ore. Lag phases were prolonged in the presence of lanthanides, particularly with ore, but methane oxidation rates converged across treatments after acclimation. Proteomic analysis revealed extensive condition-specific responses, with 724 proteins differentially expressed in Ore treatment compared to 60 under CeCl&lt;sub&gt;3&lt;/sub&gt;. XoxF3 and XoxF5 were upregulated while MxaF and its accessory proteins were downregulated, consistent with the \"lanthanide switch\". Notably, LanM was not expressed despite being encoded, whereas LutH-like receptor was downregulated under both treatments, likely reflecting regulatory control to prevent excess metal uptake. Additional upregulation of a TonB-dependent receptor and ABC transporter suggests a potential lanthanophore-mediated uptake strategy.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;This study highlights the diversity and ecological activity of Ln-binding and transport systems in MOBs, their plasmid localisation and potential mobility, and their distinct regulation under different Ln sources. The strong proteomic response to complex ore underscores the physiological flexibility of MOBs in coping with natural lanthanide forms. These findings provide a framework for ecological studies and candidate targets for biotechnological applications in methane bioconversion and sustainab","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"120"},"PeriodicalIF":5.4,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145193674","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":"Sharp but consistent fungi species composition transition during a 40-yr urbanization in a subtropical city of China.","authors":"Yapeng Hao, Weimin Wang, Qun Guo, Wanyi Zhang, Liang Kou, Jiajia Zheng, Yu Bai, Ning Ma, Jing Yang, Xiangyun Xiong, Hong Liang, Shenggong Li","doi":"10.1186/s40793-025-00695-5","DOIUrl":"10.1186/s40793-025-00695-5","url":null,"abstract":"<p><strong>Background: </strong>Rapid urbanization has profoundly impacted soil fungal dynamics and thus soil health, however, it remains poorly addressed due to lack of ideal experimental region. Taking Shenzhen of China, a megacity built within 30 years, as the study region, we analyzed the effects of rapid urbanization on soil fungal diversity, species composition, and community stability from the perspective of urbanization stages (within 10, 10-20, 20-30, 30-40, and over 40 years of urbanization), and original (forests, paddy fields, and drylands) and present (parks, streets, and residential areas) urban land-use types.</p><p><strong>Results: </strong>Results showed that soil fungi of urban areas had significantly lower Chao1 and phylogenetic diversity (PD) than that of natural ecosystem (P < 0.05), i.e., forests in this study, with the lowest PD in street. The urbanization-induced higher phosphorus (P) content and thus lower soil N/P may explain the lower PD in city areas (P < 0.05). As the urbanization proceeded, soil fungal species composition shifted and resilience stability reduced significantly within 10 years (P < 0.05) compared with forests, but then the composition gradually transitioned to a consistent state while stability recovered to a certain extent for the rest of the urbanization stages. Key phyla driving these results included Ascomycota and Mortierellomycota. Original land-use types did not significantly affect urban soil fungal diversity or composition (P > 0.05). However, SparCC-based network analysis revealed no significant differences (P > 0.05) in fungal co-occurrence patterns or stability across different land-use types and urbanization stages, suggesting that urbanization may not strongly restructure fungal interaction networks.</p><p><strong>Conclusions: </strong>Our findings shed new lights on the scientific understanding and the urban spatial planning when considering soil health under the context of rapid urbanization. Additionally, they emphasize the need to incorporate multiple analytical approaches when studying microbial community interactions.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"121"},"PeriodicalIF":5.4,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145193656","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}