Microbial Ecology最新文献

{"title":"Chronic Nitrogen Deposition Alters Diazotrophic Community Composition, Reduces Biological Nitrogen Fixation, and Restructures Fungal-Diazotroph CO-Occurrence Networks in Deadwood.","authors":"Shakhawat Hossen, Christina Groß, Friederike Roy, Harald Kellner, Matthias Noll, Werner Borken","doi":"10.1007/s00248-026-02849-5","DOIUrl":"10.1007/s00248-026-02849-5","url":null,"abstract":"<p><p>Biological nitrogen fixation (BNF) by diazotrophs contributes to increasing nitrogen (N) availability in nutrient-poor deadwood during the decomposition process. However, chronically elevated atmospheric N deposition may increase N availability, thereby reshaping diazotrophic community and suppressing BNF. We simulated high N deposition by repeatedly applying ammonium-nitrate solution to deadwood of 13 tree species over 9 years (N addition) and compared diazotrophic community composition and BNF rates with untreated controls. Deadwood N concentrations increased over time in both control and N addition, with N addition resulting in higher N concentrations at the final sampling, although significant treatment effects were detected only in Tilia and Pinus. Chronic high-N addition was associated with reduced BNF activity, with significant suppression primarily observed in coniferous deadwood, while responses among broadleaved species were weak, variable, or absent. The N addition altered diazotroph richness and community composition by increasing the abundance of Bradyrhizobium and by reducing Methylocapsa across all tree species. Under N addition, BNF correlated positively with nifH gene copy numbers in broadleaved deadwood but negatively in coniferous deadwood. Co-occurrence networks were more interconnected and modular under N addition, with diazotrophs (e.g., Azospirillum) central in broadleaved deadwood and fungi (e.g., Meliniomyces, Athelia) central in coniferous deadwood. Tree clade (coniferous vs. broadleaved) strongly shaped richness and community response, with broadleaved and coniferous species showing distinct patterns.Overall, the largely robust diversity and community composition of diazotrophs and BNF activity under high N addition suggest that moderately increasing N deposition has little influence on fungal deadwood decomposition and the function of deadwood as a carbon pool in forest ecosystems.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"89 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13433720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148664222","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":"Retraction Note: Purification and Characterization of Desferrioxamine B of Pseudomonas fluorescens and Its Application to Improve Oil Content, Nutrient Uptake, and Plant Growth in Peanuts.","authors":"S Nithyapriya, Lalitha Sundaram, Sakthi Uma Devi Eswaran, Kahkashan Perveen, Najla A Alshaikh, R Z Sayyed, Andrea Mastinu","doi":"10.1007/s00248-026-02838-8","DOIUrl":"10.1007/s00248-026-02838-8","url":null,"abstract":"","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"89 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13401521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148592680","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":"Effects of Culture History and Algal Taxonomy on Bacterial Communities in Long-maintained Filamentous Green Algae.","authors":"Ethan Wood, Bente Edvardsen, Kari Skjånes, Luka Šupraha","doi":"10.1007/s00248-026-02840-0","DOIUrl":"https://doi.org/10.1007/s00248-026-02840-0","url":null,"abstract":"<p><p>Algal cultures are widely used to study algae-bacteria interactions, yet the relative roles of algal taxonomy, culturing environment, and historical contingency in shaping bacterial communities of long-maintained monoalgal cultures remain unclear. In a two-stage experimental design, we used 16 S rRNA metabarcoding to first profile the bacterial communities of 14 filamentous freshwater algal strains from three orders (Chaetophorales, Oedogoniales, Zygnematales) maintained in two distinct culture collections, and then, in a second experiment to test community mixing using a co-culture and re-isolation design with two algal strains (Stigeoclonium sp. and Oedogonium sp.). The 14-strain profiling showed that bacterial communities were broadly similar at higher taxonomic ranks, with many shared orders within Pseudomonadota, whereas composition at the ASV level was largely algal-strain-specific. Ordination of phylogeny-aware UniFrac distances showed that culture collection of origin explained more variation in community composition than algal order, an effect reduced but not eliminated after standardizing the culture medium. The co-culture and re-isolation experiment showed that the two algal strains exchanged many bacterial community members, yet algal strain identity remained detectable after re-isolation. These results support a framework where culture history results in strain-specific ASV-level composition within recurrent higher-rank structure, and where algal-strain-specific effects on bacterial community composition become evident when cultures are exposed to a shared bacterial pool. Co-culture followed by algal re-isolation offers a practical approach to examine the persistence of algal-culture bacterial communities under mixing and may help identify candidate bacterial partners with potentially strong host-specific interactions without requiring axenic hosts.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148549428","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":"Bacterial and Green Algal Communities of Norwegian Birch Tree Bark.","authors":"Jaelle C Brealey, Marie L Davey, Bård Pedersen","doi":"10.1007/s00248-026-02841-z","DOIUrl":"https://doi.org/10.1007/s00248-026-02841-z","url":null,"abstract":"<p><p>Tree bark hosts a unique community of microorganisms, distinct from that of other plant tissues and from the microbial associates of macrophytic epiphytes. These corticolous communities are important components of tree-associated food webs. However, the factors influencing corticolous microbial diversity are understudied. We used amplicon sequencing to characterise and compare the bacterial and aerophytic algal communities colonising the bark of birch trees at three sites in southern Norway with differing histories of nitrogen deposition. Within each site, we investigated associations between the corticolous community and variation in placement on the trunk, including north-facing vs. south-facing aspect, height and trunk diameter. While the most abundant bacterial and algal taxa were similar across the three sites, there were clear differences among sites. Aspect had a strong effect at the most oceanic and open site, with increased abundance of cyanobacteria at northern compared to southern aspects. We observed a higher abundance of nitrogen-fixing cyanobacteria at the site where historical nitrogen deposition had been lowest and correspondingly higher abundance of non-diazotrophic green algae where historical nitrogen deposition had been highest. Generally, the bacterial and algal communities followed similar patterns and co-occurrence network analysis revealed that algal taxa were interspersed among bacterial clusters. Our study provides the first characterisation of both the bacterial and aerophytic algal bark-associated communities of birch, one of the most common and ecologically important trees in Norway. Our results add to the growing body of literature demonstrating that tree bark supports a complex microbial community that varies among sites.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148536387","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":"Beyond Dominant Symbionts: Low-Abundance Taxa Govern Microbial Network Topology in Sympatric Ticks.","authors":"Francisco J Márquez, Y Perez-Llano, S A Sánchez-Carrión, M De Rojas, A Caruz","doi":"10.1007/s00248-026-02842-y","DOIUrl":"https://doi.org/10.1007/s00248-026-02842-y","url":null,"abstract":"<p><p>Ticks are obligate hematophagous arthropods and major vectors of diverse bacterial, parasitic, and viral pathogens. They host complex microbial communities that critically influence their biology, fitness, and interactions with pathogens. Using 16 S rRNA gene amplicon sequencing at the amplicon sequence variant (ASV) resolution combined with co-occurrence network analysis, we characterized the bacterial communities of questing adult ticks collected in the Cazorla, Segura y Las Villas Natural Park (Jaén, Spain). A total of 83 adult ticks (27 males and 56 females) representing six sympatric species, Dermacentor marginatus (n = 39), Haemaphysalis punctata (n = 9), H. sulcata (n = 15), Hyalomma lusitanicum (n = 7), Ixodes ricinus s. l. (n = 2), and Rhipicephalus bursa (n = 11), were analyzed. After stringent quality filtering, 3.77 million high-quality reads were recovered and resolved into 407 ASVs. Due to the inherent resolution limits of the V3-V4 region for species-level discrimination, taxonomic assignments were conservatively consolidated at the genus level (101 bacterial genera). Across all tick species, the bacteriome was heavily dominated by Pseudomonadota (98.6%), with species-specific differences primarily driven by variation in obligate symbionts. Coxiella-associated ASVs predominated in multiple tick species, whereas H. lusitanicum exhibited strong dominance by Francisella and secondary representation of Candidatus Midichloria. Alpha and beta diversity analyses revealed distinct compositional patterns shaped by host identity, with lower dispersion observed in D. marginatus and R. bursa, and greater variability among Hyalomma and Haemaphysalis individuals. Spearman-based co-occurrence network analysis indicated a highly cooperative and modular structure (> 98% positive correlations) across tick species. Notably, dominant endosymbionts (Coxiella, Rickettsia, and Francisella) occupied peripheral or weakly connected positions within the networks. In contrast, ecological connectivity was governed by a distinct set of low-abundance taxa, including Roseomonas, Friedmanniella, Methylobacterium, Sphingomonas, Aureimonas, Conexibacter, Marmoricola, Mycobacterium, and Nocardioides, which acted as central hubs bridging network modules, a topology robustly validated by an independent, composition-aware (SparCC) reanalysis within the D. marginatus cohort. These comparative findings demonstrate a functional decoupling between abundance and connectivity in tick microbiomes, highlighting how the \"rare microbiome\" can drive the topological organization and potential stability of microbial communities across sympatric host species.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148520658","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":"Microbial Diversity, Structure and Predicted Carbon-cycling Pathways Show Partial Convergence in Restored and Natural Salt Marshes in Venice Lagoon.","authors":"Anjali Gopakumar, Md Masum Billah, Alessandro Vezzi, Fabio De Pascale, Davide De Battisti, Marco Bonato, Katherine A Dafforn, Laura Airoldi","doi":"10.1007/s00248-026-02836-w","DOIUrl":"https://doi.org/10.1007/s00248-026-02836-w","url":null,"abstract":"<p><p>Salt marshes are increasingly restored following widespread degradation, yet the responses of sediment microbial communities to restoration remain poorly understood, despite their central role in ecosystem functioning. We compared microbial diversity, composition, structure and predicted function between natural (N) and two types of restored salt marshes in Venice lagoon, Italy: marshes restored with tidal creeks (RC), favouring a more natural tidal exchange and creek formation at the low marsh, and marshes restored with barriers (RB), which constrain tidal flow. We analysed sediment microbial communities in the three dominant habitat types of each marsh (unvegetated low marsh, vegetated low marsh, vegetated mid marsh) by amplicon sequencing of the V4 and V5 hypervariable regions of the 16 S rRNA gene. Microbial diversity was similar across natural and restored salt marshes, but community composition and structure were different. Natural marshes were characterised by higher abundances of taxa associated with sulphate reduction and organic matter degradation (e.g. Syntrophobacterales, Bacteroidales and Desulfatiglandales), whereas restored marshes showed greater representation of Desulfobacterales, Desulfobulbales and Chromatiales. In vegetated habitats, microbial communities also differed between low- and mid-marsh elevations, with low marshes enriched in Syntrophobacterales and Desulfobulbales and mid marshes characterised by Ignavibacteriales and Defluviicoccales. Despite these taxonomic differences, predicted carbon-cycling pathways were remarkably similar across restoration types and elevations. This suggests that key microbial functions can recover even when community composition remains distinct, indicating rapid re-establishment of microbial functional potential following restoration.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148447932","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":"Unraveling the Influence of Behavioural Ecotypes on Fish Gut Microbiome: Focus on the Atlantic cod (Gadus morhua) in Icelandic Waters.","authors":"Elena Radaelli, Giorgia Palladino, Daniela Leuzzi, Daniel Scicchitano, Simone Rampelli, Silvia Turroni, Haseeb S Randhawa, Marco Candela","doi":"10.1007/s00248-026-02832-0","DOIUrl":"https://doi.org/10.1007/s00248-026-02832-0","url":null,"abstract":"<p><p>This study investigated the gut microbiome of Atlantic cod in northern Icelandic waters to assess how resident (coastal) and migratory (frontal) behavioural ecotypes influence gut microbial community composition, with a focus on the effects of ecological adaptation and the potential drivers of microbial shifts within this species. A total of 81 intestinal samples from coastal and frontal Atlantic cod collected in northern Iceland in December 2021 and January 2024 were analysed using 16S rRNA gene metabarcoding. Environmental datasets from the Copernicus Marine Service were used to assess the relationship between annual shifts in microbiome composition and changes in environmental conditions. Our results highlight that the Icelandic cod gut microbiome is a highly dynamic system primarily shaped by environmental shifts, such as warming trends and anthropogenic stressors. Because different behavioural ecotypes are inherently exposed to distinct environmental configurations, these distinct macro-scale exposures may indirectly translate into ecotype-specific microbial signatures that shape the differentiation between coastal and offshore habitats; the effects were particularly evident in the coastal populations, underscoring the greater vulnerability of nearshore habitats to environmental shifts and anthropogenic stressors. These findings suggest the role of the microbiome in ecological plasticity of Atlantic cod; concurrently, they reveal distinct ecotype-specific sensitivities to environmental shifts, particularly those of anthropogenic origin, providing a valuable framework that may support future marine conservation strategies.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148447997","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":"The Microbial and Chemical Terroir of Agarwood in French Guiana.","authors":"Kenji Maurice, Nicolas Baldovini, Alba Zaremski, Jérémie Damay, Romain Lehnebach, Yannick Estevez, Marc Ducousso","doi":"10.1007/s00248-026-02824-0","DOIUrl":"https://doi.org/10.1007/s00248-026-02824-0","url":null,"abstract":"<p><p>Agarwood is a highly valued aromatic resinous wood formed in Aquilaria species following stress or infection, yet the putative microbial drivers of its quality remain poorly understood, particularly outside its native range. In this study, we investigated the bacterial and fungal communities associated with agarwood produced from Aquilaria crassna Pierre ex Lecomte planted in French Guiana and examined their relationships with volatile chemical compounds relevant to agarwood fragrance. Using high‑throughput sequencing and comprehensive chemical profiling, we characterized microbial community composition and agarwood volatile profiles across multiple cultivation plots. Despite spatial variability in microbial assemblages, agarwood samples exhibited a conserved chemical signature dominated by chromone derivatives and sesquiterpenoids, indicating the presence of a stable chemical terroir under Guianese environmental conditions. Network analysis revealed numerous bacterial and fungal taxa significantly associated with key chemical classes, suggesting potential microbial contributions to agarwood chemical complexity through plant-microbe interactions or microbial metabolic activity, although causality remains to be established. Comparative analyses with commercial agarwood samples from South-East Asia and the Middle East revealed a distinct chemical profile for Guianese agarwood, highlighting the influence of geographic origin on agarwood quality and supporting an extension of the terroir concept to woody aromatic products. Overall, this study demonstrates that Aquilaria trees cultivated in French Guiana can produce high‑quality agarwood and provides new insights into the interplay between microbial communities and agarwood chemistry. These findings lay the groundwork for the development of locally adapted, microbiome‑informed strategies for sustainable agarwood production.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148448018","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":"Correction to: Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.","authors":"Beatriz Roncero-Ramos, Elena Romano-Rodríguez, Enrique Mateos-Naranjo, Pedro Valle-Romero, Susana Redondo-Gómez","doi":"10.1007/s00248-026-02821-3","DOIUrl":"10.1007/s00248-026-02821-3","url":null,"abstract":"","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"89 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13356076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148422416","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":"Metabarcoding Characterization of Fungal Communities in Spanish Cereals with a Special Focus on Fusarium Species.","authors":"Sergio Alías-Segura, Belén Patiño, Jéssica Gil-Serna","doi":"10.1007/s00248-026-02833-z","DOIUrl":"https://doi.org/10.1007/s00248-026-02833-z","url":null,"abstract":"<p><p>Cereal safety is a critical public health concern, as crops are frequently compromised by mycotoxin-producing fungi, particularly those from the genus Fusarium. Although metabarcoding is a powerful tool for characterizing these fungal communities, the universal internal transcribed spacer 2 (ITS2) marker lacks the resolution required to distinguish closely related species with distinct toxigenic profiles. The objective of this work was to accurately characterize the mycobiota and specific Fusarium community structure in Spanish cereal field samples. We propose a high-resolution metabarcoding workflow within the QIIME 2 environment to optimize Fusarium identification using the translation elongation factor 1-α (TEF1) gene. We developed a TEF1 Naive Bayes classifier trained on a curated database derived from FUSARIUM-ID v.3.0, expanded with eukaryotic sequences to prevent false-positive assignments. This approach was validated through direct comparison with ITS2 in the same samples. As expected, ITS2 significantly underestimates Fusarium diversity, whereas TEF1 enables precise species-level resolution within this genus. General mycobiota analysis performed using ITS2 revealed that fungal communities are shaped primarily by geographical location rather than host cereal species. Crucially, our approach confirmed the persistence of key toxigenic species, such as F. langsethiae and F. graminearum, and revealed broader diversity through the consistent detection of species often overlooked by traditional methods, including F. equiseti, F. acuminatum, and F. culmorum. We conclude that our metabarcoding framework reveals a high Fusarium diversity in Spanish cereal grains, and this knowledge is essential for designing targeted strategies to predict and mitigate mycotoxin contamination in these crops.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148422391","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}