FEMS microbiology ecology最新文献

{"title":"Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus).","authors":"Isabella Wilson, Tahlia Perry, Raphael Eisenhofer, Peggy Rismiller, Michelle Shaw, Frank Grutzner","doi":"10.1093/femsec/fiaf036","DOIUrl":"https://doi.org/10.1093/femsec/fiaf036","url":null,"abstract":"<p><p>Monotreme and marsupial development is characterised by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich environment. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation, but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiota (n = 22) during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Metataxonomic profiling using 16S rRNA gene sequencing revealed that pseudo-pouch microbial communities undergo dramatic changes during lactation, with significant differences in taxonomic composition compared with samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. Furthermore, captivity was not found to have a significant effect on pseudo-pouch microbiota. This study pioneers pouch microbiota research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programs in the future.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803030","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":"Halotolerant plant growth-promoting bacteria mediated plant salt resistance and microbiome-based solutions for sustainable agriculture in saline soils.","authors":"Hui-Ping Li, Hong-Bin Ma, Jin-Lin Zhang","doi":"10.1093/femsec/fiaf037","DOIUrl":"https://doi.org/10.1093/femsec/fiaf037","url":null,"abstract":"<p><p>Soil salinization has been the major form of soil degradation under the dual influence of climate change and high-intensity human activities, threatening global agricultural sustainability and food security. High salt concentrations induce osmotic imbalance, ion stress, oxidative damage, and other hazards to plants, resulting in retarded growth, reduced biomass and even total crop failure. Halo-tolerant plant growth promoting rhizobacteria (HT-PGPR), as a widely distributed group of beneficial soil microorganisms, are emerging as a valuable biological tool for mitigating the toxic effects of high salt concentrations and improve plant growth while remediating degraded saline soil. Here, the current status, harm and treatment measures of global soil salinization are summarized. The mechanism of salt tolerance and growth promotion induced by HT-PGPR are reviewed. We highlight that advances in multi-omics technologies are helpful for exploring the genetic and molecular mechanisms of microbiota centered on HT-PGPR to address the issue of plant losses in saline soil. Future research is urgently needed to comprehensively and robustly determine the interaction mechanism between the root microbiome centered on HT-PGPR and salt-stressed plants via advanced means to maximize the efficacy of HT-PGPR as a microbial agent.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803027","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":"Microplastic biofilms as potential hotspots for plastic biodegradation and nitrogen cycling: A metagenomic perspective.","authors":"Samantha G Fortin, Kelley Uhlig, Robert C Hale, Bongkeun Song","doi":"10.1093/femsec/fiaf035","DOIUrl":"https://doi.org/10.1093/femsec/fiaf035","url":null,"abstract":"<p><p>Microplastics are an emerging contaminant worldwide, with the potential to impact organisms and facilitate the sorption and release of chemicals. Additionally, they create a novel habitat for microbial communities, forming biofilms known as the plastisphere. While the plastisphere has been studied in select aquatic environments, those in estuarine ecosystems merit additional attention due to their proximity to plastic debris sources. Additionally, the role plastisphere communities play in nutrient cycling has rarely been examined. This study used metagenomic analysis to investigate the taxonomic composition and functional genes of developing plastisphere communities living on petroleum-based (polyethylene and polyvinyl chloride) and biopolymer-based (polylactic acid) substrates. Isolated metagenome assembled genomes (MAGs) showed plastisphere communities have the genes necessary to perform nitrification and denitrification and degrade petroleum and biopolymer-based plastics. The functions of these plastispheres have implications for estuarine nitrogen cycling and provide a possible explanation for the plastisphere microbes' competitiveness in biofilm environments. Overall, microplastics in the estuarine system provide a novel habitat for microbial communities and associated nitrogen cycling, facilitating the growth of microbes with plastic degrading capabilities.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771820","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":"Mechanisms and impacts of Agaricus urinascens fairy rings on plant diversity and microbial communities in a montane Mediterranean grassland.","authors":"Giuliano Bonanomi, Giuseppina Iacomino, Luigi Di Costanzo, Mauro Moreno, Giulio Tesei, Marina Allegrezza, Stefano Mazzoleni, Mohamed Idbella","doi":"10.1093/femsec/fiaf034","DOIUrl":"https://doi.org/10.1093/femsec/fiaf034","url":null,"abstract":"<p><p>Fungal fairy rings (FFRs) significantly influence plant communities and soil microbiota. This study investigated the development of Agaricus urinascens fairy rings in a species-rich montane Mediterranean grassland. By combining vegetation analysis, soil chemistry measurements, and next-generation sequencing, we assessed fairy rings' impact on soil properties, plants, fungi, and bacteria. Our findings reveal a fungal-driven transformation of biological communities, with significant variations across FFRs zones. At the fungal front (FF), plant biomass decreased slightly but increased more than threefold inside the ring (>1100 g/m²), favouring grasses like Brachypodium genuense over forbs. In addition, species richness dropped significantly in the FF (-40%) compared to surrounding grassland, particularly affecting perennials. Moreover, our findings reveal substantial alterations in soil properties at the FF, including a 534% increase in P₂O5, a 210% rise in electrical conductivity, and a 36% increase in soil hydrophobicity compared to the surrounding grassland. Clay content at the FF was nearly three times higher than outside the ring (162.8 vs. 57.5 g kg⁻¹), indicating potential structural modifications in the soil matrix. Organic carbon decreased by 10% in the FF, while the C/N ratio and cation exchange capacity dropped significantly. Distinct shifts in microbial composition were observed. Bacterial diversity declined at the FF, where Actinobacteria dominated (85%) and Proteobacteria dropped to 8%. Similarly, fungal diversity was lowest inside the ring but highest in the belt section, with Ascomycota reaching 97% at the FF. Certain taxa, such as Kribbella, Streptomyces, Trichoderma, Penicillium, and Dichotomopilus, coexisted with A. urinascens mycelium. Notably, hydrophobicity at the FF was linked to high calcium oxalate crystal coverage on fungal mycelium and plant roots. This may have accelerated root desiccation, ultimately leading to plant mortality. Overall, our findings provide strong evidence that fairy ring fungi act as ecosystem engineers, shaping the spatial patterns of biotic composition and diversity in Mediterranean grasslands.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763340","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":"Editorial: thematic issue on interactions across microbial ecosystems.","authors":"Søren J Sørensen, Kornelia Smalla, Mette Burmølle, Itzhak Mizrahi","doi":"10.1093/femsec/fiaf031","DOIUrl":"https://doi.org/10.1093/femsec/fiaf031","url":null,"abstract":"","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763331","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":"High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.","authors":"Linnea F M Kop, Hanna Koch, Paula Dalcin Martins, Carolina Suarez, Sabina Karačić, Frank Persson, Britt-Marie Wilén, Per Hagelia, Mike S M Jetten, Sebastian Lücker","doi":"10.1093/femsec/fiaf032","DOIUrl":"https://doi.org/10.1093/femsec/fiaf032","url":null,"abstract":"<p><p>Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7±15% but a wide range between 1.2-61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome (MAG) analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742714","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":"Contrasting alpha, beta, and gamma diversity in the littoral zones of mountain lakes: effects of habitat size and within-lake community structuring on bacterial biogeography.","authors":"Andreas Härer, Joshua Dominguez, Jonathan B Shurin, Diana J Rennison","doi":"10.1093/femsec/fiaf026","DOIUrl":"10.1093/femsec/fiaf026","url":null,"abstract":"<p><p>Research on microbial biogeography has revealed key patterns like the diversity-area relationship and distance-decay of similarity. However, how habitat size affects bacterial diversity in freshwater environments remains largely unclear. Here, we characterize bacterial communities in the littoral zones of 10 mountain lakes in the Sierra Nevada, CA, ranging in surface area from 0.92 to 71.72 ha. Despite significant habitat size effects on community composition, dominant bacterial phyla were shared across lakes. We found no evidence for diversity-area relationships, either in single samples (alpha diversity) or cumulative lake-level samples (within-lake gamma diversity), when accounting for environmental variation. Moreover, within-lake beta diversity showed little spatial structuring, with similar bacterial community composition across samples regardless of geographic distance. Gamma diversity did not reach saturation with our sample size, and lake size had no effect on the predicted sample size necessary to reach gamma diversity saturation. Our findings offer new insights into diversity-area dynamics and spatial structuring by investigating alpha, beta, and gamma diversity in freshwater environments. Notably, individual water samples captured much of the bacterial community, with strong correlations between alpha and gamma diversity. These results advance our understanding of microbial biogeography and inform sampling designs for characterizing bacterial diversity in freshwater ecosystems.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647862","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":"Cryptic iron cycling influenced by organic carbon availability in a seasonally stratified lake.","authors":"Verena Nikeleit, Markus Maisch, Daniel Straub, Sümeyya Eroglu, Jimena C Lopez-Rivoldi, Harald Strauss, Fin Ring-Hrubesh, James M Byrne, Andreas Kappler, Casey Bryce","doi":"10.1093/femsec/fiaf029","DOIUrl":"10.1093/femsec/fiaf029","url":null,"abstract":"<p><p>Iron cycling including phototrophic Fe(II) oxidation has been observed in multiple permanently stratified meromictic lakes, yet less focus has been on dimictic lakes, which seasonally overturn and are vastly more common. Here, we investigated iron cycling in a dimictic lake, Großes Heiliges Meer in northwest Germany, using 16S rRNA amplicon sequencing, as well as in-situ and lab-based experiments. Bacterial community composition in the lake follows geochemical gradients and differs markedly between oxic and anoxic conditions. Potential iron-metabolizing bacteria were found mostly in anoxic conditions at 7 and 8 m depth and were comprised of taxa from the genera Chlorobium, Thiodictyon, Sideroxydans, Geobacter, and Rhodoferrax. We were able to recreate active iron cycling (1) with an ex-situ microbial community from 8 m depth and (2) with a successful microbial enrichment culture from 7 m depth. Varying the light and organic carbon availability in lab-based experiments showed that Fe(III) reduction overshadows Fe(II) oxidation leading to a cryptic iron cycle. Overall, we could demonstrate that microbial iron cycling can be a key biogeochemical process in dimictic lakes despite regular disturbance, and that complex environmental factors such as organic substrates control the balance between Fe(II) oxidation and Fe(III) reduction.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974394/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669188","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":"Evaluation of Thiobacillus denitrificans' sustainability in nitrate-reducing Fe(II) oxidation and the potential significance of Fe(II) as a growth-supporting reductant.","authors":"Stefanie Becker, Thu Trang Dang, Ran Wei, Andreas Kappler","doi":"10.1093/femsec/fiaf024","DOIUrl":"10.1093/femsec/fiaf024","url":null,"abstract":"<p><p>The betaproteobacterium Thiobacillus denitrificans (ATCC 25259) oxidizes Fe(II) while reducing nitrate, yet its capacity for autotrophic growth as a nitrate-reducing Fe(II)-oxidizer remains uncertain. This study explored this capacity through cultivation experiments across multiple transfers, using growth medium with Fe(II) and nitrate as sole electron donor and acceptor, respectively. This setup necessitated nitrate reduction coupled to Fe(II) oxidation as the primary energy-yielding mechanism and Fe(II) as the exclusive electron donor for CO2 fixation and biomass production. Thiosulfate/nitrate pregrown T. denitrificans oxidized 42% of 10 mM Fe(II), reduced 54% of 3.5 mM nitrate, and accumulated 1.6 mM nitrite, but showed no cell growth. Subsequent transfers from this Fe(II)/nitrate culture to fresh medium with Fe(II) and nitrate showed no nitrate-reducing Fe(II) oxidation or population growth. While bacterial activity [Fe(II) oxidation, nitrate reduction] occurred in the first transfer from thiosulfate/nitrate to Fe(II)/nitrate, nitrite was produced, further reacting with Fe(II) abiotically (chemodenitrification). A kinetic model assessed enzymatic versus abiotic Fe(II) oxidation, revealing enzymatic oxidation accounted for twice as much (ca. 70%) as abiotic denitrification (ca. 30%) within 22 days. These findings suggest T. denitrificans performs the first step of denitrification with Fe(II) as an electron donor but does not achieve autotrophic growth under these conditions.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647863","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":"The bacterial community associated with the solitary resin bee Megachile tosticauda throughout its life cycle.","authors":"Elisabeth Williamson, Kelly Hill, Katja Hogendoorn, Raphael Eisenhofer","doi":"10.1093/femsec/fiaf023","DOIUrl":"10.1093/femsec/fiaf023","url":null,"abstract":"<p><p>Unlike in eusocial bees where the identity, acquisition, and function of symbiotic microbes are well understood, little is known about the relationships formed between solitary bees and bacteria. Assessing the potential role of microbes in solitary bee health is important, especially in the face of global bee declines. Early evidence suggests solitary bee microbiomes differ between bee species and development stages, but the reported bacteria are often indistinguishable from environmental taxa. Here, we use metabarcoding of the 16S rRNA gene to characterize the bacterial communities associated with solitary resin bee Megachile tosticauda. We describe the microbiome at different life cycle stages, and within pollen provisions, and investigate indirect inheritance from nesting substrate upon eclosion. The microbiome of adult M. tosticauda was consistent between samples, and the bacterial composition of larval pollen supplies changed with progressing larval development. In wild adults and pollen provisions, the genus Acinetobacter-a common nectar associate-dominated the communities. In prepupae and frass, Tyzzerella dominated, a genus that has been found in a number of other immature bee systems. Intriguingly, while wild adults did not harbour Tyzzerella, all bees that had newly emerged from the nest did. The combined observations show that M. tosticauda acquire their bacterial community from the environment, and Tyzzerella may represent a beneficial symbiont for mature brood.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11916890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556166","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}