ISME communications最新文献

{"title":"Radiolytic support for oxidative metabolism in an ancient subsurface brine system.","authors":"Devan M Nisson, Thomas L Kieft, Julio Castillo, Scott M Perl, Tullis C Onstott","doi":"10.1093/ismeco/ycae138","DOIUrl":"10.1093/ismeco/ycae138","url":null,"abstract":"<p><p>Long-isolated subsurface brine environments (Ma-Ga residence times) may be habitable if they sustainably provide substrates, e.g. through water-rock reactions, that support microbial catabolic energy yields exceeding maintenance costs. The relative inaccessibility and low biomass of such systems has led to limited understanding of microbial taxonomic distribution, metabolism, and survival under abiotic stress exposure in these extreme environments. In this study, taxonomic and metabolic annotations of 95 single-cell amplified genomes were obtained for one low biomass (10³-10⁴ cells/ml), hypersaline (246 g/L), and radiolytically enriched brine obtained from 3.1 km depth in South Africa's Moab Khotsong mine. The majority of single-cell amplified genomes belonged to three halophilic families (<i>Halomondaceae</i> (58%), <i>Microbacteriaceae</i> (24%), and <i>Idiomarinaceae</i> (8%)) and did not overlap with any family-level identifications from service water or a less saline dolomite aquifer sampled in the same mine. Functional annotation revealed complete metabolic modules for aerobic heterotrophy (organic acids and xenobiotic oxidation), fermentation, denitrification, and thiosulfate oxidation, suggesting metabolic support in a microoxic environment. Single-cell amplified genomes also contained complete modules for degradation of complex organics, amino acid and nucleotide synthesis, and motility. This work highlights a long-isolated subsurface fluid system with microbial metabolism fueled by radiolytically generated substrates, including O₂, and suggests subsurface brines with high radionuclide concentrations as putatively habitable and redox-sustainable environments over long (ka-Ga) timescales.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae138"},"PeriodicalIF":5.1,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial and fungal components of the microbiome have distinct roles in Hawaiian <i>drosophila</i> reproduction.","authors":"Matthew J Medeiros, Laura Seo, Aziel Macias, Donald K Price, Joanne Y Yew","doi":"10.1093/ismeco/ycae134","DOIUrl":"10.1093/ismeco/ycae134","url":null,"abstract":"<p><p>The microbiome provides numerous physiological benefits for host animals. The role of bacterial members of microbiomes to host physiology is well-documented. However, much less is known about the contributions and interactions of fungal members, even though fungi are integral components of many microbiomes, including those of humans and insects. Here, we used antibacterial and antifungal drugs to manipulate the gut microbiome of a Hawaiian picture-wing <i>Drosophila</i> species, <i>Drosophila grimshawi</i>, and identified distinct effects for each treatment on microbiome community stability, reproduction, and lipid metabolism. Female oogenesis, fecundity, and mating drive were significantly diminished with antifungal treatment. In contrast, male fecundity was affected by antibacterial but not antifungal treatment. For males and females, simultaneous treatment with both antibacterial and antifungal drugs resulted in severely reduced fecundity and changes in fatty acid levels and composition. Microbial transplants using frass harvested from control flies partially restored microbiome composition and female fecundity. Overall, our results reveal that antibacterial and antifungal treatments have distinct effects on host fecundity, mating behavior, and lipid metabolism, and that interkingdom interactions contribute to microbial community stability and reproduction.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae134"},"PeriodicalIF":5.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11643357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142831041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recurrent association between <i>Trichodesmium</i> colonies and calcifying amoebae.","authors":"Futing Zhang, Siyuan Wang, Anna-Neva Visser, Coco Koedooder, Meri Eichner, O Roger Anderson, Sonya T Dyhrman, Yeala Shaked","doi":"10.1093/ismeco/ycae137","DOIUrl":"10.1093/ismeco/ycae137","url":null,"abstract":"<p><p>Colonies of the N₂-fixing cyanobacterium <i>Trichodesmium</i> spp. constitute a consortium with multiple microorganisms that collectively exert ecosystem-level influence on marine carbon and nitrogen cycling, shunting newly fixed nitrogen to low nitrogen systems, and exporting both carbon and nitrogen to the deep sea. Here we identify a seasonally recurrent association between puff colonies and amoebae through a two-year survey involving over 10 000 <i>Trichodesmium</i> colonies in the Red Sea. This association was most commonly found in near-shore populations during spring. Microscopic observations revealed consistent amoebae morphology throughout the study, and both morphological characteristics and 18S rRNA gene sequencing suggested that these amoebae are likely to belong to the species <i>Trichosphaerium micrum</i>, an amoeba that forms a CaCO₃ shell. Co-cultures of <i>Trichosphaerium micrum</i> and <i>Trichodesmium</i> grown in the laboratory suggest that the amoebae feed on heterotrophic bacteria and not <i>Trichodesmium</i>, which adds a consumer dynamic to the complex microbial interactions within these colonies. Sinking experiments with fresh colonies indicated that the presence of the CaCO₃-shelled amoebae decreased colony buoyancy. As such, this novel association may accelerate <i>Trichodesmium</i> sinking rates and facilitate carbon and nitrogen export to the deep ocean. Amoebae have previously been identified in <i>Trichodesmium</i> colonies in the western North Atlantic (Bermuda and Barbados), suggesting that this type of association may be widespread. This association may add a new critical facet to the microbial interactions underpinning carbon and nitrogen fixation and fate in the present and future ocean.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae137"},"PeriodicalIF":5.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxon-specific contributions of microeukaryotes to biological carbon pump in the Oyashio region.","authors":"Qingwei Yang, Yanhui Yang, Jun Xia, Hideki Fukuda, Yusuke Okazaki, Toshi Nagata, Hiroyuki Ogata, Hisashi Endo","doi":"10.1093/ismeco/ycae136","DOIUrl":"10.1093/ismeco/ycae136","url":null,"abstract":"<p><p>Microeukaryotes are critical components of sinking particles contributing to carbon export from the surface to deep oceans. However, the knowledge of the sinking microeukaryotic communities and their dynamics is currently limited. In this study, we applied 18S rRNA gene metabarcoding to investigate the microeukaryotic communities in sinking and suspended particles distinguished by marine snow catchers during spring in the Oyashio region. Sinking particles displayed distinct communities and lower diversity than suspended particles. The community compositions of the sinking particles varied with depth, suggesting that microeukaryotes were selectively disaggregated or decomposed during settling. Prymnesiophyceae and diatoms were effectively removed, as indicated by their decreased abundance in sinking particles at increasing depths. Conversely, Dinophyceae maintained a higher abundance in sinking particles across depths, indicating resistance to disaggregation and decomposition. Spirotrichea and heterotrophic Dinophyceae were enriched in sinking particles, while marine stramenopiles groups were enriched in suspended particles. The heterotrophs in the deeper layers were mainly transported from the surface layers by increasing their relative abundance towards deep layers, indicating that they contributed to the transformation processes of sinking particles. Overall, our results demonstrate the functional differences among microeukaryotes in the biological carbon pump.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae136"},"PeriodicalIF":5.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11575449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Significant role of symbiotic bacteria in the blood digestion and reproduction of <i>Dermanyssus gallinae</i> mites.","authors":"Qi Liu, Tiancong Sun, Penglong Wang, Lifang Wang, Helena Frantova, David Hartmann, Jan Perner, Weiwei Sun, Baoliang Pan","doi":"10.1093/ismeco/ycae127","DOIUrl":"https://doi.org/10.1093/ismeco/ycae127","url":null,"abstract":"<p><p>Endosymbiotic bacteria significantly impact the fitness of their arthropod hosts. <i>Dermanyssus gallinae</i>, the poultry red mite, is a blood-feeding ectoparasite that exclusively feeds on avian blood. While there is a relatively comprehensive understanding of its microbial community structures across developmental stages based on 16S rRNA sequencing， the functional integration of these microbes within the host's physiology remains elusive. This study aims to elucidate the role of symbiotic bacteria in <i>D. gallinae</i> biology. 16S rRNA amplicon sequencing and fluorescence <i>in situ</i> hybridization revealed a prominent midgut-confinement bacterial microbiota with considerable diversity, out of which <i>Kocuria</i> and <i>Bartonella</i> A acted as the predominant bacterial genera inhabiting <i>D. gallinae</i>. The relative abundance of <i>Bartonella</i> A increased rapidly after blood-sucking, suggesting its adaptation to a blood-based diet and its pivotal role in post-engorgement activities. Some of the isolated bacterial strains from <i>D. gallinae</i> display hemolytic activity on blood agar, potentially aiding blood digestion. To corroborate this <i>in vivo</i>, antibiotic-mediated clearance was exploited to generate dysbiosed cohorts of <i>D. gallinae</i> mites, lacking some of the key bacterial species. Phenotypic assessments revealed that dysbiosed mites experienced delayed blood digestion and diminished reproductive capacity. Whole-genome sequencing identified <i>Bartonella</i> A as a new species within the genus <i>Bartonella</i>, exhibiting characteristics of an obligate symbiont. These findings underscore the significance of microbiota in poultry red mites and suggest microbiota-targeted strategies for controlling mite populations in poultry farms.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae127"},"PeriodicalIF":5.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11550332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cover crop monocultures and mixtures enhance bacterial abundance and functionality in the maize root zone.","authors":"Debjyoti Ghosh, Yijie Shi, Iris M Zimmermann, Tobias Stürzebecher, Katja Holzhauser, Martin von Bergen, Anne-Kristin Kaster, Sandra Spielvogel, Michaela A Dippold, Jochen A Müller, Nico Jehmlich","doi":"10.1093/ismeco/ycae132","DOIUrl":"https://doi.org/10.1093/ismeco/ycae132","url":null,"abstract":"<p><p>Cover cropping is an effective method to protect agricultural soils from erosion, promote nutrient and moisture retention, encourage beneficial microbial activity, and maintain soil structure. Re-utilization of winter cover crop root channels by maize roots during summer allows the cash crop to extract resources from distal regions in the soil horizon. In this study, we investigated how cover cropping during winter followed by maize (<i>Zea mays</i> L.) during summer affects the spatiotemporal composition and function of the bacterial communities in the maize rhizosphere and surrounding soil samples using quantitative polymerase chain reaction (PCR), 16S ribosomal ribonucleic acid (rRNA) gene amplicon sequencing, and metaproteomics. We found that the bacterial community differed significantly among cover crop species, soil depths, and maize growth stages. Bacterial abundance increased in reused root channels, and it continued to increase as cover crop diversity changed from monocultures to mixtures. Mixing <i>Fabaceae</i> with <i>Brassicaceae</i> or <i>Poaceae</i> enhanced the overall contributions of several steps of the bacterial carbon and nitrogen cycles, especially glycolysis and the pentose phosphate pathway. The deeper root channels of <i>Fabaceae</i> and <i>Brassicaceae</i> as compared to <i>Poaceae</i> corresponded to higher bacterial 16S rRNA gene copy numbers and improved community presence in the subsoil regimes, likely due to the increased availability of root exudates secreted by maize roots. In conclusion, root channel reuse improved the expression of metabolic pathways of the carbon and nitrogen cycles and the bacterial communities, which is beneficial to the soil and to the growing crops.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae132"},"PeriodicalIF":5.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11546721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emergence of metabolic coupling to the heterotroph <i>Alteromonas</i> promotes dark survival in <i>Prochlorococcus</i>.","authors":"Allison Coe, Rogier Braakman, Steven J Biller, Aldo Arellano, Christina Bliem, Nhi N Vo, Konnor von Emster, Elaina Thomas, Michelle DeMers, Claudia Steglich, Jef Huisman, Sallie W Chisholm","doi":"10.1093/ismeco/ycae131","DOIUrl":"10.1093/ismeco/ycae131","url":null,"abstract":"<p><p><i>Prochlorococcus</i> is found throughout the euphotic zone in the oligotrophic open ocean. Deep mixing and sinking while attached to particles can, however, transport <i>Prochlorococcus</i> cells below this sunlit zone, depriving them of light for extended periods of time. Previous work has shown that <i>Prochlorococcus</i> by itself cannot survive extended periods of darkness. However, when co-cultured with a heterotrophic microbe and subjected to repeated periods of extended darkness, <i>Prochlorococcus</i> cells develop an epigenetically inherited dark-tolerant phenotype that can survive longer periods of darkness. Here we examine the metabolic and physiological changes underlying this adaptation using co-cultures of dark-tolerant and parental strains of <i>Prochlorococcus</i>, each grown with the heterotroph <i>Alteromonas</i> under diel light:dark conditions. The relative abundance of <i>Alteromonas</i> was higher in dark-tolerant than parental co-cultures, while dark-tolerant <i>Prochlorococcus</i> cells were larger, contained less chlorophyll, and were less synchronized to the light:dark cycle. Meta-transcriptome analysis revealed that dark-tolerant co-cultures undergo a joint change, in which <i>Prochlorococcus</i> undergoes a relative shift from photosynthesis to respiration, while <i>Alteromonas</i> shifts toward using more organic acids instead of sugars. Furthermore, the transcriptome data suggested enhanced biosynthesis of amino acids and purines in dark-tolerant <i>Prochlorococcus</i> and enhanced degradation of these compounds in <i>Alteromonas</i>. Collectively, our results demonstrate that dark adaptation involves a strengthening of the metabolic coupling between <i>Prochlorococcus</i> and <i>Alteromonas</i>, presumably mediated by an enhanced, and compositionally modified, carbon exchange between the two species.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae131"},"PeriodicalIF":5.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic dissection of <i>Escherichia marmotae</i> provides insights into diversity and pathogenic potential.","authors":"Ulrike Binsker, Carlus Deneke, Hafiz Muhammad Hamid, Ashish K Gadicherla, André Göhler, Annemarie Käsbohrer, Jens A Hammerl","doi":"10.1093/ismeco/ycae126","DOIUrl":"https://doi.org/10.1093/ismeco/ycae126","url":null,"abstract":"<p><p>Anthropogenic activities enhance the interconnection of human, animal, and environmental habitats and drive the evolution and inter-niche transmission of bacteria. Clear identification of emerging bacteria and pathogen control is therefore a public health priority. In 2015, the novel <i>Escherichia</i> species <i>Escherichia marmotae</i> was assigned, but due to the lack of appropriate detection and typing technologies, the One Health impact of this species is still being unraveled. <i>E. marmotae</i> represents a missing link in the impact of <i>Escherichia</i> spp. Here, we report 25 <i>E. marmotae</i> identified by next-generation sequencing that were previously phenotypically characterized as <i>Escherichia coli</i> during national zoonosis monitoring of food-producing animals. Applying fastANI to 153 738 published <i>Escherichia</i> spp. genome assemblies, we identified further 124 <i>E. marmotae</i>, originally classified as <i>E. coli</i>. Phylogenomics of all 149 isolates reveals an undefined population structure that is independent of the ecological niche. We highlight the phenotypic, genomic, and plasmid diversity of <i>E. marmotae</i> and provide evidence for gene flow across the species. The latter is illustrated by the acquisition of antibiotic resistance plasmids and pathogenicity islands, such as the type III secretion system. Thus, our comprehensive genomic overview of an emerging potential opportunistic pathogen underlines the importance of improved detection and characterization.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae126"},"PeriodicalIF":5.1,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11546641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soil nutrient amendment increases the potential for inter-kingdom resource competition among foliar endophytes.","authors":"Zoe A Hansen, Michael R Fulcher, Nicholas Wornson, Seth A Spawn-Lee, Mitch Johnson, Zewei Song, Matthew Michalska-Smith, Georgiana May, Eric W Seabloom, Elizabeth T Borer, Linda L Kinkel","doi":"10.1093/ismeco/ycae130","DOIUrl":"10.1093/ismeco/ycae130","url":null,"abstract":"<p><p>Foliar endophytes play crucial roles in large-scale ecosystem functions such as plant productivity, decomposition, and nutrient cycling. While the possible effects of environmental nutrient supply on the growth and carbon use of endophytic microbes have critical implications for these processes, these impacts are not fully understood. Here, we examined the effects of long-term elevated nitrogen, phosphorus, potassium, and micronutrient (NPKμ) supply on culturable bacterial and fungal foliar endophytes inhabiting the prairie grass <i>Andropogon gerardii</i>. We hypothesized that elevated soil nutrients alter the taxonomic composition and carbon use phenotypes of foliar endophytes and significantly shift the potential for resource competition among microbes within leaves. We observed changes in taxonomic composition and carbon use patterns of fungal, but not bacterial, endophytes of <i>A. gerardii</i> growing in NPKμ-amended versus ambient conditions. Fungal endophytes from NPKμ-amended plants had distinct carbon use profiles and demonstrated greater specialization across carbon sources compared to control plots. Resource niche overlap between bacterial and fungal endophytes also increased with plot nutrient supply, suggesting enhanced potential for inter-kingdom competition. Collectively, this work suggests that soil nutrient enrichment alters how fungal endophyte communities exist in the foliar environment, with potentially significant implications for broad-scale ecosystem function.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae130"},"PeriodicalIF":5.1,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11586052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Growth of soil ammonia-oxidizing archaea on air-exposed solid surface.","authors":"Christiana Abiola, Joo-Han Gwak, Ui-Ju Lee, Samuel Imisi Awala, Man-Young Jung, Woojun Park, Sung-Keun Rhee","doi":"10.1093/ismeco/ycae129","DOIUrl":"10.1093/ismeco/ycae129","url":null,"abstract":"<p><p>Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOMs), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), <i>Nitrososphaera viennensis</i> EN76 and \"<i>Nitrosotenuis chungbukensis</i>\" MY2, and a soil ammonia-oxidizing bacterium, <i>Nitrosomonas europaea</i> ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of <i>N. viennensis</i> EN76 and \"<i>N. chungbukensis</i>\" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of <i>N. europaea</i> ATCC 19718 was comparable on floating filters and liquid media. <i>N. viennensis</i> EN76 and <i>N. europaea</i> ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of <i>N. viennensis</i> EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, ammonia oxidation (including ammonia monooxygenase subunit C (<i>amoC3</i>) and multicopper oxidases), and defense against H₂O₂-induced oxidative stress. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the \"Ca. Nitrosocosmicus\" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae129"},"PeriodicalIF":5.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11561398/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}