FEMS microbiology ecology最新文献_第4页

Prokaryotic morphological features and maintenance activities governed by seasonal productivity conditions. 原核生物的形态特征和维护活动受季节性生产力条件的制约。

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-09-11 DOI: 10.1093/femsec/fiae121

Ashish Verma,Dennis Amnebrink,Cheng Choo Lee,Sun Nyunt Wai,Linda Sandblad,Jarone Pinhassi,Johan Wikner

{"title":"Prokaryotic morphological features and maintenance activities governed by seasonal productivity conditions.","authors":"Ashish Verma,Dennis Amnebrink,Cheng Choo Lee,Sun Nyunt Wai,Linda Sandblad,Jarone Pinhassi,Johan Wikner","doi":"10.1093/femsec/fiae121","DOIUrl":"https://doi.org/10.1093/femsec/fiae121","url":null,"abstract":"Prokaryotic maintenance respiration and associated metabolic activities constitute a considerable proportion of the total respiration of carbon to CO2 in the ocean's mixed layer. However, seasonal influences on prokaryotic maintenance activities in terms of morphological and metabolic adaptations at low (winter) and high productivity (summer) are still unclear. To address this, we examined the natural prokaryotic communities at the mesocosm scale to analyse the differences in their morphological features and gene expression at low and high maintenance respiration, experimentally manipulated with the specific growth rate. Here, we showed that morphological features including membrane blebbing, membrane vesicles and cell‒cell connections occurred under high productivity. Metabolic adaptations associated with maintenance activities were observed under low productivity. Several Kyoto Encyclopedia of Genes and Genomes categories related to signal transduction, energy metabolism, and translational machinery supported maintenance activities under simulated winter conditions. Differential abundances of genes related to transporters, osmoregulation, nitrogen metabolism, ribosome biogenesis, and cold stress were observed. Our results demonstrate how specific growth rate in different seasons can influence resource allocation at the levels of morphological features and metabolic adaptations. This motivates further study of morphological features and their ecological role during high productivity, while investigations of metabolic adaptations during low productivity can advance our knowledge about maintenance activities.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142212922","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}

引用次数: 0

Genome reduction in novel, obligately methyl-reducing Methanosarcinales isolated from arthropod guts (Methanolapillus gen. nov. and Methanimicrococcus). 从节肢动物内脏（Methanolapillus gen.）

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-13 DOI: 10.1093/femsec/fiae111

Evgenii Protasov, Hanna Reeh, Pengfei Liu, Anja Poehlein, Katja Platt, Thomas Heimerl, Vincent Hervé, Rolf Daniel, Andreas Brune

{"title":"Genome reduction in novel, obligately methyl-reducing Methanosarcinales isolated from arthropod guts (Methanolapillus gen. nov. and Methanimicrococcus).","authors":"Evgenii Protasov, Hanna Reeh, Pengfei Liu, Anja Poehlein, Katja Platt, Thomas Heimerl, Vincent Hervé, Rolf Daniel, Andreas Brune","doi":"10.1093/femsec/fiae111","DOIUrl":"10.1093/femsec/fiae111","url":null,"abstract":"Recent metagenomic studies have identified numerous lineages of hydrogen-dependent, obligately methyl-reducing methanogens. Yet, only a few representatives have been isolated in pure culture. Here, we describe six new species with this capability in the family Methanosarcinaceae (order Methanosarcinales), which makes up a substantial fraction of the methanogenic community in arthropod guts. Phylogenomic analysis placed the isolates from cockroach hindguts into the genus Methanimicrococcus (M. hacksteinii, M. hongohii, and M. stummii) and the isolates from millipede hindguts into a new genus, Methanolapillus (M. africanus, M. millepedarum, and M. ohkumae). Members of this intestinal clade, which includes also uncultured representatives from termites and vertebrates, have substantially smaller genomes (1.6-2.2 Mbp) than other Methanosarcinales. Genome reduction was accompanied by the loss of the upper part of the Wood-Ljungdahl pathway, several energy-converting membrane complexes (Fpo, Ech, and Rnf), and various biosynthetic pathways. However, genes involved in the protection against reactive oxygen species (catalase and superoxide reductase) were conserved in all genomes, including cytochrome bd (CydAB), a high-affinity terminal oxidase that may confer the capacity for microaerobic respiration. Since host-associated Methanosarcinales are nested within omnivorous lineages, we conclude that the specialization on methyl groups is an adaptation to the intestinal environment.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897184","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}

引用次数: 0

Correction to: Methicillin-resistant Staphylococcus aureus and coagulase-negative Staphylococcus produce antimicrobial substances against members of the skin microbiota in children with atopic dermatitis. 更正：耐甲氧西林金黄色葡萄球菌和凝固酶阴性葡萄球菌对特应性皮炎患儿皮肤微生物群产生抗菌物质。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-13 DOI: 10.1093/femsec/fiae107

引用次数: 0

Candida species-specific colonization in the healthy and impaired human gastrointestinal tract as simulated using the Mucosal Ileum-SHIME® model. 使用 Mucosal Ileum-SHIME® 模型模拟健康和受损人体胃肠道中念珠菌物种特异性定植。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-13 DOI: 10.1093/femsec/fiae113

Benoît Marsaux, Frédéric Moens, Gies Vandevijver, Massimo Marzorati, Tom van de Wiele

{"title":"Candida species-specific colonization in the healthy and impaired human gastrointestinal tract as simulated using the Mucosal Ileum-SHIME® model.","authors":"Benoît Marsaux, Frédéric Moens, Gies Vandevijver, Massimo Marzorati, Tom van de Wiele","doi":"10.1093/femsec/fiae113","DOIUrl":"10.1093/femsec/fiae113","url":null,"abstract":"Candida species primarily exist as harmless commensals in the gastrointestinal tract of warm-blooded animals. However, they can also cause life-threatening infections, which are often associated with gut microbial dysbiosis. Identifying the microbial actors that restrict Candida to commensalism remains a significant challenge. In vitro models could enable a mechanistic study of the interactions between Candida and simulated colon microbiomes. Therefore, this study aimed to elucidate the spatial and temporal colonization kinetics of specific Candida, including C. albicans, C. tropicalis, and C. parapsilosis, and their relative Nakaseomyces glabratus, by using an adapted SHIME® model, simulating the ileum, and proximal and distal colons. We monitored fungal and bacterial colonization kinetics under conditions of eubiosis (commensal lifestyle) and antibiotic-induced dysbiosis (pathogenic lifestyle). Our findings highlighted the variability in the colonization potential of Candida species across different intestinal regions. The ileum compartment proved to be the most favourable environment for C. albicans and C. parapsilosis under conditions of eubiosis. Antibiotic-induced dysbiosis resulted in resurgence of opportunistic Candida species, especially C. tropicalis and C. albicans. Future research should focus on identifying specific bacterial species influencing Candida colonization resistance and explore the long-term effects of antibiotics on the mycobiome and bacteriome.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11350379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016874","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}

引用次数: 0

Single-cell measurement of microbial growth rate with Raman microspectroscopy. 利用拉曼显微光谱技术单细胞测量微生物的生长速度。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-13 DOI: 10.1093/femsec/fiae110

Tristan A Caro, Srishti Kashyap, George Brown, Claudia Chen, Sebastian H Kopf, Alexis S Templeton

{"title":"Single-cell measurement of microbial growth rate with Raman microspectroscopy.","authors":"Tristan A Caro, Srishti Kashyap, George Brown, Claudia Chen, Sebastian H Kopf, Alexis S Templeton","doi":"10.1093/femsec/fiae110","DOIUrl":"10.1093/femsec/fiae110","url":null,"abstract":"Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman-SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11347945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901478","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}

引用次数: 0

Exploring modes of microbial interactions with implications for methane cycling. 探索微生物相互作用模式对甲烷循环的影响。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-13 DOI: 10.1093/femsec/fiae112

Kristof Brenzinger, Timo Glatter, Anna Hakobyan, Marion Meima-Franke, Hans Zweers, Werner Liesack, Paul L E Bodelier

{"title":"Exploring modes of microbial interactions with implications for methane cycling.","authors":"Kristof Brenzinger, Timo Glatter, Anna Hakobyan, Marion Meima-Franke, Hans Zweers, Werner Liesack, Paul L E Bodelier","doi":"10.1093/femsec/fiae112","DOIUrl":"10.1093/femsec/fiae112","url":null,"abstract":"Methanotrophs are the sole biological sink of methane. Volatile organic compounds (VOCs) produced by heterotrophic bacteria have been demonstrated to be a potential modulating factor of methane consumption. Here, we identify and disentangle the impact of the volatolome of heterotrophic bacteria on the methanotroph activity and proteome, using Methylomonas as model organism. Our study unambiguously shows how methanotrophy can be influenced by other organisms without direct physical contact. This influence is mediated by VOCs (e.g. dimethyl-polysulphides) or/and CO2 emitted during respiration, which can inhibit growth and methane uptake of the methanotroph, while other VOCs had a stimulating effect on methanotroph activity. Depending on whether the methanotroph was exposed to the volatolome of the heterotroph or to CO2, proteomics revealed differential protein expression patterns with the soluble methane monooxygenase being the most affected enzyme. The interaction between methanotrophs and heterotrophs can have strong positive or negative effects on methane consumption, depending on the species interacting with the methanotroph. We identified potential VOCs involved in the inhibition while positive effects may be triggered by CO2 released by heterotrophic respiration. Our experimental proof of methanotroph-heterotroph interactions clearly calls for detailed research into strategies on how to mitigate methane emissions.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141912371","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}

引用次数: 0

Correction to: Responses of attached bacterial communities to blooms of the swimming shelled pteropod creseis acicula in Daya Bay, southern China. 更正：附着细菌群落对中国南部大亚湾游壳翼足目creseis acicula繁殖的响应。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-13 DOI: 10.1093/femsec/fiae108

引用次数: 0

Isolation and characterization of novel acetogenic Moorella strains for employment as potential thermophilic biocatalysts. 分离和鉴定新型醋酸菌株，将其用作潜在的嗜热生物催化剂。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-13 DOI: 10.1093/femsec/fiae109

Tim Böer, Lisa Engelhardt, Alina Lüschen, Lena Eysell, Hiroki Yoshida, Dominik Schneider, Largus T Angenent, Mirko Basen, Rolf Daniel, Anja Poehlein

{"title":"Isolation and characterization of novel acetogenic Moorella strains for employment as potential thermophilic biocatalysts.","authors":"Tim Böer, Lisa Engelhardt, Alina Lüschen, Lena Eysell, Hiroki Yoshida, Dominik Schneider, Largus T Angenent, Mirko Basen, Rolf Daniel, Anja Poehlein","doi":"10.1093/femsec/fiae109","DOIUrl":"10.1093/femsec/fiae109","url":null,"abstract":"Thermophilic acetogenic bacteria have attracted attention as promising candidates for biotechnological applications such as syngas fermentation, microbial electrosynthesis, and methanol conversion. Here, we aimed to isolate and characterize novel thermophilic acetogens from diverse environments. Enrichment of heterotrophic and autotrophic acetogens was monitored by 16S rRNA gene-based bacterial community analysis. Seven novel Moorella strains were isolated and characterized by genomic and physiological analyses. Two Moorella humiferrea isolates showed considerable differences during autotrophic growth. The M. humiferrea LNE isolate (DSM 117358) fermented carbon monoxide (CO) to acetate, while the M. humiferrea OCP isolate (DSM 117359) transformed CO to hydrogen and carbon dioxide (H2 + CO2), employing the water-gas shift reaction. Another carboxydotrophic hydrogenogenic Moorella strain was isolated from the covering soil of an active charcoal burning pile and proposed as the type strain (ACPsT) of the novel species Moorella carbonis (DSM 116161T and CCOS 2103T). The remaining four novel strains were affiliated with Moorella thermoacetica and showed, together with the type strain DSM 2955T, the production of small amounts of ethanol from H2 + CO2 in addition to acetate. The physiological analyses of the novel Moorella strains revealed isolate-specific differences that considerably increase the knowledge base on thermophilic acetogens for future applications.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11328732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906321","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}

引用次数: 0

Epibiont communities on mussels in relation to parasitism and location in the rocky intertidal zone. 贻贝上的附生虫群落与寄生和潮间带岩石区位置的关系。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-13 DOI: 10.1093/femsec/fiae101

Katherine M Davis, Laura Wegener Parfrey, Christopher D G Harley, Keith Holmes, Olivia Schaefer, Alyssa-Lois Gehman

{"title":"Epibiont communities on mussels in relation to parasitism and location in the rocky intertidal zone.","authors":"Katherine M Davis, Laura Wegener Parfrey, Christopher D G Harley, Keith Holmes, Olivia Schaefer, Alyssa-Lois Gehman","doi":"10.1093/femsec/fiae101","DOIUrl":"10.1093/femsec/fiae101","url":null,"abstract":"The factors shaping host-parasite interactions and epibiont communities in the variable rocky intertidal zone are poorly understood. California mussels, Mytilus californianus, are colonized by endolithic cyanobacterial parasites that erode the host shell. These cyanobacteria become mutualistic under certain abiotic conditions because shell erosion can protect mussels from thermal stress. How parasitic shell erosion affects or is affected by epibiotic microbial communities on mussel shells and the context dependency of these interactions is unknown. We used transplant experiments to characterize assemblages of epibiotic bacteria and endolithic parasites on mussel shells across intertidal elevation gradients. We hypothesized that living mussels, and associated epibacterial communities, could limit colonization and erosion by endolithic cyanobacteria compared with empty mussel shells. We hypothesized that shell erosion would be associated with compositional shifts in the epibacterial community and tidal elevation. We found that living mussels experienced less shell erosion than empty shells, demonstrating potential biotic regulation of endolithic parasites. Increased shell erosion was not associated with a distinct epibacterial community and was decoupled from the relative abundance of putatively endolithic taxa. Our findings suggest that epibacterial community structure is not directly impacted by the dynamic symbiosis between endolithic cyanobacteria and mussels throughout the rocky intertidal zone.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11385189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975505","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}

引用次数: 0

Moderately thermostable GH1 β-glucosidases from hyperacidophilic archaeon Cuniculiplasma divulgatum S5. 来自超嗜酸性古菌 Cuniculiplasma divulgatum S5 的中等恒温 GH1 β-葡萄糖苷酶。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-13 DOI: 10.1093/femsec/fiae114

Anna N Khusnutdinova, Hai Tran, Saloni Devlekar, Marco A Distaso, Ilya V Kublanov, Tatiana Skarina, Peter Stogios, Alexei Savchenko, Manuel Ferrer, Olga V Golyshina, Alexander F Yakunin, Peter N Golyshin

{"title":"Moderately thermostable GH1 β-glucosidases from hyperacidophilic archaeon Cuniculiplasma divulgatum S5.","authors":"Anna N Khusnutdinova, Hai Tran, Saloni Devlekar, Marco A Distaso, Ilya V Kublanov, Tatiana Skarina, Peter Stogios, Alexei Savchenko, Manuel Ferrer, Olga V Golyshina, Alexander F Yakunin, Peter N Golyshin","doi":"10.1093/femsec/fiae114","DOIUrl":"10.1093/femsec/fiae114","url":null,"abstract":"Family GH1 glycosyl hydrolases are ubiquitous in prokaryotes and eukaryotes and are utilized in numerous industrial applications, including bioconversion of lignocelluloses. In this study, hyperacidophilic archaeon Cuniculiplasma divulgatum (S5T=JCM 30642T) was explored as a source of novel carbohydrate-active enzymes. The genome of C. divulgatum encodes three GH1 enzyme candidates, from which CIB12 and CIB13 were heterologously expressed and characterized. Phylogenetic analysis of CIB12 and CIB13 clustered them with β-glucosidases from genuinely thermophilic archaea including Thermoplasma acidophilum, Picrophilus torridus, Sulfolobus solfataricus, Pyrococcus furiosus, and Thermococcus kodakarensis. Purified enzymes showed maximal activities at pH 4.5-6.0 (CIB12) and 4.5-5.5 (CIB13) with optimal temperatures at 50°C, suggesting a high-temperature origin of Cuniculiplasma spp. ancestors. Crystal structures of both enzymes revealed a classical (α/β)8 TIM-barrel fold with the active site located inside the barrel close to the C-termini of β-strands including the catalytic residues Glu204 and Glu388 (CIB12), and Glu204 and Glu385 (CIB13). Both enzymes preferred cellobiose over lactose as substrates and were classified as cellobiohydrolases. Cellobiose addition increased the biomass yield of Cuniculiplasma cultures growing on peptides by 50%, suggesting that the cellobiohydrolases expand the carbon substrate range and hence environmental fitness of Cuniculiplasma.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11376072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141912372","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}

引用次数: 0