FEMS microbiology ecology最新文献_第2页

Taxonomic and functional metagenomic assessment of a dolichospermum bloom in a large and deep lake south of the Alps. 对阿尔卑斯山以南一个大型深水湖泊中的藻华进行分类和功能元基因组评估。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-09-03 DOI: 10.1093/femsec/fiae117

Nico Salmaso, Leonardo Cerasino, Massimo Pindo, Adriano Boscaini

{"title":"Taxonomic and functional metagenomic assessment of a dolichospermum bloom in a large and deep lake south of the Alps.","authors":"Nico Salmaso, Leonardo Cerasino, Massimo Pindo, Adriano Boscaini","doi":"10.1093/femsec/fiae117","DOIUrl":"https://doi.org/10.1093/femsec/fiae117","url":null,"abstract":"Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on a population of Dolichospermum lemmermannii collected during a surface bloom in Lake Garda in the summer of 2020. Using a phylogenomic approach, the almost complete metagenome-assembled genome (MAG) obtained from the analysis allowed to clarify the taxonomic position of the species within the genus Dolichospermum and contributed to frame the taxonomy of this genus within the ADA group (Anabaena/Dolichospermum/Aphanizomenon). In addition to common functional traits represented in the central metabolism of photosynthetic cyanobacteria, the genome annotation uncovered some distinctive and adaptive traits that helped define the factors that promote and maintain bloom-forming heterocytous nitrogen-fixing Nostocales in oligotrophic lakes. In addition, genetic clusters were identified that potentially encode several secondary metabolites that were previously unknown in the populations evolving in the southern Alpine lake district. These included geosmin, anabaenopetins, and other bioactive compounds. The results expanded the knowledge of the distinctive competitive traits that drive algal blooms and provided guidance for more targeted analyses of cyanobacterial metabolites with implications for human health and water resource use.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125260","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

Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period. Unde venis?从环境储库到莴苣的细菌抗药性：跟踪生长期的微生物组和抗药性组。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-31 DOI: 10.1093/femsec/fiae118

Maria-Theresia Gekenidis, Vera Vollenweider, Aoife Joyce, Sinéad Murphy, Jean-Claude Walser, Feng Ju, Helmut Bürgmann, Jörg Hummerjohann, Fiona Walsh, David Drissner

{"title":"Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period.","authors":"Maria-Theresia Gekenidis, Vera Vollenweider, Aoife Joyce, Sinéad Murphy, Jean-Claude Walser, Feng Ju, Helmut Bürgmann, Jörg Hummerjohann, Fiona Walsh, David Drissner","doi":"10.1093/femsec/fiae118","DOIUrl":"https://doi.org/10.1093/femsec/fiae118","url":null,"abstract":"Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analyzed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil-vegetable contact to minimize resistance markers on fresh produce.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142105967","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

Dissecting negative effects of two root-associated bacteria on the growth of an invasive weed. 剖析两种根相关细菌对入侵杂草生长的负面影响。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-22 DOI: 10.1093/femsec/fiae116

Xiangyu Liu, Hocelayne Paulino Fernandes, Adam Ossowicki, Klaas Vrieling, Suzanne T E Lommen, T Martijn Bezemer

{"title":"Dissecting negative effects of two root-associated bacteria on the growth of an invasive weed.","authors":"Xiangyu Liu, Hocelayne Paulino Fernandes, Adam Ossowicki, Klaas Vrieling, Suzanne T E Lommen, T Martijn Bezemer","doi":"10.1093/femsec/fiae116","DOIUrl":"https://doi.org/10.1093/femsec/fiae116","url":null,"abstract":"Plant-associated microorganisms can negatively influence plant growth, which makes them potential biocontrol agents for weeds. Two Gammaproteobacteria, Serratia plymuthica and Pseudomonas brassicacearum, isolated from roots of Jacobaea vulgaris, an invasive weed, negatively affect its root growth. We examined whether the effects of S. plymuthica and P. brassicacearum on J. vulgaris through root inoculation are concentration-dependent and investigated if these effects were mediated by metabolites in bacterial suspensions. We also tested whether the two bacteria negatively affected seed germination and seedling growth through volatile emissions. Lastly, we investigated the host specificity of these two bacteria on nine other plant species. Both bacteria significantly reduced J. vulgaris root growth after root inoculation, with S. plymuthica showing a concentration-dependent pattern in vitro. The cell-free supernatants of both bacteria did not affect J. vulgaris root growth. Both bacteria inhibited J. vulgaris seed germination and seedling growth via volatiles, displaying distinct volatile profiles. However, these negative effects were not specific to J. vulgaris. Both bacteria negatively affect J. vulgaris through root inoculation via the activity of bacterial cells, while also producing volatiles that hinder J. vulgaris germination and seedling growth. However, their negative effects extend to other plant species, limiting their potential for weed control.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142035611","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

Caterpillar-parasitoid interactions: species-specific influences on host microbiome composition. 毛虫与寄生虫的相互作用：物种对宿主微生物组组成的特定影响。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-08-20 DOI: 10.1093/femsec/fiae115

Gabriele Gloder, Mitchel E Bourne, Maximilien A C Cuny, Christel Verreth, Sam Crauwels, Marcel Dicke, Erik H Poelman, Hans Jacquemyn, Bart Lievens

{"title":"Caterpillar-parasitoid interactions: species-specific influences on host microbiome composition.","authors":"Gabriele Gloder, Mitchel E Bourne, Maximilien A C Cuny, Christel Verreth, Sam Crauwels, Marcel Dicke, Erik H Poelman, Hans Jacquemyn, Bart Lievens","doi":"10.1093/femsec/fiae115","DOIUrl":"https://doi.org/10.1093/femsec/fiae115","url":null,"abstract":"There is increasing evidence that host-parasitoid interactions can have a pronounced impact on the microbiome of host insects, but it is unclear to what extent this is caused by the host and/or parasitoid. Here, we compared the internal and external microbiome of caterpillars of Pieris brassicae and Pieris rapae parasitised by Cotesia glomerata or Cotesia rubecula with non-parasitised caterpillars. Additionally, we investigated the internal and external microbiome of the parasitoid larvae. Both internal and external bacterial densities were significantly higher for P. brassicae than P. rapae, while no differences were found between parasitised and non-parasitised caterpillars. In contrast, parasitism significantly affected the composition of the internal and external microbiome of the caterpillars and the parasitoid larvae, but the effects were dependent on the host and parasitoid species. Irrespective of host species, a Wolbachia species was exclusively found inside caterpillars parasitised by C. glomerata, as well as in the corresponding developing parasitoid larvae. Similarly, a Nosema species was abundantly present inside parasitised caterpillars and the parasitoid larvae, but this was independent of the host and the parasitoid species. We conclude that parasitism has pronounced effects on host microbiomes, but the effects depend on both the host and parasitoid species.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008550","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