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.
{"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":"<p><p>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.</p>","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}
Maria-Theresia Gekenidis, Vera Vollenweider, Aoife Joyce, Sinéad Murphy, Jean-Claude Walser, Feng Ju, Helmut Bürgmann, Jörg Hummerjohann, Fiona Walsh, David Drissner
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.
新鲜农产品被认为对肠道抗性组的形成有很大作用。我们研究了猪粪和灌溉水质对田间种植的生菜在整个生长期的微生物组和抗性组的影响。莴苣在四种条件下生长,即结合使用粪肥的土壤改良(使用/不使用)和使用上游废水输入的河水喷灌(使用/不使用)。每周收集生菜叶片、土壤和水样,并通过细菌培养、16S rRNA 基因扩增子测序和群落总 DNA 的枪式元基因组学进行分析。培养过程中只发现了少数与临床相关的抗生素耐药菌(ARB),但随着时间的推移,莴苣上的 ARB 数量在增加,而没有观察到与治疗相关的变化。微生物组分析证实了这一时间趋势。莴苣和水中特有的抗生素耐药基因(ARGs)包括多药和 β-内酰胺 ARGs,而莴苣和土壤特有的主要是糖肽和四环素 ARGs。地表水中含有与临床相关的ARB(如产ESBL的大肠埃希氏菌或丰满沙雷氏菌),但不会对莴苣的总体抗性组产生显著影响。用粪肥种植的莴苣,尤其是幼嫩莴苣(与土壤接触增多),抗性标记(包括杀菌剂和金属抗性)有所增加。总之,虽然所有调查环境都是莴苣抗性基因组的来源,但粪肥是主要来源,尤其是在幼苗上。因此,我们建议尽量减少土壤与蔬菜的接触,以减少新鲜农产品上的抗性标记。
{"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":"<p><p>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.</p>","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}
Xiangyu Liu, Hocelayne Paulino Fernandes, Adam Ossowicki, Klaas Vrieling, Suzanne T E Lommen, T Martijn Bezemer
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.
与植物相关的微生物可对植物生长产生负面影响,这使它们成为杂草的潜在生物控制剂。从一种入侵性杂草 Jacobaea vulgaris 的根部分离出的两种伽马蛋白菌 Serratia plymuthica 和 P. brassicacearum 会对其根部生长产生负面影响。我们研究了 S. plymuthica 和 P. brassicacearum 通过根部接种对 Jacobaea vulgaris 的影响是否与浓度有关,并研究了这些影响是否由细菌悬浮液中的代谢物介导。我们还测试了这两种细菌是否会通过挥发性排放物对种子萌发和幼苗生长产生负面影响。最后,我们研究了这两种细菌对其他九种植物的寄主特异性。这两种细菌在根部接种后都会明显降低 J. vulgaris 的根系生长,其中 S. plymuthica 在体外表现出浓度依赖性模式。这两种细菌的无细胞上清液对 J. vulgaris 的根系生长没有影响。两种细菌都通过挥发性物质抑制 J. vulgaris 种子萌发和幼苗生长,并表现出不同的挥发性特征。然而,这些负面影响对 J. vulgaris 并无特异性。这两种细菌都通过细菌细胞的活性对根部接种的 J. vulgaris 产生负面影响,同时还产生挥发性物质,阻碍 J. vulgaris 的发芽和幼苗生长。不过,它们的负面影响也会延伸到其他植物物种,从而限制了它们控制杂草的潜力。
{"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":"<p><p>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.</p>","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}
Gabriele Gloder, Mitchel E Bourne, Maximilien A C Cuny, Christel Verreth, Sam Crauwels, Marcel Dicke, Erik H Poelman, Hans Jacquemyn, Bart Lievens
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.
{"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":"<p><p>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.</p>","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}
Evgenii Protasov, Hanna Reeh, Pengfei Liu, Anja Poehlein, Katja Platt, Thomas Heimerl, Vincent Hervé, Rolf Daniel, Andreas Brune
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.
{"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":"<p><p>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.</p>","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}
{"title":"Correction to: Methicillin-resistant Staphylococcus aureus and coagulase-negative Staphylococcus produce antimicrobial substances against members of the skin microbiota in children with atopic dermatitis.","authors":"","doi":"10.1093/femsec/fiae107","DOIUrl":"10.1093/femsec/fiae107","url":null,"abstract":"","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/PMC11319929/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970974","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}
Benoît Marsaux, Frédéric Moens, Gies Vandevijver, Massimo Marzorati, Tom van de Wiele
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.
{"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":"<p><p>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.</p>","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}
Tristan A Caro, Srishti Kashyap, George Brown, Claudia Chen, Sebastian H Kopf, Alexis S Templeton
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.
微生物的生长速率是了解环境地球化学和生态学的基础。然而,在单细胞水平上测量微生物活动的异质性,尤其是在复杂的种群和环境基质中测量微生物活动的异质性,仍然是一项前沿挑战。稳定同位素探测(SIP)是一种评估微生物生长的方法,涉及测量微生物生物量中同位素标签的结合情况。在这里,我们将拉曼微光谱技术作为一种 SIP 技术进行评估,特别是侧重于氘(2H)的测量,氘是微生物生物量产生的示踪剂。我们利用拉曼光谱和纳米级二次离子质谱(nanoSIMS)对生长在不同浓度氘化水中的细胞进行了相关测量,从而得出微生物 2H 的同位素定标。与拉曼光谱法相比,我们发现纳米级二次离子质谱法测量的 2H 会因样品洗涤过程中 H 的快速交换而被大量稀释。我们将源自拉曼的校准应用于微生物生长的数值模型,对控制生长率量化的因素进行了明确的参数化,并证明拉曼-SIP 可以灵敏地测量倍增时间从数小时到数年不等的微生物生长。拉曼光谱是一种快速、无损的技术,它对单细胞生长的测量是将单细胞分析应用于复杂样品基质或细胞组合的重要一步。
{"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":"<p><p>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.</p>","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}
Kristof Brenzinger, Timo Glatter, Anna Hakobyan, Marion Meima-Franke, Hans Zweers, Werner Liesack, Paul L E Bodelier
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.
{"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":"<p><p>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.</p>","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}
{"title":"Correction to: Responses of attached bacterial communities to blooms of the swimming shelled pteropod creseis acicula in Daya Bay, southern China.","authors":"","doi":"10.1093/femsec/fiae108","DOIUrl":"10.1093/femsec/fiae108","url":null,"abstract":"","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/PMC11319931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970975","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}