Fede Berckx, Daniel Wibberg, Andreas Brachmann, Ciara Morrison, Nadia B Obaid, Jochen Blom, Jörn Kalinowski, Luis G Wall, Katharina Pawlowski
Coriariaceae are a small plant family of 14-17 species and subspecies that currently have a global but disjunct distribution. All species can form root nodules in symbiosis with diazotrophic Frankia cluster-2 strains, which form the earliest divergent symbiotic clade within this bacterial genus. Studies on Frankia cluster-2 mostly have focused on strains occurring in the northern hemisphere. Except for one strain from Papua New Guinea, namely Candidatus Frankia meridionalis Cppng1, no complete genome of Frankia associated with Coriaria occurring in the southern hemisphere has been published thus far, yet the majority of the Coriariaceae species occur here. We present field sampling data of novel Frankia cluster-2 strains, representing two novel species, which are associated with Coriaria arborea and Coriaria sarmentosa in New Zealand, and with Coriaria ruscifolia in Patagonia (Argentina), in addition to identifying Ca. F. meridionalis present in New Zealand. The novel Frankia species were found to be closely related to both Ca. F. meridionalis, and a Frankia species occurring in the Philippines, Taiwan, and Japan. Our data suggest that the different Frankia cluster-2 species diverged early after becoming symbiotic circa 100 million years ago.
{"title":"Genome analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere.","authors":"Fede Berckx, Daniel Wibberg, Andreas Brachmann, Ciara Morrison, Nadia B Obaid, Jochen Blom, Jörn Kalinowski, Luis G Wall, Katharina Pawlowski","doi":"10.1093/femsec/fiae042","DOIUrl":"10.1093/femsec/fiae042","url":null,"abstract":"<p><p>Coriariaceae are a small plant family of 14-17 species and subspecies that currently have a global but disjunct distribution. All species can form root nodules in symbiosis with diazotrophic Frankia cluster-2 strains, which form the earliest divergent symbiotic clade within this bacterial genus. Studies on Frankia cluster-2 mostly have focused on strains occurring in the northern hemisphere. Except for one strain from Papua New Guinea, namely Candidatus Frankia meridionalis Cppng1, no complete genome of Frankia associated with Coriaria occurring in the southern hemisphere has been published thus far, yet the majority of the Coriariaceae species occur here. We present field sampling data of novel Frankia cluster-2 strains, representing two novel species, which are associated with Coriaria arborea and Coriaria sarmentosa in New Zealand, and with Coriaria ruscifolia in Patagonia (Argentina), in addition to identifying Ca. F. meridionalis present in New Zealand. The novel Frankia species were found to be closely related to both Ca. F. meridionalis, and a Frankia species occurring in the Philippines, Taiwan, and Japan. Our data suggest that the different Frankia cluster-2 species diverged early after becoming symbiotic circa 100 million years ago.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11074711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140193587","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}
Maria Laura Amenta, Francesca Vaccaro, Stefano Varriale, Jean Rodrigue Sangaré, Roberto Defez, Alessio Mengoni, Carmen Bianco
Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.
与在盐碱和缺水等恶劣条件下生长的植物相关的微生物群落已经形成了适应性特征,使它们能够在极端环境条件下生长和生存。本研究采用原地植物诱捕法,收集与偏远恶劣地区土壤相关的可培养微生物多样性。巴尔多(Oryza sativa cv. Baldo)和普里马杜尔小麦(Triticum durum Primadur)被用作诱捕植物,而马里(西非)偏远地区的 Oryza glaberrima 植物根部周围的土壤则被用作它们生长的基质。这两种植物招募的内生菌群落属于变形菌和固醇菌,优势菌属为芽孢杆菌、科萨科尼亚菌和肠杆菌。通过分析一些最常见的植物生长促进特性,对这些内生菌进行了定性。我们发现了耐盐碱菌株、无机磷酸盐溶解菌株和固氮菌株,其中一些菌株同时具有这三种特性。我们证实,'Baldo'主要吸收了耐盐和钾溶解内生菌,而'Primadur'选择的内生菌主要是固氮菌。应用原位植物诱捕法可以分离出具有潜在有益性状的内生菌,可用于改善水稻和小麦在不利环境条件下的生长状况。
{"title":"Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils.","authors":"Maria Laura Amenta, Francesca Vaccaro, Stefano Varriale, Jean Rodrigue Sangaré, Roberto Defez, Alessio Mengoni, Carmen Bianco","doi":"10.1093/femsec/fiae041","DOIUrl":"10.1093/femsec/fiae041","url":null,"abstract":"<p><p>Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11009874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140305370","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}
Radosław Włodarczyk, Joanna Drzewińska-Chańko, Maciej Kamiński, Włodzimierz Meissner, Jan Rapczyński, Katarzyna Janik-Superson, Dawid Krawczyk, Dominik Strapagiel, Agnieszka Ożarowska, Katarzyna Stępniewska, Piotr Minias
Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens.
{"title":"Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds.","authors":"Radosław Włodarczyk, Joanna Drzewińska-Chańko, Maciej Kamiński, Włodzimierz Meissner, Jan Rapczyński, Katarzyna Janik-Superson, Dawid Krawczyk, Dominik Strapagiel, Agnieszka Ożarowska, Katarzyna Stępniewska, Piotr Minias","doi":"10.1093/femsec/fiae040","DOIUrl":"10.1093/femsec/fiae040","url":null,"abstract":"<p><p>Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11008731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140184154","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}
Our understanding of the role of secondary metabolites in microbial communities is challenged by intrinsic limitations of culturing bacteria under laboratory conditions and hence cultivation independent approaches are needed. Here, we present a protocol termed Secondary Metabolite FISH (SecMet-FISH), combining advantages of gene-targeted fluorescence in situ hybridization (geneFISH) with in-solution methods (in-solution FISH) to detect and quantify cells based on their genetic capacity to produce secondary metabolites. The approach capitalizes on the conserved nature of biosynthetic gene clusters (BGCs) encoding adenylation (AD) and ketosynthase (KS) domains, and thus selectively targets the genetic basis of non-ribosomal peptide and polyketide biosynthesis. The concept relies on the generation of amplicon pools using degenerate primers broadly targeting AD and KS domains followed by fluorescent labeling, detection, and quantification. Initially, we obtained AD and KS amplicons from Pseuodoalteromonas rubra, which allowed us to successfully label and visualize BGCs within P. rubra cells, demonstrating the feasibility of SecMet-FISH. Next, we adapted the protocol and optimized it for hybridization in both Gram-negative and Gram-positive bacterial cell suspensions, enabling high-throughput single cell analysis by flow cytometry. Ultimately, we used SecMet-FISH to successfully distinguish secondary metabolite producers from non-producers in a five-member synthetic community.
我们对次生代谢物在微生物群落中的作用的理解受到了实验室条件下培养细菌的内在限制的挑战,因此需要独立于培养的方法。在这里,我们提出了一种称为次生代谢物 FISH(SecMet-FISH)的方案,它结合了基因靶向荧光原位杂交(geneFISH)和溶液内方法(in-solution FISH)的优势,根据细胞产生次生代谢物的基因能力来检测和量化细胞。这种方法利用了编码腺苷酸化(AD)和酮合成酶(KS)结构域的生物合成基因簇(BGCs)的保守性,从而有选择地针对非核糖体肽和多酮生物合成的遗传基础。这一概念依赖于使用广泛针对 AD 和 KS 结构域的变性引物生成扩增子池,然后进行荧光标记、检测和定量。最初,我们从红掌藻(Pseuodoalteromonas rubra)中获得了AD和KS扩增子,从而成功地标记和观察了红掌藻细胞内的BGCs,证明了SecMet-FISH的可行性。接下来,我们对该方案进行了调整和优化,以便在革兰氏阴性和革兰氏阳性细菌细胞悬浮液中进行杂交,从而能够通过流式细胞仪进行高通量单细胞分析。最终,我们利用 SecMet-FISH 成功地区分了五人合成群落中的次级代谢产物生产者和非生产者。
{"title":"SecMet-FISH: labeling, visualization, and enumeration of secondary metabolite producing microorganisms.","authors":"Yannick Buijs, Aileen Ute Geers, Iuliana Nita, Mikael Lenz Strube, Mikkel Bentzon-Tilia","doi":"10.1093/femsec/fiae038","DOIUrl":"10.1093/femsec/fiae038","url":null,"abstract":"<p><p>Our understanding of the role of secondary metabolites in microbial communities is challenged by intrinsic limitations of culturing bacteria under laboratory conditions and hence cultivation independent approaches are needed. Here, we present a protocol termed Secondary Metabolite FISH (SecMet-FISH), combining advantages of gene-targeted fluorescence in situ hybridization (geneFISH) with in-solution methods (in-solution FISH) to detect and quantify cells based on their genetic capacity to produce secondary metabolites. The approach capitalizes on the conserved nature of biosynthetic gene clusters (BGCs) encoding adenylation (AD) and ketosynthase (KS) domains, and thus selectively targets the genetic basis of non-ribosomal peptide and polyketide biosynthesis. The concept relies on the generation of amplicon pools using degenerate primers broadly targeting AD and KS domains followed by fluorescent labeling, detection, and quantification. Initially, we obtained AD and KS amplicons from Pseuodoalteromonas rubra, which allowed us to successfully label and visualize BGCs within P. rubra cells, demonstrating the feasibility of SecMet-FISH. Next, we adapted the protocol and optimized it for hybridization in both Gram-negative and Gram-positive bacterial cell suspensions, enabling high-throughput single cell analysis by flow cytometry. Ultimately, we used SecMet-FISH to successfully distinguish secondary metabolite producers from non-producers in a five-member synthetic community.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11004939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140136708","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}
Jason Bosch, Priscila Thiago Dobbler, Tomáš Větrovský, Vojtěch Tláskal, Petr Baldrian, Vendula Brabcová
Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.
{"title":"Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda.","authors":"Jason Bosch, Priscila Thiago Dobbler, Tomáš Větrovský, Vojtěch Tláskal, Petr Baldrian, Vendula Brabcová","doi":"10.1093/femsec/fiae044","DOIUrl":"10.1093/femsec/fiae044","url":null,"abstract":"<p><p>Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11030162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140848251","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}
Jennifer C Underwood, Natalie C Hall, Adam C Mumford, Ronald W Harvey, Paul A Bliznik, Kaitlyn M Jeanis
Aphanizomenon flos-aquae (AFA) is the dominant filamentous cyanobacterium that develops into blooms in Upper Klamath Lake, Oregon, each year. During AFA bloom and collapse, ecosystem conditions for endangered Lost River and shortnose suckers deteriorate, thus motivating the need to identify processes that limit AFA abundance and decline. Here, we investigate the relations between AFA and other members of the microbial community (photosynthetic and nonphotosynthetic bacteria and archaea), how those relations impact abundance and collapse of AFA, and the types of microbial conditions that suppress AFA. We found significant spatial variation in AFA relative abundance during the 2016 bloom period using 16S rRNA sequencing. The Pelican Marina site had the lowest AFA relative abundance, and this was coincident with increased relative abundance of Candidatus Sericytochromatia, Flavobacterium, and Rheinheimera, some of which are known AFA antagonists. The AFA collapse coincided with phosphorus limitation relative to nitrogen and the increased relative abundance of Cyanobium and Candidatus Sericytochromatia, which outcompete AFA when dissolved inorganic nitrogen is available. The data collected in this study indicate the importance of dissolved inorganic nitrogen combined with microbial community structure in suppressing AFA abundance.
{"title":"Relation between the relative abundance and collapse of Aphanizomenon flos-aquae and microbial antagonism in Upper Klamath Lake, Oregon.","authors":"Jennifer C Underwood, Natalie C Hall, Adam C Mumford, Ronald W Harvey, Paul A Bliznik, Kaitlyn M Jeanis","doi":"10.1093/femsec/fiae043","DOIUrl":"10.1093/femsec/fiae043","url":null,"abstract":"<p><p>Aphanizomenon flos-aquae (AFA) is the dominant filamentous cyanobacterium that develops into blooms in Upper Klamath Lake, Oregon, each year. During AFA bloom and collapse, ecosystem conditions for endangered Lost River and shortnose suckers deteriorate, thus motivating the need to identify processes that limit AFA abundance and decline. Here, we investigate the relations between AFA and other members of the microbial community (photosynthetic and nonphotosynthetic bacteria and archaea), how those relations impact abundance and collapse of AFA, and the types of microbial conditions that suppress AFA. We found significant spatial variation in AFA relative abundance during the 2016 bloom period using 16S rRNA sequencing. The Pelican Marina site had the lowest AFA relative abundance, and this was coincident with increased relative abundance of Candidatus Sericytochromatia, Flavobacterium, and Rheinheimera, some of which are known AFA antagonists. The AFA collapse coincided with phosphorus limitation relative to nitrogen and the increased relative abundance of Cyanobium and Candidatus Sericytochromatia, which outcompete AFA when dissolved inorganic nitrogen is available. The data collected in this study indicate the importance of dissolved inorganic nitrogen combined with microbial community structure in suppressing AFA abundance.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11022654/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140293236","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}
Robin Siebers, Doreen Schultz, Mohamed S Farza, Anne Brauer, Daniela Zühlke, Pierre A Mücke, Fengqing Wang, Jörg Bernhardt, Hanno Teeling, Dörte Becher, Katharina Riedel, Inga V Kirstein, Karen H Wiltshire, Katharina J Hoff, Thomas Schweder, Tim Urich, Mia M Bengtsson
Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in a shallow location (6-10 m depth) in the North Sea. Particulate fractions larger than 10 µm diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths and in sediments. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, and an important role of benthic-pelagic coupling for microbiomes in shallow environments. Our findings may have implications for the understanding of algal-bacterial interactions and carbon export during blooms in shallow-water coastal areas.
{"title":"Marine particle microbiomes during a spring diatom bloom contain active sulfate-reducing bacteria.","authors":"Robin Siebers, Doreen Schultz, Mohamed S Farza, Anne Brauer, Daniela Zühlke, Pierre A Mücke, Fengqing Wang, Jörg Bernhardt, Hanno Teeling, Dörte Becher, Katharina Riedel, Inga V Kirstein, Karen H Wiltshire, Katharina J Hoff, Thomas Schweder, Tim Urich, Mia M Bengtsson","doi":"10.1093/femsec/fiae037","DOIUrl":"10.1093/femsec/fiae037","url":null,"abstract":"<p><p>Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in a shallow location (6-10 m depth) in the North Sea. Particulate fractions larger than 10 µm diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths and in sediments. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, and an important role of benthic-pelagic coupling for microbiomes in shallow environments. Our findings may have implications for the understanding of algal-bacterial interactions and carbon export during blooms in shallow-water coastal areas.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11008741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140136707","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}
Marissa Duckett, Megan N Taylor, Claire Bowman, Nic M Vega
Microbial evolution within polymicrobial communities is a complex process. Here, we report within-species diversification within multispecies microbial communities during experimental evolution with the nematode Caenorhabditis elegans. We describe morphological diversity in the target species Chryseobacterium gleum, which developed a novel colony morphotype in a small number of replicate communities. Alternate morphotypes coexisted with original morphotypes in communities, as well as in single-species experiments using evolved isolates. We found that the original and alternate morphotypes differed in motility and in spatial expansion in the presence of C. elegans. This study provides insight into the emergence and maintenance of intraspecies diversity in the context of microbial communities.
{"title":"Parallel evolution of alternate morphotypes of Chryseobacterium gleum during experimental evolution with Caenorhabditis elegans.","authors":"Marissa Duckett, Megan N Taylor, Claire Bowman, Nic M Vega","doi":"10.1093/femsec/fiae039","DOIUrl":"10.1093/femsec/fiae039","url":null,"abstract":"<p><p>Microbial evolution within polymicrobial communities is a complex process. Here, we report within-species diversification within multispecies microbial communities during experimental evolution with the nematode Caenorhabditis elegans. We describe morphological diversity in the target species Chryseobacterium gleum, which developed a novel colony morphotype in a small number of replicate communities. Alternate morphotypes coexisted with original morphotypes in communities, as well as in single-species experiments using evolved isolates. We found that the original and alternate morphotypes differed in motility and in spatial expansion in the presence of C. elegans. This study provides insight into the emergence and maintenance of intraspecies diversity in the context of microbial communities.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11004935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140318135","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}
Eva F Leifheit, Tessa Camenzind, Anika Lehmann, Diana R Andrade-Linares, Max Fussan, Sophia Westhusen, Till M Wineberger, Matthias C Rillig
Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited to forest ecosystems. In order to better understand functional traits of saprotrophic soil fungi in grassland ecosystems, we isolated 31 fungi from a natural grassland and performed several in vitro studies testing for i) leaf and wood litter decomposition, ii) the ability to use carbon sources of differing complexity, iii) the enzyme repertoire. Decomposition strongly varied among phyla and isolates, with Ascomycota decomposing the most and Mucoromycota decomposing the least. The phylogeny of the fungi and their ability to use complex carbon were the most important predictors for decomposition. Our findings show that it is crucial to understand the role of individual members and functional groups within the microbial community. This is an important way forward to understand the role of microbial community composition for the prediction of litter decomposition and subsequent potential carbon storage in grassland soils.
{"title":"Fungal traits help to understand the decomposition of simple and complex plant litter.","authors":"Eva F Leifheit, Tessa Camenzind, Anika Lehmann, Diana R Andrade-Linares, Max Fussan, Sophia Westhusen, Till M Wineberger, Matthias C Rillig","doi":"10.1093/femsec/fiae033","DOIUrl":"10.1093/femsec/fiae033","url":null,"abstract":"<p><p>Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited to forest ecosystems. In order to better understand functional traits of saprotrophic soil fungi in grassland ecosystems, we isolated 31 fungi from a natural grassland and performed several in vitro studies testing for i) leaf and wood litter decomposition, ii) the ability to use carbon sources of differing complexity, iii) the enzyme repertoire. Decomposition strongly varied among phyla and isolates, with Ascomycota decomposing the most and Mucoromycota decomposing the least. The phylogeny of the fungi and their ability to use complex carbon were the most important predictors for decomposition. Our findings show that it is crucial to understand the role of individual members and functional groups within the microbial community. This is an important way forward to understand the role of microbial community composition for the prediction of litter decomposition and subsequent potential carbon storage in grassland soils.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11022653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140131089","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}
Beatriz Rojo-Bezares, Cristina Casado, Tania Ceniceros, María López, Gabriela Chichón, Carmen Lozano, Lidia Ruiz-Roldán, Yolanda Sáenz
Pseudomonas aeruginosa isolates were recovered from surface river water samples in La Rioja region (Spain) to characterise their antibiotic resistance, molecular typing and virulence mechanisms. Fifty-two P. aeruginosa isolates were isolated from 15 different water samples (45.4%) and belonged to 23 different pulsed-field electrophoresis (PFGE) patterns. All isolates were susceptible to all antibiotics tested, except one carbapenem-resistant P. aeruginosa that showed a premature stop codon in OprD porin. Twenty-two sequence types (STs) (six new ones) were detected among 29 selected P. aeruginosa (one strain with a different PFGE pattern per sample), with ST274 (14%) being the most frequent one. O:6 and O:3 were the predominant serotypes (31%). Seven virulotypes were detected, being 59% exoS-exoY-exoT-exoA-lasA-lasB-lasI-lasR-rhlAB-rhlI-rhlR-aprA-positive P. aeruginosa. It is noteworthy that the exlA gene was identified in three strains (10.3%), and the exoU gene in seven (24.1%), exoS in 18 (62.1%), and both exoS and exoU genes in one strain. High motility ranges were found in these strains. Twenty-seven per cent of strains produced more biofilm biomass, 90% more pyorubin, 83% more pyocyanin and 65.5% more than twice the elastase activity compared with the PAO1 strain. These results highlight the importance of rivers as temporary reservoirs and sources of P. aeruginosa transmission, and show the importance of their epidemiological surveillance in the environment.
{"title":"Pseudomonas aeruginosa from river water: antimicrobial resistance, virulence and molecular typing.","authors":"Beatriz Rojo-Bezares, Cristina Casado, Tania Ceniceros, María López, Gabriela Chichón, Carmen Lozano, Lidia Ruiz-Roldán, Yolanda Sáenz","doi":"10.1093/femsec/fiae028","DOIUrl":"10.1093/femsec/fiae028","url":null,"abstract":"<p><p>Pseudomonas aeruginosa isolates were recovered from surface river water samples in La Rioja region (Spain) to characterise their antibiotic resistance, molecular typing and virulence mechanisms. Fifty-two P. aeruginosa isolates were isolated from 15 different water samples (45.4%) and belonged to 23 different pulsed-field electrophoresis (PFGE) patterns. All isolates were susceptible to all antibiotics tested, except one carbapenem-resistant P. aeruginosa that showed a premature stop codon in OprD porin. Twenty-two sequence types (STs) (six new ones) were detected among 29 selected P. aeruginosa (one strain with a different PFGE pattern per sample), with ST274 (14%) being the most frequent one. O:6 and O:3 were the predominant serotypes (31%). Seven virulotypes were detected, being 59% exoS-exoY-exoT-exoA-lasA-lasB-lasI-lasR-rhlAB-rhlI-rhlR-aprA-positive P. aeruginosa. It is noteworthy that the exlA gene was identified in three strains (10.3%), and the exoU gene in seven (24.1%), exoS in 18 (62.1%), and both exoS and exoU genes in one strain. High motility ranges were found in these strains. Twenty-seven per cent of strains produced more biofilm biomass, 90% more pyorubin, 83% more pyocyanin and 65.5% more than twice the elastase activity compared with the PAO1 strain. These results highlight the importance of rivers as temporary reservoirs and sources of P. aeruginosa transmission, and show the importance of their epidemiological surveillance in the environment.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11004943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039071","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}