FEMS microbiology ecology最新文献_第10页

Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops 多年生农业生态系统作物之间固氮细菌群落的差异

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-17 DOI: 10.1093/femsec/fiae064

Kira Sorochkina, Willm Martens-Habbena, Catherine L Reardon, Patrick W Inglett, Sarah L Strauss

{"title":"Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops","authors":"Kira Sorochkina, Willm Martens-Habbena, Catherine L Reardon, Patrick W Inglett, Sarah L Strauss","doi":"10.1093/femsec/fiae064","DOIUrl":"https://doi.org/10.1093/femsec/fiae064","url":null,"abstract":"Biocrusts, common in natural ecosystems, are specific assemblages of microorganisms at or on the soil surface with associated microorganisms extending into the top centimeter of soil. Agroecosystem biocrusts have similar rates of nitrogen (N) fixation as those in natural ecosystems, but it is unclear how agricultural management influences their composition and function. This study examined the total bacterial and diazotrophic communities of biocrusts in a citrus orchard and a vineyard that shared similar climate and soil type but differed in management. To contrast climate and soil type, these biocrusts were also compared to those from an apple orchard. Unlike natural ecosystem biocrusts, these agroecosystem biocrusts were dominated by proteobacteria and had a lower abundance of cyanobacteria. All examined agroecosystem biocrust diazotroph communities were dominated by N-fixing cyanobacteria from the Nostocales order, similar to natural ecosystem cyanobacterial biocrusts. Lower irrigation and fertilizer in the vineyard compared to the citrus orchard could have contributed to biocrust microbial composition, whereas soil type and climate could have differentiated the apple orchard biocrust. Season did not influence bacterial and diazotrophic community composition of any these agroecosystem biocrusts. Overall, agricultural management and climatic and edaphic factors potentially influenced community composition and function of these biocrusts.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140623454","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

Interaction between phytoplankton and heterotrophic bacteria in Arctic fjords during glacial melting season as revealed by eDNA metabarcoding 通过 eDNA 代谢编码揭示冰川融化季节北极峡湾浮游植物与异养菌之间的相互作用

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-13 DOI: 10.1093/femsec/fiae059

Dukki Han, Ki-Tae Park, Haryun Kim, Tae-Hoon Kim, Man-Ki Jeong, Seung-Il Nam

{"title":"Interaction between phytoplankton and heterotrophic bacteria in Arctic fjords during glacial melting season as revealed by eDNA metabarcoding","authors":"Dukki Han, Ki-Tae Park, Haryun Kim, Tae-Hoon Kim, Man-Ki Jeong, Seung-Il Nam","doi":"10.1093/femsec/fiae059","DOIUrl":"https://doi.org/10.1093/femsec/fiae059","url":null,"abstract":"The hydrographic variability in the fjords of Svalbard significantly influences water mass properties, causing distinct patterns of microbial diversity and community composition between surface and subsurface layers. However, surveys on the phytoplankton-associated bacterial communities, pivotal to ecosystem functioning in Arctic fjords, are limited. This study investigated the interactions between phytoplankton and heterotrophic bacterial communities in Svalbard fjord waters through comprehensive eDNA metabarcoding with 16S and 18S rRNA genes. The 16S rRNA sequencing results revealed a homogenous community composition including a few dominant heterotrophic bacteria across fjord waters, whereas 18S rRNA results suggested a spatially diverse eukaryotic plankton distribution. The relative abundances of heterotrophic bacteria showed a depth-wise distribution. In contrast, the dominant phytoplankton populations exhibited variable distributions in surface waters. In the network model, the linkage of phytoplankton (Prasinophytae and Dinophyceae) to heterotrophic bacteria, particularly Actinobacteria, suggested the direct or indirect influence of bacterial contributions on the fate of phytoplankton-derived organic matter. Our prediction of the metabolic pathways for bacterial activity related to phytoplankton-derived organic matter suggested competitive advantages and symbiotic relationships between phytoplankton and heterotrophic bacteria. Our findings provide valuable insights into the response of phytoplankton-bacterial interactions to environmental changes in Arctic fjords.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584919","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

Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations 普氏旋毛虫菌株 PS-1 的萘降解途径中的基因冗余能够应对不同的底物浓度

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-13 DOI: 10.1093/femsec/fiae060

Anjela L Vogel, Katharine J Thompson, Daniel Straub, Florin Musat, Tony Gutierrez, Sara Kleindienst

{"title":"Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations","authors":"Anjela L Vogel, Katharine J Thompson, Daniel Straub, Florin Musat, Tony Gutierrez, Sara Kleindienst","doi":"10.1093/femsec/fiae060","DOIUrl":"https://doi.org/10.1093/femsec/fiae060","url":null,"abstract":"Polycyclic aromatic hydrocarbon (PAH) contamination in marine environments range from low-diffusive inputs to high loads. The influence of PAH concentration on the expression of functional genes (e.g., those encoding ring-hydroxylating dioxygenases; RHDs), has been overlooked in PAH biodegradation studies. However, understanding marker-gene expression under different PAH loads can help monitor and predict bioremediation efficiency. Here, we followed the expression (via RNA sequencing) of Cycloclasticus pugetii strain PS-1 in cell suspension experiments under different naphthalene (100 and 30 mg L-1) concentrations. We identified genes encoding previously uncharacterized RHD subunits, termed rhdPS1α and rhdPS1β, that were highly transcribed in response to naphthalene-degradation activity. Additionally, we identified six RHD subunit-encoding genes that responded to naphthalene exposure. In contrast, four RHD subunit genes were PAH-independently expressed and three other RHD subunit genes responded to naphthalene starvation. Cycloclasticus spp. could, therefore, use genetic redundancy in key PAH-degradation genes to react to varying PAH loads. This genetic redundancy may restrict the monitoring of environmental hydrocarbon-degradation activity using single-gene expression. For Cycloclasticus pugetii strain PS-1, however, the newly identified rhdPS1α and rhdPS1β genes might be potential target genes to monitor its environmental naphthalene-degradation activity.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140585204","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

Leaf surface microbiota transplantation confers resistance to the coffee leaf rust in susceptible Coffea arabica 叶面微生物群移植使易感的阿拉伯咖啡豆对咖啡叶锈病产生抗性

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-11 DOI: 10.1093/femsec/fiae049

Leandro Pio de Sousa, Jorge Maurício Costa Mondego

{"title":"Leaf surface microbiota transplantation confers resistance to the coffee leaf rust in susceptible Coffea arabica","authors":"Leandro Pio de Sousa, Jorge Maurício Costa Mondego","doi":"10.1093/femsec/fiae049","DOIUrl":"https://doi.org/10.1093/femsec/fiae049","url":null,"abstract":"Coffee leaf rust, caused by the fungus Hemileia vastatrix, became a major concern for coffee-producing countries. Additionally, there is an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers to use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla, but the protection depended on the concentration of the microbiota. Certain fungi such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora, Torula and bacteria such as Chryseobacterium, Sphingobium and especially Enterobacter and have their populations increased and may be related to the antagonism seen against H. vastatrix. Interestingly, relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplant, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust as well as help to optimize the development of biocontrol agents.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140585095","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

Powdery mildew-induced changes in phyllosphere microbial community dynamics of cucumber 白粉病诱发的黄瓜叶球微生物群落动态变化

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-11 DOI: 10.1093/femsec/fiae050

Cong Yue, Changxia Du, Xiaodan Wang, Yinqing Tan, Xingchen Liu, Huaifu Fan

{"title":"Powdery mildew-induced changes in phyllosphere microbial community dynamics of cucumber","authors":"Cong Yue, Changxia Du, Xiaodan Wang, Yinqing Tan, Xingchen Liu, Huaifu Fan","doi":"10.1093/femsec/fiae050","DOIUrl":"https://doi.org/10.1093/femsec/fiae050","url":null,"abstract":"As an important habitat for microorganisms, the phyllosphere has a great impact on plant growth and health, and changes in phyllosphere microorganisms are closely related to the occurrence of leaf diseases. However, there remains a limited understanding regarding alterations to the microbial community in the phyllosphere resulting from pathogen infections. Here, we analyzed and compared the differences in phyllosphere microorganisms of powdery mildew cucumber from three disease severity levels (0% &lt; L1 &lt; 30%, 30% ≤ L2 &lt; 50%, L3 ≥ 50%, the number represents the lesion coverage rate of powdery mildew on leaves). There were significant differences in α diversity and community structure of phyllosphere communities under different disease levels. Disease severity altered the community structure of phyllosphere microorganisms, Rosenbergiella, Rickettsia, and Cladosporium accounted for the largest proportion in the L1 disease grade, while Bacillus, Pantoea, Kocuria, and Podosphaera had the highest relative abundance in the L3 disease grade. The co-occurrence network analysis of the phyllosphere microbial community indicated that the phyllosphere bacterial community was most affected by the severity of disease. Our results suggested that with the development of cucumber powdery mildew, the symbiotic relationship between species was broken, and the entire bacterial community tended to compete.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584665","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

Bacterial diversity in agricultural drainage ditches shifts with increasing urea-N concentrations 农业排水沟中的细菌多样性随尿素氮浓度的增加而变化

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-11 DOI: 10.1093/femsec/fiae057

Sabrina A Klick, Joseph S Pitula, Amy S Collick, Eric B May, Oliva Pisani

{"title":"Bacterial diversity in agricultural drainage ditches shifts with increasing urea-N concentrations","authors":"Sabrina A Klick, Joseph S Pitula, Amy S Collick, Eric B May, Oliva Pisani","doi":"10.1093/femsec/fiae057","DOIUrl":"https://doi.org/10.1093/femsec/fiae057","url":null,"abstract":"Urea-based fertilizers applied to crop fields can enter surface waters of adjacent agricultural drainage ditches and contribute to nitrogen (N) loading to nearby watersheds. Management practices applied in drainage ditches promote N removal by the microbial communities, but little is known about the impacts of excess urea fertilizer from crop fields on the microbial diversity in these ditches. In 2017, sediments from drainage ditches next to corn and soybean fields were sampled to determine if fertilizer application and high urea-N concentrations alters bacterial diversity and urease gene abundances. A mesocosm experiment was paired with a field study to determine which bacterial groups respond to high urea-N concentrations. The bacterial diversity in the ditch next to corn fields was significantly different from the other site. The bacterial orders of Rhizobiales, Bacteroidales, Acidobacteriales, Burkholderiales, and Anaerolineales were most abundant in the ditch next to corn and increased after the addition of urea-N (0.5 mg N L−1) during the mesocosm experiment. The results of our study suggests that urea-N concentrations &gt;0.07 mg N L−1, which are higher than concentrations associated with downstream harmful algal blooms, can lead to shifts in the bacterial communities of agricultural drainage ditches.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140585172","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 analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere. 南半球最早分化的法兰克亚支系的基因组分析和生物地理分布。

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-10 DOI: 10.1093/femsec/fiae042

Fede Berckx, Daniel Wibberg, Andreas Brachmann, Ciara Morrison, Nadia B Obaid, Jochen Blom, Jörn Kalinowski, Luis G Wall, Katharina Pawlowski

{"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":"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.","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}

引用次数: 0

Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils. 在恶劣的土壤中原地种植谷物时，谷物会吸附内生细菌。

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-10 DOI: 10.1093/femsec/fiae041

Maria Laura Amenta, Francesca Vaccaro, Stefano Varriale, Jean Rodrigue Sangaré, Roberto Defez, Alessio Mengoni, Carmen Bianco

{"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":"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.","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}

引用次数: 0

Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds. 中途停留栖息地的选择促使迁徙岸鸟的肠道微生物组组成和病原体获取发生变化。

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-10 DOI: 10.1093/femsec/fiae040

Radosław Włodarczyk, Joanna Drzewińska-Chańko, Maciej Kamiński, Włodzimierz Meissner, Jan Rapczyński, Katarzyna Janik-Superson, Dawid Krawczyk, Dominik Strapagiel, Agnieszka Ożarowska, Katarzyna Stępniewska, Piotr Minias

{"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":"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.","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}

引用次数: 0

SecMet-FISH: labeling, visualization, and enumeration of secondary metabolite producing microorganisms. SecMet-FISH：对产生次级代谢物的微生物进行标记、可视化和计数。

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-04-10 DOI: 10.1093/femsec/fiae038

Yannick Buijs, Aileen Ute Geers, Iuliana Nita, Mikael Lenz Strube, Mikkel Bentzon-Tilia

{"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":"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.","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}

引用次数: 0