A. Cerqueira, Helena Santiago Lima, L. C. F. Silva, T. G. R. Veloso, S. D. de Paula, W. C. Santana, C. C. da Silva
The Melipona gut microbes differ from other social bees, with the absence of crucial corbiculate core gut symbionts and the high occurrence of environmental strains. We studied the microbial diversity and composition of three Melipona species and their honey to understand which strains are obtained by horizontal transmission (HT) from the pollination environment; or represent symbionts co-evolved with Melipona by HT from the hive/food stores or vertical transmission (VT) via social interactions. Bees harbored higher microbial alpha diversity and a different and more species-specific bacterial composition than honey. Otherwise, the fungal communities of bee and honey samples are less dissimilar. As expected, the core symbionts Snodgrassella and Gilliamella were absent in bees that had a prevalence of Lactobacillus Firm-5, environmental Lactobacillaceae, Bifidobacteriaceae and Acetobacteraceae. Also, Pectinatus and Floricoccus have habitat preferences for bees, putatively representing novel symbionts from the environment that co-evolved via VT among generations. Fructilactobacillus found in bees possibly had HT to bees from honey stores. Metschnikowia yeasts, consistent in all bees and honey samples, might have HT to bees from food stores. Similarly, Saccharomycetales might have HT from honey or plants/flowers to bees. This work contributes to the understanding of Melipona symbionts and their modes of transmission.
{"title":"Melipona stingless bees and honey microbiota reveal the diversity, composition, and modes of symbionts transmission.","authors":"A. Cerqueira, Helena Santiago Lima, L. C. F. Silva, T. G. R. Veloso, S. D. de Paula, W. C. Santana, C. C. da Silva","doi":"10.1093/femsec/fiae063","DOIUrl":"https://doi.org/10.1093/femsec/fiae063","url":null,"abstract":"The Melipona gut microbes differ from other social bees, with the absence of crucial corbiculate core gut symbionts and the high occurrence of environmental strains. We studied the microbial diversity and composition of three Melipona species and their honey to understand which strains are obtained by horizontal transmission (HT) from the pollination environment; or represent symbionts co-evolved with Melipona by HT from the hive/food stores or vertical transmission (VT) via social interactions. Bees harbored higher microbial alpha diversity and a different and more species-specific bacterial composition than honey. Otherwise, the fungal communities of bee and honey samples are less dissimilar. As expected, the core symbionts Snodgrassella and Gilliamella were absent in bees that had a prevalence of Lactobacillus Firm-5, environmental Lactobacillaceae, Bifidobacteriaceae and Acetobacteraceae. Also, Pectinatus and Floricoccus have habitat preferences for bees, putatively representing novel symbionts from the environment that co-evolved via VT among generations. Fructilactobacillus found in bees possibly had HT to bees from honey stores. Metschnikowia yeasts, consistent in all bees and honey samples, might have HT to bees from food stores. Similarly, Saccharomycetales might have HT from honey or plants/flowers to bees. This work contributes to the understanding of Melipona symbionts and their modes of transmission.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140672824","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}
Gurpreet S Kharey, V. Palace, L. Whyte, Charles W. Greer
With the increase in crude oil transport throughout Canada, the potential for spills into freshwater ecosystems has increased and additional research is needed in these sensitive environments. Large enclosures erected in a lake were used as mesocosms for this controlled experimental dilbit (diluted bitumen) spill under ambient environmental conditions. The microbial response to dilbit, the efficacy of standard remediation protocols on different shoreline types commonly found in Canadian freshwater lakes, including a testing of a shoreline washing agent were all evaluated. We found that the native microbial community did not undergo any significant shifts in composition after exposure to dilbit or the ensuing remediation treatments. Regardless of the treatment, sample type (soil, sediment, or water), or type of associated shoreline, the community remained relatively consistent over a 3-month monitoring period. Following this, metagenomic analysis of polycyclic aromatic and alkane hydrocarbon degradation mechanisms also showed that while many key genes identified in PAH and alkane biodegradation were present, their abundance did not change significantly over the course of the experiment. These results showed that the native microbial community present in a pristine freshwater lake has the prerequisite mechanisms for hydrocarbon degradation in place, and combined with standard remediation practices in use in Canada, has the genetic potential and resilience to potentially undertake bioremediation.
{"title":"Native freshwater lake microbial community response to an in situ experimental dilbit spill.","authors":"Gurpreet S Kharey, V. Palace, L. Whyte, Charles W. Greer","doi":"10.1093/femsec/fiae055","DOIUrl":"https://doi.org/10.1093/femsec/fiae055","url":null,"abstract":"With the increase in crude oil transport throughout Canada, the potential for spills into freshwater ecosystems has increased and additional research is needed in these sensitive environments. Large enclosures erected in a lake were used as mesocosms for this controlled experimental dilbit (diluted bitumen) spill under ambient environmental conditions. The microbial response to dilbit, the efficacy of standard remediation protocols on different shoreline types commonly found in Canadian freshwater lakes, including a testing of a shoreline washing agent were all evaluated. We found that the native microbial community did not undergo any significant shifts in composition after exposure to dilbit or the ensuing remediation treatments. Regardless of the treatment, sample type (soil, sediment, or water), or type of associated shoreline, the community remained relatively consistent over a 3-month monitoring period. Following this, metagenomic analysis of polycyclic aromatic and alkane hydrocarbon degradation mechanisms also showed that while many key genes identified in PAH and alkane biodegradation were present, their abundance did not change significantly over the course of the experiment. These results showed that the native microbial community present in a pristine freshwater lake has the prerequisite mechanisms for hydrocarbon degradation in place, and combined with standard remediation practices in use in Canada, has the genetic potential and resilience to potentially undertake bioremediation.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140675315","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}
Ö. Coskun, Gonzalo V. Gomez-Saez, Murat Beren, Doğacan Özcan, Suna D Günay, Viktor Elkin, Hakan Hoşgörmez, Florian Einsiedl, Wolfgang Eisenreich, W. Orsi
Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750 meter deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.
{"title":"Quantifying genome specific carbon fixation in a 750 meter deep subsurface hydrothermal microbial community.","authors":"Ö. Coskun, Gonzalo V. Gomez-Saez, Murat Beren, Doğacan Özcan, Suna D Günay, Viktor Elkin, Hakan Hoşgörmez, Florian Einsiedl, Wolfgang Eisenreich, W. Orsi","doi":"10.1093/femsec/fiae062","DOIUrl":"https://doi.org/10.1093/femsec/fiae062","url":null,"abstract":"Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750 meter deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.","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":"140694509","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}
Quinten Struik, José R. Paranaíba, Martyna Glodowska, S. Kosten, Berber M J W Meulepas, Ana B. Rios-Miguel, M. Jetten, Miquel Lurling, G. Waajen, Thomas P. A. Nijman, A. Veraart
Aquatic ecosystems are large contributors to global methane (CH4) emissions. Eutrophication significantly enhances CH4-production as it stimulates methanogenesis. Mitigation measures aimed at reducing eutrophication, such as the addition of metal salts to immobilize phosphate (PO43-), are now common practice. However, the effects of such remedies on methanogenic and methanotrophic communities-and therefore on CH4-cycling-remain largely unexplored. Here, we demonstrate that Fe(II)Cl2 addition, used as PO43- binder, differentially affected microbial CH4 cycling-processes in field experiments and batch incubations. In the field experiments, carried out in enclosures in a eutrophic pond, Fe(II)Cl2 application lowered in-situ CH4 emissions by lowering net CH4-production, while sediment aerobic CH4-oxidation rates-as found in batch incubations of sediment from the enclosures-did not differ from control. In Fe(II)Cl2-treated sediments, a decrease in net CH4-production rates could be attributed to the stimulation of iron-dependent anaerobic CH4-oxidation (Fe-AOM). In batch incubations, anaerobic CH4-oxidation and Fe(II)-production started immediately after CH4 addition, indicating Fe-AOM, likely enabled by favorable indigenous iron cycling conditions and the present methanotroph community in the pond sediment. 16S rRNA sequencing data confirmed the presence of anaerobic CH4-oxidizing archaea and both iron-reducing and iron-oxidizing bacteria in the tested sediments. Thus, besides combatting eutrophication, Fe(II)Cl2 application can mitigate CH4 emissions by reducing microbial net CH4-production and stimulating Fe-AOM.
{"title":"Fe(II)Cl2 amendment suppresses pond methane emissions by stimulating iron-dependent anaerobic oxidation of methane.","authors":"Quinten Struik, José R. Paranaíba, Martyna Glodowska, S. Kosten, Berber M J W Meulepas, Ana B. Rios-Miguel, M. Jetten, Miquel Lurling, G. Waajen, Thomas P. A. Nijman, A. Veraart","doi":"10.1093/femsec/fiae061","DOIUrl":"https://doi.org/10.1093/femsec/fiae061","url":null,"abstract":"Aquatic ecosystems are large contributors to global methane (CH4) emissions. Eutrophication significantly enhances CH4-production as it stimulates methanogenesis. Mitigation measures aimed at reducing eutrophication, such as the addition of metal salts to immobilize phosphate (PO43-), are now common practice. However, the effects of such remedies on methanogenic and methanotrophic communities-and therefore on CH4-cycling-remain largely unexplored. Here, we demonstrate that Fe(II)Cl2 addition, used as PO43- binder, differentially affected microbial CH4 cycling-processes in field experiments and batch incubations. In the field experiments, carried out in enclosures in a eutrophic pond, Fe(II)Cl2 application lowered in-situ CH4 emissions by lowering net CH4-production, while sediment aerobic CH4-oxidation rates-as found in batch incubations of sediment from the enclosures-did not differ from control. In Fe(II)Cl2-treated sediments, a decrease in net CH4-production rates could be attributed to the stimulation of iron-dependent anaerobic CH4-oxidation (Fe-AOM). In batch incubations, anaerobic CH4-oxidation and Fe(II)-production started immediately after CH4 addition, indicating Fe-AOM, likely enabled by favorable indigenous iron cycling conditions and the present methanotroph community in the pond sediment. 16S rRNA sequencing data confirmed the presence of anaerobic CH4-oxidizing archaea and both iron-reducing and iron-oxidizing bacteria in the tested sediments. Thus, besides combatting eutrophication, Fe(II)Cl2 application can mitigate CH4 emissions by reducing microbial net CH4-production and stimulating Fe-AOM.","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":"140694330","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}
Kira Sorochkina, Willm Martens-Habbena, Catherine L Reardon, Patrick W Inglett, Sarah L Strauss
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.
{"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}
Dukki Han, Ki-Tae Park, Haryun Kim, Tae-Hoon Kim, Man-Ki Jeong, Seung-Il Nam
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.
{"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}
Anjela L Vogel, Katharine J Thompson, Daniel Straub, Florin Musat, Tony Gutierrez, Sara Kleindienst
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.
{"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}
Leandro Pio de Sousa, Jorge Maurício Costa Mondego
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.
由真菌 Hemileia vastatrix 引起的咖啡叶锈病已成为咖啡生产国关注的主要问题。此外，某些菌种对杀真菌剂和育种品种的抗性也在增加，这使得生产者不得不使用其他控制方法。在这项工作中，我们将抗锈病咖啡品种（Coffea racemosa 和 Coffea stenophylla）的叶面微生物群移植到阿拉伯咖啡中，并测试了新的微生物群是否能将 H. vastatrix 造成的损害降到最低。结果表明，移植成功地控制了锈病，尤其是来自 C. stenophylla 的锈病，但保护效果取决于微生物群的浓度。某些真菌（如 Acrocalymma、Bipolaris、Didymella、Nigrospora、Setophaeosphaeria、Simplicillium、Stagonospora、Torula）和细菌（如 Chryseobacterium、Sphingobium，尤其是 Enterobacter）的数量有所增加，这可能与大锈菌的拮抗作用有关。有趣的是，泛变形菌属、甲基杆菌属和鞘氨单胞菌属细菌的相对数量在移植后有所减少，这表明它们与巨大芽胞杆菌的发展之间存在积极的相互作用。我们的研究结果可能有助于更好地了解微生物群在咖啡叶锈病中的作用，并有助于优化生物控制剂的开发。
{"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}
Cong Yue, Changxia Du, Xiaodan Wang, Yinqing Tan, Xingchen Liu, Huaifu Fan
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% < L1 < 30%, 30% ≤ L2 < 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.
{"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}
Sabrina A Klick, Joseph S Pitula, Amy S Collick, Eric B May, Oliva Pisani
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 >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.
农田施用的尿素基肥料会进入邻近农业排水沟的地表水中，造成附近流域的氮（N）负荷。排水沟中施用的管理方法可促进微生物群落对氮的清除，但人们对来自作物田的过量尿素肥料对这些排水沟中微生物多样性的影响知之甚少。2017 年，对玉米田和大豆田旁排水沟的沉积物进行了取样，以确定施肥和高浓度尿素氮是否会改变细菌多样性和脲酶基因丰度。中观宇宙实验与实地研究相结合，以确定哪些细菌群对高浓度尿素氮做出反应。玉米田旁沟渠中的细菌多样性与其他地点有显著差异。玉米田旁的沟渠中根瘤菌属、类杆菌属、酸性杆菌属、伯克霍尔德菌属和厌氧菌属的细菌数量最多，并且在中观试验期间添加尿素-N（0.5 毫克 N L-1）后，这些细菌数量有所增加。我们的研究结果表明，尿素氮浓度>0.07 mg N L-1（高于下游有害藻类大量繁殖的浓度）可导致农业排水沟细菌群落的变化。
{"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}
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