Yossi Cohen, Julia Johnke, Alfred Abed-Rabbo, Zohar Pasternak, Antonis Chatzinotas, Edouard Jurkevitch
Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics, and functions of the microbial communities in highly sewage-impacted rivers is limited in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem we show, using 16S and 18S rRNA gene-based community analysis and targeted QPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Organic compounds hydrolyzers, and nitrogen and phosphorus recyclers were lacking, pointing at a reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio-and-like-organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.
{"title":"Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream","authors":"Yossi Cohen, Julia Johnke, Alfred Abed-Rabbo, Zohar Pasternak, Antonis Chatzinotas, Edouard Jurkevitch","doi":"10.1093/femsec/fiae069","DOIUrl":"https://doi.org/10.1093/femsec/fiae069","url":null,"abstract":"Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics, and functions of the microbial communities in highly sewage-impacted rivers is limited in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem we show, using 16S and 18S rRNA gene-based community analysis and targeted QPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Organic compounds hydrolyzers, and nitrogen and phosphorus recyclers were lacking, pointing at a reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio-and-like-organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"119 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140840325","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}
Masaru Bamba, Turgut Yigit Akyol, Yusuke Azuma, Johan Quilbe, Stig Uggerhøj Andersen, Shusei Sato
The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype [G], soil microbiome [M], and growth conditions (environment) [E] are the core factors shaping root microbiome, their relationships remain unclear. In this study we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.
植物及其根系微生物组之间的生物相互作用对植物生长至关重要，尽管植物基因型[G]、土壤微生物组[M]和生长条件（环境）[E]是影响根系微生物组的核心因素，但它们之间的关系仍不清楚。在本研究中，我们采用体外交叉接种方法，重建了两种不同环境条件下 9 个莲花品种与 4 种土壤微生物组之间的相互作用，研究了 G、M 和 E 及其相互作用对莲花根系微生物组和植物生长的影响。结果表明，根部微生物组的大部分组成是由 M 和 E 决定的，而与 G 相关的（G、G × M 和 G × E）效应显著但较小。相比之下，G 和 M 之间的相互作用对植物嫩枝生长的影响比单独 M 的影响更明显。我们的研究结果还表明，大多数由 M 控制的微生物组变异对植物表型的影响很小，而 G × M 的相互作用则有更显著的影响。植物基因型与土壤微生物之间的相互作用值得更多关注，以优化作物产量和抗逆性。
{"title":"Synergistic effects of plant genotype and soil microbiome on growth in Lotus japonicus","authors":"Masaru Bamba, Turgut Yigit Akyol, Yusuke Azuma, Johan Quilbe, Stig Uggerhøj Andersen, Shusei Sato","doi":"10.1093/femsec/fiae056","DOIUrl":"https://doi.org/10.1093/femsec/fiae056","url":null,"abstract":"The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype [G], soil microbiome [M], and growth conditions (environment) [E] are the core factors shaping root microbiome, their relationships remain unclear. In this study we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"22 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140812421","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}
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups—bacterial viruses, i.e. phages—has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
{"title":"The role of rhizosphere phages in soil health","authors":"Xiaofang Wang, Yike Tang, Xiufeng Yue, Shuo Wang, Keming Yang, Yangchun Xu, Qirong Shen, Ville-Petri Friman, Zhong Wei","doi":"10.1093/femsec/fiae052","DOIUrl":"https://doi.org/10.1093/femsec/fiae052","url":null,"abstract":"While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups—bacterial viruses, i.e. phages—has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"35 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140812940","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":"51 1","pages":""},"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":"49 1","pages":""},"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":"56 1","pages":""},"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":"49 1","pages":""},"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":"95 1","pages":""},"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":"78 1","pages":""},"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}
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":" ","pages":""},"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}
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