Pub Date : 2023-06-01DOI: 10.1094/pbiomes-02-22-0007-r
John Lagergren, Mikaela Cashman, Veronica Melesse Vergara, Paul Eller, Joao Gabriel Felipe Machado Gazolla, Hari Chhetri, Jared Streich, Sharlee Climer, Peter Thornton, Wayne Joubert, Daniel Jacobson
Predicted growth in world population will put unparalleled stress on the need for sustainable energy and global food production, as well as increase the likelihood of future pandemics. In this work, we identify high-resolution environmental zones in the context of a changing climate and predict longitudinal processes relevant to these challenges. We do this using exhaustive vector comparison methods that measure the climatic similarity between all locations on Earth at high geospatial resolution relative to global-scale analyses. The results are captured as networks, in which edges between geolocations are defined if their historical climate similarities exceed a threshold. We apply Markov clustering and our novel correlation of correlations method to the resulting climatic networks, which provides unprecedented agglomerative and longitudinal views of climatic relationships across the globe. The methods performed here resulted in the fastest (9.37 × 10 18 operations/s) and one of the largest 168.7 × 10 21 operations) scientific computations ever performed, with more than 100 quadrillion edges considered for a single climatic network. Our climatic analysis reveals areas of the world experiencing rapid environmental changes, which can have important implications for global carbon fluxes and zoonotic spillover events. Correlation and network analyses of this kind are widely applicable across computational and predictive biology domains, including systems biology, ecology, carbon cycles, biogeochemistry, and zoonosis research.
{"title":"Climatic Clustering and Longitudinal Analysis with Impacts on Food, Bioenergy, and Pandemics","authors":"John Lagergren, Mikaela Cashman, Veronica Melesse Vergara, Paul Eller, Joao Gabriel Felipe Machado Gazolla, Hari Chhetri, Jared Streich, Sharlee Climer, Peter Thornton, Wayne Joubert, Daniel Jacobson","doi":"10.1094/pbiomes-02-22-0007-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-22-0007-r","url":null,"abstract":"Predicted growth in world population will put unparalleled stress on the need for sustainable energy and global food production, as well as increase the likelihood of future pandemics. In this work, we identify high-resolution environmental zones in the context of a changing climate and predict longitudinal processes relevant to these challenges. We do this using exhaustive vector comparison methods that measure the climatic similarity between all locations on Earth at high geospatial resolution relative to global-scale analyses. The results are captured as networks, in which edges between geolocations are defined if their historical climate similarities exceed a threshold. We apply Markov clustering and our novel correlation of correlations method to the resulting climatic networks, which provides unprecedented agglomerative and longitudinal views of climatic relationships across the globe. The methods performed here resulted in the fastest (9.37 × 10 18 operations/s) and one of the largest 168.7 × 10 21 operations) scientific computations ever performed, with more than 100 quadrillion edges considered for a single climatic network. Our climatic analysis reveals areas of the world experiencing rapid environmental changes, which can have important implications for global carbon fluxes and zoonotic spillover events. Correlation and network analyses of this kind are widely applicable across computational and predictive biology domains, including systems biology, ecology, carbon cycles, biogeochemistry, and zoonosis research.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136118745","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}
Pub Date : 2023-06-01DOI: 10.1094/pbiomes-02-23-0010-r
Kang Liu, Wen-jing Meng, Zhao‐lei Qu, Yue-mei Zhang, Bing Liu, Yang Ma, Lin Chang, Huimin Sun
Forest succession affects aboveground vegetation and belowground microbial community composition, in which litter degradation plays an important role in nutrient cycling. However, limited information is available on how microbial communities change during litter degradation in forests undergoing succession due to disease. In this study, the bacterial communities and functions in litter degradation along the forest succession from pure Pinus forest (PPF), mixed Pinus and Liquidambar forest (MPF and MLF) and pure Liquidambar forest (PLF) were investigated. The results showed the bacterial community richness and diversity in both needles/leaves and branch litters increased progressively with forest succession. Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria were the most abundant bacterial phyla in the litter degradation along forest succession. The abundance of Bacteroidetes in branch increased significantly, while the abundance of genus Paraburkholderia decreased along forest succession. The different forests formed distinct bacterial community structures during litter decomposition. Functionally, chemoheterotrophy was the most abundant functional guild, followed by nitrogen fixation, intracellular parasitism and urealysis. The abundance of nitrogen fixation increased significantly along forest succession. Similarly, the different forests formed distinct bacterial functional structures in the needle/leaf along the succession. However, only two functional structures were formed in the branch. These results suggest that the bacterial community and its functions undergo significant changes during forest succession, particularly from the pure pine to mixed pine forest. These results provide a clear understanding of the changes in bacterial communities and functions during litter degradation in forests undergoing disease-induced succession.
{"title":"Changes in bacterial communities and functions associated with litter degradation during forest succession caused by forest disease","authors":"Kang Liu, Wen-jing Meng, Zhao‐lei Qu, Yue-mei Zhang, Bing Liu, Yang Ma, Lin Chang, Huimin Sun","doi":"10.1094/pbiomes-02-23-0010-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-23-0010-r","url":null,"abstract":"Forest succession affects aboveground vegetation and belowground microbial community composition, in which litter degradation plays an important role in nutrient cycling. However, limited information is available on how microbial communities change during litter degradation in forests undergoing succession due to disease. In this study, the bacterial communities and functions in litter degradation along the forest succession from pure Pinus forest (PPF), mixed Pinus and Liquidambar forest (MPF and MLF) and pure Liquidambar forest (PLF) were investigated. The results showed the bacterial community richness and diversity in both needles/leaves and branch litters increased progressively with forest succession. Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria were the most abundant bacterial phyla in the litter degradation along forest succession. The abundance of Bacteroidetes in branch increased significantly, while the abundance of genus Paraburkholderia decreased along forest succession. The different forests formed distinct bacterial community structures during litter decomposition. Functionally, chemoheterotrophy was the most abundant functional guild, followed by nitrogen fixation, intracellular parasitism and urealysis. The abundance of nitrogen fixation increased significantly along forest succession. Similarly, the different forests formed distinct bacterial functional structures in the needle/leaf along the succession. However, only two functional structures were formed in the branch. These results suggest that the bacterial community and its functions undergo significant changes during forest succession, particularly from the pure pine to mixed pine forest. These results provide a clear understanding of the changes in bacterial communities and functions during litter degradation in forests undergoing disease-induced succession.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45274246","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}
Pub Date : 2023-06-01DOI: 10.1094/pbiomes-12-22-0108-ta
Abdonaser Poursalavati, Vahid Jalali Javaran, Isabelle Laforest-Lapointe, Mamadou Fall
Soil microbes play an undeniable role in sustainable agriculture, plant health, and soil management. A deeper understanding of soil microbial composition and function has been gained through next-generation sequencing. Although soil metagenomics has provided valuable information about microbial diversity, issues stemming from RNA extraction, low RNA abundance in some microbial populations (e.g., viruses), and messenger RNA enrichment have slowed the progress of soil metatranscriptomics. A variety of soil RNA extraction methods have been developed thus far yet none of the available protocols can obtain RNA with high quality, purity, and yield for third-generation sequencing. The latter requires RNA with high quality and large quantities (with no or low contamination such as humic acids). Also, use of commercial kits for in-batch soil RNA extraction is quite expensive, and these commercial kits lack buffer composition details, which prevents the optimization of protocols for different soil types. An improved and cost-effective method for extracting RNAs from mineral and organic soils is presented in this article. An acidic sodium acetate buffer and phosphate buffer with modifications to bead beating and nucleic acid precipitation lead to higher RNA yields and quality. Using this method, we obtained almost DNA-free RNA. By using nanopore's direct RNA sequencing, the extracted contamination-free RNAs were successfully sequenced. Finally, taxonomic groups such as bacteria, fungi, archaea, and viruses were classified and profiled, and functional annotation of the datasets was carried out using an in-house customized bioinformatics workflow.
{"title":"Soil Metatranscriptomics: An Improved RNA Extraction Method Toward Functional Analysis Using Nanopore Direct RNA Sequencing","authors":"Abdonaser Poursalavati, Vahid Jalali Javaran, Isabelle Laforest-Lapointe, Mamadou Fall","doi":"10.1094/pbiomes-12-22-0108-ta","DOIUrl":"https://doi.org/10.1094/pbiomes-12-22-0108-ta","url":null,"abstract":"Soil microbes play an undeniable role in sustainable agriculture, plant health, and soil management. A deeper understanding of soil microbial composition and function has been gained through next-generation sequencing. Although soil metagenomics has provided valuable information about microbial diversity, issues stemming from RNA extraction, low RNA abundance in some microbial populations (e.g., viruses), and messenger RNA enrichment have slowed the progress of soil metatranscriptomics. A variety of soil RNA extraction methods have been developed thus far yet none of the available protocols can obtain RNA with high quality, purity, and yield for third-generation sequencing. The latter requires RNA with high quality and large quantities (with no or low contamination such as humic acids). Also, use of commercial kits for in-batch soil RNA extraction is quite expensive, and these commercial kits lack buffer composition details, which prevents the optimization of protocols for different soil types. An improved and cost-effective method for extracting RNAs from mineral and organic soils is presented in this article. An acidic sodium acetate buffer and phosphate buffer with modifications to bead beating and nucleic acid precipitation lead to higher RNA yields and quality. Using this method, we obtained almost DNA-free RNA. By using nanopore's direct RNA sequencing, the extracted contamination-free RNAs were successfully sequenced. Finally, taxonomic groups such as bacteria, fungi, archaea, and viruses were classified and profiled, and functional annotation of the datasets was carried out using an in-house customized bioinformatics workflow.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136370906","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}
Pub Date : 2023-05-21DOI: 10.1094/pbiomes-12-22-0105-r
M. Parizadeh, S. Kembel, B. Mimee
Neonicotinoid insecticides are widely used to control early-season and foliar-feeding pests. Some studies have revealed their non-target impacts on pollinators and other invertebrates, but few investigated their effects on soil microbiota. Given the crucial role of soil prokaryotic and eukaryotic microbial communities in agroecosystem regulation and their contribution to soil fertility, it is critical to understand their structure and changes in response to disturbances such as pesticide application. Among these communities, free-living nematodes have the potential to indicate the ecological changes in soil caused by environmental stress and have a key role in forming and modulating soil microbial composition and function by feeding on other soil microorganisms or interacting with them. Here, we used 18S rRNA gene amplicon sequencing to characterize the effects of neonicotinoids on soil nematode communities in a three-year soybean/corn crop rotation in Quebec, Canada. We also quantified the changes in nematode-bacteria co-occurrence networks in soil exposed to neonicotinoids. We found that neonicotinoid seed treatment significantly explained variation in nematode community composition and affected the relative abundance of some nematode families, such as a decrease in the omnivorous family Dorylaimidae in neonicotinoid-treated samples. Moreover, neonicotinoids altered the patterns of nematode-bacteria co-occurrence, including the structure and taxonomic composition of the networks. However, it is unclear whether neonicotinoids affected bacterial co-occurrence networks directly or indirectly by affecting nematodes that feed on bacteria. Further research is needed to understand how neonicotinoids affect nematodes and the role of nematodes in microbial network variation in soil exposed to neonicotinoids.
{"title":"Neonicotinoid Seed Treatments Influence Soil Nematode Taxonomic Composition and the Soil Microbial Co-occurrence Networks","authors":"M. Parizadeh, S. Kembel, B. Mimee","doi":"10.1094/pbiomes-12-22-0105-r","DOIUrl":"https://doi.org/10.1094/pbiomes-12-22-0105-r","url":null,"abstract":"Neonicotinoid insecticides are widely used to control early-season and foliar-feeding pests. Some studies have revealed their non-target impacts on pollinators and other invertebrates, but few investigated their effects on soil microbiota. Given the crucial role of soil prokaryotic and eukaryotic microbial communities in agroecosystem regulation and their contribution to soil fertility, it is critical to understand their structure and changes in response to disturbances such as pesticide application. Among these communities, free-living nematodes have the potential to indicate the ecological changes in soil caused by environmental stress and have a key role in forming and modulating soil microbial composition and function by feeding on other soil microorganisms or interacting with them. Here, we used 18S rRNA gene amplicon sequencing to characterize the effects of neonicotinoids on soil nematode communities in a three-year soybean/corn crop rotation in Quebec, Canada. We also quantified the changes in nematode-bacteria co-occurrence networks in soil exposed to neonicotinoids. We found that neonicotinoid seed treatment significantly explained variation in nematode community composition and affected the relative abundance of some nematode families, such as a decrease in the omnivorous family Dorylaimidae in neonicotinoid-treated samples. Moreover, neonicotinoids altered the patterns of nematode-bacteria co-occurrence, including the structure and taxonomic composition of the networks. However, it is unclear whether neonicotinoids affected bacterial co-occurrence networks directly or indirectly by affecting nematodes that feed on bacteria. Further research is needed to understand how neonicotinoids affect nematodes and the role of nematodes in microbial network variation in soil exposed to neonicotinoids.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45942669","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}
Pub Date : 2023-05-18DOI: 10.1094/pbiomes-12-22-0106-r
Sonia Garcia Mendez, A. Persyn, C. De Tender, S. Goormachtig, A. Willems
Low temperatures greatly affect plant growth. Besides the development of own protection mechanisms, plants may rely on microorganisms to help them cope with cold. As Valerianella locusta (lamb’s lettuce) is a cold-adapted plant, it represents an interesting plant to understand how cold affects the root bacteriome. By means of amplicon sequencing of 16S rRNA genes, we identified the taxa forming the main cold root bacteriome of lamb’s lettuce. The analysis of the root microbiome of a naturally growing V. locusta population and the study of the changes in the root microbiome of cultivated V. locusta grown under cold and ambient conditions allowed us to detect four cold-responsive families, of which Oxalobacteraceae presented the strongest shift under chilling temperatures. Moreover, the plant genotype had a small, but significant, effect on the response of the root bacteriome to cold. Finally, several bacterial candidates were discovered that may possibly alleviate the effect of low temperatures on plant fitness, namely Massilia ASV2, Flavobacterium ASV5 and ASV11, or Acidovorax ASV20. However, currently, only ten cold-enriched isolates could be obtained in cultivation, of which Flavobacterium R-83141, Polaromonas R-83176, R-83177, R-83175 and Acidovorax R-83129, were able to increase either the root, shoot and/or total fresh weight of a cold sensitive ecotype of A. thaliana (Cvi-0). Our results provide an overview of the taxa forming the root microbiome of this species and of the compositional shift that occurs under cold temperature treatment, demonstrating the impact of low temperatures on the composition of the root microbiome.
{"title":"Unravelling the bacterial community composition of Valerianella locusta, a cold tolerant plant","authors":"Sonia Garcia Mendez, A. Persyn, C. De Tender, S. Goormachtig, A. Willems","doi":"10.1094/pbiomes-12-22-0106-r","DOIUrl":"https://doi.org/10.1094/pbiomes-12-22-0106-r","url":null,"abstract":"Low temperatures greatly affect plant growth. Besides the development of own protection mechanisms, plants may rely on microorganisms to help them cope with cold. As Valerianella locusta (lamb’s lettuce) is a cold-adapted plant, it represents an interesting plant to understand how cold affects the root bacteriome. By means of amplicon sequencing of 16S rRNA genes, we identified the taxa forming the main cold root bacteriome of lamb’s lettuce. The analysis of the root microbiome of a naturally growing V. locusta population and the study of the changes in the root microbiome of cultivated V. locusta grown under cold and ambient conditions allowed us to detect four cold-responsive families, of which Oxalobacteraceae presented the strongest shift under chilling temperatures. Moreover, the plant genotype had a small, but significant, effect on the response of the root bacteriome to cold. Finally, several bacterial candidates were discovered that may possibly alleviate the effect of low temperatures on plant fitness, namely Massilia ASV2, Flavobacterium ASV5 and ASV11, or Acidovorax ASV20. However, currently, only ten cold-enriched isolates could be obtained in cultivation, of which Flavobacterium R-83141, Polaromonas R-83176, R-83177, R-83175 and Acidovorax R-83129, were able to increase either the root, shoot and/or total fresh weight of a cold sensitive ecotype of A. thaliana (Cvi-0). Our results provide an overview of the taxa forming the root microbiome of this species and of the compositional shift that occurs under cold temperature treatment, demonstrating the impact of low temperatures on the composition of the root microbiome.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47953199","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}
Pub Date : 2023-05-18DOI: 10.1094/pbiomes-12-22-0107-mf
Subha Chandran, Dinesh Sanka Loganathachetti, K. Masmoudi, R. Iratni, S. Mundra
Saline groundwater irrigation is commonly used in arid regions of the Middle East and North Africa for date palm (Phoenix dactylifera) cultivation, yet little is known about its impact on root-associated fungal (RAF) communities. We investigated the impact of irrigation water sources (freshwater vs. saline groundwater) on date palm RAF diversity, communities, and their assembly processes. RAF richness was lower in roots under saline groundwater irrigation and was significantly related to soil and water electrical conductivity (EC), and only 25.3% of the total operational taxonomic units (OTUs) were strictly found in roots under saline groundwater irrigation. Overall, the RAF communities were distinct among irrigation water sources, wherein water pH and EC were the major structuring factors. The relative importance of drift assembly was higher for RAF distribution under saline groundwater irrigation. Saprotrophic and pathotrophic communities were also distinct between irrigation water sources and shaped by irrigation water pH. In addition, we found higher abundance of saprotrophic OTUs Acrocalymma vagum, Coprinopsis sp., and Myrothecium sp. in roots under saline groundwater irrigation. Summarily, we show that saline groundwater irrigation lowers RAF richness, alters overall and guild level RAF communities (saprotroph and pathotroph) which assemble mainly through drift process, wherein overall communities are shaped by irrigation water pH and EC, while saprotrophic and pathotrophic communities are structured by water pH. The high abundance of specific saprotrophs under saline groundwater irrigation indicates their potential role in nutrient cycling and plant growth promotion in arid agroecosystems.
{"title":"Irrigation water source matters: Saline groundwater irrigation lowers date palm root-associated fungal richness and alters their community structural patterns","authors":"Subha Chandran, Dinesh Sanka Loganathachetti, K. Masmoudi, R. Iratni, S. Mundra","doi":"10.1094/pbiomes-12-22-0107-mf","DOIUrl":"https://doi.org/10.1094/pbiomes-12-22-0107-mf","url":null,"abstract":"Saline groundwater irrigation is commonly used in arid regions of the Middle East and North Africa for date palm (Phoenix dactylifera) cultivation, yet little is known about its impact on root-associated fungal (RAF) communities. We investigated the impact of irrigation water sources (freshwater vs. saline groundwater) on date palm RAF diversity, communities, and their assembly processes. RAF richness was lower in roots under saline groundwater irrigation and was significantly related to soil and water electrical conductivity (EC), and only 25.3% of the total operational taxonomic units (OTUs) were strictly found in roots under saline groundwater irrigation. Overall, the RAF communities were distinct among irrigation water sources, wherein water pH and EC were the major structuring factors. The relative importance of drift assembly was higher for RAF distribution under saline groundwater irrigation. Saprotrophic and pathotrophic communities were also distinct between irrigation water sources and shaped by irrigation water pH. In addition, we found higher abundance of saprotrophic OTUs Acrocalymma vagum, Coprinopsis sp., and Myrothecium sp. in roots under saline groundwater irrigation. Summarily, we show that saline groundwater irrigation lowers RAF richness, alters overall and guild level RAF communities (saprotroph and pathotroph) which assemble mainly through drift process, wherein overall communities are shaped by irrigation water pH and EC, while saprotrophic and pathotrophic communities are structured by water pH. The high abundance of specific saprotrophs under saline groundwater irrigation indicates their potential role in nutrient cycling and plant growth promotion in arid agroecosystems.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44699405","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}
Pub Date : 2023-05-18DOI: 10.1094/pbiomes-11-22-0081-r
A. Gates, Austin French, Alexander A. Demetros, Brittni R Kelley, S. Lebeis
While plant microbiome assembly involves a series of both plant-microbe and microbe-microbe interactions, the latter is less often directly tested. Here, we investigate a role for Streptomyces strains to influence assembly of other bacteria into root microbiomes through the use of two synthetic communities (SynComs): a 21-member community including four Streptomyces strains and a 17-member community lacking those Streptomyces strains. Following inoculation with these SynComs on wildtype Arabidopsis thaliana Col-0, differential abundance modeling on root endosphere 16S rRNA gene amplicon sequencing data revealed altered abundance of four diverse SynCom members: Arthrobacter sp. 131, Agrobacterium sp. 33, Burkholderia sp. CL11, and Ralstonia sp. CL21. Modeling results were tested by seedling co-inoculation experiments with the four Streptomyces strains and differentially abundant members, which confirmed the predicted decreased abundance for Arthrobacter sp. 131, Agrobacterium sp. 33, and Ralstonia sp. CL21 when Streptomyces strains were present. We further characterized how the phytohormone salicylic acid (SA) mediates Streptomyces strains’ influence over Agrobacterium sp. 33 and Burkholderia sp. CL11 seedling colonization. While decreased colonization of Ralstonia sp. CL21 and Arthrobacter sp. 131 when Streptomyces are present were not influenced by SA, direct antibiosis of Arthrobacter sp. 131 by the Streptomyces was observed. These results highlight a role for Streptomyces mediated microbial interactions during plant root microbiome assembly as well as distinct mechanisms that mediate them. Understanding the role of microbial interactions during microbiome assembly will inform the production of beneficial microbial treatments for use in agricultural fields.
{"title":"A Streptomyces consortium contributes distinct microbial interactions during Arabidopsis thaliana microbiome assembly","authors":"A. Gates, Austin French, Alexander A. Demetros, Brittni R Kelley, S. Lebeis","doi":"10.1094/pbiomes-11-22-0081-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-22-0081-r","url":null,"abstract":"While plant microbiome assembly involves a series of both plant-microbe and microbe-microbe interactions, the latter is less often directly tested. Here, we investigate a role for Streptomyces strains to influence assembly of other bacteria into root microbiomes through the use of two synthetic communities (SynComs): a 21-member community including four Streptomyces strains and a 17-member community lacking those Streptomyces strains. Following inoculation with these SynComs on wildtype Arabidopsis thaliana Col-0, differential abundance modeling on root endosphere 16S rRNA gene amplicon sequencing data revealed altered abundance of four diverse SynCom members: Arthrobacter sp. 131, Agrobacterium sp. 33, Burkholderia sp. CL11, and Ralstonia sp. CL21. Modeling results were tested by seedling co-inoculation experiments with the four Streptomyces strains and differentially abundant members, which confirmed the predicted decreased abundance for Arthrobacter sp. 131, Agrobacterium sp. 33, and Ralstonia sp. CL21 when Streptomyces strains were present. We further characterized how the phytohormone salicylic acid (SA) mediates Streptomyces strains’ influence over Agrobacterium sp. 33 and Burkholderia sp. CL11 seedling colonization. While decreased colonization of Ralstonia sp. CL21 and Arthrobacter sp. 131 when Streptomyces are present were not influenced by SA, direct antibiosis of Arthrobacter sp. 131 by the Streptomyces was observed. These results highlight a role for Streptomyces mediated microbial interactions during plant root microbiome assembly as well as distinct mechanisms that mediate them. Understanding the role of microbial interactions during microbiome assembly will inform the production of beneficial microbial treatments for use in agricultural fields.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47551034","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}
Pub Date : 2023-05-09DOI: 10.1094/pbiomes-02-23-0005-r
Leta Larsen, D. Schlatter, Jason Nimpoeno, Carla Hines-Snider, D. Samac
Alfalfa (Medicago sativa) seeds planted in cold, wet soil are prone to seed rot, pre- and post-emergence damping-off, and seedling root rot. These diseases reduce initial stand density and impact forage yields and winter survival when root systems are stunted by infection. Successful management depends on identifying the causal agents, but isolation in pure culture is time consuming and may fail to recover slow growing organisms or those requiring special growth conditions. Here, the oomycetes in rhizosphere soil and root endospheres from eight locations with a history of poor alfalfa establishment were identified by amplicon sequence analysis. Seedling bioassays were done with bulk soil and quantitative PCR assays were done using DNA from bulk soil, rhizosphere soil, and the root endosphere for Aphanomyces euteiches, Phytophthora medicaginis, Pythium irregulare, P. sylvaticum, and P. ultimum var. ultimum. In the endosphere and rhizosphere, A. euteiches was the dominant taxon, followed by Phytophthora medicaginis and P. sansomeana, a broad host range pathogen not previously known to infect alfalfa. Pythium inflatum and Globisporangium perplexum were also significantly over-represented in roots at five of the eight locations, indicating that these taxa are commonly enriched in alfalfa roots, but had not previously been identified as alfalfa pathogens. The qPCR assays of bulk soil showed that A. euteiches and P. medicaginis were unevenly distributed in the plots and low concentrations of the pathogens led to high levels of root rot disease. These results support development of cultivars with high levels of resistance to the most common oomycete pathogens.
{"title":"Rhizosphere and root community analysis of oomycetes associated with poor alfalfa (Medicago sativa) seedling establishment","authors":"Leta Larsen, D. Schlatter, Jason Nimpoeno, Carla Hines-Snider, D. Samac","doi":"10.1094/pbiomes-02-23-0005-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-23-0005-r","url":null,"abstract":"Alfalfa (Medicago sativa) seeds planted in cold, wet soil are prone to seed rot, pre- and post-emergence damping-off, and seedling root rot. These diseases reduce initial stand density and impact forage yields and winter survival when root systems are stunted by infection. Successful management depends on identifying the causal agents, but isolation in pure culture is time consuming and may fail to recover slow growing organisms or those requiring special growth conditions. Here, the oomycetes in rhizosphere soil and root endospheres from eight locations with a history of poor alfalfa establishment were identified by amplicon sequence analysis. Seedling bioassays were done with bulk soil and quantitative PCR assays were done using DNA from bulk soil, rhizosphere soil, and the root endosphere for Aphanomyces euteiches, Phytophthora medicaginis, Pythium irregulare, P. sylvaticum, and P. ultimum var. ultimum. In the endosphere and rhizosphere, A. euteiches was the dominant taxon, followed by Phytophthora medicaginis and P. sansomeana, a broad host range pathogen not previously known to infect alfalfa. Pythium inflatum and Globisporangium perplexum were also significantly over-represented in roots at five of the eight locations, indicating that these taxa are commonly enriched in alfalfa roots, but had not previously been identified as alfalfa pathogens. The qPCR assays of bulk soil showed that A. euteiches and P. medicaginis were unevenly distributed in the plots and low concentrations of the pathogens led to high levels of root rot disease. These results support development of cultivars with high levels of resistance to the most common oomycete pathogens.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43623695","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}
Pub Date : 2023-05-02DOI: 10.1094/pbiomes-02-23-0012-p
David W. Armitage, Morgan Carter, R. Choudhury, Mitja N. P. Remus-Emsermann, C. Morris, J. Leveau, L. Kinkel, J. P. Dundore-Arias
Here we summarize the main takeaways from a symposium and hybrid virtual and in-person participatory discussion focused on the challenges of scale in understanding the ecology and management of phyllosphere microbial communities. We provide an overview of the confounding effects of spatial scale on inference in microbial ecology, the spatial organization of microbial interactions in the phyllosphere, advances and remaining gaps in measuring phyllosphere colonization across scales, and the epidemiology in the phyllosphere. We hope to motivate further discussion and the development and adoption of creative approaches to solving the challenges of scale to enhance fundamental understanding and practical management of the phyllosphere microbiomes.
{"title":"Predictive ecology and management of phyllosphere microbial communities through cross-scale synthesis","authors":"David W. Armitage, Morgan Carter, R. Choudhury, Mitja N. P. Remus-Emsermann, C. Morris, J. Leveau, L. Kinkel, J. P. Dundore-Arias","doi":"10.1094/pbiomes-02-23-0012-p","DOIUrl":"https://doi.org/10.1094/pbiomes-02-23-0012-p","url":null,"abstract":"Here we summarize the main takeaways from a symposium and hybrid virtual and in-person participatory discussion focused on the challenges of scale in understanding the ecology and management of phyllosphere microbial communities. We provide an overview of the confounding effects of spatial scale on inference in microbial ecology, the spatial organization of microbial interactions in the phyllosphere, advances and remaining gaps in measuring phyllosphere colonization across scales, and the epidemiology in the phyllosphere. We hope to motivate further discussion and the development and adoption of creative approaches to solving the challenges of scale to enhance fundamental understanding and practical management of the phyllosphere microbiomes.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46023469","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}
Pub Date : 2023-04-28DOI: 10.1094/pbiomes-11-22-0091-r
F. Huang, J. Ling, Congyi Zhu, B. Cheng, Xiao-Bing Song, A. Peng
Plant disease is an important factor that affects the plant microbiome. However, for many plant–pathogen–microbiome interactions, the influences are unknown. Citrus, comprising abundant varieties of mandarin, sweet orange, pomelo, and lemon, is widely cultivated in different production areas in China. Most of these varieties are vulnerable to citrus canker, which is caused by Xanthomonas spp. In this study, asymptomatic and cankered leaves from asymptomatic and canker-infected trees, respectively, were collected from 17 orchards in six citrus production areas and their endophytic microbiomes were compared. The effects of canker on the microbial community richness and diversity were dependent on whether the interaction type was intrakingdom (for bacteria, positive) and interkingdom (for fungi, negative), respectively. The negative effects of canker on the fungal communities might be affected by the strong correlation between Xanthomonas and Fusarium/ Gibberella species. The occurrence of canker significantly affected the composition and structure of both the endophytic fungal and bacterial communities, and altered the dominant genera of each community. In addition, canker occurrence intensified the cross-kingdom microbial interaction network, in which species of Enterobacter, Xanthomonas, Pseudomonas, and Pantoea were detected with increased roles in the network and responsible for the predominant functional genes involved in nutritional metabolism, the bacterial secretion system, and biotin metabolism. The results provide insights into the responses of the endophytic microbiome to citrus canker disease.
{"title":"Canker Disease Intensifies Cross-Kingdom Microbial Interactions in the Endophytic Microbiota of Citrus Phyllosphere","authors":"F. Huang, J. Ling, Congyi Zhu, B. Cheng, Xiao-Bing Song, A. Peng","doi":"10.1094/pbiomes-11-22-0091-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-22-0091-r","url":null,"abstract":"Plant disease is an important factor that affects the plant microbiome. However, for many plant–pathogen–microbiome interactions, the influences are unknown. Citrus, comprising abundant varieties of mandarin, sweet orange, pomelo, and lemon, is widely cultivated in different production areas in China. Most of these varieties are vulnerable to citrus canker, which is caused by Xanthomonas spp. In this study, asymptomatic and cankered leaves from asymptomatic and canker-infected trees, respectively, were collected from 17 orchards in six citrus production areas and their endophytic microbiomes were compared. The effects of canker on the microbial community richness and diversity were dependent on whether the interaction type was intrakingdom (for bacteria, positive) and interkingdom (for fungi, negative), respectively. The negative effects of canker on the fungal communities might be affected by the strong correlation between Xanthomonas and Fusarium/ Gibberella species. The occurrence of canker significantly affected the composition and structure of both the endophytic fungal and bacterial communities, and altered the dominant genera of each community. In addition, canker occurrence intensified the cross-kingdom microbial interaction network, in which species of Enterobacter, Xanthomonas, Pseudomonas, and Pantoea were detected with increased roles in the network and responsible for the predominant functional genes involved in nutritional metabolism, the bacterial secretion system, and biotin metabolism. The results provide insights into the responses of the endophytic microbiome to citrus canker disease.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46390814","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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