Pub Date : 2023-10-09DOI: 10.1094/pbiomes-07-23-0076-r
Madison Flasco, Victoria Hoyle, Garner Powell, Jacob Seiter, Alice Wise, Elizabeth Cieniewicz, Marc Fuchs
Grapevine red blotch virus (GRBV) is the causative agent of red blotch disease. Limited information is available on the seasonal variation of GRBV titer in relation to disease symptom expression in vineyards across the United States. In this study, no statistically significant difference in GRBV titer was found among asymptomatic, infected vines in June (p=0.451) and among symptomatic, infected vines in October (p=0.068) in a diseased ‘Cabernet franc’ vineyard in California, regardless of the years symptomatic, i.e., one to seven, as shown by qPCR. Similarly, there were no statistically significant differences in GRBV titer as it relates to isolates of the two phylogenetic clades in asymptomatic, infected ‘Cabernet franc’ and ‘Cabernet Sauvignon’ vines in June (p=0.138 and p=0.778, respectively) and in symptomatic, infected vines in October (p=0.806 and p=0.490, respectively). GRBV titer differed among cultivars in diseased California vineyards (p < 0.001) and increased over the course of the growing season in infected ‘Merlot’ and ‘Cabernet franc’ vines, but not in ‘Cabernet Sauvignon’ vines. Patterns observed in California were consistent in New York and Georgia vineyards. In a Geneva double curtain-trellised ‘Cabernet Sauvignon’ vineyard in Georgia, GRBV distribution was uneven between cordons, and virus titer was variable within the vine canopy in June (p=0.017) but not in October (p=0.107). This work revealed consistent patterns of GRBV titer during a growing season in different vineyards across the United States. It also highlighted relatively high virus titer in symptomless grapevines in June when Spissistilus festinus-mediated GRBV transmission is documented in northern California.
{"title":"Seasonal variation in grapevine red blotch virus titer in relation to disease symptom expression in vineyards","authors":"Madison Flasco, Victoria Hoyle, Garner Powell, Jacob Seiter, Alice Wise, Elizabeth Cieniewicz, Marc Fuchs","doi":"10.1094/pbiomes-07-23-0076-r","DOIUrl":"https://doi.org/10.1094/pbiomes-07-23-0076-r","url":null,"abstract":"Grapevine red blotch virus (GRBV) is the causative agent of red blotch disease. Limited information is available on the seasonal variation of GRBV titer in relation to disease symptom expression in vineyards across the United States. In this study, no statistically significant difference in GRBV titer was found among asymptomatic, infected vines in June (p=0.451) and among symptomatic, infected vines in October (p=0.068) in a diseased ‘Cabernet franc’ vineyard in California, regardless of the years symptomatic, i.e., one to seven, as shown by qPCR. Similarly, there were no statistically significant differences in GRBV titer as it relates to isolates of the two phylogenetic clades in asymptomatic, infected ‘Cabernet franc’ and ‘Cabernet Sauvignon’ vines in June (p=0.138 and p=0.778, respectively) and in symptomatic, infected vines in October (p=0.806 and p=0.490, respectively). GRBV titer differed among cultivars in diseased California vineyards (p < 0.001) and increased over the course of the growing season in infected ‘Merlot’ and ‘Cabernet franc’ vines, but not in ‘Cabernet Sauvignon’ vines. Patterns observed in California were consistent in New York and Georgia vineyards. In a Geneva double curtain-trellised ‘Cabernet Sauvignon’ vineyard in Georgia, GRBV distribution was uneven between cordons, and virus titer was variable within the vine canopy in June (p=0.017) but not in October (p=0.107). This work revealed consistent patterns of GRBV titer during a growing season in different vineyards across the United States. It also highlighted relatively high virus titer in symptomless grapevines in June when Spissistilus festinus-mediated GRBV transmission is documented in northern California.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135094437","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 : 2023-09-12DOI: 10.1094/pbiomes-06-23-0042-r
Brandon L. Matsumoto, Ella Tali Sieradzki, Alex Greenlon, Laura Margarita Perilla-Henao, Anneliek Maria ter Horst, Sara Geonczy, Douglas Cook, Joanne B. Emerson
Legume nodules are specialized environments on plant roots that are induced and dominated by nitrogen-fixing bacteria. Bacteriophages (phages) in these nodules could potentially provide top-down controls on population size and, therefore, function of nitrogen-fixing symbionts. Here we sought to characterize the diversity and biogeographical patterns of phages that infect nitrogen-fixing Mesorhizobium symbionts isolated from root nodules, leveraging 266 genomes of Mesorhizobium isolated from nodules and 648 nodule metagenomes collected from three species of chickpea plants (Cicer spp.) under different agricultural management practices, spanning eight countries on five continents. We identified 106 phage populations (vOTUs) in Mesorhizobium draft genomes, 37% of which were confirmed as likely prophages. These vOTUs were detected in 64% of the Mesorhizobium-dominated nodule metagenomes and 58% of Mesorhizobium isolates. Per metagenome, 1-16 putative Mesorhizobium vOTUs were detected, with over half of the nodules containing only one such vOTU. The majority of vOTUs were detected exclusively in Ethiopia, followed by India and Morocco, with the lowest richness of putative Mesorhizobium phages in countries that applied industrial Mesorhizobium inoculants to crops. Two vOTUs were identified in five or more countries and in nodules dominated by different strains of Mesorhizobium, suggesting infection of diverse Mesorhizobium hosts and long-term interactions. Beta-diversity of these Mesorhizobium phage assemblages was significantly correlated with the dominant Mesorhizobium strain, but not with measured environmental parameters. Our findings indicate that nitrogen-fixing nodules in chickpea plants can contain distinct viral assemblages, with potential impacts on the nodule microbiome that bear further exploration.
{"title":"Viruses of nitrogen-fixing <i>Mesorhizobium</i> bacteria in globally distributed chickpea root nodules","authors":"Brandon L. Matsumoto, Ella Tali Sieradzki, Alex Greenlon, Laura Margarita Perilla-Henao, Anneliek Maria ter Horst, Sara Geonczy, Douglas Cook, Joanne B. Emerson","doi":"10.1094/pbiomes-06-23-0042-r","DOIUrl":"https://doi.org/10.1094/pbiomes-06-23-0042-r","url":null,"abstract":"Legume nodules are specialized environments on plant roots that are induced and dominated by nitrogen-fixing bacteria. Bacteriophages (phages) in these nodules could potentially provide top-down controls on population size and, therefore, function of nitrogen-fixing symbionts. Here we sought to characterize the diversity and biogeographical patterns of phages that infect nitrogen-fixing Mesorhizobium symbionts isolated from root nodules, leveraging 266 genomes of Mesorhizobium isolated from nodules and 648 nodule metagenomes collected from three species of chickpea plants (Cicer spp.) under different agricultural management practices, spanning eight countries on five continents. We identified 106 phage populations (vOTUs) in Mesorhizobium draft genomes, 37% of which were confirmed as likely prophages. These vOTUs were detected in 64% of the Mesorhizobium-dominated nodule metagenomes and 58% of Mesorhizobium isolates. Per metagenome, 1-16 putative Mesorhizobium vOTUs were detected, with over half of the nodules containing only one such vOTU. The majority of vOTUs were detected exclusively in Ethiopia, followed by India and Morocco, with the lowest richness of putative Mesorhizobium phages in countries that applied industrial Mesorhizobium inoculants to crops. Two vOTUs were identified in five or more countries and in nodules dominated by different strains of Mesorhizobium, suggesting infection of diverse Mesorhizobium hosts and long-term interactions. Beta-diversity of these Mesorhizobium phage assemblages was significantly correlated with the dominant Mesorhizobium strain, but not with measured environmental parameters. Our findings indicate that nitrogen-fixing nodules in chickpea plants can contain distinct viral assemblages, with potential impacts on the nodule microbiome that bear further exploration.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135826392","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 : 2023-09-01DOI: 10.1094/pbiomes-12-21-0075-r
Heng-An Lin, Santiago Mideros
Septoria brown spot, caused by Septoria glycines, is Illinois’ most prevalent soybean disease. It is common to use foliar fungicides to control Septoria brown spot and other late-season diseases of soybean. The effects of fungicide on nontarget organisms in the phyllosphere are unknown. To study the effect of S. glycines and fungicide application on the soybean phyllosphere mycobiome, we conducted a replicated field trial and collected samples at three soybean developmental stages. Then, we sequenced full-length internal transcribed spacer and a partial large subunit region using Oxford Nanopore technologies. Sequencing and data analysis produced 3,342 operational taxonomic units. The richness of the fungal community increased with the host development. There were differences in mycobiome diversity between soybean lines at the early developmental stage but not at the reproductive stages. Inoculation with S. glycines did not affect the α diversity but some significant changes were observed for the β diversity. At the beginning seed stage (R5), fungicide application changed the composition of the fungal community. The fungicide treatment decreased the proportion of several fungal taxa but it increased the proportion of Septoria. The core mycobiome in the phyllosphere was composed of genera Gibberella, Alternaria, Didymella, Cladosporium, Plectosphaerella, Colletotrichum, and Bipolaris. Network analysis identified significant interactions between Septoria and Diaporthe, Bipolaris, and two other taxonomic units. In this study, we set Septoria as the target organism and demonstrated that metabarcoding could be a tool to quantify the effect of multiple treatments on the mycobiome community. Better understanding of the dynamics of the phyllosphere microbiome is necessary to untangle the late-season diseases of soybean.
{"title":"The Effect of <i>Septoria glycines</i> and Fungicide Application on the Soybean Phyllosphere Mycobiome","authors":"Heng-An Lin, Santiago Mideros","doi":"10.1094/pbiomes-12-21-0075-r","DOIUrl":"https://doi.org/10.1094/pbiomes-12-21-0075-r","url":null,"abstract":"Septoria brown spot, caused by Septoria glycines, is Illinois’ most prevalent soybean disease. It is common to use foliar fungicides to control Septoria brown spot and other late-season diseases of soybean. The effects of fungicide on nontarget organisms in the phyllosphere are unknown. To study the effect of S. glycines and fungicide application on the soybean phyllosphere mycobiome, we conducted a replicated field trial and collected samples at three soybean developmental stages. Then, we sequenced full-length internal transcribed spacer and a partial large subunit region using Oxford Nanopore technologies. Sequencing and data analysis produced 3,342 operational taxonomic units. The richness of the fungal community increased with the host development. There were differences in mycobiome diversity between soybean lines at the early developmental stage but not at the reproductive stages. Inoculation with S. glycines did not affect the α diversity but some significant changes were observed for the β diversity. At the beginning seed stage (R5), fungicide application changed the composition of the fungal community. The fungicide treatment decreased the proportion of several fungal taxa but it increased the proportion of Septoria. The core mycobiome in the phyllosphere was composed of genera Gibberella, Alternaria, Didymella, Cladosporium, Plectosphaerella, Colletotrichum, and Bipolaris. Network analysis identified significant interactions between Septoria and Diaporthe, Bipolaris, and two other taxonomic units. In this study, we set Septoria as the target organism and demonstrated that metabarcoding could be a tool to quantify the effect of multiple treatments on the mycobiome community. Better understanding of the dynamics of the phyllosphere microbiome is necessary to untangle the late-season diseases of soybean.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135685705","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 : 2023-09-01DOI: 10.1094/pbiomes-12-21-0080-r
Anneliek Maria ter Horst, Jane D. Fudyma, Aurélie Bak, Min Sook Hwang, Christian Santos-Medellin, Kristian Stevens, David Rizzo, Maher Al Rwahnih, Joanne B. Emerson
Pub Date : 2023-09-01DOI: 10.1094/pbiomes-08-22-0046-fi
Marco Mechan, John Mullet, Ashley Shade
Phyllosphere exudates create specialized microhabitats that shape microbial community diversity. We explored the microbiome associated with two sorghum phyllosphere exudates, the epicuticular wax and aerial root mucilage. We assessed the microbiome associated with the wax from sorghum plants over two growth stages, and the root mucilage additionally from nitrogen-fertilized and nonfertilized plants. In parallel, we isolated and characterized hundreds of bacteria from wax and mucilage, and integrated data from cultivation-independent and cultivation-dependent approaches to gain insights into exudate diversity and bacterial phenotypes. We found that Sphingomonadaceae and Rhizobiaceae families were the major taxa in the wax regardless of water availability and plant developmental stage to plants. The cultivation-independent mucilage-associated bacterial microbiome contained the families Erwiniaceae, Flavobacteriaceae, Rhizobiaceae, Pseudomonadaceae, and Sphingomonadaceae, and its structure was strongly influenced by sorghum development but only modestly influenced by fertilization. In contrast, the fungal community structure of mucilage was strongly affected by the year of sampling but not by fertilization or plant developmental stage, suggesting a decoupling of fungal–bacterial dynamics in the mucilage. Our bacterial isolate collection from wax and mucilage had several isolates that matched 100% to detected amplicon sequence variants, and were enriched on media that selected for phenotypes that included phosphate solubilization, putative diazotrophy, resistance to desiccation, capability to grow on methanol as a carbon source, and ability to grow in the presence of linalool and β-caryophyllene (terpenes in sorghum wax). This work expands our understanding of the microbiome of phyllosphere exudates and supports our long-term goal to translate microbiome research to support sorghum cultivation.
{"title":"Phyllosphere Exudates Select for Distinct Microbiome Members in Sorghum Epicuticular Wax and Aerial Root Mucilage","authors":"Marco Mechan, John Mullet, Ashley Shade","doi":"10.1094/pbiomes-08-22-0046-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-08-22-0046-fi","url":null,"abstract":"Phyllosphere exudates create specialized microhabitats that shape microbial community diversity. We explored the microbiome associated with two sorghum phyllosphere exudates, the epicuticular wax and aerial root mucilage. We assessed the microbiome associated with the wax from sorghum plants over two growth stages, and the root mucilage additionally from nitrogen-fertilized and nonfertilized plants. In parallel, we isolated and characterized hundreds of bacteria from wax and mucilage, and integrated data from cultivation-independent and cultivation-dependent approaches to gain insights into exudate diversity and bacterial phenotypes. We found that Sphingomonadaceae and Rhizobiaceae families were the major taxa in the wax regardless of water availability and plant developmental stage to plants. The cultivation-independent mucilage-associated bacterial microbiome contained the families Erwiniaceae, Flavobacteriaceae, Rhizobiaceae, Pseudomonadaceae, and Sphingomonadaceae, and its structure was strongly influenced by sorghum development but only modestly influenced by fertilization. In contrast, the fungal community structure of mucilage was strongly affected by the year of sampling but not by fertilization or plant developmental stage, suggesting a decoupling of fungal–bacterial dynamics in the mucilage. Our bacterial isolate collection from wax and mucilage had several isolates that matched 100% to detected amplicon sequence variants, and were enriched on media that selected for phenotypes that included phosphate solubilization, putative diazotrophy, resistance to desiccation, capability to grow on methanol as a carbon source, and ability to grow in the presence of linalool and β-caryophyllene (terpenes in sorghum wax). This work expands our understanding of the microbiome of phyllosphere exudates and supports our long-term goal to translate microbiome research to support sorghum cultivation.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135636433","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 : 2023-09-01DOI: 10.1094/pbiomes-08-23-0088-e
Johan H. J. Leveau, Gwyn A. Beattie, Steven E. Lindow, Walter F. Mahaffee
The phyllosphere encompasses leaves and other aerial tissues of plants, which together provide diverse habitats for micro- and macro-organisms. In this editorial for the Phytobiomes Journal Focus Issue on the Phyllosphere, we celebrate the tremendous growth and impact of phyllosphere science as a discipline by introducing and providing context for 14 articles by nearly 100 authors from over 40 institutions. These articles collectively highlight the current status of the field and offer ideas for future directions. They explore topics related to phyllosphere biodiversity, community assembly and dynamics, and the adaptive capacity of species, populations, and communities on leaf surfaces and other phyllosphere compartments. The articles also delve into the multipartite relationships that phyllosphere colonizers have with each other and with their host, and issues of global concern such as food security, food safety, and climate change. This collection of work illustrates the international, transdisciplinary and collaborative nature of phyllosphere science, the challenges that the discipline faces, and the importance of recruiting and training the next generation of phyllosphere scientists.
{"title":"Phyllosphere, Front and Center: Focus on a Formerly ‘Ecologically Neglected’ Microbial Milieu","authors":"Johan H. J. Leveau, Gwyn A. Beattie, Steven E. Lindow, Walter F. Mahaffee","doi":"10.1094/pbiomes-08-23-0088-e","DOIUrl":"https://doi.org/10.1094/pbiomes-08-23-0088-e","url":null,"abstract":"The phyllosphere encompasses leaves and other aerial tissues of plants, which together provide diverse habitats for micro- and macro-organisms. In this editorial for the Phytobiomes Journal Focus Issue on the Phyllosphere, we celebrate the tremendous growth and impact of phyllosphere science as a discipline by introducing and providing context for 14 articles by nearly 100 authors from over 40 institutions. These articles collectively highlight the current status of the field and offer ideas for future directions. They explore topics related to phyllosphere biodiversity, community assembly and dynamics, and the adaptive capacity of species, populations, and communities on leaf surfaces and other phyllosphere compartments. The articles also delve into the multipartite relationships that phyllosphere colonizers have with each other and with their host, and issues of global concern such as food security, food safety, and climate change. This collection of work illustrates the international, transdisciplinary and collaborative nature of phyllosphere science, the challenges that the discipline faces, and the importance of recruiting and training the next generation of phyllosphere scientists.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135346645","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 : 2023-08-28DOI: 10.1094/pbiomes-01-23-0001-r
V. Flores-Núñez, D. A. Camarena‐Pozos, J. D. Chávez-González, Raúl Alcalde-Vázquez, M. N. Vázquez-Sánchez, A. G. Hernández-Melgar, J. Xool-Tamayo, Aldo Moreno-Ulloa, L. Partida-Martínez
Agaves are plants native to North America that sustain life in arid and semi-arid ecosystems. Previous studies revealed that cultivated plants of Agave tequilana had lower microbial diversity and functionality than wild Agave species. Here, we tested if synthetic communities (syncoms), based on microbial hubs or taxa with enriched microbial functions, could increase microbial diversity, plant health, and productivity in A. tequilana. We applied ten syncoms on the phyllosphere of six-months-old plants of Agave tequilana in the field and monitored their development for two years. Amplicon sequencing of the 16S-rRNA-V4 and ITS2 revealed that the inoculated syncoms played a negligible or minor role in the assembly of the prokaryotic and eukaryotic phyllospheric communities associated with Agave tequilana, respectively. However, syncoms based on microbial hubs, particularly those observed in the phyllosphere associated with the wild A. salmiana (PFCS), promoted microbial communities with higher alpha diversity. Some of these syncoms-derived phyllospheric communities consumed a greater variety of carbon sources; had more complex co-occurrence networks; and increased the content of sugars (oBrix, a measure of productivity in agaves) in the stem and changed the leaf metabolome. Our work demonstrates that the application of syncoms formulated based on predicted microbe-microbe interactions and metagenomic analyses of microbial communities in cultivated and wild plant species represents an effective tool to improve the sustainability and productivity of crops of arid ecosystems.
{"title":"Synthetic communities increase microbial diversity and productivity of Agave tequilana plants in the field","authors":"V. Flores-Núñez, D. A. Camarena‐Pozos, J. D. Chávez-González, Raúl Alcalde-Vázquez, M. N. Vázquez-Sánchez, A. G. Hernández-Melgar, J. Xool-Tamayo, Aldo Moreno-Ulloa, L. Partida-Martínez","doi":"10.1094/pbiomes-01-23-0001-r","DOIUrl":"https://doi.org/10.1094/pbiomes-01-23-0001-r","url":null,"abstract":"Agaves are plants native to North America that sustain life in arid and semi-arid ecosystems. Previous studies revealed that cultivated plants of Agave tequilana had lower microbial diversity and functionality than wild Agave species. Here, we tested if synthetic communities (syncoms), based on microbial hubs or taxa with enriched microbial functions, could increase microbial diversity, plant health, and productivity in A. tequilana. We applied ten syncoms on the phyllosphere of six-months-old plants of Agave tequilana in the field and monitored their development for two years. Amplicon sequencing of the 16S-rRNA-V4 and ITS2 revealed that the inoculated syncoms played a negligible or minor role in the assembly of the prokaryotic and eukaryotic phyllospheric communities associated with Agave tequilana, respectively. However, syncoms based on microbial hubs, particularly those observed in the phyllosphere associated with the wild A. salmiana (PFCS), promoted microbial communities with higher alpha diversity. Some of these syncoms-derived phyllospheric communities consumed a greater variety of carbon sources; had more complex co-occurrence networks; and increased the content of sugars (oBrix, a measure of productivity in agaves) in the stem and changed the leaf metabolome. Our work demonstrates that the application of syncoms formulated based on predicted microbe-microbe interactions and metagenomic analyses of microbial communities in cultivated and wild plant species represents an effective tool to improve the sustainability and productivity of crops of arid ecosystems.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43650920","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 : 2023-08-28DOI: 10.1094/pbiomes-02-23-0011-r
Daniel F. Caddell, Dean J. Pettinga, Katherine B. Louie, Ben Bowen, Julie A. Sievert, Joy Hollingsworth, Rebeckah Rubanowitz, J. Dahlberg, E. Purdom, T. Northen, D. Coleman-Derr
Plant-associated microbial communities shift in composition as a result of environmental perturbations, such as drought. Recently, it has been shown that Actinobacteria are enriched in plant roots and rhizosphere during drought stress, however, the correlations between microbiome dynamics and plant response to drought are poorly understood. Here we apply a combination of bacterial community composition analysis and plant metabolite profiling in Sorghum bicolor root, rhizosphere, and soil during drought and drought-recovery to investigate potential contributions of host metabolism towards shifts in bacterial composition. Our results provide a detailed view of metabolic shifts across the plant root during drought and show that the response to rewatering differs between root and soil; additionally, we identify drought-responsive metabolites that are highly correlated with the observed changes in Actinobacteria abundance. Furthermore, our study reports that pipecolic acid is a drought-enriched metabolite in sorghum roots, and that exogenous application of pipecolic acid inhibits root growth. Finally, we show that this activity functions independently from the systemic acquired resistance pathway, and has the potential to impact Actinobacterial taxa within the root microbiome.
{"title":"Drought shifts sorghum root metabolite and microbiome profiles and enriches for pipecolic acid","authors":"Daniel F. Caddell, Dean J. Pettinga, Katherine B. Louie, Ben Bowen, Julie A. Sievert, Joy Hollingsworth, Rebeckah Rubanowitz, J. Dahlberg, E. Purdom, T. Northen, D. Coleman-Derr","doi":"10.1094/pbiomes-02-23-0011-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-23-0011-r","url":null,"abstract":"Plant-associated microbial communities shift in composition as a result of environmental perturbations, such as drought. Recently, it has been shown that Actinobacteria are enriched in plant roots and rhizosphere during drought stress, however, the correlations between microbiome dynamics and plant response to drought are poorly understood. Here we apply a combination of bacterial community composition analysis and plant metabolite profiling in Sorghum bicolor root, rhizosphere, and soil during drought and drought-recovery to investigate potential contributions of host metabolism towards shifts in bacterial composition. Our results provide a detailed view of metabolic shifts across the plant root during drought and show that the response to rewatering differs between root and soil; additionally, we identify drought-responsive metabolites that are highly correlated with the observed changes in Actinobacteria abundance. Furthermore, our study reports that pipecolic acid is a drought-enriched metabolite in sorghum roots, and that exogenous application of pipecolic acid inhibits root growth. Finally, we show that this activity functions independently from the systemic acquired resistance pathway, and has the potential to impact Actinobacterial taxa within the root microbiome.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43324562","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 : 2023-07-28DOI: 10.1094/pbiomes-04-23-0025-r
C. Martínez-Arias, J. Sobrino-Plata, J. Rodríguez-Calcerrada, J. Martín
The assembly of plant microbial communities is a complex process orchestrated by plant physiology and microbial interactions under changing environmental conditions. In this work we aim to disentangle how an aggressive vascular pathogen, Ophiostoma novo-ulmi, affects the composition of the resident mycobiome of field elm (Ulmus minor). We also aim to determine the extent to which the inoculation of beneficial endophytes buffers the changes induced by the pathogen in the resident mycobiome composition. Three U. minor genotypes, two resistant and one susceptible to O. novo-ulmi, were inoculated with i) the pathogen, ii) a consortium of three beneficial endophytes, or iii) the endophyte consortium followed by pathogen inoculation. Endophyte composition of stem samples was profiled by high throughput sequencing of the first internal transcribed spacer region of the ribosomal DNA. A total of 365 ASVs were obtained, 61 of which were core members. Pathogen colonization reduced the ASV richness while endophyte inoculation increased the Shannon diversity. In most cases, the endophyte consortium inoculation prevented most of the changes in the mycobiome composition induced by the pathogen. At the genotype level, both alpha and beta diversity varied strongly, with latent pathogens being more abundant in the susceptible genotype. Overall, the results evidence that inoculation of plant beneficial endophytes buffers the changes produced in the mycobiome by aggressive pathogens.
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