Pub Date : 2021-08-24DOI: 10.1094/pbiomes-02-21-0015-r
P. Benito, Lorena Carro, Rodrigo Bacigalupe, M. Ortúzar, M. Trujillo
An important number of Micromonospora strains have been reported from nitrogen fixing root nodules of legume and actinorhizal plants. However, the question of whether this bacterium can also be found in other parts of these plants remains unanswered. Over 150 strains were recovered from different Lupinus angustifolius and Pisum sativum tissues including leaves, stems, roots, and nodules. Ninety-seven percent of the isolates were identified by 16S rRNA gene sequence in the target genus and were associated with 27 different Micromonospora species. Plant-polymer degrading enzymes are suspected to play a role in the colonization of plants. To this end, bacterial enzymatic activity assays for amylases, cellulases, chitinases, pectinases and xylanases were determined. All strains produced xylanases and pectinases, while 98.6%, 98%, and 94.6% of them produced amylases, cellulases, and chitinases, respectively. The most productive strains included seven isolates from P. sativum and one from L. angustifolius. Strain Micromonospora lupini ML01-gfp was used to determine its capacity to reach and colonize different plant organs using P. sativum as the plant model. Stem and leaf samples were monitored by optical and fluorescence microscopy to locate the tagged strain. These results strongly suggest that Micromonospora is able, not only to infect nitrogen-fixing nodules, but also of reaching other parts of the host plant, especially the leaves.
{"title":"From roots to leaves: the capacity of Micromonospora to colonize different legume tissues","authors":"P. Benito, Lorena Carro, Rodrigo Bacigalupe, M. Ortúzar, M. Trujillo","doi":"10.1094/pbiomes-02-21-0015-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-21-0015-r","url":null,"abstract":"An important number of Micromonospora strains have been reported from nitrogen fixing root nodules of legume and actinorhizal plants. However, the question of whether this bacterium can also be found in other parts of these plants remains unanswered. Over 150 strains were recovered from different Lupinus angustifolius and Pisum sativum tissues including leaves, stems, roots, and nodules. Ninety-seven percent of the isolates were identified by 16S rRNA gene sequence in the target genus and were associated with 27 different Micromonospora species. Plant-polymer degrading enzymes are suspected to play a role in the colonization of plants. To this end, bacterial enzymatic activity assays for amylases, cellulases, chitinases, pectinases and xylanases were determined. All strains produced xylanases and pectinases, while 98.6%, 98%, and 94.6% of them produced amylases, cellulases, and chitinases, respectively. The most productive strains included seven isolates from P. sativum and one from L. angustifolius. Strain Micromonospora lupini ML01-gfp was used to determine its capacity to reach and colonize different plant organs using P. sativum as the plant model. Stem and leaf samples were monitored by optical and fluorescence microscopy to locate the tagged strain. These results strongly suggest that Micromonospora is able, not only to infect nitrogen-fixing nodules, but also of reaching other parts of the host plant, especially the leaves.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41822920","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 : 2021-08-19DOI: 10.1094/pbiomes-04-21-0030-r
A. Bintarti, A. Sulesky-Grieb, N. Stopnisek, A. Shade
Like other plant compartments, the seed harbors a microbiome. Seed microbiome members are the first to colonize a germinating seedling, and they may initiate the trajectory of microbiome assembly for the next plant generation. Therefore, the members of the seed microbiome are important for the dynamics of plant microbiome assembly and the vertical transmission of potentially beneficial symbionts. However, it remains challenging to assess the microbiome at the individual seed level (and, therefore, for the future individual plants) due to low endophytic microbial biomass, seed exudates that can select for particular members, and high plant and plastid contamination of resulting reads. Here, we report a protocol for extracting microbial DNA from an individual seed (common bean, Phaseolus vulgaris L.) with minimal disruption of host tissue, which we expect to be generalizable to other medium- and large-seed plant species. We applied this protocol to determine the 16S rRNA V4 and rRNA ITS2 amplicon composition and examine the variability of individual seeds harvested from replicate common bean plants grown under standard, controlled conditions to maintain health. Using DNA extractions from individual seeds, we compared seed-to-seed, pod-to-pod, and plant-to-plant microbiomes, and found highest microbiome variability at the plant level. This suggests that several seeds from the same plant could be pooled for microbiome assessment, given experimental designs that apply treatments at the parent plant level. This study adds protocols and insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems.
{"title":"Endophytic microbiome variation among single plant seeds","authors":"A. Bintarti, A. Sulesky-Grieb, N. Stopnisek, A. Shade","doi":"10.1094/pbiomes-04-21-0030-r","DOIUrl":"https://doi.org/10.1094/pbiomes-04-21-0030-r","url":null,"abstract":"Like other plant compartments, the seed harbors a microbiome. Seed microbiome members are the first to colonize a germinating seedling, and they may initiate the trajectory of microbiome assembly for the next plant generation. Therefore, the members of the seed microbiome are important for the dynamics of plant microbiome assembly and the vertical transmission of potentially beneficial symbionts. However, it remains challenging to assess the microbiome at the individual seed level (and, therefore, for the future individual plants) due to low endophytic microbial biomass, seed exudates that can select for particular members, and high plant and plastid contamination of resulting reads. Here, we report a protocol for extracting microbial DNA from an individual seed (common bean, Phaseolus vulgaris L.) with minimal disruption of host tissue, which we expect to be generalizable to other medium- and large-seed plant species. We applied this protocol to determine the 16S rRNA V4 and rRNA ITS2 amplicon composition and examine the variability of individual seeds harvested from replicate common bean plants grown under standard, controlled conditions to maintain health. Using DNA extractions from individual seeds, we compared seed-to-seed, pod-to-pod, and plant-to-plant microbiomes, and found highest microbiome variability at the plant level. This suggests that several seeds from the same plant could be pooled for microbiome assessment, given experimental designs that apply treatments at the parent plant level. This study adds protocols and insights to the growing toolkit of approaches to understand the plant-microbiome engagements that support the health of agricultural and environmental ecosystems.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45081773","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 : 2021-08-03DOI: 10.1094/pbiomes-02-21-0014-r
G. Williams, M. Ginzel
Thousand cankers disease (TCD) is hypothesized to have a greater impact on eastern black walnut (Juglans nigra) in urban forests and plantations compared to natural forest stands. Along with other factors, such as resource availability, the phytobiome could partly account for observed differences in disease severity across management regimes. We investigated the extent to which J. nigra-associated soil microbiomes from plantations and natural forests modulate a) the amount of necrosis caused by Geosmithia morbida Kolařík, Freeland, Utley and Tisserat in one-year-old seedlings, and b) relative abundance of rhizosphere endophytes and opportunistic pathogens Fusarium and Rhizoctonia in response to aboveground inoculation with G. morbida. Our results suggest that the microbiome from natural forest soil in central Indiana suppresses Fusarium and is indirectly suppressive of G. morbida. Natural forest soil had a greater ability to reduce the size of necrotic area caused by G. morbida compared to steam-treated soil. Inoculating stems of seedlings with G. morbida induced a shift in fungal community composition in the rhizosphere, including Fusarium and Rhizoctonia, but the direction and magnitude of the shift depended on whether seedlings were amended with forest, plantation, or steam-treated soil. In a companion experiment, necrotic area in G. morbida-inoculated seedlings was twice as high in seedlings grown from seeds that were treated with Fusarium solani relative to those grown from seeds treated with water. Our findings support the hypothesis that TCD severity can be modulated by host-mediated feedback between above- and belowground pathogens, as well as by microbial interactions in the rhizosphere.
{"title":"Forest and Plantation Soil Microbiomes Differ in Their Capacity to Suppress Feedback Between Geosmithia morbida and Rhizosphere Pathogens of J. nigra Seedlings","authors":"G. Williams, M. Ginzel","doi":"10.1094/pbiomes-02-21-0014-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-21-0014-r","url":null,"abstract":"Thousand cankers disease (TCD) is hypothesized to have a greater impact on eastern black walnut (Juglans nigra) in urban forests and plantations compared to natural forest stands. Along with other factors, such as resource availability, the phytobiome could partly account for observed differences in disease severity across management regimes. We investigated the extent to which J. nigra-associated soil microbiomes from plantations and natural forests modulate a) the amount of necrosis caused by Geosmithia morbida Kolařík, Freeland, Utley and Tisserat in one-year-old seedlings, and b) relative abundance of rhizosphere endophytes and opportunistic pathogens Fusarium and Rhizoctonia in response to aboveground inoculation with G. morbida. Our results suggest that the microbiome from natural forest soil in central Indiana suppresses Fusarium and is indirectly suppressive of G. morbida. Natural forest soil had a greater ability to reduce the size of necrotic area caused by G. morbida compared to steam-treated soil. Inoculating stems of seedlings with G. morbida induced a shift in fungal community composition in the rhizosphere, including Fusarium and Rhizoctonia, but the direction and magnitude of the shift depended on whether seedlings were amended with forest, plantation, or steam-treated soil. In a companion experiment, necrotic area in G. morbida-inoculated seedlings was twice as high in seedlings grown from seeds that were treated with Fusarium solani relative to those grown from seeds treated with water. Our findings support the hypothesis that TCD severity can be modulated by host-mediated feedback between above- and belowground pathogens, as well as by microbial interactions in the rhizosphere.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42226064","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 : 2021-08-02DOI: 10.1094/pbiomes-03-21-0019-r
Alan Harrison Wright, Shawkat Ali, Zoe Migiovsky, G. Douglas, S. Yurgel, Adèle L. Bunbury-Blanchette, Jeff Franklin, S. J. Adams, A. K. Walker
The microbiome, an influential factor affecting plant health and growth, is attracting increasing interest with respect to wine grape production. The purpose of this study was to characterize the microbiome (fungi and bacteria) of the soil, cover crop roots and grape (Vitis spp.) roots across rootstock and depth in a cool climate, organic vineyard. The cover crop consisted of a fescue (Festuca sp.) grass, while grape roots were sampled from ‘New York Muscat,’ a cool climate hybrid, across three root types (ungrafted, ‘3309C’ and ‘Riparia Gloire’) at three root depths (0–15, 15–30 and 30–50 cm). The grape root microbiome was more specialized, with fewer observed amplicon sequence variants (ASVs), for both bacteria (16S) and fungi (ITS) than found in the cover crop and the surrounding soil. Grape roots were dominated by bacterial genera Pseudomonas , Niastella and Rhizobium; most prominent fungal genera were Plectosphaerella, Trichosporon and Ilyonectria. While no correlations were found between alpha diversity metrics and soil parameters, Pseudaleuria RA was correlated with Mn, Fe and Na levels. Soil depth explained a small portion of bacterial, but not fungal, variance and taxonomic composition. Rootstock type explained a portion of both bacterial and fungal variance and taxonomic composition, substantiating the role of host plant genetics in the development of the grape root microbiome. This is the first characterization of the grape root microbiome in a cool climate Canadian vineyard.
{"title":"A Characterization of a Cool Climate Organic Vineyard’s Microbiome","authors":"Alan Harrison Wright, Shawkat Ali, Zoe Migiovsky, G. Douglas, S. Yurgel, Adèle L. Bunbury-Blanchette, Jeff Franklin, S. J. Adams, A. K. Walker","doi":"10.1094/pbiomes-03-21-0019-r","DOIUrl":"https://doi.org/10.1094/pbiomes-03-21-0019-r","url":null,"abstract":"The microbiome, an influential factor affecting plant health and growth, is attracting increasing interest with respect to wine grape production. The purpose of this study was to characterize the microbiome (fungi and bacteria) of the soil, cover crop roots and grape (Vitis spp.) roots across rootstock and depth in a cool climate, organic vineyard. The cover crop consisted of a fescue (Festuca sp.) grass, while grape roots were sampled from ‘New York Muscat,’ a cool climate hybrid, across three root types (ungrafted, ‘3309C’ and ‘Riparia Gloire’) at three root depths (0–15, 15–30 and 30–50 cm). The grape root microbiome was more specialized, with fewer observed amplicon sequence variants (ASVs), for both bacteria (16S) and fungi (ITS) than found in the cover crop and the surrounding soil. Grape roots were dominated by bacterial genera Pseudomonas , Niastella and Rhizobium; most prominent fungal genera were Plectosphaerella, Trichosporon and Ilyonectria. While no correlations were found between alpha diversity metrics and soil parameters, Pseudaleuria RA was correlated with Mn, Fe and Na levels. Soil depth explained a small portion of bacterial, but not fungal, variance and taxonomic composition. Rootstock type explained a portion of both bacterial and fungal variance and taxonomic composition, substantiating the role of host plant genetics in the development of the grape root microbiome. This is the first characterization of the grape root microbiome in a cool climate Canadian vineyard.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42777730","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 : 2021-07-08DOI: 10.1094/PBIOMES-06-21-0041-R
Vanessa L. Brisson, Jesper Richardy, S. Kosina, T. Northen, J. Vogel, A. Gaudin
Domestication and breeding have impacted interactions between plants and their microbiomes in ways that are only beginning to be understood but may have important implications for recruitment of rhizosphere microorganisms, particularly under stress conditions. We investigated the responses of a modern maize (Zea mays ssp. mays) cultivar and its wild relative, teosinte (Zea mays ssp. parviglumis), to different phosphate availabilities. We appraised responses of the plant-microbial holobiont to phosphate stresses by profiling root exudate metabolomes, and microbial communities in the root endosphere and rhizosphere. We also performed plate assays to quantify phosphate solubilizing microorganisms from the rhizosphere. While root exudate metabolite profiles were distinct between the teosinte and modern maize under high phosphate, both plants shifted exudate compositions in response to phosphate stress toward a common metabolite profile. Root and rhizosphere microbial communities also responded significantly to both plant type and the phosphate availability. A subset of bacterial and fungal taxa were differentially abundant under the different phosphate conditions, with each of the three conditions favoring different taxa. Both teosinte and maize rhizospheres harbored phosphate solubilizing microorganisms under all growth conditions. These results suggest that the root exudation response to phosphate stress was conserved through the domestication of maize from teosinte, shifting exudation levels of specific metabolites. Although microbial communities also shifted, plate-based assays did not detect selective recruitment of phosphate solubilizers in response to phosphate availability.
{"title":"Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in a Teosinte and a Modern Maize Cultivar","authors":"Vanessa L. Brisson, Jesper Richardy, S. Kosina, T. Northen, J. Vogel, A. Gaudin","doi":"10.1094/PBIOMES-06-21-0041-R","DOIUrl":"https://doi.org/10.1094/PBIOMES-06-21-0041-R","url":null,"abstract":"Domestication and breeding have impacted interactions between plants and their microbiomes in ways that are only beginning to be understood but may have important implications for recruitment of rhizosphere microorganisms, particularly under stress conditions. We investigated the responses of a modern maize (Zea mays ssp. mays) cultivar and its wild relative, teosinte (Zea mays ssp. parviglumis), to different phosphate availabilities. We appraised responses of the plant-microbial holobiont to phosphate stresses by profiling root exudate metabolomes, and microbial communities in the root endosphere and rhizosphere. We also performed plate assays to quantify phosphate solubilizing microorganisms from the rhizosphere. While root exudate metabolite profiles were distinct between the teosinte and modern maize under high phosphate, both plants shifted exudate compositions in response to phosphate stress toward a common metabolite profile. Root and rhizosphere microbial communities also responded significantly to both plant type and the phosphate availability. A subset of bacterial and fungal taxa were differentially abundant under the different phosphate conditions, with each of the three conditions favoring different taxa. Both teosinte and maize rhizospheres harbored phosphate solubilizing microorganisms under all growth conditions. These results suggest that the root exudation response to phosphate stress was conserved through the domestication of maize from teosinte, shifting exudation levels of specific metabolites. Although microbial communities also shifted, plate-based assays did not detect selective recruitment of phosphate solubilizers in response to phosphate availability.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45872783","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 : 2021-07-02DOI: 10.1094/pbiomes-03-21-0024-r
M. Sun, Senyu Chen, J. Kurle
Nutritional deficiency chlorosis especially iron-deficiency chlorosis and soybean cyst nematode (SCN) limit soybean yield. Arbuscular mycorrhizal fungi (MF) generally have beneficial effects on plant growth. The interactive effects of SCN, MF, and soil pH on leaf chlorophyll content (LCC) and growth of soybean were examined in a greenhouse experiment. The experiment was a randomized complete block design with three factors: SCN population densities, MF inoculation, and soil pH levels. SCN reduced LCC, and the effect increased with increasing time during 5-9 weeks after planting, especially in the high pH (8) soil. MF increased LCC in low pH (5.6) soil regardless of SCN population density and in the high pH soil without SCN. However, MF reduced LCC if both pH and SCN population density were high. The high SCN population density (inoculation 10,000 eggs/100 cm3 soil) reduced soybean shoot weight in all soils regardless of MF. MF increased shoot weight at pH 6.9 and pH 8 but not at pH 5.6. When MF was present, shoot weight was generally highest at pH 6.9. At high SCN when MF was absent, plant growth was better in pH 5.6 than pH 6.9 and 8 soils. This study demonstrates that SCN causes greater damage to soybean when interacting with high pH, and MF had a beneficial effect on soybean growth regardless of SCN infection in all pH soils, in spite of the negative effect of MF on LCC around 5-9 weeks after planting in high pH soil at high SCN population density.
{"title":"Interactive Effects of Soybean Cyst Nematode, Arbuscular-mycorrhizal Fungi, and Soil pH on Chlorophyll Content and Plant Growth of Soybean","authors":"M. Sun, Senyu Chen, J. Kurle","doi":"10.1094/pbiomes-03-21-0024-r","DOIUrl":"https://doi.org/10.1094/pbiomes-03-21-0024-r","url":null,"abstract":"Nutritional deficiency chlorosis especially iron-deficiency chlorosis and soybean cyst nematode (SCN) limit soybean yield. Arbuscular mycorrhizal fungi (MF) generally have beneficial effects on plant growth. The interactive effects of SCN, MF, and soil pH on leaf chlorophyll content (LCC) and growth of soybean were examined in a greenhouse experiment. The experiment was a randomized complete block design with three factors: SCN population densities, MF inoculation, and soil pH levels. SCN reduced LCC, and the effect increased with increasing time during 5-9 weeks after planting, especially in the high pH (8) soil. MF increased LCC in low pH (5.6) soil regardless of SCN population density and in the high pH soil without SCN. However, MF reduced LCC if both pH and SCN population density were high. The high SCN population density (inoculation 10,000 eggs/100 cm3 soil) reduced soybean shoot weight in all soils regardless of MF. MF increased shoot weight at pH 6.9 and pH 8 but not at pH 5.6. When MF was present, shoot weight was generally highest at pH 6.9. At high SCN when MF was absent, plant growth was better in pH 5.6 than pH 6.9 and 8 soils. This study demonstrates that SCN causes greater damage to soybean when interacting with high pH, and MF had a beneficial effect on soybean growth regardless of SCN infection in all pH soils, in spite of the negative effect of MF on LCC around 5-9 weeks after planting in high pH soil at high SCN population density.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46882371","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 : 2021-06-22DOI: 10.1094/pbiomes-03-21-0021-r
J. Doherty, J. Crouch, J. Roberts
Creeping bentgrass (Agrostis stolonifera L.) is widely used in golf course settings for its desirable playing surface characteristics, however it is highly susceptible to diseases that can disrupt surface integrity and cause significant losses despite preventative management. Understanding the influence of early plant growth and basic management practices on microbiome communities are crucial first steps to developing future efforts to harness the microbiome for plant health. This study investigated bacterial and fungal communities of creeping bentgrass foliage and rhizosphere through six months post-emergence under a controlled environment to elucidate microbiome community dynamics in response to plant age. We hypothesized that plant compartments will host distinct community structures and exhibit different responses to plant age. Our results showed that predominant bacterial phyla and fungal classes remain consistent across time and plant compartment. However, genus level classification revealed bacterial taxa differed across plant compartment while fungal taxa remained consistent. Host influence over the microbiome manifests quickly, with the largest shift in both microbial communities occurring between emergence and two months post-emergence. For example, Burkholderia and Penicillium were present at high relative abundance at emergence, but by two months post-emergence both taxa decreased significantly. Bacterial communities continued to experience significant fluctuation in rare taxa from two months post-emergence onward, while fungal community structure was driven by the fluctuation of the most common taxa. These results highlight the connection between plant age and microbial community structure in creeping bentgrass in addition to underscoring future research efforts in creeping bentgrass microbiome manipulation for plant health.
{"title":"Plant Age Influences Microbiome Communities More Than Plant Compartment in Greenhouse Grown Creeping Bentgrass","authors":"J. Doherty, J. Crouch, J. Roberts","doi":"10.1094/pbiomes-03-21-0021-r","DOIUrl":"https://doi.org/10.1094/pbiomes-03-21-0021-r","url":null,"abstract":"Creeping bentgrass (Agrostis stolonifera L.) is widely used in golf course settings for its desirable playing surface characteristics, however it is highly susceptible to diseases that can disrupt surface integrity and cause significant losses despite preventative management. Understanding the influence of early plant growth and basic management practices on microbiome communities are crucial first steps to developing future efforts to harness the microbiome for plant health. This study investigated bacterial and fungal communities of creeping bentgrass foliage and rhizosphere through six months post-emergence under a controlled environment to elucidate microbiome community dynamics in response to plant age. We hypothesized that plant compartments will host distinct community structures and exhibit different responses to plant age. Our results showed that predominant bacterial phyla and fungal classes remain consistent across time and plant compartment. However, genus level classification revealed bacterial taxa differed across plant compartment while fungal taxa remained consistent. Host influence over the microbiome manifests quickly, with the largest shift in both microbial communities occurring between emergence and two months post-emergence. For example, Burkholderia and Penicillium were present at high relative abundance at emergence, but by two months post-emergence both taxa decreased significantly. Bacterial communities continued to experience significant fluctuation in rare taxa from two months post-emergence onward, while fungal community structure was driven by the fluctuation of the most common taxa. These results highlight the connection between plant age and microbial community structure in creeping bentgrass in addition to underscoring future research efforts in creeping bentgrass microbiome manipulation for plant health.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45861124","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 : 2021-04-28DOI: 10.1094/PBIOMES-11-20-0079-R
J. hily, V. Komar, N. Poulicard, E. Vigne, O. Jacquet, Nathalie Protet, A. Spilmont, O. Lemaire
Since its identification in 2003, little has been revealed about the spread of grapevine Pinot gris virus (GPGV), an emerging grapevine virus. According to studies from Italy, GPGV transmission in the vineyard can be fast but progressive over the years. To gain new insights into the spread of GPGV infections, we tested 67 grapevines in a single vineyard parcel in southern France. These vines were sampled over eight years (2013-2020) and tested for GPGV by RT-PCR using a new primer pair designed from the recently described genetic diversity of GPGV worldwide. While focusing on a portion of the samples (20), we observed a drastic increase in newly GPGV-infected vines from 2014 (5%, 1 of 20) to 2015 (80%, 16 of 20) and 2016 (90%, 18 of 20). Infected vines were scattered throughout the vineyard with no distinct pattern of distribution and some rare vines remained negative through 2020. Using all available genomic information, we performed Bayesian-based phylogeographic analyses that identified a major intra-vineyard transmission in 2014-2015. To test our model, we analyzed 47 additional grapevines and confirmed the outbreak of GPGV in 2015, validating our in-silico projection. Interestingly, some grapevines remained negative throughout the study, in spite of their close proximity to infected plants. These results raise questions on the dynamic of vector populations and environmental conditions that may be required for virus spread to occur in the vineyard.
{"title":"Biological evidence and molecular modeling of a grapevine Pinot gris virus outbreak in a vineyard","authors":"J. hily, V. Komar, N. Poulicard, E. Vigne, O. Jacquet, Nathalie Protet, A. Spilmont, O. Lemaire","doi":"10.1094/PBIOMES-11-20-0079-R","DOIUrl":"https://doi.org/10.1094/PBIOMES-11-20-0079-R","url":null,"abstract":"Since its identification in 2003, little has been revealed about the spread of grapevine Pinot gris virus (GPGV), an emerging grapevine virus. According to studies from Italy, GPGV transmission in the vineyard can be fast but progressive over the years. To gain new insights into the spread of GPGV infections, we tested 67 grapevines in a single vineyard parcel in southern France. These vines were sampled over eight years (2013-2020) and tested for GPGV by RT-PCR using a new primer pair designed from the recently described genetic diversity of GPGV worldwide. While focusing on a portion of the samples (20), we observed a drastic increase in newly GPGV-infected vines from 2014 (5%, 1 of 20) to 2015 (80%, 16 of 20) and 2016 (90%, 18 of 20). Infected vines were scattered throughout the vineyard with no distinct pattern of distribution and some rare vines remained negative through 2020. Using all available genomic information, we performed Bayesian-based phylogeographic analyses that identified a major intra-vineyard transmission in 2014-2015. To test our model, we analyzed 47 additional grapevines and confirmed the outbreak of GPGV in 2015, validating our in-silico projection. Interestingly, some grapevines remained negative throughout the study, in spite of their close proximity to infected plants. These results raise questions on the dynamic of vector populations and environmental conditions that may be required for virus spread to occur in the vineyard.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49451643","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 : 2021-04-12DOI: 10.1094/PBIOMES-11-20-0080-A
Kenneth Dumack, M. Sapp, Tiemo von Steimker, Anna Tatjana Mänz, L. Rose, M. Bonkowski
The characterization of specific subsets of soil microbiota in the rhizosphere and endosphere has led to the recognition of plant species-specific microbiomes. Most attention has been given to microbial prokaryotes and fungi. Only recently was convincing evidence for the existence of plant species-specific protist microbiomes presented. Although protists are expected to shape the composition of bacterial and fungal communities and, thereby, directly impact plant health, a lack of cultures of these important plant-symbiotic protists has hampered their experimental exploration. To facilitate empirical plant microbiome research, we sampled Arabidopsis thaliana, established 79 cultures covering nearly all major groups of plant-symbiotic Cercozoa (protists), and have made these publicly available. We discuss our findings and propose potential roles that these protists may have in structuring the plant microbiome.
{"title":"A Call for Research: A Resource of Core Microbial Symbionts of the Arabidopsis thaliana Microbiome Ready and Awaiting Experimental Exploration","authors":"Kenneth Dumack, M. Sapp, Tiemo von Steimker, Anna Tatjana Mänz, L. Rose, M. Bonkowski","doi":"10.1094/PBIOMES-11-20-0080-A","DOIUrl":"https://doi.org/10.1094/PBIOMES-11-20-0080-A","url":null,"abstract":"The characterization of specific subsets of soil microbiota in the rhizosphere and endosphere has led to the recognition of plant species-specific microbiomes. Most attention has been given to microbial prokaryotes and fungi. Only recently was convincing evidence for the existence of plant species-specific protist microbiomes presented. Although protists are expected to shape the composition of bacterial and fungal communities and, thereby, directly impact plant health, a lack of cultures of these important plant-symbiotic protists has hampered their experimental exploration. To facilitate empirical plant microbiome research, we sampled Arabidopsis thaliana, established 79 cultures covering nearly all major groups of plant-symbiotic Cercozoa (protists), and have made these publicly available. We discuss our findings and propose potential roles that these protists may have in structuring the plant microbiome.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46087342","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 : 2021-02-25DOI: 10.1094/PBIOMES-09-20-0066-R
Carla Bridget Milazzo, Katherine G. Zulak, M. J. Muria-Gonzalez, Darcy A. B. Jones, M. Power, K. Bransgrove, M. Bunce, F. López-Ruiz
Over the last decade, the microbiome has received increasing attention as a key factor in macroorganism fitness. Sustainable pest management requires an understanding of the complex microbial endophyte communities existing symbiotically within plants and the way synthetic pesticides interact with them. Fungal endophytes are known to benefit plant growth and fitness and may deter pests and diseases. Recent advances in high-throughput sequencing (HTS) have enabled integrative microbiome studies, especially in agricultural contexts. Here, we profile the fungal endophyte community in the phyllosphere of two barley (Hordeum vulgare) cultivars exposed to two systemic foliar fungicides using metabarcoding, an HTS tool that constructs community profiles from environmental DNA. We studied the fungal nuclear ribosomal large subunit D2 and internal transcribed spacer 2 (ITS2) DNA markers through a bioinformatics pipeline introduced here. We found 88 and 128 unique amplicon sequence variants (ASVs) using the D2 and ITS2 metabarcoding assays, respectively. With principal coordinate analysis and permutational analysis of variance, ASV diversity did not change in response to barley cultivar or fungicide treatment; however, the community structure of unsprayed plants did change between two collection times 8 days apart. The workflow described here can be applied to other microbiome studies in agriculture and we hope it encourages further research into crop microbiomes to improve agroecosystem management.
{"title":"High-Throughput Metabarcoding Characterizes Fungal Endophyte Diversity in the Phyllosphere of a Barley Crop","authors":"Carla Bridget Milazzo, Katherine G. Zulak, M. J. Muria-Gonzalez, Darcy A. B. Jones, M. Power, K. Bransgrove, M. Bunce, F. López-Ruiz","doi":"10.1094/PBIOMES-09-20-0066-R","DOIUrl":"https://doi.org/10.1094/PBIOMES-09-20-0066-R","url":null,"abstract":"Over the last decade, the microbiome has received increasing attention as a key factor in macroorganism fitness. Sustainable pest management requires an understanding of the complex microbial endophyte communities existing symbiotically within plants and the way synthetic pesticides interact with them. Fungal endophytes are known to benefit plant growth and fitness and may deter pests and diseases. Recent advances in high-throughput sequencing (HTS) have enabled integrative microbiome studies, especially in agricultural contexts. Here, we profile the fungal endophyte community in the phyllosphere of two barley (Hordeum vulgare) cultivars exposed to two systemic foliar fungicides using metabarcoding, an HTS tool that constructs community profiles from environmental DNA. We studied the fungal nuclear ribosomal large subunit D2 and internal transcribed spacer 2 (ITS2) DNA markers through a bioinformatics pipeline introduced here. We found 88 and 128 unique amplicon sequence variants (ASVs) using the D2 and ITS2 metabarcoding assays, respectively. With principal coordinate analysis and permutational analysis of variance, ASV diversity did not change in response to barley cultivar or fungicide treatment; however, the community structure of unsprayed plants did change between two collection times 8 days apart. The workflow described here can be applied to other microbiome studies in agriculture and we hope it encourages further research into crop microbiomes to improve agroecosystem management.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":"1 1","pages":""},"PeriodicalIF":4.4,"publicationDate":"2021-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41756435","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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