Pub Date : 2022-12-02DOI: 10.1094/pbiomes-11-22-0092-r
K. Delventhal, Victoria P. Skillman, Xiaoping Li, P. Busby, K. Frost
For tuberizing crops like potato (Solanum tuberosum), the geocaulosphere, or the thin zone of soil in contact with and influenced by the tuber, is a distinct habitat that exists between the potato and the soil environment. Geocaulosphere soil that remains associated with the tuber after harvest is called tare soil. However, beyond potato pathogens, the microbes present in tare soil are understudied. We used ITS and 16S metabarcoding to characterize the microbial communities present in 130 tare soils of commercially produced seed potatoes used for potato production in Oregon. In 2018 and 2019, tare soils were opportunistically sampled from seed potatoes that were collected from farmers in the Columbia Basin of OR. This sampling effort included seed tubers of 23 cultivars that had originated from 40 commercial seed farms in 11 states. We identified a core microbiome consisting of 61 bacterial and 26 fungal taxa, some of which are not common to the potato microbiome, and others which have been reported to either possess biocontrol activities, promote plant growth, or cause disease in potato. Seed grower farm accounted for the greatest amount of compositional variation among tare soil microbiome samples, with more similar communities found on seed tubers grown on farms near to each other. Learning which factors shape tare soil microbial community composition and if those communities influence plant health are essential steps towards potato microbiome management.
{"title":"Characterizing variation in the bacterial and fungal tare soil microbiome of the seed potato","authors":"K. Delventhal, Victoria P. Skillman, Xiaoping Li, P. Busby, K. Frost","doi":"10.1094/pbiomes-11-22-0092-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-22-0092-r","url":null,"abstract":"For tuberizing crops like potato (Solanum tuberosum), the geocaulosphere, or the thin zone of soil in contact with and influenced by the tuber, is a distinct habitat that exists between the potato and the soil environment. Geocaulosphere soil that remains associated with the tuber after harvest is called tare soil. However, beyond potato pathogens, the microbes present in tare soil are understudied. We used ITS and 16S metabarcoding to characterize the microbial communities present in 130 tare soils of commercially produced seed potatoes used for potato production in Oregon. In 2018 and 2019, tare soils were opportunistically sampled from seed potatoes that were collected from farmers in the Columbia Basin of OR. This sampling effort included seed tubers of 23 cultivars that had originated from 40 commercial seed farms in 11 states. We identified a core microbiome consisting of 61 bacterial and 26 fungal taxa, some of which are not common to the potato microbiome, and others which have been reported to either possess biocontrol activities, promote plant growth, or cause disease in potato. Seed grower farm accounted for the greatest amount of compositional variation among tare soil microbiome samples, with more similar communities found on seed tubers grown on farms near to each other. Learning which factors shape tare soil microbial community composition and if those communities influence plant health are essential steps towards potato microbiome management.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49108084","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 : 2022-12-02DOI: 10.1094/pbiomes-11-22-0093-r
K. Delventhal, P. Busby, K. Frost
Understanding the factors influencing microbial community composition in the rhizosphere is an important step towards managing the microbiomes of globally important crops like potato (Solanum tuberosum). Potato is vegetatively propagated and seed tubers are planted with tare soil, or soil adhering to the tuber surface, from their field of origin. Bulk soil is known to influence rhizosphere microbiome composition, but whether tare soil additionally contributes to compositional variation is not known. We tested this hypothesis in a greenhouse experiment where tare soil was removed (or remained intact for controls) prior to planting in either soil from a potato field or soil from a previously uncultivated area next the potato field. We used ITS and 16S metabarcoding to characterize the fungal and bacterial rhizosphere communities of plants grown from the experimental seed tubers. We found that tare soil influenced rhizosphere microbial composition, more strongly for fungi than bacteria. As expected, bulk soil origin explained the greatest amount of variation in the rhizosphere microbiome overall, but we found no evidence that the impact of tare soil on microbial community composition differed between bulk soil origins. The magnitude of the tare soil effect did, however, depend in part on seed tuber origin. Our findings reveal that tare soil explains a significant, though modest, amount of variation in rhizosphere composition, and sets the stage for future work addressing functional consequences for plant health and productivity.
{"title":"Tare soil alters the composition of the developing the potato rhizosphere microbiome","authors":"K. Delventhal, P. Busby, K. Frost","doi":"10.1094/pbiomes-11-22-0093-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-22-0093-r","url":null,"abstract":"Understanding the factors influencing microbial community composition in the rhizosphere is an important step towards managing the microbiomes of globally important crops like potato (Solanum tuberosum). Potato is vegetatively propagated and seed tubers are planted with tare soil, or soil adhering to the tuber surface, from their field of origin. Bulk soil is known to influence rhizosphere microbiome composition, but whether tare soil additionally contributes to compositional variation is not known. We tested this hypothesis in a greenhouse experiment where tare soil was removed (or remained intact for controls) prior to planting in either soil from a potato field or soil from a previously uncultivated area next the potato field. We used ITS and 16S metabarcoding to characterize the fungal and bacterial rhizosphere communities of plants grown from the experimental seed tubers. We found that tare soil influenced rhizosphere microbial composition, more strongly for fungi than bacteria. As expected, bulk soil origin explained the greatest amount of variation in the rhizosphere microbiome overall, but we found no evidence that the impact of tare soil on microbial community composition differed between bulk soil origins. The magnitude of the tare soil effect did, however, depend in part on seed tuber origin. Our findings reveal that tare soil explains a significant, though modest, amount of variation in rhizosphere composition, and sets the stage for future work addressing functional consequences for plant health and productivity.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44003944","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 : 2022-11-15DOI: 10.1094/pbiomes-04-22-0028-fi
Shay Szymanski, R. Longley, R. Hatlen, Lexi Heger, N. Sharma, G. Bonito, T. Miles
The microbial ecology of agricultural products may provide crucial insights into the management of post-harvest fruit rots. To investigate post-harvest microbial communities of highbush blueberry (Vaccinium corymbosum), five fungicide spray programs were evaluated for their influence on the mycobiome of fruit skin and within the fruit pulp. The mycobiome was characterized by sequencing amplicons of the ITS1 region with primers ITS1f and ITS4 with the Illumina MiSeq 300bp v3 system. Two of the five programs utilized commercial biological fungicides, two utilized azoxystrobin, and one utilized a series of treatments to simulate a realistic disease management program. Fungicide applications reduced diversity of the fruit skin mycobiome (R2=0.409, p=0.0001) and had a moderate impact on the pulp mycobiome (R2=0.233, p=0.0001). The mycobiome of the fruit pulp was also more variable than the skin mycobiome. In comparison to the untreated controls, each fungicide treatment program had a strongly significant effect on the beta-diversity of the blueberry fruit skin mycobiome (R2=0.53-0.73, p=0.0001). In the pulp, three of the five treatments had moderate but significant effects on beta-diversity in comparison to the control (R2=0.10-0.18, p=0.0005-0.017). Most samples indicated that fungi belonging to Epicoccum, Papiliotrema, and Sporobolomyces were widely prevalent and abundant across treatments and tissues. Fruit pathogen Botrytis cinerea was particularly abundant in the pulp of three of fungicide treatments. Results from this study provide a baseline for future exploration of post-harvest rot pathology and provide a community context on how fungicides may alter fungal communities in agricultural systems.
{"title":"The Blueberry Fruit Mycobiome Varies by Tissue Type and Fungicide Treatment","authors":"Shay Szymanski, R. Longley, R. Hatlen, Lexi Heger, N. Sharma, G. Bonito, T. Miles","doi":"10.1094/pbiomes-04-22-0028-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-04-22-0028-fi","url":null,"abstract":"The microbial ecology of agricultural products may provide crucial insights into the management of post-harvest fruit rots. To investigate post-harvest microbial communities of highbush blueberry (Vaccinium corymbosum), five fungicide spray programs were evaluated for their influence on the mycobiome of fruit skin and within the fruit pulp. The mycobiome was characterized by sequencing amplicons of the ITS1 region with primers ITS1f and ITS4 with the Illumina MiSeq 300bp v3 system. Two of the five programs utilized commercial biological fungicides, two utilized azoxystrobin, and one utilized a series of treatments to simulate a realistic disease management program. Fungicide applications reduced diversity of the fruit skin mycobiome (R2=0.409, p=0.0001) and had a moderate impact on the pulp mycobiome (R2=0.233, p=0.0001). The mycobiome of the fruit pulp was also more variable than the skin mycobiome. In comparison to the untreated controls, each fungicide treatment program had a strongly significant effect on the beta-diversity of the blueberry fruit skin mycobiome (R2=0.53-0.73, p=0.0001). In the pulp, three of the five treatments had moderate but significant effects on beta-diversity in comparison to the control (R2=0.10-0.18, p=0.0005-0.017). Most samples indicated that fungi belonging to Epicoccum, Papiliotrema, and Sporobolomyces were widely prevalent and abundant across treatments and tissues. Fruit pathogen Botrytis cinerea was particularly abundant in the pulp of three of fungicide treatments. Results from this study provide a baseline for future exploration of post-harvest rot pathology and provide a community context on how fungicides may alter fungal communities in agricultural systems.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45601965","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 : 2022-11-15DOI: 10.1094/pbiomes-06-22-0037-a
C. Vacher, Claire Francioni, Mario Michel, Tania Fort, Julie Faivre d’Arcier, É. Chancerel, F. Delmotte, C. E. Delmas
{"title":"Fungal Metabarcoding Data for Two Grapevine Varieties (Regent and Vitis vinifera ‘Cabernet-Sauvignon’) Inoculated with Powdery Mildew (Erysiphe necator) Under Drought Conditions","authors":"C. Vacher, Claire Francioni, Mario Michel, Tania Fort, Julie Faivre d’Arcier, É. Chancerel, F. Delmotte, C. E. Delmas","doi":"10.1094/pbiomes-06-22-0037-a","DOIUrl":"https://doi.org/10.1094/pbiomes-06-22-0037-a","url":null,"abstract":"","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47990097","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 : 2022-11-02DOI: 10.1094/pbiomes-08-22-0056-r
B. Whitaker, M. Vaughan, S. McCormick
Fusarium head blight (FHB) is an economically important disease of small grains globally and is primarily caused by Fusarium graminearum in North America. Recently, microbial biocontrols have risen in importance as sustainable agents of disease control. However, the path to implementation of microbial biocontrols in agriculture will require an understanding of how microbiota impact both plant performance overall and vary with inherent host disease resistance. Using a full-factorial, controlled greenhouse experiment, we tested how seven bacterial endophyte seed soak treatments impacted both plant physiology prior to pathogen infection and FHB disease progression in Triticum aestivum (wheat). Bacterial endophyte treatments strongly impacted the light dependent reactions of photosynthesis, with changes in plant traits regulating light energy allocation and the build-up of electrochemical energy storage across the thylakoid membrane. Physiological responses were contingent on host variety. The direct effects of bacterial endophytes on wheat response to infection were weak and dependent on the inherent disease resistance of the host variety. However, disease outcomes were indirectly mediated by bacterial impacts on plant traits, with proton motive force traits emerging as common predictors of disease response across both host varieties and other traits indicating potential trade-offs in host response to bacterial inoculants and F. graminearum infection. Our results provide an alternate mechanism for microbial biocontrol efficacy other than direct antagonism with the pathogen inside the host. Furthermore, the chlorophyll-fluorescence and absorbance-based markers assessed here may have translational potential as a phenotyping tool for FHB susceptibility in wheat and other small grains.
{"title":"Biocontrol impacts on wheat physiology and Fusarium head blight outcomes are bacterial endophyte strain- and cultivar specific","authors":"B. Whitaker, M. Vaughan, S. McCormick","doi":"10.1094/pbiomes-08-22-0056-r","DOIUrl":"https://doi.org/10.1094/pbiomes-08-22-0056-r","url":null,"abstract":"Fusarium head blight (FHB) is an economically important disease of small grains globally and is primarily caused by Fusarium graminearum in North America. Recently, microbial biocontrols have risen in importance as sustainable agents of disease control. However, the path to implementation of microbial biocontrols in agriculture will require an understanding of how microbiota impact both plant performance overall and vary with inherent host disease resistance. Using a full-factorial, controlled greenhouse experiment, we tested how seven bacterial endophyte seed soak treatments impacted both plant physiology prior to pathogen infection and FHB disease progression in Triticum aestivum (wheat). Bacterial endophyte treatments strongly impacted the light dependent reactions of photosynthesis, with changes in plant traits regulating light energy allocation and the build-up of electrochemical energy storage across the thylakoid membrane. Physiological responses were contingent on host variety. The direct effects of bacterial endophytes on wheat response to infection were weak and dependent on the inherent disease resistance of the host variety. However, disease outcomes were indirectly mediated by bacterial impacts on plant traits, with proton motive force traits emerging as common predictors of disease response across both host varieties and other traits indicating potential trade-offs in host response to bacterial inoculants and F. graminearum infection. Our results provide an alternate mechanism for microbial biocontrol efficacy other than direct antagonism with the pathogen inside the host. Furthermore, the chlorophyll-fluorescence and absorbance-based markers assessed here may have translational potential as a phenotyping tool for FHB susceptibility in wheat and other small grains.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45044418","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 : 2022-09-26DOI: 10.1094/pbiomes-02-22-0012-r
J. Ata, A. Schoettle, R. Sitz, J. Caballero, Christine T. Holtz, Z. Abdo, J. Stewart
Fungal endophytic communities in needles of field-grown Pinus flexilis previously inferred to carry major gene resistance (R) to white pine blister rust (WPBR) or to lack it (S) were surveyed to identify unique microbes that may be recruited by WPBR-resistant genotypes. Resistant and susceptible trees were sampled in each of 11 P. flexilis populations for a total of 50 trees sampled. Through next-generation sequencing, this study showed a diverse needle mycobiota in P. flexilis, of which many remain unknown, regardless of the presence or absence of the WPBR resistance gene, Cr4. Ascomycota dominated the mycobiota (88.9%) followed by Basidiomycota (4.4%) and Chytridiomycota (0.03%), and the remaining 6.7% were unclassified. Shared ( n = 105) and unique ( n = 48 in R and n = 49 in S) fungal taxa, including differentially abundant operational taxonomic units, were identified that could provide insights into core mycobiota and host genotype-specific fungal groups. Marginal variation of the fungal diversity and structure was observed between host genotypes, which indicates that neither Cr4 nor the physiological differences associated with the presence or absence of the gene affects mycobiota recruitment. Instead, other parameters, including host size (diameter at breast height) and site elevation, significantly influenced the variability of the composition and structure of the fungal endophytic community. Further investigations are needed to understand the relationship of unique or differentially abundant taxa with one genotype or the other, and to determine the role of the needle mycobiota in WPBR disease development in natural stands of P. flexilis.
{"title":"Characterization of Foliar Fungal Endophyte Communities from White Pine Blister Rust Resistant and Susceptible Pinus flexilis in Natural Stands in the Southern Rocky Mountains","authors":"J. Ata, A. Schoettle, R. Sitz, J. Caballero, Christine T. Holtz, Z. Abdo, J. Stewart","doi":"10.1094/pbiomes-02-22-0012-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-22-0012-r","url":null,"abstract":"Fungal endophytic communities in needles of field-grown Pinus flexilis previously inferred to carry major gene resistance (R) to white pine blister rust (WPBR) or to lack it (S) were surveyed to identify unique microbes that may be recruited by WPBR-resistant genotypes. Resistant and susceptible trees were sampled in each of 11 P. flexilis populations for a total of 50 trees sampled. Through next-generation sequencing, this study showed a diverse needle mycobiota in P. flexilis, of which many remain unknown, regardless of the presence or absence of the WPBR resistance gene, Cr4. Ascomycota dominated the mycobiota (88.9%) followed by Basidiomycota (4.4%) and Chytridiomycota (0.03%), and the remaining 6.7% were unclassified. Shared ( n = 105) and unique ( n = 48 in R and n = 49 in S) fungal taxa, including differentially abundant operational taxonomic units, were identified that could provide insights into core mycobiota and host genotype-specific fungal groups. Marginal variation of the fungal diversity and structure was observed between host genotypes, which indicates that neither Cr4 nor the physiological differences associated with the presence or absence of the gene affects mycobiota recruitment. Instead, other parameters, including host size (diameter at breast height) and site elevation, significantly influenced the variability of the composition and structure of the fungal endophytic community. Further investigations are needed to understand the relationship of unique or differentially abundant taxa with one genotype or the other, and to determine the role of the needle mycobiota in WPBR disease development in natural stands of P. flexilis.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41680906","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 : 2022-09-08DOI: 10.1094/pbiomes-03-22-0018-r
Brett R. Lane, Amy E. Kendig, Christopher M. Wojan, Ashish Adhikari, M. Jusino, N. Kortessis, Margaret W. Simon, R. Holt, Matthew E. Smith, K. Clay, S. L. Flory, P. Harmon, E. Goss
Invasive plants, which cause substantial economic and ecological impacts, acquire both pathogens and beneficial microbes in their introduced ranges. Communities of fungal endophytes are known to mediate impacts of pathogens on plant fitness, but few studies have examined the temporal dynamics of fungal communities on invasive plants. The annual grass Microstegium vimineum, an invader of forests and riparian areas throughout the eastern US, experiences annual epidemics of disease caused by Bipolaris pathogens. Our objective was to characterize the dynamics of foliar fungal communities on M. vimineum over a growing season during a foliar disease epidemic. First, we asked how the fungal community in the phyllosphere changed over two months that corresponded with increasing disease severity. Second, we experimentally suppressed disease with fungicide in half the plots and asked how the treatment affected fungal community diversity and composition. We found increasingly diverse foliar fungal communities and substantial changes in community composition between timepoints using high-throughput amplicon sequencing of the ITS2 region. Monthly fungicide application caused shifts in fungal community composition relative to control samples. Fungicide application increased diversity at the late-season timepoint, suggesting it suppressed dominant fungicide sensitive taxa and allowed other fungal taxa to flourish. These results raise new questions regarding the roles of putative endophytes found in the phyllosphere given the limited number of pathogens known to cause disease on M. vimineum in its invasive range.
{"title":"Fungicide mediated shifts in the foliar fungal community of an invasive grass","authors":"Brett R. Lane, Amy E. Kendig, Christopher M. Wojan, Ashish Adhikari, M. Jusino, N. Kortessis, Margaret W. Simon, R. Holt, Matthew E. Smith, K. Clay, S. L. Flory, P. Harmon, E. Goss","doi":"10.1094/pbiomes-03-22-0018-r","DOIUrl":"https://doi.org/10.1094/pbiomes-03-22-0018-r","url":null,"abstract":"Invasive plants, which cause substantial economic and ecological impacts, acquire both pathogens and beneficial microbes in their introduced ranges. Communities of fungal endophytes are known to mediate impacts of pathogens on plant fitness, but few studies have examined the temporal dynamics of fungal communities on invasive plants. The annual grass Microstegium vimineum, an invader of forests and riparian areas throughout the eastern US, experiences annual epidemics of disease caused by Bipolaris pathogens. Our objective was to characterize the dynamics of foliar fungal communities on M. vimineum over a growing season during a foliar disease epidemic. First, we asked how the fungal community in the phyllosphere changed over two months that corresponded with increasing disease severity. Second, we experimentally suppressed disease with fungicide in half the plots and asked how the treatment affected fungal community diversity and composition. We found increasingly diverse foliar fungal communities and substantial changes in community composition between timepoints using high-throughput amplicon sequencing of the ITS2 region. Monthly fungicide application caused shifts in fungal community composition relative to control samples. Fungicide application increased diversity at the late-season timepoint, suggesting it suppressed dominant fungicide sensitive taxa and allowed other fungal taxa to flourish. These results raise new questions regarding the roles of putative endophytes found in the phyllosphere given the limited number of pathogens known to cause disease on M. vimineum in its invasive range.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43247735","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 : 2022-09-02DOI: 10.1094/pbiomes-10-21-0067-r
Burkhardt Flemer, S. Gulati, A. Bergna, Manuela Raendler, T. Cernava, K. Witzel, G. Berg, R. Grosch
Crops are often simultaneously threaten by abiotic and biotic stress factors but the stress response of the plant holobiont is not well understood despite the high importance to ensure future plant production. Therefore, the aim of this study was to assess the impact of individual and combined abiotic (ionic, osmotic) and biotic (Verticillium dahliae, Fusarium oxysporum) stress factors on plant performance and on the bacterial composition of the root endosphere in tomato. Structure and function of the microbiota was analyzed by 16S rRNA gene amplicon sequencing and a complementary cultivation approach including in vitro and in vivo assays. Under all stress conditions, tomato growth and photosynthetic activity was reduced. Combined abiotic stressors with F. oxysporum but not with V. dahliae infection led to an additive negative effect on plant performance. All stress conditions induced a microbiome shift, and changed the relative abundance of phyla such as Firmicutes and classes of Proteobacteria. Endophytes identified as Bacillus, Paenibacillus and Microbacterium showed tolerance to abiotic stress conditions and plant beneficial effects. Stressor-specific enrichments of beneficial bacteria in the root were discovered, e.g. Paenibacillus in roots infected with F. oxysporum, and Microbacterium in roots infected with V. dahliae. Interestingly, endophytes that were able to promote plant growth were obtained only from roots exposed to individual biotic and combined abiotic and biotic stress conditions but not individual abiotic stressors. Our study revealed stressor-specific enrichment of beneficial bacteria in tomato roots, which has implications for novel plant protection strategies.
{"title":"Biotic and abiotic stress factors induce microbiome shifts and enrichment of distinct beneficial bacteria in tomato roots","authors":"Burkhardt Flemer, S. Gulati, A. Bergna, Manuela Raendler, T. Cernava, K. Witzel, G. Berg, R. Grosch","doi":"10.1094/pbiomes-10-21-0067-r","DOIUrl":"https://doi.org/10.1094/pbiomes-10-21-0067-r","url":null,"abstract":"Crops are often simultaneously threaten by abiotic and biotic stress factors but the stress response of the plant holobiont is not well understood despite the high importance to ensure future plant production. Therefore, the aim of this study was to assess the impact of individual and combined abiotic (ionic, osmotic) and biotic (Verticillium dahliae, Fusarium oxysporum) stress factors on plant performance and on the bacterial composition of the root endosphere in tomato. Structure and function of the microbiota was analyzed by 16S rRNA gene amplicon sequencing and a complementary cultivation approach including in vitro and in vivo assays. Under all stress conditions, tomato growth and photosynthetic activity was reduced. Combined abiotic stressors with F. oxysporum but not with V. dahliae infection led to an additive negative effect on plant performance. All stress conditions induced a microbiome shift, and changed the relative abundance of phyla such as Firmicutes and classes of Proteobacteria. Endophytes identified as Bacillus, Paenibacillus and Microbacterium showed tolerance to abiotic stress conditions and plant beneficial effects. Stressor-specific enrichments of beneficial bacteria in the root were discovered, e.g. Paenibacillus in roots infected with F. oxysporum, and Microbacterium in roots infected with V. dahliae. Interestingly, endophytes that were able to promote plant growth were obtained only from roots exposed to individual biotic and combined abiotic and biotic stress conditions but not individual abiotic stressors. Our study revealed stressor-specific enrichment of beneficial bacteria in tomato roots, which has implications for novel plant protection strategies.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47410250","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 : 2022-08-16DOI: 10.1094/pbiomes-05-22-0029-r
S. Pot, C. De Tender, S. Ommeslag, I. Delcour, J. Ceusters, B. Vandecasteele, J. Debode, K. Vancampenhout
Nature management residues residues (i.e., biomass generated from the management of nature reserves) are promising peat alternatives for horticultural substrates and may have a positive effect on disease suppression because of their microbiological characteristics. Moreover, addition of fertilizer may also affect the rhizosphere microbiome and accordingly disease suppression. In this study, we determined the effect of two management residues in horticultural substrates, i.e., chopped heath and acidified soft rush, and two fertilization regimes, i.e., pure nitrogen fertilizer and compound fertilizer, on the suppression of Phytophthora on Chamaecyparis lawsoniana. The bacterial and fungal rhizosphere community was characterized using 16S rRNA and ITS2 gene metabarcoding. Soft rush with a compound fertilizer (R2) and chopped heath with a pure nitrogen fertilizer (H1) showed a disease suppressive effect and showed the largest shifts in microbial community composition compared to peat-based substrates. The disease suppressive treatments showed differences in their microbial communities. Different genera associated with described biocontrol agents for Phytophthora were found in higher amounts in those treatments. Aspergillus and Trichoderma were highly abundant in H1, while Actinomadura and Bacillus had a high abundance in R2. In addition, the relative abundances of 24 bacterial and 9 fungal genera were negatively correlated with disease severity. Several of those genera, including Bacillus, Chaetomium and Actinomadura, were significantly more abundant in one of the disease suppressive treatments. This study shows that disease suppressiveness in sustainable horticultural substrates is dependent on fertilization and can be linked to changes in the microbial rhizosphere communities.
{"title":"Suppression of Phytophthora on Chamaecyparis in sustainable horticultural substrates depends on fertilization and is linked to the rhizobiome","authors":"S. Pot, C. De Tender, S. Ommeslag, I. Delcour, J. Ceusters, B. Vandecasteele, J. Debode, K. Vancampenhout","doi":"10.1094/pbiomes-05-22-0029-r","DOIUrl":"https://doi.org/10.1094/pbiomes-05-22-0029-r","url":null,"abstract":"Nature management residues residues (i.e., biomass generated from the management of nature reserves) are promising peat alternatives for horticultural substrates and may have a positive effect on disease suppression because of their microbiological characteristics. Moreover, addition of fertilizer may also affect the rhizosphere microbiome and accordingly disease suppression. In this study, we determined the effect of two management residues in horticultural substrates, i.e., chopped heath and acidified soft rush, and two fertilization regimes, i.e., pure nitrogen fertilizer and compound fertilizer, on the suppression of Phytophthora on Chamaecyparis lawsoniana. The bacterial and fungal rhizosphere community was characterized using 16S rRNA and ITS2 gene metabarcoding. Soft rush with a compound fertilizer (R2) and chopped heath with a pure nitrogen fertilizer (H1) showed a disease suppressive effect and showed the largest shifts in microbial community composition compared to peat-based substrates. The disease suppressive treatments showed differences in their microbial communities. Different genera associated with described biocontrol agents for Phytophthora were found in higher amounts in those treatments. Aspergillus and Trichoderma were highly abundant in H1, while Actinomadura and Bacillus had a high abundance in R2. In addition, the relative abundances of 24 bacterial and 9 fungal genera were negatively correlated with disease severity. Several of those genera, including Bacillus, Chaetomium and Actinomadura, were significantly more abundant in one of the disease suppressive treatments. This study shows that disease suppressiveness in sustainable horticultural substrates is dependent on fertilization and can be linked to changes in the microbial rhizosphere communities.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45259373","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 : 2022-08-09DOI: 10.1094/pbiomes-03-22-0019-r
F. Savian, F. Marroni, P. Ermacora, G. Firrao, M. Martini
Since 2012 Kiwifruit Vine Decline Syndrome (KVDS) has severely compromised all major kiwifruit growing areas in Italy. So far, aetiological studies were mainly focused on waterlogging effects or on the isolation of microorganisms from diseased plants, thus an all-encompassing picture on KVDS microbiota is still missing. This work aims to describe oomycete and fungal communities associated with KVDS and to identify key taxa potentially involved in the disease through a metabarcoding approach on root endosphere and rhizosphere samples. Two nearby fields with similar pedoclimatic conditions were identified based on KVDS spreading during a 4-year survey (2016-2019). In total, four sampling areas were selected, one from the control field with no sign of KVDS (asymptomatic site) and three from the KVDS-affected field (diseased site): i) asymptomatic until the sampling date in 2018, ii) symptomatic since 2018, and iii) symptomatic since 2017. Total genomic DNA samples were subjected to a nested PCR approach targeting separately the ITS2 region of fungal and oomycete communities. The communities were compared in terms of alpha-and beta-diversities, and key taxa were identified using univariate differential abundance tests. Major differences in taxa distribution were observed between samples from the different sites (asymptomatic and diseased) and were mostly linked to the oomycete community. Phytophthora sojae was the main taxa characterising the diseased site and supposed to be involved in the disease and Phytopythium species were found related to the different plant health status. Finally, Dactylonectria macrodidyma, Phytopythium citrinum and Thielaviopsis basicola were also proposed as new KVDS-related pathogens.
{"title":"A metabarcoding approach to investigate fungal and oomycete communities associated with Kiwifruit Vine Decline Syndrome (KVDS) in Italy","authors":"F. Savian, F. Marroni, P. Ermacora, G. Firrao, M. Martini","doi":"10.1094/pbiomes-03-22-0019-r","DOIUrl":"https://doi.org/10.1094/pbiomes-03-22-0019-r","url":null,"abstract":"Since 2012 Kiwifruit Vine Decline Syndrome (KVDS) has severely compromised all major kiwifruit growing areas in Italy. So far, aetiological studies were mainly focused on waterlogging effects or on the isolation of microorganisms from diseased plants, thus an all-encompassing picture on KVDS microbiota is still missing. This work aims to describe oomycete and fungal communities associated with KVDS and to identify key taxa potentially involved in the disease through a metabarcoding approach on root endosphere and rhizosphere samples. Two nearby fields with similar pedoclimatic conditions were identified based on KVDS spreading during a 4-year survey (2016-2019). In total, four sampling areas were selected, one from the control field with no sign of KVDS (asymptomatic site) and three from the KVDS-affected field (diseased site): i) asymptomatic until the sampling date in 2018, ii) symptomatic since 2018, and iii) symptomatic since 2017. Total genomic DNA samples were subjected to a nested PCR approach targeting separately the ITS2 region of fungal and oomycete communities. The communities were compared in terms of alpha-and beta-diversities, and key taxa were identified using univariate differential abundance tests. Major differences in taxa distribution were observed between samples from the different sites (asymptomatic and diseased) and were mostly linked to the oomycete community. Phytophthora sojae was the main taxa characterising the diseased site and supposed to be involved in the disease and Phytopythium species were found related to the different plant health status. Finally, Dactylonectria macrodidyma, Phytopythium citrinum and Thielaviopsis basicola were also proposed as new KVDS-related pathogens.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":"1 1","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61195554","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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