Pub Date : 2023-07-24DOI: 10.1094/pbiomes-07-23-0066-mf
Selma Cadot, P. Hohmann, Ming-Hui Hsung, Martin Hartmann, Benedikt Haug, L. Wille, M. Messmer, N. Bodenhausen
Intercropping of legume and cereal crop species shows potential to reduce root disease pressures by changing root-associated microbiomes and improve nitrogen (N) use via soil N-dependent fixation of atmospheric N2 by symbiotic rhizobia. A two-year field study was conducted to evaluate the effect of pea-barley association on crop performance and on the root fungal community. Five pea cultivars (Alvesta, Karpate, Mytic, Respect, Vitra) were grown either in pure stands or mixed with one variety of barley (Atrika). We measured crop grain yield and root rot incidence and analyzed root fungal communities. In mixed stands, total grain yield was more stable compared with each pure stand, but pea root disease incidence was higher except for cv. Vitra and Karpate. The effect of cropping system on fungal alpha diversity depended on the cultivar, with cv. Vitra showing higher Shannon diversity and cv. Alvesta showing lower richness in mixed compared with pure stands. All four operational taxonomic units (OTUs) belonging to the Didymellaceae family were positively associated with pea root rot, and another disease-asssociated OTU in pea, Neoascoschyta exitialis, was found to be also part of the barley core microbiome. Eleven out of 12 OTUs belonging to the Glomeraceae family were associated with healthy roots and abundant in cv. Vitra. This study shows how the phenotype and fungal microbiome of different pea cultivars respond distinctly to intercropping. Furthermore, the identification of disease- and health-associated taxa in the pea root fungal community refines the characterization of different cultivar candidates for intercropping.
{"title":"Fungal microbiome indicators are associated with genotypic variation in pea root rot susceptibility when intercropped with barley","authors":"Selma Cadot, P. Hohmann, Ming-Hui Hsung, Martin Hartmann, Benedikt Haug, L. Wille, M. Messmer, N. Bodenhausen","doi":"10.1094/pbiomes-07-23-0066-mf","DOIUrl":"https://doi.org/10.1094/pbiomes-07-23-0066-mf","url":null,"abstract":"Intercropping of legume and cereal crop species shows potential to reduce root disease pressures by changing root-associated microbiomes and improve nitrogen (N) use via soil N-dependent fixation of atmospheric N2 by symbiotic rhizobia. A two-year field study was conducted to evaluate the effect of pea-barley association on crop performance and on the root fungal community. Five pea cultivars (Alvesta, Karpate, Mytic, Respect, Vitra) were grown either in pure stands or mixed with one variety of barley (Atrika). We measured crop grain yield and root rot incidence and analyzed root fungal communities. In mixed stands, total grain yield was more stable compared with each pure stand, but pea root disease incidence was higher except for cv. Vitra and Karpate. The effect of cropping system on fungal alpha diversity depended on the cultivar, with cv. Vitra showing higher Shannon diversity and cv. Alvesta showing lower richness in mixed compared with pure stands. All four operational taxonomic units (OTUs) belonging to the Didymellaceae family were positively associated with pea root rot, and another disease-asssociated OTU in pea, Neoascoschyta exitialis, was found to be also part of the barley core microbiome. Eleven out of 12 OTUs belonging to the Glomeraceae family were associated with healthy roots and abundant in cv. Vitra. This study shows how the phenotype and fungal microbiome of different pea cultivars respond distinctly to intercropping. Furthermore, the identification of disease- and health-associated taxa in the pea root fungal community refines the characterization of different cultivar candidates for intercropping.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49576879","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 : 2023-07-12DOI: 10.1094/pbiomes-10-22-0071-r
Glen Groben, B. Clarke, L. Kerkhof, S. Bonos, William Meyer, Yuanshuo Qu, Jing Luo, E. Walsh, Ning Zhang
The effects mycobiomes have on physiological traits in turfgrasses are poorly understood. Drought tolerance, an economically and ecologically important trait, can be influenced by symbiotic fungi. In this two-year study, we evaluated the mycobiome associated with tall fescue exposed to prolonged periods of drought stress in a rainout shelter. Twelve plants, comprised of six sets of half-sibs (progenies having one parent in common), one exhibiting a drought tolerant phenotype and the other a susceptible phenotype were selected for analysis each year. The mycobiomes associated with the shoot, root, and rhizosphere soil was evaluated for each tall fescue half-sib pair using both short-read Illumina MiSeq and long-read Oxford Nanopore Technology (ONT) MinION sequencing pipelines. Both platforms sequenced portions of the fungal nuclear ribosomal RNA genes. The Illumina MiSeq sequenced the internal transcribed spacer region (ITS, 600 bp), while the ONT MinION covered the small subunit, ITS, and partial large subunit (4,600 bp). Both sequencing pipelines revealed that the mycobiomes associated with the roots, shoots, and soil were significantly different. The ONT MinION pipeline identified more diverse fungal lineages and had higher taxonomic resolution compared to the Illumina pipeline. Our results also indicated that root pathogens may play a more important role than the endophytic or mycorrhizal symbionts in tall fescue drought stress tolerance.
{"title":"Mycobiome Analysis of Tall Fescue Grass under Drought Stress Using the Illumina MiSeq and Oxford Nanopore Technology MinION","authors":"Glen Groben, B. Clarke, L. Kerkhof, S. Bonos, William Meyer, Yuanshuo Qu, Jing Luo, E. Walsh, Ning Zhang","doi":"10.1094/pbiomes-10-22-0071-r","DOIUrl":"https://doi.org/10.1094/pbiomes-10-22-0071-r","url":null,"abstract":"The effects mycobiomes have on physiological traits in turfgrasses are poorly understood. Drought tolerance, an economically and ecologically important trait, can be influenced by symbiotic fungi. In this two-year study, we evaluated the mycobiome associated with tall fescue exposed to prolonged periods of drought stress in a rainout shelter. Twelve plants, comprised of six sets of half-sibs (progenies having one parent in common), one exhibiting a drought tolerant phenotype and the other a susceptible phenotype were selected for analysis each year. The mycobiomes associated with the shoot, root, and rhizosphere soil was evaluated for each tall fescue half-sib pair using both short-read Illumina MiSeq and long-read Oxford Nanopore Technology (ONT) MinION sequencing pipelines. Both platforms sequenced portions of the fungal nuclear ribosomal RNA genes. The Illumina MiSeq sequenced the internal transcribed spacer region (ITS, 600 bp), while the ONT MinION covered the small subunit, ITS, and partial large subunit (4,600 bp). Both sequencing pipelines revealed that the mycobiomes associated with the roots, shoots, and soil were significantly different. The ONT MinION pipeline identified more diverse fungal lineages and had higher taxonomic resolution compared to the Illumina pipeline. Our results also indicated that root pathogens may play a more important role than the endophytic or mycorrhizal symbionts in tall fescue drought stress tolerance.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48526896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-28DOI: 10.1094/pbiomes-08-22-0053-r
Jingjie Hao, Ying Yang, Stephanie L Futrell, Elisabeth A. Kelly, Claire M. Lorts, B. Nebié, S. Runo, Jinliang Yang, S. Alvarez, J. Lasky, D. Schachtman
Strigolactones are a group of small molecules that play critical roles in plant developmental processes and root biotic interactions. Strigolactones are agronomically important due to their role as a signal for the germination of a parasitic weed ( Striga spp.) that reduces yields of cereal crops worldwide. To identify the genes encoding strigolactones in sorghum and their function, we characterized two CRISPR/Cas9-mediated gene knockouts of carotenoid cleavage dioxygenase 8 ( CCD8) genes ( SbCCD8a and SbCCD8b), which have been shown in other plant species to be involved in strigolactone biosynthesis. Although strigolactones are important for the parasitization of sorghum in Africa, the functions of members of the CCD8 family have not been characterized. The impact of the knockouts on strigolactone production, plant growth and development, resistance to the parasitic weed Striga, and the root-associated microbiomes were investigated in this study. The results revealed that knockout of SbCCD8 genes in sorghum significantly reduced orobanchol production and Striga germination. Strigolactone deficiency altered the shoot and root architecture and reduced grain yield of sorghum. The knockout of the SbCCD8b gene significantly affected the rhizosphere bacterial diversity and community composition at sorghum plant grain-fill stage due to the abolition of orobanchol exudation from roots. Reduced amounts of orobanchol in root exudates also influenced root-associated fungal taxa abundance. Our findings provide new insights into potentially sustainable approaches for the recruitment of beneficial microbes and for parasitic weed control through manipulation of strigolactone production in sorghum.
{"title":"CRISPR/Cas9-Mediated Mutagenesis of Carotenoid Cleavage Dioxygenase (CCD) Genes in Sorghum Alters Strigolactone Biosynthesis and Plant Biotic Interactions","authors":"Jingjie Hao, Ying Yang, Stephanie L Futrell, Elisabeth A. Kelly, Claire M. Lorts, B. Nebié, S. Runo, Jinliang Yang, S. Alvarez, J. Lasky, D. Schachtman","doi":"10.1094/pbiomes-08-22-0053-r","DOIUrl":"https://doi.org/10.1094/pbiomes-08-22-0053-r","url":null,"abstract":"Strigolactones are a group of small molecules that play critical roles in plant developmental processes and root biotic interactions. Strigolactones are agronomically important due to their role as a signal for the germination of a parasitic weed ( Striga spp.) that reduces yields of cereal crops worldwide. To identify the genes encoding strigolactones in sorghum and their function, we characterized two CRISPR/Cas9-mediated gene knockouts of carotenoid cleavage dioxygenase 8 ( CCD8) genes ( SbCCD8a and SbCCD8b), which have been shown in other plant species to be involved in strigolactone biosynthesis. Although strigolactones are important for the parasitization of sorghum in Africa, the functions of members of the CCD8 family have not been characterized. The impact of the knockouts on strigolactone production, plant growth and development, resistance to the parasitic weed Striga, and the root-associated microbiomes were investigated in this study. The results revealed that knockout of SbCCD8 genes in sorghum significantly reduced orobanchol production and Striga germination. Strigolactone deficiency altered the shoot and root architecture and reduced grain yield of sorghum. The knockout of the SbCCD8b gene significantly affected the rhizosphere bacterial diversity and community composition at sorghum plant grain-fill stage due to the abolition of orobanchol exudation from roots. Reduced amounts of orobanchol in root exudates also influenced root-associated fungal taxa abundance. Our findings provide new insights into potentially sustainable approaches for the recruitment of beneficial microbes and for parasitic weed control through manipulation of strigolactone production in sorghum.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41687612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-27DOI: 10.1094/pbiomes-02-23-0009-fi
P. Kong, Xiaoping Li, Melissa Sharifi, A. Bordas, Chuanxue Hong
Differential tolerance of English boxwood to boxwood blight has been linked to the ratio of culturable bacterial and fungal dominance in the leaf tissue of representative samples. To further understand how the whole endophyte communities may involve the tolerance of large samples, we extracted DNA from healthy leaf tissue of previously identified 28 tolerant (T), 41 moderately tolerant (M) and 21 susceptible (S) English boxwood plants, then sequenced associated bacterial and fungal amplicons using the Nanopore MinION platform. The endophyte community did not differ in diversity among the T, M, and S plants, but differed in the abundance of bacteria and fungi, particularly between T and S samples. The bacterial genera Brevundimonas and Ammonifex had higher relative abundance in the T and M communities than in the S community which was more dominant by the fungal genera Botrytis, Thermothelomyces and Chaetomiaceae. The same results were obtained when mother and daughter samples in the T community were compared with controls in the S community, suggesting bacteria as a work force in the T community. Co-occurrence network analyses revealed that the T network had more fungal hubs but less complex with more positive connections than the S network, suggesting that the T community was supported by a healthier network. The resistance of English boxwood to blight is likely attributed to bacteria dominance and a synergic community network. This study is foundational to constructing synthetic communities and using whole communities of tolerant plants through vegetative propagation for microbe-modulated immunity.
{"title":"Leaf endophyte community composition and network structures differ between tolerant and susceptible English boxwood","authors":"P. Kong, Xiaoping Li, Melissa Sharifi, A. Bordas, Chuanxue Hong","doi":"10.1094/pbiomes-02-23-0009-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-02-23-0009-fi","url":null,"abstract":"Differential tolerance of English boxwood to boxwood blight has been linked to the ratio of culturable bacterial and fungal dominance in the leaf tissue of representative samples. To further understand how the whole endophyte communities may involve the tolerance of large samples, we extracted DNA from healthy leaf tissue of previously identified 28 tolerant (T), 41 moderately tolerant (M) and 21 susceptible (S) English boxwood plants, then sequenced associated bacterial and fungal amplicons using the Nanopore MinION platform. The endophyte community did not differ in diversity among the T, M, and S plants, but differed in the abundance of bacteria and fungi, particularly between T and S samples. The bacterial genera Brevundimonas and Ammonifex had higher relative abundance in the T and M communities than in the S community which was more dominant by the fungal genera Botrytis, Thermothelomyces and Chaetomiaceae. The same results were obtained when mother and daughter samples in the T community were compared with controls in the S community, suggesting bacteria as a work force in the T community. Co-occurrence network analyses revealed that the T network had more fungal hubs but less complex with more positive connections than the S network, suggesting that the T community was supported by a healthier network. The resistance of English boxwood to blight is likely attributed to bacteria dominance and a synergic community network. This study is foundational to constructing synthetic communities and using whole communities of tolerant plants through vegetative propagation for microbe-modulated immunity.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48489524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-27DOI: 10.1094/pbiomes-11-22-0083-r
Sandra Mosquera, Carolina Cataño Useche, Susan Saavedra, V. Villegas-Escobar
Different postharvest diseases and disorders affect avocado cv. Hass fruits. Among them, lenticel-like damages, which compromise the fruit epidermis without affecting the mesocarp, are important causes of fruit rejection worldwide. However, lenticel-like damage etiology is still unclear. In order to better comprehend this disorder, we evaluated the level of the lenticel-like damage from avocado cv. Hass fruits from two different growing regions in Colombia at different harvest seasons. We also characterized the fungal microbial communities associated with these fruits by Illumina MiSeq. We found that the level of the lenticel-like damage varies with the farm and with the harvest season, and increases during cold storage. Fungal communities and enriched taxa associated with avocado cv. Hass fruits were influenced by the farm and the lenticel-like damage level. Regardless of the farm, Ascomycetes were increased by four-fold compared to Basidiomycetes in severely damaged fruits, while in mild damage damaged fruits the ratio was equal. In particular, severely damaged fruits from the more affected farm (El Sinaí) were enriched in Colletotrichum and Pseudocercospora, while mild damage fruits from the less affected farm (La Escondida) include Cladosporium, Vishniacozyma, Meira, and Symmetrospora. Altogether, our results suggests that fungal communities of avocado cv. Hass exocarps influence the lenticel-like damage development and might be responsible for the damage differences between farms.
{"title":"Characterization of fungal communities associated with the lenticel-like damage of avocado cv. Hass in two geographical locations in Colombia","authors":"Sandra Mosquera, Carolina Cataño Useche, Susan Saavedra, V. Villegas-Escobar","doi":"10.1094/pbiomes-11-22-0083-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-22-0083-r","url":null,"abstract":"Different postharvest diseases and disorders affect avocado cv. Hass fruits. Among them, lenticel-like damages, which compromise the fruit epidermis without affecting the mesocarp, are important causes of fruit rejection worldwide. However, lenticel-like damage etiology is still unclear. In order to better comprehend this disorder, we evaluated the level of the lenticel-like damage from avocado cv. Hass fruits from two different growing regions in Colombia at different harvest seasons. We also characterized the fungal microbial communities associated with these fruits by Illumina MiSeq. We found that the level of the lenticel-like damage varies with the farm and with the harvest season, and increases during cold storage. Fungal communities and enriched taxa associated with avocado cv. Hass fruits were influenced by the farm and the lenticel-like damage level. Regardless of the farm, Ascomycetes were increased by four-fold compared to Basidiomycetes in severely damaged fruits, while in mild damage damaged fruits the ratio was equal. In particular, severely damaged fruits from the more affected farm (El Sinaí) were enriched in Colletotrichum and Pseudocercospora, while mild damage fruits from the less affected farm (La Escondida) include Cladosporium, Vishniacozyma, Meira, and Symmetrospora. Altogether, our results suggests that fungal communities of avocado cv. Hass exocarps influence the lenticel-like damage development and might be responsible for the damage differences between farms.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44113558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-14DOI: 10.1094/pbiomes-05-23-0029-mr
J. Leveau, G. Coaker, M. Marco
This Meeting-Review article offers a synthesis of the science presented and discussed at the recently held 11th-International-Symposium-on-Leaf-Surface-Microbiology, also known as Phyllosphere-2022 (University of California-Davis, 17-21 July 2022). Twice-postponed due to Covid-19, this in-person conference covered wide-ranging-but-intersecting topics related to the microbiology of leaves (and other above-ground parts of plants), including phyto-pathology, food-safety, plant-physiology, microbial-ecology, fluid-physics, vegetation-science, single-cell biology, canopy-architecture, and human-health. The overarching theme of the meeting (‘understanding-the-rules-of-phyllospheric life’) was explored in 46 podium- and 12 poster-presentations. It also fueled the formal and informal discussions among 90+ conference participants about existing and new questions in phyllosphere-microbiology. Are there first principles underlying the acquisition, assembly and succession of microbial communities in the phyllosphere? How best to define, recognize, and exploit phyllosphere-fitness of microscopic leaf dwellers? At what scales do or should we sample, interrogate, and understand the phyllosphere? What needs to be learned still that keeps us from new insights, resources and tools to produce healthier and more-nutritious plant foliage? Having the conference at UC Davis in the summer presented a unique opportunity to 'vertically-integrate' high school students from the COSMOS program into the Phyllosphere-2022 conference and allow face-to-face interactions with early-career and senior-scientists in phyllosphere-microbiology. Students thus experienced first-hand the ways in which scientists address problems that affect society and seek understanding and solutions to those problems. It represented an effective approach to engage a younger generation into thinking about research and stewardship of plants and their foliage, and more generally about the merits of a science career.
{"title":"Phyllosphere 2022: 11th International Symposium on Leaf Surface Microbiology","authors":"J. Leveau, G. Coaker, M. Marco","doi":"10.1094/pbiomes-05-23-0029-mr","DOIUrl":"https://doi.org/10.1094/pbiomes-05-23-0029-mr","url":null,"abstract":"This Meeting-Review article offers a synthesis of the science presented and discussed at the recently held 11th-International-Symposium-on-Leaf-Surface-Microbiology, also known as Phyllosphere-2022 (University of California-Davis, 17-21 July 2022). Twice-postponed due to Covid-19, this in-person conference covered wide-ranging-but-intersecting topics related to the microbiology of leaves (and other above-ground parts of plants), including phyto-pathology, food-safety, plant-physiology, microbial-ecology, fluid-physics, vegetation-science, single-cell biology, canopy-architecture, and human-health. The overarching theme of the meeting (‘understanding-the-rules-of-phyllospheric life’) was explored in 46 podium- and 12 poster-presentations. It also fueled the formal and informal discussions among 90+ conference participants about existing and new questions in phyllosphere-microbiology. Are there first principles underlying the acquisition, assembly and succession of microbial communities in the phyllosphere? How best to define, recognize, and exploit phyllosphere-fitness of microscopic leaf dwellers? At what scales do or should we sample, interrogate, and understand the phyllosphere? What needs to be learned still that keeps us from new insights, resources and tools to produce healthier and more-nutritious plant foliage? Having the conference at UC Davis in the summer presented a unique opportunity to 'vertically-integrate' high school students from the COSMOS program into the Phyllosphere-2022 conference and allow face-to-face interactions with early-career and senior-scientists in phyllosphere-microbiology. Students thus experienced first-hand the ways in which scientists address problems that affect society and seek understanding and solutions to those problems. It represented an effective approach to engage a younger generation into thinking about research and stewardship of plants and their foliage, and more generally about the merits of a science career.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47102679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-04DOI: 10.1094/pbiomes-09-22-0062-mf
E. Kudjordjie, R. Sapkota, M. Nicolaisen
The plant-associated microbiota confers beneficial traits to the plant host by promoting growth and preventing disease. It is, however, not fully understood how the host and the associated microbiota interact with pathogens. In this work, we studied how the host plant modulates its associated microbiome to suppress disease. For this, we used two Arabidopsis thaliana lines with different host responses to Fusarium oxysporum f. sp. mathioli (FOM). We isolated bacterial consortia (BCs) from FOM-infected or healthy host plants of the two lines of Arabidopsis and studied their effect on the root-associated microbiota and FOM progression in the following generations of Arabidopsis plants. Root bacterial and fungal communities were profiled using 16S rRNA and ITS amplicon sequencing, respectively, while qPCR was used for assessment of FOM quantities in shoots of Arabidopsis. Host- or pathogen-adapted BCs significantly reduced FOM quantities in shoots of both the resistant Col-0 and the susceptible Ler-0 Arabidopsis lines. Several bacterial taxa including Chthoniobacter, Bacillus, Chryseobacterium and Actinoplanes negatively correlated with FOM suggestive of an antagonistic effect. Furthermore, both host- and pathogen-adapted BCs significantly affected community composition with distinct differentially abundant taxa and co-cooccurrence network structures. Taken together, our findings suggest that using a subcommunity selection approach is a potential route for exploiting plant associated rhizosphere microbiomes for engineering disease resilient microbiomes.
植物相关微生物群通过促进生长和预防疾病，赋予植物寄主有益的性状。然而，目前还不完全清楚宿主和相关微生物群如何与病原体相互作用。在这项工作中，我们研究了寄主植物如何调节其相关微生物组来抑制疾病。为此，我们选用了两个对镰刀菌(Fusarium oxysporum f. sp. mathioli, FOM)有不同寄主反应的拟南芥品系。我们从感染了FOM的两个品系或健康的拟南芥寄主植株中分离出细菌联合体(bc)，并研究了它们对拟南芥后代根系相关微生物群和FOM进展的影响。采用16S rRNA和ITS扩增子测序技术分别对拟南芥根系细菌和真菌群落进行了分析，采用qPCR技术对拟南芥芽部FOM数量进行了评估。宿主或病原体适应的bc显著降低了抗性col0和敏感的Ler-0拟南芥品系的芽部FOM数量。几个细菌分类群，包括硫杆菌、芽孢杆菌、黄杆菌和放线素菌群，与FOM呈负相关，提示其拮抗作用。此外，宿主适应性和病原体适应性bc对群落组成都有显著影响，类群丰富度和共生网络结构差异显著。综上所述，我们的研究结果表明，使用亚群落选择方法是利用植物相关根际微生物组来设计抗病微生物组的潜在途径。
{"title":"Host and Fusarium-adapted bacterial consortia alter microbial community structures in Arabidopsis roots and suppress Fusarium oxysporum","authors":"E. Kudjordjie, R. Sapkota, M. Nicolaisen","doi":"10.1094/pbiomes-09-22-0062-mf","DOIUrl":"https://doi.org/10.1094/pbiomes-09-22-0062-mf","url":null,"abstract":"The plant-associated microbiota confers beneficial traits to the plant host by promoting growth and preventing disease. It is, however, not fully understood how the host and the associated microbiota interact with pathogens. In this work, we studied how the host plant modulates its associated microbiome to suppress disease. For this, we used two Arabidopsis thaliana lines with different host responses to Fusarium oxysporum f. sp. mathioli (FOM). We isolated bacterial consortia (BCs) from FOM-infected or healthy host plants of the two lines of Arabidopsis and studied their effect on the root-associated microbiota and FOM progression in the following generations of Arabidopsis plants. Root bacterial and fungal communities were profiled using 16S rRNA and ITS amplicon sequencing, respectively, while qPCR was used for assessment of FOM quantities in shoots of Arabidopsis. Host- or pathogen-adapted BCs significantly reduced FOM quantities in shoots of both the resistant Col-0 and the susceptible Ler-0 Arabidopsis lines. Several bacterial taxa including Chthoniobacter, Bacillus, Chryseobacterium and Actinoplanes negatively correlated with FOM suggestive of an antagonistic effect. Furthermore, both host- and pathogen-adapted BCs significantly affected community composition with distinct differentially abundant taxa and co-cooccurrence network structures. Taken together, our findings suggest that using a subcommunity selection approach is a potential route for exploiting plant associated rhizosphere microbiomes for engineering disease resilient microbiomes.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43331721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-01DOI: 10.1094/pbiomes-02-23-0014-e
J. Leveau
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