Pub Date : 2024-07-24DOI: 10.1094/pbiomes-03-24-0033-fi
Katherine M. D'Amico-Willman, Prasanna Joglekar, David F. Ritchie, Amber M. Smith, Helena Heiberger, Alejandra I. Huerta
Bacteriophages (phages), viruses that infect bacteria, have key ecological and evolutionary functions in the phytobiome. Despite the importance of phages as primary drivers for bacterial evolution, phage-bacteria interactions across spatiotemporal scales in natural, agricultural settings are underexplored. With increased interest in phage-based therapies to manage bacterial pathogens, an enhanced understanding of phage genetic and functional diversity at the population level, and how this, in turn, impacts bacterial evolution and virulence, is necessary. This study presents data on the genetic similarity among Xanthomonas arboricola pv. pruni (Xap) strains isolated from different geographic locations that display different lytic phenotypes when challenged with a panel of six phage isolates collected in the same region over four decades. The minor yet significant genetic variation among this small population of Xap strains is structured by both geographic location and response to phage infection. Phage genomes are also highly similar, with conserved and diverse genomic loci that correspond to isolation year. The six phages characterized here cluster into the Kantovirinae subfamily and possibly form a new genus. Only future studies will elucidate the role of Xap and Xapφ phage genes identified here in the virulence and lysis of Xap and how these, in turn, impact bacterial spot disease outcomes. The research and tripartite pathosystem presented here provides a unique opportunity to investigate the coevolution of phage-phytobacterial pathogen-plant host in depth in an agricultural setting with the potential to monitor the rate at which phage populations contribute to bacterial genetic diversity across geographic and temporal scales.
{"title":"Genetically similar Xanthomonas arboricola pv. pruni strains and associated phage display phenotypic and genotypic variation across 35 years","authors":"Katherine M. D'Amico-Willman, Prasanna Joglekar, David F. Ritchie, Amber M. Smith, Helena Heiberger, Alejandra I. Huerta","doi":"10.1094/pbiomes-03-24-0033-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-03-24-0033-fi","url":null,"abstract":"Bacteriophages (phages), viruses that infect bacteria, have key ecological and evolutionary functions in the phytobiome. Despite the importance of phages as primary drivers for bacterial evolution, phage-bacteria interactions across spatiotemporal scales in natural, agricultural settings are underexplored. With increased interest in phage-based therapies to manage bacterial pathogens, an enhanced understanding of phage genetic and functional diversity at the population level, and how this, in turn, impacts bacterial evolution and virulence, is necessary. This study presents data on the genetic similarity among Xanthomonas arboricola pv. pruni (Xap) strains isolated from different geographic locations that display different lytic phenotypes when challenged with a panel of six phage isolates collected in the same region over four decades. The minor yet significant genetic variation among this small population of Xap strains is structured by both geographic location and response to phage infection. Phage genomes are also highly similar, with conserved and diverse genomic loci that correspond to isolation year. The six phages characterized here cluster into the Kantovirinae subfamily and possibly form a new genus. Only future studies will elucidate the role of Xap and Xapφ phage genes identified here in the virulence and lysis of Xap and how these, in turn, impact bacterial spot disease outcomes. The research and tripartite pathosystem presented here provides a unique opportunity to investigate the coevolution of phage-phytobacterial pathogen-plant host in depth in an agricultural setting with the potential to monitor the rate at which phage populations contribute to bacterial genetic diversity across geographic and temporal scales.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141806409","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 : 2024-06-14DOI: 10.1094/pbiomes-02-24-0012-r
Elle Barnes, Kyle Hartman, Dawn Chiniquy, Wenting Zhao, Peng Liu, Cody Creech, Daniel P. Schachtman, S. Tringe
Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses such as water and nutrient limitation. While the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe-microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities, but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments as well as an increase in the modularity and proportion of positive associations which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. While stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.
{"title":"Abiotic stress reorganizes rhizosphere and endosphere network structure of Sorghum bicolor","authors":"Elle Barnes, Kyle Hartman, Dawn Chiniquy, Wenting Zhao, Peng Liu, Cody Creech, Daniel P. Schachtman, S. Tringe","doi":"10.1094/pbiomes-02-24-0012-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-24-0012-r","url":null,"abstract":"Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses such as water and nutrient limitation. While the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe-microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities, but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments as well as an increase in the modularity and proportion of positive associations which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. While stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141344507","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}
One important ecological question regarding the use of plant resistance genes against fungal pathogens concerns whether and how such resistance genes may modify pathogenic or beneficial members of the plant-associated microbiota. We studied the impact of a plant resistance gene by analyzing the mycobiota associated with Brassica napus organs over two cropping seasons. Sampling dates coincided with key stages of the life cycle of the B. napus pathogen Leptosphaeria maculans. Leaf samples were collected at three time points in autumn and spring, and stem base samples were collected at two time points a few weeks before and at harvest. Stem residues, where L. maculans survives in the intercropping season and develops sexual reproduction, were also analyzed at four time points between the two cropping seasons. The sampling was performed on two plant genotypes, Darmor and Darmor- Rlm11, only differing by the effective resistance gene against L. maculans, Rlm11. Altogether, 419 samples were analyzed using two barcode: internal transcribed spacer (ITS) and Actin. The plant organ was shown to be the main mycobiota structuring factor, as clear-cut alternation of the species suggested that each plant organ represented a specific ecological niche. The cropping season and plant genotype also significantly influenced the community structure in lower proportions. The resistance gene contributed differently to the community structure depending on the year and the organ concerned. A significant but low impact of Rlm11 on other B. napus fungal pathogens was detected. The ITS and Actin barcodes showed similar results, but the species assignation was limited for the latter.
{"title":"A Specific Resistance Gene to Leptosphaeria maculans, Rlm11, Has a Limited Impact on Brassica napus Mycobiota Compared with Plant Compartment or Cropping Season Effects","authors":"Mathilde Gorse, Lydie Kerdraon, Noémie Jacques, Angélique Gautier, Marie-Hélène Balesdent, Valérie Laval","doi":"10.1094/pbiomes-07-23-0069-r","DOIUrl":"https://doi.org/10.1094/pbiomes-07-23-0069-r","url":null,"abstract":"One important ecological question regarding the use of plant resistance genes against fungal pathogens concerns whether and how such resistance genes may modify pathogenic or beneficial members of the plant-associated microbiota. We studied the impact of a plant resistance gene by analyzing the mycobiota associated with Brassica napus organs over two cropping seasons. Sampling dates coincided with key stages of the life cycle of the B. napus pathogen Leptosphaeria maculans. Leaf samples were collected at three time points in autumn and spring, and stem base samples were collected at two time points a few weeks before and at harvest. Stem residues, where L. maculans survives in the intercropping season and develops sexual reproduction, were also analyzed at four time points between the two cropping seasons. The sampling was performed on two plant genotypes, Darmor and Darmor- Rlm11, only differing by the effective resistance gene against L. maculans, Rlm11. Altogether, 419 samples were analyzed using two barcode: internal transcribed spacer (ITS) and Actin. The plant organ was shown to be the main mycobiota structuring factor, as clear-cut alternation of the species suggested that each plant organ represented a specific ecological niche. The cropping season and plant genotype also significantly influenced the community structure in lower proportions. The resistance gene contributed differently to the community structure depending on the year and the organ concerned. A significant but low impact of Rlm11 on other B. napus fungal pathogens was detected. The ITS and Actin barcodes showed similar results, but the species assignation was limited for the latter.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140970133","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}
Plant parasitic nematodes pose a significant threat to food security. Management strategies for these pathogens are limited, and additional tools for their control are needed. Some fungi have shown promise for biocontrol, however, their success in the field has varied. In contrast, some fungal plant pathogens form synergistic associations with nematodes resulting in increased plant disease severity. However, how both groups of fungi change with different plant parasitic nematode abundances in the soil is underexplored. In this study, we used the soybean cyst nematode as a model to understand these changes. We sampled soil from 171 Ohio soybean fields in 2019 and 2021 and determined soybean cyst nematode abundance. We identified the fungi in the samples through amplicon sequencing of the 18S-ITS rDNA regions. Edaphoclimatic factors were used to classify samples into geographic regions to account for environmental differences between sampling locations. We hypothesized that fungal communities would be influenced by both region and soybean cyst nematode abundance. K-near neighbor analysis revealed that fungal communities follow regional patterns. We also found that soybean cyst nematode abundance was associated with changes in these communities regardless of the region. Two potential nematophagous fungi were found to be prevalent in Ohio through core community analysis, although they were enriched when soybean cyst nematode abundance was high. Lastly, differential network analysis showed that interactions among fungal community members change when soybean cyst nematode is present in the soil. Together these results suggest that this nematode significantly shifts the fungal community composition in field soils.
{"title":"Fungal communities shift with soybean cyst nematode abundance in soils","authors":"Melanie Medina López, Horacio Lopez-Nicora, Maria-Soledad Benitez Ponce","doi":"10.1094/pbiomes-02-24-0021-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-24-0021-r","url":null,"abstract":"Plant parasitic nematodes pose a significant threat to food security. Management strategies for these pathogens are limited, and additional tools for their control are needed. Some fungi have shown promise for biocontrol, however, their success in the field has varied. In contrast, some fungal plant pathogens form synergistic associations with nematodes resulting in increased plant disease severity. However, how both groups of fungi change with different plant parasitic nematode abundances in the soil is underexplored. In this study, we used the soybean cyst nematode as a model to understand these changes. We sampled soil from 171 Ohio soybean fields in 2019 and 2021 and determined soybean cyst nematode abundance. We identified the fungi in the samples through amplicon sequencing of the 18S-ITS rDNA regions. Edaphoclimatic factors were used to classify samples into geographic regions to account for environmental differences between sampling locations. We hypothesized that fungal communities would be influenced by both region and soybean cyst nematode abundance. K-near neighbor analysis revealed that fungal communities follow regional patterns. We also found that soybean cyst nematode abundance was associated with changes in these communities regardless of the region. Two potential nematophagous fungi were found to be prevalent in Ohio through core community analysis, although they were enriched when soybean cyst nematode abundance was high. Lastly, differential network analysis showed that interactions among fungal community members change when soybean cyst nematode is present in the soil. Together these results suggest that this nematode significantly shifts the fungal community composition in field soils.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140995564","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 : 2024-03-01DOI: 10.1094/pbiomes-09-23-0095-r
Ciara Garcia, Duke Pauli, Caroline Plecki, Hesham Alnasser, Bruno Rozzi, Sebastian Calleja, A. E. Arnold
Plant-associated microbes contribute to crop health and resilience, potentially extending or complementing plant traits under abiotic stress. Here, we tested a series of hypotheses centered on the fungal mycobiome and bacterial microbiome of field-grown sorghum (Sorghum bicolor (L.) Moench), an emerging model crop for drought resilience, which we cultivated under arid conditions. Overall, the sorghum mycobiome and microbiome differed in composition between the exterior and interior of plant tissues, between roots and leaves, and among sorghum genotypes. We did not observe variation in fungal and bacterial endophytes among performance classes of sorghum when water was plentiful, but the root-endophytic mycobiome and microbiome both shifted markedly under water limitation, with similar shifts in composition observed among multiple plant genotypes. The root-endophytic microbiome of high-performing sorghum was especially responsive to water limitation. Network analyses suggest that water limitation did not directly remodel these root-endophytic microbiomes, such that interactions of the microbiome with the host plant – rather than interactions among microbes within the microbiome – may be the most dynamic element of change when water is limited. Overall, our study points to shifts in the prevalence of particular taxa under abiotic stress and suggests that high-performing lines may have distinctive features as substrates, or strategies for actively recruiting diverse, abundant, and distinctive microbial communities to roots under water limitation. Such findings are important in the arid lands that frame marginal agriculture today and comprise an increasing proportion of agriculture in a changing world.
{"title":"The root-endophytic microbiome shifts under drought in high-performing sorghum","authors":"Ciara Garcia, Duke Pauli, Caroline Plecki, Hesham Alnasser, Bruno Rozzi, Sebastian Calleja, A. E. Arnold","doi":"10.1094/pbiomes-09-23-0095-r","DOIUrl":"https://doi.org/10.1094/pbiomes-09-23-0095-r","url":null,"abstract":"Plant-associated microbes contribute to crop health and resilience, potentially extending or complementing plant traits under abiotic stress. Here, we tested a series of hypotheses centered on the fungal mycobiome and bacterial microbiome of field-grown sorghum (Sorghum bicolor (L.) Moench), an emerging model crop for drought resilience, which we cultivated under arid conditions. Overall, the sorghum mycobiome and microbiome differed in composition between the exterior and interior of plant tissues, between roots and leaves, and among sorghum genotypes. We did not observe variation in fungal and bacterial endophytes among performance classes of sorghum when water was plentiful, but the root-endophytic mycobiome and microbiome both shifted markedly under water limitation, with similar shifts in composition observed among multiple plant genotypes. The root-endophytic microbiome of high-performing sorghum was especially responsive to water limitation. Network analyses suggest that water limitation did not directly remodel these root-endophytic microbiomes, such that interactions of the microbiome with the host plant – rather than interactions among microbes within the microbiome – may be the most dynamic element of change when water is limited. Overall, our study points to shifts in the prevalence of particular taxa under abiotic stress and suggests that high-performing lines may have distinctive features as substrates, or strategies for actively recruiting diverse, abundant, and distinctive microbial communities to roots under water limitation. Such findings are important in the arid lands that frame marginal agriculture today and comprise an increasing proportion of agriculture in a changing world.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140087965","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 : 2024-02-28DOI: 10.1094/pbiomes-12-23-0132-r
M. Kaufmann, Leilei Li, Christof Van Poucke, Nicola Rhyner, C. De Tender, Mieke Uyttendaele, Marc Heyndrickx, Cyril Zipfel, Joël F. Pothier, Cottyn Bart
Chitin amendment of peat substrate has been proven effective in promoting lettuce growth and increasing phenolic compounds in lettuce seedlings. However, the effect of chitin soil amendment on lettuce growth in mineral soil remains unexplored. The effect of chitin amendment of mineral soil on lettuce growth and metabolite changes was investigated for the first time in the present study in comparison to chitin amended peat substrate. Our findings showed that chitin addition in peat substrate increased lettuce head weight by approximately 50% at harvest, whereas this increase was 30% when added to mineral soil. Targeted metabolomics analysis indicated that chitin addition affected the phenolic compounds in lettuce seedlings, but this effect varied between soil types. Moreover, untargeted metabolomics analysis suggested that using peat substrate or mineral soil had a greater influence on produced lettuce metabolites than chitin addition. Rhizobiome analysis showed that specifically Mortierellaceae family members, known for chitin degradation and plant growth promotion, significantly increased in peat substrate upon chitin treatment. In mineral soil, three bacterial genera and five fungi, including known plant growth promoting genera, were significantly more abundant upon chitin treatment but not Mortierellaceae. We assume that the observed effects primarily stem from soil physiochemical characteristics and from chitin induced alterations in rhizobiome composition, particularly the presence of Mortierellaceae members, leading to promoted lettuce growth. Despite the variability, chitin remains an environmentally friendly alternative to synthetic fertilizers in lettuce production, but its beneficial effects are dependent on rhizobiome composition, which should be considered before chitin application.
{"title":"Soil type and associated microbiomes influences chitin’s growth-promotion effect in lettuce","authors":"M. Kaufmann, Leilei Li, Christof Van Poucke, Nicola Rhyner, C. De Tender, Mieke Uyttendaele, Marc Heyndrickx, Cyril Zipfel, Joël F. Pothier, Cottyn Bart","doi":"10.1094/pbiomes-12-23-0132-r","DOIUrl":"https://doi.org/10.1094/pbiomes-12-23-0132-r","url":null,"abstract":"Chitin amendment of peat substrate has been proven effective in promoting lettuce growth and increasing phenolic compounds in lettuce seedlings. However, the effect of chitin soil amendment on lettuce growth in mineral soil remains unexplored. The effect of chitin amendment of mineral soil on lettuce growth and metabolite changes was investigated for the first time in the present study in comparison to chitin amended peat substrate. Our findings showed that chitin addition in peat substrate increased lettuce head weight by approximately 50% at harvest, whereas this increase was 30% when added to mineral soil. Targeted metabolomics analysis indicated that chitin addition affected the phenolic compounds in lettuce seedlings, but this effect varied between soil types. Moreover, untargeted metabolomics analysis suggested that using peat substrate or mineral soil had a greater influence on produced lettuce metabolites than chitin addition. Rhizobiome analysis showed that specifically Mortierellaceae family members, known for chitin degradation and plant growth promotion, significantly increased in peat substrate upon chitin treatment. In mineral soil, three bacterial genera and five fungi, including known plant growth promoting genera, were significantly more abundant upon chitin treatment but not Mortierellaceae. We assume that the observed effects primarily stem from soil physiochemical characteristics and from chitin induced alterations in rhizobiome composition, particularly the presence of Mortierellaceae members, leading to promoted lettuce growth. Despite the variability, chitin remains an environmentally friendly alternative to synthetic fertilizers in lettuce production, but its beneficial effects are dependent on rhizobiome composition, which should be considered before chitin application.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140420536","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 : 2024-02-28DOI: 10.1094/pbiomes-07-23-0061-r
Seung Yeup Lee, Roniya Thapa Magar, Kihyuck Choi, Hyo Jeong Kim, Insoo Park, Seon-Woo Lee
Bacteriophages (phages) that infect bacterial pathogens are an alternative means of controlling bacterial diseases in humans, animals, and plants. However, the effects of targeted phage therapy on indigenous microbial community has not been fully understood. In this study, we hypothesized that phages infecting plant pathogenic bacteria play a role in modulating the microbial community in the plant rhizosphere. To explore this, we used the soil-borne plant bacterial pathogen Ralstonia pseudosolanacearum as the host bacterium and its phages as a model system in the tomato rhizosphere. The effect of phages on microbiota was compared using a narrow host range phage RpY1, and a combination of two phages (RpY2 and RpT1, termed the phage combo) with a broad host range, under the natural rhizosphere microbiota of tomato plants. Both RpY1 and phage combo altered the tomato rhizosphere microbiota. The phage combo displayed phage effects mostly in the presence of R. pseudosolanacearum. However, RpY1 affected the rhizosphere microbiota even in the absence of the host bacterium. The effect of phage RpY1 on the microbiota was further investigated in the tomato rhizosphere using a synthetic community (SynCom) mimicking the natural tomato rhizosphere microbiota. Phage RpY1 affected the microbial community structure of SynCom in the tomato rhizosphere in the absence of the host bacterium. The analyses of natural microbiota and SynCom in the tomato rhizosphere indicated an indirect effect of phage RpY1 on the microbiota. This study suggests that phage application modulates indigenous microbiota through unknown interactions with non-host bacterial members in the plant rhizosphere.
{"title":"Phage-dependent alteration of rhizosphere microbiota in tomato plants","authors":"Seung Yeup Lee, Roniya Thapa Magar, Kihyuck Choi, Hyo Jeong Kim, Insoo Park, Seon-Woo Lee","doi":"10.1094/pbiomes-07-23-0061-r","DOIUrl":"https://doi.org/10.1094/pbiomes-07-23-0061-r","url":null,"abstract":"Bacteriophages (phages) that infect bacterial pathogens are an alternative means of controlling bacterial diseases in humans, animals, and plants. However, the effects of targeted phage therapy on indigenous microbial community has not been fully understood. In this study, we hypothesized that phages infecting plant pathogenic bacteria play a role in modulating the microbial community in the plant rhizosphere. To explore this, we used the soil-borne plant bacterial pathogen Ralstonia pseudosolanacearum as the host bacterium and its phages as a model system in the tomato rhizosphere. The effect of phages on microbiota was compared using a narrow host range phage RpY1, and a combination of two phages (RpY2 and RpT1, termed the phage combo) with a broad host range, under the natural rhizosphere microbiota of tomato plants. Both RpY1 and phage combo altered the tomato rhizosphere microbiota. The phage combo displayed phage effects mostly in the presence of R. pseudosolanacearum. However, RpY1 affected the rhizosphere microbiota even in the absence of the host bacterium. The effect of phage RpY1 on the microbiota was further investigated in the tomato rhizosphere using a synthetic community (SynCom) mimicking the natural tomato rhizosphere microbiota. Phage RpY1 affected the microbial community structure of SynCom in the tomato rhizosphere in the absence of the host bacterium. The analyses of natural microbiota and SynCom in the tomato rhizosphere indicated an indirect effect of phage RpY1 on the microbiota. This study suggests that phage application modulates indigenous microbiota through unknown interactions with non-host bacterial members in the plant rhizosphere.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140421175","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 : 2024-02-21DOI: 10.1094/pbiomes-08-23-0083-r
Lindsey E. Becker, M. Cubeta
Wheat (Triticum spp.) is a staple food crop, providing a fifth of the world’s protein and caloric needs. Our research examines the impact of multi generation post-flowering drought stress on the wheat seed endophytic fungal community. Understanding how wheat seed fungal communities respond to drought stress over several generations can improve our knowledge of legacy drought stress. In this manuscript, we aim to identify seed associated fungi that play critical roles within the wheat seed under drought stress conditions. We examined the endophytic seed fungal communities of three winter wheat cultivars, Catawba, Shirley, and USG 3640. Moderate drought was imposed on a subset of plants immediately after flowering, with plants relieved from drought stress after one week. Seeds harvested from generation 1 were planted for a second generation of drought experiments. When examining post-flowering drought impact on wheat physiology, drought-exposed plants consistently exhibited lower daily transpiration rates, chlorophyll-a values, and seed yield compared to control plants, indicating that drought implementation was successful. ITS1 metabarcoding revealed that wheat seed fungal community species richness decreased during post-anthesis drought stress across both generations. We also observed that generation accounted for variation in fungal species richness and community structure, independent of drought treatment. The most abundant taxa recovered across all cultivars, treatments, and generations included Cladosporium, Penicillium, Alternaria, and Epicoccum. These results support our hypothesis that post-anthesis drought shapes the wheat seed fungal community.
{"title":"Multigenerational drought reveals a stable wheat seed fungal community","authors":"Lindsey E. Becker, M. Cubeta","doi":"10.1094/pbiomes-08-23-0083-r","DOIUrl":"https://doi.org/10.1094/pbiomes-08-23-0083-r","url":null,"abstract":"Wheat (Triticum spp.) is a staple food crop, providing a fifth of the world’s protein and caloric needs. Our research examines the impact of multi generation post-flowering drought stress on the wheat seed endophytic fungal community. Understanding how wheat seed fungal communities respond to drought stress over several generations can improve our knowledge of legacy drought stress. In this manuscript, we aim to identify seed associated fungi that play critical roles within the wheat seed under drought stress conditions. We examined the endophytic seed fungal communities of three winter wheat cultivars, Catawba, Shirley, and USG 3640. Moderate drought was imposed on a subset of plants immediately after flowering, with plants relieved from drought stress after one week. Seeds harvested from generation 1 were planted for a second generation of drought experiments. When examining post-flowering drought impact on wheat physiology, drought-exposed plants consistently exhibited lower daily transpiration rates, chlorophyll-a values, and seed yield compared to control plants, indicating that drought implementation was successful. ITS1 metabarcoding revealed that wheat seed fungal community species richness decreased during post-anthesis drought stress across both generations. We also observed that generation accounted for variation in fungal species richness and community structure, independent of drought treatment. The most abundant taxa recovered across all cultivars, treatments, and generations included Cladosporium, Penicillium, Alternaria, and Epicoccum. These results support our hypothesis that post-anthesis drought shapes the wheat seed fungal community.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140445073","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 : 2024-01-28DOI: 10.1094/pbiomes-07-23-0074-r
Alison K. Adams, Dana Landry, Virginia R. Sykes, Tara Rickman, A. Cham, Annemarie Timling, Heather M Kelly, J. Mcbeath, Bode Olukolu
As an alternative to host resistance, transgenic expression of entomocidal and antimicrobial proteins from Bacillus thuringiensis (Bt) in maize can mitigate Fusarium ear rot (FER). This study evaluates FER in Bt and conventional maize; and the role of microbes in the kernel-associated metagenome using quantitative reduced representation sequencing (qRRS). Our results revealed significant differences in FER severity across environments and varieties, and between inoculation treatments. The lower FER scores of conventional maize Spectrum-6416 relative to other varieties highlight resistant alleles in maize germplasm, while strong correlations indicate FER-induced yield loss. Mitigation of FER by the transgenes was validated by about 3-fold enrichment of Fusarium verticillioides (Fv) post-inoculation, compared to non-significant Fv enrichment in conventional maize. While the major causal pathogen of FER, Fv, was the most abundant species in the metagenomes, similar degree of correlations was observed between FER and several Fusarium spp. (0.2-0.56; Fv: 0.41-0.49). The potential FER-suppressing properties of Talaromyces stipitatus and Ustilago maydis were indicated by negative correlations with FER (-0.22 to -0.42), Fv and some Fusarium spp. The more FER resistant varieties consistently enriched for the potential FER-suppressing Burkholderia cenocepacia (negatively correlated with Fv). This suggests host genetic background-dependent recruitment of beneficial microbes that suppress pathogens and that microbe-microbe interactions play a role in FER severity. Quantitative and species/strain-level metagenomic profiles hold promise for identifying robust disease-suppressing microbes, microbes that act in synergy with pathogens, and for developing a holobiont-aware breeding strategies that accounts for host-microbiome coevolution and host genotype, microbiome/metagenome, and environment (GxGxE) interactions.
作为宿主抗性的替代方法，在玉米中转基因表达苏云金芽孢杆菌（Bt）的杀昆虫和抗微生物蛋白可减轻镰刀菌穗腐病（FER）。本研究评估了 Bt 玉米和传统玉米中的 FER，并使用定量还原表征测序（qRRS）评估了微生物在内核相关元基因组中的作用。我们的研究结果表明，不同环境、不同品种以及不同接种处理的 FER 严重程度存在显著差异。与其他品种相比，传统玉米花谱-6416的FER得分较低，这突出表明了玉米种质中的抗性等位基因，而强相关性则表明了FER诱导的产量损失。转基因对 FER 的缓解作用通过接种后禾谷镰刀菌（Fv）富集约 3 倍而得到验证，相比之下，常规玉米中的 Fv 富集并不明显。虽然 FER 的主要致病菌 Fv 是元基因组中最丰富的物种，但在 FER 和几种镰刀菌属之间也观察到了类似程度的相关性（0.2-0.56；Fv：0.41-0.49）。Talaromyces stipitatus 和 Ustilago maydis 的潜在 FER 抑制特性与 FER（-0.22 至 -0.42）、Fv 和一些镰刀菌属呈负相关，表明抗 FER 能力较强的品种始终富集潜在的 FER 抑制伯克霍尔德氏菌（与 Fv 呈负相关）。这表明宿主遗传背景依赖于有益微生物的招募，而有益微生物可抑制病原体，微生物与微生物之间的相互作用在 FER 严重程度中起一定作用。定量和物种/菌株水平的元基因组图谱有望确定强健的疾病抑制微生物、与病原体协同作用的微生物，并制定整体生物群感知的育种策略，以考虑宿主-微生物组协同进化以及宿主基因型、微生物组/元基因组和环境（GxGxE）之间的相互作用。
{"title":"Maize Kernel-Associated Metagenomes Reveal Potential Microbe-Microbe Interactions that Underlie Fusarium Ear Rot Disease","authors":"Alison K. Adams, Dana Landry, Virginia R. Sykes, Tara Rickman, A. Cham, Annemarie Timling, Heather M Kelly, J. Mcbeath, Bode Olukolu","doi":"10.1094/pbiomes-07-23-0074-r","DOIUrl":"https://doi.org/10.1094/pbiomes-07-23-0074-r","url":null,"abstract":"As an alternative to host resistance, transgenic expression of entomocidal and antimicrobial proteins from Bacillus thuringiensis (Bt) in maize can mitigate Fusarium ear rot (FER). This study evaluates FER in Bt and conventional maize; and the role of microbes in the kernel-associated metagenome using quantitative reduced representation sequencing (qRRS). Our results revealed significant differences in FER severity across environments and varieties, and between inoculation treatments. The lower FER scores of conventional maize Spectrum-6416 relative to other varieties highlight resistant alleles in maize germplasm, while strong correlations indicate FER-induced yield loss. Mitigation of FER by the transgenes was validated by about 3-fold enrichment of Fusarium verticillioides (Fv) post-inoculation, compared to non-significant Fv enrichment in conventional maize. While the major causal pathogen of FER, Fv, was the most abundant species in the metagenomes, similar degree of correlations was observed between FER and several Fusarium spp. (0.2-0.56; Fv: 0.41-0.49). The potential FER-suppressing properties of Talaromyces stipitatus and Ustilago maydis were indicated by negative correlations with FER (-0.22 to -0.42), Fv and some Fusarium spp. The more FER resistant varieties consistently enriched for the potential FER-suppressing Burkholderia cenocepacia (negatively correlated with Fv). This suggests host genetic background-dependent recruitment of beneficial microbes that suppress pathogens and that microbe-microbe interactions play a role in FER severity. Quantitative and species/strain-level metagenomic profiles hold promise for identifying robust disease-suppressing microbes, microbes that act in synergy with pathogens, and for developing a holobiont-aware breeding strategies that accounts for host-microbiome coevolution and host genotype, microbiome/metagenome, and environment (GxGxE) interactions.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139592016","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 : 2023-12-11DOI: 10.1094/pbiomes-09-23-0091-mf
Stalin W. Sarango Flores, Viviane Cordovez, B. Oyserman, N. Stopnisek, J. Raaijmakers, Pieter Van 't Hof
Plant domestication and breeding not only resulted in multiple phenotypic changes, but also impacted agricultural ecosystems where our current crops are cultivated. Most crops to date rely on the extensive use of fertilizers and pesticides to support crop growth and health. To minimize the environmental impact of these management practices, the plant microbiome got renewed attention as a large, yet untapped resource of microorganisms with beneficial effects on plant growth and health. In the past decade, it has become evident that the microbiome of plants plays a key role in nutrient acquisition, plant development and tolerance to diverse abiotic and biotic stresses. Here we review past and present knowledge of the microbiome of tomato as a model for unraveling the functional potential of plant microbiomes, the impact of domestication and the underlying genetics of microbiome assembly and activity. We also provide perspectives on how this knowledge can be adopted to enhance crop productivity and strengthen the sustainability of agricultural management practices.
{"title":"The Tomato’s Tale: Exploring taxonomy, biogeography, domestication and microbiome for enhanced resilience","authors":"Stalin W. Sarango Flores, Viviane Cordovez, B. Oyserman, N. Stopnisek, J. Raaijmakers, Pieter Van 't Hof","doi":"10.1094/pbiomes-09-23-0091-mf","DOIUrl":"https://doi.org/10.1094/pbiomes-09-23-0091-mf","url":null,"abstract":"Plant domestication and breeding not only resulted in multiple phenotypic changes, but also impacted agricultural ecosystems where our current crops are cultivated. Most crops to date rely on the extensive use of fertilizers and pesticides to support crop growth and health. To minimize the environmental impact of these management practices, the plant microbiome got renewed attention as a large, yet untapped resource of microorganisms with beneficial effects on plant growth and health. In the past decade, it has become evident that the microbiome of plants plays a key role in nutrient acquisition, plant development and tolerance to diverse abiotic and biotic stresses. Here we review past and present knowledge of the microbiome of tomato as a model for unraveling the functional potential of plant microbiomes, the impact of domestication and the underlying genetics of microbiome assembly and activity. We also provide perspectives on how this knowledge can be adopted to enhance crop productivity and strengthen the sustainability of agricultural management practices.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139010418","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：