Pub Date : 2023-04-25DOI: 10.1094/pbiomes-10-22-0069-r
Mohamed-Amine Hassani, Omar Gonzalez, Samuel S. Hunter, Gerald Holmes, Shashika Hewavitharana, Kelly Ivors, Cristina Lazcano
Plants recruit diverse microbial communities from the soil to their roots. Inter-microbial interactions and connectivity in the root microbiome play essential roles in plant health by promoting resistance to soil-borne pathogens. Yet, the understanding of these interactions under field conditions is still scarce. Using a strawberry crop model, we characterized the prokaryotic and the fungal communities in the rhizosphere and the roots of three strawberry cultivars grown under field conditions and displaying varying degrees of resistance to the soil-borne fungal pathogen Macrophomina phaseolina. We tested the hypothesis that resistant cultivars assemble distinct bacterial and fungal communities that foster microbial connectivity and mediate disease resistance. Our results show that the soil-borne pathogen, M. phaseolina, does not alter the root microbiome of the three strawberry cultivars. Microbiome comparative analysis indicated that the highly susceptible cultivar, Sweet Ann, assembled a distinct rhizosphere and root microbiome, whereas the microbiome of the strawberry cultivars Marquis and Manresa, were more similar and enriched with potential beneficial microbes. Co-occurrence network analysis revealed that the fungal pathogen, M. phaseolina, was more peripheral in the microbial network of Sweet Ann compared to Manresa and Marquis. Collectively, these results stress the role of the plant microbiome in mediating resistance against soil-borne pathogens and further suggest the role of plant genetic traits in the assembly of beneficial microbiome members. Our study reinforces the eminent role of the plant microbiome as trait selection in breeding programs and the need for further understanding of the genetic and biological mechanisms that mediate microbiome assembly. Uncovering these mechanisms will be key for the future success of plant breeding programs in their fight against soil-borne pathogens.
{"title":"Microbiome network connectivity and composition linked to disease resistance in strawberry plants","authors":"Mohamed-Amine Hassani, Omar Gonzalez, Samuel S. Hunter, Gerald Holmes, Shashika Hewavitharana, Kelly Ivors, Cristina Lazcano","doi":"10.1094/pbiomes-10-22-0069-r","DOIUrl":"https://doi.org/10.1094/pbiomes-10-22-0069-r","url":null,"abstract":"Plants recruit diverse microbial communities from the soil to their roots. Inter-microbial interactions and connectivity in the root microbiome play essential roles in plant health by promoting resistance to soil-borne pathogens. Yet, the understanding of these interactions under field conditions is still scarce. Using a strawberry crop model, we characterized the prokaryotic and the fungal communities in the rhizosphere and the roots of three strawberry cultivars grown under field conditions and displaying varying degrees of resistance to the soil-borne fungal pathogen Macrophomina phaseolina. We tested the hypothesis that resistant cultivars assemble distinct bacterial and fungal communities that foster microbial connectivity and mediate disease resistance. Our results show that the soil-borne pathogen, M. phaseolina, does not alter the root microbiome of the three strawberry cultivars. Microbiome comparative analysis indicated that the highly susceptible cultivar, Sweet Ann, assembled a distinct rhizosphere and root microbiome, whereas the microbiome of the strawberry cultivars Marquis and Manresa, were more similar and enriched with potential beneficial microbes. Co-occurrence network analysis revealed that the fungal pathogen, M. phaseolina, was more peripheral in the microbial network of Sweet Ann compared to Manresa and Marquis. Collectively, these results stress the role of the plant microbiome in mediating resistance against soil-borne pathogens and further suggest the role of plant genetic traits in the assembly of beneficial microbiome members. Our study reinforces the eminent role of the plant microbiome as trait selection in breeding programs and the need for further understanding of the genetic and biological mechanisms that mediate microbiome assembly. Uncovering these mechanisms will be key for the future success of plant breeding programs in their fight against soil-borne pathogens.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135017440","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 : 2023-04-20DOI: 10.1094/pbiomes-11-22-0078-sc
Meredith J. Persico, Suzanne M. Fleishman, D. Eissenstat, Terrence H. Bell, M. Centinari
In grapevine, metabolic activity of absorptive roots changes rapidly as roots age, but it is unclear if nearby microbial assemblages shift as well. Here, we investigated whether first-order root age impacts bacterial and fungal variation adjacent to the root surface, and if root age should be integrated into future studies on root functional traits and associated microbes. We hypothesized that microbial diversity and composition would differ between young (≤ 11 days old) and old (11.5 – 40 days old) first-order roots due to expected differences in metabolism over root lifespan (i.e., higher metabolism in young roots). Overall, we found that microbial composition was distinct between young and old absorptive roots, with stronger evidence at the phylum and ASV taxonomic levels for fungi (p = 0.003 and p = 0.038, respectively) than bacteria (p = 0.082 and p = 0.129, respectively). Furthermore, we identified differentially abundant fungal and bacterial ASVs in young and old roots that related to expected differences in root function, including instances of microbes previously described as copiotrophs more abundant adjacent to young roots and microbes described as oligotrophs and saprotrophs more abundant adjacent to old roots. In contrast to the distinct shifts in microbial composition, there was little evidence of shifts in alpha diversity (i.e., observed ASVs and Shannon diversity) between young and old roots. Our study suggests that future work on the impacts of root functional traits on localized microbial composition may improve results interpretation and reduce some variation by accounting for root age at sampling.
{"title":"The age of absorptive roots impacts root-adjacent microbial composition in grapevines","authors":"Meredith J. Persico, Suzanne M. Fleishman, D. Eissenstat, Terrence H. Bell, M. Centinari","doi":"10.1094/pbiomes-11-22-0078-sc","DOIUrl":"https://doi.org/10.1094/pbiomes-11-22-0078-sc","url":null,"abstract":"In grapevine, metabolic activity of absorptive roots changes rapidly as roots age, but it is unclear if nearby microbial assemblages shift as well. Here, we investigated whether first-order root age impacts bacterial and fungal variation adjacent to the root surface, and if root age should be integrated into future studies on root functional traits and associated microbes. We hypothesized that microbial diversity and composition would differ between young (≤ 11 days old) and old (11.5 – 40 days old) first-order roots due to expected differences in metabolism over root lifespan (i.e., higher metabolism in young roots). Overall, we found that microbial composition was distinct between young and old absorptive roots, with stronger evidence at the phylum and ASV taxonomic levels for fungi (p = 0.003 and p = 0.038, respectively) than bacteria (p = 0.082 and p = 0.129, respectively). Furthermore, we identified differentially abundant fungal and bacterial ASVs in young and old roots that related to expected differences in root function, including instances of microbes previously described as copiotrophs more abundant adjacent to young roots and microbes described as oligotrophs and saprotrophs more abundant adjacent to old roots. In contrast to the distinct shifts in microbial composition, there was little evidence of shifts in alpha diversity (i.e., observed ASVs and Shannon diversity) between young and old roots. Our study suggests that future work on the impacts of root functional traits on localized microbial composition may improve results interpretation and reduce some variation by accounting for root age at sampling.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41759255","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 : 2023-04-14DOI: 10.1094/pbiomes-02-23-0013-r
H. Schimann, C. Vacher, S. Coste, Elianne Louisanna, Tania Fort, L. Zinger
The determinants of phyllosphere microbial communities are drawing much attention given their functional importance for their plant host fitness and health. Identifying these determinants remain challenging in neotropical forests, considering the diversity of the tree hosts and the strong vertical heterogeneity of abiotic condition within the canopy and at the scale of the leaf. Here, we studied fungal and bacterial communities living in the endophytic and epiphytic phyllosphere in tree species across vertical gradients, from the top of the canopy to the ground. We used DNA metabarcoding to characterize microbial communities and measured abiotic variables and foliar traits to characterize environmental heterogeneity. The assembly of fungal communities was more driven by deterministic processes as compared to bacteria, endo- and epiphytic communities being similarly shaped by the host identity and unmeasured parameters. In contrast, in bacterial communities, the relative importance of deterministic processes decreased from endophytic to epiphytic communities. Bacterial epi- and endophytic communities were partly and differently determined by the position within the canopy, the host identity and leaf traits, suggesting an effect of the vertical gradient and a stronger selection in the inner tissues of the leaf than on its surface. The tree host exerts a selective pressure on microbial communities but the leaf as microhabitat contributes also significantly to the assembly of microbial communities. Discrepancies exist between Fungi and Bacteria that probably reflect different life-history trait and ecological strategies, emphasizing the need to study these communities jointly if we are to fully understand plant-phyllosphere interactions.
{"title":"Determinants of the vertical distribution of the phyllosphere differ between microbial groups and the epi- and endosphere","authors":"H. Schimann, C. Vacher, S. Coste, Elianne Louisanna, Tania Fort, L. Zinger","doi":"10.1094/pbiomes-02-23-0013-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-23-0013-r","url":null,"abstract":"The determinants of phyllosphere microbial communities are drawing much attention given their functional importance for their plant host fitness and health. Identifying these determinants remain challenging in neotropical forests, considering the diversity of the tree hosts and the strong vertical heterogeneity of abiotic condition within the canopy and at the scale of the leaf. Here, we studied fungal and bacterial communities living in the endophytic and epiphytic phyllosphere in tree species across vertical gradients, from the top of the canopy to the ground. We used DNA metabarcoding to characterize microbial communities and measured abiotic variables and foliar traits to characterize environmental heterogeneity. The assembly of fungal communities was more driven by deterministic processes as compared to bacteria, endo- and epiphytic communities being similarly shaped by the host identity and unmeasured parameters. In contrast, in bacterial communities, the relative importance of deterministic processes decreased from endophytic to epiphytic communities. Bacterial epi- and endophytic communities were partly and differently determined by the position within the canopy, the host identity and leaf traits, suggesting an effect of the vertical gradient and a stronger selection in the inner tissues of the leaf than on its surface. The tree host exerts a selective pressure on microbial communities but the leaf as microhabitat contributes also significantly to the assembly of microbial communities. Discrepancies exist between Fungi and Bacteria that probably reflect different life-history trait and ecological strategies, emphasizing the need to study these communities jointly if we are to fully understand plant-phyllosphere interactions.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47146332","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 : 2023-03-21DOI: 10.1094/pbiomes-01-22-0006-fi
Catherine D. Aimone, Hannah Giauque, C. Hawkes
Foliar fungal endophytes are known to alter plant physiology, but the mechanisms by which they do so remain poorly understood. We focused on how plant gene expression was altered by six fungal strains that generated "water-saver" and "water-spender" drought physiologies in a C4 grass, Panicum hallii. Water-saver physiologies have lower plant water loss, improved wilt resistance, and higher survival compared to water-spender strategies. We expected fungi within each functional group would have similar effects on P. hallii, and this was largely true for plant physiology, but not for plant gene expression. When we focused only on genes that were differentially expressed relative to fungus-free controls, we found surprisingly little overlap in plant differentially expressed genes or gene regulatory pathways across the fungal treatments, including within and between the water-saver and water-spender strategies. Nevertheless, using lasso regression we identified a small subset of genes that predicted 39% and 53% of the variation in plant wilt resistance and water loss, respectively. These results suggest that fungal effects on plant transcription may identify how they extend the plant phenotype, and the comparison across multiple fungi allows us to differentiate broadly fungal-responsive plant genes vs. those plant genes that respond only to single fungal taxa. The genes identified here could be targeted for future study to understand their function and, ultimately, represent candidates for precision breeding efforts to increase plant drought tolerance.
{"title":"Fungal symbionts generate water-saver and water-spender plant drought strategies via diverse effects on host gene expression","authors":"Catherine D. Aimone, Hannah Giauque, C. Hawkes","doi":"10.1094/pbiomes-01-22-0006-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-01-22-0006-fi","url":null,"abstract":"Foliar fungal endophytes are known to alter plant physiology, but the mechanisms by which they do so remain poorly understood. We focused on how plant gene expression was altered by six fungal strains that generated \"water-saver\" and \"water-spender\" drought physiologies in a C4 grass, Panicum hallii. Water-saver physiologies have lower plant water loss, improved wilt resistance, and higher survival compared to water-spender strategies. We expected fungi within each functional group would have similar effects on P. hallii, and this was largely true for plant physiology, but not for plant gene expression. When we focused only on genes that were differentially expressed relative to fungus-free controls, we found surprisingly little overlap in plant differentially expressed genes or gene regulatory pathways across the fungal treatments, including within and between the water-saver and water-spender strategies. Nevertheless, using lasso regression we identified a small subset of genes that predicted 39% and 53% of the variation in plant wilt resistance and water loss, respectively. These results suggest that fungal effects on plant transcription may identify how they extend the plant phenotype, and the comparison across multiple fungi allows us to differentiate broadly fungal-responsive plant genes vs. those plant genes that respond only to single fungal taxa. The genes identified here could be targeted for future study to understand their function and, ultimately, represent candidates for precision breeding efforts to increase plant drought tolerance.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45096497","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 : 2023-03-14DOI: 10.1094/pbiomes-01-23-0002-r
Alsayed Alfiky, E. Abou-Mansour, Mout De Vrieze, Floriane L' Haridon, L. Weisskopf
Potato growers worldwide are embattled in a war since more than 150-years with an enemy whose lifecycle, genome size and architecture, and economic impacts are the epitome of a plant pathogen. Phytophthora infestans (Mont.) de Bary is an oomycete that causes the notorious late blight infection in potato and tomato. In this study we explored the benefits of the multi-talented plant symbiotic fungi Trichoderma spp. and of their metabolites as potential biopesticides against P. infestans. Eleven strains of Trichoderma spp. were obtained from soil and tree barks and were identified using DNA sequence analysis. The antagonistic potential of the strains against P. infestans was first evaluated in vitro. In dual culture assays, P. infestans growth was significantly inhibited (53-95%) by different Trichoderma spp. through direct mycoparasitism, competition for space and nutrients, and/or antibiosis. The cell-free filtrates (CFF) of different Trichoderma strains were obtained, characterized for anti-Phytophthora activities as well as biochemical stability. The results indicated that Trichoderma CFF were chemically stable and strongly decreased P. infestans’ mycelial growth as well as zoospore motility and viability. Similarly, Trichoderma CFF showed significant protection against P. infestans infection in leaf disk assays. Ultra-performance liquid chromatography analysis revealed the presence of harzianic (HA), iso harzianic (iso-HA) acid and 6-Pentyl-2H-pyran-2-one (6PP) as major compounds in different Trichoderma CFF. Furthermore, selected Trichoderma strains significantly protected potato plants against soil-mediated late blight infection. Finally, Trichoderma spp. showed high compatibility with a copper-based fungicide, suggesting that both protective agents could be combined in integrated pest management program.
150多年来，世界各地的马铃薯种植者都陷入了一场战争，他们的敌人的生命周期、基因组大小和结构以及经济影响都是植物病原体的缩影。疫霉(Mont.) de Bary是一种卵菌，引起马铃薯和番茄臭名昭著的晚疫病感染。在这项研究中，我们探索了多才能植物共生真菌木霉及其代谢物作为潜在的生物农药对病原菌的益处。从土壤和树皮中分离得到11株木霉，并进行了DNA序列鉴定。首次在体外评价了菌株对病原菌的拮抗潜力。在双重培养试验中，不同木霉菌通过直接的支原体寄生、空间和营养的竞争和/或抗生素抑制了病原菌的生长(53-95%)。获得了不同木霉菌株的无细胞滤液(CFF)，并对其抗疫活性和生化稳定性进行了表征。结果表明，木霉CFF具有化学稳定性，能显著降低病原菌菌丝生长、游动孢子活力和活力。同样，木霉CFF在叶片检测中也表现出对病原菌的保护作用。超高效液相色谱分析表明，不同木霉CFF中主要化合物为哈兹酸(HA)、异哈兹酸(HA)和6-戊基- 2h -吡喃-2-酮(6PP)。此外，所选木霉菌株能显著保护马铃薯植株免受土壤介导的晚疫病感染。结果表明，木霉与铜基杀菌剂具有较高的配伍性，可用于害虫综合治理。
{"title":"Newly isolated Trichoderma spp. show multifaceted biocontrol strategies to inhibit potato late blight causal agent Phytophthora infestans both in vitro and in planta","authors":"Alsayed Alfiky, E. Abou-Mansour, Mout De Vrieze, Floriane L' Haridon, L. Weisskopf","doi":"10.1094/pbiomes-01-23-0002-r","DOIUrl":"https://doi.org/10.1094/pbiomes-01-23-0002-r","url":null,"abstract":"Potato growers worldwide are embattled in a war since more than 150-years with an enemy whose lifecycle, genome size and architecture, and economic impacts are the epitome of a plant pathogen. Phytophthora infestans (Mont.) de Bary is an oomycete that causes the notorious late blight infection in potato and tomato. In this study we explored the benefits of the multi-talented plant symbiotic fungi Trichoderma spp. and of their metabolites as potential biopesticides against P. infestans. Eleven strains of Trichoderma spp. were obtained from soil and tree barks and were identified using DNA sequence analysis. The antagonistic potential of the strains against P. infestans was first evaluated in vitro. In dual culture assays, P. infestans growth was significantly inhibited (53-95%) by different Trichoderma spp. through direct mycoparasitism, competition for space and nutrients, and/or antibiosis. The cell-free filtrates (CFF) of different Trichoderma strains were obtained, characterized for anti-Phytophthora activities as well as biochemical stability. The results indicated that Trichoderma CFF were chemically stable and strongly decreased P. infestans’ mycelial growth as well as zoospore motility and viability. Similarly, Trichoderma CFF showed significant protection against P. infestans infection in leaf disk assays. Ultra-performance liquid chromatography analysis revealed the presence of harzianic (HA), iso harzianic (iso-HA) acid and 6-Pentyl-2H-pyran-2-one (6PP) as major compounds in different Trichoderma CFF. Furthermore, selected Trichoderma strains significantly protected potato plants against soil-mediated late blight infection. Finally, Trichoderma spp. showed high compatibility with a copper-based fungicide, suggesting that both protective agents could be combined in integrated pest management program.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48399121","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 : 2023-03-07DOI: 10.1094/pbiomes-10-22-0068-r
Hyun Kim, Christopher Kim, Yong-Hwan Lee
Genetic and environmental cues affecting seed microbial communities have been investigated to assess the ecological characteristics of seed microbial communities. However, little is known concerning seed-to-seed microbial variations and ecological drivers at the single-seed level. We report rare taxa-associated heterogeneity and robustness of seed bacterial and fungal communities in individual seeds using 63 pooled and 70 single-seed samples from a single field-grown rice plant. Ordination analyses showed that seed-to-seed variation patterns could be clustered according to the originating panicle branch. Bacterial-fungal associations and in silico extinction experiments demonstrated that rare taxa contribute to the connectivity and robustness of the associations. Null modeling-based statistical analysis revealed that the distribution of rare taxa is mainly governed by dispersal limitation, whereas the distribution of prevalent taxa is mainly governed by homogeneous selection and ecological drift. Our findings provide an ecological framework for understanding the heterogeneity of seed microbial communities in a single plant; they will facilitate the development and application of seed microbiota or single microbe-based engineering strategies.
{"title":"The single-seed microbiota reveals rare taxa-associated community robustness","authors":"Hyun Kim, Christopher Kim, Yong-Hwan Lee","doi":"10.1094/pbiomes-10-22-0068-r","DOIUrl":"https://doi.org/10.1094/pbiomes-10-22-0068-r","url":null,"abstract":"Genetic and environmental cues affecting seed microbial communities have been investigated to assess the ecological characteristics of seed microbial communities. However, little is known concerning seed-to-seed microbial variations and ecological drivers at the single-seed level. We report rare taxa-associated heterogeneity and robustness of seed bacterial and fungal communities in individual seeds using 63 pooled and 70 single-seed samples from a single field-grown rice plant. Ordination analyses showed that seed-to-seed variation patterns could be clustered according to the originating panicle branch. Bacterial-fungal associations and in silico extinction experiments demonstrated that rare taxa contribute to the connectivity and robustness of the associations. Null modeling-based statistical analysis revealed that the distribution of rare taxa is mainly governed by dispersal limitation, whereas the distribution of prevalent taxa is mainly governed by homogeneous selection and ecological drift. Our findings provide an ecological framework for understanding the heterogeneity of seed microbial communities in a single plant; they will facilitate the development and application of seed microbiota or single microbe-based engineering strategies.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46881410","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 : 2023-02-27DOI: 10.1094/pbiomes-09-22-0060-r
S. Addison, M. Rúa, S. Smaill, K. Daley, B. Singh, S. Wakelin
Microbiomes play critical roles in host functioning and therefore there is increasing interest in the microbiome assembly of plants. However, sampling strategies for long-lived perennial trees need to be standardised to produce robust data that accurately represents the microbiome over time. This issue is currently unresolved because there is little evidence indicating which portion of perennial tree species (e.g., root region or surrounding soil) is the best to sample to produce the most accurate measure of microbiome communities. Our aim was to sample different compartments of a plant’s belowground microbiome to identify the optimal sampling strategy to account for the microbial community present. We found that the structure of the microbial community depends most strongly on the environment (site) and compartment of sample collected (bulk soil, rhizosphere, or rhizoplane), rather than the depth or cardinal direction of the sample. We also found that the microbial community increased in diversity with increased distance from the tree within the rhizoplane and rhizosphere. The data presented here provides systematic evidence for a pragmatic and robust sampling regime that was tested and validated across different environments and soil types while controlling for host genotype. This sampling regime will enable effective partitioning of root compartments when studying the microbiome associated with perennial tree species, allowing targeted questions about the microbiome to be explored with greater accuracy.
{"title":"Getting to the root of tree soil microbiome sampling","authors":"S. Addison, M. Rúa, S. Smaill, K. Daley, B. Singh, S. Wakelin","doi":"10.1094/pbiomes-09-22-0060-r","DOIUrl":"https://doi.org/10.1094/pbiomes-09-22-0060-r","url":null,"abstract":"Microbiomes play critical roles in host functioning and therefore there is increasing interest in the microbiome assembly of plants. However, sampling strategies for long-lived perennial trees need to be standardised to produce robust data that accurately represents the microbiome over time. This issue is currently unresolved because there is little evidence indicating which portion of perennial tree species (e.g., root region or surrounding soil) is the best to sample to produce the most accurate measure of microbiome communities. Our aim was to sample different compartments of a plant’s belowground microbiome to identify the optimal sampling strategy to account for the microbial community present. We found that the structure of the microbial community depends most strongly on the environment (site) and compartment of sample collected (bulk soil, rhizosphere, or rhizoplane), rather than the depth or cardinal direction of the sample. We also found that the microbial community increased in diversity with increased distance from the tree within the rhizoplane and rhizosphere. The data presented here provides systematic evidence for a pragmatic and robust sampling regime that was tested and validated across different environments and soil types while controlling for host genotype. This sampling regime will enable effective partitioning of root compartments when studying the microbiome associated with perennial tree species, allowing targeted questions about the microbiome to be explored with greater accuracy.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45858537","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 : 2023-02-23DOI: 10.1094/pbiomes-10-22-0072-r
S. Yurgel, B. Sallato, Tanya E. Cheeke
The phytoplasma Candidatus phytoplasma pruni (CPP), a causative agent of little cherry disease (LCD), has become an increasing problem for sweet cherry growers in Washington state, which is the largest producer of cherries in the USA. The control of LCD currently relies on the identification and removal of infected trees, which has proven to be difficult because of the prolonged asymptomatic, but still contagious state of the disease, and the lack of reliable and economical tests. Thus, the development of new approaches for early detection of LCD will be an important step in the successful control of this tree fruit disease. To identify potential microbial indicators of CPP infection we evaluated the bacterial and fungal communities in the roots of cherry trees from two different orchards that were: (i) infected with CPP and symptomatic; (ii) infected with CPP but remained asymptomatic; and (iii) healthy, non-CPP infected trees. We found significant variation in the microbiomes between the two cherry orchards, with the location being a stronger driving factor determining the fungal compared to the bacterial community. The fungal communities were less affected by the disease conditions compared to the bacterial microbiome. Overall, this study demonstrates feasibility of the microbiome approach for the early detection of LCD by CPP, but also demonstrates that more orchards need to be sampled as location was a stronger contributor to the microbiome of cherry tree roots than disease condition.
{"title":"Exploring microbial dysbiosis in orchards affected by little cherry disease","authors":"S. Yurgel, B. Sallato, Tanya E. Cheeke","doi":"10.1094/pbiomes-10-22-0072-r","DOIUrl":"https://doi.org/10.1094/pbiomes-10-22-0072-r","url":null,"abstract":"The phytoplasma Candidatus phytoplasma pruni (CPP), a causative agent of little cherry disease (LCD), has become an increasing problem for sweet cherry growers in Washington state, which is the largest producer of cherries in the USA. The control of LCD currently relies on the identification and removal of infected trees, which has proven to be difficult because of the prolonged asymptomatic, but still contagious state of the disease, and the lack of reliable and economical tests. Thus, the development of new approaches for early detection of LCD will be an important step in the successful control of this tree fruit disease. To identify potential microbial indicators of CPP infection we evaluated the bacterial and fungal communities in the roots of cherry trees from two different orchards that were: (i) infected with CPP and symptomatic; (ii) infected with CPP but remained asymptomatic; and (iii) healthy, non-CPP infected trees. We found significant variation in the microbiomes between the two cherry orchards, with the location being a stronger driving factor determining the fungal compared to the bacterial community. The fungal communities were less affected by the disease conditions compared to the bacterial microbiome. Overall, this study demonstrates feasibility of the microbiome approach for the early detection of LCD by CPP, but also demonstrates that more orchards need to be sampled as location was a stronger contributor to the microbiome of cherry tree roots than disease condition.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49185248","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 : 2023-02-20DOI: 10.1094/pbiomes-07-22-0042-r
H. Baker, Jorge R. Ibarra Caballero, C. Gleason, C. Jahn, C. Hesse, J. Stewart, I. Zasada
High throughput amplicon sequencing of nematode communities has the potential to increase our understanding of nematode community ecology. A current constraint to the widespread implementation of amplicon sequencing is the lack of sequence databases with consistent taxonomic naming schemes. Focusing on 18S sequence data, we developed NemaTaxa, a manually curated database that can be used with QIIME and mothur analysis platforms. Nematode 18S sequence data was downloaded from NCBI from which both Nematoda universal primers NF1 and 18Sr2b aligned. Taxonomic strings were trimmed to include only classical Linnaean lineages to genera within Nematoda; missing taxonomic data were completed manually. NemaTaxa was compared with other available databases, specifically PR2 and Silva v132, available for mothur using data collected from Oregon, Idaho, and Washington potato cropping systems. In general, NemaTaxa performed similar to PR2 in the number of contigs assigned to Nematoda and estimates of diversity. NemaTaxa resolves classification at the genus, family and order levels while PR2 always has a portion of sequences assigned at the class level due to incomplete taxonomic strings. The Silva v132 database available in mothur is of limited use because of the greatly reduced number of nematode sequences available in the database, making classification only possible to the level of order. NemaTaxa offers an “off the shelf” database that can be used by nonexperts in nematology wanting to explore nematode community ecology, and therefore, will allow for inclusion of nematodes in soil ecology studies that employ amplicon sequencing for other organisms such as fungi and bacteria.
{"title":"NemaTaxa: A new taxonomic database for analysis of nematode community data","authors":"H. Baker, Jorge R. Ibarra Caballero, C. Gleason, C. Jahn, C. Hesse, J. Stewart, I. Zasada","doi":"10.1094/pbiomes-07-22-0042-r","DOIUrl":"https://doi.org/10.1094/pbiomes-07-22-0042-r","url":null,"abstract":"High throughput amplicon sequencing of nematode communities has the potential to increase our understanding of nematode community ecology. A current constraint to the widespread implementation of amplicon sequencing is the lack of sequence databases with consistent taxonomic naming schemes. Focusing on 18S sequence data, we developed NemaTaxa, a manually curated database that can be used with QIIME and mothur analysis platforms. Nematode 18S sequence data was downloaded from NCBI from which both Nematoda universal primers NF1 and 18Sr2b aligned. Taxonomic strings were trimmed to include only classical Linnaean lineages to genera within Nematoda; missing taxonomic data were completed manually. NemaTaxa was compared with other available databases, specifically PR2 and Silva v132, available for mothur using data collected from Oregon, Idaho, and Washington potato cropping systems. In general, NemaTaxa performed similar to PR2 in the number of contigs assigned to Nematoda and estimates of diversity. NemaTaxa resolves classification at the genus, family and order levels while PR2 always has a portion of sequences assigned at the class level due to incomplete taxonomic strings. The Silva v132 database available in mothur is of limited use because of the greatly reduced number of nematode sequences available in the database, making classification only possible to the level of order. NemaTaxa offers an “off the shelf” database that can be used by nonexperts in nematology wanting to explore nematode community ecology, and therefore, will allow for inclusion of nematodes in soil ecology studies that employ amplicon sequencing for other organisms such as fungi and bacteria.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42694239","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 : 2023-02-07DOI: 10.1094/pbiomes-09-22-0059-r
Jin Xu, Yayu Wang, Yunzheng Zhang, Nadia Riera, Jinyun Li, K. Clark, Jin Tao, Hongyun Chen, Jiawen Wen, Wenbo Ma, Huan Liu, Nian Wang
Although plant genotypes are known to be a determinant of microbiome composition, the genetic mechanisms underlying how genotypes affect the microbiome are poorly understood. Citrus is an important, perennial fruit crop that normally contains scion grafted on the rootstock. Here, we investigated the genetic traits underlying the citrus microbiome. We sequenced the metagenome of leaf, root, and rhizosphere soil samples and the genome of corresponding citrus genotypes, which included 66 unique rootstock/scion combinations (56 scion genotypes and 9 rootstock genotypes) from one location using deep shotgun sequencing. Using a genome-wide association study (GWAS) analysis, we identified significant associations between citrus genes and a subset of genera and functional traits of the microbiome. Intriguingly, we found that bacterial secretion systems, and mobility related genes were present in SNP-associated microbial functional traits of leaf and root microbiomes, but not in rhizosphere microbiome, indicating they are important factor for bacteria to colonize inside or on leaf and root tissues, but less so in the rhizosphere. We also uncovered that chemotaxis and flagella genes play critical roles for bacteria colonizing leaf tissues, but not in root tissues and rhizosphere. Microbiome associated host genes were mainly involved in plant immunity, transporters, hormones, cell wall, and metabolism of carbohydrates, amino acids, and nitrogen. We identified genetic determinants that are associated with the abundance of Bacillus, Bradyrhizobium, Burkholderia, and Cellvibrio, genera that are known to comprise many beneficial bacteria for citrus. This study unraveled genetic traits underneath the mutual selection of citrus and microbes via GWAS analyses
{"title":"Host genetic traits underlying the composition/assembly of the citrus microbiome","authors":"Jin Xu, Yayu Wang, Yunzheng Zhang, Nadia Riera, Jinyun Li, K. Clark, Jin Tao, Hongyun Chen, Jiawen Wen, Wenbo Ma, Huan Liu, Nian Wang","doi":"10.1094/pbiomes-09-22-0059-r","DOIUrl":"https://doi.org/10.1094/pbiomes-09-22-0059-r","url":null,"abstract":"Although plant genotypes are known to be a determinant of microbiome composition, the genetic mechanisms underlying how genotypes affect the microbiome are poorly understood. Citrus is an important, perennial fruit crop that normally contains scion grafted on the rootstock. Here, we investigated the genetic traits underlying the citrus microbiome. We sequenced the metagenome of leaf, root, and rhizosphere soil samples and the genome of corresponding citrus genotypes, which included 66 unique rootstock/scion combinations (56 scion genotypes and 9 rootstock genotypes) from one location using deep shotgun sequencing. Using a genome-wide association study (GWAS) analysis, we identified significant associations between citrus genes and a subset of genera and functional traits of the microbiome. Intriguingly, we found that bacterial secretion systems, and mobility related genes were present in SNP-associated microbial functional traits of leaf and root microbiomes, but not in rhizosphere microbiome, indicating they are important factor for bacteria to colonize inside or on leaf and root tissues, but less so in the rhizosphere. We also uncovered that chemotaxis and flagella genes play critical roles for bacteria colonizing leaf tissues, but not in root tissues and rhizosphere. Microbiome associated host genes were mainly involved in plant immunity, transporters, hormones, cell wall, and metabolism of carbohydrates, amino acids, and nitrogen. We identified genetic determinants that are associated with the abundance of Bacillus, Bradyrhizobium, Burkholderia, and Cellvibrio, genera that are known to comprise many beneficial bacteria for citrus. This study unraveled genetic traits underneath the mutual selection of citrus and microbes via GWAS analyses","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43951185","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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