Phytobiomes Journal最新文献_第8页

Chronic drought differentially alters the belowground microbiome of drought tolerant and drought susceptible genotypes of Populus trichocarpa 长期干旱对毛果杨耐旱和耐旱基因型地下微生物组的影响

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-07-13 DOI: 10.1094/pbiomes-12-21-0076-r

Brandon David Kristy, A. Carrell, E. Johnston, D. Klingeman, K. Gwinn, Kimberly C. Syring, Caroline Skalla, Scott Emrich, M. Cregger

{"title":"Chronic drought differentially alters the belowground microbiome of drought tolerant and drought susceptible genotypes of Populus trichocarpa","authors":"Brandon David Kristy, A. Carrell, E. Johnston, D. Klingeman, K. Gwinn, Kimberly C. Syring, Caroline Skalla, Scott Emrich, M. Cregger","doi":"10.1094/pbiomes-12-21-0076-r","DOIUrl":"https://doi.org/10.1094/pbiomes-12-21-0076-r","url":null,"abstract":"Populus trichocarpa is an ecologically important tree species and economically important biofeedstock. Belowground, P. trichocarpa interacts with diverse microorganisms in the rhizosphere and root endosphere. These plant-microbial interactions can bolster a variety of plant processes, ranging from pathogen suppression to drought tolerance, yet we know little about the impact of chronic drought stress on P. trichocarpa’s belowground microbiomes. To investigate the interactive effect of chronic drought on belowground microbial communities across genetically different P. trichocarpa hosts, we assessed archaeal/bacterial and fungal communities within the root endosphere, rhizosphere, and surrounding bulk soil of selected genotypes in a long-term drought experiment in Boardman, OR, USA. We sequenced the 16S rRNA and ITS2 gene region on samples collected from 16 distinct P. trichocarpa genotypes in plots with full or reduced irrigation. Eight of these genotypes have been previously identified as drought tolerant while the other eight genotypes were drought susceptible. While reduced irrigation influenced the composition of every archaeal/bacterial microbiome compartment, fungal communities were only affected in the rhizosphere and bulk soil compartments. Drought-tolerant bacteria, such as Actinobacteria, were differentially abundant in reduced irrigation across all belowground microbiomes. Host drought-tolerance influenced plant-associated microbiome compartments but had little impact on the bulk soil compartment. Drought-tolerant trees were enriched for potential growth-promoting microorganisms in the root endosphere and rhizosphere, including Sphingomonas bacteria and ectomycorrhizal fungi. Overall, associations of growth-promoting microbes in drought resistant P. trichocarpa genotypes can be leveraged to improve biofeedstock productivity in regions prone to periodic drought.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41432385","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}

引用次数: 4

Passaging phyllosphere microbial communities develop suppression towards bacterial speck disease in tomato 传代根层微生物群落对番茄细菌性斑点病有抑制作用

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-06-20 DOI: 10.1094/pbiomes-05-22-0030-fi

H. Ehau-Taumaunu, K. Hockett

{"title":"Passaging phyllosphere microbial communities develop suppression towards bacterial speck disease in tomato","authors":"H. Ehau-Taumaunu, K. Hockett","doi":"10.1094/pbiomes-05-22-0030-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-05-22-0030-fi","url":null,"abstract":"Microbial community-based disease management approaches have the potential to substitute or combine with currently employed strategies. Suppressive soils are great examples of microbial communities that suppress soilborne plant disease after severe outbreaks and are maintained over multiple years or crop cycles. While there are many suppressive soil examples, to our knowledge, there are no descriptions of disease suppressive phyllosphere communities. Therefore, we investigated whether a phyllosphere microbial community could be developed through a selective passaging method to suppress disease using the model pathosystem of Pseudomonas syringae pv. tomato (Pto) and tomato. Field tomato phyllosphere microbial communities were recovered, and spray transferred to greenhouse tomato plants, after which were inoculated with Pto. Disease severity was visually estimated, and the microbial communities were recovered to be independently applied to the next passage. Overall, greenhouse passaging resulted in an increase in disease severity for all passage lines from the initial passage, which peaked at passage 4-5, followed by a sharp decline until passage 9. The disease severity at passage 9 was also significantly lower than a non-passaged Pto only comparison. Heat-treatment of passage 9 communities resulted in elevated disease severity over several subsequent passages in the growth chamber, whereas the untreated community maintained low disease. Community-only passage lines (without Pto inclusion during passaging) did not show disease suppression after subsequent pathogen introduction. This work presents an experimental approach to develop phyllosphere microbial communities in the presence of a phytopathogen to enrich for a low disease phenotype and results in maintained disease suppression.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43193956","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}

引用次数: 3

Impacts of Host Genotype and Grafting on Root, Rhizosphere, and Core Microbiomes in Theobroma cacao Seedlings 寄主基因型和嫁接对可可幼苗根系、根际和核心微生物群的影响

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-06-13 DOI: 10.1094/pbiomes-04-22-0024-r

Jennifer E. Schmidt, Alana J. Firl, Taylor M. Crow, Ashley Duval, Donald Livingstone III

{"title":"Impacts of Host Genotype and Grafting on Root, Rhizosphere, and Core Microbiomes in Theobroma cacao Seedlings","authors":"Jennifer E. Schmidt, Alana J. Firl, Taylor M. Crow, Ashley Duval, Donald Livingstone III","doi":"10.1094/pbiomes-04-22-0024-r","DOIUrl":"https://doi.org/10.1094/pbiomes-04-22-0024-r","url":null,"abstract":"Recent advances in understanding microbial contributions to plant growth and soil health have sparked interest in breeding plants that cultivate a beneficial microbiome. Yet optimizing phytobiomes requires knowledge of the genetic architecture of host influence on the associated microbiome, and this knowledge is particularly lacking in perennial crops such as Theobroma cacao. Grafting adds an additional layer of complexity: What are the relative impacts of rootstock and scion on the root and rhizosphere microbiomes? Plant-microbe interactions have rarely been investigated in Theobroma cacao despite the global significance of this crop. We sought to 1) characterize the effect of host genotype on the cacao root endophyte and rhizosphere microbiomes, 2) identify a core microbiome across six open-pollinated rootstock groups, and 3) investigate whether members of the core microbiome were linked to plant growth traits in greenhouse-grown trees. Rootstock and scion identity did not affect within-sample diversity of the root or rhizosphere microbiomes, but rootstock explained 7-13% of variation in prokaryotic communities and 9-12% of variation in fungal communities. However, rootstock genetic distance was not related to taxonomic or phylogenetic dissimilarity of the root or rhizosphere microbiomes. We identified a conserved core microbiome that contained numerous taxa found in both root and rhizosphere microbiomes. Structural topic model and multivariate regression approaches identified both co-varying groups and individual taxa within the core microbiome that were associated with metrics of plant growth and development. These preliminary results could be used to inform breeding programs and potentially soil bio-amendment strategies for cacao seedlings.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":"1 1","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41421339","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}

引用次数: 0

Drought tolerance traits in Neotropical trees correlate with the composition of phyllosphere fungal communities 新热带树木的耐旱性与叶际真菌群落的组成相关

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-06-01 DOI: 10.1094/pbiomes-04-22-0023-r

Marine C. Cambon, D. Cartry, É. Chancerel, Camille Ziegler, Sébastien Levionnois, S. Coste, C. Stahl, S. Delzon, M. Buée, B. Burban, Jocelyn Cazal, Tania Fort, Jean-Yves Goret, P. Heuret, P. Léger, Elianne Louisanna, Yves Ritter, D. Bonal, M. Roy, H. Schimann, C. Vacher

{"title":"Drought tolerance traits in Neotropical trees correlate with the composition of phyllosphere fungal communities","authors":"Marine C. Cambon, D. Cartry, É. Chancerel, Camille Ziegler, Sébastien Levionnois, S. Coste, C. Stahl, S. Delzon, M. Buée, B. Burban, Jocelyn Cazal, Tania Fort, Jean-Yves Goret, P. Heuret, P. Léger, Elianne Louisanna, Yves Ritter, D. Bonal, M. Roy, H. Schimann, C. Vacher","doi":"10.1094/pbiomes-04-22-0023-r","DOIUrl":"https://doi.org/10.1094/pbiomes-04-22-0023-r","url":null,"abstract":"Plant-associated microorganisms have shown to aid plants in coping with drought. However, the underlying mechanisms are poorly understood and there is uncertainty regarding which microbial taxa and functions are mostly involved. We explored these issues in Neotropical rainforests and identified foliar microorganisms that may play a role in drought tolerance of trees. Our objectives were to (1) test the relationship between drought tolerance traits in Neotropical trees and the diversity and composition of their foliar fungal and bacterial communities and (2) identify leaf microbial taxa positively or negatively associated with drought tolerance traits. Our results showed that the composition of leaf fungal communities, but not bacterial communities, was related to drought tolerance. We identified 27 fungal Amplicon Sequence Variants (ASVs) whose relative abundance co-varied with drought tolerance traits. Most variants were assigned to fungal clades often described as plant pathogens and increased in abundance with drought susceptibility. This greater relative abundance of leaf pathogens in the most drought-susceptible trees might increase their vulnerability to climate change. Moreover, we identified the Strelitziana and Ochroconis fungal genera as potential candidates for future culture-dependent studies aimed at understanding and improving drought tolerance in Neotropical forests.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41693215","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}

引用次数: 2

Metagenomic next⁃generation sequencing (mNGS) data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen Zymoseptoria tritici metagenomics next generation sequencing (mNGS)数据揭示了小麦侵染真菌酵母菌(Zymoseptoria tritici)的根层微生物组

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-05-26 DOI: 10.1094/pbiomes-02-22-0008-fi

Didac Barroso-Bergadà, M. Massot, Noémie Vignolles, Julie Faivre d’Arcier, É. Chancerel, E. Guichoux, A. Walker, C. Vacher, D. Bohan, V. Laval, F. Suffert

{"title":"Metagenomic next⁃generation sequencing (mNGS) data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen Zymoseptoria tritici","authors":"Didac Barroso-Bergadà, M. Massot, Noémie Vignolles, Julie Faivre d’Arcier, É. Chancerel, E. Guichoux, A. Walker, C. Vacher, D. Bohan, V. Laval, F. Suffert","doi":"10.1094/pbiomes-02-22-0008-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-02-22-0008-fi","url":null,"abstract":"The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in the wheat phyllosphere would lead to new insights into STB management. This resource announcement provides fungal and bacterial metabarcoding datasets obtained by sampling wheat leaves with and without symptoms caused by Z. tritici. Tissues were sampled from three commercial wheat varieties on three sampling dates during a cropping season. Weeds around wheat fields were sampled as well. In total, more than 450 leaf samples were collected. The pathogen Z. tritici was quantified using qPCR. We provide the raw metabarcoding datasets, the Amplicon Sequence Variant (ASV) tables obtained after bioinformatic processing, the metadata associated to each sample (sampling date, wheat variety and tissue health condition), a preliminary descriptive analysis of the data, and the code used for bioinformatic and descriptive statistical analysis.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45711233","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}

引用次数: 2

Dominance of Ciliophora and Chlorophyta among phyllosphere protists of Solanaceous plants 茄科植物叶际原生生物中的Ciliophora和叶绿体优势

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-05-19 DOI: 10.1094/pbiomes-04-22-0021-fi

Stephen J. Taerum, B. Steven, D. Gage, L. Triplett

{"title":"Dominance of Ciliophora and Chlorophyta among phyllosphere protists of Solanaceous plants","authors":"Stephen J. Taerum, B. Steven, D. Gage, L. Triplett","doi":"10.1094/pbiomes-04-22-0021-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-04-22-0021-fi","url":null,"abstract":"Phyllosphere microbiota play an important role in shaping plant health and function, but most research has focused only on bacterial and fungal communities. As a result, little is known about the composition of diverse microeukaryotes in the phyllosphere, including protist predators and algae, or how they are affected by host species or co-occurring bacteria. Using universal eukaryotic primers and a PNA clamp to block amplification of the plant 18S rRNA gene, we profiled the phyllosphere and rhizosphere microbiomes of five solanaceous crop species grown in a field plot in Connecticut, USA. Phyllosphere communities of protists, like those of bacteria, were far less diverse and more variable than those of the rhizosphere. Phyllosphere samples contained hundreds of protist sequence variants from at least seven major eukaryotic lineages, of which one-fifth were not observed in bulk soil or rhizosphere samples. Phyllosphere samples were highly enriched for a few specific sequence variants representing green algae (Chlorophyta order Chlamydomonales) and ciliates (Ciliophora class Colpodea), while rhizospheres were dominated by protists from the phylum Cercozoa. Correlation analysis identified Sphingomonas spp. bacteria as central network hubs positively associated with protists in the phyllosphere and rhizosphere. These findings indicate that while leaf surfaces host a highly variable protist community of limited diversity, certain ciliates and green algae may be well-adapted for the phyllosphere habitat.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47456332","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}

引用次数: 3

Deep-rooted plant species recruit distinct bacterial communities in subsoil than in topsoil 深根植物在底土中比在表土中吸收不同的细菌群落

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-03-14 DOI: 10.1094/pbiomes-10-21-0064-r

Frederik Bak, Annemette Lyhne-Kjærbye, Stacie Tardif, D. B. Dresbøll, O. Nybroe, M. Nicolaisen

{"title":"Deep-rooted plant species recruit distinct bacterial communities in subsoil than in topsoil","authors":"Frederik Bak, Annemette Lyhne-Kjærbye, Stacie Tardif, D. B. Dresbøll, O. Nybroe, M. Nicolaisen","doi":"10.1094/pbiomes-10-21-0064-r","DOIUrl":"https://doi.org/10.1094/pbiomes-10-21-0064-r","url":null,"abstract":"Deep-rooted plants can obtain water and nutrients from the subsoil, making them resilient to climatic changes. Plant growth and health may depend on interactions with root-associated bacteria, but the composition and assembly dynamics of deep root-associated bacterial communities are unknown, as are their ability to supply plants with nitrogen (N). Here, we investigated the root-associated communities of the three deep-rooted perennial crops, lucerne (Medicago sativa), intermediate wheatgrass (Thinopyrum intermedium), and rosinweed (Silphium integrifolium), grown in 4 m tall RootTowers, under semi-natural conditions. Across the plant species, higher bacterial abundance and lower diversity were found in the root-associated communities compared to the bulk soil communities. The deep root-associated communities were enriched in the genera Pseudarthrobacter, Pseudomonas, Rhizobium and Streptomyces, genera found to harbor a wide variety of bacterial species expressing plant beneficial traits. The composition of the deep root-associated bacterial communities were plant species specific, and clearly distinct from the shallow communities. Additionally, the deep root-associated communities comprised primarily amplicon sequence variants (ASVs) that were omnipresent in the bulk soil, and to a limited extent ASVs that could have been transported from the topsoil or potentially from the seed. Abundances of genes involved in N-cycling: amoA, nifH, nirK, nirS and nosZ showed plant species specific patterns, and indicated that intermediate wheatgrass and lucerne recruit N-fixing bacteria even at 3 m depth for N supply. This work provides the first steps toward understanding plant-microbe interactions of deep-rooted crops, which are important for evaluating these crops for use in future sustainable cropping systems.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46008467","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}

引用次数: 0

Changes in fungal and oomycete community composition following irrigation reductions aimed at increasing water use efficiency in a containerized nursery crop 减少灌溉以提高容器化苗圃作物的水分利用效率后真菌和卵菌群落组成的变化

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-02-18 DOI: 10.1094/pbiomes-09-21-0058-r

J. Del Castillo Múnera, A. Poret-Peterson, C. Swett

{"title":"Changes in fungal and oomycete community composition following irrigation reductions aimed at increasing water use efficiency in a containerized nursery crop","authors":"J. Del Castillo Múnera, A. Poret-Peterson, C. Swett","doi":"10.1094/pbiomes-09-21-0058-r","DOIUrl":"https://doi.org/10.1094/pbiomes-09-21-0058-r","url":null,"abstract":"Ornamental production in the U.S. spans an estimated 267,000 hectares and uses approximately 169,000 m3 of water yearly. Ornamental growers, particularly those with air-closed systems, are interested in implementing reduced irrigation technologies like sensor-controlled irrigation (SCI) systems to improve water use efficiency in response to water scarcity. To evaluate phytobiome impacts, we utilized an Illumina metabarcoding approach to characterize changes in fungal and oomycete rhizosphere communities of commercially grown poinsettia, complementing previous studies of single-pathogen impacts. Minor reductions (from 54% volumetric water content [VWC] to 50% VWC) did not have large effects on rhizosphere fungal community structure, but shifts in plant health status (symptomatic/ asymptomatic) correlated with shifts in fungal diversity and evenness, with an increased abundance of several taxa including Plectosphaerella cucumerina, and Fusarium sp. in symptomatic plants. Further reductions in irrigation (45% VWC, 35% VWC and 25% VWC) did not affect overall fungal community composition, but the lowest VWC increased the abundance of potential root rot pathogens like Phoma multirostrata and Plectosphaerella cucumerina. Reduced irrigation volumes decreased oomycete diversity and abundance of several known pathogens in the Phytophthora genus. Addition of a bacterial product (Companion®) with putative pathogen suppressive and drought-tolerance enhancing effects had no influence on fungal community composition or abundance, but increased abundance of some oomycete species at 45% VWC. This study shows that adoption of reduced irrigation may have greater effects on fungal vs. oomycete taxa in the system, with consistent patterns of fungal enhancement, including putative fungal pathogens and beneficial organisms, and oomycete suppression.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46132551","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}

引用次数: 1

Amplicon sequencing of Fusarium translation elongation factor 1α reveals that soil communities of Fusarium species are resilient to disturbances caused by crop and tillage practices 镰刀菌翻译延伸因子1α的扩增子测序表明，镰刀菌物种的土壤群落对作物和耕作方式造成的干扰具有抵抗力

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-02-16 DOI: 10.1094/pbiomes-09-21-0053-r

Peter M. Henry, S. I. Koehler, S. Kaur, L. Epstein, Jeffery Mitchell, T. Gordon, J. Leveau

{"title":"Amplicon sequencing of Fusarium translation elongation factor 1α reveals that soil communities of Fusarium species are resilient to disturbances caused by crop and tillage practices","authors":"Peter M. Henry, S. I. Koehler, S. Kaur, L. Epstein, Jeffery Mitchell, T. Gordon, J. Leveau","doi":"10.1094/pbiomes-09-21-0053-r","DOIUrl":"https://doi.org/10.1094/pbiomes-09-21-0053-r","url":null,"abstract":"The fungal genus Fusarium contains plant pathogens, mutualists, and commensalists. As non-pathogenic Fusarium strains can contribute to disease-suppression in soil by competition or induced plant resistance, identifying factors that influence the abundance of non-pathogenic strains could lead to strategies that enhance plant-beneficial interactions and deter pathogen invasion. We developed a Fusarium-specific translation elongation factor 1α (EF-1α) high-throughput amplicon-sequencing method with sub-species resolution. Newly designed primers enabled reads to be joined for improved quality metrics after Illumina MiSeq sequencing. By including the ‘oligotyping’ program in our bioinformatic workflow, we reconstructed Fusarium EF-1α haplotypes with 100% accuracy. We conducted simulated crop rotation experiments in soil infested with the strawberry pathogen F. oxysporum f. sp. fragariae (Fof) and the following treatments: strawberry, blackberry, raspberry, lettuce, broccoli, and fallow. We profiled root Fusarium communities with EF-1α amplicons and observed that non-pathogenic strains of F. oxysporum did not colonize crops uniformly; some strains exhibited asymptomatic host preferences. In susceptible strawberry roots, >90% of sequences corresponded to Fof. Bulk soil communities of Fusarium were remarkably stable and had minimal treatment-dependent effects after one year. Similarly, in a long-term agricultural research experiment, 18 years of conservation tillage and cover cropping did not lead to bulk soil Fusarium communities that were significantly different than controls. While the roots of rotation crops can augment the abundance of non-pathogenic F. oxysporum strains, their abundance in bulk soil is unlikely to be altered after a single year. Climate and soil physicochemical properties may have a greater effect on Fusarium community structure.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43591311","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}

引用次数: 1

Evaluation of different phyllosphere sample types for parallel metabarcoding of Fungi and Oomycetes in Vitis vinifera 葡萄不同层球样品类型对真菌和卵菌平行元条形码的评价

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2022-02-11 DOI: 10.1094/pbiomes-11-21-0072-sc

F. H. Behrens, M. Fischer

{"title":"Evaluation of different phyllosphere sample types for parallel metabarcoding of Fungi and Oomycetes in Vitis vinifera","authors":"F. H. Behrens, M. Fischer","doi":"10.1094/pbiomes-11-21-0072-sc","DOIUrl":"https://doi.org/10.1094/pbiomes-11-21-0072-sc","url":null,"abstract":"Metabarcoding is an effective and cost efficient approach to study environmental microbiomes and has become a standard method in studying microbial community structures and relative species abundance. In grapevine research on leaf microbial communities, two kinds of sample types, either leaf wash sediments representing the phyllosphere microbiome from leaf surfaces, or leaf tissue samples, e.g. leaf disks, including phyllosphere and endosphere microorganisms, are used to characterize leaf microbiomes. The goal of this study was to analyze the advantages and disadvantages of these sample preparation methods for the characterization of the phyllosphere microbiome by fungal metabarcoding with both sample types being processed from the exact same set of leaves. We used a metabarcoding strategy which is capable of detecting Fungi and Oomycetes facilitating the parallel analysis of these communities. At each sampling time point species richness was shown to be higher in leaf wash samples and differences in the community structure between samples was smaller for this sample type, as well. Furthermore, by comparing read count abundance to qPCR measured relative proportions of selected amplicon sequence variants (ASVs), a higher congruence was observed for leaf wash samples. Therefore, metabarcoding analyses of leaf samples using leaf wash sediments outperforms analyses using leaf disks and should be applied to characterize phyllosphere fungal communities. As a second goal we show that the direct comparison of metabarcoding libraries of both sample types prepared from the exact same set of leaves also provides a new strategy to identify potentially not culturable endophytes.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44749055","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}

引用次数: 3