Pub Date : 2024-07-08DOI: 10.1094/pbiomes-02-24-0023-r
Betsy A. Alford, Dagnachew Bekele, Sultan Yimer, Amna Fayyaz, N. Carrasquilla-Garcia, Peter L Chang, Calen Badger, Anandkumar Surendrarao, Eric J. B. von Wettberg, M. F. H. Munis, Kassahun Tesfaye, A. Fikre, Douglas R. Cook
Classical approaches to plant disease diagnosis assume a single pathogen/single disease paradigm. Here we revisit the presumed role of Fusarium oxysporum as the causal agent of wilting and yellowing of chickpea plants on small holder farms in Ethiopia. Contrary to expectations, detection of Fusarium DNA using conserved PCR primers failed to associate the pathogen with symptomatic plants. Instead, culture-independent sequencing of microbial communities nominated unexpected pathogens and revealed patchiness in the assembly of common microbial consortia. Surprisingly, tests of differential enrichment identified Phytophthora as the most common disease-associated taxon. More generally, across all field sites, multi-level pattern analysis identified indicator taxa whose patterns of co-occurrence demarcate discrete microbial communities and are consistent with a range of specific interactions, including mutualism and antagonism. Taken together, these data indicate that soil-borne chickpea disease in Ethiopia has heterogeneous origins, and that despite decades of emphasis and disease resistance breeding, the role of Fusarium as the frequent agent of chickpea disease in Ethiopia remains enigmatic.
植物病害诊断的传统方法假定病原体单一/病害单一。在此，我们重新审视了埃塞俄比亚小农场鹰嘴豆枯萎和黄化的病原镰刀菌的假定作用。与预期相反，使用保守的 PCR 引物检测镰刀菌 DNA 未能将病原体与有症状的植株联系起来。相反，对微生物群落进行的独立培养测序发现了意想不到的病原体，并揭示了常见微生物群落组装的零散性。令人惊讶的是，差异富集测试发现疫霉菌是最常见的病害相关类群。更广泛地说，在所有田间地点，多层次模式分析确定了指标类群，其共同出现的模式划分了离散的微生物群落，并与一系列特定的相互作用相一致，包括互作和拮抗。总之，这些数据表明，埃塞俄比亚的土传鹰嘴豆病有不同的起源，尽管几十年来一直在强调和培育抗病性，但镰刀菌作为埃塞俄比亚鹰嘴豆病的常见病原体，其作用仍然是个谜。
{"title":"Microbial community analysis offers insight into the complex origins of plant disease in a smallholder farm context","authors":"Betsy A. Alford, Dagnachew Bekele, Sultan Yimer, Amna Fayyaz, N. Carrasquilla-Garcia, Peter L Chang, Calen Badger, Anandkumar Surendrarao, Eric J. B. von Wettberg, M. F. H. Munis, Kassahun Tesfaye, A. Fikre, Douglas R. Cook","doi":"10.1094/pbiomes-02-24-0023-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-24-0023-r","url":null,"abstract":"Classical approaches to plant disease diagnosis assume a single pathogen/single disease paradigm. Here we revisit the presumed role of Fusarium oxysporum as the causal agent of wilting and yellowing of chickpea plants on small holder farms in Ethiopia. Contrary to expectations, detection of Fusarium DNA using conserved PCR primers failed to associate the pathogen with symptomatic plants. Instead, culture-independent sequencing of microbial communities nominated unexpected pathogens and revealed patchiness in the assembly of common microbial consortia. Surprisingly, tests of differential enrichment identified Phytophthora as the most common disease-associated taxon. More generally, across all field sites, multi-level pattern analysis identified indicator taxa whose patterns of co-occurrence demarcate discrete microbial communities and are consistent with a range of specific interactions, including mutualism and antagonism. Taken together, these data indicate that soil-borne chickpea disease in Ethiopia has heterogeneous origins, and that despite decades of emphasis and disease resistance breeding, the role of Fusarium as the frequent agent of chickpea disease in Ethiopia remains enigmatic.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":" 1185","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141668925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.1094/pbiomes-11-23-0121-r
Christopher Liakos, Veruskha Ibanez, P. Lebre, Mike L. Derie, Jacquie van der Waals, Lindsey du Toit, B. Dutta, Brian Kvitko, D. A. Cowan, Teresa A. Coutinho
Microbes occur in complex communities within plants as endophytes and establish a network of interactions that can influence plant health positively or negatively. Positive interactions may be synergistic and confer abiotic and biotic stress tolerance. The aim of this study was to identify bacteria and viruses present in storage onion bulbs that were symptomatic and asymptomatic for bacterial bulb rot, from crops grown in Georgia and Washington states; and to assess their potential role in the bulbs based on functions of bacterial and viral genes detected. DNA was extracted from nine asymptomatic bulbs and nine bulbs displaying symptoms of bacterial bulb rot and subjected to 16S rRNA amplicon sequencing and Metagenomic Assembled Genome (MAG) analysis. The Illumina platform was used to sequence the hypervariable region (V3-V4) of the 16S rRNA gene. The 16S rRNA amplicon profiling revealed the presence of numerous bacteria including potential onion pathogens in the genera Panteoa and Burkholderia. MAG assembly identified P. agglomerans. B. gladioli and B. cepacia, known bulb rot pathogens, including genes linked to fitness and those involved in the Type II and III secretion systems. Eighty-nine unique viral genomes were identified, of which 67 could be classified taxonomically. The bacterial and viral genomes differed significantly in asymptomatic versus symptomatic bulbs. Viral genomes showed evidence of auxiliary metabolic genes (AMGs), including genes involved in fitness and pathogenicity to bacterial hosts. The bulbs hosted endophytic bacteria and viruses, some of which were potentially beneficial, and others potentially pathogenic to onion or as hosts to bacteriophages.
微生物作为内生菌存在于植物体内的复杂群落中，并建立了一个可对植物健康产生积极或消极影响的相互作用网络。积极的相互作用可能会产生协同效应，并赋予非生物和生物胁迫耐受性。本研究旨在从佐治亚州和华盛顿州种植的有症状和无症状的贮藏洋葱球茎中鉴定细菌和病毒，并根据检测到的细菌和病毒基因的功能评估它们在球茎中的潜在作用。从 9 个无症状鳞茎和 9 个出现细菌性鳞茎腐烂症状的鳞茎中提取 DNA，并进行 16S rRNA 扩增子测序和元基因组组装基因组（MAG）分析。采用 Illumina 平台对 16S rRNA 基因的超变异区（V3-V4）进行测序。16S rRNA 扩增子分析表明存在大量细菌，包括 Panteoa 属和 Burkholderia 属中的潜在洋葱病原体。MAG 组装确定了 P. agglomerans.B. gladioli 和 B. cepacia，它们是已知的球茎腐烂病病原体，包括与适应性有关的基因以及参与 II 型和 III 型分泌系统的基因。共鉴定出 89 个独特的病毒基因组，其中 67 个可按分类学进行分类。无症状球茎与有症状球茎的细菌和病毒基因组差异显著。病毒基因组显示了辅助代谢基因（AMG），包括与细菌宿主的适应性和致病性有关的基因。鳞茎中寄生有内生细菌和病毒，其中一些可能对洋葱有益，另一些则可能对洋葱致病或作为噬菌体的宿主。
{"title":"The bacterial and viral communities associated with onion bacterial bulb rot","authors":"Christopher Liakos, Veruskha Ibanez, P. Lebre, Mike L. Derie, Jacquie van der Waals, Lindsey du Toit, B. Dutta, Brian Kvitko, D. A. Cowan, Teresa A. Coutinho","doi":"10.1094/pbiomes-11-23-0121-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-23-0121-r","url":null,"abstract":"Microbes occur in complex communities within plants as endophytes and establish a network of interactions that can influence plant health positively or negatively. Positive interactions may be synergistic and confer abiotic and biotic stress tolerance. The aim of this study was to identify bacteria and viruses present in storage onion bulbs that were symptomatic and asymptomatic for bacterial bulb rot, from crops grown in Georgia and Washington states; and to assess their potential role in the bulbs based on functions of bacterial and viral genes detected. DNA was extracted from nine asymptomatic bulbs and nine bulbs displaying symptoms of bacterial bulb rot and subjected to 16S rRNA amplicon sequencing and Metagenomic Assembled Genome (MAG) analysis. The Illumina platform was used to sequence the hypervariable region (V3-V4) of the 16S rRNA gene. The 16S rRNA amplicon profiling revealed the presence of numerous bacteria including potential onion pathogens in the genera Panteoa and Burkholderia. MAG assembly identified P. agglomerans. B. gladioli and B. cepacia, known bulb rot pathogens, including genes linked to fitness and those involved in the Type II and III secretion systems. Eighty-nine unique viral genomes were identified, of which 67 could be classified taxonomically. The bacterial and viral genomes differed significantly in asymptomatic versus symptomatic bulbs. Viral genomes showed evidence of auxiliary metabolic genes (AMGs), including genes involved in fitness and pathogenicity to bacterial hosts. The bulbs hosted endophytic bacteria and viruses, some of which were potentially beneficial, and others potentially pathogenic to onion or as hosts to bacteriophages.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"29 48","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141270672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-11DOI: 10.1094/pbiomes-01-24-0011-r
David J. Burke, Caleb Lumsden, Sarah R. Carrino-Kyker, Juliana S. Medeiros, Sharon Danielson
Tsuga canadensis (Eastern hemlock) is an important tree species in North America, but it has been subject to threats from invasive insects such as Adelges tsugae (hemlock woolly adelgid-A. tsugae). A. tsugae is native to Asia and Tsuga species from Asia are typically resistant to this insect. In this study, we examined the phyllosphere microbiome of two hemlock species native to North America and susceptible to A. tsugae (T. canadensis and T. caroliniana), as well as two species native to Asia and resistant to A. tsugae (T. chinensis and T. diversifolia). Since pesticide application is often used to treat native Tsuga species impacted by A. tsugae, we also examined the response of the microbiome and overall plant physiology to the pesticide dinotefuran in T. canadensis. We found significant differences in the bacterial and fungal microbiome among the four species of Tsuga. Dinotefuran also significantly affected bacterial communities, but not fungal communities, of T. canadensis. The genus Methylobacterium, which uses methanol produced during plant cell elongation and growth, was a significant indicator of trees not subject to dinotefuran. This suggests that dinotefuran may have reduced cell growth in treated trees. Despite changes in the microbiome, dinotefuran application did not significantly affect plant physiology; however, the coefficient of variation (CV) in dinotefuran treated trees was larger than non-treated trees. Our results suggest that the microbiome could play a role in mediating insect resistance in Tsuga species, and that pesticide application could affect the phyllosphere microbiome with implications for plant growth and resistance.
Tsuga canadensis（东方铁杉）是北美的一个重要树种，但它一直受到入侵昆虫的威胁，如 Adelges tsugae（铁杉毛毡蝽-A. tsugae）。A. tsugae原产于亚洲，而亚洲的津贺树种通常对这种昆虫具有抵抗力。在这项研究中，我们考察了两个原产于北美、易受 A. tsugae 侵害的铁杉树种（T. canadensis 和 T. caroliniana）以及两个原产于亚洲、对 A. tsugae 有抗性的树种（T. chinensis 和 T. diversifolia）的植物叶球微生物组。由于施用杀虫剂经常被用来处理受 A. tsugae 影响的土生津贺物种，我们还研究了土生津贺的微生物组和整体植物生理对杀虫剂敌克松的反应。我们发现，四种津贺属植物的细菌和真菌微生物组存在明显差异。克百威还对土杉的细菌群落产生了重大影响，但对真菌群落没有影响。利用植物细胞伸长和生长过程中产生的甲醇的甲基杆菌属是未受到克百威影响的树木的一个重要指标。这表明，克百威可能减少了经处理树木的细胞生长。尽管微生物组发生了变化，但施用克百威并没有对植物生理产生显著影响；不过，施用克百威的树木的变异系数（CV）大于未施用的树木。我们的研究结果表明，微生物组可能在介导津贺树种的抗虫性方面发挥作用，施用杀虫剂可能会影响叶球微生物组，从而对植物的生长和抗性产生影响。
{"title":"The phyllosphere microbiome in Tsuga canadensis: Relationships with resistance to the insect Adelges tsugae and effects of the pesticide dinotefuran","authors":"David J. Burke, Caleb Lumsden, Sarah R. Carrino-Kyker, Juliana S. Medeiros, Sharon Danielson","doi":"10.1094/pbiomes-01-24-0011-r","DOIUrl":"https://doi.org/10.1094/pbiomes-01-24-0011-r","url":null,"abstract":"Tsuga canadensis (Eastern hemlock) is an important tree species in North America, but it has been subject to threats from invasive insects such as Adelges tsugae (hemlock woolly adelgid-A. tsugae). A. tsugae is native to Asia and Tsuga species from Asia are typically resistant to this insect. In this study, we examined the phyllosphere microbiome of two hemlock species native to North America and susceptible to A. tsugae (T. canadensis and T. caroliniana), as well as two species native to Asia and resistant to A. tsugae (T. chinensis and T. diversifolia). Since pesticide application is often used to treat native Tsuga species impacted by A. tsugae, we also examined the response of the microbiome and overall plant physiology to the pesticide dinotefuran in T. canadensis. We found significant differences in the bacterial and fungal microbiome among the four species of Tsuga. Dinotefuran also significantly affected bacterial communities, but not fungal communities, of T. canadensis. The genus Methylobacterium, which uses methanol produced during plant cell elongation and growth, was a significant indicator of trees not subject to dinotefuran. This suggests that dinotefuran may have reduced cell growth in treated trees. Despite changes in the microbiome, dinotefuran application did not significantly affect plant physiology; however, the coefficient of variation (CV) in dinotefuran treated trees was larger than non-treated trees. Our results suggest that the microbiome could play a role in mediating insect resistance in Tsuga species, and that pesticide application could affect the phyllosphere microbiome with implications for plant growth and resistance.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"37 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140716582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01DOI: 10.1094/pbiomes-11-23-0118-r
S. Mathew, Aditya Jeevannavar, M. Helander, Manu Tamminen, Pere Puigbò, Miia Rainio, K. Saikkonen, B. Fuchs
Glyphosate, the active ingredient of glyphosate-based herbicide (GBH) controls the growth of weeds by inhibiting shikimate pathway, thereby interrupting amino acid biosynthesis in plants. However, several microbes have shikimate pathway and the action of glyphosate on these non-target organisms are ignored. Along with other agrochemicals such as phosphate fertilizers, the action of GBH is further complicated, often varying their mode of action depending on soil type or plant species. To address the impact of GBH and phosphate fertilizer, we simulated agricultural application of GBH and phosphate fertilizer in a field study, investigating the composition of endophytic microbial communities and correlation of phytohormone concentrations with the microbial diversity of potato (Solanum tuberosum). In leaves, glyphosate residues in soil from GBH treatment alone and in combination with phosphate significantly shifted bacterial community whereas phosphate alone and in combination with glyphosate significantly altered the composition of fungal community. There were no significant changes in microbial communities in roots and tubers. Plants treated with GBH showed higher ratios of potentially glyphosate-resistant bacteria, with Xanthomonadaceae and Moraxallaceae being more abundant. Additionally, phytohormone concentrations showed various correlations with bacterial and fungal diversity in different treatments. The study highlights the impact of GBH residues in soil, particularly in combination with phosphate fertilizers on the composition of plant-associated microbial communities. Together with changes in phytohormone concentrations, plant health may be affected. Moreover, future studies could provide insights to whether these agrochemicals influence plant microbiome, leading to changes in phytohormones or vice-versa.
{"title":"Glyphosate residues in soil and phosphate fertilizer affect foliar endophytic microbial community composition and phytohormone levels in potato","authors":"S. Mathew, Aditya Jeevannavar, M. Helander, Manu Tamminen, Pere Puigbò, Miia Rainio, K. Saikkonen, B. Fuchs","doi":"10.1094/pbiomes-11-23-0118-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-23-0118-r","url":null,"abstract":"Glyphosate, the active ingredient of glyphosate-based herbicide (GBH) controls the growth of weeds by inhibiting shikimate pathway, thereby interrupting amino acid biosynthesis in plants. However, several microbes have shikimate pathway and the action of glyphosate on these non-target organisms are ignored. Along with other agrochemicals such as phosphate fertilizers, the action of GBH is further complicated, often varying their mode of action depending on soil type or plant species. To address the impact of GBH and phosphate fertilizer, we simulated agricultural application of GBH and phosphate fertilizer in a field study, investigating the composition of endophytic microbial communities and correlation of phytohormone concentrations with the microbial diversity of potato (Solanum tuberosum). In leaves, glyphosate residues in soil from GBH treatment alone and in combination with phosphate significantly shifted bacterial community whereas phosphate alone and in combination with glyphosate significantly altered the composition of fungal community. There were no significant changes in microbial communities in roots and tubers. Plants treated with GBH showed higher ratios of potentially glyphosate-resistant bacteria, with Xanthomonadaceae and Moraxallaceae being more abundant. Additionally, phytohormone concentrations showed various correlations with bacterial and fungal diversity in different treatments. The study highlights the impact of GBH residues in soil, particularly in combination with phosphate fertilizers on the composition of plant-associated microbial communities. Together with changes in phytohormone concentrations, plant health may be affected. Moreover, future studies could provide insights to whether these agrochemicals influence plant microbiome, leading to changes in phytohormones or vice-versa.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"181 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140758840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-18DOI: 10.1094/pbiomes-02-24-0014-r
Josiah Marquez, A. Hajihassani
Plant-parasitic nematodes (PPNs) can be found deep in the soil profile, compounding nematode management decisions and detection. This study aimed to understand how seasonal fluctuations in edaphic factors are associated with the vertical distribution of PPNs in south Georgia’s vegetable cropping systems. Five-core composite soil samples were taken monthly (March 2020 to February 2022) at three random locations in six vegetable fields. Fields represented 4 cropping systems (vegetable plasticulture, bare-ground cucumber, and plastic-bed watermelon rotation) and two regions (north and south) sampled from five 15-cm strata (0-15 cm, 15-30 cm, 30-45 cm, 45-60 cm, and 60-75 cm). Only soil temperatures and precipitation had seasonal fluctuations, while the other edaphic factors were vertically stratified. Latitude and stratum had the strongest associations with the nematode composition, showing a clear separation between the north and south regions. Variations in soil texture, porosity, moisture, and PPN vertical distribution suggest that the illuvial zone in the north region was the main factor in differences observed between regions and strata. Seasonal fluctuations in vertical distribution were found among Meloidogyne incognita and Nanidorus spp. Higher abundances of deep-dwelling PPNs were limited to the south region in the winter for M. incognita and summer and winter for Nanidorus spp., probably due to the illuvial zone barrier in the north region. Since most root-knot nematodes dwell at ≤ 30 cm during the summer, fumigants/nematicide applications are recommended during this season to minimize the risk of deep-dwelling escapees.
{"title":"Seasonal fluctuations in plant-parasitic nematode vertical distributions and their interactions with edaphic factors in vegetable fields of South Georgia, USA","authors":"Josiah Marquez, A. Hajihassani","doi":"10.1094/pbiomes-02-24-0014-r","DOIUrl":"https://doi.org/10.1094/pbiomes-02-24-0014-r","url":null,"abstract":"Plant-parasitic nematodes (PPNs) can be found deep in the soil profile, compounding nematode management decisions and detection. This study aimed to understand how seasonal fluctuations in edaphic factors are associated with the vertical distribution of PPNs in south Georgia’s vegetable cropping systems. Five-core composite soil samples were taken monthly (March 2020 to February 2022) at three random locations in six vegetable fields. Fields represented 4 cropping systems (vegetable plasticulture, bare-ground cucumber, and plastic-bed watermelon rotation) and two regions (north and south) sampled from five 15-cm strata (0-15 cm, 15-30 cm, 30-45 cm, 45-60 cm, and 60-75 cm). Only soil temperatures and precipitation had seasonal fluctuations, while the other edaphic factors were vertically stratified. Latitude and stratum had the strongest associations with the nematode composition, showing a clear separation between the north and south regions. Variations in soil texture, porosity, moisture, and PPN vertical distribution suggest that the illuvial zone in the north region was the main factor in differences observed between regions and strata. Seasonal fluctuations in vertical distribution were found among Meloidogyne incognita and Nanidorus spp. Higher abundances of deep-dwelling PPNs were limited to the south region in the winter for M. incognita and summer and winter for Nanidorus spp., probably due to the illuvial zone barrier in the north region. Since most root-knot nematodes dwell at ≤ 30 cm during the summer, fumigants/nematicide applications are recommended during this season to minimize the risk of deep-dwelling escapees.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"347 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140232614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-15DOI: 10.1094/pbiomes-01-24-0006-r
Maya Moshe, Omer Frenkel, Noa Sela, Chagai Davidovich, Hildah Amutuhaire, E. Banin, E. Cytryn
Background: Bacterial biocontrol agents that antagonize soilborne pathogens are increasingly considered as alternatives to chemical pesticides, but their in-vivo efficacy is often inconsistent, restricting commercial use. The efficacy of a biocontrol agent can depend on rhizosphere competence and its interaction with native microbiomes, which can effect ecosystem functioning. This study investigated the capacity of a Bacillus cereus sensu lato (Bcsl) biocontrol strain (S-25) to persist on roots and in the rhizosphere of cucumber, and evaluated its impact on bacterial and fungal community composition in the rhizosphere, in the absence and presence of Rhizoctonia solani, the causative agent of damping-off disease in young seedlings. Results: Following amendment, S-25 abundance in the cucumber rhizosphere decreased by two orders of magnitude, but remained relatively high for the duration of the experiment, in contrast to the root surface where it was not detected. Amendment with S-25 significantly reduced disease incidence caused by R. solani, without reducing the relative abundance of the fungal pathogen. Interestingly, R. solani did not substantially alter the rhizosphere microbial community, whereas S-25 reduced bacterial diversity and facilitated a shift in community composition, with increased relative abundance of Gram-positive bacterium and reduced abundance of Gram-negatives. Conclusions: Collectively, this study provides important insights into the mode of persistence of biocontrol agents, and their effect on native microbiomes in the rhizosphere of pathogen-inoculated plants. It demonstrates that amendment can significantly alter local microbiomes, and suggests that optimizing amendment regimes or selecting strains with higher rhizosphere competence can enhance future biocontrol agents.
{"title":"Persistence and microbiome modification in Rhizoctonia solani inoculated rhizosphere following amendment of a Bacillus biocontrol agent","authors":"Maya Moshe, Omer Frenkel, Noa Sela, Chagai Davidovich, Hildah Amutuhaire, E. Banin, E. Cytryn","doi":"10.1094/pbiomes-01-24-0006-r","DOIUrl":"https://doi.org/10.1094/pbiomes-01-24-0006-r","url":null,"abstract":"Background: Bacterial biocontrol agents that antagonize soilborne pathogens are increasingly considered as alternatives to chemical pesticides, but their in-vivo efficacy is often inconsistent, restricting commercial use. The efficacy of a biocontrol agent can depend on rhizosphere competence and its interaction with native microbiomes, which can effect ecosystem functioning. This study investigated the capacity of a Bacillus cereus sensu lato (Bcsl) biocontrol strain (S-25) to persist on roots and in the rhizosphere of cucumber, and evaluated its impact on bacterial and fungal community composition in the rhizosphere, in the absence and presence of Rhizoctonia solani, the causative agent of damping-off disease in young seedlings. Results: Following amendment, S-25 abundance in the cucumber rhizosphere decreased by two orders of magnitude, but remained relatively high for the duration of the experiment, in contrast to the root surface where it was not detected. Amendment with S-25 significantly reduced disease incidence caused by R. solani, without reducing the relative abundance of the fungal pathogen. Interestingly, R. solani did not substantially alter the rhizosphere microbial community, whereas S-25 reduced bacterial diversity and facilitated a shift in community composition, with increased relative abundance of Gram-positive bacterium and reduced abundance of Gram-negatives. Conclusions: Collectively, this study provides important insights into the mode of persistence of biocontrol agents, and their effect on native microbiomes in the rhizosphere of pathogen-inoculated plants. It demonstrates that amendment can significantly alter local microbiomes, and suggests that optimizing amendment regimes or selecting strains with higher rhizosphere competence can enhance future biocontrol agents.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"8 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140239365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-15DOI: 10.1094/pbiomes-11-23-0122-r
Blaise Jumbam, Zahra-Bita Amiri, L. Dandurand, Inga A. Zasada, M. C. Aime
Plant-parasitic nematodes are important pathogens of agricultural crops. Of particular importance are cyst nematode species of Globodera and Heterodera which remain a major constraint to global production of crops such as potato, soybean, and wheat. Recent restrictions on the use of some synthetic nematicides has created an urgent need for alternative methods of controlling cyst nematodes. This project aimed to: (i) document fungi found associated cyst nematodes, (ii) determine if the fungi associated with cyst nematodes are dependent on growth conditions or nematode species, (iii) identify core mycobiomes for each of the eight cyst nematode species, (iv) identify the core mycobiome across all cyst nematode species studied, and (v) determine if the fungi associated with Globodera species are structured geographically. Sixty cyst nematode populations from eight species – Globodera sp., G. ellingtonae, G. pallida, G. rostochiensis, H. avenae, H. carotae, H. glycines, and H. schachtii – were collected from several geographic locations globally and screened for fungi using both culture-dependent and -independent methods. The core mycobiome was determined for each species. In total, 744 species of fungi were found associated with cyst nematodes. Fungal species shared across all cyst nematode species included Pochonia sp., Sporothrix sp., Neocosmospora solani, Exophiala equina, Mortierella sp., and Sarocladium kiliense. The core mycobiomes were conserved between cyst nematode species irrespective of their geographic origin. Cyst nematodes collected from the field or from greenhouse cultures also recruited similar core mycobiomes. These findings could be relevant when choosing fungi to evaluate as biocontrol agents against cyst nematodes.
{"title":"Analyses of fungal communities from culture-dependent and -independent studies reveal novel mycobiomes associated with Globodera and Heterodera species","authors":"Blaise Jumbam, Zahra-Bita Amiri, L. Dandurand, Inga A. Zasada, M. C. Aime","doi":"10.1094/pbiomes-11-23-0122-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-23-0122-r","url":null,"abstract":"Plant-parasitic nematodes are important pathogens of agricultural crops. Of particular importance are cyst nematode species of Globodera and Heterodera which remain a major constraint to global production of crops such as potato, soybean, and wheat. Recent restrictions on the use of some synthetic nematicides has created an urgent need for alternative methods of controlling cyst nematodes. This project aimed to: (i) document fungi found associated cyst nematodes, (ii) determine if the fungi associated with cyst nematodes are dependent on growth conditions or nematode species, (iii) identify core mycobiomes for each of the eight cyst nematode species, (iv) identify the core mycobiome across all cyst nematode species studied, and (v) determine if the fungi associated with Globodera species are structured geographically. Sixty cyst nematode populations from eight species – Globodera sp., G. ellingtonae, G. pallida, G. rostochiensis, H. avenae, H. carotae, H. glycines, and H. schachtii – were collected from several geographic locations globally and screened for fungi using both culture-dependent and -independent methods. The core mycobiome was determined for each species. In total, 744 species of fungi were found associated with cyst nematodes. Fungal species shared across all cyst nematode species included Pochonia sp., Sporothrix sp., Neocosmospora solani, Exophiala equina, Mortierella sp., and Sarocladium kiliense. The core mycobiomes were conserved between cyst nematode species irrespective of their geographic origin. Cyst nematodes collected from the field or from greenhouse cultures also recruited similar core mycobiomes. These findings could be relevant when choosing fungi to evaluate as biocontrol agents against cyst nematodes.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"15 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140240315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-08DOI: 10.1094/pbiomes-08-23-0078-r
C. McGehee, Artemis S. Louyakis, R. Raudales
The spatial distribution and diversity of plant pathogens and other microbial communities in commercial operations is the first step in identifying critical control points where crops may be at risk of disease. Our objective was to characterize the spatial variation of oomycete pathogens and bacteria across the production system of a greenhouse producing lettuce in hydroponics. We utilized DNA metabarcoding to identify oomycetes and 16S rRNA gene sequencing of bacteria from different production stages and sample types (surfaces, solutions, and roots) collected from a commercial greenhouse producing lettuce in deep-water culture. Pythium was the genus with the highest relative abundance (41 - 100%) across all production stages. Pythium dissotocum was detected in most samples, except for sowing and seeding surfaces and municipal water where Pythium myriotylum was the most abundant species. Oomycete communities showed distinct clustering by production stages and sample types, where sowing and seedling surfaces and municipal water were separated from the rest. Proteobacteria had the highest relative abundance in the surfaces at the sowing (98%) and seeding (85%) stages. Municipal water was the only sample with less than 20% relative abundance of Proteobacteria and dominated by Cyanobacteria. Negative correlations between Pythium and 13 bacteria genera points to potential antagonists in hydroponics that should be further studied. Mapping the spatial variation of oomycetes and bacterial communities in a commercial greenhouse indicates that production stage and sample type influence microbial composition and potentially the risk to disease.
{"title":"Spatial variation of oomycetes and bacteria on surfaces, solutions, and plants from a commercial hydroponic greenhouse","authors":"C. McGehee, Artemis S. Louyakis, R. Raudales","doi":"10.1094/pbiomes-08-23-0078-r","DOIUrl":"https://doi.org/10.1094/pbiomes-08-23-0078-r","url":null,"abstract":"The spatial distribution and diversity of plant pathogens and other microbial communities in commercial operations is the first step in identifying critical control points where crops may be at risk of disease. Our objective was to characterize the spatial variation of oomycete pathogens and bacteria across the production system of a greenhouse producing lettuce in hydroponics. We utilized DNA metabarcoding to identify oomycetes and 16S rRNA gene sequencing of bacteria from different production stages and sample types (surfaces, solutions, and roots) collected from a commercial greenhouse producing lettuce in deep-water culture. Pythium was the genus with the highest relative abundance (41 - 100%) across all production stages. Pythium dissotocum was detected in most samples, except for sowing and seeding surfaces and municipal water where Pythium myriotylum was the most abundant species. Oomycete communities showed distinct clustering by production stages and sample types, where sowing and seedling surfaces and municipal water were separated from the rest. Proteobacteria had the highest relative abundance in the surfaces at the sowing (98%) and seeding (85%) stages. Municipal water was the only sample with less than 20% relative abundance of Proteobacteria and dominated by Cyanobacteria. Negative correlations between Pythium and 13 bacteria genera points to potential antagonists in hydroponics that should be further studied. Mapping the spatial variation of oomycetes and bacterial communities in a commercial greenhouse indicates that production stage and sample type influence microbial composition and potentially the risk to disease.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139851580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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