Phytobiomes Journal最新文献_第2页

Spatial variation of oomycetes and bacteria on surfaces, solutions, and plants from a commercial hydroponic greenhouse 商业水培温室表面、溶液和植物上的真菌和细菌的空间变化

Phytobiomes Journal Pub Date : 2024-02-08 DOI: 10.1094/pbiomes-08-23-0078-r

C. McGehee, Artemis S. Louyakis, R. Raudales

{"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":" 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139791628","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}

引用次数: 0

Incorporating culture-independent methods to identify net syndrome-associated Fusarium species in peanuts 采用独立于培养的方法确定花生中与净综合征有关的镰刀菌菌种

Phytobiomes Journal Pub Date : 2024-02-01 DOI: 10.1094/pbiomes-10-23-0111-r

Kobi Sudakov, H. Yasuor, Amit Kumar Jaiswal, Gideon Mordukhovich, Oren Buchshtab, D. Minz, Omer Frenkel

{"title":"Incorporating culture-independent methods to identify net syndrome-associated Fusarium species in peanuts","authors":"Kobi Sudakov, H. Yasuor, Amit Kumar Jaiswal, Gideon Mordukhovich, Oren Buchshtab, D. Minz, Omer Frenkel","doi":"10.1094/pbiomes-10-23-0111-r","DOIUrl":"https://doi.org/10.1094/pbiomes-10-23-0111-r","url":null,"abstract":"Peanuts (Arachis hypogaea L.) are of significant agricultural importance due to their versatile uses, providing a valuable source of edible oil and protein-rich food products, and serving in industrial applications. Peanuts are susceptible to various diseases, one of them being net syndrome, a poorly understood threat triggered by an undefined causal agent, with symptoms including black coloring and lesions of the peanut pod which affect product quality. In this study, amplicon sequencing was harnessed to explore the fungal and bacterial populations associated with the syndrome. Using this approach, we identified a specific amplicon sequence variant (ASV) of Fusarium sp., that demonstrated a significant correlation with the presence of net syndrome symptoms in both young and mature peanuts. This finding was further validated by Koch's postulate testing, including isolation, cultivation, and application of this strain to corroborate its involvement in the net syndrome in peanuts. Our findings contribute to a better understanding of the interactions between peanuts and their microbial communities, and to the identification of previously undetermined agent involved in net syndrome and the etiology of the disease.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"56 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139872530","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}

引用次数: 0

Old foe, new host: Epidemiology, genetic diversity and pathogenic characterization of maize streak virus in rice fields from Burkina Faso 老敌人，新宿主：布基纳法索稻田中玉米条纹病毒的流行病学、遗传多样性和致病特征

Phytobiomes Journal Pub Date : 2024-02-01 DOI: 10.1094/pbiomes-08-23-0085-fi

N. Fouad, M. Barro, M. Bangratz, D. Sérémé, D. Filloux, Emmanuel Fernandez, Charlotte Julian, Nignan Saïbou, Abalo Itolou Kassankogno, Abdoul Kader Guigma, P. Roumagnac, I. Wonni, C. Tollenaere, N. Poulicard

{"title":"Old foe, new host: Epidemiology, genetic diversity and pathogenic characterization of maize streak virus in rice fields from Burkina Faso","authors":"N. Fouad, M. Barro, M. Bangratz, D. Sérémé, D. Filloux, Emmanuel Fernandez, Charlotte Julian, Nignan Saïbou, Abalo Itolou Kassankogno, Abdoul Kader Guigma, P. Roumagnac, I. Wonni, C. Tollenaere, N. Poulicard","doi":"10.1094/pbiomes-08-23-0085-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-08-23-0085-fi","url":null,"abstract":"Rice is of critical significance regarding food security worldwide including in Africa. Only two viruses impacting rice production in Africa have been deeply investigated for decades: the rice yellow mottle virus (Solemoviridae) and the rice stripe necrosis virus (Benyviridae). Using viral metagenomics, we aimed at broadening knowledge on interacting communities associated with plants in rice landscapes and exploring the diversity and the epidemiological status of viruses circulating in rice fields from Burkina Faso. We performed an epidemiological survey in this country between 2016 and 2019 involving 57 small farmer’s rice fields under two production systems (rainfed lowlands and irrigated areas). More than 2700 rice samples were collected without regard for disease symptoms following a regular scheme. In addition, wild and cultivated (maize and sugarcane) Poaceae growing nearby rice fields were also collected. Unexpectedly, metagenomics detected maize streak virus (MSV, Geminiviridae) in analyzed rice samples. Further molecular analyses using RCA-PCR showed that MSV is widely distributed and highly prevalent in both rainfed lowlands and irrigated rice areas. MSV-A and MSV-G strains were identified. MSV-G, exclusively identified so far in wild grasses, was the most prevalent strain while MSV-A, known to cause severe symptoms in maize, was sporadically identified. Using infectious clones in experimental conditions, we confirmed the pathogenicity of both MSV strains on rice. Thus, in addition to contributing to the epidemiological surveillance of rice production in Africa, our results illuminate new epidemiological and pathogenic aspects of one of the most studied plant viruses with significant economic consequences in Africa.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"119 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139826242","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}

引用次数: 0

Old foe, new host: Epidemiology, genetic diversity and pathogenic characterization of maize streak virus in rice fields from Burkina Faso 老敌人，新宿主：布基纳法索稻田中玉米条纹病毒的流行病学、遗传多样性和致病特征

Phytobiomes Journal Pub Date : 2024-02-01 DOI: 10.1094/pbiomes-08-23-0085-fi

N. Fouad, M. Barro, M. Bangratz, D. Sérémé, D. Filloux, Emmanuel Fernandez, Charlotte Julian, Nignan Saïbou, Abalo Itolou Kassankogno, Abdoul Kader Guigma, P. Roumagnac, I. Wonni, C. Tollenaere, N. Poulicard

{"title":"Old foe, new host: Epidemiology, genetic diversity and pathogenic characterization of maize streak virus in rice fields from Burkina Faso","authors":"N. Fouad, M. Barro, M. Bangratz, D. Sérémé, D. Filloux, Emmanuel Fernandez, Charlotte Julian, Nignan Saïbou, Abalo Itolou Kassankogno, Abdoul Kader Guigma, P. Roumagnac, I. Wonni, C. Tollenaere, N. Poulicard","doi":"10.1094/pbiomes-08-23-0085-fi","DOIUrl":"https://doi.org/10.1094/pbiomes-08-23-0085-fi","url":null,"abstract":"Rice is of critical significance regarding food security worldwide including in Africa. Only two viruses impacting rice production in Africa have been deeply investigated for decades: the rice yellow mottle virus (Solemoviridae) and the rice stripe necrosis virus (Benyviridae). Using viral metagenomics, we aimed at broadening knowledge on interacting communities associated with plants in rice landscapes and exploring the diversity and the epidemiological status of viruses circulating in rice fields from Burkina Faso. We performed an epidemiological survey in this country between 2016 and 2019 involving 57 small farmer’s rice fields under two production systems (rainfed lowlands and irrigated areas). More than 2700 rice samples were collected without regard for disease symptoms following a regular scheme. In addition, wild and cultivated (maize and sugarcane) Poaceae growing nearby rice fields were also collected. Unexpectedly, metagenomics detected maize streak virus (MSV, Geminiviridae) in analyzed rice samples. Further molecular analyses using RCA-PCR showed that MSV is widely distributed and highly prevalent in both rainfed lowlands and irrigated rice areas. MSV-A and MSV-G strains were identified. MSV-G, exclusively identified so far in wild grasses, was the most prevalent strain while MSV-A, known to cause severe symptoms in maize, was sporadically identified. Using infectious clones in experimental conditions, we confirmed the pathogenicity of both MSV strains on rice. Thus, in addition to contributing to the epidemiological surveillance of rice production in Africa, our results illuminate new epidemiological and pathogenic aspects of one of the most studied plant viruses with significant economic consequences in Africa.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"150 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139886272","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}

引用次数: 0

Incorporating culture-independent methods to identify net syndrome-associated Fusarium species in peanuts 采用独立于培养的方法确定花生中与净综合征有关的镰刀菌菌种

Phytobiomes Journal Pub Date : 2024-02-01 DOI: 10.1094/pbiomes-10-23-0111-r

Kobi Sudakov, H. Yasuor, Amit Kumar Jaiswal, Gideon Mordukhovich, Oren Buchshtab, D. Minz, Omer Frenkel

{"title":"Incorporating culture-independent methods to identify net syndrome-associated Fusarium species in peanuts","authors":"Kobi Sudakov, H. Yasuor, Amit Kumar Jaiswal, Gideon Mordukhovich, Oren Buchshtab, D. Minz, Omer Frenkel","doi":"10.1094/pbiomes-10-23-0111-r","DOIUrl":"https://doi.org/10.1094/pbiomes-10-23-0111-r","url":null,"abstract":"Peanuts (Arachis hypogaea L.) are of significant agricultural importance due to their versatile uses, providing a valuable source of edible oil and protein-rich food products, and serving in industrial applications. Peanuts are susceptible to various diseases, one of them being net syndrome, a poorly understood threat triggered by an undefined causal agent, with symptoms including black coloring and lesions of the peanut pod which affect product quality. In this study, amplicon sequencing was harnessed to explore the fungal and bacterial populations associated with the syndrome. Using this approach, we identified a specific amplicon sequence variant (ASV) of Fusarium sp., that demonstrated a significant correlation with the presence of net syndrome symptoms in both young and mature peanuts. This finding was further validated by Koch's postulate testing, including isolation, cultivation, and application of this strain to corroborate its involvement in the net syndrome in peanuts. Our findings contribute to a better understanding of the interactions between peanuts and their microbial communities, and to the identification of previously undetermined agent involved in net syndrome and the etiology of the disease.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"10 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139812424","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}

引用次数: 0

Endophyte mediated Populus trichocarpa water use efficiency is dependent on time of day and plant water status 内生菌介导的毛白杨水分利用效率取决于一天中的时间和植物水分状况

Phytobiomes Journal Pub Date : 2024-02-01 DOI: 10.1094/pbiomes-11-22-0077-r

Darshi Banan, Andrew W. Sher, Sharon Doty, Soo-Hyung Kim

{"title":"Endophyte mediated Populus trichocarpa water use efficiency is dependent on time of day and plant water status","authors":"Darshi Banan, Andrew W. Sher, Sharon Doty, Soo-Hyung Kim","doi":"10.1094/pbiomes-11-22-0077-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-22-0077-r","url":null,"abstract":"Endophytes are potential partners for improving the resource use efficiency of bioenergy feedstock systems such as short rotation coppiced Populus. Endophytes isolated from members of the Salicaceae family have broad host compatibility and can improve water use efficiency (WUE) through decreases in stomatal conductance. However, the literature is inconsistent with regards to the environmental conditions and temporal patterns of these benefits. This study investigates how endophyte mediated changes in Populus trichocarpa (Torr. and Gray) ‘Nisqually-1’ stomatal conductance and WUE shift with time and scale in response to water-deficit stress. Leaf gas exchange and above-ground productivity were used to evaluate the carbon and water balances of glasshouse grown plants in response to endophyte inoculation and water-deficit. Differences in stomatal conductance between control and inoculated plants were more pronounced (39.7 % decrease, Welch’s two-sample t(14.34 dfadj) = -2.358, p-value = 0.033) under water-deficit conditions in the late morning during a period of higher light intensity. The decrease in stomatal conductance accompanied a substantial increase in intrinsic WUE (iWUE) for water-deficit inoculated plants. However, increases in iWUE did not result in improvements in aboveground productivity or shoot biomass WUE (WUEsb) for water-deficit inoculated plants. This decoupling between iWUE and aboveground productivity may be an indicator of assimilate allocation to microbial metabolism as an additional carbon sink or a shift in carbon allocation towards belowground biomass. Future work should take a whole-plant approach that accounts for diurnal patterns in incident irradiance to evaluate the impact of endophyte inoculation on host WUE and stress tolerance.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"68 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139888129","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}

引用次数: 0

Endophyte mediated Populus trichocarpa water use efficiency is dependent on time of day and plant water status 内生菌介导的毛白杨水分利用效率取决于一天中的时间和植物水分状况

Phytobiomes Journal Pub Date : 2024-02-01 DOI: 10.1094/pbiomes-11-22-0077-r

Darshi Banan, Andrew W. Sher, Sharon Doty, Soo-Hyung Kim

{"title":"Endophyte mediated Populus trichocarpa water use efficiency is dependent on time of day and plant water status","authors":"Darshi Banan, Andrew W. Sher, Sharon Doty, Soo-Hyung Kim","doi":"10.1094/pbiomes-11-22-0077-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-22-0077-r","url":null,"abstract":"Endophytes are potential partners for improving the resource use efficiency of bioenergy feedstock systems such as short rotation coppiced Populus. Endophytes isolated from members of the Salicaceae family have broad host compatibility and can improve water use efficiency (WUE) through decreases in stomatal conductance. However, the literature is inconsistent with regards to the environmental conditions and temporal patterns of these benefits. This study investigates how endophyte mediated changes in Populus trichocarpa (Torr. and Gray) ‘Nisqually-1’ stomatal conductance and WUE shift with time and scale in response to water-deficit stress. Leaf gas exchange and above-ground productivity were used to evaluate the carbon and water balances of glasshouse grown plants in response to endophyte inoculation and water-deficit. Differences in stomatal conductance between control and inoculated plants were more pronounced (39.7 % decrease, Welch’s two-sample t(14.34 dfadj) = -2.358, p-value = 0.033) under water-deficit conditions in the late morning during a period of higher light intensity. The decrease in stomatal conductance accompanied a substantial increase in intrinsic WUE (iWUE) for water-deficit inoculated plants. However, increases in iWUE did not result in improvements in aboveground productivity or shoot biomass WUE (WUEsb) for water-deficit inoculated plants. This decoupling between iWUE and aboveground productivity may be an indicator of assimilate allocation to microbial metabolism as an additional carbon sink or a shift in carbon allocation towards belowground biomass. Future work should take a whole-plant approach that accounts for diurnal patterns in incident irradiance to evaluate the impact of endophyte inoculation on host WUE and stress tolerance.","PeriodicalId":509866,"journal":{"name":"Phytobiomes Journal","volume":"42 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139828249","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}

引用次数: 0