Pub Date : 2023-02-07DOI: 10.1094/pbiomes-05-22-0032-r
Dao-hui Huo, A. Malacrinò, L. Lindsey, Maria-Soledad Benitez Ponce
Crop rotational diversity can improve crop productivity, soil health, and boost soil microbial diversity. This research hypothesized that a three-year rotation of corn-soybean-wheat (CSW), compared to a two-year corn-soybean (CS) rotation, would result in a more diverse and more complex soil bacterial community, together with a greater abundance of beneficial bacteria. This was evaluated in a replicated experiment established in 2013 at two locations in Ohio (USA). The soil bacterial communities under soybean were compared between CS and CSW, at both studied sites, in 2018 and 2019, through 16S rDNA amplicon metabarcoding. Experimental site was the main driver of bacterial richness and evenness. Significant effects on bacterial community composition were observed in response to the interaction between site, rotational sequence, and year of study. Eight bacterial ASVs were identified within all CSW treatments and were not present in CS. Several taxa were differentially abundant between rotation treatments, including the genera Ralstonia being more abundant in CS. Co-occurrence networks, including hub taxa, were generally different between rotation treatments and year, with more structure observed in CSW networks for one of the studies sites. Few bacterial genera were consistently identified as hubs across all networks, including an unidentified Acidobacteriales, while other hubs were unique for CSW networks, including members of the family Gemmatimonadaceae. Finally, the composition of the bacterial communities at the northwestern site positively correlated with plant biomass and active carbon, whereas more recalcitrant pools (total C and organic water) correlated with the bacterial communities at the western site.
{"title":"Subtle responses of soil bacterial communities to corn-soybean-wheat rotation","authors":"Dao-hui Huo, A. Malacrinò, L. Lindsey, Maria-Soledad Benitez Ponce","doi":"10.1094/pbiomes-05-22-0032-r","DOIUrl":"https://doi.org/10.1094/pbiomes-05-22-0032-r","url":null,"abstract":"Crop rotational diversity can improve crop productivity, soil health, and boost soil microbial diversity. This research hypothesized that a three-year rotation of corn-soybean-wheat (CSW), compared to a two-year corn-soybean (CS) rotation, would result in a more diverse and more complex soil bacterial community, together with a greater abundance of beneficial bacteria. This was evaluated in a replicated experiment established in 2013 at two locations in Ohio (USA). The soil bacterial communities under soybean were compared between CS and CSW, at both studied sites, in 2018 and 2019, through 16S rDNA amplicon metabarcoding. Experimental site was the main driver of bacterial richness and evenness. Significant effects on bacterial community composition were observed in response to the interaction between site, rotational sequence, and year of study. Eight bacterial ASVs were identified within all CSW treatments and were not present in CS. Several taxa were differentially abundant between rotation treatments, including the genera Ralstonia being more abundant in CS. Co-occurrence networks, including hub taxa, were generally different between rotation treatments and year, with more structure observed in CSW networks for one of the studies sites. Few bacterial genera were consistently identified as hubs across all networks, including an unidentified Acidobacteriales, while other hubs were unique for CSW networks, including members of the family Gemmatimonadaceae. Finally, the composition of the bacterial communities at the northwestern site positively correlated with plant biomass and active carbon, whereas more recalcitrant pools (total C and organic water) correlated with the bacterial communities at the western site.","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":"46645616","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 : 2023-01-31DOI: 10.1094/pbiomes-11-22-0084-r
O. Sharon, Xiang Sun, S. Ezrati, Naomi Kagan-Trushina, A. Sharon
Seeds acquire fungal endophytes either from the environment or from their progenitors. These transmission modes are central in shaping the microbiome as they affect species composition and balance. We studied fungal endophyte communities (FEC) in three plant species: bread wheat (Triticum aestivum), wild emmer wheat (Triticum turgidum dicoccoides), and wild barley (Hordeum spontaneum). We conducted two experiments to test seed-to-seed transmission: (i) we compared FECs in stems and seeds collected from agricultural and natural habitats, and (ii) we grew plants under greenhouse conditions to isolate the effect of vertical transmission on the plant FECs. The analysis of seed communities revealed differences in FEC composition and diversity among plant species; however, Alternaria infectoria dominated FECs in all plant species. In field-collected plants, the number of taxa in the seeds was less than half the number in stems, and close to 90% of the seed taxa were found in stems. The FECs from stems and seeds of greenhouse-grown plants were more diverse than the FECs of original seeds; they lacked a single dominant taxon, and new seeds FECs had a similar richness and diversity to stems FECs, with only 40% overlap. The controlled environment experiment confirmed vertical transmission of certain species but also showed that external infection of the seeds is the main source for specific taxa. Our results show that many taxa can reach the seeds internally, albeit in different abundance, that both infection sources affect seed FECs composition, and that external conditions the balance between FECs within the plant.
{"title":"Transmission mode and assembly of seed fungal endophyte communities in wheat and wheat wild relatives","authors":"O. Sharon, Xiang Sun, S. Ezrati, Naomi Kagan-Trushina, A. Sharon","doi":"10.1094/pbiomes-11-22-0084-r","DOIUrl":"https://doi.org/10.1094/pbiomes-11-22-0084-r","url":null,"abstract":"Seeds acquire fungal endophytes either from the environment or from their progenitors. These transmission modes are central in shaping the microbiome as they affect species composition and balance. We studied fungal endophyte communities (FEC) in three plant species: bread wheat (Triticum aestivum), wild emmer wheat (Triticum turgidum dicoccoides), and wild barley (Hordeum spontaneum). We conducted two experiments to test seed-to-seed transmission: (i) we compared FECs in stems and seeds collected from agricultural and natural habitats, and (ii) we grew plants under greenhouse conditions to isolate the effect of vertical transmission on the plant FECs. The analysis of seed communities revealed differences in FEC composition and diversity among plant species; however, Alternaria infectoria dominated FECs in all plant species. In field-collected plants, the number of taxa in the seeds was less than half the number in stems, and close to 90% of the seed taxa were found in stems. The FECs from stems and seeds of greenhouse-grown plants were more diverse than the FECs of original seeds; they lacked a single dominant taxon, and new seeds FECs had a similar richness and diversity to stems FECs, with only 40% overlap. The controlled environment experiment confirmed vertical transmission of certain species but also showed that external infection of the seeds is the main source for specific taxa. Our results show that many taxa can reach the seeds internally, albeit in different abundance, that both infection sources affect seed FECs composition, and that external conditions the balance between FECs within the plant.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41280299","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 : 2023-01-27DOI: 10.1094/pbiomes-07-22-0045-r
Yun-Le Li, S. Vail, M. Arcand, B. Helgason
Canola (Brassica napus) is an important broadacre crop, produced under high nitrogen (N) fertilizer application. Modern canola varieties are developed under high N rates but the impacts on root-associated microbiomes of different varieties are unknown. We studied eight canola varieties spanning historical Canadian spring canola development at two sites under high and low N fertility and characterized bacterial and fungal microbiomes in the root and rhizosphere using amplicon sequencing. Environmental conditions and the resulting canola varietal responses strongly affected the root-associated bacterial and fungal microbiomes. Microbes regulated by N fertility in each canola variety were mainly Gammaproteobacteria, Bacteroidia, Actinobacteria, Sordariomycetes, Dothideomycetes, and Agaricomycetes classes. Differentially abundant (DA) microbial taxa showed that N more strongly enriched bacteria in the roots and fungi in the rhizosphere. Each variety had its specific pattern of DA-ASVs responding to soil N availability, and the profile of DA-ASVs in paired canola varieties were also altered by soil N availability, especially bacteria in rhizosphere. The yield was strongly associated with a subset of microbial taxa mainly from Proteobacteria, Actinobacteriota, and Ascomycota. These variety-dependent responses to N and links to yield performance make root-associated microbiome a promising target for improving the agronomic performance of canola by manipulating microorganisms tailored to soil fertility and plant genotype.
{"title":"Contrasting nitrogen fertilization and Brassica napus (canola) variety development impact recruitment of the root-associated microbiome","authors":"Yun-Le Li, S. Vail, M. Arcand, B. Helgason","doi":"10.1094/pbiomes-07-22-0045-r","DOIUrl":"https://doi.org/10.1094/pbiomes-07-22-0045-r","url":null,"abstract":"Canola (Brassica napus) is an important broadacre crop, produced under high nitrogen (N) fertilizer application. Modern canola varieties are developed under high N rates but the impacts on root-associated microbiomes of different varieties are unknown. We studied eight canola varieties spanning historical Canadian spring canola development at two sites under high and low N fertility and characterized bacterial and fungal microbiomes in the root and rhizosphere using amplicon sequencing. Environmental conditions and the resulting canola varietal responses strongly affected the root-associated bacterial and fungal microbiomes. Microbes regulated by N fertility in each canola variety were mainly Gammaproteobacteria, Bacteroidia, Actinobacteria, Sordariomycetes, Dothideomycetes, and Agaricomycetes classes. Differentially abundant (DA) microbial taxa showed that N more strongly enriched bacteria in the roots and fungi in the rhizosphere. Each variety had its specific pattern of DA-ASVs responding to soil N availability, and the profile of DA-ASVs in paired canola varieties were also altered by soil N availability, especially bacteria in rhizosphere. The yield was strongly associated with a subset of microbial taxa mainly from Proteobacteria, Actinobacteriota, and Ascomycota. These variety-dependent responses to N and links to yield performance make root-associated microbiome a promising target for improving the agronomic performance of canola by manipulating microorganisms tailored to soil fertility and plant genotype.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43974889","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 : 2023-01-19DOI: 10.1094/pbiomes-06-22-0038-rvw
J. Kubiriba, R. Erima, A. Tugume, W. Tinzaara, W. Tushemereirwe
Banana Xanthomonas wilt (BXW) is a destructive disease caused by Xanthomonas vasicola pv. musacearum (Xvm) bacterium that indiscriminately infects all banana varieties grown in East and Central Africa (ECA). In this region, BXW was first reported in 2001 in Uganda and was projected to eliminate >90% of Uganda’s bananas worth US$4 billion if not controlled in less than 10 years. Lack of basic information led to application of control approaches that were based on similarity of BXW symptoms to those of Moko disease of bananas. The approaches were however, unsuccessful and in 7-9 years, BXW had covered six countries and threatened to wipe out the banana industry in ECA. However, BXW has to-date been tamed, mainly due to relentless and systematic deployment of carefully crafted and packaged cultural control practices based on epidemiological information generated within target banana cropping ecosystems. In Uganda, the initial “top-down” communication approaches reached >85% banana farming communities but did not mobilize the communities enough into action; hence, only 30% impact in controlling BXW was registered. In contrast, participatory approaches mobilised farming communities into action and effectively controlled BXW at field and community levels to near eradication. The approaches effectively controlled BXW in Uganda, and consequently, in eastern Kenya, northern Tanzania, Rwanda, Burundi and DRC. This paper reviews step-wise processes leading to success over the 2 decades and identifies critical research gaps. Deployment of resistant genotypes is urgently needed as a significant addition to the BXW management tool-box to create BXW-free banana cropping systems in ECA.
{"title":"Changing dynamics in the spread and management of banana Xanthomonas wilt disease in Uganda over two decades","authors":"J. Kubiriba, R. Erima, A. Tugume, W. Tinzaara, W. Tushemereirwe","doi":"10.1094/pbiomes-06-22-0038-rvw","DOIUrl":"https://doi.org/10.1094/pbiomes-06-22-0038-rvw","url":null,"abstract":"Banana Xanthomonas wilt (BXW) is a destructive disease caused by Xanthomonas vasicola pv. musacearum (Xvm) bacterium that indiscriminately infects all banana varieties grown in East and Central Africa (ECA). In this region, BXW was first reported in 2001 in Uganda and was projected to eliminate >90% of Uganda’s bananas worth US$4 billion if not controlled in less than 10 years. Lack of basic information led to application of control approaches that were based on similarity of BXW symptoms to those of Moko disease of bananas. The approaches were however, unsuccessful and in 7-9 years, BXW had covered six countries and threatened to wipe out the banana industry in ECA. However, BXW has to-date been tamed, mainly due to relentless and systematic deployment of carefully crafted and packaged cultural control practices based on epidemiological information generated within target banana cropping ecosystems. In Uganda, the initial “top-down” communication approaches reached >85% banana farming communities but did not mobilize the communities enough into action; hence, only 30% impact in controlling BXW was registered. In contrast, participatory approaches mobilised farming communities into action and effectively controlled BXW at field and community levels to near eradication. The approaches effectively controlled BXW in Uganda, and consequently, in eastern Kenya, northern Tanzania, Rwanda, Burundi and DRC. This paper reviews step-wise processes leading to success over the 2 decades and identifies critical research gaps. Deployment of resistant genotypes is urgently needed as a significant addition to the BXW management tool-box to create BXW-free banana cropping systems in ECA.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45759251","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 : 2022-12-28DOI: 10.1094/pbiomes-12-22-0101-r
Chuntao Yin, D. Schlatter, C. Hagerty, S. Hulbert, T. Paulitz
The plant is one of the primary drivers of microbial communities in the rhizosphere. The consistent presence of same plant species over time, such as in monocropping in agriculture can drive significant changes in plant-associated microbiomes. Most of the studies with monocropping have focused on bacteria, which are involved in the natural suppression of a number of soilborne diseases, including Rhizoctonia root rot and take-all. However, few studies have examined how monocropping and root rot pathogens jointly affect the structure of fungal communities in the rhizosphere. In this greenhouse study, rhizosphere fungal communities from successive wheat plantings infected with the fungal pathogen Rhizoctonia solani AG8 were characterized using MiSeq sequencing targeting the ITS1 region of the rRNA gene. Sequence analyses revealed that distinct fungal groups clustered by planting cycles with or without AG8 inoculation, but infection with AG8 enhanced the separation of fungal communities. Clusters of fungal communities were also observed in AG8-infected and non-infected rhizospheres, whereas there was no difference in fungal communities between the rhizosphere with the least root disease and those with the worst root disease. Planting cycles significantly reduced fungal alpha diversity. The most abundant fungal genus was Mortierella which increased in relative abundance with planting cycles in AG8-infected samples. In contrast, a group of fungal genera, including Pseudogymnoascus, Gibberella, Fusarium, Fusicolla, Exophiala, and Waitea, were reduced in relative abundance with successive plantings and AG8 infection. Together, this study revealed how fungal communities change with successive wheat growth under the pressure of a soilborne fungal pathogen.
{"title":"Disease-induced assemblage of the rhizosphere fungal community in successive plantings of wheat","authors":"Chuntao Yin, D. Schlatter, C. Hagerty, S. Hulbert, T. Paulitz","doi":"10.1094/pbiomes-12-22-0101-r","DOIUrl":"https://doi.org/10.1094/pbiomes-12-22-0101-r","url":null,"abstract":"The plant is one of the primary drivers of microbial communities in the rhizosphere. The consistent presence of same plant species over time, such as in monocropping in agriculture can drive significant changes in plant-associated microbiomes. Most of the studies with monocropping have focused on bacteria, which are involved in the natural suppression of a number of soilborne diseases, including Rhizoctonia root rot and take-all. However, few studies have examined how monocropping and root rot pathogens jointly affect the structure of fungal communities in the rhizosphere. In this greenhouse study, rhizosphere fungal communities from successive wheat plantings infected with the fungal pathogen Rhizoctonia solani AG8 were characterized using MiSeq sequencing targeting the ITS1 region of the rRNA gene. Sequence analyses revealed that distinct fungal groups clustered by planting cycles with or without AG8 inoculation, but infection with AG8 enhanced the separation of fungal communities. Clusters of fungal communities were also observed in AG8-infected and non-infected rhizospheres, whereas there was no difference in fungal communities between the rhizosphere with the least root disease and those with the worst root disease. Planting cycles significantly reduced fungal alpha diversity. The most abundant fungal genus was Mortierella which increased in relative abundance with planting cycles in AG8-infected samples. In contrast, a group of fungal genera, including Pseudogymnoascus, Gibberella, Fusarium, Fusicolla, Exophiala, and Waitea, were reduced in relative abundance with successive plantings and AG8 infection. Together, this study revealed how fungal communities change with successive wheat growth under the pressure of a soilborne fungal pathogen.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2022-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45692514","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 : 2022-12-20DOI: 10.1094/pbiomes-08-22-0054-mf
Carolina Escobar Rodriguez, B. Mitter, Livio Antonielli, A. Sessitsch
The association of the plant microbiota is a successional process that starts with the seed and its intrinsic microbiota. The recently reported relevance of seeds as carriers of microbiota has encouraged investigations of the assembly of these communities in different tissues. Here, we address the contributions of both seed and soil bacterial microbiota in the assembly of communities within endospheres of adult plants by 16S rRNA gene-based Illumina sequencing. Surface-sterilized seeds of the model plant Setaria viridis L. were sown in sterile conditions and seedlings were transferred onto either their native soil or a foreign soil. Soil-derived bacterial colonizers contributed to the highest portion of endophytic microbiota, with varying community composition depending on the cultivation soil. In contrast, the contribution of seed microbiota in those of adult plants was less evident. Moreover, seedlings grown in their native soils resulted in plants with consistent endophytic assemblages, whereas a dramatic increase in variability was observed for rhizosphere and endophytic root communities of plants grown in foreign soils.
{"title":"Assembly of endophytic communities of Setaria viridis L. plants when grown in different soils and derived from different seeds","authors":"Carolina Escobar Rodriguez, B. Mitter, Livio Antonielli, A. Sessitsch","doi":"10.1094/pbiomes-08-22-0054-mf","DOIUrl":"https://doi.org/10.1094/pbiomes-08-22-0054-mf","url":null,"abstract":"The association of the plant microbiota is a successional process that starts with the seed and its intrinsic microbiota. The recently reported relevance of seeds as carriers of microbiota has encouraged investigations of the assembly of these communities in different tissues. Here, we address the contributions of both seed and soil bacterial microbiota in the assembly of communities within endospheres of adult plants by 16S rRNA gene-based Illumina sequencing. Surface-sterilized seeds of the model plant Setaria viridis L. were sown in sterile conditions and seedlings were transferred onto either their native soil or a foreign soil. Soil-derived bacterial colonizers contributed to the highest portion of endophytic microbiota, with varying community composition depending on the cultivation soil. In contrast, the contribution of seed microbiota in those of adult plants was less evident. Moreover, seedlings grown in their native soils resulted in plants with consistent endophytic assemblages, whereas a dramatic increase in variability was observed for rhizosphere and endophytic root communities of plants grown in foreign soils.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2022-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49245649","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 : 2022-12-08DOI: 10.1094/pbiomes-07-22-0044-mf
A. Persyn, Sonia Garcia Mendez, Stien Beirinckx, Sam De Meyer, A. Willems, C. De Tender, S. Goormachtig
Growth of lettuce (Lactuca sativa) is severely hampered by low temperatures, even when cultivated under greenhouse conditions. Root-associated bacteria might promote plant growth under stressful conditions. Therefore, we analyzed the effect of low temperatures on the lettuce root-associated microbiome to evaluate whether microbiome-based selection aids in the identification of bacteria that stimulate plant growth in the cold. 16S rRNA gene amplicon sequencing was used to examine the compositional differences in the lettuce root-associated microbiome when grown under low and control temperature conditions. Chilling temperatures significantly altered the lettuce root endosphere composition, whereas its effects were less severe in the rhizosphere and absent in the bulk soil. Several cold-enriched families were found, of which nine, the Oxalobacteraceae, Pseudomonadaceae, Flavobacteriaceae, Microscillaceae, Spingobacteriaceae, Comamonadaceae, Devosiaceae, Methylophilaceae and env.OPS_17, in both the rhizosphere and the root endosphere. Concurrently, a collection of lettuce root-colonizing bacteria was established and based on correlation with these families, representative isolates were screened. None of the lettuce root isolates showed growth-promoting effects, but three growth-promoting Flavobacterium strains from an available collection of grass root-colonizing bacteria were identified. Amplicon sequence variant (ASV) annotation of the lettuce and grass strains revealed that strains matching cold-enriched or highly abundant ASVs in at least one soil promoted growth in the cold. Overall our data demonstrate that microbiome analyses, combined with high-throughput bacterial isolations, might be a helpful tool to isolate effective cold growth-promoting strains.
{"title":"Digging into the lettuce cold-specific root microbiome in search of chilling stress tolerance-conferring plant growth-promoting bacteria","authors":"A. Persyn, Sonia Garcia Mendez, Stien Beirinckx, Sam De Meyer, A. Willems, C. De Tender, S. Goormachtig","doi":"10.1094/pbiomes-07-22-0044-mf","DOIUrl":"https://doi.org/10.1094/pbiomes-07-22-0044-mf","url":null,"abstract":"Growth of lettuce (Lactuca sativa) is severely hampered by low temperatures, even when cultivated under greenhouse conditions. Root-associated bacteria might promote plant growth under stressful conditions. Therefore, we analyzed the effect of low temperatures on the lettuce root-associated microbiome to evaluate whether microbiome-based selection aids in the identification of bacteria that stimulate plant growth in the cold. 16S rRNA gene amplicon sequencing was used to examine the compositional differences in the lettuce root-associated microbiome when grown under low and control temperature conditions. Chilling temperatures significantly altered the lettuce root endosphere composition, whereas its effects were less severe in the rhizosphere and absent in the bulk soil. Several cold-enriched families were found, of which nine, the Oxalobacteraceae, Pseudomonadaceae, Flavobacteriaceae, Microscillaceae, Spingobacteriaceae, Comamonadaceae, Devosiaceae, Methylophilaceae and env.OPS_17, in both the rhizosphere and the root endosphere. Concurrently, a collection of lettuce root-colonizing bacteria was established and based on correlation with these families, representative isolates were screened. None of the lettuce root isolates showed growth-promoting effects, but three growth-promoting Flavobacterium strains from an available collection of grass root-colonizing bacteria were identified. Amplicon sequence variant (ASV) annotation of the lettuce and grass strains revealed that strains matching cold-enriched or highly abundant ASVs in at least one soil promoted growth in the cold. Overall our data demonstrate that microbiome analyses, combined with high-throughput bacterial isolations, might be a helpful tool to isolate effective cold growth-promoting strains.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46493840","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 : 2022-12-02DOI: 10.1094/pbiomes-05-22-0031-rvw
A. Tugume, D. R. Mbanzibwa, T. Alicai, C. Omongo, M. Gowda
Viruses have the ability to frequently colonize new hosts and ecological niches because of their inherently high genetic and evolutionary plasticity. However, a virus may emerge and remain of no or less economic importance until changes in viral and/or environmental factors dictate its epidemiological status. An example is sweet potato mild mottle virus (SPMMV), which was first reported in the 1970s on sweetpotatoes in eastern Africa, has remained endemic in the region and poorly understood, yet accounting for 60-95% losses especially in mixed infections. Unlike other sweetpotato viruses which have a global incidence, SPMMV has never been confirmed outside eastern Africa. This implicates the region as its center of origin, but does not fully account for SPMMV’s exclusive geographic delimitation to eastern Africa. Despite its importance, several mysteries and research gaps surround SPMMV, which decelerate efforts for effective virus disease management in sweetpotato. The aim of this review is to articulate research gaps, propose pivotal scientific directions and stimulate knowledge generation for better management of virus diseases in sweetpotato. Vector-mediated transmission of SPMMV remains enigmatic. Here we postulate testable hypotheses to explain SPMMV transmission. Comparisons between SPMMV and cassava brown streak ipomoviruses demonstrate epidemiological “hallmarks” for monitoring SPMMV. Evolutionary forces on SPMMV coupled with the virus’ broad host range imply a ‘silent build up’ of better fit variants in a changing climate, and this could explode into a worse disease conundrum. These information gaps need urgent filling to ease future management of virus disease emergences in sweetpotato.
{"title":"Endemism and reemergence potential of the ipomovirus Sweet potato mild mottle virus (family Potyviridae) in Eastern Africa: half a century of mystery","authors":"A. Tugume, D. R. Mbanzibwa, T. Alicai, C. Omongo, M. Gowda","doi":"10.1094/pbiomes-05-22-0031-rvw","DOIUrl":"https://doi.org/10.1094/pbiomes-05-22-0031-rvw","url":null,"abstract":"Viruses have the ability to frequently colonize new hosts and ecological niches because of their inherently high genetic and evolutionary plasticity. However, a virus may emerge and remain of no or less economic importance until changes in viral and/or environmental factors dictate its epidemiological status. An example is sweet potato mild mottle virus (SPMMV), which was first reported in the 1970s on sweetpotatoes in eastern Africa, has remained endemic in the region and poorly understood, yet accounting for 60-95% losses especially in mixed infections. Unlike other sweetpotato viruses which have a global incidence, SPMMV has never been confirmed outside eastern Africa. This implicates the region as its center of origin, but does not fully account for SPMMV’s exclusive geographic delimitation to eastern Africa. Despite its importance, several mysteries and research gaps surround SPMMV, which decelerate efforts for effective virus disease management in sweetpotato. The aim of this review is to articulate research gaps, propose pivotal scientific directions and stimulate knowledge generation for better management of virus diseases in sweetpotato. Vector-mediated transmission of SPMMV remains enigmatic. Here we postulate testable hypotheses to explain SPMMV transmission. Comparisons between SPMMV and cassava brown streak ipomoviruses demonstrate epidemiological “hallmarks” for monitoring SPMMV. Evolutionary forces on SPMMV coupled with the virus’ broad host range imply a ‘silent build up’ of better fit variants in a changing climate, and this could explode into a worse disease conundrum. These information gaps need urgent filling to ease future management of virus disease emergences in sweetpotato.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42413447","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 : 2022-12-02DOI: 10.1094/pbiomes-11-22-0092-r
K. Delventhal, Victoria P. Skillman, Xiaoping Li, P. Busby, K. Frost
For tuberizing crops like potato (Solanum tuberosum), the geocaulosphere, or the thin zone of soil in contact with and influenced by the tuber, is a distinct habitat that exists between the potato and the soil environment. Geocaulosphere soil that remains associated with the tuber after harvest is called tare soil. However, beyond potato pathogens, the microbes present in tare soil are understudied. We used ITS and 16S metabarcoding to characterize the microbial communities present in 130 tare soils of commercially produced seed potatoes used for potato production in Oregon. In 2018 and 2019, tare soils were opportunistically sampled from seed potatoes that were collected from farmers in the Columbia Basin of OR. This sampling effort included seed tubers of 23 cultivars that had originated from 40 commercial seed farms in 11 states. We identified a core microbiome consisting of 61 bacterial and 26 fungal taxa, some of which are not common to the potato microbiome, and others which have been reported to either possess biocontrol activities, promote plant growth, or cause disease in potato. Seed grower farm accounted for the greatest amount of compositional variation among tare soil microbiome samples, with more similar communities found on seed tubers grown on farms near to each other. Learning which factors shape tare soil microbial community composition and if those communities influence plant health are essential steps towards potato microbiome management.
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