First report of Acidovorax avenae subsp. avenae causing bacterial brown stripe disease of rice in Taiwan

et al. 2020

Rice

Background The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3024 rice accessions. Findings By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial “hubs” and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities. Conclusion We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.

Section: The Functional Profile Of the Leaf Microbiomementioning

confidence: 99%

Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project

et al. 2020

Rice

“…The hubs Methylobacterium, Pseudomonas, Bacillus, Kineococcus, Azotobacter, Acidovorax, and Clostridium have also been reported as commensal, bene cials, or pathogens in other plants (Cottyn et al 2009;Bian et al 2012;Horino et al 2015;Chen et al 2018;Lai and Huang 2018). The hubs Chamaesiphon and Prochlorococcus could be part of the rice microbiome, as the paddy eld conditions like shallow water and sunlight could create an ideal environment for algae growth.…”

Section: The Functional Pro Le Of the Leaf Microbiomementioning

confidence: 99%

Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project.

et al. 2020

Preprint

Background: The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3,024 rice accessions. Findings: By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial “hubs” and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities. Conclusion: We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.

“…The hubs Methylobacterium, Pseudomonas, Bacillus, Kineococcus, Azotobacter, Acidovorax and Clostridium have been reported as commensal, bene cial or pathogens in other plants (Cottyn et al 2009;Bian et al 2012;Horino et al 2015;Chen et al 2018;Lai and Huang 2018). The hubs Chamaesiphon and Prochlorococcus could be part of the rice microbiome, as the paddy eld conditions like shallow water and sunlight could create an ideal environment for algae growth.…”

Section: The Functional Pro Le Of the Leaf Microbiomementioning

confidence: 99%

Characterization of the leaf microbiome from whole-genome sequencing data of the 3000 rice genomes project

et al. 2020

Preprint

Background: The crop microbial communities are shaped by interactions between the host, microbes and the environment, however, their relative contribution is beginning to be understood. Here, we explore these interactions in the leaf bacterial community across 3,024 rice accessions.Findings: By using unmapped DNA sequencing reads as microbial reads, we characterized the structure of the rice bacterial microbiome. We identified central bacteria taxa that emerge as microbial “hubs” and may have an influence on the network of host-microbe interactions. We found regions in the rice genome that might control the assembly of these microbial hubs. To our knowledge this is one of the first studies that uses raw data from plant genome sequencing projects to characterize the leaf bacterial communities. Conclusion: We showed, that the structure of the rice leaf microbiome is modulated by multiple interactions among host, microbes, and environment. Our data provide insight into the factors influencing microbial assemblage in the rice leaf and also opens the door for future initiatives to modulate rice consortia for crop improvement efforts.