Identification and Characterization of the Core Rice Seed Microbiome

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.

show abstract

“…1b). The average Shannon index was 3.64 + 1.2 similar to seed and root rice microbiome (Edwards et al 2015;Eyre et al 2019) (Fig. 1c).…”

Section: Diversity Of the Rice Leaf Microbiomementioning

confidence: 73%

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

Román-Reyna

Pinili

Borja

et al. 2020

Rice

View full text Add to dashboard Cite

show abstract

“…The average Shannon index was 3.64 + 1.2 similar to seed and root rice microbiome (Edwards et al 2015;Eyre et al 2019) ( Figure 1C).…”

Section: Diversity Of the Rice Leaf Microbiomementioning

confidence: 80%

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

Román-Reyna

Pinili

Borja

et al. 2020

Preprint

View full text Add to dashboard Cite

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.

show abstract

“…To better understand the microbiome dynamics from seeds to seedlings, additional analyses were performed using the four different seed compartments: outer husk, husk, outer grain and grain (Eyre et al, 2019; see Supplementary Figure 1). From outer surface to inner grain, the number of shared ASVs among seed compartments and seedling samples decreased, consistent with the observation that the number of ASVs decreased in rice seeds from outer surface to inner grain (Eyre et al, 2019).…”

Section: Changes Of Microbial Members In the Rice During Shoot And Romentioning

confidence: 99%

Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds

et al. 2020

Self Cite

View full text Add to dashboard Cite

Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents.

show abstract

Identification and Characterization of the Core Rice Seed Microbiome

Cited by 89 publications

References 54 publications

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

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

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

Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds

Contact Info

Product

Resources

About