The rice leaf microbiome has a conserved community structure controlled by complex host-microbe interactions

Abstract

26Understanding the factors that influence the outcome of crop interactions with microbes is key to 27 managing crop diseases and improving yield. While the composition, structure and functional profile of 28 crop microbial communities are shaped by complex interactions between the host, microbes and the 29 environment, the relative contribution of each of these factors is mostly unknown. Here, we profiled the 30 community composition of bacteria across leaves of 3,024 rice (Oryza sativa) accessions from field trials 31 in China and the Philippines using metagenomics. Despite significant differences in diversity between 32 environments, the structure and metabolic profiles of the microbiome appear to be conserved, suggesting 33 that microbiomes converge onto core functions. Furthermore, co-occurrence analysis identified microbial 34 hubs that regulate the network structure of the microbiome. We identified rice genomic regions controlling 35 the abundance of these hubs, enriched for processes involved in stress responses and carbohydrate 36 metabolism. We functionally validated the importance of these processes, finding that abundance of hub 37 taxa was different in rice mutants with altered cellulose and salicylate accumulation, two major 38 metabolites at the host-microbe interactions interface. By identifying key host genomic regions, host traits 39 and hub microbes that govern microbiome composition, our study opens the door to designing future 40 cropping systems. 41 42

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

“…Previous GWAS of plant-associated microbiome traits have often been conducted with leaf samples, and have not always been successful in identifying loci that correlate with microbiome phenotypes 16–18 . In this study, we compared the overall correlation between host genotype and bacterial microbiome distances across leaf, root, and rhizosphere of Sorghum bicolor , and demonstrate that of the three, the rhizosphere represents the most promising compartment for conducting experiments to untangle the heritability of the sorghum microbiome.…”

“…In plants, a recent study in Arabidopsis thaliana used phyllosphere microbial community data as the phenotypic trait in a GWAS to demonstrate that plant loci responsible for defense and cell wall integrity affect microbial community variation 16 . Several other recent phyllosphere studies performed GWAS to identify genetic factors controlling microbiome associations with mixed degrees of success 16–18 . However, to our knowledge, use of GWAS in conjunction with the root associated microbiome has yet to be explored.…”

Genome‐scale metabolic reconstruction and in silico analysis of the rice leaf blight pathogen, Xanthomonas oryzae

“…In addition, secretion of endo‐1,4‐β‐ d ‐glucanase/cellulase is an important characteristic for virulence and survival in Xoo (Figure ) as it has been observed as a common feature in all plant pathogens (Sun et al , ; Rajeshwari et al , ). Substantiating this, a recent study characterizing the rice leaf microbiome indicated a major role of cellulose in facilitating plant–microbiome interactions at the leaf interface (Roman‐reyna et al , ).…”

Metagenomic Analysis of Bacterial Community Associated with Rhizosphere and Phyllosphere of Basmati Rice

“…Previously, research work was conducted to study the microbial community residing as root endophytes of Indian rice [19], rhizospheric microbiota of two Venezuelan rice varieties [20] and phyllosphere analysis in two major rice growing areas of China and the Philippines [21]. According to our knowledge, no microbiome information is available from aromatic Basmati rice growing areas.…”