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

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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.

Bats are highly diverse and ecologically valuable mammals. They serve as host to bacteria, viruses and fungi that are either beneficial or harmful to its colony as well as to other groups of cave organisms. The bacterial diversity of two bat guano samples, C1 and C2, from Cabalyorisa Cave, Mabini, Pangasinan, Philippines were investigated using 16S rRNA gene amplicon sequencing. V3-V4 hypervariable regions were amplified and then sequenced using Illumina MiSeq 250 PE system. Reads were processed using Mothur and QIIME pipelines and assigned 12,345 OTUs for C1 and 5,408 OTUs for C2. The most dominant OTUs in C1 belong to the Proteobacteria (61.7%), Actinobacteria (19.4%), Bacteroidetes (4.2%), Firmicutes (2.7%), Chloroflexi (2.5%), candidate phylum TM7 (2.3%) and Planctomycetes (1.9%) while Proteobacteria (61.7%) and Actinobacteria (34.9%) dominated C2. Large proportion of sequence reads mainly associated with unclassified bacteria indicated possible occurrence of novel bacteria in both samples. XRF spectrophotometric analyses of C1 and C2 guano revealed significant differences in the composition of both major and trace elements. C1 guano recorded high levels of Si, Fe, Mg, Al, Mn, Ti and Cu while C2 samples registered high concentrations of Ca, P, S, Zn and Cr. Community structure of the samples were compared with other published community profiling studies from Finland (SRR868695), Meghalaya, Northeast India (SRR1793374) and Maharashtra State, India (CGS). Core microbiome among samples were determined for comparison. Variations were observed among previously studied guano samples and the Cabalyorisa Cave samples were attributed to either bat sources or age of the guano. This is the first study on bacterial diversity of guano in the Philippines through high-throughput sequencing.

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.