Oryza sativa L. Raw sequence reads
Rice germination and seedlings growth depend on several factors, including the abundance and diversity of seed microbial endophytes. Two rice varieties, NERICA 3 and NERICA 8, were used for investigating the seed-associated microbiome using the Illumina-based 16S rRNA gene. After analyses, significant differences were observed in terms of richness index between normal and abnormal seedlings that developed from sprouting seeds, although no significant species evenness index was assessed within either phenotype. Two hundred ninetytwo bacterial amplicon sequence variants were identified in seed microbiome of the rice varieties, and principal coordinate analysis revealed that microbial communities formed two distinct clusters in normal and abnormal seedling phenotypes. Overall, 38 bacteria gen-era were identified, belonging to 6 main phyla. Furthermore, the core microbiome was defined, and the differential abundance of 28 bacteria genera was assessed. Based on the collected results, putative bacterial genera were directly correlated with the development of normal seedlings. For the majority of genera that are recognised to include beneficial species, such as Brevundimonas, Sphingomonas, Exiguobacterium, Luteibacter, Microbacte-rium and Streptomyces, a significant increase of their relative abundance was found in normal seedlings. Additionally, in abnormal seedlings, we also observed an increased abundance for a few bacteria (Kosakonia and Paenibacillus) that might have controversial aspects (beneficial and pathogenic), together with the appearance of some genera (e.g. Clostridium sensu stricto) that are commonly correlated with adverse conditions for plant health. Data presented in this study may help the scientific community in further under-standing the importance of the seed microbiome for driving a correct development of rice plants at the early stages and to identify possible beneficial bacteria to ensure seeds and seedlings health for possible technological applications.