Oryza sativa L. Raw sequence reads. Oryza sativa L.

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.

水稻萌发与幼苗生长受多种因素调控，其中种子内生微生物（seed microbial endophytes）的丰度与多样性是关键影响因素之一。本研究选取NERICA 3与NERICA 8两个水稻品种，采用基于Illumina平台的16S rRNA基因测序技术，解析其种子相关微生物组（seed-associated microbiome）。分析结果显示，由萌发种子发育而成的正常幼苗与异常幼苗之间，群落丰富度指数存在显著差异；但两种表型下的物种均匀度指数均未表现出显著差异。本研究在两个水稻品种的种子微生物组中共鉴定得到292个细菌扩增子序列变体（amplicon sequence variant, ASV）；主坐标分析（principal coordinate analysis, PCoA）结果显示，对应正常与异常幼苗表型的微生物群落各自形成了两个独立的聚类簇。整体而言，共鉴定出38个细菌属，分属于6个主要的细菌门。此外，本研究明确了该体系的核心微生物组，并对28个细菌属的丰度差异进行了分析。基于所得结果，推定部分细菌属与正常幼苗的发育存在直接关联。其中，包括寡养单胞菌属（Brevundimonas）、鞘氨醇单胞菌属（Sphingomonas）、微小杆菌属（Exiguobacterium）、黄色杆菌属（Luteibacter）、微杆菌属（Microbacterium）以及链霉菌属（Streptomyces）在内的多数被报道包含有益菌株的菌属，在正常幼苗中的相对丰度均显著升高。此外，在异常幼苗中，部分兼具益生与致病双重特性的细菌——如科斯氏菌属（Kosakonia）与类芽孢杆菌属（Paenibacillus）——的相对丰度出现上升；同时还检出了通常与植物健康逆境相关的梭菌严格厌氧簇（Clostridium sensu stricto）等多个菌属。本研究所得数据可为学界进一步明晰种子微生物组在水稻早期发育中的调控作用提供参考，并有助于筛选潜在有益细菌以保障种子与幼苗健康，为相关技术应用奠定基础。