Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea.
Research Institute of Climate Change and Agriculture, National Institute of Horticultural & Herbal Science, RDA, Jeju, 63240, South Korea.
Sci Rep. 2019 Jun 26;9(1):9300. doi: 10.1038/s41598-019-45660-8.
Plant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots under natural systems, we characterized the bacterial, archaeal, and fungal communities of three belowground compartments (rhizosphere, endosphere, and bulk soil) of tomato plants collected from 23 greenhouses in 7 geographic locations of South Korea. The microbial diversity and structure varied by rhizocompartment, with the most distinctive community features found in the endosphere. The bacterial and fungal communities in the bulk soil and rhizosphere were correlated with soil physicochemical properties, such as pH, electrical conductivity, and exchangeable cation levels, while this trend was not evident in the endosphere samples. A small number of core bacterial operational taxonomic units (OTUs) present in all samples from the rhizosphere and endosphere represented more than 60% of the total relative abundance. Among these core microbes, OTUs belonging to the genera Acidovorax, Enterobacter, Pseudomonas, Rhizobium, Streptomyces, and Variovorax, members of which are known to have beneficial effects on plant growth, were more relatively abundant in the endosphere samples. A co-occurrence network analysis indicated that the microbial community in the rhizosphere had a larger and more complex network than those in the bulk soil and endosphere. The analysis also identified keystone taxa that might play important roles in microbe-microbe interactions in the community. Additionally, profiling of predicted gene functions identified many genes associated with membrane transport in the endospheric and rhizospheric communities. Overall, the data presented here provide preliminary insight into bacterial, archaeal, and fungal phylogeny, functionality, and interactions in the rhizocompartments of tomato roots under real-world environments.
植物微生物组是决定植物健康和生产力的关键因素。植物微生物组的组成和结构根据植物组织和隔室而变化，这些隔室是微生物定植的特定栖息地。为了研究与自然系统中番茄根系相关的微生物组的结构组成，我们对从韩国 7 个地理位置的 23 个温室中采集的番茄植物的三个地下隔室（根际、内围和土壤）的细菌、古菌和真菌群落进行了特征描述。微生物多样性和结构因根际隔室而异，内围的群落特征最为独特。土壤理化性质（如 pH 值、电导率和可交换阳离子水平）与土壤和根际中的细菌和真菌群落相关，但这种趋势在内围样本中并不明显。在根际和内围的所有样本中都存在的少数核心细菌操作分类单元（OTUs）代表了总相对丰度的 60%以上。在这些核心微生物中，属于 Acidovorax、Enterobacter、Pseudomonas、Rhizobium、Streptomyces 和 Variovorax 属的 OTUs，这些属的成员已知对植物生长有有益的影响，在内围样本中更为丰富。共现网络分析表明，根际微生物群落的网络比土壤和内围微生物群落的网络更大、更复杂。该分析还确定了在群落中可能对微生物相互作用发挥重要作用的关键类群。此外，预测基因功能的分析确定了内围和根围群落中许多与膜转运相关的基因。总的来说，这里提供的数据初步揭示了真实环境中番茄根系根际区细菌、古菌和真菌的系统发育、功能和相互作用。
