The innovation team of Agricultural microbial resources,  Institute of Agricultural Resources and Regional Planning (IARRP) of the Chinese Academy of Agricultural Sciences (CAAS) established the rice endophytes microbial resource library and clarified the function of the core seed endophytes and its vertical communication mechanism by multi-scale omics anaylsis.

Related results were published on the academic journal "Microbiome", which is well known in the field of microbiology.

Plant associated microbiota is called the "second genome" of plants, and the endophyte microbiome is the core of plant-related microbiome, which plays a key role in plant evolution, disease resistance, and nutrient uptake.

Based on the microbiome data of two generations of six different rice varieties from five microhabitats from four geographic locations, the research conducted an in-depth analysis and built a resource library. The preferences of rice related microbiota assembly and the dynamic changes in different rice microhabitats were illustrated. The core bacterial endophytes of rice were primarily comprised of 14 amplicon sequence variants (ASVs) and three Pantoea species and one Xanthomonas sacchari species were successfully isolated with vertical transmission characteristic. Functional genome analysis shows that these two types of bacterial genomes are simple, pathogenic characteristic free and including special secondary metabolic and enzymic genes, with the beneficial characteristics such as phosphorus dissolution and plant promotion.

This study proposed and verified the vertical transmission mechanism of the rice endophytes through omics analysis, which has innovative significance in the aspect of microorganism-plant co-evolution field. In addition, the establishment of rice endophytes microbial resource library provides a resource basis for the development and utilization of this special microorganisms. Some important microorganisms with the potential of nutrient transformation and uptake, disease and resistance will shed the light on the development of microbial fertilizers, microbial pesticides, microbial seed coating agents, and microbial preservatives.

Professor Xiaoxia Zhang and Dr. Yi-Nan Ma are the first authors of the paper, and professor Hai-Lei Wei is the corresponding author. The study was funded by the National Natural Science Foundation of China, the Fundamental Research Funds for Central Public-interest Scientific Institutions and the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences.