Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures

• Published in: PloS one Vol. 16; no. 2; p. e0246687
• Main Authors: Peng, Xiaojue, Xie, Jian, Li, Wenzhuo, Xie, Hongwei, Cai, Yaohui, Ding, Xia
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 08.02.2021; Public Library of Science (PLoS)
• Subjects: Agricultural sciences; Aquatic plants; Archaea; Archaea - genetics; Archaea - metabolism; Bacteria; Bacteria - genetics; Bacteria - metabolism; Biogeochemistry; Biology and Life Sciences; Breeding; Computer and Information Sciences; Computer programs; Deoxyribonucleic acid; DNA; Drafting software; Ecology and Environmental Sciences; Endophytes; Environmental aspects; Ethanol; Filter paper; Floods; Fluorometers; Funding; Fungi; Gene amplification; Gene Expression Profiling - methods; Genetic aspects; Insect pests; Insects; Life sciences; Microbiomes; Microbiota; Microbiota (Symbiotic organisms); Microbiota - genetics; Microorganisms; Nitrogen; Oryza - genetics; Oryza - metabolism; Oryza - microbiology; Oryza longistaminata; Pests; Phylogeny; Plant Leaves - microbiology; Plant Roots - microbiology; Quality assessment; R&D; Research & development; Research and Analysis Methods; Rhizome - genetics; Rhizome - metabolism; Rhizome - microbiology; Rhizomes; Rice; RNA, Ribosomal, 16S - genetics; rRNA 16S; Seeds; Software; Veganism; Viruses; Visualization; China; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0246687

Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O . longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O . longistaminata . The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus , Bacillus , and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter , YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae , which potentially benefits the host by facilitating CH 4 -dependent N 2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O . longistaminata in nutrient-poor environments for biofertilizer development in agriculture.