Insight into the diversity and application characters of endophytes in ramie (Boehmeria nivea L. Gaud)

Endophytes are essential for plant growth and resistance to stress. However, little is known about endophytes of ramie, which is an important fiber crop. Here, to gain insight into ramie endophytes, we collected 180 samples of three varieties ramie across four microhabitats (rhizosphere, root, stem, and leaf) in three geographic locations, and further endophyte Pseudomonas sp. B4 was isolated and its function was analyzed. The results demonstrated that microhabitat was the primary for ramie bacterial assemblage rather than geographic location or ramie variety. For endophytes, Cyanobacteria was the main phylum (>75 %, in the roots, stems, and leaves); Proteobacteria was the secondary phylum, and with relative abundance of 9.08 %, 14.97 % and 16.28 % in the roots, stems and leaves, respectively. The results of LEfSe analysis indicated Sphingomonas and Acidothermus were the biomarkers in the rhizosphere, Clostridia was the biomarker in the roots, and unidentified Chloroplast and Ralstonia were biomarkers in the stems and leaves, respectively. From the rhizosphere to the leaves, the co-occurrence network complexity gradually decreased, and the co-occurrence network of the leaves was the simplest. Proteobacteria was the key taxa according to the co‑occurrence networks analysis results. In addition, Pseudomonas sp. B4, which belongs to γ- Proteobacteria , was isolated from ramie plants and could increase plant height (19.92 %), stem diameter (10.39 %) and fiber yield (21.67 %) remarkably. Overall, this study elucidated the composition and potential functions of ramie endophytes. And, the endophyte B4 improved ramie growth and fiber yield. These findings provide a basis for understanding endophyte assembly and for managing crop microbiome for sustainable agriculture. • Bacterial assembly changed largely along with rhizosphere, root, stem, and leaf in ramie. • Microhabitat was more primary for ramie endophytes assemblage rather than geographic location and ramie variety in ramie. • Endophyte Pseudomonas sp. B4 could increase plant height, stem diameter and fiber yield remarkably.