AUTHOR=Huang Xiaoping , Zeng Zhanghui , Chen Zhehao , Tong Xiaxiu , Jiang Jie , He Chenjing , Xiang Taihe 

TITLE=Deciphering the potential of a plant growth promoting endophyte Rhizobium sp. WYJ-E13, and functional annotation of the genes involved in the metabolic pathway

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1035167

DOI=10.3389/fmicb.2022.1035167

ISSN=1664-302X

ABSTRACT=<p>Plant growth-promoting rhizobacteria (PGPR) are well-acknowledged root endophytic bacteria used for plant growth promotion. However, which metabolites produced by PGPR could promote plant growth remains unclear. Additionally, which genes are responsible for plant growth-promoting traits is also not elucidated. Thus, as comprehensive understanding of the mechanism of endophyte in growth promotion is limited, this study aimed to determine the metabolites and genes involved in plant growth-promotion. We isolated an endophytic <italic>Rhizobium</italic> sp. WYJ-E13 strain from the roots of <italic>Curcuma wenyujin</italic> Y.H. Chen <italic>et</italic> C. Ling, a perennial herb and medicinal plant. The tissue culture experiment showed its plant growth-promoting ability. The bacterium colonization in the root was confirmed by scanning electron microscopy and paraffin sectioning. Furthermore, it was noted that the WYJ-E13 strain produced cytokinin, anthranilic acid, and L-phenylalanine by metabolome analysis. Whole-genome analysis of the strain showed that it consists of a circular chromosome of 4,350,227 bp with an overall GC content of 60.34%, of a 2,149,667 bp plasmid1 with 59.86% GC, and of a 406,180 bp plasmid2 with 58.05% GC. Genome annotation identified 4,349 putative protein-coding genes, 51 tRNAs, and 9 rRNAs. The CDSs number allocated to the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and Clusters of Orthologous Genes databases were 2027, 3,175 and 3,849, respectively. Comparative genome analysis displayed that <italic>Rhizobium</italic> sp. WYJ-E13 possesses the collinear region among three species: <italic>Rhizobium acidisoli</italic> FH23, <italic>Rhizobium gallicum</italic> R602 and <italic>Rhizobium phaseoli</italic> R650. We recognized a total set of genes that are possibly related to plant growth promotion, including genes involved in nitrogen metabolism (<italic>nifU</italic>, <italic>gltA</italic>, <italic>gltB</italic>, <italic>gltD</italic>, <italic>glnA</italic>, <italic>glnD</italic>), hormone production (<italic>trp ABCDEFS</italic>), sulfur metabolism (<italic>cysD</italic>, <italic>cysE</italic>, <italic>cysK</italic>, <italic>cysN</italic>), phosphate metabolism (<italic>pstA</italic>, <italic>pstC</italic>, <italic>phoB</italic>, <italic>phoH</italic>, <italic>phoU</italic>), and root colonization. Collectively, these findings revealed the roles of WYJ-E13 strain in plant growth-promotion. To the best of our knowledge, this was the first study using whole-genome sequencing for <italic>Rhizobium</italic> sp. WYJ-E13 associated with <italic>C. wenyujin</italic>. WYJ-E13 strain has a high potential to be used as <italic>Curcuma</italic> biofertilizer for sustainable agriculture.</p>