AUTHOR=Wang Yuhu , Zhao Qianqian , Sun Zhenqi , Li Yahui , He Hongtao , Zhang Yuanyu , Yang Xiangdong , Wang Dong , Dong Baozhu , Zhou Hongyou , Zhao Mingmin , Zheng Hongli 

TITLE=Whole-genome analysis revealed the growth-promoting mechanism of endophytic bacterial strain Q2H1 in potato plants

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1035901

DOI=10.3389/fmicb.2022.1035901

ISSN=1664-302X

ABSTRACT=<sec><title>Introduction</title><p>Endophytes are non-pathogenic inhabitants of healthy plant tissues and have been found to promote plant growth and health. The endophytic bacterial strain Q2H1 was isolated from the roots of the potato and was identified to exhibit growth-promoting effects in potato plants.</p></sec><sec><title>Methods</title><p>Whole-genome sequencing was performed to reveal the mechanism underlying its growth-promoting effect. The obtained sequencing data of approximately 5.65 MB encompassed 5,533 coding sequences. Of note, nine secondary metabolite gene clusters, including siderophore gene clusters, closely associated with plant growth promotion (PGP) were predicted by antiSMASH software. Comparative genomic analysis revealed that Q2H1 belongs to the genus <italic>Peribacillus</italic>. By gene function annotation, those genes related to plant growth-promoting activities, including indole-3-acetic acid (IAA) synthesis in tryptophan metabolism, siderophore biosynthetic activity, phosphate solubilization, nitrogen fixation, and related genes, were summarized. IAA (14.4 μg/ml) was presumptively produced by Q2H1 using the Salkowski colorimetric method. A total of five genes, namely, <italic>phoU, pstB, pstA1, pstC</italic>, and <italic>pstS</italic>, were annotated for phosphate solubilization, which is associated with the ability of the Q2H1 strain to solubilize phosphate under <italic>in vitro</italic> conditions.</p></sec><sec><title>Results</title><p>It is revealed that genes in the Q2H1 genome associated with nitrogen fixation belonged to three groups, namely, nitrogen fixation (<italic>nifU, sufU, salA</italic>, and <italic>nifS</italic>), nitrogen metabolism (<italic>nirA, nrtB</italic>, and <italic>nasA</italic>), and glutamate synthesis (<italic>glnA, gltB, gltD</italic>, and <italic>gudB</italic>), supported by evidence that Q2H1 grew on medium without nitrogen. We have also identified a siderophore gene cluster located on the chromosome of Q2H1, including seven genes (<italic>viz., rbsR, rhbf, rhbE, rhbD, rhbC, rhbA, ddc</italic>, and an unknown gene). In the <italic>in vitro</italic> assay, a prominent brown circle around the colony was produced on the chrome azurol S medium at 48 and 72 h post-inoculation, indicating that the siderophore gene cluster in Q2H1 harbored the ability to produce siderophores.</p></sec><sec><title>Conclusion</title><p>In summary, these findings implied that identifying strain-specific genes for their metabolic pathways in bacterial endophytes may reveal a variety of significant functions of plant growth-promoting mechanisms.</p></sec>