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

Abstract

IntroductionEndophytes 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.MethodsWhole-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 Peribacillus. 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, phoU, pstB, pstA1, pstC, and pstS, were annotated for phosphate solubilization, which is associated with the ability of the Q2H1 strain to solubilize phosphate under in vitro conditions.ResultsIt is revealed that genes in the Q2H1 genome associated with nitrogen fixation belonged to three groups, namely, nitrogen fixation (nifU, sufU, salA, and nifS), nitrogen metabolism (nirA, nrtB, and nasA), and glutamate synthesis (glnA, gltB, gltD, and gudB), 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 (viz., rbsR, rhbf, rhbE, rhbD, rhbC, rhbA, ddc, and an unknown gene). In the in vitro 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.ConclusionIn 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.

Whole-genome analysis revealed the growth-promoting and biological control mechanism of the endophytic bacterial strain Bacillus halotolerans Q2H2, with strong antagonistic activity in potato plants

“…The endophytic strain Q2H2 was isolated from potato roots (Atlantic variety) and stored at −80°C in 50% glycerol. The cells were cultured in Luria-Bertani (LB) medium, as described by Wang et al (2022b) .…”

“…The PCR system and program were operated according to the Taq polymerase instructions (TaKaRa, Dalian, China). Genomic DNA was used as the template for PCR amplification ( Table 1 ; Wang et al, 2022b ). The PCR products were purified and sequenced by BGI (Shenzhen, China).…”

“…The sample preparation and genome sequencing methods have previously been described by Wang et al (2022b) . Q2H2 samples were sent to Biomarker Technologies (Beijing, China) for genome sequencing using single-molecule real-time sequencing on the PacBio platform.…”

“…Genome component analysis and functional annotation of Q2H2 were performed using a method described by Wang et al (2022b) .…”

Culturable Bacterial Endophytes of Wild White Poplar (Populus alba L.) Roots: A First Insight into Their Plant Growth-Stimulating and Bioaugmentation Potential

“…The members of Peribacillus genus has been previously identified as an endophyte of pine, and genetically close strains Q2H1 and P. castrilensis as growth-promoting bacteria in potato and tomato, respectively [107,108]. One of the most interesting features of Peribacillus sp.…”