Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2T

Abstract

Endophytes can facilitate the improvement of plant growth and health in agriculturally important crops, yet their genomes and secondary metabolites remain largely unexplored. We previously isolated Saccharibacillus brassicae strain ATSA2T from surface-sterilized seeds of kimchi cabbage and represented a novel species of the genus Saccharibacillus. In this study, we evaluated the plant growth-promoting (PGP) effect of strain ATSA2T in kimchi cabbage, bok choy, and pepper plants grown in soils. We found a significant effect on the shoot and root biomass, and chlorophyll contents following strain ATSA2T treatment. Strain ATSA2T displayed PGP traits such as indole acetic acid (IAA, 62.9 μg/mL) and siderophore production, and phosphate solubilization activity. Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition (fhuABD, afuABC, fbpABC, and fepCDG) and phosphate solubilization (pstABCHS, phoABHLU, and phnCDEP) and other phytohormone biosynthesis genes, including indole-3-acetic acid (trpABCDEFG), in the genome. Interestingly, the secondary metabolites cerecidin, carotenoid, siderophore (staphylobactin), and bacillaene underlying plant growth promotion were found in the whole genome via antiSMASH analysis. Overall, physiological testing and genome analysis data provide comprehensive insights into plant growth-promoting mechanisms, suggesting the relevance of strain ATSA2T in agricultural biotechnology.

Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter

“…Nevertheless, other iron-siderophores involved in siderophore uptake were identified in the genomes, including a ferric uptake regulator ( perR ), and the iron ABC transporters afuABC and fbpABC . Furthermore, similar to our study, both ABC transporters in Saccharibacillus brassicae (Jiang et al 2023 ) and Virgibacillus halodenitrificans (Sharma et al 2023 ) were identified as siderophore transport systems. Therefore, we suggest that L. irui may be able to acquire iron and make it available to plants.…”

“…The four pst genes ( pstS , pstC , pstA , and pstB ) from the phosphate-specific transport (Pst), an important bacterial transport system for phosphate, were also present in all genomes analyzed. Previously, Yuan et al ( 2022 ) and Jiang et al ( 2023 ) had also reported the presence of pstABCS in the plant growth-promoting bacteria Paenibacillus peoriae and Saccharibacillus brassicae , respectively.…”

“…Iron is an essential nutrient required for plant growth but is not available to plants due to its low bioavailability in soil (Jiang et al 2023 ). The biosynthetic gene cluster dhbABCDEF is responsible for the synthesis of the iron-siderophore bacillibactin, and it has been detected in Bacillus amyloliquefaciens (Niazi et al 2014 ) and Bacillus velezensis (Rabbee et al 2019 ).…”

“…Various studies have used whole-genome sequencing and comparative analysis to delve into the intricate bacterial mechanisms that contribute to the promotion of plant growth. Examples include investigations on Bacillus pumilus strain SF-4 (Iqbal et al 2021 ), Bacillus subtilis BS87 (Chandra et al 2021 ), Saccharibacillus brassicae ATSA2 (Jiang et al 2023 ), and Paenibacillus peoriae ZBSF16 (Yuan et al 2022 ). Numerous studies highlight the plant growth-promoting abilities of Lysinibacillus (Ahsan and Shimizu 2021 ; Naureen et al 2017 ; Pantoja-Guerra et al 2023 ; Sahu et al 2018 ).…”

Penicillium citrinum Provides Transkingdom Growth Benefits in Choy Sum (Brassica rapa var. parachinensis)

“…Current trends in agriculture are focused towards reducing the input of inorganic fertilizers and the use of PGP microbes to achieve sustainability. Mentioned hitherto, the world of PGP microbes remains unexplored as far as Choy Sum is concerned, although some reports have described such beneficial microbes and endophytic fungi in other Brassicaceae species [6][7][8][9][10]. Plant growth-promoting rhizobacteria (PGPR) colonize roots and enhance plant growth directly and indirectly [11,12].…”