Genome-Guided Insights into the Plant Growth Promotion Capabilities of the Physiologically Versatile Bacillus aryabhattai Strain AB211

Abstract

Bacillus aryabhattai AB211 is a plant growth promoting, Gram-positive firmicute, isolated from the rhizosphere of tea (Camellia sinensis), one of the oldest perennial crops and a major non-alcoholic beverage widely consumed all over the world. The whole genome of B. aryabhattai AB211 was sequenced, annotated and evaluated with special focus on genomic elements related to plant microbe interaction. It’s genome sequence reveals the presence of a 5,403,026 bp chromosome. A total of 5226 putative protein-coding sequences, 16 rRNA, 120 tRNA, 8 ncRNAs, 58 non-protein coding genes, and 11 prophage regions were identified. Genome sequence comparisons between strain AB211 and other related environmental strains of B. aryabhattai, identified about 3558 genes conserved among all B. aryabhattai genomes analyzed. Most of the common genes involved in plant growth promotion activities were found to be present within core genes of all the genomes used for comparison, illustrating possible common plant growth promoting traits shared among all the strains of B. aryabhattai. Besides the core genes, some genes were exclusively identified in the genome of strain AB211. Functional annotation of the genes predicted in the strain AB211 revealed the presence of genes responsible for mineral phosphate solubilization, siderophores, acetoin, butanediol, exopolysaccharides, flagella biosynthesis, surface attachment/biofilm formation, and indole acetic acid production, most of which were experimentally verified in the present study. Genome analysis and experimental evidence suggested that AB211 has robust central carbohydrate metabolism implying that this bacterium can efficiently utilize the root exudates and other organic materials as an energy source. Genes for the production of peroxidases, catalases, and superoxide dismutases, that confer resistance to oxidative stresses in plants were identified in AB211 genome. Besides these, genes for heat shock tolerance, cold shock tolerance, glycine-betaine production, and antibiotic/heavy metal resistance that enable bacteria to survive biotic/abiotic stress were also identified. Based on the genome sequence information and experimental evidence as presented in this study, strain AB211 appears to be metabolically diverse and exhibits tremendous potential as a plant growth promoting bacterium.

Increase in phenolic compounds of Coriandrum sativum L. after the application of a Bacillus halotolerans biofertilizer

“…Soil microorganisms have been described having as an important role in natural phosphorus cycling, as a result of solubilizing and precipitating phosphorus processes. In general, these processes depend on pH and soil type . According to several enzymes involved in making insoluble phosphorous compounds available for plant cellular growth, biological solubilization is currently a focus of great special attention.…”

“…Whole transcriptomic analysis of the strain Bacillus amyloliquefacines SQR9 colonising maize plant roots revealed that some of the most upregulated genes were related to biofilm formation . The genome of other reported PGPR Bacillus strains also included genes linked to mineral phosphate solubilization, siderophore and exopolysaccharide production, and root surface attachment …”

“…In general, these processes depend on pH and soil type. 29 According to several enzymes involved in making insoluble phosphorous compounds available for plant cellular growth, biological solubilization is currently a focus of great special attention. The results of the present study are in agreement with the studies by Banerjee et al 30 and Maheswar and Sathiyavani, 31 which also report several Bacillus strains with higher phosphate solubilizing activity.…”

“…34 The genome of other reported PGPR Bacillus strains also included genes linked to mineral phosphate solubilization, siderophore and exopolysaccharide production, and root surface attachment. 29 It is commonly accepted that efficient PGPR strains colonize roots under a wide range of conditions, predominantly by forming biofilms. 35 Bacterial plant root attachment is essential for successful colonization.…”

Causes and consequences of soil bacterial rarity

“…However, even if rare species are demonstrated to have a large influence on ecosystem functions, it is often not clear whether the rare species themselves are involved in supporting this function or if they do so by affecting more abundant species. One way to test the functional potential of a bacterial species is whole genome sequencing, which is becoming increasingly affordable and builds on an increasing database of reference genomes (Land et al 2015, Bhattacharyya et al 2017. Still, actual functional traits have to be tested experimentally by isolating the respective species.…”