Genome wide underpinning of antagonistic and plant beneficial attributes of Bacillus sp. SBA12

Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health

Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.

Phylogenetic and Structural Analysis of Bacterial Nitrilases for the Biodegradation of Nitrile Compounds

BACKGROUND

Microbial nitrilases play a vital role in the biodegradation of nitrilecontaining pollutants, effluent treatments in chemical and textile industries, and the biosynthesis of Indole-3-acetic acid (IAA) from tryptophan in plants. However, the lack of structural information limits the correlation between its activity and substrate specificity.

METHODS

The present study involves the genome mining of bacteria for the distribution and diversity of nitrilases, their phylogenetic analysis and structural characterization for motifs/ domains, followed by interaction with substrates.

RESULTS

Here, we mined the bacterial genomes for nitrilases and correlated their functions to hypothetical, uncharacterized, or putative ones. The comparative genomics revealed four AcNit, As7Nit, Cn5Nit and Cn9Nit predicted nitrilases encoding genes as uncharacterized subgroups of the nitrilase superfamily. The annotation of these nitrilases encoding genes revealed relatedness with nitrilase hydratases and cyanoalanine hydratases. At the proteomics level, the motif analysis of these protein sequences predicted a single motif of 20-28 aa, with glutamate (E), lysine (K) and cysteine (C) residues as a part of catalytic triad along with several other residues at the active site. The structural analysis of the nitrilases revealed geometrical and close conformation in the form of α-helices and β-sheets arranged in a sandwich structure. The catalytic residues constituted the substrate binding pocket and exhibited the broad nitrile substrate spectra for aromatic and aliphatic nitriles-containing compounds. The aromatic amino acid residues Y159 in the active site were predicted to be responsible for substrate specificity. The substitution of non-aromatic alanine residue in place of Y159 completely disrupted the catalytic activity for indole-3-acetonitrile (IAN).

CONCLUSION

The present study reports genome mining and simulation of structure-function relationship for uncharacterized bacterial nitrilases and their role in the biodegradation of pollutants and xenobiotics, which could be of applications in different industrial sectors.

Genomic and Phenotypic Insights into the Potential of Bacillus subtilis YB-15 Isolated from Rhizosphere to Biocontrol against Crown Rot and Promote Growth of Wheat

Fusarium crown rot caused by Fusarium pseudograminearum is one of the most devastating diseases of wheat worldwide causing major yield and economic losses. In this study, strain YB-15 was isolated from soil of wheat rhizosphere and classified as Bacillus subtilis by average nucleotide identity analysis. It significantly reduced Fusarium crown rot with a control efficacy of 81.50% and significantly improved the growth of wheat seedlings by increasing root and shoot fresh weight by 11.4% and 4.2%, respectively. Reduced Fusarium crown rot may have been due to direct antagonism by the production of β-1, 3-glucanase, amylase, protease and cellulase, or by the ability of B. subtilis YB-15 to induce defense-related enzyme activities of wheat seedlings, both alone and in seedlings infected with F. pseudograminearum. Improved plant growth may be related to the ability of B. subtilis YB-15 to secrete indole acetic acid and siderophores, as well as to solubilize phosphorus. In addition, the genome of strain YB-15 was determined, resulting in a complete assembled circular genome of 4,233,040 bp with GC content of 43.52% consisting of 4207 protein-encoding genes. Sequencing the B. subtilis YB-15 genome further revealed genes for encoding carbohydrate-active enzymes, biosynthesis of various secondary metabolites, nutrient acquisition, phytohormone production, chemotaxis and motility, which could explain the potential of strain YB-15 to be plant growth-promoting bacteria and biological control agent. B. subtilis YB-15 appears to be a promising biocontrol agent against Fusarium crown rot as well as for wheat growth promotion.

Combination of rhizosphere bacteria isolated from resistant potato plants for biocontrol of potato late blight

BACKGROUND

Potato late blight (PLB) caused by Phytophthora infestans is one of the most devastating plant diseases. The heavy use of chemical control agents is at odds with the development of sustainable and environmentally friendly agriculture practices. It is necessary to screen the antagonistic microorganisms of P. infestans and provide a new choice of PLB biocontrol.

RESULTS

In vitro, eight bacterial strains (A, B, C, D, E, F, G, H) isolated from the rhizosphere of resistant potato plants had a significant inhibitory effect on the mycelium growth of P. infestans, and the inhibition rate was 35.02-79.20%. These isolates were assigned to Streptomyces, Pseudomonas, Saccharothrix and Nocardiopsis by phylogenetic analysis of 16S rRNA genes. Their physiological and biochemical characteristics suggested that they can produce cellulase and catalase, which may help to inhibit the infection of P. infestans. In vivo, each strain significantly inhibited the infection of P. infestans after individual inoculation into potato tubers, and no strains posed a pathogenic threat to tubers. In the field environment, multibacterial treatment significantly reduced the disease index. Compared with the control, multibacterial and single H treatment significantly increased the microbial species and abundance of the potato rhizosphere and enriched potential beneficial bacteria such as Rhizobiaceae. Meanwhile, multi-bacterial and single H treatment significantly reduced the abundance of Enterobacteriaceae and Bacillaceae.

CONCLUSION

Our results provide some valuable native strains from the potato rhizosphere with the ability to inhibit P. infestans in vivo and in vitro, which may be a new option for PLB biocontrol. © 2021 Society of Chemical Industry.

Genomic Organization of Streptomyces flavotricini NGL1 and Streptomyces erythrochromogenes HMS4 Reveals Differential Plant Beneficial Attributes and Laccase Production Capabilities

The genus Streptomyces has been explored in industrial sectors due to its endurance to environmental stresses, the production of a plethora of biomolecules, the biological remediation of soils, and alleviating plant stresses. The whole genome of NGL1 and HMS4 was sequenced due to the specific laccase activity against 2,6-dimethoxyphenol (2,6-DMP) and differential plant beneficial attributes. The deduced genome of 8.85 Mbp and 7.73 Mbp in size with a G+C content of 72.03% and 72.3% was obtained for NGL1 and HMS4, respectively. A total of 8438 and 7322 protein coding genes, 155 (130 tRNA, 25 rRNA) and 145 tRNA (121 tRNA, 24 rRNA) coding genes were predicted in NGL1 and HMS4, respectively. The comparative genomics of NGL1 and HMS4 showed 185 and 162 genes encoding for carbohydrate-active enzymes, respectively. The genomic ability of these strains to encode carbohydrate-active enzymes, laccase, and diversity of BGCs, along with plant beneficial attributes to suppress the plant pathogens can be used for several industrial and agricultural applications.

Genomic Analysis of Endophytic Bacillus cereus T4S and Its Plant Growth-Promoting Traits

Insights into plant endophytic microbes and their exploration in agriculture have provided opportunities for sustainable plant health and food safety. Notable endophytic Bacillus species with plant growth-promoting traits have been documented; nevertheless, information on genome analysis of B. cereus associated with the sunflower in South Africa has not been studied. Therefore, we present whole-genome sequence of agriculturally important B. cereus strain T4S isolated from sunflower plants. The NextSeq Illumina sequencing yielded 7,255,762 bp sequence reads, 151 bp average read length, 5,945,881 bp genome size, 56 tRNA, 63 rRNA, and G + C content of 34.8%. The phylogeny analysis of strain T4S was similar to B. cereus NJ-W. Secondary metabolites, such as petrobactin, bacillibactin, bacitracin, molybdenum factor, zwittermicin, and fengycin underlining bacterial biocontrol efficacy against phytopathogens were found in the T4S genome. The predicted novel genes in the bacterial genome mediating the complex metabolic pathways can provide a genetic basis in understanding endosphere biology and their multiple functions thereof in crop improvement. Interestingly, seed and root inoculation with strain T4S contributed to sunflower yield under greenhouse experiments. Hence, the detection of notable genes specific for plant growth promotion as validated under in vitro screening, promisingly, suggests the relevance of strain T4S in agricultural biotechnology.

Antifungal Mechanism of Volatile Organic Compounds Produced by Bacillus subtilis CF-3 on Colletotrichum gloeosporioides Assessed Using Omics Technology

Bacillus subtilis is commonly used as a biocontrol bacterium owing to its strong antifungal activity, broad-spectrum inhibition, and general safety. In this study, the inhibitory effects of volatile organic compounds (VOCs) produced by B. subtilis CF-3 on Colletotrichum gloeosporioides, a major destructive phytopathogen of litchi anthracnose, were analyzed using proteomics and transcriptomics. Differentially expressed genes (DEGs) and proteins (DEPs) indicated that the inhibition of C. gloeosporioides by B. subtilis CF-3 VOCs downregulated the expression of genes related to cell membrane fluidity, cell wall integrity, energy metabolism, and production of cell wall-degrading enzymes. Particularly, those important DEGs and DEPs related to the ergosterol biosynthetic and biosynthesis of unsaturated fatty acids are most significantly influenced. 2,4-di-tert-butylphenol, a characteristic component of B. subtilis CF-3 VOCs, also showed a similar effect on C. gloeosporioides. Our results provide a theoretical basis for the potential application of B. subtilis CF-3 in the postharvest protection of fruits and vegetables.