Genome analysis of a halophilic Virgibacillus halodenitrificans ASH15 revealed salt adaptation, plant growth promotion, and isoprenoid biosynthetic machinery

Abstract

Globally, due to widespread dispersion, intraspecific diversity, and crucial ecological components of halophilic ecosystems, halophilic bacteria is considered one of the key models for ecological, adaptative, and biotechnological applications research in saline environments. With this aim, the present study was to enlighten the plant growth-promoting features and investigate the systematic genome of a halophilic bacteria, Virgibacillus halodenitrificans ASH15, through single-molecule real-time (SMRT) sequencing technology. Results showed that strain ASH15 could survive in high salinity up to 25% (w/v) NaCl concentration and express plant growth-promoting traits such as nitrogen fixation, plant growth hormones, and hydrolytic enzymes, which sustain salt stress. The results of pot experiment revealed that strain ASH15 significantly enhanced sugarcane plant growth (root shoot length and weight) under salt stress conditions. Moreover, the sequencing analysis of the strain ASH15 genome exhibited that this strain contained a circular chromosome of 3,832,903 bp with an average G+C content of 37.54%: 3721 predicted protein-coding sequences (CDSs), 24 rRNA genes, and 62 tRNA genes. Genome analysis revealed that the genes related to the synthesis and transport of compatible solutes (glycine, betaine, ectoine, hydroxyectoine, and glutamate) confirm salt stress as well as heavy metal resistance. Furthermore, functional annotation showed that the strain ASH15 encodes genes for root colonization, biofilm formation, phytohormone IAA production, nitrogen fixation, phosphate metabolism, and siderophore production, which are beneficial for plant growth promotion. Strain ASH15 also has a gene resistance to antibiotics and pathogens. In addition, analysis also revealed that the genome strain ASH15 has insertion sequences and CRISPRs, which suggest its ability to acquire new genes through horizontal gene transfer and acquire immunity to the attack of viruses. This work provides knowledge of the mechanism through which V. halodenitrificans ASH15 tolerates salt stress. Deep genome analysis, identified MVA pathway involved in biosynthesis of isoprenoids, more precisely “Squalene.” Squalene has various applications, such as an antioxidant, anti-cancer agent, anti-aging agent, hemopreventive agent, anti-bacterial agent, adjuvant for vaccines and drug carriers, and detoxifier. Our findings indicated that strain ASH15 has enormous potential in industries such as in agriculture, pharmaceuticals, cosmetics, and food.

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.…”

Fertilising Maize with Bio-Based Mineral Fertilisers Gives Similar Growth to Conventional Fertilisers and Does Not Alter Soil Microbiome

“…This cluster encompasses a broader range of genera, predominantly comprising PGPR species or indicators of soil health. Notable genera in this cluster include Bdellovibrio, Massilia, Phormidium, Phormidesmis, Acidovorax, Flavobacterium, Olivibacter, Arthrobacter, Kocuria, Noviherbaspirillum, and Nafulsella, previously mentioned as beneficial microorganisms; as well as Dyadobacter, known as a PGPR commonly present in the rhizosphere that enhances crop yield [81]; Streptomyces, commonly found in plant microbiomes with PGPR characteristics [82]; Rubrobacter, associated with potassium absorption and soil health [69,83]; Virgibacillus, housing halophytic PGPR species [84,85]; Pseudonocardia, a P-solubilizing bacterium and disease-suppressive bacterial agent [86,87]; Nocardioides, possessing PGPR capabilities to mitigate saline stress conditions [88,89]; and Promicromonospora, a PGPR producing gibberellins and mitigating the adverse effects of salinity and osmotic stress [90,91].…”

Synergistic interactions of nanoparticles and plant growth promoting rhizobacteria enhancing soil-plant systems: a multigenerational perspective

“…Because the soils carry out a wide range of ecological functions, it is characterized from the viewpoint of those functions. From the perspectives of concurrent agriculture and the environment, it is described as “the capacity of a soil to function within ecosystem and land-use boundaries to sustain biological productivity, maintain environmental quality, and promote plant and animal health” ( Verma et al., 2022d ; Anikwe and Ife, 2023 ; Sharma et al., 2023 ). The main chemical elements of soil quality are soil organic matter, pH, and accessible macronutrients (nitrogen, phosphorus, and potassium).…”

“…Application of Enterobacter, Pseudomonas, Azospirillum, Agrobacterium and NPs enhanced sustainable agriculture production. The interactive use of PGPR and NPs may enhance seed germination frequency, height of plants, dry-fresh biomass, and crop productivity than the single use of PGPR or NPs ( Medina-Velo et al., 2017 ; Fadiji et al., 2022 ; Sharma et al., 2023 ). This combination can work in different directions.…”

“…Most PGPRs have been reported and confirmed to improve plant productivity by reducing environmental challenges ( Singh et al., 2021 ; Kumari et al., 2023a ). Through both direct and indirect strategies, it may enhance the overall quality of soil and plant yield ( Figure 1 ) ( Sharma et al., 2023 ; Rajput et al., 2023a ). The functions of PGPR occur through direct mechanisms such as nitrogen fixation, phosphate, and potassium solubilization, and the production of growth-promoting phytohormones like indole acetic acid (IAA) and siderophores.…”