Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes

Abstract

Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation. 16S rRNA gene sequence analysis has indicated the dominance of halophilic/halotolerant phylotypes affiliated to Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Acidobacteria. A functional metagenomics approach led to the identification of osmotolerant clones SSR1, SSR4, SSR6, SSR2 harboring BCAA_ABCtp, GSDH, STK_Pknb, and duf3445 genes. Furthermore, transposon mutagenesis, genetic, physiological and functional studies in close association has confirmed the role of these genes in osmotolerance. Enhancement in host osmotolerance possibly though the cytosolic accumulation of amino acids, reducing equivalents and osmolytes involving BCAA-ABCtp, GSDH, and STKc_PknB. Decoding of the genetic elements prevalent within these microbes can be exploited either as such for ameliorating soils or their genetically modified forms can assist crops to resist and survive in saline environment.

Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem

“…The other strategy is the “low-salt-in” strategy, which involves accumulating low-molecular-weight organic compounds (e.g., amino acids and carbohydrates) within the cell to exclude salt from the cell (35). Previous culture-independent studies detected dominant halophilic and halotolerant taxa affiliated with the bacterial phyla Proteobacteria , Actinobacteria , Bacteroidetes , and Gemmatimonadetes (36, 37). The microbial taxa belonging to Proteobacteria , Bacteroidetes , Actinobacteria , and Halobacteria detected in this study have a high-salinity niche preference (Fig.…”

Extreme Osmotolerance and Halotolerance in Food-Relevant Yeasts and the Role of Glycerol-Dependent Cell Individuality

“…Glycerol is the most common compatible solute in yeasts grown on glucose (Babazadeh et al, 2017), but other species accumulate arabitol or mannitol (Van Eck et al, 1993), or glycine/betaine in bacteria (Welsh, 2000). Nevertheless, metagenomic profiling of microbial populations from saline environments has shown enrichment of conserved osmotolerance gene functions (Ahmed et al, 2018).…”

Isolation of gene conferring salt tolerance from halophilic bacteria of Lunsu, Himachal Pradesh, India

“…Similarly, Ahmed et al [19] reported recombinant plasmids named as pSSR1, pSSR4, pSSR6, and pSSR21, which showed significant growth in the presence of NaCl [4.0% (w/v)] and KCl [5.5% (w/v)] as compared to E. coli (DH10B) strain carrying empty plasmid vector (pUC19) [19].…”

“…Ahmed et al [19] reported a putative branched-chain amino acid (BCAA) ABC transporter gene (BCAA_ABCTP) (putative BCAA_ABCTP) gene, which was subcloned (pSSR1C1) in salt-sensitive E. coli strain MKH13. The transformed strain bearing pSSR1C1 showed a significant growth in the presence of NaCl [3.0% (w/v)] and KCl [3.7% (w/v)] as compared to the strain carrying only the empty vector (pUC19) [19]. In another study, a metagenomic library from the human gut microbiota was screened for potential salttolerant clones [23].…”