Understanding microbial salt-stress biology through “omic” approaches

Halotolerant microorganisms are capable of growing in the absence as well as in the presence of relatively high salt concentrations. The biology of the salt affected habitats is studied using high throughput “omic” approaches consisting of metagenomics, transcriptomics, metatranscriptomics, metabolomics, and proteomics. The study of Metagenome-assembled genomes of uncultured halophilic microbes has uncovered the genomic basis of salt stress tolerance in “yet to culture” microorganisms. Also, functional metagenomic approaches have been used to decipher the novel genes from uncultured microbes and their possible role in microbial salt-stress tolerance. A recently published collaborative review helped in understanding microbial salt-stress biology and it also summarized the key molecular processes contributing to microbial salt-stress response.

Microorganisms employ two different strategies to adjust to hypersaline conditions: ‘salt-out’ strategy and ‘salt-in’ strategy. ‘salt-out’ strategy is adopted by halotolerant microbes while ‘salt-in’ strategy is common in halophiles. The review article described the important genes governing microbial halotolerance. The description of many genes, gene clusters or operons that are reported to play an important role in microbial salt-stress response are mostly related to compatible osmolyte biosynthesis. Ectoine biosynthesis gene cluster is considered as a potential marker gene for halotolerance in bacteria. A brief and comprehensive description of genes related to compatible osmolyte biosynthesis, along with their encoded enzymes is presented in the review.

Ectoine biosynthesis: an osmoadaptive response to salt stress is reported in bacteria and is conventionally believed to be absent in Archaea, and Eukarya. The annotation of the genome sequences of ammonia oxidizing archaea has first time lead to the observation about the presence of genes for ectoine biosynthesis even in ammonia-oxidizing archaea. Later, ectoine biosynthetic genes were observed in methanogen genome as well. But the mere presence of the ectoine biosynthesis genes in the genomes of archaea and methanogen does not imply that these genes are functional and ectoine synthesis do exist in Archaea. Further genomic and molecular studies uncovered the uncommon instance of ectoine biosynthesis in Archaea.

Microbes adopting ‘high salt-in’ strategy, display different genomic features. The ‘salt-in’ strategy is well documented in haloarchaea and extremely halophilic bacteria like Salinibacter ruber. The genome of obligate halophiles adopting ‘salt-in’ strategy possess distinct genomic and molecular features supporting a halophilic lifestyle. Most of the halophiles have highly acidic proteome. The halophiles relying on ‘salt-in’ strategy have evolved unique molecular features that differentiate them from microbes adopting ‘salt-out’ strategy for halotolerance.

Genome-resolved metagenomics offer a great opportunity to explore the niche adaptation and metabolic potential of uncultivated microbes. The MAGs obtained can serve as the blueprint for understanding the physiology and salt-stress adaptation strategies of uncultured microbes. The metagenomic genome reconstruction has been applied to recover the genomes of uncultured halophiles.

Using functional metagenomic approach, molecular basis of halotolerance in uncultured microbes is studied. The halotolerant metagenomic clones are studied for the identification and characterization of genes present in metagenomic DNA insert which actually renders the salt tolerance to such metagenomic clones. The techniques like transposon mutagenesis are also used to confirm the role of identified genes in halotolerance. A number of salt-tolerant genes are identified using functional metagenomics. But there are few limitations to metagenomics approach. The major limitation is because many genes/ORFs imparting salt stress tolerance to metagenomic clones, tend to annotate as the hypothetical protein and some even do not show similarity to any other known protein in the database.

The review also covered the detailed transcriptomic studies in microbial halotolerance research like microarray-based gene expression studies for salt-stress response and next-generation sequencing-based transcriptomic studies. The review also provide proteomic insights into microbial halotolerance, metabolic basis of microbial salt-tolerance.

“Omic'”-based microbial halotolerance research suffer few shortcomings like scarce information about halophiles confronting low salt conditions, halophiles warranting reassessment of ‘salt-in’ and ‘salt-out’ delimitations etc. The review concludes that the “Omic” landscape of microbial salt stress tolerance is as vast as the salt afflicted habitats on the earth landscape. It is important to undertake detailed and comprehensive studies that can generate in-depth data at different “Omic” levels on a single biological sample, in order to generate the systems biology view of microbial salt-stress tolerance

Reference: https://www.tandfonline.com/doi/full/10.1080/1040841X.2020.1819770