Comparative Analysis of Growth Requirements and Genomic Potential in Halophilic Archaea from Kazakhstan: Linking Metabolic Pathway Content to Phenotypic Adaptation

Abstract

Halophilic archaea are extremophiles that inhabit hypersaline settings due to unique molecular adaptations. Despite their biotechnological potential, most mechanistic studies have concentrated on a single model organism (Halobacterium salinarum NRC-1), leaving the physiological diversity of wild haloarchaeal communities little understood. Three novel, phylogenetically different halophilic archaea strains; Halobacterium salinarum (KBTZ01) (HS), Halomicrobium sp. (KBTZ05) (HM), and Haloarcula sp. KBTZ06 (HA); were isolated from Lake Kobeituz, a hypersaline lake in northern Kazakhstan, but no genotype-to-phenotype investigation of these strains has been conducted prior to this work. This thesis combines comparative genomic analysis with experimental evaluations of carbon source use and pH/buffer adjustment. The genetic study revealed three distinct metabolic profiles: HS maintained the arginine deiminase pathway, as well as histidine and tryptophan catabolism, and bacteriorhodopsin (bop), but was deficient in the complete biosynthesis of several amino acids; HM had a full set of amino-acid biosynthesis genes but was missing amino-acid catabolism and bacteriorhodopsin, and showed enrichment in enzymes that act on complex carbohydrates; HA had the largest set of genes, including a complete arginase-urease operon and the highest numbers of aminotransferase copies. Experimental growth testing confirmed these predictions: HS required external amino acids (scavenger phenotype), HM required an extra carbohydrate (carbohydrate specialist), and HA flourished in all examined settings (metabolic generalist). Experiment results on the environmental conditions, pH and buffer system, concluded that HEPES and Tris consistently outperformed PIPES, while HEPES also being overall more stable and resulting in better growth across the three strains. Moreover, HM was the most sensitive to acidic environments, while HS and HA actively alkalinized their medium during growth. These findings present the first genotype-phenotype framework for haloarchaea native to Kazakhstan.