Multiomics Reveals the Mechanism of Natranaerobius thermophilus Adaptation to Combined Hypersaline, Alkaline, and Elevated Temperature Environments

The halophilic alkalithermophile N. thermophilus grows optimally at the combined extremes of 3.3–3.9 M Na⁺, pH 9.5, and 53 °C. This study aims to uncover its unique adaptations to the combined extremes of high salt, alkaline pH, and high temperature. Due to the difficulties of genetic manipulation, we used a multiomics approach to reveal the comprehensive transcriptomic, proteomic, and metabolomic landscapes of N. thermophilus under the triple extremes. Specifically, two distinct conditions were evaluated: high salt-alkaline-thermal (HSAT, 4 M Na⁺/ pH 9.8/52 °C) stress and low salt-alkaline-thermal (LSAT, 3 M Na⁺/ pH 8.8/42 °C) stress. Under HSAT stress, N. thermophilus increased the level of saturated fatty acids and uncharged polar lipids to remodel its cell membrane, enhanced Na⁺-driven flagellar motility, accumulated various compatible solutes, redirected amino acid metabolism for energy, and adjusted the activity of ion transporters and chaperones. These findings exemplify the “No Free Lunch” principle in polyextremophiles. By examining changes in gene, protein, and metabolic regulation levels in N. thermophilus under the simultaneous influence of three extremes, this study provides a comprehensive analysis of the survival mechanisms of polyextremophiles in hypersaline, alkaline, and high-temperature environments. Our findings offer valuable insights into the origins of life on Earth and the potential for extraterrestrial life.