Uncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis

Abstract

There are few naturally occurring environments where both acid and salinity stress exist together, consequently, there has been little evolutionary pressure for microorganisms to develop systems that enable them to deal with both stresses simultaneously. Members of the genus Acidihalobacter are iron- and sulfur-oxidizing, halotolerant acidophiles that have developed the ability to tolerate acid and saline stress and, therefore, have the potential to bioleach ores with brackish or saline process waters under acidic conditions. The genus consists of four members, A. prosperus DSM 5130 T , A. prosperus DSM 14174, A. prosperus F5 and “ A. ferrooxidans ” DSM 14175. An in depth genome comparison was undertaken in order to provide a more comprehensive description of the mechanisms of halotolerance used by the different members of this genus. Pangenome analysis identified 29, 3 and 9 protein families related to halotolerance in the core, dispensable and unique genomes, respectively. The genes for halotolerance showed K a /K s ratios between 0 and 0.2, confirming that they are conserved and stabilized. All the Acidihalobacter genomes contained similar genes for the synthesis and transport of ectoine, which was recently found to be the dominant osmoprotectant in A. prosperus DSM 14174 and A. prosperus DSM 5130 T . Similarities also existed in genes encoding low affinity potassium pumps, however, A. prosperus DSM 14174 was also found to contain genes encoding high affinity potassium pumps. Furthermore, only A. prosperus DSM 5130 T and “ A. ferrooxidans ” DSM 14175 contained genes allowing the uptake of taurine as an osmoprotectant. Variations were also seen in genes encoding proteins involved in the synthesis and/or transport of periplasmic glucans, sucrose, proline, and glycine betaine. This suggests that versatility exists in the Acidihalobacter genus in terms of the mechanisms they can use for halotolerance. This information is useful for developing hypotheses for the search for life on exoplanets and moons.

Insights into the Metabolism and Evolution of the Genus Acidiphilium , a Typical Acidophile in Acid Mine Drainage

“…HGT-derived alkaline phosphatases (Alp), which release phosphate groups from various compounds, and phosphate import systems encoded by pstSACB and pitA were present in all clades of Acidiphilium . Compatible solute uptake and biosynthesis as well as potassium uptake are known as common strategies to counteract osmotic stress ( 53 , 54 ). The HGT-derived biosynthetic pathway of the compatible solute hydroxyectoine conferred by the gene cluster ectRABCD-ask ( 55 ) was detected in the genomes of clades III and IV.…”

Osmotic Imbalance, Cytoplasm Acidification and Oxidative Stress Induction Support the High Toxicity of Chloride in Acidophilic Bacteria

“…nov. (=DSM14175) (45 g/L NaCl), and Alicyclobacillus sp. S09 have been isolated (Huber and Stetter, 1989; Bobadilla-Fazzini et al, 2014; Issotta et al, 2016; Dopson et al, 2017; Huynh et al, 2017; Khaleque et al, 2019). The mechanisms that these or other acidophilic microorganisms use to withstand the osmotic stress are recently being investigated.…”

Glutathione synthetase overexpression in Acidithiobacillus ferrooxidans improves halotolerance of iron oxidation

“…The discovery of these new Acidihalobacter spp. has spurred the investigation of the genetic mechanisms responsible for their halotolerance (16, 17). It has been shown that these bacterial species have adopted a biphasic salting out approach to increase their internal osmolarity by transporting potassium into the cytoplasm and synthesizing compatible solutes such as proline, ectoine, and periplasmic glucans (18).…”

“…As such, it is becoming an excellent chassis to apply synthetic biology approaches to overcome challenging conditions in novel bioleaching applications (26). As the mechanisms of halotolerance in acidophilic halotolerant species have been uncovered, this offers new opportunities to develop genetically engineered strains of A. ferrooxidans that would thrive under even harsher conditions (17). Furthermore, previous studies have reported that genes associated with glutathione in A. ferrooxidans respond to various forms of oxidative stress (27-30).…”