Theoretical Model of the Structure and the Reaction Mechanisms of Sulfur Oxygenase Reductase in <i>Acidithiobacillus thiooxidans</i>

Effect of Introduction of Exogenous Strain Acidithiobacillus thiooxidans A01 on Structure and Function of Adsorbed and Planktonic Microbial Consortia During Bioleaching of Low-Grade Copper Sulfide

The introduction of Acidithiobacillus thiooxidans A01 strengthens the positive interactions between physiologically distinct microorganisms and enhances the bioleaching ability of the consortium. However, the effect of introducing an exogenous strain, A. thiooxidans A01 on the structure and function of the adsorbed and planktonic microbial consortia during bioleaching of low-grade copper sulfide remains unclear. In this study, A. thiooxidans A01 was introduced into an indigenous leaching microbial community on the 0th (group B), 24th (group C), and 36th day (group D). Results revealed that the copper leaching efficiency was highest in group D, in which the Cu2+ concentration in the solution reached 251.5 mg/L on day 48, which was 18.5% higher than that of the control (group A, no addition of A. thiooxidans A01). Restriction fragment length polymorphism (RFLP) analysis of the microbial community in group D revealed the presence of Leptospirillum ferriphilum, Acidithiobacillus ferrooxidans, Acidithiobacillus caldus, Sulfobacillus sp., Acidiphilium spp., and Acidithiobacillus albertensis before introduction of A. thiooxidans A01 on the 36th or 48th day; however, A. albertensis was absent on day 48 in group A. Further, the proportion of dominant A. caldus, L. ferriphilum, and A. ferrooxidans became altered. The results of real-time PCR in group D showed that A. thiooxidans A01 was primarily adsorbed on the surface of the ore, with the adsorption reaching the maxima on day 42; while the free A. thiooxidans A01 in solution grew slowly, reaching its maximum concentration on day 45. Compared with that in the control group, the abundance of both free and attached A. caldus and Sulfobacillus sp. decreased following the introduction of A. thiooxidans A01, while that of L ferriphilum, A. ferrooxidans, and Acidiphilium sp. increased. Functional gene arrays data indicated that the abundance of genes involved in sulfide and iron oxidation in L. ferriphilum and A. ferrooxidans, as well as that of the metal (loid) resistance genes of A. ferrooxidans, L. ferriphilum, and Acidiphilium sp. increased, while the abundance of genes involved in sulfur metabolism in A. caldus and Sulfolobus spp. decreased. Taken together, these results provide useful information for application of bioleaching of copper sulfide in industry.

Acidithiobacillus thiooxidans and its potential application

Acidithiobacillus thiooxidans (A. thiooxidans) is a widespread, mesophilic, obligately aerobic, extremely acidophilic, rod-shaped, and chemolithoautotrophic gram-negative gammaproteobacterium. It can obtain energy and electrons from the oxidation of reducible sulfur, and it can fix carbon dioxide and assimilate nitrate, nitrite, and ammonium to satisfy carbon and nitrogen requirement. This bacterium exists as different genomovars and its genome size range from 3.02 to 3.97 Mb. Here, we highlight the recent advances in the understanding of the general biological features of A. thiooxidans, as well as the genetic diversity and the sulfur oxidation pathway system. Additionally, the potential applications of A. thiooxidans were summarized including the recycling of metals from metal-bearing ores, electric wastes, and sludge, the improvement of alkali-salinity soils, and the removal of sulfur from sulfur-containing solids and gases.

In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle

The coinage “pan-genome” was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species’ basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species’ core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H₂ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H₂ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillusthermosulfidooxidans Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains.IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.

Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics

Acidithiobacillus caldus is an extremely acidophilic sulfur-oxidizer with specialized characteristics, such as tolerance to low pH and heavy metal resistance. To gain novel insights into its genetic complexity, we chosen six A. caldus strains for comparative survey. All strains analyzed in this study differ in geographic origins as well as in ecological preferences. Based on phylogenomic analysis, we clustered the six A. caldus strains isolated from various ecological niches into two groups: group 1 strains with smaller genomes and group 2 strains with larger genomes. We found no obvious intraspecific divergence with respect to predicted genes that are related to central metabolism and stress management strategies between these two groups. Although numerous highly homogeneous genes were observed, high genetic diversity was also detected. Preliminary inspection provided a first glimpse of the potential correlation between intraspecific diversity at the genome level and environmental variation, especially geochemical conditions. Evolutionary genetic analyses further showed evidence that the difference in environmental conditions might be a crucial factor to drive the divergent evolution of A. caldus species. We identified a diverse pool of mobile genetic elements including insertion sequences and genomic islands, which suggests a high frequency of genetic exchange in these harsh habitats. Comprehensive analysis revealed that gene gains and losses were both dominant evolutionary forces that directed the genomic diversification of A. caldus species. For instance, horizontal gene transfer and gene duplication events in group 2 strains might contribute to an increase in microbial DNA content and novel functions. Moreover, genomes undergo extensive changes in group 1 strains such as removal of potential non-functional DNA, which results in the formation of compact and streamlined genomes. Taken together, the findings presented herein show highly frequent gene turnover of A. caldus species that inhabit extremely acidic environments, and shed new light on the contribution of gene turnover to the evolutionary adaptation of acidophiles.

Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments

Many studies have investigated the mechanisms underlying the survival and growth of certain organisms in extremely acidic environments known to be harmful to most prokaryotes and eukaryotes. Acidithiobacillus and Leptospirillum spp. are dominant bioleaching bacteria widely used in bioleaching systems, which are characterized by extremely acidic environments. To survive and grow in such settings, these acidophiles utilize shared molecular mechanisms that allow life in extreme conditions. In this review, we have summarized the results of published genomic analyses, which underscore the ability of iron- and/or sulfur-oxidizing autotrophic acidophiles belonging to the genera Acidithiobacillus and Leptospirillum to adapt to acidic environmental conditions. Several lines of evidence point at the metabolic diversity and multiplicity of pathways involved in the survival of these organisms. The ability to thrive in adverse environments requires versatile activation of structural and functional adaptive responses, including bacterial adhesion, motility, and resistance to heavy metals. We have highlighted recent developments centered on the key survival mechanisms employed by dominant extremophiles, and have laid the foundation for future studies focused on the ability of acidophiles to thrive in extremely acidic environments.

Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation

Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.