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

Abstract

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.

Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1

“…SCN63-17 clustered together. This result is consistent with the results of an earlier study that found six Novosphingobium strains were correlated with their isolation sources (Gan et al, 2013 ), and in a CV tree of Acidithiobacillus caldus , three strains from a copper mine clustered together (Zhang et al, 2016 ). However, most of the subclades in the phylogenetic trees had more ambiguity in habitat specificity.…”

“…Further analysis showed that when more strains were included in phylogenetic trees, the trend to cluster according to habitat was more mixed. This suggests that specific environment variations also may influence genome structure (Lin et al, 2013 ; Ji et al, 2014 ; Zhang et al, 2016 ).…”

“…More GIs were identified on chromosomes than on the plasmids in the six complete genomes (Table 2 ). Previous studies have shown that GIs were relevant to niche-specific adaptation (Wu et al, 2011 ; Zhang et al, 2016 ), so the prevalence of GIs in the 22 Novosphingobium genomes may imply rapid adaptation occurred to give them a survival advantage in diverse environments.…”

“…Insertion sequences (ISs) were detected by BLAST comparisons ( E -value ≤ 1e −5 ) against the ISFinder database (Siguier et al, 2006 ). IslandViewer 4 (Bertelli et al, 2017 ), which integrates IslandPick (Langille et al, 2008 ), IslandPathDIMOB (Hsiao et al, 2003 ), and SIGI-HMM (Waack et al, 2006 ), were used to predict genomic islands (GIs), as described previously (Zhang et al, 2016 ). CRISPR arrays were detected using the CRISPRFinder (Grissa et al, 2007 ) online server to perform BLAST searches against dbCRISPR (CRISPR database).…”

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

“…Genome functional annotation was performed using the Rapid Annotations using Subsystems Technology (RAST) platform (http://rast.nmpdr.org/) (92). Subsequently, protein sequences and corresponding annotation were acquired as previously described (43,93). PanOCT version 3.18 (94), with an E value cutoff of 0.00001 and sequence identity cutoff of 65%, was applied for the identification of orthologs that were shared between species or strains.…”