Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes

Abstract

The iron-oxidizing species Acidithiobacillus ferrivorans is one of few acidophiles able to oxidize ferrous iron and reduced inorganic sulfur compounds at low temperatures (<10°C). To complete the genome of At. ferrivorans strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. The At. ferrivorans CF27 genome comprises a 3,409,655 bp chromosome and a 46,453 bp plasmid. At. ferrivorans CF27 possesses genes allowing its adaptation to cold, metal(loid)-rich environments, as well as others that enable it to sense environmental changes, allowing At. ferrivorans CF27 to escape hostile conditions and to move toward favorable locations. Interestingly, the genome of At. ferrivorans CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. Furthermore, several genes specific to At. ferrivorans CF27 have been identified that could be responsible for the phenotypic differences of this strain compared to other Acidithiobacillus species. Most genes located inside At. ferrivorans CF27-specific gene clusters which have been analyzed were expressed by both ferrous iron-grown and sulfur-attached cells, indicating that they are not pseudogenes and may play a role in both situations. Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups.

Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C

“…This relatively low pairwise nucleotide identity is attributed to high genetic heterogeneity in IO-2C genome which might be consequence of adaptation to hostile environmental conditions, i.e. pH stress or horizontal gene transfer over a long period of time 11 , which contributed to the large number of unique genes (292 genes including genes of unknown function and pseudogenes). Genome annotations revealed about 2, 927 protein coding sequences, 42 tRNAs, 5 rRNAs and 131 pseudogenes (Fig.…”

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

“…Genome sequencing can be an important first step in characterizing a new organism as it provides critical genetic information required to elucidate biochemical pathways underpinning its metabolic capabilities and survival mechanisms. Several acidophiles have been sequenced and comparative genomics has shed light on their metabolic processes (Tyson et al, 2004; Levicán et al, 2008; Valdés et al, 2008, 2010; Zhou et al, 2008; Cárdenas et al, 2010, 2012; Zhang et al, 2016a,b; Tran et al, 2017). The sequencing of the genomes of the members of the Acidihalobacter genus (Ossandon et al, 2014; Khaleque et al, 2017a,b,c) has provided an opportunity to better study the mechanisms of survival used by these acidophilic, halotolerant acidophiles.…”

Determinants of Copper Resistance in Acidithiobacillus Ferrivorans ACH Isolated from the Chilean Altiplano

“…Additionally, the amino acid sequence of both rusticyanin genes (rusA and rusB) found in the ACH genome was identical (100%) to those from the SS3 strain ( Figure S3B,C). On the other hand, Tran and collaborators reported the presence of at least seventeen genes involved in CF27 strain copper resistance (copZ, copA, copB, cusCBA-like, and putative phosphate transporter (Pho84)) [27]. Comparing these genes to those from the ACH strain, we found a high similarity only with copZ (100%) (AFERRI_420163), cusC (98%) (AFERRI_10103), and copA (99%) (AFERRI_140009).…”

“…However, A. ferrivorans' ability to tolerate high heavy metal concentrations remains mostly unexplored, mainly because its psychrotolerant capacity draws greater research interest. Nevertheless, although there is information about genetic determinants for heavy metal resistance in A. ferrivorans, most research has focused only on identifying the presence/absence of genes potentially involved in these processes [23,26,27]. In this case, several genes involved in copper resistance (including RND and Cop systems) have been identified in the SS3, CF27, and YL15 genomes [23,26,27].…”

“…Nevertheless, although there is information about genetic determinants for heavy metal resistance in A. ferrivorans, most research has focused only on identifying the presence/absence of genes potentially involved in these processes [23,26,27]. In this case, several genes involved in copper resistance (including RND and Cop systems) have been identified in the SS3, CF27, and YL15 genomes [23,26,27]. However, the function and capacity of those genes to yield the copper-resistant phenotype has not yet been demonstrated, nor has it been correlated with processes at low temperatures.…”