Genomic Analysis of a Newly Isolated Acidithiobacillus ferridurans JAGS Strain Reveals Its Adaptation to Acid Mine Drainage

Abstract

Acidithiobacillus ferridurans JAGS is a newly isolated acidophile from an acid mine drainage (AMD). The genome of isolate JAGS was sequenced and compared with eight other published genomes of Acidithiobacillus. The pairwise mutation distance (Mash) and average nucleotide identity (ANI) revealed that isolate JAGS had a close evolutionary relationship with A. ferridurans JCM18981, but whole-genome alignment showed that it had higher similarity in genomic structure with A. ferrooxidans species. Pan-genome analysis revealed that nine genomes were comprised of 4601 protein coding sequences, of which 43% were core genes (1982) and 23% were unique genes (1064). A. ferridurans species had more unique genes (205–246) than A. ferrooxidans species (21–234). Functional gene categorizations showed that A. ferridurans strains had a higher portion of genes involved in energy production and conversion while A. ferrooxidans had more for inorganic ion transport and metabolism. A high abundance of kdp, mer and ars genes, as well as mobile genetic elements, was found in isolate JAGS, which might contribute to its resistance to harsh environments. These findings expand our understanding of the evolutionary adaptation of Acidithiobacillus and indicate that A. ferridurans JAGS is a promising candidate for biomining and AMD biotreatment applications.

Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle

“…The presence of sqs gene in Acidithiobacillaceae coding for squalene biosynthesis in a single reaction (as compared with the three reactions in T. tepidarius ) may also represent an important evolutionary energetic advantage for hopanoid biosynthesis, which, along with the hpn FGAIJKNLHM gene cluster, allows to synthetize and modify hopanoids. The second line in Acidithiobacillaceae presented a pool of accessory genes for buffering of intracellular pH, including decarboxylation of glutamate, urea hydrolysis, and hydration of CO 2 , and antiporters export excess protons by coupling the uptake of Na + ( Chen et al, 2021 ). This functional redundancy may represent a key strategy for acidophiles to live across different pH ranges and “hedge bet” in rapidly changing acidic environments, where it is hypothesized that the cost of maintaining genetic redundancy is offset by the ability to expeditiously adjust to environmental fluxes.…”

“…Low pH mitigation mechanisms have been investigated in acidophiles ( Baker-Austin and Dopson, 2007 ; Li et al, 2011 ; Ullrich et al, 2016a ; Colman et al, 2018 ; Vergara et al, 2020 ; Chen et al, 2021 ; Mayer et al, 2021 ; Sriaporn et al, 2021 ). These studies show that horizontal gene transfer (HGT), gene mutation, and gene loss trajectories in evolution allow adaptation and survival of prokaryotes in extreme conditions ( Foster, 2004 ; Ullrich et al, 2016a ; Zhang et al, 2017 ; Vergara et al, 2020 ).…”

Genetic Engineering of Acidithiobacillus ferridurans Using CRISPR Systems To Mitigate Toxic Release in Biomining

“…A. ferridurans JAGS, which is a dominant strain newly isolated from an acidic mine drainage (AMD) sample collected in September 2010 from Clarabelle Mill, near Sudbury, Ontario, Canada, , was cultured in different 9K liquid media as specified in the experimental design. Specifically, we used 9K-Fe, 9K-S, and 9K-PO media, which were prepared by combining 9K basic solution (3.0 g (NH 4 ) 2 SO 4 , 0.5 g K 2 HPO 4 , 0.5 g MgSO 4 ·7H 2 O, and 0.1 g KCl in 1 L) with 44.22 g FeSO 4 ·7H 2 O, 5 g S 0 , or 50 g pyrrhotite tailings (PO, Fe (1– x ) S, x = 0–0.125 with ∼1% Ni), respectively.…”

“…They are capable of oxidizing iron and/or sulfur to derive energy and fix carbon dioxide as their primary carbon source . Members of Acidithiobacillus are well-known for their efficient biomining capabilities and are harnessed to recover metals and rare earth elements from a variety of sources, such as ores, mine tailings, electric wastes, and spent batteries. − Their highly adaptive nature and ability to thrive under extreme conditions make them promising candidates for bioremediation and biomining applications and future space biomining missions. , Nonetheless, the utilization of Acidithiobacillus in biomining presents several challenges that need to be addressed, such as excess sulfuric acid generation, a long growth cycle, a low biomining rate, and a lack of selectivity when releasing metals . Synthetic biology offers promising solutions to these problems.…”

Genetic engineering of Acidithiobacillus ferridurans with CRISPR-Cas9/dCas9 systems

“…In this study, we used A. ferridurans JAGS for the genetic engineering, which we isolated from an acidic mine drainage (AMD) sample collected in September 2010 from Clarabelle Mill, near Sudbury, Ontario, Canada [27]. Its genome was sequenced and analyzed in our previous research [28]. E. coli was grown at 37 o C in Luria-Bertani (LB) broth or on LB agar plates.…”