Draft Genome Sequence of the Sulfobacillus thermosulfidooxidans Cutipay Strain, an Indigenous Bacterium Isolated from a Naturally Extreme Mining Environment in Northern Chile

Abstract

Sulfobacillus thermosulfidooxidans strain Cutipay is a mixotrophic, acidophilic, moderately thermophilic bacterium isolated from mining environments of the north of Chile, making it an interesting subject for studying the bioleaching of copper. We introduce the draft genome sequence and annotation of this strain, which provide insights into its mechanisms for heavy metal resistance. Sulfobacillus thermosulfidooxidans strain Cutipay has been identified as a sulfur-and iron-oxidizing, Gram-positive, sporulating, acidophilic, and moderately thermophilic bacterium. It was microbiologically characterized as having an optimum growth temperature of 45°C and an optimum pH range of 2.0 to 2.5 when growing in the presence of Fe 2ϩ and/or sulfur supplemented with yeast extract. It was originally named Cutipay from the indigenous Mapudungun word meaning "coming from the water," because it was isolated from naturally occurring effluents in the extreme mining environment of the north of Chile. Using phylogenetic analyses, it was identified as a Sulfobacillus thermosulfidooxidans species first described by Golovacheva and Karaviako in 1978 (2).The draft genome sequence of S. thermosulfidooxidans strain Cutipay was determined by whole-genome shotgun sequencing using a mixed technology strategy consisting of a run of the Ion Torrent PGM 316 Chip (8) on an unpaired library and two runs of the Roche 454 -GS Junior pyrosequencing platform (6) on one 3-kb mate pair library and 1 unpaired library generating a 116ϫ coverage. Assembly was performed using wgs-assembler (Celera Assembler) version 7 (7). Identification of coding regions and annotation were performed using protocols described in references 3 and 5.The Sulfobacillus thermosulfidooxidans Cutipay strain draft genome was assembled in 47 contigs. Using mate information, the final assembly has 3,862,012 total bp in 35 scaffolds. The maximum scaffold length is 1,134,202 bp, and the minimum length is 1,007 bp. The scaffold length has a mean of 110,343 bp, a median of 30,355 bp, and an N 50 length of 509,367 bp, while the genome has a GC content of 49.3%, which is similar to that of Sulfobacillus thermosulfidooxidans subspecies thermotolerans (4).According to our analysis, 3,600 putative genes and 54 tRNAs were predicted. Three 5S, 16S, and 23S partial operons were found. Carbon and sulfur metabolism enzymes described previously have also been identified (1). Differences between arsenic resistances in the arsRB operon were found. The arsRB operon includes arsR regulator, arsB arsenite efflux pump, kumamolisin-As precursor, and glycosyl transferase codifying genes previously described in S. thermosulfidooxidans strain VKM B-1269 (9, 10). We have found another open reading frame (ORF) with no homology between the genes for glycosyl transferase and kumamolisin-As precursor present in S. thermosulfidooxidans strain Cutipay and a putative arsC in another region of the genome. The arsC gene codes for an arsenate reductase not previously described in S. thermosulfidooxidans (9, 10), indic...

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

“…Sulfobacillus spp. are known as mixotrophic acidophiles that are capable of assimilating organic and inorganic carbon (30,34,42,51). Similar to the published Sulfobacillus genomes (30, 31), a full suite of genes involved in the Calvin-Benson-Bassham cycle were predicted in all strains ( Fig.…”

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

“…Other phenotypic differences such as metal tolerance, temperature tolerance, and use of different carbon compounds set these organisms apart [ 5 , 11 , 13 ]. Genomes for two of these species— S. acidophilus and S. thermosulfidooxidans —have been previously reported [ 2 , 16 – 18 ] and an additional S. thermosulfidooxidans genome is deposited in the publicly available “Integrated Microbial Genomes and Metagenomes” (IMG) database [ 19 ]. Here we present five new draft genomes of Sulfobacillus organisms assembled from metagenomic data.…”

Microbial biogeochemistry of Boiling Springs Lake: a physically dynamic, oligotrophic, low‐pH geothermal ecosystem

“…BSL is geologically and chemically distinct from caldera-type volcanic lakes typified by the Uzon Caldera (Kamchatka, Russia) and features within the Rotorua geothermal field in New Zealand (McColl & Forsyth, 1973;Mroczek et al, 2004) and from high chloride, lower sulfate features characteristic of the liquid-dominated geothermal systems in Yellowstone National Park (YNP; Thompson, 1985;McCleskey et al, 2004;Inskeep & McDermott, 2005;Janik & McLaren, 2010). However, it is much warmer than coal mining lakes of more similar water chemistry (Travisany et al, 2012) restricting the eukaryotic community to entirely microbial taxa, and BSL's basin depth and structure are obscured by suspended sediments that limit light penetration. However, it is much warmer than coal mining lakes of more similar water chemistry (Travisany et al, 2012) restricting the eukaryotic community to entirely microbial taxa, and BSL's basin depth and structure are obscured by suspended sediments that limit light penetration.…”

“…Compared to well-studied AMD sites such as the Rio Tinto (Justice et al, 2012) or Iron Mountain Mine (Edwards et al, 1999), BSL is a much more dilute sulfuric acid solution, and contains extremely low burdens of heavy metals, as well as low nutrients (Siering et al, 2006). However, it is much warmer than coal mining lakes of more similar water chemistry (Travisany et al, 2012) restricting the eukaryotic community to entirely microbial taxa, and BSL's basin depth and structure are obscured by suspended sediments that limit light penetration. Additionally, as an 'aquatic island' in an alpine forest, BSL receives allochthonous organic material from the surrounding vegetation (conifer needles and woody debris).…”