Complete Genome Sequence of the Extremely Thermoacidophilic Archaeon Acidianus manzaensis YN-25.

The complete genome of Acidianus manzaensis YN-25 consists of a chromosome of 2,687,463 bp, with a G+C content of 30.62% and 2,746 coding DNA sequences. This archaeon contains a series of specific genes involved in the oxidation of elemental sulfur and reduced inorganic sulfur compounds.

GENOME ANNOUNCEMENT

Bioleaching exploits acidophilic microorganisms to recover valuable metals, for instance, Au and Cu, from ores in the processes conducted at temperatures ranging from ambient to 80°C (1, 2). Higher-temperature operations with consortia of extremely thermoacidophilic archaea can improve the yield of target metals and reduce the problematic passivation on ore surfaces. Acidianus manzaensis is a novel thermoacidophilic archaeon of the Acidianus genus which is capable of oxidizing elemental sulfur and reduced inorganic sulfur compounds (RISCs) (3, 4). This strain has shown excellent capacity for metal recovery and high efficiency of chalcopyrite bioleaching (5–7). To investigate the mechanism that enables A. manzaensis to survive and proliferate during the biohydrometallurgical processes and to further research relevant metabolic pathways, such as sulfur oxidation, we performed whole-genome sequencing of A. manzaensis YN-25.

The strain A. manzaensis YN-25 was isolated from an acid thermal spring in Tengchong, China (4). The cells were cultivated with 9K basic medium [3.0 g/liter (NH4)2SO4, 0.5 g/liter MgSO4·7H2O, 0.5 g/liter K2HPO4, 0.1 g/liter KCl, 0.01 g/liter Ca(NO3)2] added with 0.2 g/liter yeast extract as a growth factor. Elemental sulfur was used as the electron donor (170 rpm at 65°C). The genomic DNA of A. manzaensis was extracted by the TIANamp DNA kit (Tiangen, Beijing, China) and sequenced using a combined strategy of the Illumina HiSeq 4000 (Illumina, USA) and PacBio RSII (Pacific Biosciences, USA) platforms (8). The genome sequence was assembled using the SOAPdenovo software (9). The coding DNA sequences (CDSs) were predicted by Glimmer (10). Function annotation was completed by homologous comparison of each putative gene against the public databases, including the Kyoto Encyclopedia of Genes and Genomes, the Clusters of Orthologous Groups of proteins, Swiss-Prot, the nonredundant protein database, and Gene Ontology. In addition, rRNAs and tRNAs were predicted by RNAmmer and tRNAscan-SE, respectively.

The A. manzaensis YN-25 complete genome consists of a circular chromosome of 2,687,463 bp, with a G+C content of 30.62%. The genome is predicted to contain 2,746 CDSs. The number of tandem repeat sequences is 110 (6,113 bp), which makes up 0.2275% of the genome. The numbers of tRNAs and rRNAs are 42 and 2, respectively.

A. manzaensis YN-25 encodes several enzymes involved in the oxidation of sulfur and RISCs, including the sulfur oxygenase-reductase, thiosulfate:quinone oxidoreductase, and tetrathionate hydrolase. Electrons generated from sulfur and RISC oxidation enter the electron transport chain via quinone. Terminal quinol oxidases, like aa ubiquinol oxidase, receive electrons from quinone and transfer them to O2 coupled with ATP generation. Some electrons can be transmitted to the NADH complex to produce NADH by NADH-quinone oxidoreductase. The complete genome of A. manzaensis YN-25 provides novel insights into biologically catalyzed metal sulfide oxidation.

Accession number(s).

The complete genome sequence of A. manzaensis YN-25 has been deposited in GenBank under the accession number CP020477. The version described in this paper is the first version, CP020477.1.