acidithiobacillus ferrooxidans ( a. ferrooxidans ) is a gram - negative , extremely acidophilic , mesophilic , chemolithotrophic bacterium and the most well - studied acidophilic organism which is usually found in acid environments such as acid mine drainage , . due to its bioleaching capabilities
, it is an important member of microbial consortia involved in the industrial recovery of metal under mesophilic conditions ( bioleaching or biomining ) .
recently , a. ferrooxidans has played important roles in bioleaching and harnesse environmental contamination , .
like in other acidophilic iron - oxidizing bacterium , it grows optimally at about 35  c in 9k inorganic medium at extremely low ph ( ph  1.02.0 ) and fixes both carbon and nitrogen from the atmosphere .
a. ferrooxidans derives energy from oxidizing reduced sulfur compounds and fe ions to form sulfate and fe , respectively .
dna was isolated from 1.01.5  g of cell paste using qiagen genomic 500 dna kit ( qiagen , hil - den , germany ) with a modified protocol , st / ft , for cell lysis , as described in valdes et al . .
draft genome sequence of a. ferrooxidans type strain dlc-5 was obtained in illumina hiseq2000 sequencing technology by shanghai majorbio bio - pharm technology co. , ltd .
( shanghai , china ) , using the short oligonucleotides alignment program ( soap ) denovo alignment tool ( http://soap.genomics.org.cn/ ) processes reads assemble . a library containing 300-bp inserts
was constructed . altogether , 6,372,268 paired reads ; 398,580 single reads ; total 1,079,535,272  bp bases with average coverage of 221.1  . reads were filtered to remove adapter sequences , low - quality bases ( phred score , <  20 ) , removing the 5 end that contains the bases of it is not a , g , c , t before shearing , remove reads with the containing 10% of n , giving up adapter and small fragments of length less than 25  bp after qualitative pruning .
the reads were assembled into 881 contigs ( >  1000  bp ; contig n50 , 102  bp ; contig n90 , 569  bp ) and 573 scaffolds ( >  1000  bp ; scaffold n50 , 71  bp ; scaffold n90 , 333  bp ) . until now , two genome sequences of a. ferrooxidans strains atcc 23270 and atcc 53993 are available in the public databases , .
these genomic data are useful for the experimental identification of unique proteins or estimation of the phylogenetic relationship among the related strains
. strain dlc-5 ( cctcc - m 2014362 ) is the type strain of a. ferrooxidans , isolated from wudalianchi in heihe of heilongjiang province , and the type species of the genus acidithiobacillus , which currently contains five species .
the draft genome sequences of strain dlc-5 have great importance to provide more explicit information for the physiology and metabolic potential of a. ferrooxidans .
further analysis of the genome sequence via gene engineering might improve the oxidation of fe efficiency by strain dlc-5 .
the genome includes two plasmids , for a total size of 3,142,890  bp , with one circular chromosome of 1,832,305  bp ( 58.3% gc content ) . for the main chromosome , 4299  bp genes
3250  bp of protein coding genes were assigned to a putative function with the remaining annotated as hypothetical proteins
. the properties and the statistics of the genome are summarized in table 1 . the distribution of genes into cogs functional categories is presented in table 2 .
extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms are widely distributed in the extreme acidic environment . in this study
, we analyzed the genome sequence of a. ferrooxidans dlc-5 , which was isolated from acid mine drainage in northeast china .
it may contribute to further studies on important process for bioleaching and acid mine drainage production , such as biofilm formation , energy resources utilization and quorum sensing that could play a role in a possible interrelationship of bioleaching heaps and other acidic environments .
in addition , combining with genomes of other members in acidithiobacillus , will make an important advance in understanding of the ecological roles that acidithiobacillus species play in those acidic environments and their relationships with other extremely acidophilic microorganisms .
the sequence of a. ferrooxidans dlc-5 under this whole genome shotgun project has been deposited at ddbj / embl / genbank under the accession jnnh00000000.1 .
 acidithiobacillus ferrooxidans type strain dlc-5 , isolated from wudalianchi in heihe of heilongjiang province , china . here , 
 we present the draft genome of strain dlc-5 which contains 4,232,149  bp in 2745 contigs with 57.628% gc content and includes 32,719 protein - coding genes and 64 trna - encoding genes . the genome sequence can be accessed at ddbj / embl / genbank under the accession no . 
 jnnh00000000.1 . 
Direct link to deposited data
Experimental design, materials and methods
Nucleotide sequence accession number
Competing interests