Abstract
We report here the draft genome sequence of Ardenticatena maritima 110S, the first sequenced member of class Ardenticatenia of the phylum Chloroflexi. This thermophilic organism is capable of a range of physiologies, including aerobic respiration and iron reduction. It also encodes a complete denitrification pathway with a novel nitric oxide reductase.
GENOME ANNOUNCEMENT
Ardenticatena maritima 110S was originally isolated from an iron-rich coastal hydrothermal field in the Kirishima Volcanic Belt of Japan (1). Closely related strains have been reported from hot springs (2) and hydrothermal vents (3). A. maritima is a filamentous nonmotile organism that can facultatively reduce nitrate and iron (1). It grows optimally at 50 to 70°C and pH 7.0 (pH range, 5.5 to 8.0).
The genome of A. maritima 110S (DSM 23922) was sequenced as part of a project to expand the phylogenetic breadth of Chloroflexi genomes. Genome sequencing was performed at SeqMatic using the Illumina MiSeq sequencing platform. SPAdes 3.1.1 (4) was used to assemble the genome. The genome was screened for contaminants based on sequence coverage, G+C composition, and BLAST hits of conserved single-copy genes. Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline. The draft genome is 3.62 Mb in size, assembled into 12 contigs. It contains 3,041 genes, 2,578 coding sequences (CDSs), 2 16S RNAs, 46 tRNAs, and 10 clustered regularly interspaced short palindromic repeat (CRISPR) arrays. It is estimated to be ~99% (111/111) complete based on conserved single-copy genes.
Analysis of the A. maritima genome revealed the presence of many genes responsible for its physiological breadth. A. maritima encodes a branched aerobic respiratory chain, including complex I (NADH dehydrogenase), complex II (succinate dehydrogenase), complex III (cytochrome bc complex), and three oxygen reductases (A- and B-family heme-copper oxygen reductases and bd oxidase). B-family heme-copper oxygen reductases are commonly found in aerobic thermophiles, enabling growth with the low oxygen levels found in thermal systems (5). A. maritima also encodes a complete denitrification pathway composed of nitrate reductase (NapA), nitrite reductase (NirK), a novel nitric oxide reductase (eNOR) (6), and nitrous oxide reductase (NosZ). Interestingly, the eNOR is found in an operon with NirK, suggesting that these genes are coregulated. No genes were found for either lipopolysaccharide (LPS) biosynthesis or outer membrane proteins, consistent with the proposal that Chloroflexi have only one membrane (7).
Nucleotide sequence accession number.
This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession no. LGKN00000000.
ACKNOWLEDGMENTS
Genomic DNA was obtained from the Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH. Sequencing was performed at SeqMatic, Fremont, CA.
This work was funded in part by the Center for Environmental Microbial Interactions (CEMI) at Caltech, the Packard Foundation (to W.W.F.), the Agouron Institute (to J.H. and W.W.F.), and NSF GRFP (to L.M.W.).
Footnotes
Citation Hemp J, Ward LM, Pace LA, Fischer WW. 2015. Draft genome sequence of Ardenticatena maritima 110S, a thermophilic nitrate- and iron-reducing member of the Chloroflexi class Ardenticatenia. Genome Announc 3(6):e01347-15. doi:10.1128/genomeA.01347-15.
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