Abstract
We present the draft genome of Thermanaerothrix daxensis GNS-1, a thermophilic member of the Chloroflexi phylum. This organism was initially characterized as a nonmotile, strictly anaerobic fermenter; however, genome analysis demonstrates that it encodes genes for a flagellum and multiple pathways for aerobic and anaerobic respiration.
GENOME ANNOUNCEMENT
Thermanaerothrix daxensis GNS-1 was isolated from a deep groundwater aquifer (149 m) housed within sedimentary strata of the large Mesozoic and Tertiary Aquitaine Basin in southwestern France (1). Closely related strains have been reported from a hot spring in Yellowstone National Park (2), a hot spring in southwestern Taiwan, geothermal soil, a thermophilic anaerobic digestive sludge, and a thermophilic electrochemical cell (3). T. daxensis is a filamentous, nonsporulating organism that can ferment a number of sugars and organic acids (1). It grows optimally at 65°C (range 50 to 73°C) and pH 7 (range pH 5.8 to 8.5) (1).
The genome of Thermanaerothrix daxensis GNS-1 (DSM 23592) 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 version 3.1.1 (4) was used to assemble the genome. The genome was screened for contaminants based on sequence coverage, GC composition, and BLAST hits of conserved single-copy genes. Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline. The draft genome is 3.06 Mb in size, assembled into 6 contigs. It encodes 2,798 genes, 2,395 coding sequences, 1 16S RNA, 47 tRNAs, and 4 CRISPR arrays. It is estimated to be ~95% complete based on conserved single-copy genes (106/111).
Genome analysis of T. daxensis detected the presence of aerobic and anaerobic respiration pathways, hinting at a richer physiology than previously recognized. It encodes for Complex I (NADH dehydrogenase), Complex II (succinate dehydrogenase), and an aerobic CO dehydrogenase. It also has two aerobic respiration modules; an A-family heme-copper oxygen reductase coupled to an alternative complex III (ACIII) (5), and a quinol bd oxidase (6). In addition, T. daxensis has two respiratory nitrite reductases; NirS, which reduces NO2− to NO, and NrfA that reduces NO2− to NH4+. The genome provides no evidence for the presence of LPS biosynthesis genes or outer membrane proteins, suggesting that this organism has only one membrane (7). Furthermore, it encodes for a Gram-positive flagella and is likely motile under certain physiological conditions.
Nucleotide sequence accession number.
This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession number LGKO00000000.
ACKNOWLEDGMENTS
Genomic DNA was obtained from the Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH. Sequencing was performed at Seqmatic, Fremont, CA, USA.
This work was funded in part by the Center for Environmental Microbial Interactions (CEMI) at Caltech, the Packard Foundation (W.W.F.), the Agouron Institute (J.H. and W.W.F.), and NSF GRFP (L.M.W.).
Footnotes
Citation Pace LA, Hemp J, Ward LM, Fischer WW. 2015. Draft genome of Thermanaerothrix daxensis GNS-1, a thermophilic facultative anaerobe from the Chloroflexi class Anaerolineae. Genome Announc 3(6):e01354-15. doi:10.1128/genomeA.01354-15.
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