Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture

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1 School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
2 School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
3 Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
4 School of Chemical Engineering, University of New South Wales, Sydney, New South Wales, Australia
5 Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales, Australia
DOI
10.7287/peerj.preprints.27718v1
Published
Accepted
Subject Areas
Genomics, Microbiology, Environmental Contamination and Remediation
Keywords
Peptococcaceae, dichloromethane, whole genome sequencing, phylogeny
Copyright
© 2019 Holland et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Holland SI, Edwards RJ, Ertan H, Wong YK, Russell TL, Deshpande NP, Manefield M, Lee MJ. 2019. Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture. PeerJ Preprints 7:e27718v1

Abstract

Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, "DCMF", was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the Peptococcaceae family. The DCMF genome is large in comparison to known DCM-fermenting bacteria and includes 96 predicted methylamine methyltransferases, which may provide clues to the basis of its DCM metabolism. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, available at http://www.slimsuite.unsw.edu.au/research/dcmf/.

Author Comment

This is a submission to PeerJ for review.

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