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

Sophie I Holland; Richard J Edwards; Haluk Ertan; Yie Kuan Wong; Tonia L Russell; Nandan P Deshpande; Michael J Manefield; Matthew Lee

doi:10.7717/peerj.7775

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

PeerJ. 2019 Oct 2:7:e7775. doi: 10.7717/peerj.7775. eCollection 2019.

Authors

Sophie I Holland^#¹, Richard J Edwards^#², Haluk Ertan^{3

4}, Yie Kuan Wong², Tonia L Russell⁵, Nandan P Deshpande², Michael J Manefield^{1

4}, Matthew Lee¹

Affiliations

¹ UNSW Water Research Centre, 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.

^# Contributed equally.

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 SMRT^TM 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. It includes an abundance of methyltransferases, which may provide clues to the basis of its DCM metabolism, as well as potential to metabolise additional methylated substrates such as quaternary amines. 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, http://www.slimsuite.unsw.edu.au/research/dcmf/.

Keywords: Dichloromethane; Peptococcaceae; Phylogeny; Whole genome sequencing.

Grants and funding

Sophie I. Holland was supported by an Australian Government Research Training Program scholarship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.