Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture
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 B...
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PeerJ Inc.
2019-10-01
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| author | Sophie I. Holland Richard J. Edwards Haluk Ertan Yie Kuan Wong Tonia L. Russell Nandan P. Deshpande Michael J. Manefield Matthew Lee |
| author_facet | Sophie I. Holland Richard J. Edwards Haluk Ertan Yie Kuan Wong Tonia L. Russell Nandan P. Deshpande Michael J. Manefield Matthew Lee |
| author_sort | Sophie I. Holland |
| collection | DOAJ |
| description | 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. 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/. |
| first_indexed | 2024-03-09T06:37:18Z |
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| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:37:18Z |
| publishDate | 2019-10-01 |
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| spelling | doaj.art-7955417b1a984101a1b2b73638c642042023-12-03T10:56:36ZengPeerJ Inc.PeerJ2167-83592019-10-017e777510.7717/peerj.7775Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment cultureSophie I. Holland0Richard J. Edwards1Haluk Ertan2Yie Kuan Wong3Tonia L. Russell4Nandan P. Deshpande5Michael J. Manefield6Matthew Lee7UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, AustraliaSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, AustraliaDepartment of Molecular Biology and Genetics, Istanbul University, Istanbul, TurkeySchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, AustraliaRamaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales, AustraliaSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, AustraliaUNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, AustraliaUNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, AustraliaBacteria 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. 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/.https://peerj.com/articles/7775.pdfPeptococcaceaeDichloromethaneWhole genome sequencingPhylogeny |
| spellingShingle | Sophie I. Holland Richard J. Edwards Haluk Ertan Yie Kuan Wong Tonia L. Russell Nandan P. Deshpande Michael J. Manefield Matthew Lee Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture PeerJ Peptococcaceae Dichloromethane Whole genome sequencing Phylogeny |
| title | Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture |
| title_full | Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture |
| title_fullStr | Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture |
| title_full_unstemmed | Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture |
| title_short | Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture |
| title_sort | whole genome sequencing of a novel dichloromethane fermenting peptococcaceae from an enrichment culture |
| topic | Peptococcaceae Dichloromethane Whole genome sequencing Phylogeny |
| url | https://peerj.com/articles/7775.pdf |
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