'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family

Sara Kleindienst; Steven A Higgins; Despina Tsementzi; Gao Chen; Konstantinos T Konstantinidis; E Erin Mack; Frank E Löffler

doi:10.1016/j.syapm.2016.12.001

'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family

Syst Appl Microbiol. 2017 Apr;40(3):150-159. doi: 10.1016/j.syapm.2016.12.001. Epub 2016 Dec 21.

Authors

Sara Kleindienst¹, Steven A Higgins², Despina Tsementzi³, Gao Chen⁴, Konstantinos T Konstantinidis⁵, E Erin Mack⁶, Frank E Löffler⁷

Affiliations

¹ University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA. Electronic address: sara.kleindienst@uni-tuebingen.de.
² University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.
³ Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA.
⁴ Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.
⁵ Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA; School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
⁶ Corporate Remediation Group, E. I. DuPont de Nemours and Company, Newark, DE 19714, USA.
⁷ University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA. Electronic address: frank.loeffler@utk.edu.

PMID: 28292625
DOI: 10.1016/j.syapm.2016.12.001

Abstract

Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader does not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160±3μmolL^-1 d^-1. The DCM degrader attained 5.25×10⁷±1.0×10⁷ cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4±0.8μm long and 0.4±0.1μm wide. Based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, 'Candidatus Dichloromethanomonas elyunquensis'.

Keywords: Anaerobic dichloromethane degradation; Metagenome binning; Peptococcaceae; ‘Candidatus Dichloromethanomonas elyunquensis’.

MeSH terms

Chromatography, Gas
Environmental Microbiology
In Situ Hybridization, Fluorescence
Methylene Chloride / chemistry
Methylene Chloride / metabolism*
Open Reading Frames
Peptococcaceae / classification*
Peptococcaceae / genetics
Peptococcaceae / isolation & purification
Peptococcaceae / metabolism*
Phylogeny
RNA, Ribosomal, 16S / genetics
Sequence Analysis, DNA

Substances

RNA, Ribosomal, 16S
Methylene Chloride