TY - JOUR
T1 - Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ‘Candidatus Formimonas warabiya’ strain DCMF
AU - Holland, Sophie I.
AU - Vázquez-Campos, Xabier
AU - Ertan, Haluk
AU - Edwards, Richard J.
AU - Manefield, Michael J.
AU - Lee, Matthew
N1 - Funding Information:
Mass spectrometric analysis for this work was carried out at the Bioanalytical Mass Spectrometry Facility (BMSF), UNSW and was supported in part by infrastructure funding from the New South Wales Government as part of its co-investment in the National Collaborative Research Infrastructure Strategy. We are grateful to Ling Zhong at the BMSF for her assistance with LC–MS/MS. This research includes computations using the computational cluster Katana supported by Research Technology Services at UNSW Sydney. We acknowledge the Dharawal Language Program and thank the Eastern Zone Gujaga Aboriginal Corporation (Gujaga) for granting a non-exclusive license to use the placename, Warabiya, in the candidate species name for the bacterial lineage under investigation.
Funding Information:
Mass spectrometric analysis for this work was carried out at the Bioanalytical Mass Spectrometry Facility (BMSF), UNSW and was supported in part by infrastructure funding from the New South Wales Government as part of its co-investment in the National Collaborative Research Infrastructure Strategy. We are grateful to Ling Zhong at the BMSF for her assistance with LC–MS/MS. This research includes computations using the computational cluster Katana supported by Research Technology Services at UNSW Sydney. We acknowledge the Dharawal Language Program and thank the Eastern Zone Gujaga Aboriginal Corporation (Gujaga) for granting a non-exclusive license to use the placename, Warabiya, in the candidate species name for the bacterial lineage under investigation.
Funding Information:
SH was supported by an Australian Government Research Training Program Scholarship. XV-C acknowledges support from the New South Wales State Government RAAP scheme and the National Collaborative Research Infrastructure Strategy. RE was funded by the Australian Research Council (ARC LP160100610).
Publisher Copyright:
Copyright © 2022 Holland, Vázquez-Campos, Ertan, Edwards, Manefield and Lee.
PY - 2022/12/7
Y1 - 2022/12/7
N2 - Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood–Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, ‘Candidatus Formimonas warabiya’ strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.
AB - Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood–Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, ‘Candidatus Formimonas warabiya’ strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.
KW - anaerobic dechlorination
KW - dichloromethane
KW - glycine betaine
KW - metaproteomics
KW - methyltransferase
KW - subsurface
KW - Wood–Ljungdahl pathway
UR - http://www.scopus.com/inward/record.url?scp=85144323427&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2022.1035247
DO - 10.3389/fmicb.2022.1035247
M3 - Article
C2 - 36569084
AN - SCOPUS:85144323427
SN - 1664-302X
VL - 13
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
M1 - 1035247
ER -