1
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Chen G, Yang Y, Yan J, Löffler FE. Metabolite cross-feeding enables concomitant catabolism of chlorinated methanes and chlorinated ethenes in synthetic microbial assemblies. THE ISME JOURNAL 2024; 18:wrae090. [PMID: 38818735 PMCID: PMC11170663 DOI: 10.1093/ismejo/wrae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/19/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
Isolate studies have been a cornerstone for unraveling metabolic pathways and phenotypical (functional) features. Biogeochemical processes in natural and engineered ecosystems are generally performed by more than a single microbe and often rely on mutualistic interactions. We demonstrate the rational bottom-up design of synthetic, interdependent co-cultures to achieve concomitant utilization of chlorinated methanes as electron donors and organohalogens as electron acceptors. Specialized anaerobes conserve energy from the catabolic conversion of chloromethane or dichloromethane to formate, H2, and acetate, compounds that the organohalide-respiring bacterium Dehalogenimonas etheniformans strain GP requires to utilize cis-1,2-dichloroethenene and vinyl chloride as electron acceptors. Organism-specific qPCR enumeration matched the growth of individual dechlorinators to the respective functional (i.e. dechlorination) traits. The metabolite cross-feeding in the synthetic (co-)cultures enables concomitant utilization of chlorinated methanes (i.e. chloromethane and dichloromethane) and chlorinated ethenes (i.e. cis-1,2-dichloroethenene and vinyl chloride) without the addition of an external electron donor (i.e. formate and H2). The findings illustrate that naturally occurring chlorinated C1 compounds can sustain anaerobic food webs, an observation with implications for the development of interdependent, mutualistic communities, the sustenance of microbial life in oligotrophic and energy-deprived environments, and the fate of chloromethane/dichloromethane and chlorinated electron acceptors (e.g. chlorinated ethenes) in pristine environments and commingled contaminant plumes.
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Affiliation(s)
- Gao Chen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States
| | - Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Jun Yan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, United States
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2
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Anaerobic biodegradation of chloroform and dichloromethane with a Dehalobacter enrichment culture. Appl Environ Microbiol 2021; 88:e0197021. [PMID: 34936839 DOI: 10.1128/aem.01970-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chloroform (CF) and dichloromethane (DCM) are among the more commonly identified chlorinated aliphatic compounds found in contaminated soil and groundwater. Complete dechlorination of CF has been reported under anaerobic conditions by microbes that respire CF to DCM and others that biodegrade DCM. The objectives of this study were to ascertain if a commercially available bioaugmentation enrichment culture (KB-1® Plus CF) uses an oxidative or fermentative pathway for biodegradation of DCM; and to determine if the products from DCM biodegradation can support organohalide respiration of CF to DCM in the absence of an exogenous electron donor. In various treatments with the KB-1® Plus CF culture to which 14C-CF was added, the predominant product was 14CO2, indicating that oxidation is the predominant pathway for DCM. Recovery of 14C-DCM when biodegradation was still in progress confirmed that CF first undergoes reductive dechlorination to DCM. 14C-labeled organic acids, including acetate and propionate, were also recovered, suggesting that synthesis of organic acids provides a sink for the electron equivalents from oxidation of DCM. When the biomass was washed to remove organic acids from prior additions of exogenous electron donor and only CF and DCM were added, the culture completely dechlorinated CF. The total amount of DCM added was not sufficient to provide the electron equivalents needed to reduce CF to DCM. Thus, the additional reducing power came via the DCM generated from CF reduction. Nevertheless, the rate of CF consumption was considerably slower in comparison to treatments that received an exogenous electron donor. IMPORTANCE Chloroform (CF) and dichloromethane (DCM) are among the more commonly identified chlorinated aliphatic compounds found in contaminated soil and groundwater. One way to address this problem is to add microbes to the subsurface that can biodegrade these compounds. While microbes are known that can accomplish this task, less is known about the pathways used under anaerobic conditions. Some use an oxidative pathway, resulting mainly in carbon dioxide. Others use a fermentative pathway, resulting in formation of organic acids. In this study, a commercially available bioaugmentation enrichment culture (KB-1® Plus CF) was evaluated using carbon-14 labelled chloroform. The main product formed was carbon dioxide, indicating the use of an oxidative pathway. The reducing power gained from oxidation was shown to support reductive dechlorination of CF to DCM. The results demonstrate the potential to achieve full dechlorination of CF and DCM to nonhazardous products that are difficult to identify in the field.
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3
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Holland SI, Ertan H, Montgomery K, Manefield MJ, Lee M. Novel dichloromethane-fermenting bacteria in the Peptococcaceae family. THE ISME JOURNAL 2021; 15:1709-1721. [PMID: 33452483 PMCID: PMC8163858 DOI: 10.1038/s41396-020-00881-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/29/2020] [Accepted: 12/09/2020] [Indexed: 01/29/2023]
Abstract
Dichloromethane (DCM; CH2Cl2) is a toxic groundwater pollutant that also has a detrimental effect on atmospheric ozone levels. As a dense non-aqueous phase liquid, DCM migrates vertically through groundwater to low redox zones, yet information on anaerobic microbial DCM transformation remains scarce due to a lack of cultured organisms. We report here the characterisation of DCMF, the dominant organism in an anaerobic enrichment culture (DFE) capable of fermenting DCM to the environmentally benign product acetate. Stable carbon isotope experiments demonstrated that the organism assimilated carbon from DCM and bicarbonate via the Wood-Ljungdahl pathway. DCMF is the first anaerobic DCM-degrading population also shown to metabolise non-chlorinated substrates. It appears to be a methylotroph utilising the Wood-Ljungdahl pathway for metabolism of methyl groups from methanol, choline, and glycine betaine. The flux of these substrates from subsurface environments may either directly (DCM, methanol) or indirectly (choline, glycine betaine) affect the climate. Community profiling and cultivation of cohabiting taxa in culture DFE without DCMF suggest that DCMF is the sole organism in this culture responsible for substrate metabolism, while the cohabitants persist via necromass recycling. Genomic and physiological evidence support placement of DCMF in a novel genus within the Peptococcaceae family, 'Candidatus Formimonas warabiya'.
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Affiliation(s)
- Sophie I Holland
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Haluk Ertan
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael J Manefield
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia.
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4
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Chen G, Jiang N, Villalobos Solis MI, Kara Murdoch F, Murdoch RW, Xie Y, Swift CM, Hettich RL, Löffler FE. Anaerobic Microbial Metabolism of Dichloroacetate. mBio 2021; 12:e00537-21. [PMID: 33906923 PMCID: PMC8092247 DOI: 10.1128/mbio.00537-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising "Candidatus Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H2, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated "Candidatus Dichloromethanomonas elyunquensis" strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg-1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.IMPORTANCE Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination. Despite the ubiquitous presence of DCA, its fate under anoxic conditions has remained obscure. We discovered an anaerobic bacterium capable of metabolizing DCA, identified the enzyme responsible for DCA dehalogenation, and elucidated a novel DCA fermentation pathway. The findings have implications for the turnover of DCA and the carbon and electron flow in electron acceptor-depleted environments and the human gastrointestinal tract.
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Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Nannan Jiang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Fadime Kara Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert Waller Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Yongchao Xie
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cynthia M Swift
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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5
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Mineralization versus fermentation: evidence for two distinct anaerobic bacterial degradation pathways for dichloromethane. ISME JOURNAL 2020; 14:959-970. [PMID: 31907367 DOI: 10.1038/s41396-019-0579-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/11/2019] [Accepted: 12/17/2019] [Indexed: 01/03/2023]
Abstract
Dichloromethane (DCM) is an anthropogenic pollutant with ozone destruction potential that is also formed naturally. Under anoxic conditions, fermentation of DCM to acetate and formate has been reported in axenic culture Dehalobacterium formicoaceticum, and to acetate, H2 and CO2 in mixed culture RM, which harbors the DCM degrader 'Candidatus Dichloromethanomonas elyunquensis'. RM cultures produced 28.1 ± 2.3 μmol of acetate from 155.6 ± 9.3 μmol DCM, far less than the one third (i.e., about 51.9 µmol) predicted based on the assumed fermentation model, and observed in cultures of Dehalobacterium formicoaceticum. Temporal metabolite analyses using gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy revealed that no 13C-labeled acetate was formed in 13C-DCM-grown RM cultures, indicating acetate was not a direct product of DCM metabolism. The data were reconciled with DCM mineralization and H2 consumption via CO2 reduction to acetate and methane by homoacetogenic and methanogenic partner populations, respectively. In contrast, Dehalobacterium formicoaceticum produced 13C-labeled acetate and formate from 13C-DCM, consistent with a fermentation pathway. Free energy change calculations predicted that organisms with the mineralization pathway are the dominant DCM consumers in environments with H2 <100 ppmv. These findings have implications for carbon and electron flow in environments where DCM is introduced through natural production processes or anthropogenic activities.
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6
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Holland SI, Edwards RJ, Ertan H, Wong YK, Russell TL, Deshpande NP, Manefield MJ, Lee M. Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture. PeerJ 2019; 7:e7775. [PMID: 31592187 PMCID: PMC6778437 DOI: 10.7717/peerj.7775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/27/2019] [Indexed: 01/07/2023] Open
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. 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/.
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Affiliation(s)
- Sophie I. Holland
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Haluk Ertan
- Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
- School of Chemical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Yie Kuan Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Tonia L. Russell
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales, Australia
| | - Nandan P. Deshpande
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael J. Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales, Australia
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7
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Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism. Appl Environ Microbiol 2019; 85:AEM.02768-18. [PMID: 30658979 DOI: 10.1128/aem.02768-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/08/2019] [Indexed: 11/20/2022] Open
Abstract
Dichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader "Candidatus Dichloromethanomonas elyunquensis" strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/cofactor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM's genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase of Dehalococcoides mccartyi strain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase of Dehalobacter sp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway.IMPORTANCE Naturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader "Candidatus Dichloromethanomonas elyunquensis" strain RM, suggesting that reductive dechlorination and methyl group transfer play roles in anaerobic DCM degradation. These findings suggest that the characterized DCM-degrading bacterium Dehalobacterium formicoaceticum and "Candidatus Dichloromethanomonas elyunquensis" strain RM utilize distinct strategies for carbon-chlorine bond cleavage, indicating that multiple pathways evolved for anaerobic DCM metabolism. The specific proteins (e.g., RDases and methyltransferases) identified in strain RM may have value as biomarkers for monitoring anaerobic DCM degradation in natural and contaminated environments.
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8
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Chen G, Shouakar-Stash O, Phillips E, Justicia-Leon SD, Gilevska T, Sherwood Lollar B, Mack EE, Seger ES, Löffler FE. Dual Carbon-Chlorine Isotope Analysis Indicates Distinct Anaerobic Dichloromethane Degradation Pathways in Two Members of Peptococcaceae. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8607-8616. [PMID: 29975517 DOI: 10.1021/acs.est.8b01583] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Dichloromethane (DCM) is a probable human carcinogen and frequent groundwater contaminant and contributes to stratospheric ozone layer depletion. DCM is degraded by aerobes harboring glutathione-dependent DCM dehalogenases; however, DCM contamination occurs in oxygen-deprived environments, and much less is known about anaerobic DCM metabolism. Some members of the Peptococcaceae family convert DCM to environmentally benign products including acetate, formate, hydrogen (H2), and inorganic chloride under strictly anoxic conditions. The current study applied stable carbon and chlorine isotope fractionation measurements to the axenic culture Dehalobacterium formicoaceticum and to the consortium RM comprising DCM degrader Candidatus Dichloromethanomonas elyunquensis. Degradation-associated carbon and chlorine isotope enrichment factors (εC and εCl) of -42.4 ± 0.7‰ and -5.3 ± 0.1‰, respectively, were measured in D. formicoaceticum cultures. A similar εCl of -5.2 ± 0.1‰, but a substantially lower εC of -18.3 ± 0.2‰, were determined for Ca. Dichloromethanomonas elyunquensis. The εC and εCl values resulted in distinctly different dual element C-Cl isotope correlations (ΛC/Cl = Δδ13C/Δδ37Cl) of 7.89 ± 0.12 and 3.40 ± 0.03 for D. formicoaceticum and Ca. Dichloromethanomonas elyunquensis, respectively. The distinct ΛC/Cl values obtained for the two cultures imply mechanistically distinct C-Cl bond cleavage reactions, suggesting that members of Peptococcaceae employ different pathways to metabolize DCM. These findings emphasize the utility of dual carbon-chlorine isotope analysis to pinpoint DCM degradation mechanisms and to provide an additional line of evidence that detoxification is occurring at DCM-contaminated sites.
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Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology, Department of Civil and Environmental Engineering, and Department of Microbiology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Orfan Shouakar-Stash
- Isotope Tracer Technologies Inc. (IT2) , Waterloo , Ontario N2 V 1Z5 , Canada
- Department of Earth and Environmental Sciences , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
- School of Engineering , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Elizabeth Phillips
- Department of Earth Sciences , University of Toronto , Toronto , Ontario M5S 3B1 , Canada
| | - Shandra D Justicia-Leon
- School of Biology , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Tetyana Gilevska
- Department of Earth Sciences , University of Toronto , Toronto , Ontario M5S 3B1 , Canada
| | | | - E Erin Mack
- DuPont Corporate Remediation Group , E. I. DuPont de Nemours and Company , Wilmington , Delaware 19805 , United States
| | - Edward S Seger
- The Chemours Company , Wilmington , Delaware 19899 , United States
| | - Frank E Löffler
- Center for Environmental Biotechnology, Department of Civil and Environmental Engineering, and Department of Microbiology , University of Tennessee , Knoxville , Tennessee 37996 , United States
- Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division , University of Tennessee and Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Department of Biosystems Engineering and Soil Science , University of Tennessee , Knoxville , Tennessee 37996 , United States
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9
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Wright J, Kirchner V, Bernard W, Ulrich N, McLimans C, Campa MF, Hazen T, Macbeth T, Marabello D, McDermott J, Mackelprang R, Roth K, Lamendella R. Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation. Front Microbiol 2017; 8:2300. [PMID: 29213257 PMCID: PMC5702783 DOI: 10.3389/fmicb.2017.02300] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023] Open
Abstract
The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.
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Affiliation(s)
- Justin Wright
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States.,Wright Labs, LLC, Huntingdon, PA, United States
| | - Veronica Kirchner
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - William Bernard
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Nikea Ulrich
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Christopher McLimans
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Maria F Campa
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
| | - Terry Hazen
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States.,Department of Microbiology, University of Tennessee, Knoxville, TN, United States.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
| | | | | | | | - Rachel Mackelprang
- Department of Biology, California State University Northridge, Northridge, PA, United States
| | - Kimberly Roth
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Regina Lamendella
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States.,Wright Labs, LLC, Huntingdon, PA, United States
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10
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Chen G, Kleindienst S, Griffiths DR, Mack EE, Seger ES, Löffler FE. Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture. Environ Microbiol 2017; 19:4784-4796. [DOI: 10.1111/1462-2920.13945] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology; University of Tennessee; Knoxville TN 37996 USA
- Department of Civil and Environmental Engineering; University of Tennessee; Knoxville TN 37996 USA
| | - Sara Kleindienst
- Center for Environmental Biotechnology; University of Tennessee; Knoxville TN 37996 USA
- Oak Ridge National Laboratory; University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division; Oak Ridge TN 37831 USA
- Center for Applied Geosciences; Department of Geosciences, Eberhard Karls University Tübingen; Tübingen 72074 Germany
| | | | - E. Erin Mack
- Corporate Remediation Group; E. I. DuPont de Nemours and Company; Wilmington DE 19805 USA
| | | | - Frank E. Löffler
- Center for Environmental Biotechnology; University of Tennessee; Knoxville TN 37996 USA
- Department of Civil and Environmental Engineering; University of Tennessee; Knoxville TN 37996 USA
- Oak Ridge National Laboratory; University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division; Oak Ridge TN 37831 USA
- Department of Microbiology; University of Tennessee; Knoxville TN 37996 USA
- Department of Biosystems Engineering and Soil Science; University of Tennessee; Knoxville TN 37996 USA
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Chen G, Murdoch RW, Mack EE, Seger ES, Löffler FE. Complete Genome Sequence of Dehalobacterium formicoaceticum Strain DMC, a Strictly Anaerobic Dichloromethane-Degrading Bacterium. GENOME ANNOUNCEMENTS 2017; 5:e00897-17. [PMID: 28912314 PMCID: PMC5597755 DOI: 10.1128/genomea.00897-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 07/26/2017] [Indexed: 01/17/2023]
Abstract
Dehalobacterium formicoaceticum utilizes dichloromethane as the sole energy source in defined anoxic bicarbonate-buffered mineral salt medium. The products are formate, acetate, inorganic chloride, and biomass. The bacterium's genome was sequenced using PacBio, assembled, and annotated. The complete genome consists of one 3.77-Mb circular chromosome harboring 3,935 predicted protein-encoding genes.
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Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Robert W Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - E Erin Mack
- Corporate Remediation Group, E. I. DuPont de Nemours and Company, Newark, Delaware, USA
| | | | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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12
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Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21. GENOME ANNOUNCEMENTS 2017; 5:5/30/e00622-17. [PMID: 28751386 PMCID: PMC5532824 DOI: 10.1128/genomea.00622-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from samples of environments contaminated with halogenated pollutants and capable of using dichloromethane as its sole carbon and energy source, was determined.
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13
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Kleindienst S, Higgins SA, Tsementzi D, Chen G, Konstantinidis KT, Mack EE, Löffler FE. 'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. Syst Appl Microbiol 2016; 40:150-159. [PMID: 28292625 DOI: 10.1016/j.syapm.2016.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
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'.
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Affiliation(s)
- Sara Kleindienst
- 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.
| | - Steven A Higgins
- 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
| | - Despina Tsementzi
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA
| | - Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Konstantinos T Konstantinidis
- 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
| | - E Erin Mack
- Corporate Remediation Group, E. I. DuPont de Nemours and Company, Newark, DE 19714, USA
| | - Frank E Löffler
- 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.
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