1
|
Wu M, Zhao D, Gu B, Wang Z, Hu J, Yu Z, Yu J. Efficient degradation of aqueous dichloromethane by an enhanced microbial electrolysis cell: Degradation kinetics, microbial community and metabolic mechanisms. J Environ Sci (China) 2024; 139:150-159. [PMID: 38105043 DOI: 10.1016/j.jes.2023.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/08/2023] [Accepted: 05/22/2023] [Indexed: 12/19/2023]
Abstract
Dichloromethane (DCM) has been listed as a toxic and harmful water pollutant, and its removal needs attention. Microbial electrolysis cells (MECs) are viewed as a promising alternative for pollutant removal, which can be strengthened from two aspects: microbial inoculation and acclimation. In this study, the MEC for DCM degradation was inoculated with the active sludge enhanced by Methylobacterium rhodesianum H13 (strain H13) and then acclimated in the form of a microbial fuel cell (MFC). Both the introduction of strain H13 and the initiation in MFC form significantly promoted DCM degradation. The degradation kinetics were fitted by the Haldane model, with Vmax, Kh, Ki and vmax values of 103.2 mg/L/hr, 97.8 mg/L, 268.3 mg/L and 44.7 mg/L/hr/cm2, respectively. The cyclic voltammogram implies that DCM redox reactions became easier with the setup of MEC, and the electrochemical impedance spectrogram shows that the acclimated and enriched microbes reduced the charge transfer resistance from the electrode to the electrolyte. In the biofilm, the dominant genera shifted from Geobacter to Hyphomicrobium in acclimation stages. Moreover, Methylobacterium played an increasingly important role. DCM metabolism mainly occurred through the hydrolytic glutathione S-transferase pathway, given that the gene dcmA was identified rather than the dhlA and P450/MO. The exogenous electrons facilitated the reduction of GSSG, directly or indirectly accelerating the GSH-catalyzed dehalogenation. This study provides support for the construction of an efficient and stable MEC for DCM removal in water environment.
Collapse
Affiliation(s)
- Meng Wu
- College of Environment, College of Biotechnology and Bioengineering, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Di Zhao
- Shentuo Environment (Hangzhou) Co. Ltd., Hangzhou 311121, China
| | - Bing Gu
- Zhejiang Tianyi Environmental Co. Ltd., Hangzhou 310000, China
| | - Ziru Wang
- College of Environment, College of Biotechnology and Bioengineering, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jun Hu
- College of Environment, College of Biotechnology and Bioengineering, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Zhiliang Yu
- College of Environment, College of Biotechnology and Bioengineering, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jianming Yu
- College of Environment, College of Biotechnology and Bioengineering, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China.
| |
Collapse
|
2
|
Genome-Wide Transcription Start Sites Mapping in Methylorubrum Grown with Dichloromethane and Methanol. Microorganisms 2022; 10:microorganisms10071301. [PMID: 35889020 PMCID: PMC9320726 DOI: 10.3390/microorganisms10071301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Dichloromethane (DCM, methylene chloride) is a toxic halogenated volatile organic compound massively used for industrial applications, and consequently often detected in the environment as a major pollutant. DCM biotransformation suggests a sustainable decontamination strategy of polluted sites. Among methylotrophic bacteria able to use DCM as a sole source of carbon and energy for growth, Methylorubrum extorquens DM4 is a longstanding reference strain. Here, the primary 5′-ends of transcripts were obtained using a differential RNA-seq (dRNA-seq) approach to provide the first transcription start site (TSS) genome-wide landscape of a methylotroph using DCM or methanol. In total, 7231 putative TSSs were annotated and classified with respect to their localization to coding sequences (CDSs). TSSs on the opposite strand of CDS (antisense TSS) account for 31% of all identified TSSs. One-third of the detected TSSs were located at a distance to the start codon inferior to 250 nt (average of 84 nt) with 7% of leaderless mRNA. Taken together, the global TSS map for bacterial growth using DCM or methanol will facilitate future studies in which transcriptional regulation is crucial, and efficient DCM removal at polluted sites is limited by regulatory processes.
Collapse
|
3
|
Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms 2020; 8:microorganisms8121876. [PMID: 33260855 PMCID: PMC7760279 DOI: 10.3390/microorganisms8121876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/23/2022] Open
Abstract
Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for Hyphomicrobium sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain. For this, we designed a pan-proteomics database comprising the annotated genome sequences of 13 distinct Hyphomicrobium strains. Compared to growth with methanol, growth with DCM induces drastic changes in the proteome of strain MC8b. Dichloromethane dehalogenase DcmA was detected by differential pan-proteomics, but only with poor sequence coverage, suggesting atypical characteristics of the DCM dehalogenation system in this strain. More peptides were assigned to DcmA by error-tolerant search, warranting subsequent sequencing of the genome of strain MC8b, which revealed a highly divergent set of dcm genes in this strain. This suggests that the dcm enzymatic system is less strongly conserved than previously believed, and that substantial molecular evolution of dcm genes has occurred beyond their horizontal transfer in the bacterial domain. Our study showed the power of pan-proteomics for quick characterization of new strains belonging to branches of the Tree of Life that are densely genome-sequenced.
Collapse
|
4
|
Hermon L, Denonfoux J, Hellal J, Joulian C, Ferreira S, Vuilleumier S, Imfeld G. Dichloromethane biodegradation in multi-contaminated groundwater: Insights from biomolecular and compound-specific isotope analyses. WATER RESEARCH 2018; 142:217-226. [PMID: 29885622 DOI: 10.1016/j.watres.2018.05.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/25/2018] [Accepted: 05/30/2018] [Indexed: 06/08/2023]
Abstract
Dichloromethane (DCM) is a widespread and toxic industrial solvent which often co-occurs with chlorinated ethenes at polluted sites. Biodegradation of DCM occurs under both oxic and anoxic conditions in soils and aquifers. Here we investigated in situ and ex situ biodegradation of DCM in groundwater sampled from the industrial site of Themeroil (France), where DCM occurs as a major co-contaminant of chloroethenes. Carbon isotopic fractionation (εC) for DCM ranging from -46 to -22‰ were obtained under oxic or denitrifying conditions, in mineral medium or contaminated groundwater, and for laboratory cultures of Hyphomicrobium sp. strain GJ21 and two new DCM-degrading strains isolated from the contaminated groundwater. The extent of DCM biodegradation (B%) in the aquifer, as evaluated by compound-specific isotope analysis (δ13C), ranged from 1% to 85% applying DCM-specific εC derived from reference strains and those determined in this study. Laboratory groundwater microcosms under oxic conditions showed DCM biodegradation rates of up to 0.1 mM·day-1, with concomitant chloride release. Dehalogenase genes dcmA and dhlA involved in DCM biodegradation ranged from below 4 × 102 (boundary) to 1 × 107 (source zone) copies L-1 across the contamination plume. High-throughput sequencing on the 16S rrnA gene in groundwater samples showed that both contaminant level and terminal electron acceptor processes (TEAPs) influenced the distribution of genus-level taxa associated with DCM biodegradation. Taken together, our results demonstrate the potential of DCM biodegradation in multi-contaminated groundwater. This integrative approach may be applied to contaminated aquifers in the future, in order to identify microbial taxa and pathways associated with DCM biodegradation in relation to redox conditions and co-contamination levels.
Collapse
Affiliation(s)
- L Hermon
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France; BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - J Denonfoux
- Service Recherche, Développement et Innovation-Communautés Microbiennes, GenoScreen Lille, France
| | - J Hellal
- BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - C Joulian
- BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - S Ferreira
- Service Recherche, Développement et Innovation-Communautés Microbiennes, GenoScreen Lille, France
| | - S Vuilleumier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
| | - G Imfeld
- Université de Strasbourg, CNRS/EOST, LHyGeS UMR 7517, Laboratory of Hydrology and Geochemistry of Strasbourg, Strasbourg, France.
| |
Collapse
|
5
|
Malla MA, Dubey A, Yadav S, Kumar A, Hashem A, Abd Allah EF. Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches. Front Microbiol 2018; 9:1132. [PMID: 29915565 PMCID: PMC5994547 DOI: 10.3389/fmicb.2018.01132] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/14/2018] [Indexed: 12/24/2022] Open
Abstract
Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.
Collapse
Affiliation(s)
- Muneer A Malla
- Department of Zoology, Dr. Harisingh Gour University, Sagar, India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University, Sagar, India
| | - Shweta Yadav
- Department of Zoology, Dr. Harisingh Gour University, Sagar, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University, Sagar, India
| | - Abeer Hashem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
6
|
N-terminome and proteogenomic analysis of the Methylobacterium extorquens DM4 reference strain for dichloromethane utilization. J Proteomics 2018; 179:131-139. [DOI: 10.1016/j.jprot.2018.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 12/29/2022]
|