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Pioli S, Clagnan E, Chowdhury AA, Bani A, Borruso L, Ventura M, Tonon G, Brusetti L. Structural and functional microbial diversity in deadwood respond to decomposition dynamics. Environ Microbiol 2023; 25:2351-2367. [PMID: 37403552 DOI: 10.1111/1462-2920.16459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions.
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Affiliation(s)
- Silvia Pioli
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Monterotondo Scalo (RM), Italy
| | - Elisa Clagnan
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Atif Aziz Chowdhury
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Alessia Bani
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Maurizio Ventura
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Giustino Tonon
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
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2
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Hussain B, Chen JS, Huang SW, Tsai IS, Rathod J, Hsu BM. Underpinning the ecological response of mixed chlorinated volatile organic compounds (CVOCs) associated with contaminated and bioremediated groundwaters: A potential nexus of microbial community structure and function for strategizing efficient bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122215. [PMID: 37473850 DOI: 10.1016/j.envpol.2023.122215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/22/2023]
Abstract
Understanding the structure, dynamics, and functionality of microbial communities is essential for developing sustainable and effective bioremediation strategies, particularly for sites contaminated with mixed chlorinated volatile organic compounds (CVOCs), which can make the biodegradation process more complex and challenging. In this study, 16S rRNA amplicon sequencing revealed a significant change in microbial distribution in response to CVOCs contamination. The loss of sensitive taxa such as Proteobacteria and Acidobacteriota was observed, while CVOCs-resistant taxa such as Campilobacterota were found significantly enriched in contaminated sites. Additionally, varying abundances of crucial enzymes involved in the sequential biodegradation of CVOCs were expressed depending on the contamination level. Association analysis revealed that specific genera such as Sulfurospirillum, Azospira, Trichlorobacter, Acidiphilium, and Magnetospririllum could relatively survive under higher levels of CVOC contamination, whereas pH, ORP and temperature had a negative influence in their abundance and distribution. However, Dechloromonas, Thiobacillus, Pseudarcicella, Hydrogenophaga, and Sulfuritalea showed a negative relationship with CVOC contamination, highlighting their sensitivity towards CVOC contamination. These findings provide valuable insights into the relationship among ecological responses, the groundwater bacterial community, and their functionality in response to mixed CVOC contamination, offering a fundamental basis for developing effective and sustainable bioremediation strategies for CVOC-contaminated groundwater systems.
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Affiliation(s)
- Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Shih-Wei Huang
- Institute of Environmental Toxin and Emerging Contaminant, Cheng Shiu University, Kaohsiung, Taiwan; Center for Environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung, Taiwan
| | - I-Sen Tsai
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Doctoral Program in Science, Technology, Environment and Mathematics, National Chung Cheng University, Chiayi, Taiwan
| | - Jagat Rathod
- Department of Environmental Biotechnology, Gujarat Biotechnology University, Near Gujarat International Finance and Tec (GIFT)-City, Gandhinagar, Gujarat, India
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan.
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3
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Ahmad K, Roy Ghatak H, Ahuja S. Optimal production of vanillin and 4-hydroxybenzaldehyde from rice straw hydrolysis residue (RSHR) over TiO2/UV and ZnO/UV system. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Verstraete W, Yanuka‐Golub K, Driesen N, De Vrieze J. Engineering microbial technologies for environmental sustainability: choices to make. Microb Biotechnol 2022; 15:215-227. [PMID: 34875143 PMCID: PMC8719809 DOI: 10.1111/1751-7915.13986] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/21/2021] [Indexed: 11/27/2022] Open
Abstract
Microbial technologies have provided solutions to key challenges in our daily lives for over a century. In the debate about the ongoing climate change and the need for planetary sustainability, microbial ecology and microbial technologies are rarely considered. Nonetheless, they can bring forward vital solutions to decrease and even prevent long-term effects of climate change. The key to the success of microbial technologies is an effective, target-oriented microbiome management. Here, we highlight how microbial technologies can play a key role in both natural, i.e. soils and aquatic ecosystems, and semi-natural or even entirely human-made, engineered ecosystems, e.g. (waste) water treatment and bodily systems. First, we set forward fundamental guidelines for effective soil microbial resource management, especially with respect to nutrient loss and greenhouse gas abatement. Next, we focus on closing the water circle, integrating resource recovery. We also address the essential interaction of the human and animal host with their respective microbiomes. Finally, we set forward some key future potentials, such as microbial protein and the need to overcome microphobia for microbial products and services. Overall, we conclude that by relying on the wisdom of the past, we can tackle the challenges of our current era through microbial technologies.
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Affiliation(s)
- Willy Verstraete
- Center for Microbial Ecology and Technology (CMET)Faculty of Bioscience EngineeringGhent UniversityCoupure Links 653GentB‐9000Belgium
- Avecom NVIndustrieweg 122PWondelgem9032Belgium
| | - Keren Yanuka‐Golub
- The Institute of Applied ResearchThe Galilee SocietyP.O. Box 437Shefa‐AmrIsrael
| | | | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET)Faculty of Bioscience EngineeringGhent UniversityCoupure Links 653GentB‐9000Belgium
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5
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1,2-DCA Natural Attenuation Evaluation in Groundwater: Insight by Dual Isotope 13C/37Cl and Molecular Analysis Approach. WATER 2021. [DOI: 10.3390/w13050728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Natural attenuation (NA) processes represent a valuable option in groundwater remediation. At a heavily 1,2-dichloroethane (1,2-DCA) contaminated site, Compound-Specific Isotope Analysis (CSIA) in combination with Biological Molecular Tools (BMTs) were implemented as a rigorous characterization approach to evaluate the occurrence of Natural Attenuation in the proximity of the source area. By the use of microcosm experiments, the potential for natural and enhanced biodegradation under anaerobic conditions was documented, following the dichloroelimination pathway. Enrichment factors of −9.1‰ and −11.3‰ were obtained for 13C while Geobacter spp. and reductive dehalogenase genes (rdhs) were identified as main site-specific biomarkers. At pilot scale, enrichments of 13.5‰ and 6.3‰ for δ13C and δ37Cl, respectively, high levels of reductive dehalogenase (rdh group VI) along with the dominance of Geobacter spp. indicated the occurrence of significant dichloroelimination processes in groundwater under anaerobic conditions. By using the site-specific enrichment factors, degradation extents over approximately 70–80% were estimated, highlighting the relevant potential of NA in 1,2-DCA degradation in the vicinity of the source area at the site. The proposed fine-tuned protocol, including CSIA and BMTs, is proven to be effective as a groundwater remediation strategy, properly assessing and monitoring NA at site scale.
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Ang TF, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018; 23:E1100. [PMID: 29735886 PMCID: PMC6100074 DOI: 10.3390/molecules23051100] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.
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Affiliation(s)
- Thiau-Fu Ang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Jonathan Maiangwa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Wang Y, Feng Y, Cao X, Liu Y, Xue S. Insights into the molecular mechanism of dehalogenation catalyzed by D-2-haloacid dehalogenase from crystal structures. Sci Rep 2018; 8:1454. [PMID: 29362453 PMCID: PMC5780510 DOI: 10.1038/s41598-017-19050-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/17/2017] [Indexed: 11/09/2022] Open
Abstract
D-2-haloacid dehalogenases (D-DEXs) catalyse the hydrolytic dehalogenation of D-2-haloacids, releasing halide ions and producing the corresponding 2-hydroxyacids. A structure-guided elucidation of the catalytic mechanism of this dehalogenation reaction has not been reported yet. Here, we report the catalytic mechanism of a D-DEX, HadD AJ1 from Pseudomonas putida AJ1/23, which was elucidated by X-ray crystallographic analysis and the H218O incorporation experiment. HadD AJ1 is an α-helical hydrolase that forms a homotetramer with its monomer including two structurally axisymmetric repeats. The product-bound complex structure was trapped with L-lactic acid in the active site, which is framed by the structurally related helices between two repeats. Site-directed mutagenesis confirmed the importance of the residues lining the binding pocket in stabilizing the enzyme-substrate complex. Asp205 acts as a key catalytic residue and is responsible for activating a water molecule along with Asn131. Then, the hydroxyl group of the water molecule directly attacks the C2 atom of the substrate to release the halogen ion instead of forming an enzyme-substrate ester intermediate as observed in L-2-haloacid dehalogenases. The newly revealed structural and mechanistic information on D-DEX may inspire structure-based mutagenesis to engineer highly efficient haloacid dehalogenases.
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Affiliation(s)
- Yayue Wang
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanbin Feng
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xupeng Cao
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Yinghui Liu
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Song Xue
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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8
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Kunze C, Diekert G, Schubert T. Subtle changes in the active site architecture untangled overlapping substrate ranges and mechanistic differences of two reductive dehalogenases. FEBS J 2017; 284:3520-3535. [DOI: 10.1111/febs.14258] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/20/2017] [Accepted: 08/30/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Cindy Kunze
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena Germany
| | - Torsten Schubert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena Germany
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9
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Bretón-Deval L, Rios-Leal E, Poggi-Varaldo HM, Ponce-Noyola T. Biodegradability of Nonionic Surfactant Used in the Remediation of Groundwaters Polluted with PCE. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2016; 88:2159-2168. [PMID: 28661332 DOI: 10.2175/106143016x14733681695564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The objective of this work was to evaluate the degradation of the nonionic surfactant Tween 80 by a PCE-degrading consortium anchored in bioparticles of fluidized bed bioreactors used in onsite remediation. Batch lab-scale bioreactors were set with dominant denitrifying (DN), methanogenic (M), and aerobic (Ab) metabolisms. Tween 80 at 100 mg/L was the sole source of carbon and energy. Denitrifying bioreactors had the highest surfactant removal (70%). Tween removals in M and Ab bioreactors were 53 and 37%, respectively. Removals of organic matter (COD) closely followed the efficiencies reported for Tween. This strongly suggested that degradation of Tween 80 occurred. Positive consequences of Tween degradation in remediation are first, the surfactant will not become an environmental/health liability by remaining as a recalcitrant or toxic substance in aquifers or in treated effluents; and second, savings on aeration could be achieved by conducting Tween 80 degradation in anaerobic conditions, either DN or M.
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Affiliation(s)
- Luz Bretón-Deval
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
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10
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Leitão P, Rossetti S, Nouws HPA, Danko AS, Majone M, Aulenta F. Bioelectrochemically-assisted reductive dechlorination of 1,2-dichloroethane by a Dehalococcoides-enriched microbial culture. BIORESOURCE TECHNOLOGY 2015; 195:78-82. [PMID: 26099437 DOI: 10.1016/j.biortech.2015.06.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 06/04/2023]
Abstract
The aim of this study was to verify the possibility to use a polarized graphite electrode as an electron donor for the reductive dechlorination of 1,2-dichloroethane, an ubiquitous groundwater contaminant. The rate of 1,2-DCA dechlorination almost linearly increased by decreasing the set cathode potential over a broad range of set cathode potentials (i.e., from -300 mV to -900 mV vs. the standard hydrogen electrode). This process was primarily dependent on electrolytic H2 generation. On the other hand, reductive dechlorination proceeded (although quite slowly) with a very high Coulombic efficiency (near 70%) at a set cathode potential of -300 mV, where no H2 production occurred. Under this condition, reductive dechlorination was likely driven by direct electron uptake from the surface of the polarized electrode. Taken as a whole, this study further extends the range of chlorinated contaminants which can be treated with bioelectrochemical systems.
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Affiliation(s)
- Patrícia Leitão
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km. 29.300, 00015 Monterotondo (RM), Italy; CERENA, Department of Mining Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; REQUIMTE/LAQV, Institute of Engineering of Porto, Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 431, 4200-072 Porto, Portugal
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km. 29.300, 00015 Monterotondo (RM), Italy
| | - Henri P A Nouws
- REQUIMTE/LAQV, Institute of Engineering of Porto, Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 431, 4200-072 Porto, Portugal
| | - Anthony S Danko
- CERENA, Department of Mining Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Mauro Majone
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km. 29.300, 00015 Monterotondo (RM), Italy.
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11
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Wang Y, Cao X, Feng Y, Xue S. Environment-induced conformational and functional changes of L-2-haloacid dehalogenase. J Biosci Bioeng 2015; 121:491-6. [PMID: 26508534 DOI: 10.1016/j.jbiosc.2015.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/11/2015] [Accepted: 09/11/2015] [Indexed: 11/29/2022]
Abstract
2-Haloacid dehalogenases have been highly studied due to their potential applications in chemical industries and bioremediation. Although biochemical and structural characterizations of the enzyme have been detailed, no information was available regarding environmental effects on the structure-function relationship. Here, circular dichroism spectroscopy (CD) was used to investigate the correlation between changes on the conformation and the function of l-2-haloacid dehalogenase (HadL AJ1) from the Pseudomonas putida induced by the environmental factors. Decreased α-helix and increased β-sheet contents were observed in the structure of HadL AJ1 along with activity losses caused by pH, temperature and inhibitors. Regardless of which factor above-mentioned existed, more than 65.0% of HadL AJ1 activity could be remained if its α-helix content was over 12.0%. The maintenance of α-helical structure in HadL AJ1 was indispensable to its catalysis, while β-sheet increase restricts its activity. This study revealed the variation of enzymatic activity due to environmental conditions resulting in structural changes monitored by CD, which contributed to rational modification and was instructive for predicting changes of the enzymatic activity during application.
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Affiliation(s)
- Yayue Wang
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xupeng Cao
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yanbin Feng
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Song Xue
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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12
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Wang SY, Kuo YC, Huang YZ, Huang CW, Kao CM. Bioremediation of 1,2-dichloroethane contaminated groundwater: Microcosm and microbial diversity studies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 203:97-106. [PMID: 25863886 DOI: 10.1016/j.envpol.2015.03.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 06/04/2023]
Abstract
In this study, the effectiveness of bioremediating 1,2-dichloroethane (DCA)-contaminated groundwater under different oxidation-reduction processes was evaluated. Microcosms were constructed using indigenous bacteria and activated sludge as the inocula and cane molasses and a slow polycolloid-releasing substrate (SPRS) as the primary substrates. Complete DCA removal was obtained within 30 days under aerobic and reductive dechlorinating conditions. In anaerobic microcosms with sludge and substrate addition, chloroethane, vinyl chloride, and ethene were produced. The microbial communities and DCA-degrading bacteria in microcosms were characterized by 16S rRNA-based denatured-gradient-gel electrophoresis profiling and nucleotide sequence analyses. Real-time polymerase chain reaction was applied to evaluate the variations in Dehalococcoides spp. and Desulfitobacterium spp. Increase in Desulfitobacterium spp. indicates that the growth of Desulfitobacterium might be induced by DCA. Results indicate that DCA could be used as the primary substrate under aerobic conditions. The increased ethene concentrations imply that dihaloelimination was the dominate mechanism for DCA biodegradation.
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Affiliation(s)
- S Y Wang
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Y C Kuo
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Y Z Huang
- Bioenvironmental Engineering Department, Chung Yuan University, Chung Li, Taiwan
| | - C W Huang
- Deaprtment of Biological Science, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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13
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Diverse Reductive Dehalogenases Are Associated with Clostridiales-Enriched Microcosms Dechlorinating 1,2-Dichloroethane. BIOMED RESEARCH INTERNATIONAL 2015; 2015:242856. [PMID: 26273600 PMCID: PMC4529907 DOI: 10.1155/2015/242856] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 03/06/2015] [Indexed: 11/17/2022]
Abstract
The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales. Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community.
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14
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Parthasarathy A, Stich TA, Lohner ST, Lesnefsky A, Britt RD, Spormann AM. Biochemical and EPR-spectroscopic investigation into heterologously expressed vinyl chloride reductive dehalogenase (VcrA) from Dehalococcoides mccartyi strain VS. J Am Chem Soc 2015; 137:3525-32. [PMID: 25686300 PMCID: PMC4516053 DOI: 10.1021/ja511653d] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reductive dehalogenases play a critical role in the microbial detoxification of aquifers contaminated with chloroethenes and chlorethanes by catalyzing the reductive elimination of a halogen. We report here the first heterologous production of vinyl chloride reductase VcrA from Dehalococcoides mccartyi strain VS. Heterologously expressed VcrA was reconstituted to its active form by addition of hydroxocobalamin/adenosylcobalamin, Fe(3+), and sulfide in the presence of mercaptoethanol. The kinetic properties of reconstituted VcrA catalyzing vinyl chloride reduction with Ti(III)-citrate as reductant and methyl viologen as mediator were similar to those obtained previously for VcrA as isolated from D. mccartyi strain VS. VcrA was also found to catalyze a novel reaction, the environmentally important dihaloelimination of 1,2-dichloroethane to ethene. Electron paramagnetic resonance (EPR) spectroscopic studies with reconstituted VcrA in the presence of mercaptoethanol revealed the presence of Cob(II)alamin. Addition of Ti(III)-citrate resulted in the appearance of a new signal characteristic of a reduced [4Fe-4S] cluster and the disappearance of the Cob(II)alamin signal. UV-vis absorption spectroscopy of Ti(III)citrate-treated samples revealed the formation of two new absorption maxima characteristic of Cob(I)alamin. No evidence for the presence of a [3Fe-4S] cluster was found. We postulate that during the reaction cycle of VcrA, a reduced [4Fe-4S] cluster reduces Co(II) to Co(I) of the enzyme-bound cobalamin. Vinyl chloride reduction to ethene would be initiated when Cob(I)alamin transfers an electron to the substrate, generating a vinyl radical as a potential reaction intermediate.
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Affiliation(s)
- Anutthaman Parthasarathy
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Svenja T. Lohner
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Ann Lesnefsky
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Alfred M. Spormann
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
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Analysis of hydrocarbon-contaminated groundwater metagenomes as revealed by high-throughput sequencing. Mol Biotechnol 2013; 54:900-12. [PMID: 23307295 DOI: 10.1007/s12033-012-9639-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The tendency for chlorinated aliphatics and aromatic hydrocarbons to accumulate in environments such as groundwater and sediments poses a serious environmental threat. In this study, the metabolic capacity of hydrocarbon (aromatics and chlorinated aliphatics)-contaminated groundwater in the KwaZulu-Natal province of South Africa has been elucidated for the first time by analysis of pyrosequencing data. The taxonomic data revealed that the metagenomes were dominated by the phylum Proteobacteria (mainly Betaproteobacteria). In addition, Flavobacteriales, Sphingobacteria, Burkholderiales, and Rhodocyclales were the predominant orders present in the individual metagenomes. These orders included microorganisms (Flavobacteria, Dechloromonas aromatica RCB, and Azoarcus) involved in the degradation of aromatic compounds and various other hydrocarbons that were present in the groundwater. Although the metabolic reconstruction of the metagenome represented composite cell networks, the information obtained was sufficient to address questions regarding the metabolic potential of the microbial communities and to correlate the data to the contamination profile of the groundwater. Genes involved in the degradation of benzene and benzoate, heavy metal-resistance mechanisms appeared to provide a survival strategy used by the microbial communities. Analysis of the pyrosequencing-derived data revealed that the metagenomes represent complex microbial communities that have adapted to the geochemical conditions of the groundwater as evidenced by the presence of key enzymes/genes conferring resistance to specific contaminants. Thus, pyrosequencing analysis of the metagenomes provided insights into the microbial activities in hydrocarbon-contaminated habitats.
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Buttet GF, Holliger C, Maillard J. Functional genotyping of Sulfurospirillum spp. in mixed cultures allowed the identification of a new tetrachloroethene reductive dehalogenase. Appl Environ Microbiol 2013; 79:6941-7. [PMID: 23995945 PMCID: PMC3811552 DOI: 10.1128/aem.02312-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/28/2013] [Indexed: 11/20/2022] Open
Abstract
Reductive dehalogenases are the key enzymes involved in the anaerobic respiration of organohalides such as the widespread groundwater pollutant tetrachloroethene. The increasing number of available bacterial genomes and metagenomes gives access to hundreds of new putative reductive dehalogenase genes that display a high level of sequence diversity and for which substrate prediction remains very challenging. In this study, we present the development of a functional genotyping method targeting the diverse reductive dehalogenases present in Sulfurospirillum spp., which allowed us to unambiguously identify a new reductive dehalogenase from our tetrachloroethene-dechlorinating SL2 bacterial consortia. The new enzyme, named PceATCE, shows 92% sequence identity with the well-characterized PceA enzyme of Sulfurospirillum multivorans, but in contrast to the latter, it is restricted to tetrachloroethene as a substrate. Its apparent higher dechlorinating activity with tetrachloroethene likely allowed its selection and maintenance in the bacterial consortia among other enzymes showing broader substrate ranges. The sequence-substrate relationships within tetrachloroethene reductive dehalogenases are also discussed.
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Affiliation(s)
- Géraldine F Buttet
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Lausanne, Switzerland
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Delgado AG, Parameswaran P, Fajardo-Williams D, Halden RU, Krajmalnik-Brown R. Role of bicarbonate as a pH buffer and electron sink in microbial dechlorination of chloroethenes. Microb Cell Fact 2012; 11:128. [PMID: 22974059 PMCID: PMC3511292 DOI: 10.1186/1475-2859-11-128] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 09/04/2012] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Buffering to achieve pH control is crucial for successful trichloroethene (TCE) anaerobic bioremediation. Bicarbonate (HCO3-) is the natural buffer in groundwater and the buffer of choice in the laboratory and at contaminated sites undergoing biological treatment with organohalide respiring microorganisms. However, HCO3- also serves as the electron acceptor for hydrogenotrophic methanogens and hydrogenotrophic homoacetogens, two microbial groups competing with organohalide respirers for hydrogen (H2). We studied the effect of HCO3- as a buffering agent and the effect of HCO3--consuming reactions in a range of concentrations (2.5-30 mM) with an initial pH of 7.5 in H2-fed TCE reductively dechlorinating communities containing Dehalococcoides, hydrogenotrophic methanogens, and hydrogenotrophic homoacetogens. RESULTS Rate differences in TCE dechlorination were observed as a result of added varying HCO3- concentrations due to H2-fed electrons channeled towards methanogenesis and homoacetogenesis and pH increases (up to 8.7) from biological HCO3- consumption. Significantly faster dechlorination rates were noted at all HCO3- concentrations tested when the pH buffering was improved by providing 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) as an additional buffer. Electron balances and quantitative PCR revealed that methanogenesis was the main electron sink when the initial HCO3- concentrations were 2.5 and 5 mM, while homoacetogenesis was the dominant process and sink when 10 and 30 mM HCO3- were provided initially. CONCLUSIONS Our study reveals that HCO3- is an important variable for bioremediation of chloroethenes as it has a prominent role as an electron acceptor for methanogenesis and homoacetogenesis. It also illustrates the changes in rates and extent of reductive dechlorination resulting from the combined effect of electron donor competition stimulated by HCO3- and the changes in pH exerted by methanogens and homoacetogens.
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Affiliation(s)
- Anca G Delgado
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, PO Box 875001, Tempe, AZ 85287-5701, USA
- School of Life Sciences, Arizona State University, Tempe, USA
| | - Prathap Parameswaran
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, PO Box 875001, Tempe, AZ 85287-5701, USA
| | - Devyn Fajardo-Williams
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, PO Box 875001, Tempe, AZ 85287-5701, USA
| | - Rolf U Halden
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, PO Box 875001, Tempe, AZ 85287-5701, USA
- Ira A Fulton Schools of Engineering, Arizona State University, Tempe, USA
| | - Rosa Krajmalnik-Brown
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, PO Box 875001, Tempe, AZ 85287-5701, USA
- Ira A Fulton Schools of Engineering, Arizona State University, Tempe, USA
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Dell'Anno A, Beolchini F, Rocchetti L, Luna GM, Danovaro R. High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2012; 167:85-92. [PMID: 22542785 DOI: 10.1016/j.envpol.2012.03.043] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 05/31/2023]
Abstract
We investigated changes of bacterial abundance and biodiversity during bioremediation experiments carried out on oxic and anoxic marine harbor sediments contaminated with hydrocarbons. Oxic sediments, supplied with inorganic nutrients, were incubated in aerobic conditions at 20 °C and 35 °C for 30 days, whereas anoxic sediments, amended with organic substrates, were incubated in anaerobic conditions at the same temperatures for 60 days. Results reported here indicate that temperature exerted the main effect on bacterial abundance, diversity and assemblage composition. At higher temperature bacterial diversity and evenness increased significantly in aerobic conditions, whilst decreased in anaerobic conditions. In both aerobic and anaerobic conditions, biodegradation efficiencies of hydrocarbons were significantly and positively related with bacterial richness and evenness. Overall results presented here suggest that bioremediation strategies, which can sustain high levels of bacterial diversity rather than the selection of specific taxa, may significantly increase the efficiency of hydrocarbon degradation in contaminated marine sediments.
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Affiliation(s)
- Antonio Dell'Anno
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
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Microbial Resource Management revisited: successful parameters and new concepts. Appl Microbiol Biotechnol 2011; 90:861-71. [DOI: 10.1007/s00253-011-3223-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 02/24/2011] [Accepted: 02/24/2011] [Indexed: 12/21/2022]
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