1
|
Xu G, Zhao S, He J. Underexplored Organohalide-Respiring Bacteria in Sewage Sludge Debrominating Polybrominated Diphenyl Ethers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39031078 DOI: 10.1021/acs.est.4c00906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2024]
Abstract
Polybrominated diphenyl ethers (PBDEs) are persistent organic pollutants prevalent in the environment. Organohalide-respiring bacteria (OHRB) can attenuate PBDEs via reductive debromination, but often producing toxic end-products. Debromination of PBDEs to diphenyl ether remains a rare phenomenon and is so far specifically associated with Dehalococcoides isolated from e-waste polluted sites. The occurrence of PBDE debromination in other ecosystems and underpinning OHRB are underexplored. Here we found that debromination of PBDEs is a common trait of sewage sludge microbiota, and diphenyl ether was produced as the end-product at varying quantities (0.6-52.9% mol of the parent PBDEs) in 76 of 84 cultures established with bioreactor sludge. Diverse debromination pathways converting PBDEs to diphenyl ether, including several new routes, were identified. Although Dehalococcoides contributed to PBDE debromination, Dehalogenimonas, Dehalobacter, and uncultivated Dehalococcoidia likely played more important roles than previously recognized. Multiple reductive dehalogenase genes (including bdeA, pcbA4, pteA, and tceA) were also prevalent and coexisted in bioreactor sludge. Collectively, these findings contribute to enhancing our comprehension of the environmental fate of PBDEs, expanding the diversity of microorganisms catalyzing PBDE debromination, and developing consortia for bioremediation application.
Collapse
Affiliation(s)
- Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, 117576 Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, 117576 Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, 117576 Singapore
| |
Collapse
|
2
|
Alsharif SM, Ismaeil M, Saeed AM, El-Sayed WS. Metagenomic 16S rRNA analysis and predictive functional profiling revealed intrinsic organohalides respiration and bioremediation potential in mangrove sediment. BMC Microbiol 2024; 24:176. [PMID: 38778276 PMCID: PMC11110206 DOI: 10.1186/s12866-024-03291-8] [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: 11/21/2023] [Accepted: 04/03/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Mangrove sediment microbes are increasingly attracting scientific attention due to their demonstrated capacity for diverse bioremediation activities, encompassing a wide range of environmental contaminants. MATERIALS AND METHODS The microbial communities of five Avicennia marina mangrove sediment samples collected from Al Rayyis White Head, Red Sea (KSA), were characterized using Illumina amplicon sequencing of the 16S rRNA genes. RESULTS Our study investigated the microbial composition and potential for organohalide bioremediation in five mangrove sediments from the Red Sea. While Proteobacteria dominated four microbiomes, Bacteroidetes dominated the fifth. Given the environmental concerns surrounding organohalides, their bioremediation is crucial. Encouragingly, we identified phylogenetically diverse organohalide-respiring bacteria (OHRB) across all samples, including Dehalogenimonas, Dehalococcoides, Anaeromyxobacter, Desulfuromonas, Geobacter, Desulfomonile, Desulfovibrio, Shewanella and Desulfitobacterium. These bacteria are known for their ability to dechlorinate organohalides through reductive dehalogenation. PICRUSt analysis further supported this potential, predicting the presence of functional biomarkers for organohalide respiration (OHR), including reductive dehalogenases targeting tetrachloroethene (PCE) and 3-chloro-4-hydroxyphenylacetate in most sediments. Enrichment cultures studies confirmed this prediction, demonstrating PCE dechlorination by the resident microbial community. PICRUSt also revealed a dominance of anaerobic metabolic processes, suggesting the microbiome's adaptation to the oxygen-limited environment of the sediments. CONCLUSION This study provided insights into the bacterial community composition of five mangrove sediments from the Red Sea. Notably, diverse OHRB were detected across all samples, which possess the metabolic potential for organohalide bioremediation through reductive dehalogenation pathways. Furthermore, PICRUSt analysis predicted the presence of functional biomarkers for OHR in most sediments, suggesting potential intrinsic OHR activity by the enclosed microbial community.
Collapse
Affiliation(s)
- Sultan M Alsharif
- Department of Biology, College of Science, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Mohamed Ismaeil
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt.
| | - Ali M Saeed
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Wael S El-Sayed
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| |
Collapse
|
3
|
Broniatowski M, Wydro P. Interactions of Brominated Flame Retardants with Membrane Models of Dehalogenating Bacteria: Langmuir Monolayer and Grazing Incidence X-ray Diffraction Studies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10600-10614. [PMID: 38721840 PMCID: PMC11112749 DOI: 10.1021/acs.langmuir.4c00518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024]
Abstract
Brominated flame retardants (BFRs) are small organic molecules containing several bromine substituents added to plastics to limit their flammability. BFRs can constitute up to 30% of the weight of some plastics, which is why they are produced in large quantities. Along with plastic waste and microplastic particles, BFRs end up in the soil and can easily leach causing contamination. As polyhalogenated molecules, multiple BFRs were classified as persistent organic pollutants (POPs), meaning that their biodegradation in the soils is especially challenging. However, some anaerobic bacteria as Dehaloccocoides can dehalogenate BFRs, which is important in the bioremediation of contaminated soils. BFRs are hydrophobic, can accumulate in plasma membranes, and disturb their function. On the other hand, limited membrane accumulation is necessary for BFR dehalogenation. To study the BFR-membrane interaction, we created membrane models of soil dehalogenating bacteria and tested their interactions with seven legacy and novel BFRs most common in soils. Phospholipid Langmuir monolayers with appropriate composition were used as membrane models. These membranes were doped in the selected BFRs, and the incorporation of BFR molecules into the phospholipid matrix and also the effects of BFR presence on membrane physical properties and morphology were studied. It turned out that the seven BFRs differed significantly in their membrane affinity. For some, the incorporation was very limited, and others incorporated effectively and could affect membrane properties, while one of the tested molecules induced the formation of bilayer domains in the membranes. Thus, Langmuir monolayers can be effectively used for pretesting BFR membrane activity.
Collapse
Affiliation(s)
- Marcin Broniatowski
- Department
of Environmental Chemistry, Faculty of Chemistry, the Jagiellonian University in Kraków, ul. Gronostajowa 2, Kraków 30-387, Poland
| | - Paweł Wydro
- Department
of Physical Chemistry and Electrochemistry, Faculty of Chemistry, the Jagiellonian University in Kraków, ul. Gronostajowa 2, Kraków 30-387, Poland
| |
Collapse
|
4
|
Zhong H, Lyu H, Wang Z, Tian J, Wu Z. Application of dissimilatory iron-reducing bacteria for the remediation of soil and water polluted with chlorinated organic compounds: Progress, mechanisms, and directions. CHEMOSPHERE 2024; 352:141505. [PMID: 38387660 DOI: 10.1016/j.chemosphere.2024.141505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Chlorinated organic compounds are widely used as solvents, but they are pollutants that can have adverse effects on the environment and human health. Dissimilatory iron-reducing bacteria (DIRB) such as Shewanella and Geobacter have been applied to treat a wide range of halogenated organic compounds due to their specific biological properties. Until now, there has been no systematic review on the mechanisms of direct or indirect degradation of halogenated organic compounds by DIRB. This work summarizes the discussion of DIRB's ability to enhance the dechlorination of reaction systems through different pathways, both biological and biochemical. For biological dechlorination, some DIRB have self-dechlorination capabilities that directly dechlorinate by hydrolysis. Adjustment of dechlorination genes through genetic engineering can improve the dechlorination capabilities of DIRB. DIRB can also adjust the capacity for the microbial community to dechlorinate and provide nutrients to enhance the expression of dechlorination genes in other bacteria. In biochemical dechlorination, DIRB bioconverts Fe(III) to Fe(II), which is capable of dichlorination. On this basis, the DIRB-driven Fenton reaction can efficiently degrade chlorinated organics by continuously maintaining anoxic conditions to generate Fe(II) and oxic conditions to generate H2O2. DIRB can drive microbial fuel cells due to their electroactivity and have a good dechlorination capacity at low levels of energy consumption. The contribution of DIRB to the removal of pesticides, antibiotics and POPs is summarized. Then the DIRB electron transfer mechanism is discussed, which is core to their ability to dechlorinate. Finally, the prospect of future work on the removal of chlorine-containing organic pollutants by DIRB is presented, and the main challenges and further research directions are suggested.
Collapse
Affiliation(s)
- Hua Zhong
- Tianjin Key Laboratory of Clean Energy and Pollution Control, Hebei Engineering Research Center of Pollution Control in Power System, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Honghong Lyu
- Tianjin Key Laboratory of Clean Energy and Pollution Control, Hebei Engineering Research Center of Pollution Control in Power System, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, China.
| | - Zhiqiang Wang
- Tianjin Key Laboratory of Clean Energy and Pollution Control, Hebei Engineering Research Center of Pollution Control in Power System, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Jingya Tian
- Tianjin Key Laboratory of Clean Energy and Pollution Control, Hebei Engineering Research Center of Pollution Control in Power System, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Zhineng Wu
- Tianjin Key Laboratory of Clean Energy and Pollution Control, Hebei Engineering Research Center of Pollution Control in Power System, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, China.
| |
Collapse
|
5
|
Vigneron A, Guyoneaud R, Goñi-Urriza M. Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1551-1562. [PMID: 38197744 DOI: 10.1021/acs.est.3c08386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.
Collapse
Affiliation(s)
- Adrien Vigneron
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| |
Collapse
|
6
|
Lin M, Pan C, Qian C, Tang F, Zhao S, Guo J, Zhang Y, Song J, Rittmann BE. Core taxa, co-occurrence pattern, diversity, and metabolic pathways contributing to robust anaerobic biodegradation of chlorophenol. ENVIRONMENTAL RESEARCH 2024; 241:117591. [PMID: 37926226 DOI: 10.1016/j.envres.2023.117591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
It is hard to achieve robustness in anaerobic biodegradation of trichlorophenol (TCP). We hypothesized that specific combinations of environmental factors determine phylogenetic diversity and play important roles in the decomposition and stability of TCP-biodegrading bacteria. The anaerobic bioreactor was operated at 35 °C (H condition) or 30 °C (L condition) and mainly fed with TCP (from 28 μM to 180 μM) and organic material. Metagenome sequencing was combined with 16S rRNA gene amplicon sequencing for the microbial community analysis. The results exhibited that the property of robustness occurred in specific conditions. The corresponding co-occurrence and diversity patterns suggest high collectivization, degree and evenness for robust communities. Two types of core functional taxa were recognized: dechlorinators (unclassified Anaerolineae, Thermanaerothrix and Desulfovibrio) and ring-opening members (unclassified Proteobacteria, Methanosarcina, Methanoperedens, and Rubrobacter). The deterministic process of the expansion of niche of syntrophic bacteria at higher temperatures was confirmed. The reductive and hydrolytic dechlorination mechanisms jointly lead to C-Cl bond cleavage. H ultimately adapted to the stress of high TCP loading, with more abundant ring-opening enzyme (EC 3.1.1.45, ∼55%) and hydrolytic dechlorinase (EC 3.8.1.5, 26.5%) genes than L (∼47%, 10.5%). The functional structure (based on KEGG) in H was highly stable despite the high loading of TCP (up to 60 μM), but not in L. Furthermore, an unknown taxon with multiple functions (dechlorinating and ring-opening) was found based on genetic sequencing; its functional contribution of EC 3.8.1.5 in H (26.5%) was higher than that in L (10.5%), and it possessed a new metabolic pathway for biodegradation of halogenated aromatic compounds. This new finding is supplementary to the robust mechanisms underlying organic chlorine biodegradation, which can be used to support the engineering, regulation, and design of synthetic microbiomes.
Collapse
Affiliation(s)
- Ming Lin
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Chenhui Pan
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Chenyi Qian
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Fei Tang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Siwen Zhao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Jun Guo
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Department of Environmental Science and Engineering, Fudan University, Shanghai, 200238, PR China
| | - Yongming Zhang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Jiaxiu Song
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China.
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, 85287-5701, USA
| |
Collapse
|
7
|
Lin R, Xie L, Zheng X, Patience DOD, Duan X. Advances and challenges in biocathode microbial electrolysis cells for chlorinated organic compounds degradation from electroactive perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167141. [PMID: 37739072 DOI: 10.1016/j.scitotenv.2023.167141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023]
Abstract
Microbial electrolysis cell (MEC) is a promising in-situ strategy for chlorinated organic compound (COC) pollution remediation due to its high efficiency, low energy input, and long-term potential. Reductive dechlorination as the most critical step in COC degradation which takes place primarily in the cathode chamber of MECs is a complex biochemical process driven by the behavior of electrons. However, no information is currently available on the internal mechanism of MEC in dechlorination from the perspective of the whole electron transfer procedure and its dependent electrode materials. This review addresses the underlying mechanism of MEC on the fundamental of the generation (electron donor), transmission (transfer pathway), utilization (functional microbiota) and reception (electron acceptor) of electrons in dechlorination. In addition, the vital role of varied cathode materials involved in the entire electron transfer procedure during COC dechlorination is emphasized. Subsequently, suggestions for future research, including model construction, cathode material modification, and expanding the applicability of MECs to removal gaseous COCs have been proposed. This paper enriches the mechanism of COC degradation by MEC, and thus provides the theoretical support for the scale-up bioreactors for efficient COC removal.
Collapse
Affiliation(s)
- Rujing Lin
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Xiaomei Zheng
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Dzedzemo-On Dufela Patience
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xu Duan
- Key Laboratory of Yangtze River Water Environment, Ministry of Education; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| |
Collapse
|
8
|
Du X, Zhang X, Liu J, Zhang Z, Wu L, Bai X, Tan C, Gong Y, Zhang Y, Li H. Establishment of evaluation system for biological remediation on organic pollution in groundwater using slow-release agents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166522. [PMID: 37625714 DOI: 10.1016/j.scitotenv.2023.166522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
In situ bioremediation through slow-release agents can continuously degrade organic pollutants for a long time and have high application potential in solving problems such as tailing and rebound. However, the existing evaluation system is difficult to reflect the performance of bioremediation through slow-release agents, which is not conducive to the promotion of technology. It is urgent to establish a targeted evaluation system. Therefore, based on the multi-criteria decision-making method (MCDA), a comprehensive evaluation model was established. The evaluation index system was constructed for bioremediation through slow-release agents consisting of 16 indicators including pollutant degradation rate, agent preparation cost, engineering operation and maintenance cost, secondary pollution, long-term degradation stability, slow release time, slow release stability, increase in functional microbial flora, increase in total DNA content, agent particle size, solid agent morphology, liquid agent viscosity, dispersibility in aqueous phase, zeta potential, operability of agent preparation, and engineering operation management difficulty. Then, the weight of the indicators was determined by using the best-worst method (BWM), and evaluation criteria was established based on relevant norms and literature. Both and the indicators aggregation simple additive weighting (SAW) method constitute a quantitative evaluation model. The above content together constitutes a new evaluation system for biological remediation on organic pollution in groundwater using slow-release agents, which was defined as AOBS evaluation system. In order to verify the rationality and scientificity of the evaluation system, a typical bioremediation slow-release agent was evaluated using the established AOBS evaluation system. The results showed that the evaluation system could reasonably and comprehensively evaluate bioremediation through slow-release agents and provide suggestions for agent improvement.
Collapse
Affiliation(s)
- Xinyue Du
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 102616, China
| | - Xiaoran Zhang
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 102616, China.
| | - Junfeng Liu
- Department of Water Conservancy and Civil Engineering, Beijing Vocational College of Agriculture, Beijing 102442, China
| | - Ziyang Zhang
- Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 102616, China
| | - Liyuan Wu
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 102616, China
| | - Xiaojuan Bai
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 102616, China
| | - Chaohong Tan
- Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 102616, China
| | - Yongwei Gong
- Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 102616, China
| | - Yuling Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China
| | - Haiyan Li
- Centre for Urban Environmental Remediation, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center, Beijing University of Civil Engineering and Architecture, Beijing 102616, China; Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 102616, China
| |
Collapse
|
9
|
Cimmino L, Duarte AG, Ni D, Ekundayo BE, Pereira IAC, Stahlberg H, Holliger C, Maillard J. Structure of a membrane-bound menaquinol:organohalide oxidoreductase. Nat Commun 2023; 14:7038. [PMID: 37923808 PMCID: PMC10624902 DOI: 10.1038/s41467-023-42927-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
Organohalide-respiring bacteria are key organisms for the bioremediation of soils and aquifers contaminated with halogenated organic compounds. The major players in this process are respiratory reductive dehalogenases, corrinoid enzymes that use organohalides as substrates and contribute to energy conservation. Here, we present the structure of a menaquinol:organohalide oxidoreductase obtained by cryo-EM. The membrane-bound protein was isolated from Desulfitobacterium hafniense strain TCE1 as a PceA2B2 complex catalysing the dechlorination of tetrachloroethene. Two catalytic PceA subunits are anchored to the membrane by two small integral membrane PceB subunits. The structure reveals two menaquinone molecules bound at the interface of the two different subunits, which are the starting point of a chain of redox cofactors for electron transfer to the active site. In this work, the structure elucidates how energy is conserved during organohalide respiration in menaquinone-dependent organohalide-respiring bacteria.
Collapse
Affiliation(s)
- Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Babatunde E Ekundayo
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|
10
|
Soder-Walz JM, Wasmund K, Deobald D, Vicent T, Adrian L, Marco-Urrea E. Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses. Environ Microbiol 2023; 25:2604-2620. [PMID: 37452527 DOI: 10.1111/1462-2920.16464] [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: 02/22/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
Dehalobacter (Firmicutes) encompass obligate organohalide-respiring bacteria used for bioremediation of groundwater contaminated with halogenated organics. Various aspects of their biochemistry remain unknown, including the identities and interactions of respiratory proteins. Here, we sequenced the genome of Dehalobacter sp. strain 8M and analysed its protein expression. Strain 8M encodes 22 reductive dehalogenase homologous (RdhA) proteins. RdhA D8M_v2_40029 (TmrA) was among the two most abundant proteins during growth with trichloromethane and 1,1,2-trichloroethane. To examine interactions of respiratory proteins, we used blue native gel electrophoresis together with dehalogenation activity tests and mass spectrometry. The highest activities were found in gel slices with the highest abundance of TmrA. Protein distributions across gel lanes provided biochemical evidence that the large and small subunits of the membrane-bound [NiFe] uptake hydrogenase (HupL and HupS) interacted strongly and that HupL/S interacted weakly with RdhA. Moreover, the interaction of RdhB and membrane-bound b-type cytochrome HupC was detected. RdhC proteins, often encoded in rdh operons but without described function, migrated in a protein complex not associated with HupL/S or RdhA. This study provides the first biochemical evidence of respiratory protein interactions in Dehalobacter, discusses implications for the respiratory architecture and advances the molecular comprehension of this unique respiratory chain.
Collapse
Affiliation(s)
- Jesica M Soder-Walz
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Darja Deobald
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Lorenz Adrian
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| |
Collapse
|
11
|
Stevenson Z, Tong H, Swanner ED. Insights on biotic and abiotic 2,4-dichlorophenoxyacetic acid degradation by anaerobic iron-cycling bacteria. JOURNAL OF ENVIRONMENTAL QUALITY 2023; 52:1092-1101. [PMID: 37689985 DOI: 10.1002/jeq2.20513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/29/2023] [Indexed: 09/11/2023]
Abstract
The use of the phenoxy herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been steadily increasing in recent years due to its selectivity against broad-leafed weeds and use on genetically modified crops resistant to 2,4-D. This increases the likelihood of 2,4-D persisting in agriculturally impacted soils, sediments, and aquatic systems. Aerobic microorganisms are capable of degrading 2,4-D enzymatically. Anaerobic degradation also occurs, though the enzymatic pathway is unclear. Iron-reducing bacteria (FeRB) have been hypothesized to augment anaerobic degradation through the production of a chemically reactive Fe(II) adsorbed to Fe(III) oxyhydroxides. To test whether this iron species can catalyze abiotic degradation of 2,4-D, an enrichment culture (BLA1) containing a photosynthetic Fe(II)-oxidizing bacterium (FeOB) "Candidatus Chlorobium masyuteum" and the FeRB "Candidatus Pseudopelobacter ferreus", both of which lacked known 2,4-D degradation genes was investigated. BLA1 produces Fe(II)-adsorbed to Fe(III) oxyhydroxides during alternating photoautotrophic iron oxidation and dark iron reduction (amended with acetate) cycles. No 2,4-D degradation occurred during iron oxidation by FeOB Ca. C. masyuteum or during iron reduction by FeRB Ca. P. ferreus under any incubation conditions tested (i.e., +/-Fe(II), +/-cells, and +/-light), or due to the presence of Fe(II) adsorbed to Fe(III) oxyhydroxides. Our results cast doubt on the hypothesis that the mineral-bound Fe(II) species augments the anaerobic degradation of 2,4-D in anoxic soils and waters by iron-cycling bacteria, and further justify the need to identify the genetic underpinnings of anaerobic 2,4-D degradation.
Collapse
Affiliation(s)
- Zackry Stevenson
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, Iowa, USA
| | - Hui Tong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Elizabeth D Swanner
- Department of Geological and Atmospheric Sciences, Iowa State University, Ames, Iowa, USA
| |
Collapse
|
12
|
Fisher K, Halliwell T, Payne KAP, Ragala G, Hay S, Rigby SEJ, Leys D. Efficient NADPH-dependent dehalogenation afforded by a self-sufficient reductive dehalogenase. J Biol Chem 2023; 299:105086. [PMID: 37495113 PMCID: PMC10463259 DOI: 10.1016/j.jbc.2023.105086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Reductive dehalogenases are corrinoid and iron-sulfur cluster-containing enzymes that catalyze the reductive removal of a halogen atom. The oxygen-sensitive and membrane-associated nature of the respiratory reductive dehalogenases has hindered their detailed kinetic study. In contrast, the evolutionarily related catabolic reductive dehalogenases are oxygen tolerant, with those that are naturally fused to a reductase domain with similarity to phthalate dioxygenase presenting attractive targets for further study. We present efficient heterologous expression of a self-sufficient catabolic reductive dehalogenase from Jhaorihella thermophila in Escherichia coli. Combining the use of maltose-binding protein as a solubility-enhancing tag with the btuCEDFB cobalamin uptake system affords up to 40% cobalamin occupancy and a full complement of iron-sulfur clusters. The enzyme is able to efficiently perform NADPH-dependent dehalogenation of brominated and iodinated phenolic compounds, including the flame retardant tetrabromobisphenol, under both anaerobic and aerobic conditions. NADPH consumption is tightly coupled to product formation. Surprisingly, corresponding chlorinated compounds only act as competitive inhibitors. Electron paramagnetic resonance spectroscopy reveals loss of the Co(II) signal observed in the resting state of the enzyme under steady-state conditions, suggesting accumulation of Co(I)/(III) species prior to the rate-limiting step. In vivo reductive debromination activity is readily observed, and when the enzyme is expressed in E. coli strain W, supports growth on 3-bromo-4-hydroxyphenylacetic as a sole carbon source. This demonstrates the potential for catabolic reductive dehalogenases for future application in bioremediation.
Collapse
Affiliation(s)
- Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Tom Halliwell
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl A P Payne
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Gabriel Ragala
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Stephen E J Rigby
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| |
Collapse
|
13
|
Löffler P, Escher BI, Baduel C, Virta MP, Lai FY. Antimicrobial Transformation Products in the Aquatic Environment: Global Occurrence, Ecotoxicological Risks, and Potential of Antibiotic Resistance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37335844 DOI: 10.1021/acs.est.2c09854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
The global spread of antimicrobial resistance (AMR) is concerning for the health of humans, animals, and the environment in a One Health perspective. Assessments of AMR and associated environmental hazards mostly focus on antimicrobial parent compounds, while largely overlooking their transformation products (TPs). This review lists antimicrobial TPs identified in surface water environments and examines their potential for AMR promotion, ecological risk, as well as human health and environmental hazards using in silico models. Our review also summarizes the key transformation compartments of TPs, related pathways for TPs reaching surface waters and methodologies for studying the fate of TPs. The 56 antimicrobial TPs covered by the review were prioritized via scoring and ranking of various risk and hazard parameters. Most data on occurrences to date have been reported in Europe, while little is known about antibiotic TPs in Africa, Central and South America, Asia, and Oceania. Occurrence data on antiviral TPs and other antibacterial TPs are even scarcer. We propose evaluation of structural similarity between parent compounds and TPs for TP risk assessment. We predicted a risk of AMR for 13 TPs, especially TPs of tetracyclines and macrolides. We estimated the ecotoxicological effect concentrations of TPs from the experimental effect data of the parent chemical for bacteria, algae and water fleas, scaled by potency differences predicted by quantitative structure-activity relationships (QSARs) for baseline toxicity and a scaling factor for structural similarity. Inclusion of TPs in mixtures with their parent increased the ecological risk quotient over the threshold of one for 7 of the 24 antimicrobials included in this analysis, while only one parent had a risk quotient above one. Thirteen TPs, from which 6 were macrolide TPs, posed a risk to at least one of the three tested species. There were 12/21 TPs identified that are likely to exhibit a similar or higher level of mutagenicity/carcinogenicity, respectively, than their parent compound, with tetracycline TPs often showing increased mutagenicity. Most TPs with increased carcinogenicity belonged to sulfonamides. Most of the TPs were predicted to be mobile but not bioaccumulative, and 14 were predicted to be persistent. The six highest-priority TPs originated from the tetracycline antibiotic family and antivirals. This review, and in particular our ranking of antimicrobial TPs of concern, can support authorities in planning related intervention strategies and source mitigation of antimicrobials toward a sustainable future.
Collapse
Affiliation(s)
- Paul Löffler
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala SE-75007, Sweden
| | - Beate I Escher
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research, UZ, 04318 Leipzig, Germany
- Eberhard Karls University Tübingen, Environmental Toxicology, Department of Geosciences, 72076 Tübingen, Germany
| | - Christine Baduel
- Université Grenoble Alpes, IRD, CNRS, Grenoble INP, IGE, 38 050 Grenoble, France
| | - Marko P Virta
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, Helsinki 00100, Finland
| | - Foon Yin Lai
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Uppsala SE-75007, Sweden
| |
Collapse
|
14
|
Yu Y, Zhang Y, Liu Y, Lv M, Wang Z, Wen LL, Li A. In situ reductive dehalogenation of groundwater driven by innovative organic carbon source materials: Insights into the organohalide-respiratory electron transport chain. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131243. [PMID: 36989787 DOI: 10.1016/j.jhazmat.2023.131243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 02/24/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
In situ bioremediation using organohalide-respiring bacteria (OHRB) is a prospective method for the removal of persistent halogenated organic pollutants from groundwater, as OHRB can utilize H2 or organic compounds produced by carbon source materials as electron donors for cell growth through organohalide respiration. However, few previous studies have determined the suitability of different carbon source materials to the metabolic mechanism of reductive dehalogenation from the perspective of electron transfer. The focus of this critical review was to reveal the interactions and relationships between carbon source materials and functional microbes, in terms of the electron transfer mechanism. Furthermore, this review illustrates some innovative strategies that have used the physiological characteristics of OHRB to guide the optimization of carbon source materials, improving the abundance of indigenous dehalogenated bacteria and enhancing electron transfer efficiency. Finally, it is proposed that future research should combine multi-omics analysis with machine learning (ML) to guide the design of effective carbon source materials and optimize current dehalogenation bioremediation strategies to reduce the cost and footprint of practical groundwater bioremediation applications.
Collapse
Affiliation(s)
- Yang Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yueyan Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yuqing Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Mengran Lv
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zeyi Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Li-Lian Wen
- College of Resource and Environmental Science, Hubei University, Wuhan 430062, China.
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| |
Collapse
|
15
|
Puigserver D, Herrero J, Carmona JM. Mobilization pilot test of PCE sources in the transition zone to aquitards by combining mZVI and biostimulation with lactic acid. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162751. [PMID: 36921871 DOI: 10.1016/j.scitotenv.2023.162751] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/05/2023] [Accepted: 03/05/2023] [Indexed: 05/06/2023]
Abstract
The potential toxic and carcinogenic effects of chlorinated solvents in groundwater on human health and aquatic ecosystems require very effective remediation strategies of contaminated groundwater to achieve the low legal cleanup targets required. The transition zones between aquifers and bottom aquitards occur mainly in prograding alluvial fan geological contexts. Hence, they are very frequent from a hydrogeological point of view. The transition zone consists of numerous thin layers of fine to coarse-grained clastic fragments (e.g., medium sands and gravels), which alternate with fine-grained materials (clays and silts). When the transition zones are affected by DNAPL spills, free-phase pools accumulate on the less conductive layers. Owing to the low overall conductivity of this zone, the pools are very recalcitrant. Little field research has been done on transition zone remediation techniques. Injection of iron microparticles has the disadvantage of the limited accessibility of this reagent to reach the entire source of contamination. Biostimulation of indigenous microorganisms in the medium has the disadvantage that few of the microorganisms are capable of complete biodegradation to total mineralization of the parent contaminant and metabolites. A field pilot test was conducted at a site where a transition zone existed in which DNAPL pools of PCE had accumulated. In particular, the interface with the bottom aquitard was where PCE concentrations were the highest. In this pilot test, a combined strategy using ZVI in microparticles and biostimulation with lactate in the form of lactic acid was conducted. Throughout the test it was found that the interdependence of the coupled biotic and abiotic processes generated synergies between these processes. This resulted in a greater degradation of the PCE and its transformation products. With the combination of the two techniques, the mobilization of the contaminant source of PCE was extremely effective.
Collapse
Affiliation(s)
- Diana Puigserver
- Department of Mineralogy, Petrology and Applied Geology. Faculty of Earth Sciences, University of Barcelona (UB), Water Research Institute (IdRA-UB), Serra Húnter Tenure-elegible Lecturer, C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| | - Jofre Herrero
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB), Water Research Institute (IdRA-UB), C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| | - José M Carmona
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB), Water Research Institute (IdRA-UB), C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| |
Collapse
|
16
|
Zhang X, Wang Z, Li Z, Shaik S, Wang B. [4Fe–4S]-Mediated Proton-Coupled Electron Transfer Enables the Efficient Degradation of Chloroalkenes by Reductive Dehalogenases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xuan Zhang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Zhen Li
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Binju Wang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| |
Collapse
|
17
|
Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
Collapse
Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
| |
Collapse
|
18
|
Wang S, He J, Shen C, Manefield MJ. Editorial: Organohalide respiration: New findings in metabolic mechanisms and bioremediation applications, Volume II. Front Microbiol 2022; 13:1112309. [PMID: 36590394 PMCID: PMC9800048 DOI: 10.3389/fmicb.2022.1112309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Affiliation(s)
- Shanquan Wang
- Environmental Microbiome Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China,*Correspondence: Shanquan Wang ✉
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Michael J. Manefield
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
19
|
Czinnerova M, Stejskal V, Markova K, Nosek J, Riha J, Sevcu A. Field application of glycerol to enhance reductive dechlorination of chlorinated ethenes and its impact on microbial community. CHEMOSPHERE 2022; 309:136640. [PMID: 36181841 DOI: 10.1016/j.chemosphere.2022.136640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/02/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Chlorinated ethenes (CEs) are common and persistent contaminants of soil and groundwater. Their degradation is mostly driven by a process of bacterial reductive dechlorination (also called organohalide respiration) in anaerobic conditions. This study summarizes the outcomes of the long-term in-situ application of glycerol for the enhanced reductive dechlorination of CEs on a highly contaminated site. Glycerol injection resulted in an almost immediate increase in the abundance of fermentative Firmicutes, which produce essential sources of carbon (acetate) and electrons (H2) for organohalide-respiring bacteria (OHRB) and change groundwater conditions to be suitable for OHRB growth. The decreased redox potential of groundwater promoted also the proliferation of sulfate-reducing bacteria, which compete for electron donors with OHRB but at the same time support their growth by producing essential corrinoids and acetate. A considerable increase in the abundance of OHRB Dehalococcoides, concurrently with vinyl chloride (VC) reductase gene levels, was revealed by real time polymerase chain reaction (qPCR) method. Consistent with the shifts in bacterial populations, the concentrations of pollutants tetrachloroethylene and trichloroethylene decreased during the monitoring period, with rising levels of cis-1,2-dichloroethylene, VC, and most importantly, the final CE degradation products: ethene and ethane. Our study implies the importance of syntrophic bacterial interactions for successful and complete CE degradation and evaluates glycerol as convenient substrate to enhance reductive dechlorination and as an effective source of electrons for OHRB.
Collapse
Affiliation(s)
- Marie Czinnerova
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic; Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
| | - Vojtech Stejskal
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Kristyna Markova
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jaroslav Nosek
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jakub Riha
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic; Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Alena Sevcu
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic; Faculty of Science, Humanities and Education, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
| |
Collapse
|
20
|
Community-integrated multi-omics facilitates screening and isolation of the organohalide dehalogenation microorganism. Innovation (N Y) 2022; 4:100355. [PMID: 36506298 PMCID: PMC9730224 DOI: 10.1016/j.xinn.2022.100355] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
A variety of anthropogenic organohalide contaminants generated from industry are released into the environment and thus cause serious pollution that endangers human health. In the present study, we investigated the microbial community composition of industrial saponification wastewater using 16S rRNA sequencing, providing genomic insights of potential organohalide dehalogenation bacteria (OHDBs) by metagenomic sequencing. We also explored yet-to-culture OHDBs involved in the microbial community. Microbial diversity analysis reveals that Proteobacteria and Patescibacteria phyla dominate microbiome abundance of the wastewater. In addition, a total of six bacterial groups (Rhizobiales, Rhodobacteraceae, Rhodospirillales, Flavob a cteriales, Micrococcales, and Saccharimonadales) were found as biomarkers in the key organohalide removal module. Ninety-four metagenome-assembled genomes were reconstructed from the microbial community, and 105 hydrolytic dehalogenase genes within 42 metagenome-assembled genomes were identified, suggesting that the potential for organohalide hydrolytic dehalogenation is present in the microbial community. Subsequently, we characterized the organohalide dehalogenation of an isolated OHDB, Microbacterium sp. J1-1, which shows the dehalogenation activities of chloropropanol, dichloropropanol, and epichlorohydrin. This study provides a community-integrated multi-omics approach to gain functional OHDBs for industrial organohalide dehalogenation.
Collapse
|
21
|
Barnum TP, Coates JD. The biogeochemical cycling of chlorine. GEOBIOLOGY 2022; 20:634-649. [PMID: 35851523 DOI: 10.1111/gbi.12513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/24/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Chlorine has important roles in the Earth's systems. In different forms, it helps balance the charge and osmotic potential of cells, provides energy for microorganisms, mobilizes metals in geologic fluids, alters the salinity of waters, and degrades atmospheric ozone. Despite this importance, there has not been a comprehensive summary of chlorine's geobiology. Here, we unite different areas of recent research to describe a biogeochemical cycle for chlorine. Chlorine enters the biosphere through volcanism and weathering of rocks and is sequestered by subduction and the formation of evaporite sediments from inland seas. In the biosphere, chlorine is converted between solid, dissolved, and gaseous states and in oxidation states ranging from -1 to +7, with the soluble, reduced chloride ion as its most common form. Living organisms and chemical reactions change chlorine's form through oxidation and reduction and the addition and removal of chlorine from organic molecules. Chlorine can be transported through the atmosphere, and the highest oxidation states of chlorine are produced by reactions between sunlight and trace chlorine gases. Partial oxidation of chlorine occurs across the biosphere and creates reactive chlorine species that contribute to the oxidative stress experienced by living cells. A unified view of this chlorine cycle demonstrates connections between chlorine biology, chemistry, and geology that affect life on the Earth.
Collapse
Affiliation(s)
- Tyler P Barnum
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - John D Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| |
Collapse
|
22
|
Di Franca ML, Matturro B, Crognale S, Zeppilli M, Dell’Armi E, Majone M, Petrangeli Papini M, Rossetti S. Microbiome Composition and Dynamics of a Reductive/Oxidative Bioelectrochemical System for Perchloroethylene Removal: Effect of the Feeding Composition. Front Microbiol 2022; 13:951911. [PMID: 35923400 PMCID: PMC9340161 DOI: 10.3389/fmicb.2022.951911] [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: 05/24/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Chlorinated solvents still represent an environmental concern that requires sustainable and innovative bioremediation strategies. This study describes the microbiome composition of a novel bioelectrochemical system (BES) based on sequential reductive/oxidative dechlorination for complete perchloroethylene (PCE) removal occurring in two separate but sequential chambers. The BES has been tested under various feeding compositions [i.e., anaerobic mineral medium (MM), synthetic groundwater (SG), and real groundwater (RG)] differing in presence of sulfate, nitrate, and iron (III). In addition, the main biomarkers of the dechlorination process have been monitored in the system under various conditions. Among them, Dehalococcoides mccartyi 16S rRNA and reductive dehalogenase genes (tceA, bvcA, and vcrA) involved in anaerobic dechlorination have been quantified. The etnE and etnC genes involved in aerobic dechlorination have also been quantified. The feeding composition affected the microbiome, in particular when the BES was fed with RG. Sulfuricurvum, enriched in the reductive compartment, operated with MM and SG, suggesting complex interactions in the sulfur cycle mostly including sulfur oxidation occurring at the anodic counter electrode (MM) or coupled to nitrate reduction (SG). Moreover, the known Mycobacterium responsible for natural attenuation of VC by aerobic degradation was found abundant in the oxidative compartment fed with RG, which was in line with the high VC removal observed (92 ± 2%). D. mccartyi was observed in all the tested conditions ranging from 8.78E + 06 (with RG) to 2.35E + 07 (with MM) 16S rRNA gene copies/L. tceA was found as the most abundant reductive dehalogenase gene in all the conditions explored (up to 2.46 E + 07 gene copies/L in MM). The microbiome dynamics and the occurrence of biomarkers of dechlorination, along with the kinetic performance of the system under various feeding conditions, suggested promising implications for the scale-up of the BES, which couples reductive with oxidative dechlorination to ensure the complete removal of highly chlorinated ethylene and mobile low-chlorinated by-products.
Collapse
Affiliation(s)
- Maria L. Di Franca
- Water Research Institute-National Research Council (IRSA-CNR), Rome, Italy
| | - Bruna Matturro
- Water Research Institute-National Research Council (IRSA-CNR), Rome, Italy
- *Correspondence: Bruna Matturro,
| | - Simona Crognale
- Water Research Institute-National Research Council (IRSA-CNR), Rome, Italy
| | - Marco Zeppilli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Mauro Majone
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Simona Rossetti
- Water Research Institute-National Research Council (IRSA-CNR), Rome, Italy
| |
Collapse
|
23
|
Hudari MSB, Richnow H, Vogt C, Nijenhuis I. Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review. FEMS Microbiol Ecol 2022; 98:6638985. [PMID: 35810002 DOI: 10.1093/femsec/fiac081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.
Collapse
Affiliation(s)
- Mohammad Sufian Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| |
Collapse
|
24
|
Hu Y, Chen J, Wang C, Wang P, Gao H, Zhang J, Zhang B, Cui G, Zhao D. Insight into microbial degradation of hexabromocyclododecane (HBCD) in lake sediments under different hydrodynamic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154358. [PMID: 35259383 DOI: 10.1016/j.scitotenv.2022.154358] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Hexabromocyclododecane (HBCD), an emerging persistent organic pollutant, has been widely detected in aquatic ecosystems with various hydrodynamic conditions, however, the effects of hydrodynamic changes on microbial degradation of HBCD in aquatic sediment remains unclear. Here, we conducted an annular flume experiment to characterize variation in HBCD removal from contaminated sediment under three hydrodynamic conditions with different flow velocities, as well as clarify the underlying microbial mechanisms. We detected significant HBCD removal and bromine ion generation in all contaminated sediments, and microbial reduction debromination was an important process for HBCD removal. At the end of the 49-day experiment, both HBCD removal percentage and the bromine ion concentration were significantly lower under dynamic water condition with higher sediment redox potential, compared with static water conditions. The dynamic water conditions resulted a relatively high sediment redox potential and decreased the iron reduction rate and the abundance of organohalide-respiring bacteria (OHRB) in the genera Geobatcer, Dehalogenimonas, Dehalobacter, and Dehalococcoide, which reduced the microbial degradation of HBCD in contaminated sediments. The community composition of both total bacteria and OHRB also differed significantly among hydrodynamic conditions. Some bacterial groups with HBCD degradation abilities such as Pseudomonas and Sulfuricurvum were less abundant under dynamic water conditions, and the HBCD degradation efficiencies were lower. These findings enhance our understanding of the bioremediation potential of HBCD-contaminated sediments in different hydrodynamic areas.
Collapse
Affiliation(s)
- Yu Hu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Jingjing Zhang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Bo Zhang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Ge Cui
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Dan Zhao
- Kunming Engineering Corporation Limited, Power China, 115 People's East Road, Kunming 650216, PR China
| |
Collapse
|
25
|
Lee M, Liang G, Holland SI, O'Farrell C, Osborne K, Manefield MJ. Dehalobium species implicated in 2,3,7,8-tetrachlorodibenzo-p-dioxin dechlorination in the contaminated sediments of Sydney Harbour Estuary. MARINE POLLUTION BULLETIN 2022; 179:113690. [PMID: 35504213 DOI: 10.1016/j.marpolbul.2022.113690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Polychlorinated dibenzo-p-dioxins and furans (PCDD/F) are some of the most environmentally recalcitrant and toxic compounds. They occur naturally and as by-products of anthropogenic activity. Sydney Harbour Estuary (Sydney, Australia), is heavily contaminated with PCDD/F. Analysis of sediment cores revealed that the contamination source area in Homebush Bay continues to have one of the highest levels of PCDD/F contamination in the world (5207 pg WHO-TEQ g-1) with >50% of the toxicity attributed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), the most toxic PCDD/F congener. Comparison of congener profiles at the contamination source area with surrounding bays and historical data provided evidence for the attenuation of 2,3,7,8-TCDD and other congeners at the source area. This finding was supported by the detection of di-, mono- and unchlorinated dibenzo-p-dioxin. Microbial community analysis of sediments by 16S rRNA amplicon sequencing revealed an abundance of lineages from the class Dehalococcoidia (up to 15% of the community), including the genus Dehalobium (up to 0.5%). Anaerobic seawater enrichment cultures using perchloroethene as more biologically available growth substrate enriched the Dehalobium population by more than six-fold. The enrichment culture then proved capable of reductively dechlorinating 2,3,7,8-TCDD to 2,3,7-TriCDD and octachlorodibenzo-p-dibenzodioxin (OCDD) to hepta and hexa congeners. This work is the first to show microbial reductive dehalogenation of 2,3,7,8-TCDD with a bacterium from outside the Dehalococcoides genus, and one of only a few that demonstrates PCDD/F dechlorination in a marine environment.
Collapse
Affiliation(s)
- Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia.
| | - Gan Liang
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Sophie I Holland
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | | | - Keith Osborne
- New South Wales Department of Planning and Environment, Lidcombe, NSW 2141, Australia
| | - Michael J Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| |
Collapse
|
26
|
Halliwell T, Fisher K, Rigby SEJ, Leys D. Heterologous production and biophysical characterization of catabolic Nitratireductor pacificus pht-3B reductive dehalogenase. Methods Enzymol 2022; 668:327-347. [PMID: 35589200 DOI: 10.1016/bs.mie.2022.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Reductive dehalogenases provide a possible route to the biotechnological remediation of widespread anthropogenic environmental organohalide contamination. These bacterial enzymes employ cobalamin and an internal electron transfer chain of two [4Fe-4S] clusters to remove halide ions from organohalides, leaving an organic molecule more amenable to further transformations. Detailed protocols for the cloning, heterologous expression, purification, crystallization and characterization of the catabolic dehalogenase from Nitratireductor pacificus pht-3B (NpRdhA) are presented, together with insight into enzyme turnover, substrate selectivity and the use of electron paramagnetic resonance (EPR) spectroscopy as an active site probe.
Collapse
Affiliation(s)
- Tom Halliwell
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Karl Fisher
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Stephen E J Rigby
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - David Leys
- School of Chemistry, University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
27
|
Puigserver D, Herrero J, Nogueras X, Cortés A, Parker BL, Playà E, Carmona JM. Biotic and abiotic reductive dechlorination of chloroethenes in aquitards. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151532. [PMID: 34752872 DOI: 10.1016/j.scitotenv.2021.151532] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Chlorinated solvents occur as dense nonaqueous phase liquid (DNAPL) or as solutes when dissolved in water. They are present in many pollution sites in urban and industrial areas. They are toxic, carcinogenic, and highly recalcitrant in aquifers and aquitards. In the latter case, they migrate by molecular diffusion into the matrix. When aquitards are fractured, chlorinated solvents also penetrate as a free phase through the fractures. The main objective of this study was to analyze the biogeochemical processes occurring inside the matrix surrounding fractures and in the joint-points zones. The broader implications of this objective derive from the fact that, incomplete natural degradation of contaminants in aquitards generates accumulation of daughter products. This causes steep concentration gradients and back-diffusion fluxes between aquitards and high hydraulic conductivity layers. This offers opportunities to develop remediation strategies based, for example, on the coupling of biotic and reactive abiotic processes. The main results showed: 1) Degradation occurred especially in the matrix adjacent to the orthogonal network of fractures and textural heterogeneities, where texture contrasts favored microbial development because these zones constituted ecotones. 2) A dechlorinating bacterium not belonging to the Dehalococcoides genus, namely Propionibacterium acnes, survived under the high concentrations of dissolved perchloroethene (PCE) in contact with the PCE-DNAPL and was able to degrade it to trichloroethene (TCE). Dehalococcoides genus was able to conduct PCE reductive dechlorination at least up to cis-1,2-dichloroethene (cDCE), which shows again the potential of the medium to degrade chloroethenes in aquitards. 3) Degradation of PCE in the matrix resulted from the coupling of reactive abiotic and biotic processes-in the first case, promoted by Fe2+ sorbed to iron oxides, and in the latter case, related to dechlorinating microorganisms. The dechlorination resulting from these coupling processes is slow and limited by the need for an adequate supply of electron donors.
Collapse
Affiliation(s)
- Diana Puigserver
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB), Water Research Institute (IdRA-UB), Serra Húnter Tenure-elegible Lecturer, C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| | - Jofre Herrero
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB), Water Research Institute (IdRA-UB). C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| | - Xènia Nogueras
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB). C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain; Health Section of the City Council of Mataró (Barcelona), Specialized Support Technician, Carrer de la Riera, 48, 08301 Mataró, Barcelona, Spain.
| | - Amparo Cortés
- Department of Biology, Health and Environment, Faculty of Pharmacy, University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain.
| | - Beth L Parker
- School of Engineering, University of Guelph, 50, Stone Road East, Guelph, N1G 2W1, Ontario, Canada.
| | - E Playà
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB). C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| | - José M Carmona
- Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona (UB), Water Research Institute (IdRA-UB). C/ Martí i Franquès, s/n, E-08028 Barcelona, Spain.
| |
Collapse
|
28
|
|
29
|
Korbel KL, Greenfield P, Hose GC. Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150870. [PMID: 34627912 DOI: 10.1016/j.scitotenv.2021.150870] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/21/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.
Collapse
Affiliation(s)
- K L Korbel
- Department of Biological Sciences, Macquarie University, Australia.
| | | | - G C Hose
- Department of Biological Sciences, Macquarie University, Australia
| |
Collapse
|
30
|
Zhu X, Wang X, Li N, Wang Q, Liao C. Bioelectrochemical system for dehalogenation: A review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 293:118519. [PMID: 34793908 DOI: 10.1016/j.envpol.2021.118519] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/26/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Halogenated organic compounds are persistent pollutants, whose persistent contamination and rapid spread seriously threaten human health and the safety of ecosystems. It is difficult to remove them completely by traditional physicochemical techniques. In-situ remediation utilizing bioelectrochemical technology represents a promising strategy for degradation of halogenated organic compounds, which can be achieved through potential modulation. In this review, we summarize the reactor configuration of microbial electrochemical dehalogenation systems and relevant organohalide-respiring bacteria. We also highlight the mechanisms of electrode potential regulation of microbial dehalogenation and the role of extracellular electron transfer in dehalogenation process, and further discuss the application of bioelectrochemical technology in bioremediation of halogenated organic compounds. Therefore, this review summarizes the status of research on microbial electrochemical dehalogenation systems from macroscopic to microscopic levels, providing theoretical support for the development of rapid and efficient in situ bioremediation technologies for halogenated organic compounds contaminated sites, as well as insights for the removal of refractory fluorides.
Collapse
Affiliation(s)
- Xuemei Zhu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Qi Wang
- Beijing Construction Engineering Group Environmental Remediation Co. Ltd. and National Engineering Laboratory for Site Remediation Technologies, Beijing, 100015, China
| | - Chengmei Liao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin, 300350, China.
| |
Collapse
|
31
|
Differentiating closely affiliated Dehalococcoides lineages by a novel genetic marker identified via computational pangenome analysis. Appl Environ Microbiol 2021; 88:e0218121. [PMID: 34910572 DOI: 10.1128/aem.02181-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As a group, Dehalococcoides dehalogenate a wide range of organohalide pollutants but the range of organohalide compounds that can be utilized for reductive dehalogenation differs among the Dehalococcoides strains. Dehalococcoides lineages cannot be reliably disambiguated in mixed communities using typical phylogenetic markers, which often confounds bioremediation efforts. Here, we describe a computational approach to identify Dehalococcoides genetic markers with improved discriminatory resolution. Screening core genes from the Dehalococcoides pangenome for degree of similarity and frequency of 100% identity found a candidate genetic marker encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function. This gene exhibits the fewest completely identical amino acid sequences and among the lowest average amino acid sequence identity in the core pangenome. Primers targeting BNR could effectively discriminate between 40 available BNR sequences (in silico) and 10 different Dehalococcoides isolates (in vitro). Amplicon sequencing of BNR fragments generated from 22 subsurface soil samples revealed a total of 109 amplicon sequence variants, suggesting a high diversity of Dehalococcoides distributed in environment. Therefore, the BNR gene can serve as an alternative genetic marker to differentiate strains of Dehalococcoides in complicated microbial communities. Importance The challenge of discriminating between phylogenetically similar but functionally distinct bacterial lineages is particularly relevant to the development of technologies seeking to exploit the metabolic or physiological characteristics of specific members of bacterial genera. A computational approach was developed to expedite screening of potential genetic markers among phylogenetically affiliated bacteria. Using this approach, a gene encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function was selected and evaluated as a genetic marker to differentiate strains of Dehalococcoides, an environmentally relevant genus of bacteria whose members can transform and detoxify a range of halogenated organic solvents and persistent organic pollutants, in complex microbial communities to demonstrate the validity of the approach. Moreover, many apparently phylogenetically distinct, currently uncharacterized Dehalococcoides were detected in environmental samples derived from contaminated sites.
Collapse
|
32
|
He H, Li Y, Shen R, Shim H, Zeng Y, Zhao S, Lu Q, Mai B, Wang S. Environmental occurrence and remediation of emerging organohalides: A review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118060. [PMID: 34479159 DOI: 10.1016/j.envpol.2021.118060] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/02/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
As replacements for "old" organohalides, such as polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs), "new" organohalides have been developed, including decabromodiphenyl ethane (DBDPE), short-chain chlorinated paraffins (SCCPs), and perfluorobutyrate (PFBA). In the past decade, these emerging organohalides (EOHs) have been extensively produced as industrial and consumer products, resulting in their widespread environmental distribution. This review comprehensively summarizes the environmental occurrence and remediation methods for typical EOHs. Based on the data collected from 2015 to 2021, these EOHs are widespread in both abiotic (e.g., dust, air, soil, sediment, and water) and biotic (e.g., bird, fish, and human serum) matrices. A significant positive correlation was found between the estimated annual production amounts of EOHs and their environmental contamination levels, suggesting the prohibition of both production and usage of EOHs as a critical pollution-source control strategy. The strengths and weaknesses, as well as the future prospects of up-to-date remediation techniques, such as photodegradation, chemical oxidation, and biodegradation, are critically discussed. Of these remediation techniques, microbial reductive dehalogenation represents a promising in situ remediation method for removal of EOHs, such as perfluoroalkyl and polyfluoroalkyl substances (PFASs) and halogenated flame retardants (HFRs).
Collapse
Affiliation(s)
- Haozheng He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yiyang Li
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Rui Shen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hojae Shim
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau SAR, 999078, China
| | - Yanhong Zeng
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Siyan Zhao
- School of Environmental Science and Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China; State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
| | - Bixian Mai
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| |
Collapse
|
33
|
Giannari D, Ho CH, Mahadevan R. A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PLoS Comput Biol 2021; 17:e1009060. [PMID: 34723959 PMCID: PMC8584699 DOI: 10.1371/journal.pcbi.1009060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/11/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.
Collapse
Affiliation(s)
- Dafni Giannari
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- The Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
34
|
In Situ Bioremediation of a Chlorinated Hydrocarbon Plume: A Superfund Site Field Pilot Test. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112110005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The North Railroad Avenue Plume, discovered in 1989, contained chlorinated solvent groundwater plumes extending over 23.5 hectares (58 acres) and three hydrostratigraphic units. The source contaminant, tetrachloroethene, stemmed from release at a dry cleaner/laundromat business. The anaerobic biodegradation byproducts trichloroethene, isomers of dichloroethene (DCE), and vinyl chloride were detected in groundwater samples collected prior to remedial action. The impacted aquifers are the sole source drinking water aquifers for the communities near the site. Following the remedial investigation and feasibility study, the selected alternative for full-scale remedial action at the site was enhanced reductive dichlorination (ERD) focused on four treatment areas: the shallow source zone, the shallow hotspot area, the shallow downgradient area, and the deep zone. Pilot testing, which was conducted in the source zone and hotspot areas, is the subject of this paper. The primary objectives of the pilot test were to obtain the necessary information to select an ERD treatment formulation, dose, and frequency of dosing for use during full-scale remedial action, as well as to refine the site’s hydrogeologic conceptual site model and design parameters. Four (4) test cells, each of which contained well pairs of injection and downgradient extraction wells, were used to test ERD bio-amendment formulations: ethyl lactate, dairy whey, emulsified vegetable oil (EVO), and a combination of EVO and a hydrogen gas infusion. A conservative tracer, bromide, was added to the recirculation flow to record tracer breakthrough, peak, and dissipation at extraction wells. The results of these dipole tracer tests were used to reassess the hydraulic conductivity and hydrodynamic dispersity used in the remedial design. In addition to water quality analyses of contaminants and substrates, groundwater samples were also analyzed for biological analyses before, during, and after the addition of bioamendment. Analyses of phospholipid fatty acids and deoxyribonucleic acid (DNA) extracts from fresh groundwater samples informed decisions on the capacity for complete ERD without DCE stalling and tracked the shifts in the bacterial and archaeal taxonomy and phylogeny stemming from the addition of bioamendments. The pilot test concluded that EVO was the most suitable, considering (1) support of the native microbial consortia for ERD, (2) mechanics and hydraulics of the remediation system, and (3) sustainability/retention of the substrate in the subsurface. Along with EVO, the addition of a nutrient broth derived from brewery waste accelerated and sustained the desired conditions and microbial diversity and population levels. The pilot test results were also used to assess the utilization kinetics of the injected substrates based on total organic carbon (TOC) concentrations measured in the groundwater. After determining that substrate utilization followed Monod kinetics, a TOC threshold at 300 milligrams per liter, equivalent to approximately twice its half-saturation constant was established. Full scale treatment dosing and dose frequency were designed around this threshold, assuming the maximum substrate utilization would yield optimum ERD.
Collapse
|
35
|
Semerád J, Ševců A, Nguyen NHA, Hrabák P, Špánek R, Bobčíková K, Pospíšková K, Filip J, Medřík I, Kašlík J, Šafařík I, Filipová A, Nosek J, Pivokonský M, Cajthaml T. Discovering the potential of an nZVI-biochar composite as a material for the nanobioremediation of chlorinated solvents in groundwater: Degradation efficiency and effect on resident microorganisms. CHEMOSPHERE 2021; 281:130915. [PMID: 34029963 DOI: 10.1016/j.chemosphere.2021.130915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/22/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Abiotic and biotic remediation of chlorinated ethenes (CEs) in groundwater from a real contaminated site was studied using biochar-based composites containing nanoscale zero-valent iron (nZVI/BC) and natural resident microbes/specific CE degraders supported by a whey addition. The material represented by the biochar matrix decorated by isolated iron nanoparticles or their aggregates, along with the added whey, was capable of a stepwise dechlorination of CEs. The tested materials (nZVI/BC and BC) were able to decrease the original TCE concentration by 99% in 30 days. Nevertheless, regarding the transformation products, it was clear that biotic as well as abiotic transformation mechanisms were involved in the transformation process when nonchlorinated volatiles (i.e., methane, ethane, ethene, and acetylene) were detected after the application of nZVI/BC and nZVI/BC with whey. The whey addition caused a massive increase in bacterial biomass in the groundwater samples (monitored by 16S rRNA sequencing and qPCR) that corresponded with the transformation of trichloro- and dichloro-CEs, and this process was accompanied by the formation of less chlorinated products. Moreover, the biostimulation step also eliminated the adverse effect caused by nZVI/BC (decrease in microbial biomass after nZVI/BC addition). The nZVI/BC material or its aging products, and probably together with vinyl chloride-respiring bacteria, were able to continue the further reductive dechlorination of dichlorinated CEs into nonhalogenated volatiles. Overall, the results of the present study demonstrate the potential, feasibility, and environmental safety of this nanobioremediation approach.
Collapse
Affiliation(s)
- Jaroslav Semerád
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic
| | - Alena Ševců
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic.
| | - Nhung H A Nguyen
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Pavel Hrabák
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Roman Špánek
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Kateřina Bobčíková
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Kristýna Pospíšková
- Regional Centre of Advanced Technologies and Materials, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Jan Filip
- Regional Centre of Advanced Technologies and Materials, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Ivo Medřík
- Regional Centre of Advanced Technologies and Materials, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Josef Kašlík
- Regional Centre of Advanced Technologies and Materials, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Ivo Šafařík
- Regional Centre of Advanced Technologies and Materials, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic; Department of Nanobiotechnology, Biology Centre, ISB, CAS, Na Sadkach 7, 370 05, Ceske Budejovice, Czech Republic
| | - Alena Filipová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic
| | - Jaroslav Nosek
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Martin Pivokonský
- Institute of Hydrodynamics of the Czech Academy of Sciences, Pod Patankou 30/5, CZ-166 12, Prague 6, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic.
| |
Collapse
|
36
|
Wackett LP. Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances. Microb Biotechnol 2021; 15:773-792. [PMID: 34570953 PMCID: PMC8913905 DOI: 10.1111/1751-7915.13928] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Poly‐ and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today’s society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called ‘forever chemicals’ due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.
Collapse
Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, 55108, USA
| |
Collapse
|
37
|
A Microcosm Treatability Study for Evaluating Wood Mulch-Based Amendments as Electron Donors for Trichloroethene (TCE) Reductive Dechlorination. WATER 2021. [DOI: 10.3390/w13141949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, wood mulch-based amendments were tested in a bench-scale microcosm experiment in order to assess the treatability of saturated soils and groundwater from an industrial site contaminated by chlorinated ethenes. Wood mulch was tested alone as the only electron donor in order to assess its potential for stimulating the biological reductive dechlorination. It was also tested in combination with millimetric iron filings in order to assess the ability of the additive to accelerate/improve the bioremediation process. The efficacy of the selected amendments was compared with that of unamended control microcosms. The results demonstrated that wood mulch is an effective natural and low-cost electron donor to stimulate the complete reductive dechlorination of chlorinated solvents to ethene. Being a side-product of the wood industry, mulch can be used in environmental remediation, an approach which perfectly fits the principles of circular economy and addresses the compelling needs of a sustainable and low environmental impact remediation. The efficacy of mulch was further improved by the co-presence of iron filings, which accelerated the conversion of vinyl chloride into the ethene by increasing the H2 availability rather than by catalyzing the direct abiotic dechlorination of contaminants. Chemical analyses were corroborated by biomolecular assays, which confirmed the stimulatory effect of the selected amendments on the abundance of Dehalococcoides mccartyi and related reductive dehalogenase genes. Overall, this paper further highlights the application potential and environmental sustainability of wood mulch-based amendments as low-cost electron donors for the biological treatment of chlorinated ethenes.
Collapse
|
38
|
Matturro B, Majone M, Aulenta F, Rossetti S. Correlations between maximum reductive dechlorination rates and specific biomass parameters in Dehalococcoides mccartyi consortia enriched on chloroethenes PCE, TCE and cis-1,2-DCE. FEMS Microbiol Ecol 2021; 97:6253249. [PMID: 33899920 DOI: 10.1093/femsec/fiab064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/23/2021] [Indexed: 01/04/2023] Open
Abstract
One of the challenges to implementing the modeling of the biological reductive dechlorination (RD) process is the evaluation of biological parameters that represent the abundance/activity levels of the microorganisms involved in the biodegradation of chloroethenes. Here we report a combined analysis of kinetic and specific biomass parameters conducted on three dechlorinating consortia enriched on PCE, TCE and cis-1,2-DCE. In these consortia, Dehalococcoides mccartyi (Dhc) represented ≥70% of the bacterial population identified via 16S rRNA gene amplicon sequencing. Quantitative biomolecular methods were used to generate specific biomass parameters targeting either the Dhc population (16S rRNA genes or cells) or specific genes encoding RD process-involved reductive dehalogenases. The correlation factor between the abundance of active Dhc cells or tceA gene copies and maximum RD rates allowed to predict an increment of 7E+09 of active Dhc cells or 5E+09 tceA gene copies/L under controlled conditions. Diversely, the utilization of gene transcripts as biomass parameters for RD modeling did not provide reliable correlations with kinetic performances. This study provides valuable insights for further modeling of the RD process through the utilization of specific biomass parameters.
Collapse
Affiliation(s)
- B Matturro
- Water Research Institute, IRSA-CNR, Via Salaria km 29.300, Monterotondo (RM) 00015, Italy
| | - M Majone
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - F Aulenta
- Water Research Institute, IRSA-CNR, Via Salaria km 29.300, Monterotondo (RM) 00015, Italy
| | - S Rossetti
- Water Research Institute, IRSA-CNR, Via Salaria km 29.300, Monterotondo (RM) 00015, Italy
| |
Collapse
|
39
|
Lu Q, Liu J, He H, Liang Z, Qiu R, Wang S. Waste activated sludge stimulates in situ microbial reductive dehalogenation of organohalide-contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125189. [PMID: 33858119 DOI: 10.1016/j.jhazmat.2021.125189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Due to its enriched organic matter, nutrients and growth cofactors, as well as a diverse range of microorganisms, waste activated sludge (WAS) might be an ideal additive to stimulate organohalide respiration for in situ bioremediation of organohalide-contaminated sites. In this study, we investigated the biostimulation and bioaugmentation impacts of WAS-amendment on the performance and microbiome in tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) dechlorinating microcosms. Results demonstrated that WAS-amendment increased PCE- and PCBs-dechlorination rate as much as 6.06 and 10.67 folds, respectively. The presence of WAS provided a favorable growth niche for organohalide-respiring bacteria (OHRB), including redox mediation and generation of electron donors and carbon sources. Particularly for the PCE dechlorination, indigenous Geobacter and WAS-derived Dehalococcoides were identified to play key roles in PCE-to-dichloroethene (DCE) and DCE-to-ethene dechlorination, respectively. Similar biostimulation and bioaugmentation effects of WAS-amendment were observed on both PCE- and PCBs-dechlorination in three different soils, i.e., laterite, brown loam and paddy soil. Risk assessment suggested low potential ecological risk of WAS amendment in remediation of organohalide-contaminated soil. Overall, this study provided an economic and efficient strategy to stimulate the organohalide respiration-based bioremediation in field applications.
Collapse
Affiliation(s)
- Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Jinting Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Haozheng He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhiwei Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China
| | - Rongliang Qiu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510275, China.
| |
Collapse
|
40
|
Kruse S, Türkowsky D, Birkigt J, Matturro B, Franke S, Jehmlich N, von Bergen M, Westermann M, Rossetti S, Nijenhuis I, Adrian L, Diekert G, Goris T. Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene. THE ISME JOURNAL 2021; 15:1794-1809. [PMID: 33479489 PMCID: PMC8163811 DOI: 10.1038/s41396-020-00887-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/04/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Microbial communities involving dehalogenating bacteria assist in bioremediation of areas contaminated with halocarbons. To understand molecular interactions between dehalogenating bacteria, we co-cultured Sulfurospirillum multivorans, dechlorinating tetrachloroethene (PCE) to cis-1,2-dichloroethene (cDCE), and Dehalococcoides mccartyi strains BTF08 or 195, dehalogenating PCE to ethene. The co-cultures were cultivated with lactate as electron donor. In co-cultures, the bacterial cells formed aggregates and D. mccartyi established an unusual, barrel-like morphology. An extracellular matrix surrounding bacterial cells in the aggregates enhanced cell-to-cell contact. PCE was dehalogenated to ethene at least three times faster in the co-culture. The dehalogenation was carried out via PceA of S. multivorans, and PteA (a recently described PCE dehalogenase) and VcrA of D. mccartyi BTF08, as supported by protein abundance. The co-culture was not dependent on exogenous hydrogen and acetate, suggesting a syntrophic relationship in which the obligate hydrogen consumer D. mccartyi consumes hydrogen and acetate produced by S. multivorans. The cobamide cofactor of the reductive dehalogenase-mandatory for D. mccartyi-was also produced by S. multivorans. D. mccartyi strain 195 dechlorinated cDCE in the presence of norpseudo-B12 produced by S. multivorans, but D. mccartyi strain BTF08 depended on an exogenous lower cobamide ligand. This observation is important for bioremediation, since cofactor supply in the environment might be a limiting factor for PCE dehalogenation to ethene, described for D. mccartyi exclusively. The findings from this co-culture give new insights into aggregate formation and the physiology of D. mccartyi within a bacterial community.
Collapse
Affiliation(s)
- Stefan Kruse
- grid.9613.d0000 0001 1939 2794Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Dominique Türkowsky
- grid.7492.80000 0004 0492 3830Department Molecular Systems Biology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Jan Birkigt
- grid.7492.80000 0004 0492 3830Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Bruna Matturro
- grid.435629.f0000 0004 1755 3971Water Research Institute, IRSA-CNR, Monterotondo, Rome, Italy
| | - Steffi Franke
- grid.7492.80000 0004 0492 3830Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany ,Present Address: Eurofins Institute Dr. Appelt Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- grid.7492.80000 0004 0492 3830Department Molecular Systems Biology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Martin von Bergen
- grid.7492.80000 0004 0492 3830Department Molecular Systems Biology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Martin Westermann
- grid.275559.90000 0000 8517 6224Center for Electron Microscopy of the University Hospital Jena, Jena, Germany
| | - Simona Rossetti
- grid.435629.f0000 0004 1755 3971Water Research Institute, IRSA-CNR, Monterotondo, Rome, Italy
| | - Ivonne Nijenhuis
- grid.7492.80000 0004 0492 3830Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Lorenz Adrian
- grid.6734.60000 0001 2292 8254Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany ,grid.7492.80000 0004 0492 3830Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Gabriele Diekert
- grid.9613.d0000 0001 1939 2794Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Tobias Goris
- grid.9613.d0000 0001 1939 2794Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany ,grid.418213.d0000 0004 0390 0098Present Address: German Institute of Human Nutrition, Department Molecular Toxicology, Research Group Intestinal Microbiology, Potsdam-Rehbrücke, Nuthetal, Germany
| |
Collapse
|
41
|
Balabanova L, Averianova L, Marchenok M, Son O, Tekutyeva L. Microbial and Genetic Resources for Cobalamin (Vitamin B12) Biosynthesis: From Ecosystems to Industrial Biotechnology. Int J Mol Sci 2021; 22:ijms22094522. [PMID: 33926061 PMCID: PMC8123684 DOI: 10.3390/ijms22094522] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Many microbial producers of coenzyme B12 family cofactors together with their metabolically interdependent pathways are comprehensively studied and successfully used both in natural ecosystems dominated by auxotrophs, including bacteria and mammals, and in the safe industrial production of vitamin B12. Metabolic reconstruction for genomic and metagenomic data and functional genomics continue to mine the microbial and genetic resources for biosynthesis of the vital vitamin B12. Availability of metabolic engineering techniques and usage of affordable and renewable sources allowed improving bioprocess of vitamins, providing a positive impact on both economics and environment. The commercial production of vitamin B12 is mainly achieved through the use of the two major industrial strains, Propionobacterium shermanii and Pseudomonas denitrificans, that involves about 30 enzymatic steps in the biosynthesis of cobalamin and completely replaces chemical synthesis. However, there are still unresolved issues in cobalamin biosynthesis that need to be elucidated for future bioprocess improvements. In the present work, we review the current state of development and challenges for cobalamin (vitamin B12) biosynthesis, describing the major and novel prospective strains, and the studies of environmental factors and genetic tools effecting on the fermentation process are reported.
Collapse
Affiliation(s)
- Larissa Balabanova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
- Correspondence:
| | - Liudmila Averianova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Maksim Marchenok
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Oksana Son
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Liudmila Tekutyeva
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| |
Collapse
|
42
|
Russum S, Lam KJK, Wong NA, Iddamsetty V, Hendargo KJ, Wang J, Dubey A, Zhang Y, Medrano-Soto A, Saier MH. Comparative population genomic analyses of transporters within the Asgard archaeal superphylum. PLoS One 2021; 16:e0247806. [PMID: 33770091 PMCID: PMC7997004 DOI: 10.1371/journal.pone.0247806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/15/2021] [Indexed: 01/02/2023] Open
Abstract
Upon discovery of the first archaeal species in the 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, the organization of the three-domain tree of life has been challenged following the discovery of archaeal lineages such as the TACK and Asgard superphyla. The Asgard Superphylum has emerged as the closest archaeal ancestor to eukaryotes, potentially improving our understanding of the evolution of life forms. We characterized the transportomes and their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- and Loki-archaeota as well as the fully sequenced genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 that belongs to the Loki phylum. Using the Transporter Classification Database (TCDB) as reference, candidate transporters encoded within the proteomes were identified based on sequence similarity, alignment coverage, compatibility of hydropathy profiles, TMS topologies and shared domains. Identified transport systems were compared within the Asgard superphylum as well as within dissimilar eukaryotic, archaeal and bacterial organisms. From these analyses, we infer that Asgard organisms rely mostly on the transport of substrates driven by the proton motive force (pmf), the proton electrochemical gradient which then can be used for ATP production and to drive the activities of secondary carriers. The results indicate that Asgard archaea depend heavily on the uptake of organic molecules such as lipid precursors, amino acids and their derivatives, and sugars and their derivatives. Overall, the majority of the transporters identified are more similar to prokaryotic transporters than eukaryotic systems although several instances of the reverse were documented. Taken together, the results support the previous suggestions that the Asgard superphylum includes organisms that are largely mixotrophic and anaerobic but more clearly define their metabolic potential while providing evidence regarding their relatedness to eukaryotes.
Collapse
Affiliation(s)
- Steven Russum
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Katie Jing Kay Lam
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Nicholas Alan Wong
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Vasu Iddamsetty
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Kevin J. Hendargo
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Jianing Wang
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Aditi Dubey
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Yichi Zhang
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
| | - Arturo Medrano-Soto
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
- * E-mail: (MHS); (AMS)
| | - Milton H. Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America
- * E-mail: (MHS); (AMS)
| |
Collapse
|
43
|
Shen R, Yu L, Xu P, Liang Z, Lu Q, Liang D, He Z, Wang S. Water content as a primary parameter determines microbial reductive dechlorination activities in soil. CHEMOSPHERE 2021; 267:129152. [PMID: 33316619 DOI: 10.1016/j.chemosphere.2020.129152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
Organohalide-respiring bacteria (OHRB) remove halogens from a variety of organohalides, which have been utilized for in situ remediation of different contaminated sites, e.g., groundwater, sediment and soil. Nonetheless, dehalogenation activities of OHRB and consequent remediation efficiencies can be synergistically affected by water content, soil type and inoculated/indigenous OHRB, which need to be disentangled to identify the key driving parameter and to elucidate the underlying mechanism. In this study, we investigated the impacts of water content (0-100%), soil type (laterite, brown soil and black soil) and inoculated OHRB (Dehalococcoides mccartyi CG1 and a river sediment culture) on reductive dechlorination of perchloroethene (PCE) and polychlorinated biphenyls (PCBs), as well as on associated microbial communities. Results suggested that the water content as a primary rate-limiting parameter governed dechlorination activities in environmental matrices, particularly in the soil, possibly through mediation of cell-to-organohalide mobility of OHRB. By contrast, interestingly, organohalide-dechlorinating microbial communities were predominantly clustered based on soil types, rather than water contents or inoculated OHRB. This study provided knowledge on the impacts of major parameters on OHRB-mediated reductive dechlorination in groundwater, sediment and soil for future optimization of in situ bioremediation of organohalides.
Collapse
Affiliation(s)
- Rui Shen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Ling Yu
- Analysis and Test Center, Guangdong University of Technology, Guangzhou, 510006, China
| | - Pan Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Zhiwei Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Dawei Liang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Space & Environment, Beihang University, Beijing, 100191, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006, China.
| |
Collapse
|
44
|
Zerva I, Remmas N, Kagalou I, Melidis P, Ariantsi M, Sylaios G, Ntougias S. Effect of Chlorination on Microbiological Quality of Effluent of a Full-Scale Wastewater Treatment Plant. Life (Basel) 2021; 11:68. [PMID: 33477775 PMCID: PMC7832327 DOI: 10.3390/life11010068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/10/2021] [Accepted: 01/14/2021] [Indexed: 11/17/2022] Open
Abstract
The evaluation of effluent wastewater quality mainly relies on the assessment of conventional bacterial indicators, such as fecal coliforms and enterococci; however, little is known about opportunistic pathogens, which can resist chlorination and may be transmitted in aquatic environments. In contrast to conventional microbiological methods, high-throughput molecular techniques can provide an accurate evaluation of effluent quality, although a limited number of studies have been performed in this direction. In this work, high-throughput amplicon sequencing was employed to assess the effectiveness of chlorination as a disinfection method for secondary effluents. Common inhabitants of the intestinal tract, such as Bacteroides, Arcobacter and Clostridium, and activated sludge denitrifiers capable of forming biofilms, such as Acidovorax, Pseudomonas and Thauera, were identified in the chlorinated effluent. Chloroflexi with dechlorination capability and the bacteria involved in enhanced biological phosphorus removal, i.e., Candidatus Accumulibacter and Candidatus Competibacter, were also found to resist chlorination. No detection of Escherichia indicates the lack of fecal coliform contamination. Mycobacterium spp. were absent in the chlorinated effluent, whereas toxin-producing cyanobacteria of the genera Anabaena and Microcystis were identified in low abundances. Chlorination significantly affected the filamentous bacteria Nocardioides and Gordonia, whereas Zoogloea proliferated in the disinfected effluent. Moreover, perchlorate/chlorate- and organochlorine-reducing bacteria resisted chlorination.
Collapse
Affiliation(s)
- Ioanna Zerva
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
- Department of Civil Engineering, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece;
| | - Nikolaos Remmas
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
| | - Ifigeneia Kagalou
- Department of Civil Engineering, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece;
| | - Paraschos Melidis
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
| | - Marina Ariantsi
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
| | - Georgios Sylaios
- Department of Environmental Engineering, Laboratory of Ecological Engineering and Technology, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece;
| | - Spyridon Ntougias
- Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Democritus University of Thrace, Vas. Sofias 12, 67132 Xanthi, Greece; (I.Z.); (N.R.); (P.M.); (M.A.)
| |
Collapse
|
45
|
Li T, Wen J, Li B, Ding S, Wang W. Biological effects of tourmaline treatment on Dehalococcoides spp. during the reductive dechlorination of trichloroethylene. RSC Adv 2021; 11:12086-12094. [PMID: 35423729 PMCID: PMC8697016 DOI: 10.1039/d0ra10830h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/08/2021] [Indexed: 11/26/2022] Open
Abstract
In the present study, to develop the application of biostimulation for the in situ remediation of trichloroethylene (TCE) in contaminated groundwater/soil, a mixed culture containing Dehalococcoides spp. was employed to investigate the biological effects of the polarized mineral tourmaline on the dechlorination performance, community structure, cell proliferation and expression of two model gene (tceA and vcrA) coding for reductive dehalogenases (Rdase). It was observed that tourmaline could speed up the biological dechlorination of TCE by promoting the growth and metabolism of the bacteria, impacting the expression of RDase genes. Compared with the bacteria system, the time for the complete removal of TCE was reduced from 7 d to 4 d when 5 g L−1 tourmaline was added to the bacterial system, and the yield of the innocuous product ethene increased from 53% to 91% on the 15th day of reaction. At this time, the community similarity of the tourmaline-added bacteria system and the bacteria system was 83.1%. The Dehalococcoides spp. in the tourmaline system grew 2 times more than that in the bacteria system. Moreover, an increase in the expression levels and decrease in the relative expression ratios of the functional genes (tceA and vcrA) were observed with the addition of tourmaline. The above analysis provides a molecular basis for the investigation of the biostimulation process by minerals. To explore the application of mineral in bioremediation of contaminated aquifers, this study investigated tourmaline-induced changes in TCE degradation, community structure, cell proliferation and gene expression of dechlorinating bacteria.![]()
Collapse
Affiliation(s)
- Tielong Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria
- Tianjin Key Laboratory of Environmental Remediation and Pollution Control
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution
- College of Environmental Science and Engineering
- Nankai University
| | - Jiaxin Wen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria
- Tianjin Key Laboratory of Environmental Remediation and Pollution Control
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution
- College of Environmental Science and Engineering
- Nankai University
| | - Bingjie Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria
- Tianjin Key Laboratory of Environmental Remediation and Pollution Control
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution
- College of Environmental Science and Engineering
- Nankai University
| | - Shihu Ding
- MOE Key Laboratory of Pollution Processes and Environmental Criteria
- Tianjin Key Laboratory of Environmental Remediation and Pollution Control
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution
- College of Environmental Science and Engineering
- Nankai University
| | - Wei Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria
- Tianjin Key Laboratory of Environmental Remediation and Pollution Control
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution
- College of Environmental Science and Engineering
- Nankai University
| |
Collapse
|
46
|
Kumar VV. Microbial Remediation: A Natural Approach for Environmental Pollution Management. Fungal Biol 2021. [DOI: 10.1007/978-3-030-54422-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
47
|
Halliwell T, Fisher K, Payne KAP, Rigby SEJ, Leys D. Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope. Microorganisms 2020; 8:microorganisms8091344. [PMID: 32887524 PMCID: PMC7565698 DOI: 10.3390/microorganisms8091344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 11/17/2022] Open
Abstract
Reductive dehalogenases are responsible for the reductive cleavage of carbon-halogen bonds during organohalide respiration. A variety of mechanisms have been proposed for these cobalamin and [4Fe-4S] containing enzymes, including organocobalt, radical, or cobalt-halide adduct based catalysis. The latter was proposed for the oxygen-tolerant Nitratireductor pacificus pht-3B catabolic reductive dehalogenase (NpRdhA). Here, we present the first substrate bound NpRdhA crystal structures, confirming a direct cobalt–halogen interaction is established and providing a rationale for substrate preference. Product formation is observed in crystallo due to X-ray photoreduction. Protein engineering enables rational alteration of substrate preference, providing a future blue print for the application of this and related enzymes in bioremediation.
Collapse
Affiliation(s)
- Tom Halliwell
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (T.H.); (K.F.); (K.A.P.P.); (S.E.J.R.)
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (T.H.); (K.F.); (K.A.P.P.); (S.E.J.R.)
| | - Karl A. P. Payne
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (T.H.); (K.F.); (K.A.P.P.); (S.E.J.R.)
- Future Biomanufacturing Research Hub (FutureBRH), Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Stephen E. J. Rigby
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (T.H.); (K.F.); (K.A.P.P.); (S.E.J.R.)
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; (T.H.); (K.F.); (K.A.P.P.); (S.E.J.R.)
- Correspondence: ; Tel.: +44-161-306-51-50
| |
Collapse
|
48
|
Romero-Cedillo L, Poggi-Varaldo HM, Santoyo-Salazar J, Escamilla-Alvarado C, Matsumoto-Kuwabara Y, Ponce-Noyola MT, Bretón-Deval L, García-Rocha M. Biological synthesis of iron nanoparticles using hydrolysates from a waste-based biorefinery. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:28649-28669. [PMID: 32347480 DOI: 10.1007/s11356-020-08729-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
The purpose of this work was to produce iron nanoparticles (Fe-NP) by microbial pathway from anaerobic bacteria grown in anaerobic fluidized bed reactors (AnFBRs) that constitute a new stage of a waste-based biorefinery. Bioparticles from biological fluidized bed reactors from a biorefinery of organic fraction of municipal solid wastes (that produces hydrolysates rich in reducing sugars) were nanodecorated (embedded nanobioparticle or nanodecorated bioparticle, ENBP) by biological reduction of iron salts. Factors "origin of bioparticles" (either from hydrogenogenic or methanogenic fluidized bed reactor) and "type of iron precursor salt" (iron chloride or iron citrate) were explored. SEM and high-resolution transmission electron microscopy (HRTEM) showed amorphous distribution of nanoparticles (NP) on the bioparticles surface, although small structures that are nanoparticle-like could be seen in the SEM micrographs. Some agglomeration of NPs was confirmed by DLS. Average NP size was lower in general for NP in ENBP-M than ENBP-H according to HRTEM. The factors did not have a significant influence on the specific surface area of NPs, which was high and in the range 490 to 650 m2 g-1. Analysis by EDS displayed consistent iron concentration 60-65% iron in nanoparticles present in ENBP-M (bioparticles previously grown in methanogenic bioreactor), whereas the iron concentration in NPs present in ENBP-H (bioparticles previously grown in hydrogenogenic bioreactor) was more variable in a range from 8.5 to 62%, depending on the iron salt. X-ray diffraction patterns showed the typical peaks for magnetite at 35° (3 1 1), 43° (4 0 0), and 62° (4 0 0); moreover, siderite diffraction pattern was found at 26° (0 1 2), 38° (1 1 0), and 42° (1 1 3). Results of infrared analysis of ENBP in our work were congruent with presence of magnetite and occasionally siderite determined by XRD analysis as well as presence of both Fe+2 and F+3 (and selected satellite signal peaks) observed by XPS. Our results on the ENBPs hold promise for water treatment, since iron NPs are commonly used in wastewater technologies that treat a wide variety of pollutants. Finally, the biological production of ENBP coupled to a biorefinery could become an environmentally friendly platform for nanomaterial biosynthesis as well as an additional source of revenues for a waste-based biorefinery.
Collapse
Affiliation(s)
- Leticia Romero-Cedillo
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV del IPN, P.O. Box 17-740, 07000, Mexico City, Mexico
- Environmental Biotechnology and Renewable Energies Group, CINVESTAV del IPN, P.O. Box 14-740, 07000, Mexico City, Mexico
| | - Héctor M Poggi-Varaldo
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV del IPN, P.O. Box 17-740, 07000, Mexico City, Mexico.
- Environmental Biotechnology and Renewable Energies Group, CINVESTAV del IPN, P.O. Box 14-740, 07000, Mexico City, Mexico.
| | - Jaime Santoyo-Salazar
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV del IPN, P.O. Box 17-740, 07000, Mexico City, Mexico
| | - Carlos Escamilla-Alvarado
- Centre for Research on Biotechnology and Nanotechnology (CIByN), Faculty of Chemical Sciences, Engineering and Sustainable Bioprocesses Group, UANL, Parque de Investigación e Innovación Tecnológica, km 10 Autopista al Aeropuerto Internacional Mariano Escobedo, 66629, Apodaca, Nuevo León, Mexico
| | - Yasuhiro Matsumoto-Kuwabara
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV del IPN, P.O. Box 17-740, 07000, Mexico City, Mexico
| | - M Teresa Ponce-Noyola
- Departamento de Biotecnología y Bioingeniería, CINVESTAV del IPN, Mexico City, Mexico
| | - Luz Bretón-Deval
- Cátedras Conacyt - Instituto de Biotecnología, UNAM, Av. Universidad 2001, Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Miguel García-Rocha
- Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV del IPN, P.O. Box 17-740, 07000, Mexico City, Mexico
| |
Collapse
|
49
|
Waseem H, Ali J, Syed JH, Jones KC. Establishing the relationship between molecular biomarkers and biotransformation rates: Extension of knowledge for dechlorination of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114676. [PMID: 33618452 DOI: 10.1016/j.envpol.2020.114676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic reductive treatment technologies offer cost-effective and large-scale treatment of chlorinated compounds, including polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The information about the degradation rates of these compounds in natural settings is critical but difficult to obtain because of slow degradation processes. Establishing a relationship between biotransformation rate and abundance of biomarkers is one of the most critical challenges faced by the bioremediation industry. When solved for a given contaminant, it may result in significant cost savings because of serving as a basis for action. In the current review, we have summarized the studies highlighting the use of biomarkers, particularly DNA and RNA, as a proxy for reductive dechlorination of chlorinated ethenes. As the use of biomarkers for predicting biotransformation rates has not yet been executed for PCDD/Fs, we propose the extension of the same knowledge for dioxins, where slow degradation rates further necessitate the need for developing the biomarker-rate relationship. For this, we have first retrieved and calculated the bioremediation rates of different PCDD/Fs and then highlighted the key sequences that can be used as potential biomarkers. We have also discussed the implications and hurdles in developing such a relationship. Improvements in current techniques and collaboration with some other fields, such as biokinetic modeling, can improve the predictive capability of the biomarkers so that they can be used for effectively predicting biotransformation rates of dioxins and related compounds. In the future, a valid and established relationship between biomarkers and biotransformation rates of dioxin may result in significant cost savings, whilst also serving as a basis for action.
Collapse
Affiliation(s)
- Hassan Waseem
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA; Department of Biotechnology, University of Sialkot, Sialkot, Punjab 51310, Pakistan
| | - Jafar Ali
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Jabir Hussain Syed
- Department of Meteorology, COMSATS University, Tarlai Kalan Park Road, Islamabad, 45550, Pakistan.
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| |
Collapse
|
50
|
Zenteno-Rojas A, Martínez-Romero E, Castañeda-Valbuena D, Rincón-Molina CI, Ruíz-Valdiviezo VM, Meza-Gordillo R, Villalobos-Maldonado JJ, Vences-Guzmán MÁ, Rincón-Rosales R. Structure and diversity of native bacterial communities in soils contaminated with polychlorinated biphenyls. AMB Express 2020; 10:124. [PMID: 32651884 PMCID: PMC7351888 DOI: 10.1186/s13568-020-01058-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/02/2020] [Indexed: 11/20/2022] Open
Abstract
Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) are a group of high-risk synthetic substances for human and environmental health. Currently, the study of sites contaminated by the spillage of equipment PCBs containing have been considered targeted areas for the study of bacterial communities with potential for PCBs degradation. There in isolation of bacterial strains is vital for use in biodegradable processes, such as bacterial bioaugmentation, which accelerates the development of phenomena such as natural attenuation of contaminated sites. The objective of this study was to assess biodiversity of bacteria contained in anthropogenic contaminated soils (HS and HP) with PCBs compared to a control sample without contaminant and the modified forest (F) and agricultural (A) soil in the laboratory with 100 mg L−1 PCB. For the analysis of 16S rRNA genes amplified from DNA extracted from the soils evaluated, the latest generation of Illumina Miseq and Sanger sequencing for the cultivable strains were detected. The bacteria identified as the most abundant bacterial phyla for HS and HP soil was Proteobacteria (56.7%) and Firmicutes (22.9%), which decreased in F and A soils. The most abundant bacterial genera were Burkholderia, Bacillus, Acinetobacter, Comamonas and Cupriavidus. Several species identified in this study, such as Bacillus cereus, Burkholderia cepacia, Comamonas testosteroni and Acinetobacter pittii have been reported as PCBs degraders. Finally, by means of a principal component analysis (PCA), a correlation between the physical and chemical characteristics of the soils in relation to the relative abundances of the bacteria identified was obtained. The C/N ratio was directly related to the control soil (without contaminant), while SOM maintained a relationship with F and A soils and the bacterial abundances were directly related to Hs and Hp soils due to the presence of aroclor 1260. Bacteria with the ability to tolerate high concentrations of this pollutant are considered for future use in biostimulation and bioaugmentation processes in contaminated soils.
Collapse
|