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Swaney MH, Henriquez N, Campbell T, Handelsman J, Kalan LR. Skin-associated Corynebacterium amycolatum shares cobamides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591522. [PMID: 38712214 PMCID: PMC11071462 DOI: 10.1101/2024.04.28.591522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The underlying interactions that occur to maintain skin microbiome composition, function, and overall skin health are largely unknown. Often, these types of interactions are mediated by microbial metabolites. Cobamides, the vitamin B12 family of cofactors, are essential for metabolism in many bacteria, but are only synthesized by a small fraction of prokaryotes, including certain skin-associated species. Therefore, we hypothesize that cobamide sharing mediates skin community dynamics. Preliminary work predicts that several skin-associated Corynebacterium species encode de novo cobamide biosynthesis and that their abundance is associated with skin microbiome diversity. Here, we show that commensal Corynebacterium amycolatum produces cobamides and that this synthesis can be tuned by cobalt limitation. To demonstrate cobamide sharing by C. amycolatum, we employed a co-culture assay using an E. coli cobamide auxotroph and show that C. amycolatum produces sufficient cobamides to support E. coli growth, both in liquid co-culture and when separated spatially on solid medium. We also generated a C. amycolatum non-cobamide-producing strain (cob-) using UV mutagenesis that contains mutated cobamide biosynthesis genes cobK and cobO and confirm that disruption of cobamide biosynthesis abolishes support of E. coli growth through cobamide sharing. Our study provides a unique model to study metabolite sharing by microorganisms, which will be critical for understanding the fundamental interactions that occur within complex microbiomes and for developing approaches to target the human microbiota for health advances.
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Affiliation(s)
- M H Swaney
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI, USA
| | - N Henriquez
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - T Campbell
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
| | - J Handelsman
- Wisconsin Institute for Discovery, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin, Madison, WI, USA
| | - L R Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, CAN
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, CAN
- David Braley Centre for Antibiotic Discovery, Hamilton, ON, CAN
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2
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Liu M, Su X, Yuan J, Chen Y, Huang X, Yang X, Zheng J, Li Q, Xu J, He Y. Residual effects of chlorinated organic pollutants on microbial community and natural redox processes in coastal wetlands. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133364. [PMID: 38176260 DOI: 10.1016/j.jhazmat.2023.133364] [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: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024]
Abstract
Chlorinated organic pollutants (COPs) are common in flooded environments. To examine the residual status and effects of COPs on flooded environments, a survey of 7 coastal wetlands in Zhejiang, East China was conducted. Total COP concentrations detected from 95.69 to 412.76 ng g-1 dw. Gamma-HCH and o,p'-DDT posed the greatest risk with exceedance rates of 100% according to sediment quality guidelines. Samples with higher COP pollution had higher microbial diversity, more complex microbial networks, more deterministic community assembly processes and lower microbiome stability, indicating an improved soil function for balance cycle of substances, especially for COP degradation. Further analysis using quantitative real-time PCR suggested COP-dechlorination interacted with natural redox processes, especially sulfate reduction and methanogenesis. The positive correlation between CH4 and pentachlorobenzene indicated a potential increase in greenhouse gas emissions caused by COP pollution. Correlation between dsr gene and COPs demonstrated the ability of sulfate-reducing bacteria to degrade COPs. Particularly, facultative OHRB such as sulfate-reducing bacteria hold significant importance in the process of COP-dechlorination. This finding provides a reference for COP pollution remediation. Collectively, our study offers new insight into the residual effect of COPs in coastal wetlands and contributes to an improved understanding of bioremediation strategies for COP pollution.
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Affiliation(s)
- Meng Liu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin Su
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Yuan
- Department of Urban Studies and Planning, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuxuan Chen
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaowei Huang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xueling Yang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinjin Zheng
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qinfen Li
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan He
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou 310058, China.
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3
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Dang H, Ewald JM, Mattes TE. Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16386-16398. [PMID: 37856784 PMCID: PMC10621002 DOI: 10.1021/acs.est.3c05439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Growth of organohalide-respiring bacteria such as Dehalococcoides mccartyi on halogenated organics (e.g., polychlorinated biphenyls (PCBs)) at contaminated sites or in enrichment culture requires interaction and support from other microbial community members. To evaluate naturally occurring interactions between Dehalococcoides and key supporting microorganisms (e.g., production of H2, acetate, and corrinoids) in PCB-contaminated sediments, metagenomic and metatranscriptomic sequencing was conducted on DNA and RNA extracted from sediment microcosms, showing evidence of both Dehalococcoides growth and PCB dechlorination. Using a genome-resolved approach, 160 metagenome-assembled genomes (MAGs), including three Dehalococcoides MAGs, were recovered. A novel reductive dehalogenase gene, distantly related to the chlorophenol dehalogenase gene cprA (pairwise amino acid identity: 23.75%), was significantly expressed. Using MAG gene expression data, 112 MAGs were assigned functional roles (e.g., corrinoid producers, acetate/H2 producers, etc.). A network coexpression analysis of all 160 MAGs revealed correlations between 39 MAGs and the Dehalococcoides MAGs. The network analysis also showed that MAGs assigned with functional roles that support Dehalococcoides growth (e.g., corrinoid assembly, and production of intermediates required for corrinoid synthesis) displayed significant coexpression correlations with Dehalococcoides MAGs. This work demonstrates the power of genome-resolved metagenomic and metatranscriptomic analyses, which unify taxonomy and function, in investigating the ecology of dehalogenating microbial communities.
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Affiliation(s)
- Hongyu Dang
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
| | - Jessica M. Ewald
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
| | - Timothy E. Mattes
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
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Xu G, Zhao S, Chen C, Zhang N, He J. Alleviating Chlorinated Alkane Inhibition on Dehalococcoides to Achieve Detoxification of Chlorinated Aliphatic Cocontaminants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15112-15122. [PMID: 37772791 DOI: 10.1021/acs.est.3c04535] [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: 09/30/2023]
Abstract
Cocontamination by multiple chlorinated solvents is a prevalent issue in groundwater, presenting a formidable challenge for effective remediation. Despite the recognition of this issue, a comprehensive assessment of microbial detoxification processes involving chloroethenes and associated cocontaminants, along with the underpinning microbiome, remains absent. Moreover, strategies to mitigate the inhibitory effects of cocontaminants have not been reported. Here, we revealed that chloroform exhibited the most potent inhibitory effects, followed by 1,1,1-trichloroethane and 1,1,2-trichloroethane, on dechlorination of dichloroethenes (DCEs) in Dehalococcoides-containing consortia. The observed inhibition could be attributed to suppression of biosynthesis and enzymatic activity of reductive dehalogenases and growth of Dehalococcoides. Notably, cocontaminants more profoundly inhibited Dehalococcoides populations harboring the vcrA gene than those possessing the tceA gene, thereby explaining the accumulation of vinyl chloride under cocontaminant stress. Nonetheless, we successfully ameliorated cocontaminant inhibition by augmentation with Desulfitobacterium sp. strain PR owing to its ability to attenuate cocontaminants, resulting in concurrent detoxification of DCEs, trichloroethanes, and chloroform. Microbial community analyses demonstrated obvious alterations in taxonomic composition, structure, and assembly of the dechlorinating microbiome in the presence of cocontaminants, and introduction of strain PR reshaped the dechlorinating microbiome to be similar to its original state in the absence of cocontaminants. Altogether, these findings contribute to developing bioremediation technologies to clean up challenging sites polluted with multiple chlorinated solvents.
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Affiliation(s)
- Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Chen Chen
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Ning Zhang
- College of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang, Henan 471003, China
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
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5
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Wu Z, Yu X, Liu G, Li W, Lu L, Li P, Xu X, Jiang J, Wang B, Qiao W. Sustained detoxification of 1,2-dichloroethane to ethylene by a symbiotic consortium containing Dehalococcoides species. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 325:121443. [PMID: 36921661 DOI: 10.1016/j.envpol.2023.121443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/19/2023] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
1,2-Dichloroethane (1,2-DCA) is a ubiquitous volatile halogenated organic pollutant in groundwater and soil, which poses a serious threat to the ecosystem and human health. Microbial reductive dechlorination has been recognized as an environmentally-friendly strategy for the remediation of sites contaminated with 1,2-DCA. In this study, we obtained an anaerobic microbiota derived from 1,2-DCA contaminated groundwater, which was able to sustainably convert 1,2-DCA into non-toxic ethylene with an average dechlorination rate of 30.70 ± 11.06 μM d-1 (N = 6). The microbial community profile demonstrated that the relative abundance of Dehalococcoides species increased from 0.53 ± 0.08% to 44.68 ± 3.61% in parallel with the dechlorination of 1,2-DCA. Quantitative PCR results showed that the Dehalococcoides species 16S rRNA gene increased from 2.40 ± 1.71 × 108 copies∙mL-1 culture to 4.07 ± 2.45 × 108 copies∙mL-1 culture after dechlorinating 110.69 ± 30.61 μmol of 1,2-DCA with a growth yield of 1.55 ± 0.93 × 108 cells per μmol Cl- released (N = 6), suggesting that Dehalococcoides species used 1,2-DCA for organohalide respiration to maintain cell growth. Notably, the relative abundances of Methanobacterium sp. (p = 0.0618) and Desulfovibrio sp. (p = 0.0001995) also increased significantly during the dechlorination of 1,2-DCA and were clustered in the same module with Dehalococcoides species in the co-occurrence network. These results hinted that Dehalococcoides species, the obligate organohalide-respiring bacterium, exhibited potential symbiotic relationships with Methanobacterium and Desulfovibrio species. This study illustrates the importance of microbial interactions within functional microbiota and provides a promising microbial resource for in situ bioremediation in sites contaminated with 1,2-DCA.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianghua Lu
- Jiangsu Provincial Key Laboratory of Environmental Engineering, Jiangsu Provincial Academy of Environmental Science, Nanjing 210036, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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6
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Howley E, Ki D, Krajmalnik-Brown R, Torres CI. Geobacter sulfurreducens' Unique Metabolism Results in Cells with a High Iron and Lipid Content. Microbiol Spectr 2022; 10:e0259322. [PMID: 36301091 PMCID: PMC9769739 DOI: 10.1128/spectrum.02593-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/24/2022] [Indexed: 01/07/2023] Open
Abstract
Geobacter sulfurreducens is a ubiquitous iron-reducing bacterium in soils, and in engineered systems, it can respire an electrode to produce measurable electric current. Its unique metabolism, heavily dependent on an extensive network of cytochromes, requires a unique cell composition. In this work, we used metallomics, cell fraction and elemental analyses, and transcriptomics to study and analyze the cell composition of G. sulfurreducens. Elemental composition studies (C, H, O, N, and ash content) showed high C:O and H:O ratios of approximately 1.7:1 and 0.25:1, indicative of more reduced cell composition that is consistent with high lipid content. Our study shows that G. sulfurreducens cells have a large amount of iron (2 ± 0.2 μg/g dry weight) and lipids (32 ± 0.5% dry weight/dry weight) and that this composition does not change whether the cells are grown with a soluble or an insoluble electron acceptor. The high iron concentration, higher than similar microorganisms, is attributed to the production of cytochromes that are abundant in transcriptomic analyses in both solid and soluble electron acceptor growth. The unique cell composition of G. sulfurreducens must be considered when growing this microorganism for lab studies and commercial applications. IMPORTANCE Geobacter sulfurreducens is an electroactive microorganism. In nature, it grows on metallic minerals by transferring electrons to them, effectively "breathing" metals. In a manmade system, it respires an electrode to produce an electric current. It has become a model organism for the study of electroactive organisms. There are potential biotechnological applications of an organism that can bridge the gap between biology and electrical signal and, as a ubiquitous iron reducer in soils around the world, G. sulfurreducens has an impact on the global iron cycle. We measured the concentrations of metals, macromolecules, and basic elements in G. sulfurreducens to define this organism's composition. We also used gene expression data to discuss which proteins those metals could be associated with. We found that G. sulfurreducens has a large amount of lipid and iron compared to other bacteria-these observations are important for future microbiologists and biotechnologists working with the organism.
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Affiliation(s)
- Ethan Howley
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - Dongwon Ki
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- Division of Living and the Built Environment Research, Seoul Institute of Technology, Seoul, South Korea
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - César I. Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Engineering of Matter Transport and Energy, Arizona State University, Tempe, Arizona, USA
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Hallberg ZF, Seth EC, Thevasundaram K, Taga ME. Comparative Analysis of Corrinoid Profiles across Host-Associated and Environmental Samples. Biochemistry 2022; 61:2791-2796. [PMID: 36037062 DOI: 10.1021/acs.biochem.2c00367] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Vitamin B12 (the cyanated form of cobalamin cofactors) is best known for its essential role in human health. In addition to its function in human metabolism, cobalamin also plays important roles in microbial metabolism and can impact microbial community function. Cobalamin is a member of the structurally diverse family of cofactors known as cobamides that are produced exclusively by certain prokaryotes. Cobamides are considered shared nutrients in microbial communities because the majority of bacteria that possess cobamide-dependent enzymes cannot synthesize cobamides de novo. Furthermore, different microbes have evolved metabolic specificity for particular cobamides, and therefore, the availability of cobamides in the environment is important for cobamide-dependent microbes. Determining the cobamides present in an environment of interest is essential for understanding microbial metabolic interactions. By examining the abundances of different cobamides in diverse environments, including 10 obtained in this study, we find that, contrary to its preeminence in human metabolism, cobalamin is relatively rare in many microbial habitats. Comparison of cobamide profiles of mammalian gastrointestinal samples and wood-feeding insects reveals that host-associated cobamide abundances vary and that fecal cobamide profiles differ from those of their host gastrointestinal tracts. Environmental cobamide profiles obtained from aquatic, soil, and contaminated groundwater samples reveal that the cobamide compositions of environmental samples are highly variable. As the only commercially available cobamide, cobalamin is routinely supplied during microbial culturing efforts. However, these findings suggest that cobamides specific to a given microbiome may yield greater insight into nutrient utilization and physiological processes that occur in these habitats.
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Affiliation(s)
- Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Erica C Seth
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Kersh Thevasundaram
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, California 94720, United States
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Holland SI, Vázquez-Campos X, Ertan H, Edwards RJ, Manefield MJ, Lee M. Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ' Candidatus Formimonas warabiya' strain DCMF. Front Microbiol 2022; 13:1035247. [PMID: 36569084 PMCID: PMC9768040 DOI: 10.3389/fmicb.2022.1035247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood-Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, 'Candidatus Formimonas warabiya' strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.
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Affiliation(s)
- Sophie I. Holland
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Haluk Ertan
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia,Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael J. Manefield
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,*Correspondence: Matthew Lee,
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9
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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.
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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.
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10
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Meng L, Xie L, Hirose Y, Nishiuchi T, Yoshida N. Reduced graphene oxide increases cells with enlarged outer membrane of Citrifermentans bremense and exopolysaccharides secretion. Biosens Bioelectron 2022; 218:114754. [DOI: 10.1016/j.bios.2022.114754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
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11
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Chen J, Xu F, Yang K, Chen C, Wan J, Shen C. The amendment of Organic matters enhances the anaerobic dechlorination of Polychlorinated Biphenyls in Paddy Soil. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 109:393-400. [PMID: 35687131 DOI: 10.1007/s00128-022-03563-x] [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: 01/05/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The toxicity of high-chlorinated polychlorinated biphenyls (PCBs) can be efficiently reduced through anaerobic dechlorination. However, this approach suffers a lot in face of in situ microbial remediations, like a shortage of biomass. In this study, we showed that the amendment of organic matters could help microbiota in paddy soil with anaerobic dechlorination and greatly shortened the lag period. The presence of organic matters offered a better environment for dechlorinating bacteria. They provided not only a more strictly anaerobic milieu but also copious carbon sources. By using high-throughput 16S rRNA gene sequencing, genera Dehalobacter, Dehalobacterium, and Desulfitobacterium capable of dechlorination were identified in enriched cultures. Taken together, this study proved that extra organic matters can promote anaerobic dechlorination in paddy soil slurry microcosm systems, which provides new insights into the bioremediation of PCB-contaminated soils.
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Affiliation(s)
- Jingwen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Fengjun Xu
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Kai Yang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Chen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
- Department of Civil and Environmental Engineering, National University of Singapore, Queenstown, Singapore
| | - Jixing Wan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, China.
- Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, 310058, Hangzhou, China.
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12
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Ewald JM, Schnoor JL, Mattes TE. Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants. FEMS Microbiol Ecol 2022; 98:6602352. [PMID: 35665806 DOI: 10.1093/femsec/fiac067] [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: 12/15/2021] [Revised: 04/27/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.
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Affiliation(s)
- Jessica M Ewald
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Jerald L Schnoor
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
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13
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Meng L, Yoshida N, Li Z. Soil microorganisms facilitated the electrode-driven trichloroethene dechlorination to ethene by Dehalococcoides species in a bioelectrochemical system. ENVIRONMENTAL RESEARCH 2022; 209:112801. [PMID: 35093309 DOI: 10.1016/j.envres.2022.112801] [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: 11/11/2021] [Revised: 12/17/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Bioelectrochemical dechlorination using organohalide-respiring bacteria (ORBs) is a promising technique for remediating contaminated groundwater. Generally, a longer enrichment period is required for selecting the ORB consortia to achieve bioelectrochemical dechlorination. However, the full dechloriantion is difficult to be achieved due to the absence of functional species (e.g. Dehalococcoides) in previously used enrich cultures. To overcome these challenges, bioelectrochemical dechlorination using a culture enriched with the pre-augmented Dehalococcoides was performed for the first time in this study. A two-chamber bioelectrochemical system (BES) inoculated with a pure Dehalococcoides culture and paddy soil with an applied voltage of -0.3 V (versus a standard hydrogen electrode) as the sole electron donor was used to achieve dechlorination. The ethene formation rate was 10-100 times higher than that in previous studies, indicating that inoculating the system with a pure Dehalococcoides culture and soil microorganisms gave effective full dechlorination performance. Microbial community analysis and bioelectrochemical analysis indicated that Desulfosporosinus species may have facilitated dechlorination through syntrophic interactions with Dehalococcoides. The results indicated that adding Dehalococcoides cells before operating a bioelectrochemical system is an effective way of achieving full dechlorination.
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Affiliation(s)
- Lingyu Meng
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya, 466-8555, Japan.
| | - Naoko Yoshida
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya, 466-8555, Japan
| | - Zhiling Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
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14
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Jiang L, Yang Y, Jin H, Wang H, Swift CM, Xie Y, Schubert T, Löffler FE, Yan J. Geobacter sp. Strain IAE Dihaloeliminates 1,1,2-Trichloroethane and 1,2-Dichloroethane. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3430-3440. [PMID: 35239320 DOI: 10.1021/acs.est.1c05952] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chlorinated ethanes, including 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA), are widespread groundwater contaminants. Enrichment cultures XRDCA and XRTCA derived from river sediment dihaloeliminated 1,2-DCA to ethene and 1,1,2-TCA to vinyl chloride (VC), respectively. The XRTCA culture subsequently converted VC to ethene via hydrogenolysis. Microbial community profiling demonstrated the enrichment of Geobacter 16S rRNA gene sequences in both the XRDCA and XRTCA cultures, and Dehalococcoides mccartyi (Dhc) sequences were only detected in the ethene-producing XRTCA culture. The presence of a novel Geobacter population, designated as Geobacter sp. strain IAE, was identified by the 16S rRNA gene-targeted polymerase chain reaction and Sanger sequencing. Time-resolved population dynamics attributed the dihaloelimination activity to strain IAE, which attained the growth yields of 0.93 ± 0.06 × 107 and 1.18 ± 0.14 × 107 cells per μmol Cl- released with 1,2-DCA and 1,1,2-TCA as electron acceptors, respectively. In contrast, Dhc growth only occurred during VC-to-ethene hydrogenolysis. Our findings discover a Geobacter sp. strain capable of respiring multiple chlorinated ethanes and demonstrate the involvement of a broader diversity of organohalide-respiring bacteria in the detoxification of 1,2-DCA and 1,1,2-TCA.
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Affiliation(s)
- Lisi Jiang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Huijuan Jin
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyan Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cynthia M Swift
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Yongchao Xie
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Torsten Schubert
- Research Group Anaerobic Microbiology, Friedrich Schiller University, Jena 07743, Germany
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jun Yan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
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15
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Li H, Wei S, Liu N, Du Y, Ding G. Interspecies transfer of biosynthetic cobalamin for complete dechlorination of trichloroethene by Dehalococcoides mccartyi. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2022; 85:1335-1350. [PMID: 35290215 DOI: 10.2166/wst.2022.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Complete dechlorination of trichloroethene (TCE) by Dehalococcoides mccartyi is catalyzed by reductive dehalogenases (RDases), which possess cobalamin as the crucial cofactor. However, virtually all D. mccartyi isolated thus far are corrinoid auxotrophs. The exogenous addition of commercially available cobalamin for TCE-contaminated site decontamination is costly. In this study, TCE reduction by a D. mccartyi-containing microbial consortium utilizing biosynthetic cobalamin generated by interior corrinoid-producing organisms within this microbial consortium was studied. The results confirmed that subcultures without exogenous cobalamin in the medium were apparently unaffected and were able to successively metabolize TCE to nonchlorinated ethene. The 2-bromoethanesulfonate and ampicillin resistance tests results suggested that ampicillin-sensitive bacteria rather than methanogenic archaea within this microbial consortium were responsible for biosynthesizing cobalamin. Moreover, relatively stable carbon isotopic enrichment factor (ɛ-carbon) values of TCE were obtained regardless of whether exogenous cobalamin or selective inhibitors existed in the medium, indicating that the cobalamin biosynthesized by these organisms was absorbed and utilized by D. mccartyi for RDase synthesis and eventually participated in TCE reduction. Finally, the Illumina MiSeq sequencing analysis indicated that Desulfitobacterium and Acetobacterium in this microbial consortium were responsible for the de novo cobalamin biosynthesis to fulfill the requirements of D. mccartyi for TCE metabolism.
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Affiliation(s)
- Haijun Li
- 801 Institute of Hydrogeology and Engineering Geology, Shandong Provincial Bureau of Geology & Mineral Resources, Jinan 250014, Shandong, China E-mail: ; College of Chemical and Environmental Engineering, Sichuan University of Science and Engineering, Zigong 64300, Sichuan, China
| | - Shanming Wei
- 801 Institute of Hydrogeology and Engineering Geology, Shandong Provincial Bureau of Geology & Mineral Resources, Jinan 250014, Shandong, China E-mail:
| | - Na Liu
- Institute of Groundwater and Earth Science, Jinan University, 510632 Guangzhou, China
| | - Yalu Du
- 801 Institute of Hydrogeology and Engineering Geology, Shandong Provincial Bureau of Geology & Mineral Resources, Jinan 250014, Shandong, China E-mail:
| | - Guantao Ding
- 801 Institute of Hydrogeology and Engineering Geology, Shandong Provincial Bureau of Geology & Mineral Resources, Jinan 250014, Shandong, China E-mail:
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16
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Berthomieu R, Pérez-Bernal MF, Santa-Catalina G, Desmond-Le Quéméner E, Bernet N, Trably E. Mechanisms underlying Clostridium pasteurianum's metabolic shift when grown with Geobacter sulfurreducens. Appl Microbiol Biotechnol 2021; 106:865-876. [PMID: 34939136 DOI: 10.1007/s00253-021-11736-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/08/2021] [Accepted: 12/11/2021] [Indexed: 10/19/2022]
Abstract
Recently, a study showed that glycerol fermentation by Clostridium pasteurianum could be metabolically redirected when the electroactive bacterium Geobacter sulfurreducens was added in the culture. It was assumed that this metabolic shift of the fermentative species resulted from an interspecies electron transfer. The aim of this study was to find out the mechanisms used for this interaction and how they affect the metabolism of C. pasteurianum. To get insights into the mechanisms involved, several coculture setups and RNA sequencing with differential expression analysis were performed. As a result, a putative interaction model was proposed: G. sulfurreducens produces cobamide molecules that possibly modify C. pasteurianum metabolic pathway at the key enzyme glycerol dehydratase, and affect its vanadium nitrogenase expression. In addition, the results suggested that G. sulfurreducens' electrons could enter C. pasteurianum through its transmembrane flavin-bound polyferredoxin and cellular cytochrome b5-rubredoxin interplay, putatively reinforcing the metabolic shift. Unravelling the mechanisms behind the interaction between fermentative and electroactive bacteria helps to better understand the role of bacterial interactions in fermentation setups. KEY POINTS: • C. pasteurianum-G. sulfurreducens interaction inducing a metabolic shift is mediated • C. pasteurianum's metabolic shift in coculture might be induced by cobamides • Electrons possibly enter C. pasteurianum through a multiflavin polyferredoxin.
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Affiliation(s)
| | | | | | | | | | - Eric Trably
- INRAE, Univ Montpellier, LBE, Narbonne, France.
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17
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Liu J, Bao Y, Zhang X, Zhang K, Chen S, Wu H, He J. Proteiniclasticum sediminis sp. nov., an obligate anaerobic bacterium isolated from anaerobic sludge. Antonie van Leeuwenhoek 2021; 114:1541-1549. [PMID: 34401954 DOI: 10.1007/s10482-021-01620-9] [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: 05/19/2021] [Accepted: 07/08/2021] [Indexed: 11/26/2022]
Abstract
An obligate anaerobic bacterial BAD-10 T was isolated from anaerobic acetochlor-degrading sludge. The strain was Gram-stain negative, curved rod-shaped, non-motile and non-spore-forming. Growth was observed in PYT medium at pH 6.0-9.0 (optimum, pH 7.5), at 25-47 °C (37 °C) and with 0-1.0% NaCl (w/v, 0%). Strain BAD-10 T could degrade acetochlor. The major fermentation products from peptone-yeast (PY) medium were acetate and butyrate. The predominant cellular fatty acids were iso-C15:0 FAME, anteiso-C15:0 FAME and C16:0 FAME. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain BAD-10 T showed closest affiliation to Proteiniclasticum ruminis D3RC-2 T, with a sequence similarity of 97.6%. Genome sequencing revealed a genome size of 2,983,986 bp, a G + C content of 51.4 mol% and protein-coding genes of 3,102. The average nucleotide identity and in silico DNA-DNA hybridization values between strain BAD-10 T and Proteiniclasticum ruminis D3RC-2 T were 71.0% and 20.4%, respectively, which were below the standard thresholds for species differentiation. On the basis of phenotypic, physiological and phylogenetic evidence, strain BAD-10 T represents a novel species in the genus Proteiniclasticum, for which the name Proteiniclasticum sediminis sp. nov. is proposed. Strain BAD-10 T (= CCTCC AB 2021091 T = KCTC 25288 T) is the type strain of the proposed novel species.
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Affiliation(s)
- Junwei Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Yixuan Bao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Xuan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Kaiyun Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Shuaimin Chen
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, Jilin, 130033, People's Republic of China
| | - Haiyan Wu
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, Jilin, 130033, People's Republic of China.
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China.
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18
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Wu B, Liu F, Fang W, Yang T, Chen GH, He Z, Wang S. Microbial sulfur metabolism and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146085. [PMID: 33714092 DOI: 10.1016/j.scitotenv.2021.146085] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.
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Affiliation(s)
- Bo Wu
- 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
| | - Feifei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Wenwen Fang
- 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
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, 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.
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19
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Liang Y, Lu Q, Liang Z, Liu X, Fang W, Liang D, Kuang J, Qiu R, He Z, Wang S. Substrate-dependent competition and cooperation relationships between Geobacter and Dehalococcoides for their organohalide respiration. ISME COMMUNICATIONS 2021; 1:23. [PMID: 37938613 PMCID: PMC9723705 DOI: 10.1038/s43705-021-00025-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 05/19/2023]
Abstract
Obligate and non-obligate organohalide-respiring bacteria (OHRB) play central roles in the geochemical cycling and environmental bioremediation of organohalides. Their coexistence and interactions may provide functional redundancy and community stability to assure organohalide respiration efficiency but, at the same time, complicate isolation and characterization of specific OHRB. Here, we employed a growth rate/yield tradeoff strategy to enrich and isolate a rare non-obligate tetrachloroethene (PCE)-respiring Geobacter from a Dehalococcoides-predominant microcosm, providing experimental evidence for the rate/yield tradeoff theory in population selection. Surprisingly, further physiological and genomic characterizations, together with co-culture experiments, revealed three unique interactions (i.e., free competition, conditional competition and syntrophic cooperation) between Geobacter and Dehalococcoides for their respiration of PCE and polychlorinated biphenyls (PCBs), depending on both the feeding electron donors (acetate/H2 vs. propionate) and electron acceptors (PCE vs. PCBs). This study provides the first insight into substrate-dependent interactions between obligate and non-obligate OHRB, as well as a new strategy to isolate fastidious microorganisms, for better understanding of the geochemical cycling and bioremediation of organohalides.
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Affiliation(s)
- Yongyi 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, 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, 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, China
| | - Xiaokun 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, China
| | - Wenwen Fang
- 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, China
| | - Dawei Liang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Space & Environment, Beihang University, Beijing, China
| | - Jialiang Kuang
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - 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, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 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, 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, China.
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20
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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.
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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.
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21
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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.
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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
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22
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Yan J, Wang J, Villalobos Solis MI, Jin H, Chourey K, Li X, Yang Y, Yin Y, Hettich RL, Löffler FE. Respiratory Vinyl Chloride Reductive Dechlorination to Ethene in TceA-Expressing Dehalococcoides mccartyi. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:4831-4841. [PMID: 33683880 DOI: 10.1021/acs.est.0c07354] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioremediation of chlorinated ethenes in anoxic aquifers hinges on organohalide-respiring Dehalococcoidia expressing vinyl chloride (VC) reductive dehalogenase (RDase). The tceA gene encoding the trichloroethene-dechlorinating RDase TceA is frequently detected in contaminated groundwater but not recognized as a biomarker for VC detoxification. We demonstrate that tceA-carrying Dehalococcoides mccartyi (Dhc) strains FL2 and 195 grow with VC as an electron acceptor when sufficient vitamin B12 (B12) is provided. Strain FL2 cultures that received 50 μg L-1 B12 completely dechlorinated VC to ethene at rates of 14.80 ± 1.30 μM day-1 and attained 1.64 ± 0.11 × 108 cells per μmol of VC consumed. Strain 195 attained similar growth yields of 1.80 ± 1.00 × 108 cells per μmol of VC consumed, and both strains could be consecutively transferred with VC as the electron acceptor. Proteomic analysis demonstrated TceA expression in VC-grown strain FL2 cultures. Resequencing of the strain FL2 and strain 195 tceA genes identified non-synonymous substitutions, although their consequences for TceA function are currently unknown. The finding that Dhc strains expressing TceA respire VC can explain ethene formation at chlorinated solvent sites, where quantitative polymerase chain reaction analysis indicates that tceA dominates the RDase gene pool.
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Affiliation(s)
- Jun Yan
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jingjing Wang
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Huijuan Jin
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Karuna Chourey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiuying Li
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Yi Yang
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
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23
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Organohalide-Respiring Bacteria at the Heart of Anaerobic Metabolism in Arctic Wet Tundra Soils. Appl Environ Microbiol 2021; 87:AEM.01643-20. [PMID: 33187999 DOI: 10.1128/aem.01643-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/10/2020] [Indexed: 11/20/2022] Open
Abstract
Recent work revealed an active biological chlorine cycle in coastal Arctic tundra of northern Alaska. This raised the question of whether chlorine cycling was restricted to coastal areas or if these processes extended to inland tundra. The anaerobic process of organohalide respiration, carried out by specialized bacteria like Dehalococcoides, consumes hydrogen gas and acetate using halogenated organic compounds as terminal electron acceptors, potentially competing with methanogens that produce the greenhouse gas methane. We measured microbial community composition and soil chemistry along an ∼262-km coastal-inland transect to test for the potential of organohalide respiration across the Arctic Coastal Plain and studied the microbial community associated with Dehalococcoides to explore the ecology of this group and its potential to impact C cycling in the Arctic. Concentrations of brominated organic compounds declined sharply with distance from the coast, but the decrease in organic chlorine pools was more subtle. The relative abundances of Dehalococcoides were similar across the transect, except for being lower at the most inland site. Dehalococcoides correlated with other strictly anaerobic genera, plus some facultative ones, that had the genetic potential to provide essential resources (hydrogen, acetate, corrinoids, or organic chlorine). This community included iron reducers, sulfate reducers, syntrophic bacteria, acetogens, and methanogens, some of which might also compete with Dehalococcoides for hydrogen and acetate. Throughout the Arctic Coastal Plain, Dehalococcoides is associated with the dominant anaerobes that control fluxes of hydrogen, acetate, methane, and carbon dioxide. Depending on seasonal electron acceptor availability, organohalide-respiring bacteria could impact carbon cycling in Arctic wet tundra soils.IMPORTANCE Once considered relevant only in contaminated sites, it is now recognized that biological chlorine cycling is widespread in natural environments. However, linkages between chlorine cycling and other ecosystem processes are not well established. Species in the genus Dehalococcoides are highly specialized, using hydrogen, acetate, vitamin B12-like compounds, and organic chlorine produced by the surrounding community. We studied which neighbors might produce these essential resources for Dehalococcoides species. We found that Dehalococcoides species are ubiquitous across the Arctic Coastal Plain and are closely associated with a network of microbes that produce or consume hydrogen or acetate, including the most abundant anaerobic bacteria and methanogenic archaea. We also found organic chlorine and microbes that can produce these compounds throughout the study area. Therefore, Dehalococcoides could control the balance between carbon dioxide and methane (a more potent greenhouse gas) when suitable organic chlorine compounds are available to drive hydrogen and acetate uptake.
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Chen Z, Tang X, Qiao W, Puentes Jácome LA, Edwards EA, He Y, Xu J. Nanoscale zero-valent iron reduction coupled with anaerobic dechlorination to degrade hexachlorocyclohexane isomers in historically contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2020; 400:123298. [PMID: 32947703 DOI: 10.1016/j.jhazmat.2020.123298] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Hexachlorocyclohexane (HCH) isomers pose potential threats to the environment and to public health due to their persistence and high toxicity. In this study, nanoscale zero-valent iron (nZVI) coupled with microbial degradation by indigenous microorganisms with and without biostimulation was employed to remediate soils highly polluted with HCH. The degradation efficiency of total HCHs in both the "nZVI-only" and "Non-amendment" treatments was approximately 50 %, while in the treatment amended with nZVI and acetate, 85 % of total HCHs was removed. Addition of nZVI and acetate resulted in enrichment of anaerobic microorganisms. The results of quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing revealed that Desulfotomaculum, Dehalobacter, Geobacter, and Desulfuromonas likely contributed to the depletion of HCH isomers. Moreover, some abiotic factors also favored this removal process, including pH, and the generation of iron sulfides as revealed by the result of Mössbauer spectrometer analysis. Our research provides an improved remediation strategy for soils polluted with HCH isomers and an understanding of the synergistic effect of nZVI and indigenous microorganisms.
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Affiliation(s)
- Zhengzheng Chen
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xianjin Tang
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenjing Qiao
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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25
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Dulay H, Tabares M, Kashefi K, Reguera G. Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. Front Microbiol 2020; 11:600463. [PMID: 33324382 PMCID: PMC7726332 DOI: 10.3389/fmicb.2020.600463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.
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Affiliation(s)
- Hunter Dulay
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Marcela Tabares
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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26
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Sokolovskaya OM, Shelton AN, Taga ME. Sharing vitamins: Cobamides unveil microbial interactions. Science 2020; 369:369/6499/eaba0165. [PMID: 32631870 DOI: 10.1126/science.aba0165] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study-from individual isolates, to synthetic consortia, to complex communities-have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda N Shelton
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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27
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Wen LL, Li Y, Zhu L, Zhao HP. Influence of non-dechlorinating microbes on trichloroethene reduction based on vitamin B 12 synthesis in anaerobic cultures. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113947. [PMID: 31931416 DOI: 10.1016/j.envpol.2020.113947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/28/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
In this study, the YH consortium, an ethene-producing culture, was used to evaluate the effect of vitamin B12 (VB12) on trichloroethene (TCE) dechlorination by transferring the original TCE-reducing culture with or without adding exogenous VB12. Ultra-high performance liquid chromatography - tandem mass spectrometry (UPLC-MS/MS) was applied to detect the concentrations of VB12 and its lower ligand 5,6-dimethylbenzimidazole (DMB) in the cultures. After three successive VB12 starvation cycles, the dechlorination of TCE stopped mostly at cis-dichloroethene (cDCE), and no ethene was found; methane production increased significantly, and no VB12 was detected. Results suggest that the co-cultured microbes may not be able to provide enough VB12 as a cofactor for the growth of Dehalococcoides in the YH culture, possibly due to the competition for corrinoids between Dehalococcoides and methanogens. The relative abundances of 16 S rRNA gene of Dehalococcoides and reductive dehalogenase genes tceA or vcrA were lower in the cultures without VB12 compared with the cultures with VB12. VB12 limitation changed the microbial community structures of the consortia. In the absence of VB12, the microbial community shifted from dominance of Chloroflexi to Proteobacteria after three consecutive VB12 starvation cycles, and the dechlorinating genus Dehalococcoides declined from 42.9% to 13.5%. In addition, Geobacter, Clostridium, and Desulfovibrio were also present in the cultures without VB12. Furthermore, the abundance of archaea increased under VB12 limited conditions. Methanobacterium and Methanosarcina were the predominant archaea in the culture without VB12.
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Affiliation(s)
- Li-Lian Wen
- College of Resource and Environmental Science, Hubei University, Wuhan, 430062, China; MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - Yaru Li
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - Lizhong Zhu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China.
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28
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Molenda O, Puentes Jácome LA, Cao X, Nesbø CL, Tang S, Morson N, Patron J, Lomheim L, Wishart DS, Edwards EA. Insights into origins and function of the unexplored majority of the reductive dehalogenase gene family as a result of genome assembly and ortholog group classification. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:663-678. [PMID: 32159535 DOI: 10.1039/c9em00605b] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Organohalide respiring bacteria (OHRB) express reductive dehalogenases for energy conservation and growth. Some of these enzymes catalyze the reductive dehalogenation of chlorinated and brominated pollutants in anaerobic subsurface environments, providing a valuable ecosystem service. Dehalococcoides mccartyi strains have been most extensively studied owing to their ability to dechlorinate all chlorinated ethenes - most notably carcinogenic vinyl chloride - to ethene. The genomes of OHRB, particularly obligate OHRB, often harbour multiple putative reductive dehalogenase genes (rdhA), most of which have yet to be characterized. We recently sequenced and closed the genomes of eight new strains, increasing the number of available D. mccartyi genomes in NCBI from 16 to 24. From all available OHRB genomes, we classified predicted translations of reductive dehalogenase genes using a previously established 90% amino acid pairwise identity cut-off to identify Ortholog Groups (OGs). Interestingly, the majority of D. mccartyi dehalogenase gene sequences, once classified into OGs, exhibited a remarkable degree of synteny (gene order) in all genomes sequenced to date. This organization was not apparent without the classification. A high degree of synteny indicates that differences arose from rdhA gene loss rather than recombination. Phylogenetic analysis suggests that most rdhA genes have a long evolutionary history in the Dehalococcoidia with origin prior to speciation of Dehalococcoides and Dehalogenimonas. We also looked for evidence of synteny in the genomes of other species of OHRB. Unfortunately, there are too few closed Dehalogenimonas genomes to compare at this time. There is some partial evidence for synteny in the Dehalobacter restrictus genomes, but here too more closed genomes are needed for confirmation. Interestingly, we found that the rdhA genes that encode enzymes that catalyze dehalogenation of industrial pollutants are the only rdhA genes with strong evidence of recent lateral transfer - at least in the genomes examined herein. Given the utility of the RdhA sequence classification to comparative analyses, we are building a public web server () for the community to use, which allows users to add and classify new sequences, and download the entire curated database of reductive dehalogenases.
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Affiliation(s)
- Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada.
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29
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Deobald D, Hanna R, Shahryari S, Layer G, Adrian L. Identification and characterization of a bacterial core methionine synthase. Sci Rep 2020; 10:2100. [PMID: 32034217 PMCID: PMC7005905 DOI: 10.1038/s41598-020-58873-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/20/2020] [Indexed: 11/18/2022] Open
Abstract
Methionine synthases are essential enzymes for amino acid and methyl group metabolism in all domains of life. Here, we describe a putatively anciently derived type of methionine synthase yet unknown in bacteria, here referred to as core-MetE. The enzyme appears to represent a minimal MetE form and transfers methyl groups from methylcobalamin instead of methyl-tetrahydrofolate to homocysteine. Accordingly, it does not possess the tetrahydrofolate binding domain described for canonical bacterial MetE proteins. In Dehalococcoides mccartyi strain CBDB1, an obligate anaerobic, mesophilic, slowly growing organohalide-respiring bacterium, it is encoded by the locus cbdbA481. In line with the observation to not accept methyl groups from methyl-tetrahydrofolate, all known genomes of bacteria of the class Dehalococcoidia lack metF encoding for methylene-tetrahydrofolate reductase synthesizing methyl-tetrahydrofolate, but all contain a core-metE gene. We heterologously expressed core-MetECBDB in E. coli and purified the 38 kDa protein. Core-MetECBDB exhibited Michaelis-Menten kinetics with respect to methylcob(III)alamin (KM ≈ 240 µM) and L-homocysteine (KM ≈ 50 µM). Only methylcob(III)alamin was found to be active as methyl donor with a kcat ≈ 60 s-1. Core-MetECBDB did not functionally complement metE-deficient E. coli strain DH5α (ΔmetE::kan) suggesting that core-MetECBDB and the canonical MetE enzyme from E. coli have different enzymatic specificities also in vivo. Core-MetE appears to be similar to a MetE-ancestor evolved before LUCA (last universal common ancestor) using methylated cobalamins as methyl donor whereas the canonical MetE consists of a tandem repeat and might have evolved by duplication of the core-MetE and diversification of the N-terminal part to a tetrahydrofolate-binding domain.
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Affiliation(s)
- Darja Deobald
- Leipzig University, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Permoserstraße 15, 04318, Leipzig, Germany
| | - Rafael Hanna
- Leipzig University, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
- Freiburg University, Institute of Pharmaceutical Sciences, Stefan-Meier-Straße 19, 79104, Freiburg im Breisgau, Germany
| | - Shahab Shahryari
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Permoserstraße 15, 04318, Leipzig, Germany
| | - Gunhild Layer
- Leipzig University, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
- Freiburg University, Institute of Pharmaceutical Sciences, Stefan-Meier-Straße 19, 79104, Freiburg im Breisgau, Germany
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, Isotope Biogeochemistry, Permoserstraße 15, 04318, Leipzig, Germany.
- Technische Universität Berlin, Chair of Geobiotechnology, Ackerstraße 76, 13355, Berlin, Germany.
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30
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Flexible Cobamide Metabolism in Clostridioides ( Clostridium) difficile 630 Δ erm. J Bacteriol 2020; 202:JB.00584-19. [PMID: 31685533 DOI: 10.1128/jb.00584-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/26/2019] [Indexed: 01/05/2023] Open
Abstract
Clostridioides (Clostridium) difficile is an opportunistic pathogen known for its ability to colonize the human gut under conditions of dysbiosis. Several aspects of its carbon and amino acid metabolism have been investigated, but its cobamide (vitamin B12 and related cofactors) metabolism remains largely unexplored. C. difficile has seven predicted cobamide-dependent pathways encoded in its genome in addition to a nearly complete cobamide biosynthesis pathway and a cobamide uptake system. To address the importance of cobamides to C. difficile, we studied C. difficile 630 Δerm and mutant derivatives under cobamide-dependent conditions in vitro Our results show that C. difficile can use a surprisingly diverse array of cobamides for methionine and deoxyribonucleotide synthesis and can use alternative metabolites or enzymes, respectively, to bypass these cobamide-dependent processes. C. difficile 630 Δerm produces the cobamide pseudocobalamin when provided the early precursor 5-aminolevulinic acid or the late intermediate cobinamide (Cbi) and produces other cobamides if provided an alternative lower ligand. The ability of C. difficile 630 Δerm to take up cobamides and Cbi at micromolar or lower concentrations requires the transporter BtuFCD. Genomic analysis revealed genetic variations in the btuFCD loci of different C. difficile strains, which may result in differences in the ability to take up cobamides and Cbi. These results together demonstrate that, like other aspects of its physiology, cobamide metabolism in C. difficile is versatile.IMPORTANCE The ability of the opportunistic pathogen Clostridioides difficile to cause disease is closely linked to its propensity to adapt to conditions created by dysbiosis of the human gut microbiota. The cobamide (vitamin B12) metabolism of C. difficile has been underexplored, although it has seven metabolic pathways that are predicted to require cobamide-dependent enzymes. Here, we show that C. difficile cobamide metabolism is versatile, as it can use a surprisingly wide variety of cobamides and has alternative functions that can bypass some of its cobamide requirements. Furthermore, C. difficile does not synthesize cobamides de novo but produces them when given cobamide precursors. A better understanding of C. difficile cobamide metabolism may lead to new strategies to treat and prevent C. difficile-associated disease.
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De Mandal S, Mathipi V, Muthukumaran RB, Gurusubramanian G, Lalnunmawii E, Kumar NS. Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:778. [PMID: 31784843 DOI: 10.1007/s10661-019-7879-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
The discharge of solid and liquid waste from domestic, municipal, and hospital premises pollutes the soil and river ecosystems. However, the diversity and functions of the microbial communities present in these polluted environments are not well understood and may contain harmful microbial communities with specialized metabolic potential. In this present study, we adapted the Illumina sequencing technology to analyze microbial communities and their metabolic capabilities in polluted environments. A total of 1113884 sequences of v3-v4 hypervariable region of the 16S rRNA were obtained using Illumina sequencing and assigned to the corresponding taxonomical ranks using Greengenes databases. Proteobacteria and Bacteroidetes were dominantly present in all the four studied sites (solid waste dumping site (SWD); Chite river site (CHR), Turial river site (TUR), and Tuikual river site (TUKR)). It was found that the SWD was dominated by Firmicutes, Actinobacteria; CHR by Acidobacteria, Verrucomicrobia, Planctomycetes; TUR by Verrucomicrobia, Acidobacteria; and TUKR by Verrucomicrobia and Firmicutes, respectively. The dominant bacterial genus present in all samples was Acinetobacter, Flavobacterium, Prevotella, Corynebacterium, Comamonas, Bacteroides, Wautersiella, Cloacibacterium, Stenotrophomonas, Sphingobacterium, and Pseudomonas. Twenty-seven putative bacterial pathogens were identified from the contaminated sites belonging to Salmonella enterica, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. Functional analysis showed a high representation of genes in the KEGG pathway involved in the metabolism of amino acids and carbohydrates and identified several genes associated with antibiotic resistance and xenobiotic degradation in these environments, which can be a serious problem for human health and environment. The results from this research will provide a new understanding of the possible management practices to minimize the spread of pathogenic microorganisms in the environment.
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Affiliation(s)
- Surajit De Mandal
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | | | | | | | - Esther Lalnunmawii
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
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Sokolovskaya OM, Mok KC, Park JD, Tran JLA, Quanstrom KA, Taga ME. Cofactor Selectivity in Methylmalonyl Coenzyme A Mutase, a Model Cobamide-Dependent Enzyme. mBio 2019; 10:e01303-19. [PMID: 31551329 PMCID: PMC6759758 DOI: 10.1128/mbio.01303-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/23/2019] [Indexed: 12/25/2022] Open
Abstract
Cobamides, a uniquely diverse family of enzyme cofactors related to vitamin B12, are produced exclusively by bacteria and archaea but used in all domains of life. While it is widely accepted that cobamide-dependent organisms require specific cobamides for their metabolism, the biochemical mechanisms that make cobamides functionally distinct are largely unknown. Here, we examine the effects of cobamide structural variation on a model cobamide-dependent enzyme, methylmalonyl coenzyme A (CoA) mutase (MCM). The in vitro binding affinity of MCM for cobamides can be dramatically influenced by small changes in the structure of the lower ligand of the cobamide, and binding selectivity differs between bacterial orthologs of MCM. In contrast, variations in the lower ligand have minor effects on MCM catalysis. Bacterial growth assays demonstrate that cobamide requirements of MCM in vitro largely correlate with in vivo cobamide dependence. This result underscores the importance of enzyme selectivity in the cobamide-dependent physiology of bacteria.IMPORTANCE Cobamides, including vitamin B12, are enzyme cofactors used by organisms in all domains of life. Cobamides are structurally diverse, and microbial growth and metabolism vary based on cobamide structure. Understanding cobamide preference in microorganisms is important given that cobamides are widely used and appear to mediate microbial interactions in host-associated and aquatic environments. Until now, the biochemical basis for cobamide preferences was largely unknown. In this study, we analyzed the effects of the structural diversity of cobamides on a model cobamide-dependent enzyme, methylmalonyl-CoA mutase (MCM). We found that very small changes in cobamide structure could dramatically affect the binding affinity of cobamides to MCM. Strikingly, cobamide-dependent growth of a model bacterium, Sinorhizobium meliloti, largely correlated with the cofactor binding selectivity of S. meliloti MCM, emphasizing the importance of cobamide-dependent enzyme selectivity in bacterial growth and cobamide-mediated microbial interactions.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
- Department of Chemistry, University of California Berkeley, Berkeley, California, USA
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Jong Duk Park
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Jennifer L A Tran
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Kathryn A Quanstrom
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, USA
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Complete Genome Sequence of Dehalococcoides mccartyi Strain FL2, a Trichloroethene-Respiring Anaerobe Isolated from Pristine Freshwater Sediment. Microbiol Resour Announc 2019; 8:8/33/e00558-19. [PMID: 31416865 PMCID: PMC6696640 DOI: 10.1128/mra.00558-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Dehalococcoides mccartyi strain FL2 couples growth to hydrogen oxidation and reductive dechlorination of trichloroethene and cis- and trans-1,2-dichloroethenes. Strain FL2 has a 1.42-Mb genome with a G+C content of 47.0% and carries 1,465 protein-coding sequences, including 24 reductive dehalogenase genes.
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Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges. J Ind Microbiol Biotechnol 2019; 46:1343-1358. [PMID: 31278525 DOI: 10.1007/s10295-019-02211-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/01/2019] [Indexed: 02/07/2023]
Abstract
Functional differentiation and metabolite exchange enable microbial consortia to perform complex metabolic tasks and efficiently cycle the nutrients. Inspired by the cooperative relationships in environmental microbial consortia, synthetic microbial consortia have great promise for studying the microbial interactions in nature and more importantly for various engineering applications. However, challenges coexist with promises, and the potential of consortium-based technologies is far from being fully harnessed. Thorough understanding of the underlying molecular mechanisms of microbial interactions is greatly needed for the rational design and optimization of defined consortia. These knowledge gaps could be potentially filled with the assistance of the ongoing revolution in systems biology and synthetic biology tools. As current fundamental and technical obstacles down the road being removed, we would expect new avenues with synthetic microbial consortia playing important roles in biological and environmental engineering processes such as bioproduction of desired chemicals and fuels, as well as biodegradation of persistent contaminants.
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Mao X, Stenuit B, Tremblay J, Yu K, Tringe SG, Alvarez-Cohen L. Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor. WATER RESEARCH 2019; 158:146-156. [PMID: 31035191 PMCID: PMC7053656 DOI: 10.1016/j.watres.2019.04.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 05/13/2023]
Abstract
A trichloroethene (TCE)-dechlorinating community (CANAS) maintained in a completely mixed flow reactor was established from a semi-batch enrichment culture (ANAS) and was monitored for 400 days at a low solids retention time (SRT) under electron acceptor limitation. Around 85% of TCE supplied to CANAS (0.13 mmol d-1) was converted to ethene at a rate of 0.1 mmol d-1, with detection of low production rates of vinyl chloride (6.8 × 10-3 mmol d-1) and cis-dichloroethene (2.3 × 10-3 mmol d-1). Two distinct Dehalococcoides mccartyi strains (ANAS1 and ANAS2) were stably maintained at 6.2 ± 2.8 × 108 cells mL-1 and 5.8 ± 1.2 × 108 cells mL-1, respectively. Electron balance analysis showed 107% electron recovery, in which 6.1% were involved in dechlorination. 16 S rRNA amplicon sequencing revealed a structural regime shift between ANAS and CANAS while maintaining robust TCE dechlorination due to similar relative abundances of D. mccartyi and functional redundancy among each functional guild supporting D. mccartyi activity. D. mccartyi transcriptomic analysis identified the genes encoding for ribosomal RNA and the reductive dehalogenases tceA and vcrA as the most expressed genes in CANAS, while hup and vhu were the most critical hydrogenases utilized by D. mccartyi in the community.
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Affiliation(s)
- Xinwei Mao
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720-1710, USA
| | - Benoit Stenuit
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720-1710, USA
| | | | - Ke Yu
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720-1710, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Walnut Creek, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, 94720-1710, USA; Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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El-Athman F, Adrian L, Jekel M, Putschew A. Abiotic reductive deiodination of iodinated organic compounds and X-ray contrast media catalyzed by free corrinoids. CHEMOSPHERE 2019; 221:212-218. [PMID: 30640003 DOI: 10.1016/j.chemosphere.2019.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/27/2018] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Iodinated X-ray contrast media are known for their stability concerning deiodination in the aquatic environment under aerobic conditions. In this study, we demonstrate the abiotic reductive deiodination of the iodinated contrast media iopromide, iopamidol and diatrizoate in the presence of corrinoids. In addition, triiodinated benzoic acid derivatives with iodine atoms bound at different positions were investigated. Corrinoids like cyanocobalamin (vitamin B12) and dicyanocobinamide served as electron shuttles and as catalysts between the reducing agent (e.g., titanium (III) citrate) and the electron accepting iodinated compound. The concentration decrease of the iodinated compounds followed first-order kinetics with rate constant kobs depending on the iodinated compound. A linear correlation between the rate of iodide release and the corrinoid concentration was observed, with deiodination rates for dicyanocobinamide twice as high as for vitamin B12. Reducing agents with a less negative standard redox potential like dithiothreitol or cysteine caused slower deiodination as the cobalt center was only reduced to its CoII oxidation state. With a temperature increase from 11 to 23 °C, the concentrations of released iodide doubled. A complete deiodination was only observed for the iodinated contrast media but not for structurally similar iodinated benzoic acid derivatives.
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Affiliation(s)
- Fatima El-Athman
- Technische Universität Berlin, Department of Environmental Science and Technology, Chair of Water Quality Engineering, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Lorenz Adrian
- Helmholtz-Centre for Environmental Research GmbH - UFZ, Department Isotope Biogeochemistry, Permoserstraße 15, 04318 Leipzig, Germany; Technische Universität Berlin, Department of Biotechnology, Chair of Geobiotechnology, Ackerstraße 76, 13355 Berlin, Germany
| | - Martin Jekel
- Technische Universität Berlin, Department of Environmental Science and Technology, Chair of Water Quality Engineering, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Anke Putschew
- Technische Universität Berlin, Department of Environmental Science and Technology, Chair of Water Quality Engineering, Straße des 17. Juni 135, 10623 Berlin, Germany.
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Teng Y, Xu Y, Wang X, Christie P. Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation. Front Microbiol 2019; 10:106. [PMID: 30837956 PMCID: PMC6383490 DOI: 10.3389/fmicb.2019.00106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/17/2019] [Indexed: 01/30/2023] Open
Abstract
Hydrogen (H2) metabolism has attracted considerable interest because the activities of H2-producing and consuming microbes shape the global H2 cycle and may have vital relationships with the global cycling of other elements. There are many pathways of microbial H2 emission and consumption which may affect the structure and function of microbial communities. A wide range of microbial groups employ H2 as an electron donor to catalyze the reduction of pollutants such as organohalides, azo compounds, and trace metals. Syntrophy coupled mutualistic interaction between H2-producing and H2-consuming microorganisms can transfer H2 and be accompanied by the removal of toxic compounds. Moreover, hydrogenases have been gradually recognized to have a key role in the progress of pollutant degradation. This paper reviews recent advances in elucidating role of H2 metabolism involved in syntrophy and hydrogenases in environmental bioremediation. Further investigations should focus on the application of bioenergy in bioremediation to make microbiological H2 metabolism a promising remediation strategy.
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Affiliation(s)
- Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Hermon L, Hellal J, Denonfoux J, Vuilleumier S, Imfeld G, Urien C, Ferreira S, Joulian C. Functional Genes and Bacterial Communities During Organohalide Respiration of Chloroethenes in Microcosms of Multi-Contaminated Groundwater. Front Microbiol 2019; 10:89. [PMID: 30809199 PMCID: PMC6379275 DOI: 10.3389/fmicb.2019.00089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/16/2019] [Indexed: 02/01/2023] Open
Abstract
Microcosm experiments with CE-contaminated groundwater from a former industrial site were set-up to evaluate the relationships between biological CE dissipation, dehalogenase genes abundance and bacterial genera diversity. Impact of high concentrations of PCE on organohalide respiration was also evaluated. Complete or partial dechlorination of PCE, TCE, cis-DCE and VC was observed independently of the addition of a reducing agent (Na2S) or an electron donor (acetate). The addition of either 10 or 100 μM PCE had no effect on organohalide respiration. qPCR analysis of reductive dehalogenases genes (pceA, tceA, vcrA, and bvcA) indicated that the version of pceA gene found in the genus Dehalococcoides [hereafter named pceA(Dhc)] and vcrA gene increased in abundance by one order of magnitude during the first 10 days of incubation. The version of the pceA gene found, among others, in the genus Dehalobacter, Sulfurospirillum, Desulfuromonas, and Geobacter [hereafter named pceA(Dhb)] and bvcA gene showed very low abundance. The tceA gene was not detected throughout the experiment. The proportion of pceA(Dhc) or vcrA genes relative to the universal 16S ribosomal RNA (16S rRNA) gene increased by up to 6-fold upon completion of cis-DCE dissipation. Sequencing of 16S rRNA amplicons indicated that the abundance of Operational Taxonomic Units (OTUs) affiliated to dehalogenating genera Dehalococcoides, Sulfurospirillum, and Geobacter represented more than 20% sequence abundance in the microcosms. Among organohalide respiration associated genera, only abundance of Dehalococcoides spp. increased up to fourfold upon complete dissipation of PCE and cis-DCE, suggesting a major implication of Dehalococcoides in CEs organohalide respiration. The relative abundance of pceA and vcrA genes correlated with the occurrence of Dehalococcoides and with dissipation extent of PCE, cis-DCE and CV. A new type of dehalogenating Dehalococcoides sp. phylotype affiliated to the Pinellas group, and suggested to contain both pceA(Dhc) and vcrA genes, may be involved in organohalide respiration of CEs in groundwater of the study site. Overall, the results demonstrate in situ dechlorination potential of CE in the plume, and suggest that taxonomic and functional biomarkers in laboratory microcosms of contaminated groundwater following pollutant exposure can help predict bioremediation potential at contaminated industrial sites.
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Affiliation(s)
- Louis Hermon
- Geomicrobiology and Environmental Monitoring Unit, Bureau de Recherches Géologiques et Minières (BRGM), Orléans, France.,CNRS, GMGM UMR 7156, Genomics and Microbiology, Université de Strasbourg, Strasbourg, France
| | - Jennifer Hellal
- Geomicrobiology and Environmental Monitoring Unit, Bureau de Recherches Géologiques et Minières (BRGM), Orléans, France
| | - Jérémie Denonfoux
- Service Recherche, Développement et Innovation-Communautés Microbiennes, GenoScreen, SAS, Lille, France
| | - Stéphane Vuilleumier
- CNRS, GMGM UMR 7156, Genomics and Microbiology, Université de Strasbourg, Strasbourg, France
| | - Gwenaël Imfeld
- CNRS/EOST, LHyGeS UMR 7517, Laboratory of Hydrology and Geochemistry of Strasbourg, Université de Strasbourg, Strasbourg, France
| | - Charlotte Urien
- Service Recherche, Développement et Innovation-Communautés Microbiennes, GenoScreen, SAS, Lille, France
| | - Stéphanie Ferreira
- Service Recherche, Développement et Innovation-Communautés Microbiennes, GenoScreen, SAS, Lille, France
| | - Catherine Joulian
- Geomicrobiology and Environmental Monitoring Unit, Bureau de Recherches Géologiques et Minières (BRGM), Orléans, France
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Genome-Guided Identification of Organohalide-Respiring Deltaproteobacteria from the Marine Environment. mBio 2018; 9:mBio.02471-18. [PMID: 30563901 PMCID: PMC6299228 DOI: 10.1128/mbio.02471-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The marine environment is a major reservoir for both anthropogenic and natural organohalides, and reductive dehalogenation is thought to be an important process in the overall cycling of these compounds. Here we demonstrate that the capacity of organohalide respiration appears to be widely distributed in members of marine Deltaproteobacteria. The identification of reductive dehalogenase genes in diverse Deltaproteobacteria and the confirmation of their dehalogenating activity through functional assays and transcript analysis in select isolates extend our knowledge of organohalide-respiring Deltaproteobacteria diversity. The presence of functional reductive dehalogenase genes in diverse Deltaproteobacteria implies that they may play an important role in organohalide respiration in the environment. Organohalide compounds are widespread in the environment as a result of both anthropogenic activities and natural production. The marine environment, in particular, is a major reservoir of organohalides, and reductive dehalogenation is thought to be an important process in the overall cycling of these compounds. Deltaproteobacteria are important members of the marine microbiota with diverse metabolic capacities, and reductive dehalogenation has been observed in some Deltaproteobacteria. In this study, a comprehensive survey of Deltaproteobacteria genomes revealed that approximately 10% contain reductive dehalogenase (RDase) genes, which are found within a common gene neighborhood. The dehalogenating potential of select RDase A-containing Deltaproteobacteria and their gene expression were experimentally verified. Three Deltaproteobacteria strains isolated from marine environments representing diverse species, Halodesulfovibrio marinisediminis, Desulfuromusa kysingii, and Desulfovibrio bizertensis, were shown to reductively dehalogenate bromophenols and utilize them as terminal electron acceptors in organohalide respiration. Their debrominating activity was not inhibited by sulfate or elemental sulfur, and these species are either sulfate- or sulfur-reducing bacteria. The analysis of RDase A gene transcripts indicated significant upregulation induced by 2,6-dibromophenol. This study extends our knowledge of the phylogenetic diversity of organohalide-respiring bacteria and their functional RDase A gene diversity. The identification of reductive dehalogenase genes in diverse Deltaproteobacteria and confirmation of their organohalide-respiring capability suggest that Deltaproteobacteria play an important role in natural organohalide cycling.
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Schubert T, von Reuß SH, Kunze C, Paetz C, Kruse S, Brand-Schön P, Nelly AM, Nüske J, Diekert G. Guided cobamide biosynthesis for heterologous production of reductive dehalogenases. Microb Biotechnol 2018; 12:346-359. [PMID: 30549216 PMCID: PMC6389850 DOI: 10.1111/1751-7915.13339] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/23/2018] [Accepted: 10/30/2018] [Indexed: 12/01/2022] Open
Abstract
Cobamides (Cbas) are essential cofactors of reductive dehalogenases (RDases) in organohalide‐respiring bacteria (OHRB). Changes in the Cba structure can influence RDase function. Here, we report on the cofactor versatility or selectivity of Desulfitobacterium RDases produced either in the native organism or heterologously. The susceptibility of Desulfitobacterium hafniense strain DCB‐2 to guided Cba biosynthesis (i.e. incorporation of exogenous Cba lower ligand base precursors) was analysed. Exogenous benzimidazoles, azabenzimidazoles and 4,5‐dimethylimidazole were incorporated by the organism into Cbas. When the type of Cba changed, no effect on the turnover rate of the 3‐chloro‐4‐hydroxy‐phenylacetate‐converting enzyme RdhA6 and the 3,5‐dichlorophenol‐dehalogenating enzyme RdhA3 was observed. The impact of the amendment of Cba lower ligand precursors on RDase function was also investigated in Shimwellia blattae, the Cba producer used for the heterologous production of Desulfitobacterium RDases. The recombinant tetrachloroethene RDase (PceAY51) appeared to be non‐selective towards different Cbas. However, the functional production of the 1,2‐dichloroethane‐dihaloeliminating enzyme (DcaA) of Desulfitobacterium dichloroeliminans was completely prevented in cells producing 5,6‐dimethylbenzimidazolyl‐Cba, but substantially enhanced in cells that incorporated 5‐methoxybenzimidazole into the Cba cofactor. The results of the study indicate the utilization of a range of different Cbas by Desulfitobacterium RDases with selected representatives apparently preferring distinct Cbas.
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Affiliation(s)
- Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Stephan H von Reuß
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Cindy Kunze
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Christian Paetz
- Research Group Biosynthesis/NMR, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Stefan Kruse
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Peggy Brand-Schön
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Anita Mac Nelly
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Jörg Nüske
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743, Jena, Germany
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Dang H, Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM. Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13914-13924. [PMID: 30427665 DOI: 10.1021/acs.est.8b04895] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Shotgun sequencing was used for the quantification of taxonomic and functional biomarkers associated with chlorinated solvent bioremediation in 20 groundwater samples (five sites), following bioaugmentation with SDC-9. The analysis determined the abundance of (1) genera associated with chlorinated solvent degradation, (2) reductive dehalogenase (RDases) genes, (3) genes associated with 1,4-dioxane removal, (4) genes associated with aerobic chlorinated solvent degradation, and (5) D. mccartyi genes associated with hydrogen and corrinoid metabolism. The taxonomic analysis revealed numerous genera previously linked to chlorinated solvent degradation, including Dehalococcoides, Desulfitobacterium, and Dehalogenimonas. The functional gene analysis indicated vcrA and tceA from D. mccartyi were the RDases with the highest relative abundance. Reads aligning with both aerobic and anaerobic biomarkers were observed across all sites. Aerobic solvent degradation genes, etnC or etnE, were detected in at least one sample from each site, as were pmoA and mmoX. The most abundant 1,4-dioxane biomarker detected was Methylosinus trichosporium OB3b mmoX. Reads aligning to thmA or Pseudonocardia were not found. The work illustrates the importance of shotgun sequencing to provide a more complete picture of the functional abilities of microbial communities. The approach is advantageous over current methods because an unlimited number of functional genes can be quantified.
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Affiliation(s)
- Hongyu Dang
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Yogendra H Kanitkar
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Paul B Hatzinger
- APTIM , 17 Princess Road , Lawrenceville , New Jersey 08648 , United States
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
- Center for Microbial Ecology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Alison M Cupples
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
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Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics. ISME JOURNAL 2018; 13:789-804. [PMID: 30429574 PMCID: PMC6461909 DOI: 10.1038/s41396-018-0304-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/14/2018] [Accepted: 10/04/2018] [Indexed: 11/08/2022]
Abstract
The vitamin B12 family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level. While 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0.6% of Bacteroidetes have the complete pathway, yet 96% of species in this phylum have cobamide-dependent enzymes. The form of cobamide produced by the bacteria could be predicted for 58% of cobamide-producing species, based on the presence of signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 17% of bacteria have partial biosynthetic pathways, yet have the potential to salvage cobamide precursors. Bacteria with a partial cobamide biosynthesis pathway include those in a newly defined, experimentally verified category of bacteria lacking the first step in the biosynthesis pathway. These predictions highlight the importance of cobamide and cobamide precursor salvaging as examples of nutritional dependencies in bacteria.
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43
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Chau ATT, Lee M, Adrian L, Manefield MJ. Syntrophic Partners Enhance Growth and Respiratory Dehalogenation of Hexachlorobenzene by Dehalococcoides mccartyi Strain CBDB1. Front Microbiol 2018; 9:1927. [PMID: 30186256 PMCID: PMC6113397 DOI: 10.3389/fmicb.2018.01927] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/30/2018] [Indexed: 11/19/2022] Open
Abstract
This study investigated syntrophic interactions between chlorinated benzene respiring Dehalococcoides mccartyi strain CBDB1 and fermenting partners (Desulfovibrio vulgaris, Syntrophobacter fumaroxidans, and Geobacter lovleyi) during hexachlorobenzene respiration. Dechlorination rates in syntrophic co-cultures were enhanced 2-3 fold compared to H2 fed CBDB1 pure cultures (0.23 ± 0.04 μmol Cl− day−1). Syntrophic partners were also able to supply cobalamins to CBDB1, albeit with 3–10 fold lower resultant dechlorination activity compared to cultures receiving exogenous cyanocobalamin. Strain CBDB1 pure cultures accumulated ~1 μmol of carbon monoxide per 87.5 μmol Cl− released during hexachlorobenzene respiration resulting in decreases in dechlorination activity. The syntrophic partners investigated were shown to consume carbon monoxide generated by CBDB1, thus relieving carbon monoxide autotoxicity. Accumulation of lesser chlorinated chlorobenzene congeners (1,3- and 1,4-dichlorobenzene and 1,3,5-trichlorobenzene) also inhibited dechlorination activity and their removal from the headspace through adsorption to granular activated carbon was shown to restore activity. Proteomic analysis revealed co-culturing strain CBDB1 with Geobacter lovleyi upregulated CBDB1 genes associated with reductive dehalogenases, hydrogenases, formate dehydrogenase, and ribosomal proteins. These data provide insight into CBDB1 ecology and inform strategies for application of CBDB1 in ex situ hexachlorobenzene destruction technologies.
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Affiliation(s)
- Anh T T Chau
- College of Agriculture and Applied Biology, Cantho University, Can Tho, Vietnam.,School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Michael J Manefield
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia.,School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
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44
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Mattes TE, Ewald JM, Liang Y, Martinez A, Awad A, Richards P, Hornbuckle KC, Schnoor JL. PCB dechlorination hotspots and reductive dehalogenase genes in sediments from a contaminated wastewater lagoon. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:16376-16388. [PMID: 28803405 PMCID: PMC6206866 DOI: 10.1007/s11356-017-9872-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/31/2017] [Indexed: 05/04/2023]
Abstract
Polychlorinated biphenyls (PCBs) are a class of persistent organic pollutants that are distributed worldwide. Although industrial PCB production has stopped, legacy contamination can be traced to several different commercial mixtures (e.g., Aroclors in the USA). Despite their persistence, PCBs are subject to naturally occurring biodegradation processes, although the microbes and enzymes involved are poorly understood. The biodegradation potential of PCB-contaminated sediments in a wastewater lagoon located in Virginia (USA) was studied. Total PCB concentrations in sediments ranged from 6.34 to 12,700 mg/kg. PCB congener profiles in sediment sample were similar to Aroclor 1248; however, PCB congener profiles at several locations showed evidence of dechlorination. The sediment microbial community structure varied among samples but was dominated by Proteobacteria and Firmicutes. The relative abundance of putative dechlorinating Chloroflexi (including Dehalococcoides sp.) was 0.01-0.19% among the sediment samples, with Dehalococcoides sp. representing 0.6-14.8% of this group. Other possible PCB dechlorinators present included the Clostridia and the Geobacteraceae. A PCR survey for potential PCB reductive dehalogenase genes (RDases) yielded 11 sequences related to RDase genes in PCB-respiring Dehalococcoides mccartyi strain CG5 and PCB-dechlorinating D. mccartyi strain CBDB1. This is the first study to retrieve potential PCB RDase genes from unenriched PCB-contaminated sediments.
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Affiliation(s)
- Timothy E Mattes
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA.
| | - Jessica M Ewald
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Yi Liang
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Andres Martinez
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Andrew Awad
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Patrick Richards
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Keri C Hornbuckle
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Jerald L Schnoor
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
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45
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Pérez-de-Mora A, Lacourt A, McMaster ML, Liang X, Dworatzek SM, Edwards EA. Chlorinated Electron Acceptor Abundance Drives Selection of Dehalococcoides mccartyi ( D. mccartyi) Strains in Dechlorinating Enrichment Cultures and Groundwater Environments. Front Microbiol 2018; 9:812. [PMID: 29867784 PMCID: PMC5968391 DOI: 10.3389/fmicb.2018.00812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/10/2018] [Indexed: 01/23/2023] Open
Abstract
Dehalococcoides mccartyi (D. mccartyi) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes within their respective genomes. While multiple rdhA genes have been sequenced, the activity of the corresponding proteins has been identified in only a few cases. Examples include the enzymes whose substrates are groundwater contaminants such as trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC). The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used as biomarkers of growth in field samples. In this study, we monitored an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed D. mccartyi-containing culture KB-1 to monitor population shifts in more detail. Quantitative PCR (qPCR) assays were developed for 15 D. mccartyi rdhA genes and used to measure population diversity in 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to D. mccartyi 16S rRNA gene copies revealed the presence of multiple distinct D. mccartyi strains in each culture, many more than the two strains inferred from 16S rRNA analysis. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi strains and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples from two bioaugmented field sites (Canada and United Kingdom). Growth of the dominant D. mccartyi strain in KB-1 was detected at the United Kingdom site. At both field sites, the measurement of relative rdhA abundances revealed D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene. These shifts indicate a selective pressure of the most abundant chlorinated electron acceptor, as was also observed in lab cultures. These results also suggest that reductive dechlorination at contaminated sites is brought about by multiple strains of D. mccartyi whether or not the site is bioaugmented. Understanding the driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.
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Affiliation(s)
- Alfredo Pérez-de-Mora
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Research Unit Analytical Biogeochemistry, Department of Environmental Sciences, Helmholtz Zentrum München, Neuherberg, Germany
| | - Anna Lacourt
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Xiaoming Liang
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Elizabeth A Edwards
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
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46
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Selective Utilization of Benzimidazolyl-Norcobamides as Cofactors by the Tetrachloroethene Reductive Dehalogenase of Sulfurospirillum multivorans. J Bacteriol 2018; 200:JB.00584-17. [PMID: 29378885 DOI: 10.1128/jb.00584-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/19/2018] [Indexed: 12/18/2022] Open
Abstract
The organohalide-respiring bacterium Sulfurospirillum multivorans produces a unique cobamide, namely, norpseudo-B12, which serves as cofactor of the tetrachloroethene (PCE) reductive dehalogenase (PceA). As previously reported, a replacement of the adeninyl moiety, the lower base of the cofactor, by exogenously applied 5,6-dimethylbenzimidazole led to inactive PceA. To explore the general effect of benzimidazoles on the PCE metabolism, the susceptibility of the organism for guided biosynthesis of various singly substituted benzimidazolyl-norcobamides was investigated, and their use as cofactor by PceA was analyzed. Exogenously applied 5-methylbenzimidazole (5-MeBza), 5-hydroxybenzimidazole (5-OHBza), and 5-methoxybenzimidazole (5-OMeBza) were found to be efficiently incorporated as lower bases into norcobamides (NCbas). Structural analysis of the NCbas by nuclear magnetic resonance spectroscopy uncovered a regioselectivity in the utilization of these precursors for NCba biosynthesis. When 5-MeBza was added, a mixture of 5-MeBza-norcobamide and 6-MeBza-norcobamide was formed, and the PceA enzyme activity was affected. In the presence of 5-OHBza, almost exclusively 6-OHBza-norcobamide was produced, while in the presence of 5-OMeBza, predominantly 5-OMeBza-norcobamide was detected. Both NCbas were incorporated into PceA, and no negative effect on the PceA activity was observed. In crystal structures of PceA, both NCbas were bound in the base-off mode with the 6-OHBza and 5-OMeBza lower bases accommodated by the same solvent-exposed hydrophilic pocket that harbors the adenine as the lower base of authentic norpseudo-B12 In this study, a selective production of different norcobamide isomers containing singly substituted benzimidazoles as lower bases is shown, and unique structural insights into their utilization as cofactors by a cobamide-containing enzyme are provided.IMPORTANCE Guided biosynthesis of norcobamides containing singly substituted benzimidazoles as lower bases by the organohalide-respiring epsilonproteobacterium Sulfurospirillum multivorans is reported. An unprecedented specificity in the formation of norcobamide isomers containing hydroxylated or methoxylated benzimidazoles was observed that implicated a strict regioselectivity of the norcobamide biosynthesis in the organism. In contrast to 5,6-dimethylbenzimidazolyl-norcobamide, the incorporation of singly substituted benzimidazolyl-norcobamides as a cofactor into the tetrachloroethene reductive dehalogenase was not impaired. The enzyme was found to be functional with different isomers and not limited to the use of adeninyl-norcobamide. Structural analysis of the enzyme equipped with either adeninyl- or benzimidazolyl-norcobamide cofactors visualized for the first time structurally different cobamides bound in base-off conformation to the cofactor-binding site of a cobamide-containing enzyme.
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47
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Schubert T, Adrian L, Sawers RG, Diekert G. Organohalide respiratory chains: composition, topology and key enzymes. FEMS Microbiol Ecol 2018; 94:4923014. [DOI: 10.1093/femsec/fiy035] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/28/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, D-04318 Leipzig, Germany
- Department of Geobiotechnology, Technische Universität Berlin, Ackerstraße 74, D-13355 Berlin, Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
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48
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Yan J, Bi M, Bourdon AK, Farmer AT, Wang PH, Molenda O, Quaile AT, Jiang N, Yang Y, Yin Y, Şimşir B, Campagna SR, Edwards EA, Löffler FE. Purinyl-cobamide is a native prosthetic group of reductive dehalogenases. Nat Chem Biol 2017; 14:8-14. [PMID: 29106396 PMCID: PMC6081238 DOI: 10.1038/nchembio.2512] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 10/02/2017] [Indexed: 01/21/2023]
Abstract
Cobamides such as vitamin B12 are structurally conserved, cobalt-containing tetrapyrrole biomolecules that have essential biochemical functions in all domains of life. In organohalide respiration, a vital biological process for the global cycling of natural and anthropogenic organohalogens, cobamides are the requisite prosthetic groups for carbon-halogen bond-cleaving reductive dehalogenases. This study reports the biosynthesis of a new cobamide with unsubstituted purine as the lower base and assigns unsubstituted purine a biological function by demonstrating that Coα-purinyl-cobamide (purinyl-Cba) is the native prosthetic group in catalytically active tetrachloroethene reductive dehalogenases of Desulfitobacterium hafniense. Cobamides featuring different lower bases are not functionally equivalent, and purinyl-Cba elicits different physiological responses in corrinoid-auxotrophic, organohalide-respiring bacteria. Given that cobamide-dependent enzymes catalyze key steps in essential metabolic pathways, the discovery of a novel cobamide structure and the realization that lower bases can effectively modulate enzyme activities generate opportunities to manipulate functionalities of microbiomes.
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Affiliation(s)
- Jun Yan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.,Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, P.R. China.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Meng Bi
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Allen K Bourdon
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Abigail T Farmer
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew T Quaile
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Nannan Jiang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
| | - Yi Yang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Burcu Şimşir
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA.,Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
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49
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Xu Y, He Y, Tang X, Brookes PC, Xu J. Reconstruction of microbial community structures as evidences for soil redox coupled reductive dechlorination of PCP in a mangrove soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 596-597:147-157. [PMID: 28431359 DOI: 10.1016/j.scitotenv.2017.04.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/07/2017] [Accepted: 04/09/2017] [Indexed: 05/26/2023]
Abstract
The aim was to investigate the influence of pentachlorophenol (PCP) on the soil microbial communities and the coupled mechanism between PCP reductive dechlorination and soil redox under anaerobic condition. Accordingly, a slurry incubation experiment was carried out in which bacterial and archaeal communities were detected by MiSeq amplicon sequencing. The original microbial community balance was gradually disrupted and new microbial structure was reconstructed subsequently through self-regulation and acclimation during PCP transformation, coupling with the changes of soil biogeochemical redox dynamics. The phylum Bacteroidetes predominated during the earlier PCP dechlorination period and then was progressively replaced by Proteobacteria and Firmicutes groups when PCP was mostly transformed into 2,3,4,5-TeCP and 3,4,5-TCP. Heatmap and hierarchical cluster analysis revealed the Clostridium-like, Geobacter-like and Dehalococcoides-like organisms enriched concurrently during PCP reductive dechlorination processes. The relative abundance changes of the redox-active microorganisms, together with their relevance to the corresponding biogeochemical redox processes, showed that PCP dechlorination, Fe(III) and SO42- reduction, as well as methanogenesis were coupled terminal electron accepting processes. The combined analysis of the microbial function, the affinity for substrates (H2 and acetate) and the sensitivity for PCP toxicity by microorganisms might explain why electron transport chain has changed in soil biogeochemical redox process. Our study offers a comprehensive description of the impact of PCP on the soil microbial community structures, which could be very useful for understanding the regulation of soil nutrient and energy transfer during biogeochemical cycling processes in soils with significant inputs of exogenous pollutants.
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Affiliation(s)
- Yan Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China.
| | - Xianjin Tang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Philip C Brookes
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
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50
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Affiliation(s)
- Maeva Fincker
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
| | - Alfred M. Spormann
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
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