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Lorah MM, He K, Blaney L, Akob DM, Harris C, Tokranov A, Hopkins Z, Shedd BP. Anaerobic biodegradation of perfluorooctane sulfonate (PFOS) and microbial community composition in soil amended with a dechlorinating culture and chlorinated solvents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172996. [PMID: 38719042 DOI: 10.1016/j.scitotenv.2024.172996] [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: 02/21/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Perfluorooctane sulfonate (PFOS), one of the most frequently detected per- and polyfluoroalkyl substances (PFAS) occurring in soil, surface water, and groundwater near sites contaminated with aqueous film-forming foam (AFFF), has proven to be recalcitrant to many destructive remedies, including chemical oxidation. We investigated the potential to utilize microbially mediated reduction (bioreduction) to degrade PFOS and other PFAS through addition of a known dehalogenating culture, WBC-2, to soil obtained from an AFFF-contaminated site. A substantial decrease in total mass of PFOS (soil and water) was observed in microcosms amended with WBC-2 and chlorinated volatile organic compound (cVOC) co-contaminants - 46.4 ± 11.0 % removal of PFOS over the 45-day experiment. In contrast, perfluorooctanoate (PFOA) and 6:2 fluorotelomer sulfonate (6:2 FTS) concentrations did not decrease in the same microcosms. The low or non-detectable concentrations of potential metabolites in full PFAS analyses, including after application of the total oxidizable precursor assay, indicated that defluorination occurred to non-fluorinated compounds or ultrashort-chain PFAS. Nevertheless, additional research on the metabolites and degradation pathways is needed. Population abundances of known dehalorespirers did not change with PFOS removal during the experiment, making their association with PFOS removal unclear. An increased abundance of sulfate reducers in the genus Desulfosporosinus (Firmicutes) and Sulfurospirillum (Campilobacterota) was observed with PFOS removal, most likely linked to initiation of biodegradation by desulfonation. These results have important implications for development of in situ bioremediation methods for PFAS and advancing knowledge of natural attenuation processes.
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Affiliation(s)
- Michelle M Lorah
- U.S. Geological Survey, Maryland-Delaware-D.C. Water Science Center, Baltimore, MD 21228, USA.
| | - Ke He
- University of Maryland Baltimore County, Department of Chemical, Biochemical, and Environmental Engineering, Baltimore, MD 21250, USA
| | - Lee Blaney
- University of Maryland Baltimore County, Department of Chemical, Biochemical, and Environmental Engineering, Baltimore, MD 21250, USA
| | - Denise M Akob
- U.S. Geological Survey, Geology, Energy, & Minerals Science Center, Reston, VA 20192, USA
| | - Cassandra Harris
- U.S. Geological Survey, Geology, Energy, & Minerals Science Center, Reston, VA 20192, USA
| | - Andrea Tokranov
- U.S. Geological Survey, New England Water Science Center, Pembroke, NH 03275, USA
| | - Zachary Hopkins
- U.S. Geological Survey, Eastern Ecological Science Center, Kearneysville, WV 25430, USA
| | - Brian P Shedd
- U.S. Army Corps of Engineers, U.S. DOD Environmental Programs Branch, Environmental Division, Headquarters, Washington, D.C. 20314, USA
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2
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Chen G, Yang Y, Yan J, Löffler FE. Metabolite cross-feeding enables concomitant catabolism of chlorinated methanes and chlorinated ethenes in synthetic microbial assemblies. THE ISME JOURNAL 2024; 18:wrae090. [PMID: 38818735 PMCID: PMC11170663 DOI: 10.1093/ismejo/wrae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/19/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
Isolate studies have been a cornerstone for unraveling metabolic pathways and phenotypical (functional) features. Biogeochemical processes in natural and engineered ecosystems are generally performed by more than a single microbe and often rely on mutualistic interactions. We demonstrate the rational bottom-up design of synthetic, interdependent co-cultures to achieve concomitant utilization of chlorinated methanes as electron donors and organohalogens as electron acceptors. Specialized anaerobes conserve energy from the catabolic conversion of chloromethane or dichloromethane to formate, H2, and acetate, compounds that the organohalide-respiring bacterium Dehalogenimonas etheniformans strain GP requires to utilize cis-1,2-dichloroethenene and vinyl chloride as electron acceptors. Organism-specific qPCR enumeration matched the growth of individual dechlorinators to the respective functional (i.e. dechlorination) traits. The metabolite cross-feeding in the synthetic (co-)cultures enables concomitant utilization of chlorinated methanes (i.e. chloromethane and dichloromethane) and chlorinated ethenes (i.e. cis-1,2-dichloroethenene and vinyl chloride) without the addition of an external electron donor (i.e. formate and H2). The findings illustrate that naturally occurring chlorinated C1 compounds can sustain anaerobic food webs, an observation with implications for the development of interdependent, mutualistic communities, the sustenance of microbial life in oligotrophic and energy-deprived environments, and the fate of chloromethane/dichloromethane and chlorinated electron acceptors (e.g. chlorinated ethenes) in pristine environments and commingled contaminant plumes.
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Affiliation(s)
- Gao Chen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States
| | - Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Jun Yan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, United States
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3
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Sun Y, Yin Y, He G, Cha G, Ayala-del-Río HL, González G, Konstantinidis KT, Löffler FE. pH selects for distinct N 2O-reducing microbiomes in tropical soil microcosms. ISME COMMUNICATIONS 2024; 4:ycae070. [PMID: 38808123 PMCID: PMC11131594 DOI: 10.1093/ismeco/ycae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.
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Affiliation(s)
- Yanchen Sun
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Yongchao Yin
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, MA 02148, United States
| | - Guang He
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
| | - Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | | | - Grizelle González
- USDA Forest Service, International Institute of Tropical Forestry, San Juan 00926, Puerto Rico
| | | | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
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4
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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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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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Zhu G, Chao H, Sun M, Jiang Y, Ye M. Toxicity sharing model of earthworm intestinal microbiome reveals shared functional genes are more powerful than species in resisting pesticide stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 446:130646. [PMID: 36587599 DOI: 10.1016/j.jhazmat.2022.130646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Earthworm intestinal bacteria and indigenous soil bacteria work closely during various biochemical processes and play a crucial role in maintaining the internal stability of the soil environment. However, the response mechanism of these bacterial communities to external pesticide disturbance is unknown. In this study, soil and earthworm gut contents were metagenomically sequenced after exposure to various concentrations of nitrochlorobenzene (0-1026.7 mg kg-1). A high degree of similarity was found between the microbial community composition and abundance in the worm gut and soil, both of which decreased significantly (P < 0.05) under elevated pesticide stress. The toxicity sharing model (TSM) showed that the toxicity sharing capacity was 97.4-125.7 % and 100.4-130.2 % for Egenes (genes in the worm gut) and Emet(degradation genes in the worm gut) in the earthworm intestinal microbiome, respectively. This indicated that the earthworm intestinal microbiome assisted in relieving the pesticide toxicity of the indigenous soil microbiome. This study showed that the TSM could quantitatively describe the toxic effect of pesticides on the earthworm intestinal microbiome. It provides a new analytical model for investigating the ecological alliance between earthworm intestinal microbiome and indigenous soil microbiome under pesticide stress while contributing a more profound understanding of the potential to use earthworms to mitigate pesticide pollution in soils and develop earthworm-based soil remediation techniques.
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Affiliation(s)
- Guofan Zhu
- National Engineering Laboratort of Soil Nutrients Management, Pollution Control and Remediation Technoligies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huizhen Chao
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China
| | - Mao Ye
- National Engineering Laboratort of Soil Nutrients Management, Pollution Control and Remediation Technoligies, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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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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8
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May AL, Xie Y, Kara Murdoch F, Michalsen MM, Löffler FE, Campagna SR. Metabolome patterns identify active dechlorination in bioaugmentation consortium SDC-9™. Front Microbiol 2022; 13:981994. [PMID: 36386687 PMCID: PMC9641191 DOI: 10.3389/fmicb.2022.981994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 12/01/2023] Open
Abstract
Ultra-high performance liquid chromatography-high-resolution mass spectrometry (UPHLC-HRMS) is used to discover and monitor single or sets of biomarkers informing about metabolic processes of interest. The technique can detect 1000's of molecules (i.e., metabolites) in a single instrument run and provide a measurement of the global metabolome, which could be a fingerprint of activity. Despite the power of this approach, technical challenges have hindered the effective use of metabolomics to interrogate microbial communities implicated in the removal of priority contaminants. Herein, our efforts to circumvent these challenges and apply this emerging systems biology technique to microbiomes relevant for contaminant biodegradation will be discussed. Chlorinated ethenes impact many contaminated sites, and detoxification can be achieved by organohalide-respiring bacteria, a process currently assessed by quantitative gene-centric tools (e.g., quantitative PCR). This laboratory study monitored the metabolome of the SDC-9™ bioaugmentation consortium during cis-1,2-dichloroethene (cDCE) conversion to vinyl chloride (VC) and nontoxic ethene. Untargeted metabolomics using an UHPLC-Orbitrap mass spectrometer and performed on SDC-9™ cultures at different stages of the reductive dechlorination process detected ~10,000 spectral features per sample arising from water-soluble molecules with both known and unknown structures. Multivariate statistical techniques including partial least squares-discriminate analysis (PLSDA) identified patterns of measurable spectral features (peak patterns) that correlated with dechlorination (in)activity, and ANOVA analyses identified 18 potential biomarkers for this process. Statistical clustering of samples with these 18 features identified dechlorination activity more reliably than clustering of samples based only on chlorinated ethene concentration and Dhc 16S rRNA gene abundance data, highlighting the potential value of metabolomic workflows as an innovative site assessment and bioremediation monitoring tool.
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Affiliation(s)
- Amanda L. May
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Yongchao Xie
- Department of Civil and Environmental Engineering, Tickle College of Engineering, University of Tennessee, Knoxville, TN, United States
| | - Fadime Kara Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Mandy M. Michalsen
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, United States
| | - Frank E. Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
- Department of Civil and Environmental Engineering, Tickle College of Engineering, University of Tennessee, Knoxville, TN, United States
- Department of Microbiology, College of Arts and Sciences, The University of Tennessee, Knoxville, TN, United States
- Department of Biosystems Engineering and Soil Science, Herbert College of Agriculture, The University of Tennessee, Knoxville, TN, United States
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
| | - Shawn R. Campagna
- Department of Chemistry, College of Arts and Sciences, The University of Tennessee, Knoxville, TN, United States
- Biological and Small Molecule Mass Spectrometry Core, College of Arts and Sciences, The University of Tennessee, Knoxville, TN, United States
- University of Tennessee-Oak Ridge Innovation Institute, University of Tennessee, Knoxville, TN, United States
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9
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Hudari MSB, Richnow H, Vogt C, Nijenhuis I. Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review. FEMS Microbiol Ecol 2022; 98:6638985. [PMID: 35810002 DOI: 10.1093/femsec/fiac081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.
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Affiliation(s)
- Mohammad Sufian Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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10
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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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11
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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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12
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Matturro B, Zepilli M, Lai A, Majone M, Rossetti S. Metagenomic Analysis Reveals Microbial Interactions at the Biocathode of a Bioelectrochemical System Capable of Simultaneous Trichloroethylene and Cr(VI) Reduction. Front Microbiol 2021; 12:747670. [PMID: 34659183 PMCID: PMC8516407 DOI: 10.3389/fmicb.2021.747670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023] Open
Abstract
Bioelectrochemical systems (BES) are attractive and versatile options for the bioremediation of organic or inorganic pollutants, including trichloroethylene (TCE) and Cr(VI), often found as co-contaminants in the environment. The elucidation of the microbial players’ role in the bioelectroremediation processes for treating multicontaminated groundwater is still a research need that attracts scientific interest. In this study, 16S rRNA gene amplicon sequencing and whole shotgun metagenomics revealed the leading microbial players and the primary metabolic interactions occurring in the biofilm growing at the biocathode where TCE reductive dechlorination (RD), hydrogenotrophic methanogenesis, and Cr(VI) reduction occurred. The presence of Cr(VI) did not negatively affect the TCE degradation, as evidenced by the RD rates estimated during the reactor operation with TCE (111±2 μeq/Ld) and TCE/Cr(VI) (146±2 μeq/Ld). Accordingly, Dehalococcoides mccartyi, the primary biomarker of the RD process, was found on the biocathode treating both TCE (7.82E+04±2.9E+04 16S rRNA gene copies g−1 graphite) and TCE/Cr(VI) (3.2E+07±2.37E+0716S rRNA gene copies g−1 graphite) contamination. The metagenomic analysis revealed a selected microbial consortium on the TCE/Cr(VI) biocathode. D. mccartyi was the sole dechlorinating microbe with H2 uptake as the only electron supply mechanism, suggesting that electroactivity is not a property of this microorganism. Methanobrevibacter arboriphilus and Methanobacterium formicicum also colonized the biocathode as H2 consumers for the CH4 production and cofactor suppliers for D. mccartyi cobalamin biosynthesis. Interestingly, M. formicicum also harbors gene complexes involved in the Cr(VI) reduction through extracellular and intracellular mechanisms.
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Affiliation(s)
| | - Marco Zepilli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Agnese Lai
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Mauro Majone
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
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13
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Chen K, Liu Z, Wang X, Yu C, Ye J, Yu C, Wang F, Shen C. Enhancement of perchloroethene dechlorination by a mixed dechlorinating culture via magnetic nanoparticle-mediated isolation method. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147421. [PMID: 33964769 DOI: 10.1016/j.scitotenv.2021.147421] [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: 10/21/2020] [Revised: 04/25/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Highly enriched active dechlorinating cultures are important in advancing microbial remediation technology. This study attempted to enrich a rapid perchloroethene (PCE) dechlorinating culture via magnetic nanoparticle-mediated isolation (MMI). MMI is a novel method that can separate the fast-growing and slow-growing population in a microbial community without labelling. In the MMI process, PCE dechlorination was enhanced but the subsequent trichloroethene (TCE) dechlorination was inhibited, with TCE cumulative rate reached up to 80.6% within 70 days. Meanwhile, the microbial community was also changed, with fast-growing genera like Dehalobacterium and Petrimonas enriched, and slow-growing Methanosarcina almost ruled out. Relative abundances of several major genera including Petrimonas and Methanosarcina were positively related to TCE dechlorination rate and the relative abundance of Dehalococcoides. On the other hand, Dehalobacterium was negatively related to TCE dechlorination rate and Dehalococcoides abundance, suggesting potential competition between Dehalobacterium and Dehalococcoides. The regrowth of Methanosarcina coupled well with the recovery of TCE dechlorination capacity, which implied the important role of methanogens in TCE dechlorination. Via MMI method, a simpler but more active microbial consortium could be established to enhance PCE remediation efficiency. Methanogens may act as the indicators or biomarkers for TCE dechlorination, suggesting that methanogenic activity should also be monitored when enriching dechlorination cultures and remediating PCE contaminated sites. CAPSULE: A rapid perchloroethene dechlorinator was gotten via magnetic nanoparticles and dechlorination of trichloroethene coupled well with growth of Methanosarcina.
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Affiliation(s)
- Kezhen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zefan Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaomin Wang
- Ecological Environmental Science Design and Research Institute of Zhejiang Province, Hangzhou 310007, China
| | - Chungui Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Junxiang Ye
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chunna Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Feier Wang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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14
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Fenner K, Elsner M, Lueders T, McLachlan MS, Wackett LP, Zimmermann M, Drewes JE. Methodological Advances to Study Contaminant Biotransformation: New Prospects for Understanding and Reducing Environmental Persistence? ACS ES&T WATER 2021; 1:1541-1554. [PMID: 34278380 PMCID: PMC8276273 DOI: 10.1021/acsestwater.1c00025] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 05/14/2023]
Abstract
Complex microbial communities in environmental systems play a key role in the detoxification of chemical contaminants by transforming them into less active metabolites or by complete mineralization. Biotransformation, i.e., transformation by microbes, is well understood for a number of priority pollutants, but a similar level of understanding is lacking for many emerging contaminants encountered at low concentrations and in complex mixtures across natural and engineered systems. Any advanced approaches aiming to reduce environmental exposure to such contaminants (e.g., novel engineered biological water treatment systems, design of readily degradable chemicals, or improved regulatory assessment strategies to determine contaminant persistence a priori) will depend on understanding the causal links among contaminant removal, the key driving agents of biotransformation at low concentrations (i.e., relevant microbes and their metabolic activities), and how their presence and activity depend on environmental conditions. In this Perspective, we present the current understanding and recent methodological advances that can help to identify such links, even in complex environmental microbiomes and for contaminants present at low concentrations in complex chemical mixtures. We discuss the ensuing insights into contaminant biotransformation across varying environments and conditions and ask how much closer we have come to designing improved approaches to reducing environmental exposure to contaminants.
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Affiliation(s)
- Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Martin Elsner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95448 Bayreuth, Germany
| | - Michael S McLachlan
- Department of Environmental Science (ACES), Stockholm University, 106 91 Stockholm, Sweden
| | - Lawrence P Wackett
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Michael Zimmermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, 85748 Garching, Germany
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15
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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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16
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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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17
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Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila. mBio 2020; 11:mBio.02507-20. [PMID: 33293380 PMCID: PMC7733943 DOI: 10.1128/mbio.02507-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cobamides, comprising the vitamin B12 family of cobalt-containing cofactors, are required for metabolism in all domains of life, including most bacteria. Cobamides have structural variability in the lower ligand, and selectivity for particular cobamides has been observed in most organisms studied to date. The beneficial human gut bacterium Akkermansia muciniphila provides metabolites to other members of the gut microbiota by breaking down host mucin, but most of its other metabolic functions have not been investigated. A. muciniphila strain MucT is known to use cobamides, the vitamin B12 family of cofactors with structural diversity in the lower ligand. However, A. muciniphila MucT is unable to synthesize cobamides de novo, and the specific forms that can be used by A. muciniphila have not been examined. We found that the levels of growth of A. muciniphila MucT were nearly identical with each of seven cobamides tested, in contrast to nearly all bacteria that had been studied previously. Unexpectedly, this promiscuity is due to cobamide remodeling—the removal and replacement of the lower ligand—despite the absence of the canonical remodeling enzyme CbiZ in A. muciniphila. We identified a novel enzyme, CbiR, that is capable of initiating the remodeling process by hydrolyzing the phosphoribosyl bond in the nucleotide loop of cobamides. CbiR does not share similarity with other cobamide remodeling enzymes or B12-binding domains and is instead a member of the apurinic/apyrimidinic (AP) endonuclease 2 enzyme superfamily. We speculate that CbiR enables bacteria to repurpose cobamides that they cannot otherwise use in order to grow under cobamide-requiring conditions; this function was confirmed by heterologous expression of cbiR in Escherichia coli. Homologs of CbiR are found in over 200 microbial taxa across 22 phyla, suggesting that many bacteria may use CbiR to gain access to the diverse cobamides present in their environment.
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18
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Waseem H, Ali J, Syed JH, Jones KC. Establishing the relationship between molecular biomarkers and biotransformation rates: Extension of knowledge for dechlorination of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114676. [PMID: 33618452 DOI: 10.1016/j.envpol.2020.114676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic reductive treatment technologies offer cost-effective and large-scale treatment of chlorinated compounds, including polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The information about the degradation rates of these compounds in natural settings is critical but difficult to obtain because of slow degradation processes. Establishing a relationship between biotransformation rate and abundance of biomarkers is one of the most critical challenges faced by the bioremediation industry. When solved for a given contaminant, it may result in significant cost savings because of serving as a basis for action. In the current review, we have summarized the studies highlighting the use of biomarkers, particularly DNA and RNA, as a proxy for reductive dechlorination of chlorinated ethenes. As the use of biomarkers for predicting biotransformation rates has not yet been executed for PCDD/Fs, we propose the extension of the same knowledge for dioxins, where slow degradation rates further necessitate the need for developing the biomarker-rate relationship. For this, we have first retrieved and calculated the bioremediation rates of different PCDD/Fs and then highlighted the key sequences that can be used as potential biomarkers. We have also discussed the implications and hurdles in developing such a relationship. Improvements in current techniques and collaboration with some other fields, such as biokinetic modeling, can improve the predictive capability of the biomarkers so that they can be used for effectively predicting biotransformation rates of dioxins and related compounds. In the future, a valid and established relationship between biomarkers and biotransformation rates of dioxin may result in significant cost savings, whilst also serving as a basis for action.
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Affiliation(s)
- Hassan Waseem
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA; Department of Biotechnology, University of Sialkot, Sialkot, Punjab 51310, Pakistan
| | - Jafar Ali
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Jabir Hussain Syed
- Department of Meteorology, COMSATS University, Tarlai Kalan Park Road, Islamabad, 45550, Pakistan.
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
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19
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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: 88] [Impact Index Per Article: 22.0] [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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20
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Murray A, Maillard J, Rolle M, Broholm M, Holliger C. Impact of iron- and/or sulfate-reduction on a cis-1,2-dichloroethene and vinyl chloride respiring bacterial consortium: experiments and model-based interpretation. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:740-750. [PMID: 32003373 DOI: 10.1039/c9em00544g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Process understanding of microbial communities containing organohalide-respiring bacteria (OHRB) is important for effective bioremediation of chlorinated ethenes. The impact of iron and sulfate reduction on cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC) dechlorination by a consortium containing the OHRB Dehalococcoides spp. was investigated using multiphase batch experiments. The OHRB consortium was found to contain endogenous iron- and sulfate-reducing bacteria (FeRB and SRB). A biogeochemical model was developed and used to quantify the mass transfer, aquatic geochemical, and microbial processes that occurred in the multiphase batch system. It was determined that the added SRB had the most significant impact on contaminant degradation. Addition of the SRB increased maximum specific substrate utilization rates, kmax, of cDCE and VC by 129% and 294%, respectively. The added FeRB had a slight stimulating effect on VC dechlorination when exogenous SRB were absent, but when cultured with the added SRB, FeRB moderated the SRB's stimulating effect. This study demonstrates that subsurface microbial community interactions are more complex than categorical, guild-based competition for resources such as electron donor.
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Affiliation(s)
- Alexandra Murray
- Department of Environmental Engineering, Technical University of Denmark, Bld 115, 2800 Lyngby, DK-2800, Denmark.
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21
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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: 9] [Impact Index Per Article: 2.3] [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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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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Li Y, Wen LL, Zhao HP, Zhu L. Addition of Shewanella oneidensis MR-1 to the Dehalococcoides-containing culture enhances the trichloroethene dechlorination. ENVIRONMENT INTERNATIONAL 2019; 133:105245. [PMID: 31683156 DOI: 10.1016/j.envint.2019.105245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/28/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Dehalococcoides is able to completely dehalogenate tetrachloroethene (PCE) and trichloroethene (TCE) to ethene (ETH). However, the dechlorination efficiency of Dehalococcoides is low and result in the accumulation of toxic intermediates. In this study, Shewanella oneidensis MR-1 (S. oneidensis MR-1) was added to the Dehalococcoides-containing culture and the complete TCE to ETH dechlorination was shortened from 24 days to 16 days. Dehalococcoides-targeted 16S rRNA gene and two model reductive dehalogenase (RDase) genes (tceA and vcrA), responsible for dechlorinating TCE to vinyl chloride (VC) and VC to ETH respectively, were characterized. Results showed that S. oneidensis MR-1 has no effect on the cell growth while the RDase genes expression was up-regulated and the RDase activity of Dehalococcoides was elevated. The mRNA abundance of vcrA increased approximately tenfold along with the increased concentration of vitamin B12 (cyanocobalamin). Interestingly, the addition of S. oneidensis MR-1 increased the concentration of vitamin B12 by affecting the microbial community structure. Therefore, the addition of S. oneidensis MR-1 might have a positive effect on regulating the activity of RDase of functional microorganisms and uptake of vitamin B12, and further provided a practical vision of chloroethene dechlorination by the Dehalococcoides-containing culture.
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Affiliation(s)
- Yaru Li
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Organic Pollution Process and Control, Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Li-Lian Wen
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; College of Resource and Environmental Science, Hubei University, Wuhan 430062, China
| | - He-Ping Zhao
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Organic Pollution Process and Control, Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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24
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Gude S, Taga ME. Multi-faceted approaches to discovering and predicting microbial nutritional interactions. Curr Opin Biotechnol 2019; 62:58-64. [PMID: 31597114 DOI: 10.1016/j.copbio.2019.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 01/07/2023]
Abstract
Nearly all microbes rely on other species in their environment to provide nutrients they are unable to produce. Nutritional interactions include not only the exchange of carbon and nitrogen compounds, but also amino acids and cofactors. Interactions involving cross-feeding of cobamides, the vitamin B12 family of cofactors, have been developed as a model for nutritional interactions across species and environments. In addition to experimental studies, new developments in culture-independent methodologies such as genomics and modeling now enable the prediction of nutritional interactions in a broad range of organisms including those that cannot be cultured in the laboratory. New insights into the mechanisms and evolution of microbial nutritional interactions are beginning to emerge by combining experimental, genomic, and modeling approaches.
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Affiliation(s)
- Sebastian Gude
- Department of Plant & Microbial Biology, University of California, Berkeley, CA USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, CA USA.
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Puentes Jácome LA, Wang PH, Molenda O, Li YXJJ, Islam MA, Edwards EA. Sustained Dechlorination of Vinyl Chloride to Ethene in Dehalococcoides-Enriched Cultures Grown without Addition of Exogenous Vitamins and at Low pH. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11364-11374. [PMID: 31441646 DOI: 10.1021/acs.est.9b02339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trichloroethene (TCE) bioremediation has been demonstrated at field sites using microbial cultures harboring TCE-respiring Dehalococcoides whose growth is cobalamin (vitamin B12)-dependent. Bioaugmentation cultures grown ex situ with ample exogenous vitamins and at neutral pH may become vitamin-limited or inhibited by acidic pH once injected into field sites, resulting in incomplete TCE dechlorination and accumulation of vinyl chloride (VC). Here, we report growth of the Dehalococcoides-containing bioaugmentation culture KB-1 in a TCE-amended mineral medium devoid of vitamins and in a VC-amended mineral medium at low pH (6.0 and 5.5). In these cultures, Acetobacterium, which can synthesize 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, and Sporomusa are dominant acetogens. At neutral pH, Acetobacterium supports complete TCE dechlorination by Dehalococcoides at millimolar levels with a substantial increase in cobalamin (∼20-fold). Sustained dechlorination of VC to ethene was achieved at pH as low as 5.5. Below pH 5.0, dechlorination was not stimulated by DMB supplementation but was restored by raising pH to neutral. Cell-extract assays revealed that vinyl chloride reductase activity declines significantly below pH 6.0 and is undetectable below pH 5.0. This study highlights the importance of cobamide-producing populations and pH in microbial dechlorinating communities for successful bioremediation at field sites.
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Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Yi Xuan Jine-Jine Li
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - M Ahsanul Islam
- 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
- Department of Cell and Systems Biology , University of Toronto , Toronto , Ontario M5S 3G5 , Canada
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26
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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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Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater. Sci Rep 2019; 9:10604. [PMID: 31332202 PMCID: PMC6646388 DOI: 10.1038/s41598-019-46901-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/10/2019] [Indexed: 12/15/2022] Open
Abstract
Dehalococcoides mccartyi (Dhc) bacterial strains expressing active reductive dehalogenase (RDase) enzymes play key roles in the transformation and detoxification of chlorinated pollutants, including chlorinated ethenes. Site monitoring regimes traditionally rely on qPCR to assess the presence of Dhc biomarker genes; however, this technique alone cannot directly inform about dechlorination activity. To supplement gene-centric approaches and provide a more reliable proxy for dechlorination activity, we sought to demonstrate a targeted proteomics approach that can characterize Dhc mediated dechlorination in groundwater contaminated with chlorinated ethenes. Targeted peptide selection was conducted in axenic cultures of Dhc strains 195, FL2, and BAV1. These experiments yielded 37 peptides from housekeeping and structural proteins (i.e., GroEL, EF-TU, rpL7/L2 and the S-layer), as well as proteins involved in the reductive dechlorination activity (i.e., FdhA, TceA, and BvcA). The application of targeted proteomics to a defined bacterial consortium and contaminated groundwater samples resulted in the detection of FdhA peptides, which revealed active dechlorination with Dhc strain-level resolution, and the detection of RDases peptides indicating specific reductive dechlorination steps. The results presented here show that targeted proteomics can be applied to groundwater samples and provide protein level information about Dhc dechlorination activity.
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Chevallier ML, Della-Negra O, Chaussonnerie S, Barbance A, Muselet D, Lagarde F, Darii E, Ugarte E, Lescop E, Fonknechten N, Weissenbach J, Woignier T, Gallard JF, Vuilleumier S, Imfeld G, Le Paslier D, Saaidi PL. Natural Chlordecone Degradation Revealed by Numerous Transformation Products Characterized in Key French West Indies Environmental Compartments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:6133-6143. [PMID: 31082212 DOI: 10.1021/acs.est.8b06305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Production and use of the insecticide chlordecone has caused long-term environmental pollution in the James River area and the French West Indies (FWI) that has resulted in acute human-health problems and a social crisis. High levels of chlordecone in FWI soils, even after its ban decades ago, and the absence of detection of transformation products (TPs), have suggested that chlordecone is virtually nonbiodegradable in the environment. Here, we investigated laboratory biodegradation, consisting of bacterial liquid cultures and microcosms inoculated with FWI soils, using a dual nontargeted GC-MS and LC-HRMS approach. In addition to previously reported, partly characterized hydrochlordecones and polychloroindenes (families A and B), we discovered 14 new chlordecone TPs, assigned to four families (B, C, D, and E). Organic synthesis and NMR analyses allowed us to achieve the complete structural elucidation of 19 TPs. Members of TP families A, B, C, and E were detected in soil, sediment, and water samples from Martinique and include 17 TPs not initially found in commercial chlordecone formulations. 2,4,5,6,7-Pentachloroindene was the most prominent TP, with levels similar to those of chlordecone. Overall, our results clearly show that chlordecone pollution extends beyond the parent chlordecone molecule and includes a considerable number of previously undetected TPs. Structural diversity of the identified TPs illustrates the complexity of chlordecone degradation in the environment and raises the possibility of extensive worldwide pollution of soil and aquatic ecosystems by chlordecone TPs.
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Affiliation(s)
- Marion L Chevallier
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Oriane Della-Negra
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Sébastien Chaussonnerie
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Agnès Barbance
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Delphine Muselet
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Florian Lagarde
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Ekaterina Darii
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Edgardo Ugarte
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS - UPR , 2301 Bâtiment 27, 1 avenue de la Terrasse , 91198 Gif-sur-Yvette Cedex, France
| | - Nuria Fonknechten
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Jean Weissenbach
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Thierry Woignier
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE , Avenue Escadrille Normandie Niemen , 13397 Marseille , France
- IRD, UMR IMBE , Campus Agro Environnemental Caraïbes B. P. 214 Petit Morne , 97235 Le Lamentin, Martinique , France
| | - Jean-François Gallard
- Institut de Chimie des Substances Naturelles, CNRS - UPR , 2301 Bâtiment 27, 1 avenue de la Terrasse , 91198 Gif-sur-Yvette Cedex, France
| | - Stéphane Vuilleumier
- Génétique Moléculaire, Génomique, Microbiologie (GMGM) , Université de Strasbourg, UMR 7156 CNRS , 4 allée Konrad Roentgen , 67000 Strasbourg , France
| | - Gwenaël Imfeld
- Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS) , Université de Strasbourg , UMR 7517 CNRS/EOST, 1 Rue Blessig , 67084 Strasbourg Cedex, France
| | - Denis Le Paslier
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
| | - Pierre-Loïc Saaidi
- Génomique Métabolique, Genoscope , Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay , 91057 , Evry , France
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Lihl C, Douglas LM, Franke S, Pérez-de-Mora A, Meyer AH, Daubmeier M, Edwards EA, Nijenhuis I, Sherwood Lollar B, Elsner M. Mechanistic Dichotomy in Bacterial Trichloroethene Dechlorination Revealed by Carbon and Chlorine Isotope Effects. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4245-4254. [PMID: 30857389 DOI: 10.1021/acs.est.8b06643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Tetrachloroethene (PCE) and trichloroethene (TCE) are significant groundwater contaminants. Microbial reductive dehalogenation at contaminated sites can produce nontoxic ethene but often stops at toxic cis-1,2-dichloroethene ( cis-DCE) or vinyl chloride (VC). The magnitude of carbon relative to chlorine isotope effects (as expressed by ΛC/Cl, the slope of δ13C versus δ37Cl regressions) was recently recognized to reveal different reduction mechanisms with vitamin B12 as a model reactant for reductive dehalogenase activity. Large ΛC/Cl values for cis-DCE reflected cob(I)alamin addition followed by protonation, whereas smaller ΛC/Cl values for PCE evidenced cob(I)alamin addition followed by Cl- elimination. This study addressed dehalogenation in actual microorganisms and observed identical large ΛC/Cl values for cis-DCE (ΛC/Cl = 10.0 to 17.8) that contrasted with identical smaller ΛC/Cl for TCE and PCE (ΛC/Cl = 2.3 to 3.8). For TCE, the trend of small ΛC/Cl could even be reversed when mixed cultures were precultivated on VC or DCEs and subsequently confronted with TCE (ΛC/Cl = 9.0 to 18.2). This observation provides explicit evidence that substrate adaptation must have selected for reductive dehalogenases with different mechanistic motifs. The patterns of ΛC/Cl are consistent with practically all studies published to date, while the difference in reaction mechanisms offers a potential answer to the long-standing question of why bioremediation frequently stalls at cis-DCE.
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Affiliation(s)
- Christina Lihl
- Institute of Groundwater Ecology , Helmholtz Zentrum München , Ingolstädter Landstrasse 1 , 85764 Neuherberg , Germany
| | - Lisa M Douglas
- Department of Earth Sciences , University of Toronto , Toronto , Ontario M5S 3B5 , Canada
| | - Steffi Franke
- Department for Isotope Biogeochemistry , Helmholtz-Centre for Environmental Research, UFZ , Permoserstrasse 15 , 04318 Leipzig , Germany
| | - Alfredo Pérez-de-Mora
- Institute of Groundwater Ecology , Helmholtz Zentrum München , Ingolstädter Landstrasse 1 , 85764 Neuherberg , Germany
| | - Armin H Meyer
- Institute of Groundwater Ecology , Helmholtz Zentrum München , Ingolstädter Landstrasse 1 , 85764 Neuherberg , Germany
| | - Martina Daubmeier
- Institute of Groundwater Ecology , Helmholtz Zentrum München , Ingolstädter Landstrasse 1 , 85764 Neuherberg , Germany
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Ivonne Nijenhuis
- Department for Isotope Biogeochemistry , Helmholtz-Centre for Environmental Research, UFZ , Permoserstrasse 15 , 04318 Leipzig , Germany
| | | | - Martin Elsner
- Institute of Groundwater Ecology , Helmholtz Zentrum München , Ingolstädter Landstrasse 1 , 85764 Neuherberg , Germany
- Chair of Analytical Chemistry and Water Chemistry , Technical University of Munich , Marchioninistrasse 17 , 81377 Munich , Germany
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30
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Xu G, Lu Q, Yu L, Wang S. Tetrachloroethene primes reductive dechlorination of polychlorinated biphenyls in a river sediment microcosm. WATER RESEARCH 2019; 152:87-95. [PMID: 30665163 DOI: 10.1016/j.watres.2018.12.061] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/02/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
Halo-priming is an effective approach to initiate microbial reductive dechlorination of polychlorinated biphenyls (PCBs) at contaminated sites, of which the application has been restricted by introducing extra pollutants generated from priming organohalides. In this study, tetrachloroethene (PCE) was demonstrated to be an effective priming compound to enhance PCB dechlorination both in a PCB-dechlorinating pure culture and a river sediment microcosm. In the isolated PCB-dechlorinating Dehalococcoides mccartyi CG1, PCB dechlorination activities were stimulated by adding 0.05-0.2 mM PCE, and were inhibited when further increasing PCE concentrations. Both in vivo and in vitro experiments showed that PCBs and PCE were synchronously dechlorinated in D. mccartyi CG1. In a river sediment microcosm, which was established to mimic in situ biostimulation of PCB dechlorination, 0.2 mM PCE could significantly improve para-chlorine removal from both PCB180 (2345-245-CB) and Aroclor 1260, and increase the relative abundance of indigenous dechlorinating Dehalococcoides for more than 20 times (from <0.1% to 2.3-5.0%). At the same time, PCE as a priming compound was completely dechlorinated to non-toxic ethene. Overall, this study provided an efficient strategy to stimulate in situ bioremediation of PCBs.
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Affiliation(s)
- Guofang Xu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Qihong Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China; Environmental Microbiome Research Center, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Ling Yu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China; Environmental Microbiome Research Center, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Shanquan Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China; Environmental Microbiome Research Center, Sun Yat-Sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510006, China.
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31
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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 2019; 12:346-359. [PMID: 30549216 PMCID: PMC6389850 DOI: 10.1111/1751-7915.13339] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [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 MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Stephan H. von Reuß
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyHans‐Knöll‐Straße 8D‐07745JenaGermany
- Present address:
Laboratory for Bioanalytical ChemistryInstitute of ChemistryUniversity of NeuchâtelAvenue de Bellevaux 512000NeuchâtelSwitzerland
| | - Cindy Kunze
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
- Present address:
DECHEMA‐ForschungsinstitutTheodor‐Heuss‐Allee 25D‐60486Frankfurt am MainGermany
| | - Christian Paetz
- Research Group Biosynthesis/NMRMax Planck Institute for Chemical EcologyHans‐Knöll‐Straße 8D‐07745JenaGermany
| | - Stefan Kruse
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Peggy Brand‐Schön
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Anita Mac Nelly
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Jörg Nüske
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Gabriele Diekert
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
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32
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Türkowsky D, Jehmlich N, Diekert G, Adrian L, von Bergen M, Goris T. An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research. FEMS Microbiol Ecol 2019; 94:4830072. [PMID: 29390082 DOI: 10.1093/femsec/fiy013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
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33
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Yin Y, Yan J, Chen G, Murdoch FK, Pfisterer N, Löffler FE. Nitrous Oxide Is a Potent Inhibitor of Bacterial Reductive Dechlorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:692-701. [PMID: 30558413 PMCID: PMC6944068 DOI: 10.1021/acs.est.8b05871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Organohalide-respiring bacteria are key players for the turnover of organohalogens. At sites impacted with chlorinated ethenes, bioremediation promotes reductive dechlorination; however, stoichiometric conversion to environmentally benign ethene is not always achieved. We demonstrate that nitrous oxide (N2O), a compound commonly present in groundwater, inhibits organohalide respiration. N2O concentrations in the low micromolar range decreased dechlorination rates and resulted in incomplete dechlorination of tetrachloroethene (PCE) in Geobacter lovleyi strain SZ and of cis-1,2-dichloroethene ( cDCE) and vinyl chloride (VC) in Dehalococcoides mccartyi strain BAV1 axenic cultures. Presumably, N2O interferes with reductive dechlorination by reacting with super-reduced Co(I)-corrinoids of reductive dehalogenases, which is supported by the finding that N2O did not inhibit corrinoid-independent fumarate-to-succinate reduction in strain SZ. Kinetic analyses revealed a best fit to the noncompetitive Michaelis-Menten inhibition model and determined N2O inhibitory constants, KI, for PCE and cDCE dechlorination of 40.8 ± 3.8 and 21.2 ± 3.5 μM in strain SZ and strain BAV1, respectively. The lowest KI value of 9.6 ± 0.4 μM was determined for VC to ethene reductive dechlorination in strain BAV1, suggesting that this crucial dechlorination step for achieving detoxification is most susceptible to N2O inhibition. Groundwater N2O concentrations exceeding 100 μM are not uncommon, especially in watersheds impacted by nitrate runoff from agricultural sources. Thus, dissolved N2O measurements can inform about cDCE and VC stalls at sites impacted with chlorinated ethenes.
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Affiliation(s)
- Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jun Yan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Liaoning 110016, People’s Republic of China
| | - Gao Chen
- 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
| | - Fadime Kara Murdoch
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nina Pfisterer
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Frank E. Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- 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 Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Corresponding Author: Phone: (865) 974-4933.
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34
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Niño de Guzmán GT, Hapeman CJ, Millner PD, Torrents A, Jackson D, Kjellerup BV. Presence of organohalide-respiring bacteria in and around a permeable reactive barrier at a trichloroethylene-contaminated Superfund site. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:766-776. [PMID: 30228068 DOI: 10.1016/j.envpol.2018.08.095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/29/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Trichloroethylene (TCE) is one of the most common groundwater contaminants in the United States; however clean-up efforts are a challenge due to its physical and chemical properties. TCE and several of its degradation products were detected in the groundwater of the Beaver Dam Road Landfill site (Beltsville, MD) at concentrations above accepted maximum contaminant levels. A permeable reactive barrier (i.e., biowall) was installed to remediate the groundwater. Microbial infiltration and colonization of the biowall with native site bacteria was expected to occur. An array of molecular biological tools was applied to survey the microbial community for presence of organohalide-respiring microorganisms at the site. Microorganisms belonging to methanogens, acetogens, sulfate-reducing bacteria, and chlorinated aliphatic hydrocarbon-metabolizing bacteria were identified, thus making way for the application of the microbial populations in the biowall bioaugmentation efforts. In concomitant laboratory studies, molecular approaches were used to monitor continuously-fed column reactors containing saturated biowall material spiked with a commercially-available, Dehalococcoides-containing culture (SDC-9), with or without zero-valent iron (ZVI) shavings. The column without ZVI had the highest abundance of Dehalococcoides spp. (2.7 × 106 cells g-1 material, S.D. = 3.8 × 105 cells g-1 material), while the addition of ZVI did not affect the overall population. Although the addition of ZVI and biostimulation did change ratios of the Dehalococcoides strains, the results suggests that if ZVI would be applied as a biowall material amendment, biostimulation would not be required to maintain a Dehalococcoides population. These experimental results will be utilized in future remediation and/or biowall expansion plans to utilize the natural resources most effectively at the biowall site.
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Affiliation(s)
| | - Cathleen J Hapeman
- US Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Patricia D Millner
- US Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Alba Torrents
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA
| | - Dana Jackson
- US Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Birthe V Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA.
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35
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Marcet TF, Cápiro NL, Yang Y, Löffler FE, Pennell KD. Impacts of low-temperature thermal treatment on microbial detoxification of tetrachloroethene under continuous flow conditions. WATER RESEARCH 2018; 145:21-29. [PMID: 30114555 DOI: 10.1016/j.watres.2018.07.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 07/20/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Coupling in situ thermal treatment (ISTT) with microbial reductive dechlorination (MRD) has the potential to enhance contaminant degradation and reduce cleanup costs compared to conventional standalone remediation technologies. Impacts of low-temperature ISTT on Dehalococcoides mccartyi (Dhc), a relevant species in the anaerobic degradation of cis-1,2-dichloroethene (cis-DCE) and vinyl chloride (VC) to nontoxic ethene, were assessed in sand-packed columns under dynamic flow conditions. Dissolved tetrachloroethene (PCE; 258 ± 46 μM) was introduced to identical columns bioaugmented with the PCE-to-ethene dechlorinating consortium KB-1®. Initial column temperatures represented a typical aquifer (15 °C) or a site undergoing low-temperature ISTT (35 °C), and were subsequently increased to 35 and 74 °C, respectively, to assess temperature impacts on reductive dechlorination activity. In the 15 °C column, PCE was transformed primarily to cis-DCE (159 ± 2 μM), which was further degraded to VC (164 ± 3 μM) and ethene (30 ± 0 μM) within 17 pore volumes (PVs) after the temperature was increased to 35 °C. Regardless of the initial column temperature, ethene constituted >50 mol% of effluent degradation products in both columns after 73-74 PVs at 35 °C, indicating that MRD performance was greatly improved under low-temperature ISTT conditions. Increasing the temperature of the column initially at 35 °C resulted in continued VC and ethene production until a temperature of approximately 43 °C was reached, at which point Dhc activity substantially decreased. The abundance of the vcrA reductive dehalogenase gene exceeded that of the bvcA gene by 1-2.5 orders of magnitude at 15 °C, but this relationship inversed at temperatures >35 °C, suggesting Dhc strain-specific responses to temperature. These findings demonstrate improved MRD performance with low-temperature thermal treatment and emphasize potential synergistic effects at sites undergoing ISTT.
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Affiliation(s)
- Tyler F Marcet
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA 02155, United States
| | - Natalie L Cápiro
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA 02155, United States.
| | - Yi Yang
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States
| | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States; Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, TN 37996, United States; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Kurt D Pennell
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA 02155, United States; School of Engineering, Brown University, Providence, RI 02912, United States.
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36
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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: 118] [Impact Index Per Article: 19.7] [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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37
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Wilmoth JL, Moran MA, Thompson A. Transient O 2 pulses direct Fe crystallinity and Fe(III)-reducer gene expression within a soil microbiome. MICROBIOME 2018; 6:189. [PMID: 30352628 PMCID: PMC6199725 DOI: 10.1186/s40168-018-0574-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Many environments contain redox transition zones, where transient oxygenation events can modulate anaerobic reactions that influence the cycling of iron (Fe) and carbon (C) on a global scale. In predominantly anoxic soils, this biogeochemical cycling depends on Fe mineral composition and the activity of mixed Fe(III)-reducer populations that may be altered by periodic pulses of molecular oxygen (O2). METHODS We repeatedly exposed anoxic (4% H2:96% N2) suspensions of soil from the Luquillo Critical Zone Observatory to 1.05 × 102, 1.05 × 103, and 1.05 × 104 mmol O2 kg-1 soil h-1 during pulsed oxygenation treatments. Metatranscriptomic analysis and 57Fe Mössbauer spectroscopy were used to investigate changes in Fe(III)-reducer gene expression and Fe(III) crystallinity, respectively. RESULTS Slow oxygenation resulted in soil Fe-(oxyhydr)oxides of higher crystallinity (38.1 ± 1.1% of total Fe) compared to fast oxygenation (30.6 ± 1.5%, P < 0.001). Transcripts binning to the genomes of Fe(III)-reducers Anaeromyxobacter, Geobacter, and Pelosinus indicated significant differences in extracellular electron transport (e.g., multiheme cytochrome c, multicopper oxidase, and type-IV pilin gene expression), adhesion/contact (e.g., S-layer, adhesin, and flagellin gene expression), and selective microbial competition (e.g., bacteriocin gene expression) between the slow and fast oxygenation treatments during microbial Fe(III) reduction. These data also suggest that diverse Fe(III)-reducer functions, including cytochrome-dependent extracellular electron transport, are associated with type-III fibronectin domains. Additionally, the metatranscriptomic data indicate that Methanobacterium was significantly more active in the reduction of CO2 to CH4 and in the expression of class(III) signal peptide/type-IV pilin genes following repeated fast oxygenation compared to slow oxygenation. CONCLUSIONS This study demonstrates that specific Fe(III)-reduction mechanisms in mixed Fe(III)-reducer populations are uniquely sensitive to the rate of O2 influx, likely mediated by shifts in soil Fe(III)-(oxyhydr)oxide crystallinity. Overall, we provide evidence that transient oxygenation events play an important role in directing anaerobic pathways within soil microbiomes, which is expected to alter Fe and C cycling in redox-dynamic environments.
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Affiliation(s)
- Jared Lee Wilmoth
- Department of Crop and Soil Sciences, University of Georgia, Athens, 30602, GA, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Aaron Thompson
- Department of Crop and Soil Sciences, University of Georgia, Athens, 30602, GA, USA.
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38
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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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39
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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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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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Heckel B, McNeill K, Elsner M. Chlorinated Ethene Reactivity with Vitamin B12 Is Governed by Cobalamin Chloroethylcarbanions as Crossroads of Competing Pathways. ACS Catal 2018. [DOI: 10.1021/acscatal.7b02945] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Benjamin Heckel
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, D-81377 Munich, Germany
| | - Kristopher McNeill
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, CH-8092 Zurich, Switzerland
| | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, D-81377 Munich, Germany
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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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43
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Yang Y, Higgins SA, Yan J, Şimşir B, Chourey K, Iyer R, Hettich RL, Baldwin B, Ogles DM, Löffler FE. Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes. ISME JOURNAL 2017; 11:2767-2780. [PMID: 28809851 DOI: 10.1038/ismej.2017.127] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 06/12/2017] [Accepted: 06/16/2017] [Indexed: 12/15/2022]
Abstract
Organohalide-respiring bacteria have key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene. 16S rRNA gene amplicon and qPCR analyses revealed a predominance of Dhgm sequences, but Dehalococcoides mccartyi (Dhc) biomarker genes were not detected. The enumeration of Dhgm 16S rRNA genes demonstrated VC-dependent growth, and 6.55±0.64 × 108 cells were measured per μmole of chloride released. Metagenome sequencing enabled the assembly of a Dhgm draft genome, and 52 putative reductive dehalogenase (RDase) genes were identified. Proteomic workflows identified a putative VC RDase with 49 and 56.1% amino acid similarity to the known VC RDases VcrA and BvcA, respectively. A survey of 1,173 groundwater samples collected from 111 chlorinated solvent-contaminated sites in the United States and Australia revealed that Dhgm 16S rRNA genes were frequently detected and outnumbered Dhc in 65% of the samples. Dhgm are likely greater contributors to reductive dechlorination of chlorinated solvents in contaminated aquifers than is currently recognized, and non-polluted environments represent sources of organohalide-respiring bacteria with novel RDase genes.
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Affiliation(s)
- Yi Yang
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Steven A Higgins
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jun Yan
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Burcu Şimşir
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Robert L Hettich
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | | | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
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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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45
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Liang Y, Cook LJ, Mattes TE. Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13760-13774. [PMID: 28401391 DOI: 10.1007/s11356-017-8948-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
Assessment and monitoring of microbial community dynamics is useful when tracking the progress of vinyl chloride (VC) bioremediation strategies, particularly in dilute plumes where apparent VC attenuation rates are low. In a long-term field study, the abundance and the activity of microbial VC degraders were tracked in three monitoring wells (MW05, MW25, and MW19) along a dilute VC plume at Naval Air Station (NAS) Oceana. High-throughput sequencing of partial 16S ribosomal RNA (rRNA) genes and transcripts revealed diverse groundwater microbial communities and showed that methanotrophs and anaerobic respirers (e.g., methanogens, sulfate reducers, and iron reducers) were among the most active and abundant guilds. Quantitative PCR analysis showed that among bacterial guilds with a potential to contribute to VC biodegradation, methanotrophs were the most abundant and active microbial group. Ethene-oxidizing bacterial populations were less abundant and relatively inactive compared to methanotrophs. In MW19, expression of functional genes associated with both aerobic VC oxidation and anaerobic VC reduction was observed. Overall, our results reveal that the groundwater community contains various active bacterial guilds previously associated with metabolic and cometabolic VC degradation processes either under aerobic and anaerobic conditions that might have contributed to the slowly decreasing VC concentrations at the NAS Oceana site over the 6-year study period.
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Affiliation(s)
- Yi Liang
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Laura J Cook
- CH2M 5701 Cleveland Street Suite 200, Virginia Beach, VA, 23462, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA.
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46
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Schubert T. The organohalide-respiring bacterium Sulfurospirillum multivorans: a natural source for unusual cobamides. World J Microbiol Biotechnol 2017; 33:93. [DOI: 10.1007/s11274-017-2258-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/01/2017] [Indexed: 01/27/2023]
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47
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Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions. Appl Environ Microbiol 2017; 83:AEM.03508-16. [PMID: 28188205 DOI: 10.1128/aem.03508-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/04/2017] [Indexed: 12/21/2022] Open
Abstract
The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions.
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48
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Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. ISME JOURNAL 2016; 11:626-640. [PMID: 27898054 DOI: 10.1038/ismej.2016.158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/25/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022]
Abstract
Two novel chlorinated alkane-respiring Dehalobacter restrictus strains CF and DCA were isolated from the same enrichment culture, ACT-3, and characterized. The closed genomes of these highly similar sister strains were previously assembled from metagenomic sequence data and annotated. The isolation of the strains enabled experimental verification of predicted annotations, particularly focusing on irregularities or predicted gaps in central metabolic pathways and cofactor biosynthesis. Similar to D. restrictus strain PER-K23, strains CF and DCA require arginine, histidine and threonine for growth, although the corresponding biosynthesis pathways are predicted to be functional. Using strain CF to experimentally verify annotations, we determined that the predicted defective serine biosynthesis pathway can be rescued with a promiscuous serine hydroxymethyltransferase. Strain CF grew without added thiamine although the thiamine biosynthesis pathway is predicted to be absent; intracellular thiamine diphosphate, the cofactor of carboxylases in central metabolism, was not detected in cell extracts. Thus, strain CF may use amino acids to replenish central metabolites, portending entangled metabolite exchanges in ACT-3. Consistent with annotation, strain CF possesses a functional corrinoid biosynthesis pathway, demonstrated by increasing corrinoid content during growth and guided cobalamin biosynthesis in corrinoid-free medium. Chloroform toxicity to corrinoid-producing methanogens and acetogens may drive the conservation of corrinoid autotrophy in Dehalobacter strains. Heme detection in strain CF cell extracts suggests the 'archaeal' heme biosynthesis pathway also functions in anaerobic Firmicutes. This study reinforces the importance of incorporating enzyme promiscuity and cofactor availability in genome-scale functional predictions and identifies essential nutrient interdependencies in anaerobic dechlorinating microbial communities.
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49
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Ferrer A, Rivera J, Zapata C, Norambuena J, Sandoval Á, Chávez R, Orellana O, Levicán G. Cobalamin Protection against Oxidative Stress in the Acidophilic Iron-oxidizing Bacterium Leptospirillum Group II CF-1. Front Microbiol 2016; 7:748. [PMID: 27242761 PMCID: PMC4876134 DOI: 10.3389/fmicb.2016.00748] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/03/2016] [Indexed: 11/30/2022] Open
Abstract
Members of the genus Leptospirillum are aerobic iron-oxidizing bacteria belonging to the phylum Nitrospira. They are important members of microbial communities that catalyze the biomining of sulfidic ores, thereby solubilizing metal ions. These microorganisms live under extremely acidic and metal-loaded environments and thus must tolerate high concentrations of reactive oxygen species (ROS). Cobalamin (vitamin B12) is a cobalt-containing tetrapyrrole cofactor involved in intramolecular rearrangement reactions and has recently been suggested to be an intracellular antioxidant. In this work, we investigated the effect of the exogenous addition of cobalamin on oxidative stress parameters in Leptospirillum group II strain CF-1. Our results revealed that the external supplementation of cobalamin reduces the levels of intracellular ROSs and the damage to biomolecules, and also stimulates the growth and survival of cells exposed to oxidative stress exerted by ferric ion, hydrogen peroxide, chromate and diamide. Furthermore, exposure of strain CF-1 to oxidative stress elicitors resulted in the transcriptional activation of the cbiA gene encoding CbiA of the cobalamin biosynthetic pathway. Altogether, these data suggest that cobalamin plays an important role in redox protection of Leptospirillum strain CF-1, supporting survival of this microorganism under extremely oxidative environmental conditions. Understanding the mechanisms underlying the protective effect of cobalamin against oxidative stress may help to develop strategies to make biomining processes more effective.
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Affiliation(s)
- Alonso Ferrer
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Javier Rivera
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Claudia Zapata
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Javiera Norambuena
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Álvaro Sandoval
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Renato Chávez
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Omar Orellana
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile Santiago, Chile
| | - Gloria Levicán
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
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