1
|
Hernández-Ospina DA, Osorio-González CS, Miri S, Kaur Brar S. New perspectives on the anaerobic degradation of BTEX: Mechanisms, pathways, and intermediates. CHEMOSPHERE 2024; 361:142490. [PMID: 38821131 DOI: 10.1016/j.chemosphere.2024.142490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024]
Abstract
Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries posing significant health risks to humans and wildlife. Unlike conventional clean-up methods used, biological approaches such as bioremediation can provide a more energy and labour-efficient and environmentally friendly option for sensitive areas such as nature reserves and cities, protecting biodiversity and public health. BTEX contamination is often concentrated in the subsurface of these locations where oxygen is rapidly depleted, and biodegradation relies on anaerobic processes. Thus, it is critical to understand the anaerobic biodegradation characteristics as it has not been explored to a major extent. This review presents novel insights into the degradation mechanisms under anaerobic conditions and presents a detailed description and interconnection between them. BTEX degradation can follow four activation mechanisms: hydroxylation, carboxylation, methylation, and fumarate addition. Hydroxylation is one of the mechanisms that explains the transformation of benzene into phenol, toluene into benzyl alcohol or p-cresol, and ethylbenzene into 1-phenylethanol. Carboxylation to benzoate is thought to be the primary mechanism of degradation for benzene. Despite being poorly understood, benzene methylation has been also reported. Moreover, fumarate addition is the most widely reported mechanism, present in toluene, ethylbenzene, and xylene degradation. Further research efforts are required to better elucidate new and current alternative catabolic pathways. Likewise, a comprehensive analysis of the enzymes involved as well as the development of advance tools such as omic tools can reveal bottlenecks degradation steps and create more effective on-site strategies to address BTEX pollution.
Collapse
Affiliation(s)
- Diego A Hernández-Ospina
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, Canada, M3J 1P3
| | - Carlos S Osorio-González
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, Canada, M3J 1P3
| | - Saba Miri
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, Canada, M3J 1P3
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, Canada, M3J 1P3.
| |
Collapse
|
2
|
Zhang R, Ye Z, Guo X, Yang Y, Li G. Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater. ENVIRONMENT INTERNATIONAL 2024; 188:108755. [PMID: 38772206 DOI: 10.1016/j.envint.2024.108755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.
Collapse
Affiliation(s)
- Ruihuan Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhencheng Ye
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| |
Collapse
|
3
|
Ni S, Lv W, Ji Z, Wang K, Mei Y, Li Y. Progress of Crude Oil Gasification Technology Assisted by Microorganisms in Reservoirs. Microorganisms 2024; 12:702. [PMID: 38674646 PMCID: PMC11051786 DOI: 10.3390/microorganisms12040702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Crude oil gasification bacteria, including fermenting bacteria, hydrocarbon-oxidizing bacteria, reducing bacteria, and methanogenic bacteria, participate in multi-step reactions involving initial activation, intermediate metabolism, and the methanogenesis of crude oil hydrocarbons. These bacteria degrade crude oil into smaller molecules such as hydrogen, carbon dioxide, acetic acid, and formic acid. Ultimately, they convert it into methane, which can be utilized or stored as a strategic resource. However, the current challenges in crude oil gasification include long production cycles and low efficiency. This paper provides a summary of the microbial flora involved in crude oil gasification, the gasification metabolism pathways within reservoirs, and other relevant information. It specifically focuses on analyzing the factors that affect the efficiency of crude oil gasification metabolism and proposes suggestions for improving this efficiency. These studies deepen our understanding of the potential of reservoir ecosystems and provide valuable insights for future reservoir development and management.
Collapse
Affiliation(s)
- Shumin Ni
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Weifeng Lv
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
- State Key Laboratory of Enhanced Oil Recovery, Research Institute of Petroleum Exploration and Development, CNPC, Beijing 100083, China
| | - Zemin Ji
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Kai Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Yuhao Mei
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Yushu Li
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| |
Collapse
|
4
|
Hussain N, Muccee F, Hammad M, Mohiuddin F, Bunny SM, Shahab A. Molecular and metabolic characterization of petroleum hydrocarbons degrading Bacillus cereus. Pol J Microbiol 2024; 73:107-120. [PMID: 38437466 PMCID: PMC10911661 DOI: 10.33073/pjm-2024-012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Hydrocarbon constituents of petroleum are persistent, bioaccumulated, and bio-magnified in living tissues, transported to longer distances, and exert hazardous effects on human health and the ecosystem. Bioaugmentation with microorganisms like bacteria is an emerging approach that can mitigate the toxins from environmental sources. The present study was initiated to target the petroleum-contaminated soil of gasoline stations situated in Lahore. Petroleum degrading bacteria were isolated by serial dilution method followed by growth analysis, biochemical and molecular characterization, removal efficiency estimation, metabolites extraction, and GC-MS of the metabolites. Molecular analysis identified the bacterium as Bacillus cereus, which exhibited maximum growth at 72 hours and removed 75% petroleum. Biochemical characterization via the Remel RapID™ ONE panel system showed positive results for arginine dehydrolase (ADH), ornithine decarboxylase (ODC), lysine decarboxylase (LDC), o-nitrophenyl-β-D-galactosidase (ONPG), p-nitrophenyl-β-D-glucosidase (βGLU), p-nitrophenyl-N-acetyl-β-D-glucosaminidase (NAG), malonate (MAL), adonitol fermentation (ADON), and tryptophane utilization (IND). GC-MS-based metabolic profiling identified alcohols (methyl alcohol, o-, p- and m-cresols, catechol, and 3-methyl catechol), aldehydes (methanone, acetaldehyde, and m-tolualdehyde), carboxylic acid (methanoic acid, cis,cis-muconic acid, cyclohexane carboxylic acid and benzoic acid), conjugate bases of carboxylic acids (benzoate, cis,cis-muconate, 4-hydroxybenzoate, and pyruvate) and cycloalkane (cyclohexene). It suggested the presence of methane, methylcyclohexane, toluene, xylene, and benzene degradation pathways in B. cereus.
Collapse
Affiliation(s)
- Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain Campus, Al Ain, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi Campus, Abu Dhabi, United Arab Emirates
| | - Fatima Muccee
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
| | - Muhammad Hammad
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
| | - Farhan Mohiuddin
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
| | - Saboor Muarij Bunny
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
| | - Aansa Shahab
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, Pakistan
| |
Collapse
|
5
|
Zehnle H, Otersen C, Benito Merino D, Wegener G. Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin. Front Microbiol 2023; 14:1279865. [PMID: 37840718 PMCID: PMC10570749 DOI: 10.3389/fmicb.2023.1279865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.
Collapse
Affiliation(s)
- Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Carolin Otersen
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| |
Collapse
|
6
|
Heker I, Haberhauer G, Meckenstock RU. Naphthalene Carboxylation in the Sulfate-Reducing Enrichment Culture N47 Is Proposed to Proceed via 1,3-Dipolar Cycloaddition to the Cofactor Prenylated Flavin Mononucleotide. Appl Environ Microbiol 2023; 89:e0192722. [PMID: 36815794 PMCID: PMC10057960 DOI: 10.1128/aem.01927-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/12/2023] [Indexed: 02/24/2023] Open
Abstract
Polycyclic aromatic hydrocarbons are persistent pollutants of anthropogenic or natural origin in the environment and accumulate in anoxic habitats. In this study, we investigated the mechanism of the enzyme naphthalene carboxylase as a model reaction for polycyclic aromatic hydrocarbon activation by carboxylation. An enzyme assay was established with cell extracts of the highly enriched culture N47. In assays without addition of ATP, naphthalene carboxylase catalyzed a stable isotope exchange of the carboxyl group of naphthoate with 13C-labeled bicarbonate buffer, which can only occur via a partial backwards reaction of the naphthalene carboxylase reaction to an intermediate that does not include the carboxyl group. Hence, a new carboxyl group from the labeled bicarbonate is added upon forward reaction to the naphthoate. This indicates that the reaction mechanism consists of two or more steps and that at least the latter steps are reversible and ATP independent. Naphthalene carboxylation assays were carried out in deuterated buffer and revealed the incorporation of 0, 1, 2, or 3 deuterium atoms in the final product naphthoyl-coenzyme A, indicating that the reaction is fully reversible. Putative reaction mechanisms were tested by quantum mechanical calculations. The proposed mechanism of the reaction consists of three steps: the activation of the naphthalene by 1,3-dipolar cycloaddition of the cofactor prFMN to naphthalene, release of a proton and rearomatization producing a stable intermediate, and a carboxylation with a reverse 1,3-dipolar cycloaddition and cleavage of the bond to the cofactor producing 2-naphthoate. IMPORTANCE Pollution with polycyclic aromatic hydrocarbons poses a great hazard to humans and animals, with considerable long-term effects. The anaerobic degradation of polycyclic aromatic hydrocarbons in anoxic zones and anaerobic growth of such organisms is very slow, leading to only poor investigation of the degradation pathways, so far. In this work, we elucidated the mechanism of naphthalene carboxylase, a key enzyme in anaerobic naphthalene degradation. This is the first mechanism proposed for a carboxylase targeting nonsubstituted (polycyclic) aromatic compounds and can serve as a model for the initial activation reaction in the anaerobic degradation of benzene or nonsubstituted polycyclic aromatic hydrocarbons, as well as similar enzymatic reactions from the expanding class of UbiD-like (de)carboxylases.
Collapse
Affiliation(s)
- Isabelle Heker
- Institute for Environmental Microbiology and Biotechnology, Aquatic Microbiology, University Duisburg-Essen, Essen, Germany
| | - Gebhard Haberhauer
- Institute for Organic Chemistry, University Duisburg-Essen, Essen, Germany
| | - Rainer U. Meckenstock
- Institute for Environmental Microbiology and Biotechnology, Aquatic Microbiology, University Duisburg-Essen, Essen, Germany
| |
Collapse
|
7
|
Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
Collapse
Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| |
Collapse
|
8
|
Kaneshiro AK, Datar PM, Marsh ENG. Negative Cooperativity in the Mechanism of Prenylated-Flavin-Dependent Ferulic Acid Decarboxylase: A Proposal for a "Two-Stroke" Decarboxylation Cycle. Biochemistry 2023; 62:53-61. [PMID: 36521056 DOI: 10.1021/acs.biochem.2c00460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ferulic acid decarboxylase (FDC) catalyzes the reversible carboxylation of various substituted phenylacrylic acids to produce the correspondingly substituted styrenes and CO2. FDC is a member of the UbiD family of enzymes that use prenylated-FMN (prFMN) to catalyze decarboxylation reactions on aromatic rings and C-C double bonds. Although a growing number of prFMN-dependent enzymes have been identified, the mechanism of the reaction remains poorly understood. Here, we present a detailed pre-steady-state kinetic analysis of the FDC-catalyzed reaction of prFMN with both styrene and phenylacrylic acid. Based on the pattern of reactivity observed, we propose a "two-stroke" kinetic model in which negative cooperativity between the two subunits of the FDC homodimer plays an important and previously unrecognized role in catalysis. In this model, catalysis is initiated at the high-affinity active site, which reacts with phenylacrylate to yield, after decarboxylation, the covalently bound styrene-prFMN cycloadduct. In the second stage of the catalytic cycle, binding of the second substrate molecule to the low-affinity active site drives a conformational switch that interconverts the high-affinity and low-affinity active sites. This switching of affinity couples the energetically unfavorable cycloelimination of styrene from the first site with the energetically favorable cycloaddition and decarboxylation of phenylacrylate at the second site. We note as a caveat that, at this point, the complexity of the FDC kinetics leaves open other mechanistic interpretations and that further experiments will be needed to more firmly establish or refute our proposal.
Collapse
|
9
|
Castro AR, Martins G, Salvador AF, Cavaleiro AJ. Iron Compounds in Anaerobic Degradation of Petroleum Hydrocarbons: A Review. Microorganisms 2022; 10:2142. [PMID: 36363734 PMCID: PMC9695802 DOI: 10.3390/microorganisms10112142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 09/22/2023] Open
Abstract
Waste and wastewater containing hydrocarbons are produced worldwide by various oil-based industries, whose activities also contribute to the occurrence of oil spills throughout the globe, causing severe environmental contamination. Anaerobic microorganisms with the ability to biodegrade petroleum hydrocarbons are important in the treatment of contaminated matrices, both in situ in deep subsurfaces, or ex situ in bioreactors. In the latter, part of the energetic value of these compounds can be recovered in the form of biogas. Anaerobic degradation of petroleum hydrocarbons can be improved by various iron compounds, but different iron species exert distinct effects. For example, Fe(III) can be used as an electron acceptor in microbial hydrocarbon degradation, zero-valent iron can donate electrons for enhanced methanogenesis, and conductive iron oxides may facilitate electron transfers in methanogenic processes. Iron compounds can also act as hydrocarbon adsorbents, or be involved in secondary abiotic reactions, overall promoting hydrocarbon biodegradation. These multiple roles of iron are comprehensively reviewed in this paper and linked to key functional microorganisms involved in these processes, to the underlying mechanisms, and to the main influential factors. Recent research progress, future perspectives, and remaining challenges on the application of iron-assisted anaerobic hydrocarbon degradation are highlighted.
Collapse
Affiliation(s)
- Ana R. Castro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Gilberto Martins
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Andreia F. Salvador
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Ana J. Cavaleiro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| |
Collapse
|
10
|
Guo S, Toth CRA, Luo F, Chen X, Xiao J, Edwards EA. Transient Oxygen Exposure Causes Profound and Lasting Changes to a Benzene-Degrading Methanogenic Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13036-13045. [PMID: 36083837 PMCID: PMC9496526 DOI: 10.1021/acs.est.2c02624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
We investigated the impact of oxygen on a strictly anaerobic, methanogenic benzene-degrading enrichment culture derived decades ago from oil-contaminated sediment. The culture includes a benzene fermenter from Deltaproteobacteria candidate clade Sva0485 (referred to as ORM2) and methanogenic archaea. A one-time injection of 0.1 mL air , simulating a small leak into 30 mL batch culture bottle, had no measurable impact on benzene degradation rates, although retrospectively, a tiny enrichment of aerobic taxa was detected. A subsequent 100 times larger injection of air stalled methanogenesis and caused drastic perturbation of the microbial community. A benzene-degrading Pseudomonas became highly enriched and consumed all available oxygen. Anaerobic benzene-degrading ORM2 cell numbers plummeted during this time; re-growth and associated recovery of methanogenic benzene degradation took almost 1 year. These results highlight the oxygen sensitivity of this methanogenic culture and confirm that the mechanism for anaerobic biotransformation of benzene is independent of oxygen, fundamentally different from established aerobic pathways, and is carried out by distinct microbial communities. The study also highlights the importance of including microbial decay in characterizing and modeling mixed microbial communities.
Collapse
Affiliation(s)
| | | | | | - Xu Chen
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Johnny Xiao
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| |
Collapse
|
11
|
Natural Source Zone Depletion (NSZD) Quantification Techniques: Innovations and Future Directions. SUSTAINABILITY 2022. [DOI: 10.3390/su14127027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Natural source zone depletion (NSZD) is an emerging technique for sustainable and cost-effective bioremediation of light non-aqueous phase liquid (LNAPL) in oil spill sites. Depending on regulatory objectives, NSZD has the potential to be used as either the primary or sole LNAPL management technique. To achieve this goal, NSZD rate (i.e., rate of bulk LNAPL mass depletion) should be quantified accurately and precisely. NSZD has certain characteristic features that have been used as surrogates to quantify the NSZD rates. This review highlights the most recent trends in technology development for NSZD data collection and rate estimation, with a focus on the operational and technical advantages and limitations of the associated techniques. So far, four principal techniques are developed, including concentration gradient (CG), dynamic closed chamber (DCC), CO2 trap and thermal monitoring. Discussions revolving around two techniques, “CO2 trap” and “thermal monitoring”, are expanded due to the particular attention to them in the current industry. The gaps of knowledge relevant to the NSZD monitoring techniques are identified and the issues which merit further research are outlined. It is hoped that this review can provide researchers and practitioners with sufficient information to opt the best practice for the research and application of NSZD for the management of LNAPL impacted sites.
Collapse
|
12
|
Wang A, Shao P. Effects of Organic Maceral on Biogenic Coalbed Gas Generation from Bituminous Coal. ACS OMEGA 2022; 7:18139-18145. [PMID: 35664615 PMCID: PMC9161391 DOI: 10.1021/acsomega.2c01821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Clarifying the effect of organic maceral on biogenic coalbed gas generation is important to understand the mechanism of biogenic coalbed gas generation and to develop bioengineering of coalbed gas. Bituminous coals in the Huainan mining area of China were selected as the research object, and the organic macerals were enriched through manual separation and floatation-sedimentation experiments first. Then, the simulated biogas generation experiments were carried out by using raw coal, single vitrinite, and inertinite, respectively. The results showed that all the bituminous coal, vitrinite, and inertinite could be biodegraded to generate biogas. The gas production yield of vitrinite was11.5 mL/g, which was more than that of raw coal (9.8 mL/g) and inertinite (6.26 mL/g). The production processes showed the stage characteristics of rapid increase and continuous decrease, but the gas production peak of inertinite lagged behind that of raw coal and vitrinite. Vitrinite content was positively correlated with total gas production, while inertinite could inhibit biogas production. CH4 composition in simulated biogas from vitrinite was the most, and that from inertinite was the least, while there was a positive correlation between vitrinite content and CH4 composition. The above evidence showed that vitrinite in bituminous coal is more easily biodegradable. There were significant positive correlations between chloroform bitumen "A", H, and H/C to total gas production, and they can be used as important indicators to evaluate the output of coalbed biogas.
Collapse
Affiliation(s)
- Aikuan Wang
- Key
Laboratory of Coalbed Methane Resources & Reservoir Formation
Process, Ministry of Education, China University
of Mining & Technology, Xuzhou 221008, China
- School
of Resources and Geosciences, China University
of Mining & Technology, Xuzhou 221116, China
| | - Pei Shao
- Department
of Surveying and Planning, Shangqiu Normal
University, Shangqiu 476000, China
| |
Collapse
|
13
|
Haddad PG, Mura J, Castéran F, Guignard M, Ranchou-Peyruse M, Sénéchal P, Larregieu M, Isaure MP, Svahn I, Moonen P, Le Hécho I, Hoareau G, Chiquet P, Caumette G, Dequidt D, Cézac P, Ranchou-Peyruse A. Biological, geological and chemical effects of oxygen injection in underground gas storage aquifers in the setting of biomethane deployment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150690. [PMID: 34600980 DOI: 10.1016/j.scitotenv.2021.150690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/15/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
The last few years have seen the proliferation of anaerobic digestion plants to produce biomethane. Oxygen (O2) traces added to biogas during the desulfurization process are co-injected in the gas network and can be stored in Underground Gas Storage (UGS). However, there are no data available for the undesirable effects of O2 on these anoxic environments, especially on deep aquifers. In addition to mineral alteration, O2 can have an impact on the anaerobic autochthonous microbial life. In our study, the storage conditions of an UGS aquifer were reproduced in a high-pressure reactor and bio-geo-chemical interactions between the aqueous, gas and solid phases were studied. Sulfate was depleted from the liquid phase for three consecutive times during the first 130 days of incubation reproducing the storage conditions (36 °C, 60 bar, methane with 1% CO2). Sulfate-reducers, such as Desulfovibrionaceae, were identified from the high-pressure system. Simulations with PHREEQC were used to determine the thermodynamic equilibrium to confirm any gas consumption. CO2 quantities decreased in the gas phase, suggesting its use as carbon source by microbial life. Benzene and toluene, hydrocarbons found in traces and known to be biodegradable in storages, were monitored and a decrease of toluene was revealed and associated to the Peptococcaceae family. Afterwards, O2 was added as 1% of the gas phase, corresponding to the maximum quantity found in biomethane after desulfurization process. Re-oxidation of sulfide to sulfate was observed along with the end of sulfate reducing activity and toluene biodegradation and the disappearance of most of the community. H2 surprisingly appeared and accumulated as soon as hydrogenotrophic sulfate-reducers decreased. H2 would be produced via the necromass fermentation accomplished by microorganisms able to resist the oxic conditions of 4.42·10-4 mol.Kgw-1 of O2. The solid phase composed essentially of quartz, presented no remarkable changes.
Collapse
Affiliation(s)
- Perla G Haddad
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France
| | - Jean Mura
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France
| | - Franck Castéran
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France; Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France
| | - Marion Guignard
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Magali Ranchou-Peyruse
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France; Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Pascale Sénéchal
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, DMEX, Pau, France
| | - Marie Larregieu
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Isabelle Svahn
- Bordeaux Imaging Center (BIC), CNRS, Université de Bordeaux, Bordeaux, France
| | - Peter Moonen
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, DMEX, Pau, France
| | - Isabelle Le Hécho
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Guilhem Hoareau
- Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, TOTAL, LFCR, Pau, France
| | - Pierre Chiquet
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Teréga, Pau, France
| | - Guilhem Caumette
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Teréga, Pau, France
| | - David Dequidt
- STORENGY - Geosciences Department, Bois-Colombes, France
| | - Pierre Cézac
- Universite de Pau et Pays de l'Adour, E2S UPPA, LaTEP, Pau, France; Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France
| | - Anthony Ranchou-Peyruse
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, 64000 Pau, France; Universite de Pau et Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
| |
Collapse
|
14
|
Khot V, Zorz J, Gittins DA, Chakraborty A, Bell E, Bautista MA, Paquette AJ, Hawley AK, Novotnik B, Hubert CRJ, Strous M, Bhatnagar S. CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. Front Microbiol 2022; 12:764058. [PMID: 35069469 PMCID: PMC8767102 DOI: 10.3389/fmicb.2021.764058] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/08/2021] [Indexed: 02/04/2023] Open
Abstract
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.
Collapse
Affiliation(s)
- Varada Khot
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jackie Zorz
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Daniel A Gittins
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Anirban Chakraborty
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Emma Bell
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - María A Bautista
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Alexandre J Paquette
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K Hawley
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Breda Novotnik
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Casey R J Hubert
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marc Strous
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Srijak Bhatnagar
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
15
|
Phan HV, Kurisu F, Kiba K, Furumai H. Optimized Cultivation and Syntrophic Relationship of Anaerobic Benzene-Degrading Enrichment Cultures under Methanogenic Conditions. Microbes Environ 2021; 36. [PMID: 34433738 PMCID: PMC8446749 DOI: 10.1264/jsme2.me21028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Current challenges in the anaerobic bioremediation of benzene are the lack of capable cultures and limited knowledge on the biodegradation pathway. Under methanogenic conditions, benzene may be mineralized by syntrophic interactions between microorganisms, which are poorly understood. The present study developed an optimized formula for anoxic medium to successfully promote the growth of the putative benzene degrader Deltaproteobacterium Hasda-A and enhance the benzene degradation activity of methanogenic enrichment cultures. Within 70 d of incubation, the benzene degradation activity and relative abundance of Hasda-A in cultures in the new defined medium increased from 0.5 to >3 mg L–1 d–1 and from 2.5% to >17%, respectively. Together with Hasda-A, we found a strong positive relationship between the abundances of superphylum OD1 bacteria, three methanogens (Methanoregula, Methanolinea, and Methanosaeta) and benzene degradation activity. The syntrophic relationship between these microbial taxa and Hasda-A was then demonstrated in a correlation analysis of longitudinal data. The involvement of methanogenesis in anaerobic benzene mineralization was confirmed by inhibition experiments. The high benzene degradation activity and growth of Hasda-A were quickly recovered in successive dilutions of enrichment cultures, proving the feasibility of using the medium developed in the present study to produce highly capable cultures. The present results will facilitate practical applications in bioremediation and research on the molecular mechanisms underlying benzene activation and syntrophic interactions in benzene mineralization.
Collapse
Affiliation(s)
- Hop V Phan
- JSPS International Research Fellow, Research Center for Water Environment Technology, The University of Tokyo
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, The University of Tokyo
| | - Koichiro Kiba
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, The University of Tokyo
| |
Collapse
|
16
|
Marshall SA, Payne KAP, Fisher K, Titchiner GR, Levy C, Hay S, Leys D. UbiD domain dynamics underpins aromatic decarboxylation. Nat Commun 2021; 12:5065. [PMID: 34417452 PMCID: PMC8379154 DOI: 10.1038/s41467-021-25278-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
The widespread UbiD enzyme family utilises the prFMN cofactor to achieve reversible decarboxylation of acrylic and (hetero)aromatic compounds. The reaction with acrylic compounds based on reversible 1,3-dipolar cycloaddition between substrate and prFMN occurs within the confines of the active site. In contrast, during aromatic acid decarboxylation, substantial rearrangement of the substrate aromatic moiety associated with covalent catalysis presents a molecular dynamic challenge. Here we determine the crystal structures of the multi-subunit vanillic acid decarboxylase VdcCD. We demonstrate that the small VdcD subunit acts as an allosteric activator of the UbiD-like VdcC. Comparison of distinct VdcCD structures reveals domain motion of the prFMN-binding domain directly affects active site architecture. Docking of substrate and prFMN-adduct species reveals active site reorganisation coupled to domain motion supports rearrangement of the substrate aromatic moiety. Together with kinetic solvent viscosity effects, this establishes prFMN covalent catalysis of aromatic (de)carboxylation is afforded by UbiD dynamics.
Collapse
Affiliation(s)
- Stephen A. Marshall
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK ,grid.4991.50000 0004 1936 8948Present Address: Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Karl A. P. Payne
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl Fisher
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Gabriel R. Titchiner
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Colin Levy
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Sam Hay
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| |
Collapse
|
17
|
Toth CRA, Luo F, Bawa N, Webb J, Guo S, Dworatzek S, Edwards EA. Anaerobic Benzene Biodegradation Linked to the Growth of Highly Specific Bacterial Clades. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:7970-7980. [PMID: 34041904 DOI: 10.1021/acs.est.1c00508] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Reliance on bioremediation to remove benzene from anoxic environments has proven risky for decades but for unknown reasons. Research has revealed a strong link between anaerobic benzene biodegradation and the enrichment of highly specific microbes, including Thermincola in the family Peptococcaceae and the deltaproteobacterial Candidate Sva0485 clade. Using aquifer materials from Canadian Forces Base Borden, we compared five bioremediation approaches in batch microcosms. Under conditions simulating natural attenuation or sulfate biostimulation, benzene was not degraded after 1-2 years of incubation and no enrichment of known benzene-degrading microbes occurred. In contrast, nitrate-amended microcosms reported benzene biodegradation coincident with significant growth of Thermincola spp., along with a functional gene presumed to catalyze anaerobic benzene carboxylation (abcA). Inoculation with 2.5% of a methanogenic benzene-degrading consortium containing Sva0485 (Deltaproteobacteria ORM2) resulted in benzene biodegradation in the presence of sulfate or under methanogenic conditions. The presence of other hydrocarbon co-contaminants decreased the rates of benzene degradation by a factor of 2 to 4. Tracking the abundance of the abcA gene and 16S rRNA genes specific for benzene-degrading Thermincola and Sva0485 is recommended to monitor benzene bioremediation in anoxic groundwater systems to further uncover growth-rate-limiting conditions for these two intriguing phylotypes.
Collapse
Affiliation(s)
- Courtney R A Toth
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Nancy Bawa
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Jennifer Webb
- SiREM, 130 Stone Road West, Guelph, Ontario N1G 3Z2, Canada
| | - Shen Guo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | | | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| |
Collapse
|
18
|
Melkonian C, Fillinger L, Atashgahi S, da Rocha UN, Kuiper E, Olivier B, Braster M, Gottstein W, Helmus R, Parsons JR, Smidt H, van der Waals M, Gerritse J, Brandt BW, Röling WFM, Molenaar D, van Spanning RJM. High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. Commun Biol 2021; 4:530. [PMID: 33953314 PMCID: PMC8099898 DOI: 10.1038/s42003-021-01948-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.
Collapse
Affiliation(s)
- Chrats Melkonian
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Lucas Fillinger
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Esther Kuiper
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brett Olivier
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martin Braster
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willi Gottstein
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Jan Gerritse
- Unit Subsurface and Groundwater Systems, Deltares, Utrecht, The Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wilfred F M Röling
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rob J M van Spanning
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
19
|
Aleku GA, Roberts GW, Titchiner GR, Leys D. Synthetic Enzyme-Catalyzed CO 2 Fixation Reactions. CHEMSUSCHEM 2021; 14:1781-1804. [PMID: 33631048 PMCID: PMC8252502 DOI: 10.1002/cssc.202100159] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/25/2021] [Indexed: 05/11/2023]
Abstract
In recent years, (de)carboxylases that catalyze reversible (de)carboxylation have been targeted for application as carboxylation catalysts. This has led to the development of proof-of-concept (bio)synthetic CO2 fixation routes for chemical production. However, further progress towards industrial application has been hampered by the thermodynamic constraint that accompanies fixing CO2 to organic molecules. In this Review, biocatalytic carboxylation methods are discussed with emphases on the diverse strategies devised to alleviate the inherent thermodynamic constraints and their application in synthetic CO2 -fixation cascades.
Collapse
Affiliation(s)
- Godwin A. Aleku
- Department of BiochemistryUniversity of Cambridge80 Tennis Court RoadCambridgeCB2 1GAUK
| | - George W. Roberts
- Manchester Institute of BiotechnologyDepartment of ChemistryUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Gabriel R. Titchiner
- Manchester Institute of BiotechnologyDepartment of ChemistryUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - David Leys
- Manchester Institute of BiotechnologyDepartment of ChemistryUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| |
Collapse
|
20
|
Lee K, Ulrich A. Indigenous microbial communities in Albertan sediments are capable of anaerobic benzene biodegradation under methanogenic, sulfate-reducing, nitrate-reducing, and iron-reducing redox conditions. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:524-534. [PMID: 32892398 DOI: 10.1002/wer.1454] [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: 03/10/2020] [Revised: 08/13/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
Alberta is a major center for oil and gas production, and correspondingly harbors hundreds of unresolved contamination sites by environmental hazards such as benzene (C6 H6 ). Due to its cost-effectiveness, bioremediation has become a promising strategy for C6 H6 removal. Contamination sites typically take on an anaerobic context, which complicates the energetics of contamination sites and is a subject that is scarcely broached in studies of Albertan sediments. This study examines the innate potential for indigenous microbial communities in Albertan sediments to remove C6 H6 in a multitude of reduced conditions. Community profiles of these sediments were analyzed by 16S rRNA gene amplicon sequencing, and removal rates and reaction stoichiometries were observed by gas chromatography and ion chromatography. Organisms belonging to known primary degrader taxa were identified, including Geobacter (iron-reducing), and Peptococcaceae (nitrate-reducing). Furthermore, benzene removal patterns of the cultures were similar to those observed in previously reported microcosms, with lag times between 70 and 168 days and removal rates between 3.27 and 12.70 µM/day. Such information could support a more comprehensive survey of Albertan sediment consortia, which may eventually be utilized in informing future remediation efforts in the province. PRACTITIONER POINTS: ●Clay and sand sediments originating from Northern Alberta could remove benzene under methanogenic, sulfate-reducing, iron-reducing, and nitrate-reducing conditions. ●Degradation profiles were broadly comparable to those of reported cultures from other geographical locales. ●Key degrader taxa observed included Geobacter (Fe3+ -reducing) and Peptococcaceae ( NO 3 - -reducing). ●Knowledge gained can be the start of a more extensive survey of Albertan sediments. Eventually, this collection of information can be used to generate robust C6 H6 -degrading cultures that can be implemented for bioaugmentation and be implemented in informing remediation strategies in soil and water matrices for priority contamination cases such as leaking underground storage tanks and orphan wells.
Collapse
Affiliation(s)
- Korris Lee
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Ania Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
21
|
Payne KAP, Marshall SA, Fisher K, Rigby SEJ, Cliff MJ, Spiess R, Cannas DM, Larrosa I, Hay S, Leys D. Structure and Mechanism of Pseudomonas aeruginosa PA0254/HudA, a prFMN-Dependent Pyrrole-2-carboxylic Acid Decarboxylase Linked to Virulence. ACS Catal 2021; 11:2865-2878. [PMID: 33763291 PMCID: PMC7976604 DOI: 10.1021/acscatal.0c05042] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/04/2021] [Indexed: 11/29/2022]
Abstract
The UbiD family of reversible (de)carboxylases depends on the recently discovered prenylated-FMN (prFMN) cofactor for activity. The model enzyme ferulic acid decarboxylase (Fdc1) decarboxylates unsaturated aliphatic acids via a reversible 1,3-cycloaddition process. Protein engineering has extended the Fdc1 substrate range to include (hetero)aromatic acids, although catalytic rates remain poor. This raises the question how efficient decarboxylation of (hetero)aromatic acids is achieved by other UbiD family members. Here, we show that the Pseudomonas aeruginosa virulence attenuation factor PA0254/HudA is a pyrrole-2-carboxylic acid decarboxylase. The crystal structure of the enzyme in the presence of the reversible inhibitor imidazole reveals a covalent prFMN-imidazole adduct is formed. Substrate screening reveals HudA and selected active site variants can accept a modest range of heteroaromatic compounds, including thiophene-2-carboxylic acid. Together with computational studies, our data suggests prFMN covalent catalysis occurs via electrophilic aromatic substitution and links HudA activity with the inhibitory effects of pyrrole-2-carboxylic acid on P. aeruginosa quorum sensing.
Collapse
Affiliation(s)
- Karl A. P. Payne
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Stephen A. Marshall
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Stephen E. J. Rigby
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Reynard Spiess
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Diego M. Cannas
- Department of Chemistry, University of Manchester, Chemistry Building, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Igor Larrosa
- Department of Chemistry, University of Manchester, Chemistry Building, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
22
|
Taylor NM, Toth CRA, Collins V, Mussone P, Gieg LM. The Effect of an Adsorbent Matrix on Recovery of Microorganisms from Hydrocarbon-Contaminated Groundwater. Microorganisms 2021; 9:microorganisms9010090. [PMID: 33401442 PMCID: PMC7823327 DOI: 10.3390/microorganisms9010090] [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: 11/16/2020] [Revised: 12/11/2020] [Accepted: 12/24/2020] [Indexed: 01/04/2023] Open
Abstract
The microbial degradation of recalcitrant hydrocarbons is an important process that can contribute to the remediation of oil and gas-contaminated environments. Due to the complex structure of subsurface terrestrial environments, it is important to identify the microbial communities that may be contributing to biodegradation processes, along with their abilities to metabolize different hydrocarbons in situ. In this study, a variety of adsorbent materials were assessed for their ability to trap both hydrocarbons and microorganisms in contaminated groundwater. Of the materials tested, a porous polymer resin (Tenax-TA) recovered the highest diversity of microbial taxa in preliminary experiments and was selected for additional (microcosm-based) testing. Oxic and anoxic experiments were prepared with groundwater collected from a contaminated aquifer to assess the ability of Tenax-TA to adsorb two environmental hydrocarbon contaminants of interest (toluene and benzene) while simultaneously providing a surface for microbial growth and hydrocarbon biodegradation. Microorganisms in oxic microcosms completely degraded both targets within 14 days of incubation, while anoxically-incubated microorganisms metabolized toluene but not benzene in less than 80 days. Community analysis of Tenax-TA-associated microorganisms revealed taxa highly enriched in sessile hydrocarbon-degrading treatments, including Saprospiraceae, Azoarcus, and Desulfoprunum, which may facilitate hydrocarbon degradation. This study showed that Tenax-TA can be used as a matrix to effectively trap both microorganisms and hydrocarbons in contaminated environmental systems for assessing and studying hydrocarbon-degrading microorganisms of interest.
Collapse
Affiliation(s)
- Nicole M. Taylor
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada;
| | - Courtney R. A. Toth
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada;
| | - Victoria Collins
- Applied BioNanotechnology Industrial Research Chair Program, Northern Alberta Institute of Technology, 11762-106 Street, Edmonton, AB T5G 2R1, Canada; (V.C.); (P.M.)
| | - Paolo Mussone
- Applied BioNanotechnology Industrial Research Chair Program, Northern Alberta Institute of Technology, 11762-106 Street, Edmonton, AB T5G 2R1, Canada; (V.C.); (P.M.)
| | - Lisa M. Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada;
- Correspondence:
| |
Collapse
|
23
|
Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K. New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. Front Microbiol 2020; 11:590049. [PMID: 33304336 PMCID: PMC7701123 DOI: 10.3389/fmicb.2020.590049] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
Collapse
Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | | | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| |
Collapse
|
24
|
Zhang Z, Sun J, Guo H, Wang C, Fang T, Rogers MJ, He J, Wang H. Anaerobic biodegradation of phenanthrene by a newly isolated nitrate-dependent Achromobacter denitrificans strain PheN1 and exploration of the biotransformation processes by metabolite and genome analyses. Environ Microbiol 2020; 23:908-923. [PMID: 32812321 DOI: 10.1111/1462-2920.15201] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/15/2020] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread and harmful contaminants and are more persistent under anaerobic conditions. The bioremediation of PAHs in anaerobic zones has been enhanced by treating the contamination with nitrate, which is thermodynamically favourable, cost-effective, and highly soluble. However, anaerobic PAHs biotransformation processes that employ nitrate as an electron acceptor have not been fully explored. In this study, we investigated the anaerobic biotransformation of PAHs by strain PheN1, a newly isolated phenanthrene-degrading denitrifier, using phenanthrene as a model compound. PheN1 is phylogenetically closely related to Achromobacter denitrificans and reduces nitrate to nitrite (not N2 ) during the anaerobic phenanthrene degradation process. Phenanthrene biotransformation processes were detected using gas chromatography-mass spectrometry and were further examined by reverse transcription-quantitative PCR and genome analyses. Carboxylation and methylation were both found to be the initial steps in the phenanthrene degradation process. Downstream biotransformation processed benzene compounds and cyclohexane derivatives. This study describes the isolation of an anaerobic phenanthrene-degrading bacterium along with the pure-culture evidence of phenanthrene biotransformation processes with nitrate as an electron acceptor. The findings in this study can improve our understanding of anaerobic PAHs biodegradation processes and guide PAHs bioremediation by adding nitrate to anaerobic environments.
Collapse
Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Tingting Fang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| |
Collapse
|
25
|
Structure and Functions of Hydrocarbon-Degrading Microbial Communities in Bioelectrochemical Systems. WATER 2020. [DOI: 10.3390/w12020343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bioelectrochemical systems (BESs) exploit the interaction between microbes and electrodes. A field of application thereof is bioelectrochemical remediation, an effective strategy in environments where the absence of suitable electron acceptors limits classic bioremediation approaches. Understanding the microbial community structure and genetic potential of anode biofilms is of great interest to interpret the mechanisms occurring in BESs. In this study, by using a whole metagenome sequencing approach, taxonomic and functional diversity patterns in the inoculum and on the anodes of three continuous-flow BES for the removal of phenol, toluene, and BTEX were obtained. The genus Geobacter was highly enriched on the anodes and two reconstructed genomes were taxonomically related to the Geobacteraceae family. To functionally characterize the microbial community, the genes coding for the anaerobic degradation of toluene, ethylbenzene, and phenol were selected as genetic markers for the anaerobic degradation of the pollutants. The genes related with direct extracellular electron transfer (EET) were also analyzed. The inoculum carried the genetic baggage for the degradation of aromatics but lacked the capacity of EET while anodic bacterial communities were able to pursue both processes. The metagenomic approach provided useful insights into the ecology and complex functions within hydrocarbon-degrading electrogenic biofilms.
Collapse
|
26
|
Bailey SS, Payne KAP, Saaret A, Marshall SA, Gostimskaya I, Kosov I, Fisher K, Hay S, Leys D. Enzymatic control of cycloadduct conformation ensures reversible 1,3-dipolar cycloaddition in a prFMN-dependent decarboxylase. Nat Chem 2019; 11:1049-1057. [PMID: 31527849 PMCID: PMC6817360 DOI: 10.1038/s41557-019-0324-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/02/2019] [Indexed: 11/21/2022]
Abstract
The UbiD enzyme plays an important role in bacterial ubiquinone (coenzyme Q) biosynthesis. It belongs to a family of reversible decarboxylases that interconvert propenoic or aromatic acids with the corresponding alkenes or aromatic compounds using a prenylated flavin (prFMN) cofactor. This cofactor is suggested to support (de)carboxylation through a reversible 1,3-dipolar cycloaddition process. Here we report an atomic-level description of the reaction of the UbiD related ferulic acid decarboxylase with substituted propenoic and propiolic acids (data ranging from 1.01 to 1.39 Å). The enzyme is only able to couple (de)carboxylation of cinnamic acid-type compounds to reversible 1,3-dipolar cycloaddition, while formation of dead-end prFMN cycloadducts occurs with distinct propenoic and propiolic acids. The active site imposes considerable strain on covalent intermediates formed with cinnamic and phenylpropiolic acids. Strain reduction through mutagenesis negatively affects catalytic rates with cinnamic acid, indicating a direct link between enzyme-induced strain and catalysis that is supported by computational studies.
Collapse
Affiliation(s)
- Samuel S Bailey
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Karl A P Payne
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Annica Saaret
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Stephen A Marshall
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Irina Gostimskaya
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Iaroslav Kosov
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Karl Fisher
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK.
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK.
| |
Collapse
|
27
|
Payer SE, Faber K, Glueck SM. Non-Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives. Adv Synth Catal 2019; 361:2402-2420. [PMID: 31379472 PMCID: PMC6644310 DOI: 10.1002/adsc.201900275] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Indexed: 12/20/2022]
Abstract
The utilization of carbon dioxide as a C1-building block for the production of valuable chemicals has recently attracted much interest. Whereas chemical CO2 fixation is dominated by C-O and C-N bond forming reactions, the development of novel concepts for the carboxylation of C-nucleophiles, which leads to the formation of carboxylic acids, is highly desired. Beside transition metal catalysis, biocatalysis has emerged as an attractive method for the highly regioselective (de)carboxylation of electron-rich (hetero)aromatics, which has been recently further expanded to include conjugated α,β-unsaturated (acrylic) acid derivatives. Depending on the type of substrate, different classes of enzymes have been explored for (i) the ortho-carboxylation of phenols catalyzed by metal-dependent ortho-benzoic acid decarboxylases and (ii) the side-chain carboxylation of para-hydroxystyrenes mediated by metal-independent phenolic acid decarboxylases. Just recently, the portfolio of bio-carboxylation reactions was complemented by (iii) the para-carboxylation of phenols and the decarboxylation of electron-rich heterocyclic and acrylic acid derivatives mediated by prenylated FMN-dependent decarboxylases, which is the main focus of this review. Bio(de)carboxylation processes proceed under physiological reaction conditions employing bicarbonate or (pressurized) CO2 when running in the energetically uphill carboxylation direction. Aiming to facilitate the application of these enzymes in preparative-scale biotransformations, their catalytic mechanism and substrate scope are analyzed in this review.
Collapse
Affiliation(s)
- Stefan E. Payer
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Kurt Faber
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Silvia M. Glueck
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| |
Collapse
|
28
|
Marshall SA, Payne KAP, Fisher K, White MD, Ní Cheallaigh A, Balaikaite A, Rigby SEJ, Leys D. The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry. Nat Commun 2019; 10:2357. [PMID: 31142738 PMCID: PMC6541611 DOI: 10.1038/s41467-019-10220-1] [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: 01/28/2019] [Accepted: 04/23/2019] [Indexed: 11/09/2022] Open
Abstract
The UbiX-UbiD enzymes are widespread in microbes, acting in concert to decarboxylate alpha-beta unsaturated carboxylic acids using a highly modified flavin cofactor, prenylated FMN (prFMN). UbiX serves as the flavin prenyltransferase, extending the isoalloxazine ring system with a fourth non-aromatic ring, derived from sequential linkage between a dimethylallyl moiety and the FMN N5 and C6. Using structure determination and solution studies of both dimethylallyl monophosphate (DMAP) and dimethyallyl pyrophosphate (DMAPP) dependent UbiX enzymes, we reveal the first step, N5-C1' bond formation, is contingent on the presence of a dimethylallyl substrate moiety. Hence, an SN1 mechanism similar to other prenyltransferases is proposed. Selected variants of the (pyro)phosphate binding site are unable to catalyse subsequent Friedel-Crafts alkylation of the flavin C6, but can be rescued by addition of (pyro)phosphate. Thus, retention of the (pyro)phosphate leaving group is required for C6-C3' bond formation, resembling pyrophosphate initiated class I terpene cyclase reaction chemistry.
Collapse
Affiliation(s)
- Stephen A Marshall
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Karl A P Payne
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Mark D White
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, New South Wales, Australia
| | - Aisling Ní Cheallaigh
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
- Centre for Synthesis and Chemical Biology, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Arune Balaikaite
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Stephen E J Rigby
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.
| |
Collapse
|
29
|
Payne KA, Marshall SA, Fisher K, Cliff MJ, Cannas DM, Yan C, Heyes DJ, Parker DA, Larrosa I, Leys D. Enzymatic Carboxylation of 2-Furoic Acid Yields 2,5-Furandicarboxylic Acid (FDCA). ACS Catal 2019; 9:2854-2865. [PMID: 31057985 PMCID: PMC6497424 DOI: 10.1021/acscatal.8b04862] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/06/2019] [Indexed: 11/29/2022]
Abstract
![]()
The
biological production of FDCA is of considerable value as a potential
replacement for petrochemical-derived monomers such as terephthalate,
used in polyethylene terephthalate (PET) plastics. HmfF belongs to
an uncharacterized branch of the prenylated flavin (prFMN) dependent
UbiD family of reversible (de)carboxylases and is proposed to convert
2,5-furandicarboxylic acid (FDCA) to furoic acid in vivo. We present
a detailed characterization of HmfF and demonstrate that HmfF can
catalyze furoic acid carboxylation at elevated CO2 levels
in vitro. We report the crystal structure of a thermophilic HmfF from Pelotomaculum thermopropionicum, revealing that the
active site located above the prFMN cofactor contains a furoic acid/FDCA
binding site composed of residues H296-R304-R331 specific to the HmfF
branch of UbiD enzymes. Variants of the latter are compromised in
activity, while H296N alters the substrate preference to pyrrole compounds.
Solution studies and crystal structure determination of an engineered
dimeric form of the enzyme revealed an unexpected key role for a UbiD
family wide conserved Leu residue in activity. The structural insights
into substrate and cofactor binding provide a template for further
exploitation of HmfF in the production of FDCA plastic precursors
and improve our understanding of catalysis by members of the UbiD
enzyme family.
Collapse
Affiliation(s)
- Karl A.P. Payne
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Stephen A. Marshall
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Diego M. Cannas
- School of Chemistry, University of Manchester, Chemistry Building, Oxford Road, Manchester M13 9PL, U.K
| | - Cunyu Yan
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - David A. Parker
- Innovation/Biodomain, Shell International Exploration and Production, Westhollow Technology Center, 3333 Highway 6 South, Houston, Texas 77082-3101, United States
| | - Igor Larrosa
- School of Chemistry, University of Manchester, Chemistry Building, Oxford Road, Manchester M13 9PL, U.K
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| |
Collapse
|
30
|
Junghare M, Spiteller D, Schink B. Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME JOURNAL 2019; 13:1252-1268. [PMID: 30647456 DOI: 10.1038/s41396-019-0348-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 12/13/2022]
Abstract
Syntrophorhabdus aromaticivorans is a syntrophically fermenting bacterium that can degrade isophthalate (3-carboxybenzoate). It is a xenobiotic compound which has accumulated in the environment for more than 50 years due to its global industrial usage and can cause negative effects on the environment. Isophthalate degradation by the strictly anaerobic S. aromaticivorans was investigated to advance our understanding of the degradation of xenobiotics introduced into nature, and to identify enzymes that might have ecological significance for bioremediation. Differential proteome analysis of isophthalate- vs benzoate-grown cells revealed over 400 differentially expressed proteins of which only four were unique to isophthalate-grown cells. The isophthalate-induced proteins include a phenylacetate:CoA ligase, a UbiD-like decarboxylase, a UbiX-like flavin prenyltransferase, and a hypothetical protein. These proteins are encoded by genes forming a single gene cluster that putatively codes for anaerobic conversion of isophthalate to benzoyl-CoA. Subsequently, benzoyl-CoA is metabolized by the enzymes of the anaerobic benzoate degradation pathway that were identified in the proteomic analysis. In vitro enzyme assays with cell-free extracts of isophthalate-grown cells indicated that isophthalate is activated to isophthalyl-CoA by an ATP-dependent isophthalate:CoA ligase (IPCL), and subsequently decarboxylated to benzoyl-CoA by a UbiD family isophthalyl-CoA decarboxylase (IPCD) that requires a prenylated flavin mononucleotide (prFMN) cofactor supplied by UbiX to effect decarboxylation. Phylogenetic analysis revealed that IPCD is a novel member of the functionally diverse UbiD family (de)carboxylases. Homologs of the IPCD encoding genes are found in several other bacteria, such as aromatic compound-degrading denitrifiers, marine sulfate-reducers, and methanogenic communities in a terephthalate-degrading reactor. These results suggest that metabolic strategies adapted for degradation of isophthalate and other phthalate are conserved between microorganisms that are involved in the anaerobic degradation of environmentally relevant aromatic compounds.
Collapse
Affiliation(s)
- Madan Junghare
- Microbial Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
| | - Dieter Spiteller
- Chemical Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Bernhard Schink
- Microbial Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| |
Collapse
|
31
|
Carboxylation of Hydroxyaromatic Compounds with HCO3− by Enzyme Catalysis: Recent Advances Open the Perspective for Valorization of Lignin-Derived Aromatics. Catalysts 2019. [DOI: 10.3390/catal9010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This review focuses on recent advances in the field of enzymatic carboxylation reactions of hydroxyaromatic compounds using HCO3− (as a CO2 source) to produce hydroxybenzoic and other phenolic acids in mild conditions with high selectivity and moderate to excellent yield. Nature offers an extensive portfolio of enzymes catalysing reversible decarboxylation of hydroxyaromatic acids, whose equilibrium can be pushed towards the side of the carboxylated products. Extensive structural and mutagenesis studies have allowed recent advances in the understanding of the reaction mechanism of decarboxylase enzymes, ultimately enabling an improved yield and expansion of the scope of the reaction. The topic is of particular relevance today as the scope of the carboxylation reactions can be extended to include lignin-related compounds in view of developing lignin biorefinery technology.
Collapse
|
32
|
Keller AH, Kleinsteuber S, Vogt C. Anaerobic Benzene Mineralization by Nitrate-Reducing and Sulfate-Reducing Microbial Consortia Enriched From the Same Site: Comparison of Community Composition and Degradation Characteristics. MICROBIAL ECOLOGY 2018; 75:941-953. [PMID: 29124312 DOI: 10.1007/s00248-017-1100-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/26/2017] [Indexed: 05/22/2023]
Abstract
Benzene mineralization under nitrate-reducing conditions was successfully established in an on-site reactor continuously fed with nitrate and sulfidic, benzene-containing groundwater extracted from a contaminated aquifer. Filling material from the reactor columns was used to set up anoxic enrichment cultures in mineral medium with benzene as electron donor and sole organic carbon source and nitrate as electron acceptor. Benzene degradation characteristics and community composition under nitrate-reducing conditions were monitored and compared to those of a well-investigated benzene-mineralizing consortium enriched from the same column system under sulfate-reducing conditions. The nitrate-reducing cultures degraded benzene at a rate of 10.1 ± 1.7 μM d-1, accompanied by simultaneous reduction of nitrate to nitrite. The previously studied sulfate-reducing culture degraded benzene at similar rates. Carbon and hydrogen stable isotope enrichment factors determined for nitrate-dependent benzene degradation differed significantly from those of the sulfate-reducing culture (ΛH/C nitrate = 12 ± 3 compared to ΛH/C sulfate = 28 ± 3), indicating different benzene activation mechanisms under the two conditions. The nitrate-reducing community was mainly composed of Betaproteobacteria, Ignavibacteria, and Anaerolineae. Azoarcus and a phylotype related to clone Dok59 (Rhodocyclaceae) were the dominant genera, indicating an involvement in nitrate-dependent benzene degradation. The primary benzene degrader of the sulfate-reducing consortium, a phylotype belonging to the Peptococcaceae, was absent in the nitrate-reducing consortium.
Collapse
Affiliation(s)
- Andreas H Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, 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.
| |
Collapse
|
33
|
A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways. Sci Rep 2018. [PMID: 29540736 PMCID: PMC5852087 DOI: 10.1038/s41598-018-22617-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.
Collapse
|
34
|
Qiao W, Luo F, Lomheim L, Mack EE, Ye S, Wu J, Edwards EA. Natural Attenuation and Anaerobic Benzene Detoxification Processes at a Chlorobenzene-Contaminated Industrial Site Inferred from Field Investigations and Microcosm Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:22-31. [PMID: 29178800 DOI: 10.1021/acs.est.7b04145] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A five-year site investigation was conducted at a former chemical plant in Nanjing, China. The main contaminants were 1,2,4-trichlorobenzene (TCB) reaching concentrations up to 7300 μg/L, dichlorobenzene (DCB) isomers, monochlorobenzene (MCB), and benzene. Over time, these contaminants naturally attenuated to below regulatory levels under anaerobic conditions. To confirm the transformation processes and to explore the mechanisms, a corresponding laboratory microcosm study was completed demonstrating that 1,2,4-TCB was dechlorinated to 1,2-DCB, 1,3-DCB, and 1,4-DCB in approximately 2%/10%/88% molar proportions. The DCB isomers were dechlorinated via MCB to benzene, and, finally, benzene was degraded under prevailing sulfate-reducing conditions. Dechlorination could not be attributed to known dechlorinators Dehalobacter or Dehalococcoides, while anaerobic benzene degradation was mediated by microbes affiliated to a Deltaproteobacterium ORM2, previously associated with this activity. Unidentified organic compounds, possibly aromatic compounds related to past on-site production processes, were fueling the dechlorination reactions in situ. The microcosm study confirmed transformation processes inferred from field data and provided needed assurance for natural attenuation. Activity-based microcosm studies are often omitted from site characterization in favor of rapid and less expensive molecular surveys. However, the value of microcosm studies for confirming transformation processes, establishing electron balances, assessing cocontaminant inhibition, and validating appropriate monitoring tools is clear. At complex sites impacted by multiple compounds with poorly characterized transformation mechanisms, activity assays provide valuable data to incorporate into the conceptual site model to most effectively inform remediation alternatives.
Collapse
Affiliation(s)
- Wenjing Qiao
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Elizabeth Erin Mack
- DuPont Corporate Remediation Group , Wilmington, Delaware 19805, United States
| | - Shujun Ye
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| |
Collapse
|
35
|
van der Waals MJ, Atashgahi S, da Rocha UN, van der Zaan BM, Smidt H, Gerritse J. Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition. Appl Microbiol Biotechnol 2017; 101:5175-5188. [PMID: 28321487 PMCID: PMC5486827 DOI: 10.1007/s00253-017-8214-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/27/2017] [Accepted: 03/04/2017] [Indexed: 11/26/2022]
Abstract
Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions. Benzene was degraded at a rate of 0.15 μmol/mg protein/day and a first-order rate constant of 3.04/day which was fourfold higher than rates reported previously. Bacteria belonging to the Peptococcaceae were found to play an important role in this anaerobic benzene-degrading biofilm culture, but also members of the Anaerolineaceae were predicted to be involved in benzene degradation or benzene metabolite degradation based on Illumina MiSeq analysis of 16S ribosomal RNA genes. Biomass retention in the reactor using a filtration finger resulted in reduction of benzene degradation capacity. Detection of the benzene carboxylase encoding gene, abcA, and benzoic acid in the culture vessel indicated that benzene degradation proceeds through an initial carboxylation step.
Collapse
Affiliation(s)
- Marcelle J van der Waals
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands.
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Siavash Atashgahi
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- VU University of Amsterdam, Department of Molecular Cell Physiology, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Bas M van der Zaan
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jan Gerritse
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| |
Collapse
|
36
|
Lin CI, McCarty RM, Liu HW. The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems. Angew Chem Int Ed Engl 2017; 56:3446-3489. [PMID: 27505692 PMCID: PMC5477795 DOI: 10.1002/anie.201603291] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 01/05/2023]
Abstract
Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as "name reactions". This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical-mediated, and rearrangements, which are subdivided by name reactions.
Collapse
Affiliation(s)
- Chia-I Lin
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Reid M McCarty
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| |
Collapse
|
37
|
Ranchou‐Peyruse M, Gasc C, Guignard M, Aüllo T, Dequidt D, Peyret P, Ranchou‐Peyruse A. The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer. Microb Biotechnol 2017; 10:469-479. [PMID: 27766749 PMCID: PMC5328808 DOI: 10.1111/1751-7915.12426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/15/2016] [Accepted: 09/18/2016] [Indexed: 01/04/2023] Open
Abstract
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation. In order to reveal the potential for biodegradation of these compounds within a shorter time frame, an innovative approach named the solution hybrid selection method, which combines sequence capture by hybridization and next-generation sequencing, was applied to the same original water sample. The bssA and bssA-like genes were investigated as they are considered good biomarkers for the potential of toluene and xylene biodegradation. Unlike a PCR approach which failed to detect these genes directly from formation water, this innovative strategy demonstrated the presence of the bssA and bssA-like genes in this oligotrophic ecosystem, probably harboured by Peptococcaceae. The sequence capture by hybridization shows significant potential to reveal the presence of genes of functional interest which have low-level representation in the biosphere.
Collapse
Affiliation(s)
- Magali Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Cyrielle Gasc
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Marion Guignard
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Thomas Aüllo
- TIGF – Transport et Infrastructures Gaz France40 Avenue de l'Europe, CS2052264000PauFrance
| | - David Dequidt
- STORENGY – Geosciences DepartmentBois‐ColombesFrance
| | - Pierre Peyret
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Anthony Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| |
Collapse
|
38
|
Lin C, McCarty RM, Liu H. Die Enzymologie organischer Umwandlungen: Namensreaktionen in biologischen Systemen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201603291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chia‐I. Lin
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Reid M. McCarty
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Hung‐wen Liu
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| |
Collapse
|
39
|
Lueders T. The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers. FEMS Microbiol Ecol 2016; 93:fiw220. [PMID: 27810873 PMCID: PMC5400083 DOI: 10.1093/femsec/fiw220] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/10/2016] [Indexed: 12/24/2022] Open
Abstract
The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ. 13C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation.
Collapse
Affiliation(s)
- Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| |
Collapse
|
40
|
Liu J, Wang B, Tai C, Wu L, Zhao H, Guan J, Chen L. An Effective Method to Detect Volatile Intermediates Generated in the Bioconversion of Coal to Methane by Gas Chromatography-Mass Spectrometry after In-Situ Extraction Using Headspace Solid-Phase Micro-Extraction under Strict Anaerobic Conditions. PLoS One 2016; 11:e0163949. [PMID: 27695055 PMCID: PMC5047463 DOI: 10.1371/journal.pone.0163949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 09/16/2016] [Indexed: 02/06/2023] Open
Abstract
Bioconversion of coal to methane has gained increased attention in recent decades because of its economic and environmental advantages. However, the mechanism of this process is difficult to study in depth, partly because of difficulties associated with the analysis of intermediates generated in coal bioconversion. In this investigation, we report on an effective method to analyze volatile intermediates generated in the bioconversion of coal under strict anaerobic conditions. We conduct in-situ extraction of intermediates using headspace solid-phase micro-extraction followed by detection by gas chromatography-mass spectrometry. Bioconversion simulation equipment was modified and combined with a solid-phase micro-extraction device. In-situ extraction could be achieved by using the combined units, to avoid a breakdown in anaerobic conditions and to maintain the experiment continuity. More than 30 intermediates were identified qualitatively in the conversion process, and the variation in trends of some typical intermediates has been discussed. Volatile organic acids (C2–C7) were chosen for a quantitative study of the intermediates because of their importance during coal bioconversion to methane. Fiber coating, extraction time, and solution acidity were optimized in the solid-phase micro-extraction procedure. The pressure was enhanced during the bioconversion process to investigate the influence of headspace pressure on analyte extraction. The detection limits of the method ranged from 0.0006 to 0.02 mmol/L for the volatile organic acids and the relative standard deviations were between 4.6% and 11.5%. The volatile organic acids (C2–C7) generated in the bioconversion process were 0.01–1.15 mmol/L with a recovery range from 80% to 105%. The developed method is useful for further in-depth research on the bioconversion of coal to methane.
Collapse
Affiliation(s)
- Jianmin Liu
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, China
- National Key Laboratory of Coal and Coal-bed Methane Simultaneous Extraction, Jincheng, China
| | - Baoyu Wang
- National Key Laboratory of Coal and Coal-bed Methane Simultaneous Extraction, Jincheng, China
| | - Chao Tai
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, China
- National Key Laboratory of Coal and Coal-bed Methane Simultaneous Extraction, Jincheng, China
- * E-mail:
| | - Li Wu
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, China
| | - Han Zhao
- National Key Laboratory of Coal and Coal-bed Methane Simultaneous Extraction, Jincheng, China
| | - Jiadong Guan
- National Key Laboratory of Coal and Coal-bed Methane Simultaneous Extraction, Jincheng, China
| | - Linyong Chen
- National Key Laboratory of Coal and Coal-bed Methane Simultaneous Extraction, Jincheng, China
| |
Collapse
|
41
|
An unusual strategy for the anoxic biodegradation of phthalate. ISME JOURNAL 2016; 11:224-236. [PMID: 27392087 DOI: 10.1038/ismej.2016.91] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 11/09/2022]
Abstract
In the past two decades, the study of oxygen-independent degradation of widely abundant aromatic compounds in anaerobic bacteria has revealed numerous unprecedented enzymatic principles. Surprisingly, the organisms, metabolites and enzymes involved in the degradation of o-phthalate (1,2-dicarboxybenzene), mainly derived from phthalate esters that are annually produced at the million ton scale, are sparsely known. Here, we demonstrate a previously unknown capacity of complete phthalate degradation in established aromatic compound-degrading, denitrifying model organisms of the genera Thauera, Azoarcus and 'Aromatoleum'. Differential proteome analyses revealed phthalate-induced gene clusters involved in uptake and conversion of phthalate to the central intermediate benzoyl-CoA. Enzyme assays provided in vitro evidence for the formation of phthaloyl-CoA by a succinyl-CoA- and phthalate-specific CoA transferase, which is essential for the subsequent oxygen-sensitive decarboxylation to benzoyl-CoA. The extreme instability of the phthaloyl-CoA intermediate requires highly balanced CoA transferase and decarboxylase activities to avoid its cellular accumulation. Phylogenetic analysis revealed phthaloyl-CoA decarboxylase as a novel member of the UbiD-like, (de)carboxylase enzyme family. Homologs of the encoding gene form a phylogenetic cluster and are found in soil, freshwater and marine bacteria; an ongoing global distribution of a possibly only recently evolved degradation pathway is suggested.
Collapse
|
42
|
Meckenstock RU, Boll M, Mouttaki H, Koelschbach JS, Cunha Tarouco P, Weyrauch P, Dong X, Himmelberg AM. Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:92-118. [DOI: 10.1159/000441358] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.
Collapse
|
43
|
von Netzer F, Kuntze K, Vogt C, Richnow HH, Boll M, Lueders T. Functional Gene Markers for Fumarate-Adding and Dearomatizing Key Enzymes in Anaerobic Aromatic Hydrocarbon Degradation in Terrestrial Environments. J Mol Microbiol Biotechnol 2016; 26:180-94. [PMID: 26959523 DOI: 10.1159/000441946] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Anaerobic degradation is a key process in many environments either naturally or anthropogenically exposed to petroleum hydrocarbons. Considerable advances into the biochemistry and physiology of selected anaerobic degraders have been achieved over the last decades, especially for the degradation of aromatic hydrocarbons. However, researchers have only recently begun to explore the ecology of complex anaerobic hydrocarbon degrader communities directly in their natural habitats, as well as in complex laboratory systems using tools of molecular biology. These approaches have mainly been facilitated by the establishment of a suite of targeted marker gene assays, allowing for rapid and directed insights into the diversity as well as the identity of intrinsic degrader populations and degradation potentials established at hydrocarbon-impacted sites. These are based on genes encoding either peripheral or central key enzymes in aromatic compound breakdown, such as fumarate-adding benzylsuccinate synthases or dearomatizing aryl-coenzyme A reductases, or on aromatic ring-cleaving hydrolases. Here, we review recent advances in this field, explain the different detection methodologies applied, and discuss how the detection of site-specific catabolic gene markers has improved the understanding of processes at contaminated sites. Functional marker gene-based strategies may be vital for the development of a more elaborate population-based assessment and prediction of aromatic degradation potentials in hydrocarbon-impacted environments.
Collapse
Affiliation(s)
- Frederick von Netzer
- Helmholtz Zentrum Mx00FC;nchen - German Research Center for Environmental Health, Institute of Groundwater Ecology, Neuherberg, Germany
| | | | | | | | | | | |
Collapse
|
44
|
Heider J, Schühle K, Frey J, Schink B. Activation of Acetone and Other Simple Ketones in Anaerobic Bacteria. J Mol Microbiol Biotechnol 2016; 26:152-64. [PMID: 26958851 DOI: 10.1159/000441500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Acetone and other ketones are activated for subsequent degradation through carboxylation by many nitrate-reducing, phototrophic, and obligately aerobic bacteria. Acetone carboxylation leads to acetoacetate, which is subsequently activated to a thioester and degraded via thiolysis. Two different types of acetone carboxylases have been described, which require either 2 or 4 ATP equivalents as an energy supply for the carboxylation reaction. Both enzymes appear to combine acetone enolphosphate with carbonic phosphate to form acetoacetate. A similar but more complex enzyme is known to carboxylate the aromatic ketone acetophenone, a metabolic intermediate in anaerobic ethylbenzene metabolism in denitrifying bacteria, with simultaneous hydrolysis of 2 ATP to 2 ADP. Obligately anaerobic sulfate-reducing bacteria activate acetone to a four-carbon compound as well, but via a different process than bicarbonate- or CO2-dependent carboxylation. The present evidence indicates that either carbon monoxide or a formyl residue is used as a cosubstrate, and that the overall ATP expenditure of this pathway is substantially lower than in the known acetone carboxylase reactions.
Collapse
Affiliation(s)
- Johann Heider
- Laboratory of Microbiology, LOEWE Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany
| | | | | | | |
Collapse
|
45
|
Aüllo T, Berlendis S, Lascourrèges JF, Dessort D, Duclerc D, Saint-Laurent S, Schraauwers B, Mas J, Patriarche D, Boesinger C, Magot M, Ranchou-Peyruse A. New Bio-Indicators for Long Term Natural Attenuation of Monoaromatic Compounds in Deep Terrestrial Aquifers. Front Microbiol 2016; 7:122. [PMID: 26904000 PMCID: PMC4746249 DOI: 10.3389/fmicb.2016.00122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/22/2016] [Indexed: 11/13/2022] Open
Abstract
Deep subsurface aquifers despite difficult access, represent important water resources and, at the same time, are key locations for subsurface engineering activities for the oil and gas industries, geothermal energy, and CO2 or energy storage. Formation water originating from a 760 m-deep geological gas storage aquifer was sampled and microcosms were set up to test the biodegradation potential of BTEX by indigenous microorganisms. The microbial community diversity was studied using molecular approaches based on 16S rRNA genes. After a long incubation period, with several subcultures, a sulfate-reducing consortium composed of only two Desulfotomaculum populations was observed able to degrade benzene, toluene, and ethylbenzene, extending the number of hydrocarbonoclastic-related species among the Desulfotomaculum genus. Furthermore, we were able to couple specific carbon and hydrogen isotopic fractionation during benzene removal and the results obtained by dual compound specific isotope analysis (𝜀C = -2.4‰ ± 0.3‰; 𝜀H = -57‰ ± 0.98‰; AKIEC: 1.0146 ± 0.0009, and AKIEH: 1.5184 ± 0.0283) were close to those obtained previously in sulfate-reducing conditions: this finding could confirm the existence of a common enzymatic reaction involving sulfate-reducers to activate benzene anaerobically. Although we cannot assign the role of each population of Desulfotomaculum in the mono-aromatic hydrocarbon degradation, this study suggests an important role of the genus Desulfotomaculum as potential biodegrader among indigenous populations in subsurface habitats. This community represents the simplest model of benzene-degrading anaerobes originating from the deepest subterranean settings ever described. As Desulfotomaculum species are often encountered in subsurface environments, this study provides some interesting results for assessing the natural response of these specific hydrologic systems in response to BTEX contamination during remediation projects.
Collapse
Affiliation(s)
- Thomas Aüllo
- Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux UMR 5254, Equipe Environnement et MicrobiologiePau, France
| | - Sabrina Berlendis
- Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux UMR 5254, Equipe Environnement et MicrobiologiePau, France
| | | | - Daniel Dessort
- TOTAL – Centre-Scientifique-Technique-Jean-FegerPau, France
| | | | - Stéphanie Saint-Laurent
- Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux UMR 5254, Equipe Environnement et MicrobiologiePau, France
| | | | - Johan Mas
- Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux UMR 5254, Equipe Environnement et MicrobiologiePau, France
| | | | | | - Michel Magot
- Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux UMR 5254, Equipe Environnement et MicrobiologiePau, France
| | - Anthony Ranchou-Peyruse
- Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-Chimie Pour l’Environnement et les Matériaux UMR 5254, Equipe Environnement et MicrobiologiePau, France
| |
Collapse
|
46
|
Comparison of bacterial and archaeal communities in depth-resolved zones in an LNAPL body. Appl Microbiol Biotechnol 2015; 100:3347-60. [PMID: 26691516 DOI: 10.1007/s00253-015-7106-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Advances in our understanding of the microbial ecology at sites impacted by light non-aqueous phase liquids (LNAPLs) are needed to drive development of optimized bioremediation technologies, support longevity models, and develop culture-independent molecular tools. In this study, depth-resolved characterization of geochemical parameters and microbial communities was conducted for a shallow hydrocarbon-impacted aquifer. Four distinct zones were identified based on microbial community structure and geochemical data: (i) an aerobic, low-contaminant mass zone at the top of the vadose zone; (ii) a moderate to high-contaminant mass, low-oxygen to anaerobic transition zone in the middle of the vadose zone; (iii) an anaerobic, high-contaminant mass zone spanning the bottom of the vadose zone and saturated zone; and (iv) an anaerobic, low-contaminant mass zone below the LNAPL body. Evidence suggested that hydrocarbon degradation is mediated by syntrophic fermenters and methanogens in zone III. Upward flux of methane likely contributes to promoting anaerobic conditions in zone II by limiting downward flux of oxygen as methane and oxygen fronts converge at the top of this zone. Observed sulfate gradients and microbial communities suggested that sulfate reduction and methanogenesis both contribute to hydrocarbon degradation in zone IV. Pyrosequencing revealed that Syntrophus- and Methanosaeta-related species dominate bacterial and archaeal communities, respectively, in the LNAPL body below the water table. Observed phylotypes were linked with in situ anaerobic hydrocarbon degradation in LNAPL-impacted soils.
Collapse
|
47
|
Tan B, Ng C, Nshimyimana JP, Loh LL, Gin KYH, Thompson JR. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Front Microbiol 2015; 6:1027. [PMID: 26441948 PMCID: PMC4585245 DOI: 10.3389/fmicb.2015.01027] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/10/2015] [Indexed: 12/20/2022] Open
Abstract
Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.
Collapse
Affiliation(s)
- BoonFei Tan
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
| | - Charmaine Ng
- Department of Civil and Environmental Engineering, National University of SingaporeSingapore, Singapore
| | - Jean Pierre Nshimyimana
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological UniversitySingapore, Singapore
| | - Lay Leng Loh
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
- Department of Civil and Environmental Engineering, National University of SingaporeSingapore, Singapore
| | - Karina Y.-H. Gin
- Department of Civil and Environmental Engineering, National University of SingaporeSingapore, Singapore
| | - Janelle R. Thompson
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, CambridgeMA, USA
| |
Collapse
|
48
|
Tan B, Jane Fowler S, Laban NA, Dong X, Sensen CW, Foght J, Gieg LM. Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. THE ISME JOURNAL 2015; 9:2028-45. [PMID: 25734684 PMCID: PMC4542035 DOI: 10.1038/ismej.2015.22] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 11/09/2022]
Abstract
Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities.
Collapse
Affiliation(s)
- Boonfei Tan
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - S Jane Fowler
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Nidal Abu Laban
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Xiaoli Dong
- Visual Genomics Centre, Faculty of Medicine, Calgary, Alberta, Canada
| | | | - Julia Foght
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
49
|
White MD, Payne KAP, Fisher K, Marshall SA, Parker D, Rattray NJW, Trivedi DK, Goodacre R, Rigby SEJ, Scrutton NS, Hay S, Leys D. UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis. Nature 2015; 522:502-6. [PMID: 26083743 PMCID: PMC4988493 DOI: 10.1038/nature14559] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/13/2015] [Indexed: 12/25/2022]
Abstract
Ubiquinone (also known as coenzyme Q) is a ubiquitous lipid-soluble redox cofactor that is an essential component of electron transfer chains. Eleven genes have been implicated in bacterial ubiquinone biosynthesis, including ubiX and ubiD, which are responsible for decarboxylation of the 3-octaprenyl-4-hydroxybenzoate precursor. Despite structural and biochemical characterization of UbiX as a flavin mononucleotide (FMN)-binding protein, no decarboxylase activity has been detected. Here we report that UbiX produces a novel flavin-derived cofactor required for the decarboxylase activity of UbiD. UbiX acts as a flavin prenyltransferase, linking a dimethylallyl moiety to the flavin N5 and C6 atoms. This adds a fourth non-aromatic ring to the flavin isoalloxazine group. In contrast to other prenyltransferases, UbiX is metal-independent and requires dimethylallyl-monophosphate as substrate. Kinetic crystallography reveals that the prenyltransferase mechanism of UbiX resembles that of the terpene synthases. The active site environment is dominated by π systems, which assist phosphate-C1' bond breakage following FMN reduction, leading to formation of the N5-C1' bond. UbiX then acts as a chaperone for adduct reorientation, via transient carbocation species, leading ultimately to formation of the dimethylallyl C3'-C6 bond. Our findings establish the mechanism for formation of a new flavin-derived cofactor, extending both flavin and terpenoid biochemical repertoires.
Collapse
Affiliation(s)
- Mark D White
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Karl A P Payne
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Karl Fisher
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Stephen A Marshall
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - David Parker
- Innovation/Biodomain, Shell International Exploration and Production, Westhollow Technology Center, 3333 Highway 6 South, Houston, Texas 77082-3101, USA
| | - Nicholas J W Rattray
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Drupad K Trivedi
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Royston Goodacre
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Stephen E J Rigby
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Nigel S Scrutton
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - Sam Hay
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| | - David Leys
- Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
| |
Collapse
|
50
|
Teske A, Callaghan AV, LaRowe DE. Biosphere frontiers of subsurface life in the sedimented hydrothermal system of Guaymas Basin. Front Microbiol 2014; 5:362. [PMID: 25132832 PMCID: PMC4117188 DOI: 10.3389/fmicb.2014.00362] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/26/2014] [Indexed: 12/24/2022] Open
Abstract
Temperature is one of the key constraints on the spatial extent, physiological and phylogenetic diversity, and biogeochemical function of subsurface life. A model system to explore these interrelationships should offer a suitable range of geochemical regimes, carbon substrates and temperature gradients under which microbial life can generate energy and sustain itself. In this theory and hypothesis article, we make the case for the hydrothermally heated sediments of Guaymas Basin in the Gulf of California as a suitable model system where extensive temperature and geochemical gradients create distinct niches for active microbial populations in the hydrothermally influenced sedimentary subsurface that in turn intercept and process hydrothermally generated carbon sources. We synthesize the evidence for high-temperature microbial methane cycling and sulfate reduction at Guaymas Basin - with an eye on sulfate-dependent oxidation of abundant alkanes - and demonstrate the energetic feasibility of these latter types of deep subsurface life in previously drilled Guaymas Basin locations of Deep-Sea Drilling Project 64.
Collapse
Affiliation(s)
- Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel HillChapel Hill, NC, USA
| | - Amy V. Callaghan
- Department of Microbiology and Plant Biology, University of OklahomaNorman, OK, USA
| | - Douglas E. LaRowe
- Department of Earth Sciences, University of Southern CaliforniaLos Angeles, CA, USA
| |
Collapse
|