1
|
Tucci M, Fernández-Verdejo D, Resitano M, Ciacia P, Guisasola A, Blánquez P, Marco-Urrea E, Cruz Viggi C, Matturro B, Crognale S, Aulenta F. Toluene-driven anaerobic biodegradation of chloroform in a continuous-flow bioelectrochemical reactor. CHEMOSPHERE 2023; 338:139467. [PMID: 37437617 DOI: 10.1016/j.chemosphere.2023.139467] [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: 03/31/2023] [Revised: 06/12/2023] [Accepted: 07/09/2023] [Indexed: 07/14/2023]
Abstract
Subsurface co-contamination by multiple pollutants can be challenging for the design of bioremediation strategies since it may require promoting different and often antagonistic degradation pathways. Here, we investigated the simultaneous degradation of toluene and chloroform (CF) in a continuous-flow anaerobic bioelectrochemical reactor. As a result, 47 μmol L-1 d-1 of toluene and 60 μmol L-1 d-1 of CF were concurrently removed, when the anode was polarized at +0.4 V vs. Standard Hydrogen Electrode (SHE). Analysis of the microbial community structure and key functional genes allowed to identify the involved degradation pathways. Interestingly, when acetate was supplied along with toluene, to simulate the impact of a readily biodegradable substrate on process performance, toluene degradation was adversely affected, likely due to competitive inhibition effects. Overall, this study proved the efficacy of the developed bioelectrochemical system in simultaneously treating multiple groundwater contaminants, paving the way for the application in real-world scenarios.
Collapse
Affiliation(s)
- Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - David Fernández-Verdejo
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Marco Resitano
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - Pamela Ciacia
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - Albert Guisasola
- GENOCOV, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Paqui Blánquez
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Ernest Marco-Urrea
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy.
| |
Collapse
|
2
|
Tucci M, Viggi CC, Crognale S, Matturro B, Rossetti S, Capriotti AL, Cavaliere C, Cerrato A, Montone CM, Harnisch F, Aulenta F. Insights into the syntrophic microbial electrochemical oxidation of toluene: a combined chemical, electrochemical, taxonomical, functional gene-based, and metaproteomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157919. [PMID: 35964739 DOI: 10.1016/j.scitotenv.2022.157919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of aromatic hydrocarbons in anoxic contaminated environments is typically limited by the lack of bioavailable electron acceptors. Microbial electrochemical technologies (METs) are able to provide a virtually inexhaustible electron acceptor in the form of a solid electrode. Recently, we provided first experimental evidence for the syntrophic degradation of toluene in a continuous-flow bioelectrochemical reactor known as the "bioelectric well". Herein, we further analyzed the structure and function of the electroactive toluene-degrading microbiome using a suite of chemical, electrochemical, phylogenetic, proteomic, and functional gene-based analyses. The bioelectric well removed 83 ± 7 % of the toluene from the influent with a coulombic efficiency of 84 %. Cyclic voltammetry allowed to identify the formal potentials of four putative electron transfer sites, which ranged from -0.2 V to +0.1 V vs. SHE, consistent with outer membrane c-type cytochromes and pili of electroactive Geobacter species. The biofilm colonizing the surface of the anode was indeed highly enriched in Geobacter species. On the other hand, the planktonic communities thriving in the bulk of the reactor harbored aromatic hydrocarbons degraders and fermentative propionate-producing microorganisms, as revealed by phylogenetic and proteomic analyses. Most likely, propionate, acetate or other VFAs produced in the bulk liquid from the degradation of toluene were utilized as substrates by the electroactive biofilm. Interestingly, key-functional genes related to the degradation of toluene were found both in the biofilm and in the planktonic communities. Taken as a whole, the herein reported results highlight the importance of applying a comprehensive suite of techniques to unravel the complex cooperative metabolisms occurring in METs.
Collapse
Affiliation(s)
- Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy
| | | | - Chiara Cavaliere
- Department of Chemistry, Sapienza - University of Rome, Rome, Italy
| | - Andrea Cerrato
- Department of Chemistry, Sapienza - University of Rome, Rome, Italy
| | | | - Falk Harnisch
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo, RM, Italy.
| |
Collapse
|
3
|
Wackett LP. Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances. Microb Biotechnol 2021; 15:773-792. [PMID: 34570953 PMCID: PMC8913905 DOI: 10.1111/1751-7915.13928] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Poly‐ and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today’s society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called ‘forever chemicals’ due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.
Collapse
Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, 55108, USA
| |
Collapse
|
4
|
Simultaneous removal of hydrocarbons and sulfate from groundwater using a “bioelectric well”. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
5
|
Tomei MC, Mosca Angelucci D, Clagnan E, Brusetti L. Anaerobic biodegradation of phenol in wastewater treatment: achievements and limits. Appl Microbiol Biotechnol 2021; 105:2195-2224. [PMID: 33630152 DOI: 10.1007/s00253-021-11182-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/09/2021] [Accepted: 02/14/2021] [Indexed: 11/30/2022]
Abstract
Anaerobic biodegradation of toxic compounds found in industrial wastewater is an attractive solution allowing the recovery of energy and resources but it is still challenging due to the low kinetics making the anaerobic process not competitive against the aerobic one. In this review, we summarise the present state of knowledge on the anaerobic biodegradation process for phenol, a typical target compound employed in toxicity studies on industrial wastewater treatment. The objective of this article is to provide an overview on the microbiological and technological aspects of anaerobic phenol degradation and on the research needs to fill the gaps still hindering the diffusion of the anaerobic process. The first part is focused on the microbiology and extensively presents and characterises phenol-degrading bacteria and biodegradation pathways. In the second part, dedicated to process feasibility, anaerobic and aerobic biodegradation kinetics are analysed and compared, and strategies to enhance process performance, i.e. advanced technologies, bioaugmentation, and biostimulation, are critically analysed and discussed. The final section provides a summary of the research needs. Literature data analysis shows the feasibility of anaerobic phenol biodegradation at laboratory and pilot scale, but there is still a consistent gap between achieved aerobic and anaerobic performance. This is why current research demand is mainly related to the development and optimisation of powerful technologies and effective operation strategies able to enhance the competitiveness of the anaerobic process. Research efforts are strongly justified because the anaerobic process is a step forward to a more sustainable approach in wastewater treatment.Key points• Review of phenol-degraders bacteria and biodegradation pathways.• Anaerobic phenol biodegradation kinetics for metabolic and co-metabolic processes.• Microbial and technological strategies to enhance process performance.
Collapse
Affiliation(s)
- M Concetta Tomei
- Water Research Institute, C.N.R., Via Salaria km 29.300, CP 10, 00015, Monterotondo Stazione Rome, Italy.
| | - Domenica Mosca Angelucci
- Water Research Institute, C.N.R., Via Salaria km 29.300, CP 10, 00015, Monterotondo Stazione Rome, Italy
| | - Elisa Clagnan
- Ricicla Group - DiSAA, University of Milan, Via Celoria 2, 20133, Milano, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen - Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| |
Collapse
|
6
|
Appel L, Willistein M, Dahl C, Ermler U, Boll M. Functional diversity of prokaryotic HdrA(BC) modules: Role in flavin-based electron bifurcation processes and beyond. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148379. [PMID: 33460586 DOI: 10.1016/j.bbabio.2021.148379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
In methanogenic archaea, the archetypical complex of heterodisulfide reductase (HdrABC) and hydrogenase (MvhAGD) couples the endergonic reduction of CO2 by H2 to the exergonic reduction of the CoB-S-S-CoM heterodisulfide by H2 via flavin-based electron bifurcation. Presently known enzymes containing HdrA(BC)-like components play key roles in methanogenesis, acetogenesis, respiratory sulfate reduction, lithotrophic reduced sulfur compound oxidation, aromatic compound degradation, fermentations, and probably many further processes. This functional diversity is achieved by a modular architecture of HdrA(BC) enzymes, where a big variety of electron input/output modules may be connected either directly or via adaptor modules to the HdrA(BC) components. Many, but not all HdrA(BC) complexes are proposed to catalyse a flavin-based electron bifurcation/confurcation. Despite the availability of HdrA(BC) crystal structures, fundamental questions of electron transfer and energy coupling processes remain. Here, we address the common properties and functional diversity of HdrA(BC) core modules integrated into electron-transfer machineries of outstanding complexity.
Collapse
Affiliation(s)
- Lena Appel
- Fakultät für Biologie - Mikrobiologie, Universität Freiburg, Freiburg, Germany
| | - Max Willistein
- Fakultät für Biologie - Mikrobiologie, Universität Freiburg, Freiburg, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Matthias Boll
- Fakultät für Biologie - Mikrobiologie, Universität Freiburg, Freiburg, Germany.
| |
Collapse
|
7
|
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
|
8
|
Abstract
Tungsten is the heaviest element used in biological systems. It occurs in the active sites of several bacterial or archaeal enzymes and is ligated to an organic cofactor (metallopterin or metal binding pterin; MPT) which is referred to as tungsten cofactor (Wco). Wco-containing enzymes are found in the dimethyl sulfoxide reductase (DMSOR) and the aldehyde:ferredoxin oxidoreductase (AOR) families of MPT-containing enzymes. Some depend on Wco, such as aldehyde oxidoreductases (AORs), class II benzoyl-CoA reductases (BCRs) and acetylene hydratases (AHs), whereas others may incorporate either Wco or molybdenum cofactor (Moco), such as formate dehydrogenases, formylmethanofuran dehydrogenases or nitrate reductases. The obligately tungsten-dependent enzymes catalyze rather unusual reactions such as ones with extremely low-potential electron transfers (AOR, BCR) or an unusual hydration reaction (AH). In recent years, insights into the structure and function of many tungstoenzymes have been obtained. Though specific and unspecific ABC transporter uptake systems have been described for tungstate and molybdate, only little is known about further discriminative steps in Moco and Wco biosynthesis. In bacteria producing Moco- and Wco-containing enzymes simultaneously, paralogous isoforms of the metal insertase MoeA may be specifically involved in the molybdenum- and tungsten-insertion into MPT, and in targeting Moco or Wco to their respective apo-enzymes. Wco-containing enzymes are of emerging biotechnological interest for a number of applications such as the biocatalytic reduction of CO2, carboxylic acids and aromatic compounds, or the conversion of acetylene to acetaldehyde.
Collapse
|
9
|
Weyrauch P, Heker I, Zaytsev AV, von Hagen CA, Arnold ME, Golding BT, Meckenstock RU. The 5,6,7,8-Tetrahydro-2-Naphthoyl-Coenzyme A Reductase Reaction in the Anaerobic Degradation of Naphthalene and Identification of Downstream Metabolites. Appl Environ Microbiol 2020; 86:e00996-20. [PMID: 32444470 PMCID: PMC7376553 DOI: 10.1128/aem.00996-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/15/2020] [Indexed: 11/20/2022] Open
Abstract
Anaerobic degradation of polycyclic aromatic hydrocarbons has been investigated mostly with naphthalene as a model compound. Naphthalene degradation by sulfate-reducing bacteria proceeds via carboxylation to 2-naphthoic acid, formation of a coenzyme A thioester, and subsequent reduction to 5,6,7,8-tetrahydro-2-naphthoyl-coenzyme A (THNCoA), which is further reduced to hexahydro-2-naphthoyl-CoA (HHNCoA) by tetrahydronaphthoyl-CoA reductase (THNCoA reductase), an enzyme similar to class I benzoyl-CoA reductases. When analyzing THNCoA reductase assays with crude cell extracts and NADH as electron donor via liquid chromatography-mass spectrometry (LC-MS), scanning for putative metabolites, we found that small amounts of the product of an HHNCoA hydratase were formed in the assays, but the downstream conversion by an NAD+-dependent β-hydroxyacyl-CoA dehydrogenase was prevented by the excess of NADH in those assays. Experiments with alternative electron donors indicated that 2-oxoglutarate can serve as an indirect electron donor for the THNCoA-reducing system via a 2-oxoglutarate:ferredoxin oxidoreductase. With 2-oxoglutarate as electron donor, THNCoA was completely converted and further metabolites resulting from subsequent β-oxidation-like reactions and hydrolytic ring cleavage were detected. These metabolites indicate a downstream pathway with water addition to HHNCoA and ring fission via a hydrolase acting on a β'-hydroxy-β-oxo-decahydro-2-naphthoyl-CoA intermediate. Formation of the downstream intermediate cis-2-carboxycyclohexylacetyl-CoA, which is the substrate for the previously described lower degradation pathway leading to the central metabolism, completes the anaerobic degradation pathway of naphthalene.IMPORTANCE Anaerobic degradation of polycyclic aromatic hydrocarbons is poorly investigated despite its significance in anoxic sediments. Using alternative electron donors for the 5,6,7,8-tetrahydro-2-naphthoyl-CoA reductase reaction, we observed intermediary metabolites of anaerobic naphthalene degradation via in vitro enzyme assays with cell extracts of anaerobic naphthalene degraders. The identified metabolites provide evidence that ring reduction terminates at the stage of hexahydro-2-naphthoyl-CoA and a sequence of β-oxidation-like degradation reactions starts with a hydratase acting on this intermediate. The final product of this reaction sequence was identified as cis-2-carboxycyclohexylacetyl-CoA, a compound for which a further downstream degradation pathway has recently been published (P. Weyrauch, A. V. Zaytsev, S. Stephan, L. Kocks, et al., Environ Microbiol 19:2819-2830, 2017, https://doi.org/10.1111/1462-2920.13806). Our study reveals the first ring-cleaving reaction in the anaerobic naphthalene degradation pathway. It closes the gap between the reduction of the first ring of 2-naphthoyl-CoA by 2-napthoyl-CoA reductase and the lower degradation pathway starting from cis-2-carboxycyclohexylacetyl-CoA, where the second ring cleavage takes place.
Collapse
Affiliation(s)
- Philip Weyrauch
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Isabelle Heker
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Andrey V Zaytsev
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Meike E Arnold
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Bernard T Golding
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | |
Collapse
|
10
|
Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
Collapse
Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| |
Collapse
|
11
|
Anselmann SEL, Löffler C, Stärk HJ, Jehmlich N, von Bergen M, Brüls T, Boll M. The class II benzoyl-coenzyme A reductase complex from the sulfate-reducing Desulfosarcina cetonica. Environ Microbiol 2019; 21:4241-4252. [PMID: 31430028 DOI: 10.1111/1462-2920.14784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/06/2019] [Accepted: 08/18/2019] [Indexed: 12/17/2022]
Abstract
Benzoyl-CoA reductases (BCRs) catalyse a key reaction in the anaerobic degradation pathways of monocyclic aromatic substrates, the dearomatization of benzoyl-CoA (BzCoA) to cyclohexa-1,5-diene-1-carboxyl-CoA (1,5-dienoyl-CoA) at the negative redox potential limit of diffusible enzymatic substrate/product couples (E°' = -622 mV). A 1-MDa class II BCR complex composed of the BamBCDEGHI subunits has so far only been isolated from the Fe(III)-respiring Geobacter metallireducens. It is supposed to drive endergonic benzene ring reduction at an active site W-pterin cofactor by flavin-based electron bifurcation. Here, we identified multiple copies of putative genes encoding the structural components of a class II BCR in sulfate reducing, Fe(III)-respiring and syntrophic bacteria. A soluble 950 kDa Bam[(BC)2 DEFGHI]2 complex was isolated from extracts of Desulfosarcina cetonica cells grown with benzoate/sulfate. Metal and cofactor analyses together with the identification of conserved binding motifs gave rise to 4 W-pterins, two selenocysteines, six flavin adenine dinucleotides, four Zn, and 48 FeS clusters. The complex exhibited 1,5-dienoyl-CoA-, NADPH- and ferredoxin-dependent oxidoreductase activities. Our results indicate that high-molecular class II BCR metalloenzyme machineries are remarkably conserved in strictly anaerobic bacteria with regard to subunit architecture and cofactor content, but their subcellular localization and electron acceptor preference may differ as a result of adaptations to variable energy metabolisms.
Collapse
Affiliation(s)
| | - Claudia Löffler
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Hans-Joachim Stärk
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany.,Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, 04103, Leipzig, Germany
| | - Thomas Brüls
- CEA, DRF, IBFJ, Genoscope, Evry, France.,CNRS-UMR8030, Université d'Evry Val d'Essonne and Université Paris-Saclay, Evry, France
| | - Matthias Boll
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| |
Collapse
|
12
|
James KL, Kung JW, Crable BR, Mouttaki H, Sieber JR, Nguyen HH, Yang Y, Xie Y, Erde J, Wofford NQ, Karr EA, Loo JA, Ogorzalek Loo RR, Gunsalus RP, McInerney MJ. Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids. Environ Microbiol 2019; 21:1833-1846. [PMID: 30895699 PMCID: PMC6488403 DOI: 10.1111/1462-2920.14601] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/12/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Syntrophy is essential for the efficient conversion of organic carbon to methane in natural and constructed environments, but little is known about the enzymes involved in syntrophic carbon and electron flow. Syntrophus aciditrophicus strain SB syntrophically degrades benzoate and cyclohexane-1-carboxylate and catalyses the novel synthesis of benzoate and cyclohexane-1-carboxylate from crotonate. We used proteomic, biochemical and metabolomic approaches to determine what enzymes are used for fatty, aromatic and alicyclic acid degradation versus for benzoate and cyclohexane-1-carboxylate synthesis. Enzymes involved in the metabolism of cyclohex-1,5-diene carboxyl-CoA to acetyl-CoA were in high abundance in S. aciditrophicus cells grown in pure culture on crotonate and in coculture with Methanospirillum hungatei on crotonate, benzoate or cyclohexane-1-carboxylate. Incorporation of 13 C-atoms from 1-[13 C]-acetate into crotonate, benzoate and cyclohexane-1-carboxylate during growth on these different substrates showed that the pathways are reversible. A protein conduit for syntrophic reverse electron transfer from acyl-CoA intermediates to formate was detected. Ligases and membrane-bound pyrophosphatases make pyrophosphate needed for the synthesis of ATP by an acetyl-CoA synthetase. Syntrophus aciditrophicus, thus, uses a core set of enzymes that operates close to thermodynamic equilibrium to conserve energy in a novel and highly efficient manner.
Collapse
Affiliation(s)
- Kimberly L. James
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Johannes W. Kung
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Bryan R. Crable
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Housna Mouttaki
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Jessica R. Sieber
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Hong H. Nguyen
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Yanan Yang
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Yongming Xie
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Jonathan Erde
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Neil Q. Wofford
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| | - Elizabeth A. Karr
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
- Price Family Foundation Institute of Structural Biology,
University of Oklahoma, Norman, OK, 73019
| | - Joseph A. Loo
- UCLA DOE Institute, University of California, Los Angeles
CA 90095
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Rachel R. Ogorzalek Loo
- UCLA DOE Institute, University of California, Los Angeles
CA 90095
- Department of Chemistry & Biochemistry, University of
California, Los Angeles 90095
| | - Robert P. Gunsalus
- Department of Microbiology, Immunology, and Molecular
Genetics, University of California, Los Angeles, CA, USA
- UCLA-Molecular Biology Institute, University of California,
Los Angeles, CA USA
- UCLA DOE Institute, University of California, Los Angeles
CA 90095
| | - Michael J. McInerney
- Department of Microbiology and Plant Biology, University of
Oklahoma, Norman, OK, 73019
| |
Collapse
|
13
|
One-megadalton metalloenzyme complex in Geobacter metallireducens involved in benzene ring reduction beyond the biological redox window. Proc Natl Acad Sci U S A 2019; 116:2259-2264. [PMID: 30674680 DOI: 10.1073/pnas.1819636116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Reversible biological electron transfer usually occurs between redox couples at standard redox potentials ranging from +0.8 to -0.5 V. Dearomatizing benzoyl-CoA reductases (BCRs), key enzymes of the globally relevant microbial degradation of aromatic compounds at anoxic sites, catalyze a biological Birch reduction beyond the negative limit of this redox window. The structurally characterized BamBC subunits of class II BCRs accomplish benzene ring reduction at an active-site tungsten cofactor; however, the mechanism and components involved in the energetic coupling of endergonic benzene ring reduction have remained hypothetical. We present a 1-MDa, membrane-associated, Bam[(BC)2DEFGHI]2 complex from the anaerobic bacterium Geobacter metallireducens harboring 4 tungsten, 4 zinc, 2 selenocysteines, 6 FAD, and >50 FeS cofactors. The results suggest that class II BCRs catalyze electron transfer to the aromatic ring, yielding a cyclic 1,5-dienoyl-CoA via two flavin-based electron bifurcation events. This work expands our knowledge of energetic couplings in biology by high-molecular-mass electron bifurcating machineries.
Collapse
|
14
|
Qian HX, Liao RZ. QM/MM Study of Tungsten-Dependent Benzoyl-Coenzyme A Reductase: Rationalization of Regioselectivity and Predication of W vs Mo Selectivity. Inorg Chem 2018; 57:10667-10678. [DOI: 10.1021/acs.inorgchem.8b01328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui-Xia Qian
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
15
|
Tiedt O, Fuchs J, Eisenreich W, Boll M. A catalytically versatile benzoyl-CoA reductase, key enzyme in the degradation of methyl- and halobenzoates in denitrifying bacteria. J Biol Chem 2018; 293:10264-10274. [PMID: 29769313 DOI: 10.1074/jbc.ra118.003329] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/15/2018] [Indexed: 12/22/2022] Open
Abstract
Class I benzoyl-CoA (BzCoA) reductases (BCRs) are key enzymes in the anaerobic degradation of aromatic compounds. They catalyze the ATP-dependent reduction of the central BzCoA intermediate and analogues of it to conjugated cyclic 1,5-dienoyl-CoAs probably by a radical-based, Birch-like reduction mechanism. Discovered in 1995, the enzyme from the denitrifying bacterium Thauera aromatica (BCRTar) has so far remained the only isolated and biochemically accessible BCR, mainly because BCRs are extremely labile, and their heterologous production has largely failed so far. Here, we describe a platform for the heterologous expression of the four structural genes encoding a designated 3-methylbenzoyl-CoA reductase from the related denitrifying species Thauera chlorobenzoica (MBRTcl) in Escherichia coli This reductase represents the prototype of a distinct subclass of ATP-dependent BCRs that were proposed to be involved in the degradation of methyl-substituted BzCoA analogues. The recombinant MBRTcl had an αβγδ-subunit architecture, contained three low-potential [4Fe-4S] clusters, and was highly oxygen-labile. It catalyzed the ATP-dependent reductive dearomatization of BzCoA with 2.3-2.8 ATPs hydrolyzed per two electrons transferred and preferentially dearomatized methyl- and chloro-substituted analogues in meta- and para-positions. NMR analyses revealed that 3-methylbenzoyl-CoA is regioselectively reduced to 3-methyl-1,5-dienoyl-CoA. The unprecedented reductive dechlorination of 4-chloro-BzCoA to BzCoA probably via HCl elimination from a reduced intermediate allowed for the previously unreported growth of T. chlorobenzoica on 4-chlorobenzoate. The heterologous expression platform established in this work enables the production, isolation, and characterization of bacterial and archaeal BCR and BCR-like radical enzymes, for many of which the function has remained unknown.
Collapse
Affiliation(s)
- Oliver Tiedt
- From the Fakultät für Biologie-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany and
| | - Jonathan Fuchs
- From the Fakultät für Biologie-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany and
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Technische Universität München, 85747 Garching, Germany
| | - Matthias Boll
- From the Fakultät für Biologie-Mikrobiologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany and
| |
Collapse
|
16
|
Sperfeld M, Rauschenbach C, Diekert G, Studenik S. Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation. WATER RESEARCH 2018; 132:146-157. [PMID: 29324294 DOI: 10.1016/j.watres.2017.12.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
We analyzed a coal tar polluted aquifer of a former gasworks site in Thuringia (Germany) for the presence and function of aromatic compound-degrading bacteria (ACDB) by 16S rRNA Illumina sequencing, bamA clone library sequencing and cultivation attempts. The relative abundance of ACDB was highest close to the source of contamination. Up to 44% of total 16S rRNA sequences were affiliated to ACDB including genera such as Azoarcus, Georgfuchsia, Rhodoferax, Sulfuritalea (all Betaproteobacteria) and Pelotomaculum (Firmicutes). Sequencing of bamA, a functional gene marker for the anaerobic benzoyl-CoA pathway, allowed further insights into electron-accepting processes in the aquifer: bamA sequences of mainly nitrate-reducing Betaproteobacteria were abundant in all groundwater samples, whereas an additional sulfate-reducing and/or fermenting microbial community (Deltaproteobacteria, Firmicutes) was restricted to a highly contaminated, sulfate-depleted groundwater sampling well. By conducting growth experiments with groundwater as inoculum and nitrate as electron acceptor, organisms related to Azoarcus spp. were identified as key players in the degradation of toluene and ethylbenzene. An organism highly related to Georgfuchsia toluolica G5G6 was enriched with p-xylene, a particularly recalcitrant compound. The anaerobic degradation of p-xylene requires a metabolic trait that was not described for members of the genus Georgfuchsia before. In line with this, we were able to identify a putative 4-methylbenzoyl-CoA reductase gene cluster in the respective enrichment culture, which is possibly involved in the anaerobic degradation of p-xylene.
Collapse
Affiliation(s)
- Martin Sperfeld
- Institute of Microbiology, Friedrich Schiller University Jena, Department of Applied and Ecological Microbiology, Philosophenweg 12, 07743 Jena, Germany
| | | | - Gabriele Diekert
- Institute of Microbiology, Friedrich Schiller University Jena, Department of Applied and Ecological Microbiology, Philosophenweg 12, 07743 Jena, Germany
| | - Sandra Studenik
- Institute of Microbiology, Friedrich Schiller University Jena, Department of Applied and Ecological Microbiology, Philosophenweg 12, 07743 Jena, Germany.
| |
Collapse
|
17
|
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
|
18
|
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
|
19
|
Boll M, Kung JW, Ermler U, Martins BM, Buckel W. Fermentative Cyclohexane Carboxylate Formation in Syntrophus aciditrophicus. J Mol Microbiol Biotechnol 2016; 26:165-79. [PMID: 26959729 DOI: 10.1159/000440881] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Short-chain fatty acids such as acetic, propionic, butyric or lactic acids are typical primary fermentation products in the anaerobic feeding chain. Fifteen years ago, a novel fermentation type was discovered in the obligately anaerobic Deltaproteobacterium Syntrophus aciditrophicus. During fermentative growth with crotonate and/or benzoate, acetate is formed in the oxidative branch and cyclohexane carboxylate in the reductive branch. In both cases cyclohexa-1,5-diene-1-carboxyl-CoA (Ch1,5CoA) is a central intermediate that is either formed by a class II benzoyl-CoA reductase (fermentation of benzoate) or by reverse reactions of the benzoyl-CoA degradation pathway (fermentation of crotonate). Here, we summarize the current knowledge of the enzymology involved in fermentations yielding cyclohexane carboxylate as an excreted product. The characteristic enzymes involved are two acyl-CoA dehydrogenases specifically acting on Ch1,5CoA and cyclohex-1-ene-1-carboxyl-CoA. Both enzymes are also employed during the syntrophic growth of S. aciditrophicus with cyclohexane carboxylate as the carbon source in coculture with a methanogen. An investigation of anabolic pathways in S. aciditrophicus revealed a rather unusual pathway for glutamate synthesis involving a Re-citrate synthase. Future work has to address the unresolved question concerning which components are involved in reoxidation of the NADH formed in the oxidative branch of the unique cyclohexane carboxylate fermentation pathway in S. aciditrophicus.
Collapse
Affiliation(s)
- Matthias Boll
- Mikrobiologie, Fakultx00E4;t fx00FC;r Biologie, Albert-Ludwigs-Universitx00E4;t Freiburg, Freiburg, Germany
| | | | | | | | | |
Collapse
|
20
|
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
|
21
|
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
|
22
|
Boll M, Einsle O, Ermler U, Kroneck PMH, Ullmann GM. Structure and Function of the Unusual Tungsten Enzymes Acetylene Hydratase and Class II Benzoyl-Coenzyme A Reductase. J Mol Microbiol Biotechnol 2016; 26:119-37. [PMID: 26959374 DOI: 10.1159/000440805] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In biology, tungsten (W) is exclusively found in microbial enzymes bound to a bis-pyranopterin cofactor (bis-WPT). Previously known W enzymes catalyze redox oxo/hydroxyl transfer reactions by directly coordinating their substrates or products to the metal. They comprise the W-containing formate/formylmethanofuran dehydrogenases belonging to the dimethyl sulfoxide reductase (DMSOR) family and the aldehyde:ferredoxin oxidoreductase (AOR) families, which form a separate enzyme family within the Mo/W enzymes. In the last decade, initial insights into the structure and function of two unprecedented W enzymes were obtained: the acetaldehyde forming acetylene hydratase (ACH) belongs to the DMSOR and the class II benzoyl-coenzyme A (CoA) reductase (BCR) to the AOR family. The latter catalyzes the reductive dearomatization of benzoyl-CoA to a cyclic diene. Both are key enzymes in the degradation of acetylene (ACH) or aromatic compounds (BCR) in strictly anaerobic bacteria. They are unusual in either catalyzing a nonredox reaction (ACH) or a redox reaction without coordinating the substrate or product to the metal (BCR). In organic chemical synthesis, analogous reactions require totally nonphysiological conditions depending on Hg2+ (acetylene hydration) or alkali metals (benzene ring reduction). The structural insights obtained pave the way for biological or biomimetic approaches to basic reactions in organic chemistry.
Collapse
Affiliation(s)
- Matthias Boll
- Fakultx00E4;t fx00FC;r Biologie/Mikrobiologie, Institut fx00FC;r Biochemie, Albert-Ludwigs-Universitx00E4;t Freiburg, Freiburg, Germany
| | | | | | | | | |
Collapse
|
23
|
Rabus R, Boll M, Golding B, Wilkes H. Anaerobic Degradation of p-Alkylated Benzoates and Toluenes. J Mol Microbiol Biotechnol 2016; 26:63-75. [PMID: 26960059 DOI: 10.1159/000441144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The anaerobic degradation of 4-alkylbenzoates and 4-alkyltoluenes is to date a rarely reported microbial capacity. The newly isolated Alphaproteobacterium Magnetospirillum sp. strain pMbN1 represents the first pure culture demonstrated to degrade 4-methylbenzoate completely to CO2 in a process coupled to denitrification. Differential proteogenomic studies in conjunction with targeted metabolite analyses and enzyme activity measurements elucidated a specific 4-methylbenzoyl-coenzyme A (CoA) pathway in this bacterium alongside the classical central benzoyl-CoA pathway. Whilst these two pathways are analogous, in the former the p-methyl group is retained and its 4-methylbenzoyl-CoA reductase (MbrCBAD) is phylogenetically distinct from the archetypical class I benzoyl-CoA reductase (BcrCBAD). Subsequent global regulatory studies on strain pMbN1 grown with binary or ternary substrate mixtures revealed benzoate to repress the anaerobic utilization of 4-methylbenzoate and succinate. The shared nutritional property of betaproteobacterial 'Aromatoleum aromaticum' pCyN1 and Thauera sp. strain pCyN2 is the anaerobic degradation of the plant-derived hydrocarbon p-cymene (4-isopropyltoluene) coupled to denitrification. Notably, the two strains employ two different peripheral pathways for the conversion of p-cymene to 4-isopropylbenzoyl-CoA as the possible first common intermediate. In 'A. aromaticum' pCyN1 a putative p-cymene dehydrogenase (CmdABC) is proposed to hydroxylate the benzylic methyl group, which is subsequently further oxidized to the CoA-thioester. In contrast, Thauera sp. strain pCyN2 employs a reaction sequence analogous to the known anaerobic toluene pathway, involving a distinct branching (4-isopropylbenzyl)succinate synthase (IbsABCDEF).
Collapse
Affiliation(s)
- Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | | | | | | |
Collapse
|
24
|
Li ZL, Nan J, Huang C, Liang B, Liu WZ, Cheng HY, Zhang C, Zhang D, Kong D, Kanamaru K, Kobayashi T, Wang AJ, Katayama A. Spatial Abundance and Distribution of Potential Microbes and Functional Genes Associated with Anaerobic Mineralization of Pentachlorophenol in a Cylindrical Reactor. Sci Rep 2016; 6:19015. [PMID: 26750760 PMCID: PMC4707460 DOI: 10.1038/srep19015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/02/2015] [Indexed: 01/19/2023] Open
Abstract
Functional interplays of microbial activity, genetic diversity and contaminant transformation are poorly understood in reactors for mineralizing halogenated aromatics anaerobically. Here, we investigated abundance and distribution of potential microbes and functional genes associated with pentachlorophenol (PCP) anaerobic mineralization in a continuous-flow cylindrical reactor (15 cm in length). PCP dechlorination and the metabolite (phenol) were observed at segments 0–8 cm from inlet, where key microbes, including potential reductive dechlorinators (Dehalobacter, Sulfurospirillum, Desulfitobacterium and Desulfovibrio spp.) and phenol degraders (Cryptanaerobacter and Syntrophus spp.), as well as putative functional genes, including putative chlorophenol reductive dehalogenase (cprA) and benzoyl-CoA reductase (bamB), were highly enriched simultaneously. Five types of putative cprAs, three types of putative bamBs and seven types of putative nitrogenase reductase (nifHs) were determined, with their copy numbers decreased gradually from inlet to outlet. Distribution of chemicals, bacteria and putative genes confirmed PCP dechlorination and phenol degradation accomplished in segments 0–5 cm and 0–8 cm, respectively, contributing to a high PCP mineralization rate of 3.86 μM d−1. Through long-term incubation, dechlorination, phenol degradation and nitrogen fixation bacteria coexisted and functioned simultaneously near inlet (0–8 cm), verified the feasibility of anaerobic mineralization of halogenated aromatics in the compact reactor containing multiple functional microbes.
Collapse
Affiliation(s)
- Zhi-Ling Li
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090 China.,Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa, Nagoya 464-8603 Japan
| | - Jun Nan
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090 China
| | - Cong Huang
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090 China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Wen-Zong Liu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Hao-Yi Cheng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Chunfang Zhang
- Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa, Nagoya 464-8603 Japan
| | - Dongdong Zhang
- Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa, Nagoya 464-8603 Japan
| | - Deyong Kong
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090 China
| | - Kyoko Kanamaru
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601 Japan
| | - Tetsuo Kobayashi
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601 Japan
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology, Harbin 150090 China.,Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Arata Katayama
- Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa, Nagoya 464-8603 Japan.,Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603 Japan
| |
Collapse
|
25
|
Weinert T, Huwiler SG, Kung JW, Weidenweber S, Hellwig P, Stärk HJ, Biskup T, Weber S, Cotelesage JJH, George GN, Ermler U, Boll M. Structural basis of enzymatic benzene ring reduction. Nat Chem Biol 2015; 11:586-91. [PMID: 26120796 DOI: 10.1038/nchembio.1849] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/15/2015] [Indexed: 12/19/2022]
Abstract
In chemical synthesis, the widely used Birch reduction of aromatic compounds to cyclic dienes requires alkali metals in ammonia as extremely low-potential electron donors. An analogous reaction is catalyzed by benzoyl-coenzyme A reductases (BCRs) that have a key role in the globally important bacterial degradation of aromatic compounds at anoxic sites. Because of the lack of structural information, the catalytic mechanism of enzymatic benzene ring reduction remained obscure. Here, we present the structural characterization of a dearomatizing BCR containing an unprecedented tungsten cofactor that transfers electrons to the benzene ring in an aprotic cavity. Substrate binding induces proton transfer from the bulk solvent to the active site by expelling a Zn(2+) that is crucial for active site encapsulation. Our results shed light on the structural basis of an electron transfer process at the negative redox potential limit in biology. They open the door for biological or biomimetic alternatives to a basic chemical synthetic tool.
Collapse
Affiliation(s)
| | - Simona G Huwiler
- Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Johannes W Kung
- Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Hans-Joachim Stärk
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research UFZ, Leipzig, Germany
| | - Till Biskup
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Julien J H Cotelesage
- 1] Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada. [2] Canadian Light Source, Saskatoon, Saskatchewan, Canada
| | - Graham N George
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ulrich Ermler
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Matthias Boll
- Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| |
Collapse
|
26
|
Schmid G, René SB, Boll M. Enzymes of the benzoyl-coenzyme A degradation pathway in the hyperthermophilic archaeon Ferroglobus placidus. Environ Microbiol 2015; 17:3289-300. [PMID: 25630364 DOI: 10.1111/1462-2920.12785] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/09/2015] [Accepted: 01/14/2015] [Indexed: 12/28/2022]
Abstract
The Fe(III)-respiring Ferroglobus placidus is the only known archaeon and hyperthermophile for which a complete degradation of aromatic substrates to CO2 has been reported. Recent genome and transcriptome analyses proposed a benzoyl-coenzyme A (CoA) degradation pathway similar to that found in the phototrophic Rhodopseudomonas palustris, which involves a cyclohex-1-ene-1-carboxyl-CoA (1-enoyl-CoA) forming, ATP-dependent key enzyme benzoyl-CoA reductase (BCR). In this work, we demonstrate, by first in vitro studies, that benzoyl-CoA is ATP-dependently reduced by two electrons to cyclohexa-1,5-dienoyl-CoA (1,5-dienoyl-CoA), which is further degraded by hydration to 6-hydroxycyclohex-1-ene-1-carboxyl-CoA (6-OH-1-enoyl-CoA); upon addition of NAD(+) , the latter was subsequently converted to β-oxidation intermediates. The four candidate genes of BCR were heterologously expressed, and the enriched, oxygen-sensitive enzyme catalysed the two-electron reduction of benzoyl-CoA to 1,5-dienoyl-CoA. A gene previously assigned to a 2,3-didehydropimeloyl-CoA hydratase was heterologously expressed and shown to act as a typical 1,5-dienoyl-CoA hydratase that does not accept 1-enoyl-CoA. A gene previously assigned to a 1-enoyl-CoA hydratase was heterologously expressed and identified to code for a bifunctional crotonase/3-OH-butyryl-CoA dehydrogenase. In summary, the results consistently provide biochemical evidence that F. placidus and probably other archaea predominantly degrade aromatics via the Thauera/Azoarcus type and not or only to a minor extent via the predicted R. palustris-type benzoyl-CoA degradation pathway.
Collapse
Affiliation(s)
- Georg Schmid
- Microbiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg, 79104, Germany
| | - Sandra Bosch René
- Microbiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg, 79104, Germany
| | - Matthias Boll
- Microbiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg, 79104, Germany
| |
Collapse
|
27
|
Li ZL, Nan J, Yang JQ, Jin X, Katayama A, Wang AJ. Temporal distributions of functional microbes and putative genes associated with halogenated phenol anaerobic dehalogenation and further mineralization. RSC Adv 2015. [DOI: 10.1039/c5ra16815e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Growth interactions of functional dehalogenators, degraders and genes (cprAandbamB) during anaerobic mineralization of HACs in an enriched consortium.
Collapse
Affiliation(s)
- Zhi-ling Li
- State Key Laboratory of Urban Water Resources and Environment
- Harbin Institute of Technology
- Harbin 150090
- China
- EcoTopia Science Institute
| | - Jun Nan
- State Key Laboratory of Urban Water Resources and Environment
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Jia-qi Yang
- State Key Laboratory of Urban Water Resources and Environment
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Xiao Jin
- Department of Civil Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Arata Katayama
- EcoTopia Science Institute
- Nagoya University
- Nagoya 464-8603
- Japan
- Department of Civil Engineering
| | - Ai-jie Wang
- State Key Laboratory of Urban Water Resources and Environment
- Harbin Institute of Technology
- Harbin 150090
- China
- Key Laboratory of Environmental Biotechnology
| |
Collapse
|
28
|
Estelmann S, Blank I, Feldmann A, Boll M. Two distinct old yellow enzymes are involved in naphthyl ring reduction during anaerobic naphthalene degradation. Mol Microbiol 2014; 95:162-72. [PMID: 25424741 DOI: 10.1111/mmi.12875] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2014] [Indexed: 11/29/2022]
Abstract
The 2-naphthoyl-coenzyme A (NCoA) reductase (NCR) is so far the only characterized enzyme involved in the anaerobic degradation of the environmentally relevant polycyclic aromatic hydrocarbons. The old yellow enzyme (OYE) family member apparently reduced the nonactivated naphthyl ring to 5,6,7,8-tetrahydro-2-napthoyl-CoA (THNCoA). In this work, the candidate genes of three NCRs from the sulphate-reducing, naphthalene-degrading N47 and NaphS2 cultures were expressed in Escherichia coli. The isolated products contained flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN) a [4Fe-4S] cluster and catalyzed only the two-electron reduction of NCoA to 5,6-dihydro-2-naphthoyl-CoA (5,6-DHNCoA) at a very negative E°' = -493 mV. All NCRs exhibited high NCoA-forming DHNCoA oxidase activities that are proposed to be involved in oxygen-detoxification during naphthalene degradation. Extracts of N47 and NaphS2 catalyzed the reduction of 5,6-DHNCoA to THNCoA. Genes putatively coding for 5,6-DHNCR from N47 and NaphS2 were heterologously expressed in E. coli. The enriched enzyme products specifically catalyzed the reduction of 5,6-DHNCoA to THNCoA at E°' = -375 mV. With the three NCRs and two 5,6-DHNCRs, five OYEs have been characterized that are involved in the reduction of the nonsubstituted naphthyl-ring system; these unprecedented enzymatic reactions expand our knowledge of the functional diversity of OYE.
Collapse
Affiliation(s)
- Sebastian Estelmann
- Microbiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | | | | | | |
Collapse
|
29
|
Buckel W, Kung JW, Boll M. The benzoyl-coenzyme a reductase and 2-hydroxyacyl-coenzyme a dehydratase radical enzyme family. Chembiochem 2014; 15:2188-94. [PMID: 25204868 DOI: 10.1002/cbic.201402270] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg (Germany)
| | | | | |
Collapse
|
30
|
Enzymes involved in a novel anaerobic cyclohexane carboxylic acid degradation pathway. J Bacteriol 2014; 196:3667-74. [PMID: 25112478 DOI: 10.1128/jb.02071-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The anaerobic degradation of cyclohexane carboxylic acid (CHC) has so far been studied only in Rhodopseudomonas palustris, in which CHC is activated to cyclohexanoyl coenzyme A (cyclohexanoyl-CoA [CHCoA]) and then dehydrogenated to cyclohex-1-ene-1-carboxyl-CoA (CHeneCoA). This intermediate is further degraded by reactions of the R. palustris-specific benzoyl-CoA degradation pathway of aromatic compounds. However, CHeneCoA is not an intermediate in the degradation of aromatic compounds in all other known anaerobic bacteria; consequently, degradation of CHC was mostly unknown in anaerobic bacteria. We identified a previously unknown CHC degradation pathway in the Fe(III)-reducing Geobacter metallireducens by determining the following CHC-induced in vitro activities: (i) the activation of CHC to CHCoA by a succinyl-CoA:CHC CoA transferase, (ii) the 1,2-dehydrogenation of CHCoA to CHeneCoA by CHCoA dehydrogenase, and (iii) the unusual 1,4-dehydrogenation of CHeneCoA to cyclohex-1,5-diene-1-carboxyl-CoA. This last represents a previously unknown joint intermediate of the CHC and aromatic compound degradation pathway in bacteria other than R. palustris. The enzymes catalyzing the three reactions were purified and characterized as specific enzymes after heterologous expression of the encoding genes. Quantitative reverse transcription-PCR revealed that expression of these genes was highly induced during growth with CHC but not with benzoate. The newly identified CHC degradation pathway is suggested to be present in nearly all CHC-degrading anaerobic bacteria, including denitrifying, Fe(III)-reducing, sulfate-reducing, and fermenting bacteria. Remarkably, all three CHC degradation pathways always link CHC catabolism to the catabolic pathways of aromatic compounds. We propose that the capacity to use CHC as a carbon source evolved from already-existing aromatic compound degradation pathways.
Collapse
|
31
|
Porter AW, Young LY. Benzoyl-CoA, a universal biomarker for anaerobic degradation of aromatic compounds. ADVANCES IN APPLIED MICROBIOLOGY 2014; 88:167-203. [PMID: 24767428 DOI: 10.1016/b978-0-12-800260-5.00005-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Aromatic compounds are a major component of the global carbon pool and include a diverse range of compounds such as humic acid, lignin, amino acids, and industrial contaminants. Due to the prevalence of aromatic compounds in the environment, aerobic and anaerobic microorganisms have evolved mechanisms by which to metabolize that available carbon. Less well understood are the anaerobic pathways. We now know that anaerobic metabolism of a variety of monoaromatic compounds can be initiated in a number of different ways, and a key metabolite for these pathways is benzoyl-CoA. Chemicals can have different upstream anaerobic degradation pathways yet can still be assessed by targeting the downstream benzoyl-CoA pathway. In this pathway, we propose that the ring opening hydrolase, encoded by the bamA gene, is especially useful because, in contrast to the benzoyl-CoA reductase, it is detected under a number of respiratory settings, including denitrifying, iron-reducing, sulfate-reducing, and fermentative conditions, and has a wide distribution in the environment. This review examines the bamA gene in enrichment cultures and environmental DNA extracts to consider whether it can be used as a biomarker for anaerobic aromatic degradation. Given the number of potential upstream inputs from natural and man-made monoaromatic compounds, the benzoyl-CoA pathway and the bamA gene in particular may play an important role in the global carbon cycle that has thus far been overlooked.
Collapse
Affiliation(s)
- Abigail W Porter
- Department of Environmental Science, School of Biological and Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA.
| | - Lily Y Young
- Department of Environmental Science, School of Biological and Environmental Sciences, Rutgers University, New Brunswick, New Jersey, USA
| |
Collapse
|
32
|
Kuever J, Visser M, Loeffler C, Boll M, Worm P, Sousa DZ, Plugge CM, Schaap PJ, Muyzer G, Pereira IAC, Parshina SN, Goodwin LA, Kyrpides NC, Detter J, Woyke T, Chain P, Davenport KW, Rohde M, Spring S, Klenk HP, Stams AJM. Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. Stand Genomic Sci 2014; 9:821-39. [PMID: 25197466 PMCID: PMC4148979 DOI: 10.4056/sigs.5209235] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes.
Collapse
Affiliation(s)
- Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Michael Visser
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Claudia Loeffler
- Albert-Ludwigs-University Freiburg, Institute of Biology II, Freiburg, Germany
| | - Matthias Boll
- Albert-Ludwigs-University Freiburg, Institute of Biology II, Freiburg, Germany
| | - Petra Worm
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Diana Z Sousa
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Caroline M Plugge
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Peter J Schaap
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, The Netherlands
| | - Gerard Muyzer
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ines A C Pereira
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofiya N Parshina
- Winogradsky Institute of Microbiology Russian Academy of Sciences, Moscow, Russia
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Janine Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Karen W Davenport
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alfons J M Stams
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands ; University of Minho, Centre of Biological Engineering, Braga, Portugal
| |
Collapse
|
33
|
Primers: Functional Genes for Anaerobic Hydrocarbon Degrading Microbes. SPRINGER PROTOCOLS HANDBOOKS 2014. [DOI: 10.1007/8623_2014_44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
34
|
Boll M, Löffler C, Morris BEL, Kung JW. Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes. Environ Microbiol 2013; 16:612-27. [PMID: 24238333 DOI: 10.1111/1462-2920.12328] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/03/2013] [Indexed: 11/28/2022]
Abstract
Next to carbohydrates, aromatic compounds are the second most abundant class of natural organic molecules in living organic matter but also make up a significant proportion of fossil carbon sources. Only microorganisms are capable of fully mineralizing aromatic compounds. While aerobic microbes use well-studied oxygenases for the activation and cleavage of aromatic rings, anaerobic bacteria follow completely different strategies to initiate catabolism. The key enzymes related to aromatic compound degradation in anaerobic bacteria are comprised of metal- and/or flavin-containing cofactors, of which many use unprecedented radical mechanisms for C-H bond cleavage or dearomatization. Over the past decade, the increasing number of completed genomes has helped to reveal a large variety of anaerobic degradation pathways in Proteobacteria, Gram-positive microbes and in one archaeon. This review aims to update our understanding of the occurrence of aromatic degradation capabilities in anaerobic microorganisms and serves to highlight characteristic enzymatic reactions involved in (i) the anoxic oxidation of alkyl side chains attached to aromatic rings, (ii) the carboxylation of aromatic rings and (iii) the reductive dearomatization of central arylcarboxyl-coenzyme A intermediates. Depending on the redox potential of the electron acceptors used and the metabolic efficiency of the cell, different strategies may be employed for identical overall reactions.
Collapse
Affiliation(s)
- Matthias Boll
- Institute for Biology II, University of Freiburg, Freiburg, Germany
| | | | | | | |
Collapse
|
35
|
Kim SJ, Park SJ, Cha IT, Min D, Kim JS, Chung WH, Chae JC, Jeon CO, Rhee SK. Metabolic versatility of toluene-degrading, iron-reducing bacteria in tidal flat sediment, characterized by stable isotope probing-based metagenomic analysis. Environ Microbiol 2013; 16:189-204. [DOI: 10.1111/1462-2920.12277] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/28/2022]
Affiliation(s)
- So-Jeong Kim
- Department of Microbiology; Chungbuk National University; Cheongju 361-763 Korea
| | - Soo-Je Park
- Department of Biology; Jeju National University; Jeju 690-756 Korea
| | - In-Tae Cha
- Department of Microbiology; Chungbuk National University; Cheongju 361-763 Korea
| | - Deullae Min
- Center for Gas Analysis; Korea Research Institute of Standards and Science; 267 Gajeong-ro, Yuseong-gu Daejeon 305-340 Korea
| | - Jin-Seog Kim
- Center for Gas Analysis; Korea Research Institute of Standards and Science; 267 Gajeong-ro, Yuseong-gu Daejeon 305-340 Korea
| | - Won-Hyung Chung
- Korean Bioinformation Center; Korean Research Institute of Bioscience and Bioengineering; Daejeon 305-806 Korea
| | - Jong-Chan Chae
- Division of Biotechnology; Chonbuk National University; Iksan 570-752 Korea
| | - Che Ok Jeon
- School of Biological Sciences; Chung-Ang University; Seoul 156-756 Korea
| | - Sung-Keun Rhee
- Department of Microbiology; Chungbuk National University; Cheongju 361-763 Korea
| |
Collapse
|
36
|
Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi. ISME JOURNAL 2013; 8:383-97. [PMID: 23966099 DOI: 10.1038/ismej.2013.143] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 06/24/2013] [Accepted: 07/22/2013] [Indexed: 12/27/2022]
Abstract
Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are widely distributed in the marine subsurface, yet metabolic properties of the many uncultivated lineages are completely unknown. This study therefore analysed genomic content from a single DEH cell designated 'DEH-J10' obtained from the sediments of Aarhus Bay, Denmark. Real-time PCR showed the DEH-J10 phylotype was abundant in upper sediments but was absent below 160 cm below sea floor. A 1.44 Mbp assembly was obtained and was estimated to represent up to 60.8% of the full genome. The predicted genome is much larger than genomes of cultivated DEH and appears to confer metabolic versatility. Numerous genes encoding enzymes of core and auxiliary beta-oxidation pathways were identified, suggesting that this organism is capable of oxidising various fatty acids and/or structurally related substrates. Additional substrate versatility was indicated by genes, which may enable the bacterium to oxidise aromatic compounds. Genes encoding enzymes of the reductive acetyl-CoA pathway were identified, which may also enable the fixation of CO2 or oxidation of organics completely to CO2. Genes encoding a putative dimethylsulphoxide reductase were the only evidence for a respiratory terminal reductase. No evidence for reductive dehalogenase genes was found. Genetic evidence also suggests that the organism could synthesise ATP by converting acetyl-CoA to acetate by substrate-level phosphorylation. Other encoded enzymes putatively conferring marine adaptations such as salt tolerance and organo-sulphate sulfohydrolysis were identified. Together, these analyses provide the first insights into the potential metabolic traits that may enable members of the DEH to occupy an ecological niche in marine sediments.
Collapse
|
37
|
Kung JW, Seifert J, von Bergen M, Boll M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J Bacteriol 2013; 195:3193-200. [PMID: 23667239 PMCID: PMC3697644 DOI: 10.1128/jb.00322-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/07/2013] [Indexed: 11/20/2022] Open
Abstract
The strictly anaerobic Syntrophus aciditrophicus is a fermenting deltaproteobacterium that is able to degrade benzoate or crotonate in the presence and in the absence of a hydrogen-consuming partner. During growth in pure culture, both substrates are dismutated to acetate and cyclohexane carboxylate. In this work, the unknown enzymes involved in the late steps of cyclohexane carboxylate formation were studied. Using enzyme assays monitoring the oxidative direction, a cyclohex-1-ene-1-carboxyl-CoA (Ch1CoA)-forming cyclohexanecarboxyl-CoA (ChCoA) dehydrogenase was purified and characterized from S. aciditrophicus and after heterologous expression of its gene in Escherichia coli. In addition, a cyclohexa-1,5-diene-1-carboxyl-CoA (Ch1,5CoA)-forming Ch1CoA dehydrogenase was characterized after purification of the heterologously expressed gene. Both enzymes had a native molecular mass of 150 kDa and were composed of a single, 40- to 45-kDa subunit; both contained flavin adenine dinucleotide (FAD) as a cofactor. While the ChCoA dehydrogenase was competitively inhibited by Ch1CoA in the oxidative direction, Ch1CoA dehydrogenase further converted the product Ch1,5CoA to benzoyl-CoA. The results obtained suggest that Ch1,5CoA is a common intermediate in benzoate and crotonate fermentation that serves as an electron-accepting substrate for the two consecutively operating acyl-CoA dehydrogenases characterized in this work. In the case of benzoate fermentation, Ch1,5CoA is formed by a class II benzoyl-CoA reductase; in the case of crotonate fermentation, Ch1,5CoA is formed by reversing the reactions of the benzoyl-CoA degradation pathway that are also employed during the oxidative (degradative) branch of benzoate fermentation.
Collapse
Affiliation(s)
- Johannes W. Kung
- Microbiology, Institute of Biology II, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jana Seifert
- Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, Germany
- Helmholtz Centre for Environmental Research, Department of Metabolomics, Leipzig, Germany
| | - Matthias Boll
- Microbiology, Institute of Biology II, University of Freiburg, Freiburg im Breisgau, Germany
| |
Collapse
|
38
|
Eberlein C, Johannes J, Mouttaki H, Sadeghi M, Golding BT, Boll M, Meckenstock RU. ATP-dependent/-independent enzymatic ring reductions involved in the anaerobic catabolism of naphthalene. Environ Microbiol 2013; 15:1832-41. [PMID: 23336264 DOI: 10.1111/1462-2920.12076] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/12/2012] [Accepted: 12/13/2012] [Indexed: 11/26/2022]
Abstract
Polycyclic aromatic hydrocarbons are among the most hazardous environmental pollutants. However, in contrast to aerobic degradation, the respective degradation pathways in anaerobes are greatly unknown which has so far prohibited many environmental investigations. In this work, we studied the enzymatic dearomatization reactions involved in the degradation of the PAH model compounds naphthalene and 2-methylnaphthalene in the sulfate-reducing enrichment culture N47. Cell extracts of N47 grown on naphthalene catalysed the sodium dithionite-dependent four-electron reduction of the key intermediate 2-naphthoyl-coenzyme A (NCoA) to 5,6,7,8-tetrahydro-2-naphthoyl-CoA (THNCoA). The NCoA reductase activity was independent of ATP and was, surprisingly, not sensitive to oxygen. In cell extracts in the presence of various electron donors the product THNCoA was further reduced by a two-electron reaction to most likely a conjugated hexahydro-2-naphthoyl-CoA isomer (HHNCoA). The reaction assigned to THNCoA reductase strictly depended on ATP and was oxygen-sensitive with a half-life time between 30 s and 1 min when exposed to air. The rate was highest with NADH as electron donor. The results indicate that two novel and completely different dearomatizing ring reductases are involved in anaerobic naphthalene degradation. While the THNCoA reducing activity shows some properties of ATP-dependent class I benzoyl-CoA reductases, NCoA reduction appears to be catalysed by a previously unknown class of dearomatizing aryl-carboxyl-CoA reductases.
Collapse
|
39
|
Philipp B, Schink B. Different strategies in anaerobic biodegradation of aromatic compounds: nitrate reducers versus strict anaerobes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:469-478. [PMID: 23760891 DOI: 10.1111/j.1758-2229.2011.00304.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Mononuclear aromatic compounds are degraded anaerobically through pathways that are basically different from those used in the presence of oxygen. Whereas aerobic degradation destabilizes the aromatic π-electron system by oxidative steps through oxygenase reactions, anaerobic degradation is most often initiated by a reductive attack. The benzoyl-CoA pathway is the most important metabolic route in this context, and a broad variety of mononuclear aromatics, including phenol, cresols, toluene, xylenes and ethylbenzene, are channelled into this pathway through various modification reactions. Multifunctional phenolic compounds are metabolized via the reductive resorcinol pathway, the oxidative resorcinol pathway with hydroxyhydroquinone as key intermediate, and the phloroglucinol pathway. Comparison of the various pathways used for modification and degradation of aromatics in the absence of oxygen indicates that the strategies of breakdown of these compounds are largely determined by the redox potentials of the electron acceptors used, and by the overall reaction energetics. Consequently, nitrate reducers quite often use strategies for primary attack on aromatic compounds that differ from those used by sulfate-reducing, iron-reducing or fermenting bacteria.
Collapse
Affiliation(s)
- Bodo Philipp
- Department of Biology, University of Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany
| | | |
Collapse
|
40
|
Grein F, Ramos AR, Venceslau SS, Pereira IAC. Unifying concepts in anaerobic respiration: insights from dissimilatory sulfur metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:145-60. [PMID: 22982583 DOI: 10.1016/j.bbabio.2012.09.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
Abstract
Behind the versatile nature of prokaryotic energy metabolism is a set of redox proteins having a highly modular character. It has become increasingly recognized that a limited number of redox modules or building blocks appear grouped in different arrangements, giving rise to different proteins and functionalities. This modularity most likely reveals a common and ancient origin for these redox modules, and is obviously reflected in similar energy conservation mechanisms. The dissimilation of sulfur compounds was probably one of the earliest biological strategies used by primitive organisms to obtain energy. Here, we review some of the redox proteins involved in dissimilatory sulfur metabolism, focusing on sulfate reducing organisms, and highlight links between these proteins and others involved in different processes of anaerobic respiration. Noteworthy are links to the complex iron-sulfur molybdoenzyme family, and heterodisulfide reductases of methanogenic archaea. We discuss how chemiosmotic and electron bifurcation/confurcation may be involved in energy conservation during sulfate reduction, and how introduction of an additional module, multiheme cytochromes c, opens an alternative bioenergetic strategy that seems to increase metabolic versatility. Finally, we highlight new families of heterodisulfide reductase-related proteins from non-methanogenic organisms, which indicate a widespread distribution for these protein modules and may indicate a more general involvement of thiol/disulfide conversions in energy metabolism. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
Collapse
Affiliation(s)
- Fabian Grein
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | | | | |
Collapse
|
41
|
Juárez JF, Zamarro MT, Eberlein C, Boll M, Carmona M, Díaz E. Characterization of the mbd cluster encoding the anaerobic 3-methylbenzoyl-CoA central pathway. Environ Microbiol 2012; 15:148-66. [PMID: 22759228 DOI: 10.1111/j.1462-2920.2012.02818.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mbd cluster encoding genes of the 3-methylbenzoyl-CoA pathway involved in the anaerobic catabolism of 3-methylbenzoate and m-xylene was characterized for the first time in the denitrifying β-Proteobacterium Azoarcus sp. CIB. The mbdA gene product was identified as a 3-methylbenzoate-CoA ligase required for 3-methylbenzoate activation; its substrate spectrum was unique in activating all three methylbenzoate isomers. An inducible 3-methylbenzoyl-CoA reductase (mbdONQP gene products), displaying significant amino acid sequence similarities to known class I benzoyl-CoA reductases catalysed the ATP-dependent reduction of 3-methylbenzoyl-CoA to a methyldienoyl-CoA. The mbdW gene encodes a methyldienoyl-CoA hydratase that hydrated the methyldienoyl-CoA to a methyl-6-hydroxymonoenoyl-CoA compound. The mbd cluster also contains the genes predicted to be involved in the subsequent steps of the 3-methylbenzoyl-CoA pathway as well as the electron donor system for the reductase activity. Whereas the catabolic mbd genes are organized in two divergent inducible operons, the putative mbdR regulatory gene was transcribed separately and showed constitutive expression. The efficient expression of the mbd genes required the oxygen-dependent AcpR activator, and it was subject of carbon catabolite repression by some organic acids and amino acids. Sequence analyses suggest that the mbd gene cluster was recruited by Azoarcus sp. CIB through horizontal gene transfer.
Collapse
Affiliation(s)
- Javier F Juárez
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
42
|
Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers. Appl Microbiol Biotechnol 2012; 94:851-73. [PMID: 22476263 DOI: 10.1007/s00253-012-4025-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 02/06/2023]
Abstract
Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.
Collapse
|
43
|
Identification and characterization of a succinyl-coenzyme A (CoA):benzoate CoA transferase in Geobacter metallireducens. J Bacteriol 2012; 194:2501-8. [PMID: 22408161 DOI: 10.1128/jb.00306-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Geobacter metallireducens is a Fe(III)-respiring deltaproteobacterium and serves as a model organism for aromatic compound-degrading, obligately anaerobic bacteria. In this study, a genetic system was established for G. metallireducens using nitrate as an alternative electron acceptor. Surprisingly, disruption of the benzoate-induced bamY gene, encoding a benzoate coenzyme A (CoA) ligase, reproducibly showed an increased biomass yield in comparison to the wild type during growth with benzoate but not during growth with acetate. Complementation of bamY in trans converted the biomass yield back to the wild-type level. Growth of the bamY mutant with benzoate can be rationalized by the identification of a previously unknown succinyl-CoA:benzoate CoA transferase activity; it represents an additional, energetically less demanding mode of benzoate activation. The activity was highly enriched from extracts of cells grown on benzoate, yielding a 50-kDa protein band; mass spectrometric analysis identified the corresponding benzoate-induced gene annotated as a CoA transferase. It was heterologously expressed in Escherichia coli and characterized as a specific succinyl-CoA:benzoate CoA transferase. The newly identified enzyme in conjunction with a benzoate-induced succinyl-CoA synthetase links the tricarboxylic acid cycle to the upper benzoyl-CoA degradation pathway during growth on aromatic growth substrates.
Collapse
|
44
|
Holmes DE, Risso C, Smith JA, Lovley DR. Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus. THE ISME JOURNAL 2012; 6:146-57. [PMID: 21776029 PMCID: PMC3246244 DOI: 10.1038/ismej.2011.88] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 06/07/2011] [Accepted: 06/07/2011] [Indexed: 01/02/2023]
Abstract
Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (>80° C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as having a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA (coenzyme A) reductase (BCR) found in all strictly anaerobic bacteria, but has instead genes coding for a bzd-type ATP-consuming class I BCR, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for phenol carboxylation proceeding through a phenylphosphate intermediate were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative reverse transcriptase polymerase chain reaction demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates vs growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism are highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets.
Collapse
Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA.
| | | | | | | |
Collapse
|
45
|
Abstract
Aromatic compounds are both common growth substrates for microorganisms and prominent environmental pollutants. The crucial step in their degradation is overcoming the resonance energy that stabilizes the ring structure. The classical strategy for degradation comprises an attack by oxygenases that hydroxylate and finally cleave the ring with the help of activated molecular oxygen. Here, we describe three alternative strategies used by microorganisms to degrade aromatic compounds. All three of these methods involve the use of CoA thioesters and ring cleavage by hydrolysis. However, these strategies are based on different ring activation mechanisms that consist of either formation of a non-aromatic ring-epoxide under oxic conditions, or reduction of the aromatic ring under anoxic conditions using one of two completely different systems.
Collapse
|
46
|
Combined application of PCR-based functional assays for the detection of aromatic-compound-degrading anaerobes. Appl Environ Microbiol 2011; 77:5056-61. [PMID: 21602396 DOI: 10.1128/aem.00335-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To explore the reliability of assays that detect aromatic-compound-degrading anaerobes, a combination of three functional-gene-targeting assays was applied to microcosms from benzene-contaminated aquifers. Results of the assays were consistent and suggest that species related to the genera Azoarcus and Geobacter dominated benzene degradation at the individual sites.
Collapse
|
47
|
Monitoring the metabolic status of geobacter species in contaminated groundwater by quantifying key metabolic proteins with Geobacter-specific antibodies. Appl Environ Microbiol 2011; 77:4597-602. [PMID: 21551286 DOI: 10.1128/aem.00114-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simple and inexpensive methods for assessing the metabolic status and bioremediation activities of subsurface microorganisms are required before bioremediation practitioners will adopt molecular diagnosis of the bioremediation community as a routine practice for guiding the development of bioremediation strategies. Quantifying gene transcripts can diagnose important aspects of microbial physiology during bioremediation but is technically challenging and does not account for the impact of translational modifications on protein abundance. An alternative strategy is to directly quantify the abundance of key proteins that might be diagnostic of physiological state. To evaluate this strategy, an antibody-based quantification approach was developed to investigate subsurface Geobacter communities. The abundance of citrate synthase corresponded with rates of metabolism of Geobacter bemidjiensis in chemostat cultures. During in situ bioremediation of uranium-contaminated groundwater the quantity of Geobacter citrate synthase increased with the addition of acetate to the groundwater and decreased when acetate amendments stopped. The abundance of the nitrogen-fixation protein, NifD, increased as ammonium became less available in the groundwater and then declined when ammonium concentrations increased. In a petroleum-contaminated aquifer, the abundance of BamB, an enzyme subunit involved in the anaerobic degradation of mono-aromatic compounds by Geobacter species, increased in zones in which Geobacter were expected to play an important role in aromatic hydrocarbon degradation. These results suggest that antibody-based detection of key metabolic proteins, which should be readily adaptable to standardized kits, may be a feasible method for diagnosing the metabolic state of microbial communities responsible for bioremediation, aiding in the rational design of bioremediation strategies.
Collapse
|
48
|
Lovley DR, Ueki T, Zhang T, Malvankar NS, Shrestha PM, Flanagan KA, Aklujkar M, Butler JE, Giloteaux L, Rotaru AE, Holmes DE, Franks AE, Orellana R, Risso C, Nevin KP. Geobacter: the microbe electric's physiology, ecology, and practical applications. Adv Microb Physiol 2011; 59:1-100. [PMID: 22114840 DOI: 10.1016/b978-0-12-387661-4.00004-5] [Citation(s) in RCA: 384] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.
Collapse
Affiliation(s)
- Derek R Lovley
- Department of Microbiology and Environmental Biotechnology Center, University of Massachusetts, Amherst, Massachusetts, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|