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Lequan Q, Yanan F, Xianda Z, Mengyuan B, Chenyu L, Shijin W. Mechanisms and high-value applications of phthalate isomers degradation pathways in bacteria. World J Microbiol Biotechnol 2024; 40:247. [PMID: 38904858 DOI: 10.1007/s11274-024-04060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
Phthalate isomers are key intermediates in the biodegradation of pollutants including waste polyethylene terephthalate (PET) plastics and plasticizers. So far, an increasing number of phthalate isomer-degrading strains have been isolated, and their degradation pathways show significant diversity. In this paper, we comprehensively review the current status of research on the degrading bacteria, degradation characteristics, aerobic and anaerobic degradation pathways, and degradation genes (clusters) of phthalate isomers, and discuss the current shortcomings and challenges. Moreover, the degradation process of phthalate isomers produces many important aromatic precursor molecules, which can be used to produce higher-value derivative chemicals, and the modification of their degradation pathways holds good prospects. Therefore, this review also highlights the current progress made in modifying the phthalate isomer degradation pathway and explores its potential for high-value applications.
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Affiliation(s)
- Qiu Lequan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
| | - Fu Yanan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhou Xianda
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Bao Mengyuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Li Chenyu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Wu Shijin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
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2
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Kümpel C, Grosser M, Tanabe TS, Dahl C. Fe/S proteins in microbial sulfur oxidation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119732. [PMID: 38631440 DOI: 10.1016/j.bbamcr.2024.119732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
Iron-sulfur clusters serve as indispensable cofactors within proteins across all three domains of life. Fe/S clusters emerged early during the evolution of life on our planet and the biogeochemical cycle of sulfur is one of the most ancient and important element cycles. It is therefore no surprise that Fe/S proteins have crucial roles in the multiple steps of microbial sulfur metabolism. During dissimilatory sulfur oxidation in prokaryotes, Fe/S proteins not only serve as electron carriers in several steps, but also perform catalytic roles, including unprecedented reactions. Two cytoplasmic enzyme systems that oxidize sulfane sulfur to sulfite are of particular interest in this context: The rDsr pathway employs the reverse acting dissimilatory sulfite reductase rDsrAB as its key enzyme, while the sHdr pathway utilizes polypeptides resembling the HdrA, HdrB and HdrC subunits of heterodisulfide reductase from methanogenic archaea. Both pathways involve components predicted to bind unusual noncubane Fe/S clusters acting as catalysts for the formation of disulfide or sulfite. Mapping of Fe/S cluster machineries on the sulfur-oxidizing prokaryote tree reveals that ISC, SUF, MIS and SMS are all sufficient to meet the Fe/S cluster maturation requirements for operation of the sHdr or rDsr pathways. The sHdr pathway is dependent on lipoate-binding proteins that are assembled by a novel pathway, involving two Radical SAM proteins, namely LipS1 and LipS2. These proteins coordinate sulfur-donating auxiliary Fe/S clusters in atypical patterns by three cysteines and one histidine and act as lipoyl synthases by jointly inserting two sulfur atoms to an octanoyl residue. This article is part of a Special Issue entitled: Biogenesis and Function of Fe/S proteins.
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Affiliation(s)
- Carolin Kümpel
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Martina Grosser
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
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Bruns S, Cakić N, Mitschke N, Kopke BJ, Rabus R, Wilkes H. A Novel Coenzyme A Analogue in the Anaerobic, Sulfate-Reducing, Marine Bacterium Desulfobacula toluolica Tol2 T. Chembiochem 2023; 24:e202200584. [PMID: 36331165 PMCID: PMC10107677 DOI: 10.1002/cbic.202200584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022]
Abstract
Coenzyme A (CoA) thioesters are formed during anabolic and catabolic reactions in every organism. Degradation pathways of growth-supporting substrates in bacteria can be predicted by differential proteogenomic studies. Direct detection of proposed metabolites such as CoA thioesters by high-performance liquid chromatography coupled with high-resolution mass spectrometry can confirm the reaction sequence and demonstrate the activity of these degradation pathways. In the metabolomes of the anaerobic sulfate-reducing bacterium Desulfobacula toluolica Tol2T grown with different substrates various CoA thioesters, derived from amino acid, fatty acid or alcohol metabolism, have been detected. Additionally, the cell extracts of this bacterium revealed a number of CoA analogues with molecular masses increased by 1 dalton. By comparing the chromatographic and mass spectrometric properties of synthetic reference standards with those of compounds detected in cell extracts of D. toluolica Tol2T and by performing co-injection experiments, these analogues were identified as inosino-CoAs. These CoA thioesters contain inosine instead of adenosine as the nucleoside. To the best of our knowledge, this finding represents the first detection of naturally occurring inosino-CoA analogues.
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Affiliation(s)
- Stefan Bruns
- Institute for Chemistry and Biology of the, Marine Environment (ICBM), Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Nevenka Cakić
- Institute for Chemistry and Biology of the, Marine Environment (ICBM), Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Nico Mitschke
- Institute for Chemistry and Biology of the, Marine Environment (ICBM), Marine Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Bernd Johann Kopke
- Institute for Chemistry and Biology of the, Marine Environment (ICBM), Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the, Marine Environment (ICBM), General and Molecular Microbiology, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the, Marine Environment (ICBM), Organic Geochemistry, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
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Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic Aromatoleum aromaticum EbN1 T. mSystems 2022; 7:e0068522. [PMID: 36445109 PMCID: PMC9765128 DOI: 10.1128/msystems.00685-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Members of the genus Aromatoleum thrive in diverse habitats and use a broad range of recalcitrant organic molecules coupled to denitrification or O2 respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1T, we studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate, and acetate utilized under nitrate-reducing versus oxic conditions. Integrated multi-omics (transcriptome, proteome, and metabolome) covered most of the catabolic network (199 genes) and allowed for the refining of knowledge of the degradation modules studied. Their substrate-dependent regulation showed differing degrees of specificity, ranging from high with 3-(4-hydroxyphenyl)propanoate to mostly relaxed with benzoate. For benzoate, the transcript and protein formation were essentially constitutive, contrasted by that of anoxia-specific versus oxia-specific metabolite profiles. The matrix factorization of transcriptomic data revealed that the anaerobic modules accounted for most of the variance across the degradation network. The respiration network appeared to be constitutive, both on the transcript and protein levels, except for nitrate reductase (with narGHI expression occurring only under nitrate-reducing conditions). The anoxia/nitrate-dependent transcription of denitrification genes is apparently controlled by three FNR-type regulators as well as by NarXL (all constitutively formed). The resequencing and functional reannotation of the genome fostered a genome-scale metabolic model, which is comprised of 655 enzyme-catalyzed reactions and 731 distinct metabolites. The model predictions for growth rates and biomass yields agreed well with experimental stoichiometric data, except for 3-(4-hydroxyphenyl)propanoate, with which 4-hydroxybenzoate was exported. Taken together, the combination of multi-omics, growth physiology, and a metabolic model advanced our knowledge of an environmentally relevant microorganism that differs significantly from other bacterial model strains. IMPORTANCE Aromatic compounds are abundant constituents not only of natural organic matter but also of bulk industrial chemicals and fuel components of environmental concern. Considering the widespread occurrence of redox gradients in the biosphere, facultative anaerobic degradation specialists can be assumed to play a prominent role in the natural mineralization of organic matter and in bioremediation at contaminated sites. Surprisingly, differential multi-omics profiling of the A. aromaticum EbN1T studied here revealed relaxed regulatory stringency across its four main physiological modi operandi (i.e., O2-independent and O2-dependent degradation reactions versus denitrification and O2 respiration). Combining multi-omics analyses with a genome-scale metabolic model aligned with measured growth performances establishes A. aromaticum EbN1T as a systems-biology model organism and provides unprecedented insights into how this bacterium functions on a holistic level. Moreover, this experimental platform invites future studies on eco-systems and synthetic biology of the environmentally relevant betaproteobacterial Aromatoleum/Azoarcus/Thauera cluster.
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Chen SC, Ji J, Popp D, Jaekel U, Richnow HH, Sievert SM, Musat F. Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist. Environ Microbiol 2022; 24:1964-1976. [PMID: 35257474 DOI: 10.1111/1462-2920.15956] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 11/30/2022]
Abstract
The metabolic potential of the sulfate-reducing bacterium Desulfosarcina sp. strain BuS5, currently the only pure culture able to oxidize the volatile alkanes propane and butane without oxygen, was investigated via genomics, proteomics and physiology assays. Complete genome sequencing revealed that strain BuS5 encodes a single alkyl-succinate synthase, an enzyme which apparently initiates oxidation of both propane and butane. The formed alkyl-succinates are oxidized to CO2 via beta oxidation and the oxidative Wood-Ljungdahl pathways as shown by proteogenomics analyses. Strain BuS5 conserves energy via the canonical sulfate reduction pathway and electron bifurcation. An ability to utilize long-chain fatty acids, mannose and oligopeptides, suggested by automated annotation pipelines, was not supported by physiology assays and in-depth analyses of the corresponding genetic systems. Consistently, comparative genomics revealed a streamlined BuS5 genome with a remarkable paucity of catabolic modules. These results establish strain BuS5 as an exceptional metabolic specialist, able to grow only with propane and butane, for which we propose the name Desulfosarcina aeriophaga BuS5. This highly restrictive lifestyle, most likely the result of habitat-driven evolutionary gene loss, may provide D. aeriophaga BuS5 a competitive edge in sediments impacted by natural gas seeps. Etymology: Desulfosarcina aeriophaga, aério (Greek): gas; phágos (Greek): eater; D. aeriophaga: a gas eating or gas feeding Desulfosarcina.
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Affiliation(s)
- Song-Can Chen
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jiaheng Ji
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | | | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
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6
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Ranchou-Peyruse M, Guignard M, Casteran F, Abadie M, Defois C, Peyret P, Dequidt D, Caumette G, Chiquet P, Cézac P, Ranchou-Peyruse A. Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer. Front Microbiol 2021; 12:688929. [PMID: 34721313 PMCID: PMC8549729 DOI: 10.3389/fmicb.2021.688929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L-1 and a phosphate content of 0.02mg.L-1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria ("Candidatus Acetothermia") with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.
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Affiliation(s)
- Magali Ranchou-Peyruse
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
| | - Marion Guignard
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Franck Casteran
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Maïder Abadie
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
| | - Clémence Defois
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - David Dequidt
- STORENGY – Geosciences Department, Bois-Colombes, France
| | - Guilhem Caumette
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Chiquet
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Cézac
- Laboratoire de thermique, énergétique et procédés IPRA, EA1932, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
| | - Anthony Ranchou-Peyruse
- IPREM, Institut des Sciences Analytiques et de Physico-Chimie pour l’Environnement et les Matériaux, Université de Pau & Pays Adour/E2S-UPPA, Pau, France
- Joint Laboratory SEnGA, UPPA-E2S-Teréga, Pau, France
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7
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Li WL, Dong X, Lu R, Zhou YL, Zheng PF, Feng D, Wang Y. Microbial ecology of sulfur cycling near the sulfate-methane transition of deep-sea cold seep sediments. Environ Microbiol 2021; 23:6844-6858. [PMID: 34622529 DOI: 10.1111/1462-2920.15796] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 11/27/2022]
Abstract
Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate-methane transition zone (SMTZ) of deep-sea cold seeps. How the sulfur cycling is mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow SMTZ in three of eight sediment cores sampled from two cold seep areas in the South China Sea. One hundred ten genomes representing sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) strains were identified from three SMTZ-bearing cores. In the layers above SMTZ, SOB were mostly constituted by Campylobacterota, Gammaproteobacteria and Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for oxidation of sulfide and thiosulfate in near-surface sediment layers. In the layers below the SMTZ, the deltaproteobacterial SRB genomes and metatranscriptomes revealed CO2 fixation by Wood-Ljungdahl pathway, sulfate reduction and nitrogen fixation for syntrophic or fermentative lifestyle. A total of 68% of the metagenome assembled genomes were not adjacent to known species in a phylogenomic tree, indicating a high diversity of bacteria involved in sulfur cycling. With the large number of genomes for SOB and SRB, our study uncovers the microbial populations that potentially mediate sulfur metabolism and associated carbon and nitrogen cycles, which sheds light on complex biogeochemical processes in deep-sea environments.
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Affiliation(s)
- Wen-Li Li
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Rui Lu
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Li Zhou
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng-Fei Zheng
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
| | - Dong Feng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong Wang
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
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8
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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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9
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Wang W, Tao J, Yu K, He C, Wang J, Li P, Chen H, Xu B, Shi Q, Zhang C. Vertical Stratification of Dissolved Organic Matter Linked to Distinct Microbial Communities in Subtropic Estuarine Sediments. Front Microbiol 2021; 12:697860. [PMID: 34354693 PMCID: PMC8329499 DOI: 10.3389/fmicb.2021.697860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/08/2021] [Indexed: 12/01/2022] Open
Abstract
Dissolved organic matter (DOM) provides carbon substrates and energy sources for sediment microbes driving benthic biogeochemical processes. The interactions between microbes and DOM are dynamic and complex and require the understanding based on fine-scale microbial community and physicochemical profiling. In this study, we characterized the porewater DOM composition in a 300-cm sediment core from the Pearl River estuary, China, and examined the interactions between DOM and archaeal and bacterial communities. DOM composition were highly stratified and associated with changing microbial communities. Compared to bacteria, the amplicon sequence variants of archaea showed significant Pearson correlations (r ≥ 0.65, P < 0.01) with DOM molecules of low H/C ratios, high C number and double bond equivalents, indicating that the distribution of archaea was closely correlated to recalcitrant DOM while bacteria were associated with relatively labile compounds. This was supported by the presence of auxiliary enzyme families essential for lignin degradation and bcrABCD, UbiX genes for anaerobic aromatic reduction in metagenome-assembled genomes of Bathyarchaeia. Our study demonstrates that niche differentiation between benthic bacteria and archaea may have important consequences in carbon metabolism, particularly for the transformation of recalcitrant organic carbon that may be predominant in aged marine sediments.
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Affiliation(s)
- Wenxiu Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Jianchang Tao
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Penghui Li
- School of Marine Science, Sun Yat-sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Hongmei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Bu Xu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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10
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Kivenson V, Paul BG, Valentine DL. An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria. Front Microbiol 2021; 12:680620. [PMID: 34335502 PMCID: PMC8318568 DOI: 10.3389/fmicb.2021.680620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/20/2021] [Indexed: 01/04/2023] Open
Abstract
Marine benthic environments may be shaped by anthropogenic and other localized events, leading to changes in microbial community composition evident decades after a disturbance. Marine sediments in particular harbor exceptional taxonomic diversity and can shed light on distinctive evolutionary strategies. Genetic code expansion is a strategy that increases the structural and functional diversity of proteins in cells, by repurposing stop codons to encode non-canonical amino acids: pyrrolysine (Pyl) and selenocysteine (Sec). Here, we report both a study of the microbiome at a deep sea industrial waste dumpsite and an unanticipated discovery of codon reassignment in its most abundant member, with potential ramifications for interpreting microbial interactions with ocean-dumped wastes. The genomes of abundant Deltaproteobacteria from the sediments of a deep-ocean chemical waste dump site have undergone genetic code expansion. Pyl and Sec in these organisms appear to augment trimethylamine (TMA) and one-carbon metabolism, representing an increased metabolic versatility. The inferred metabolism of these sulfate-reducing bacteria places them in competition with methylotrophic methanogens for TMA, a contention further supported by earlier isotope tracer studies and reanalysis of metatranscriptomic studies. A survey of genomic data further reveals a broad geographic distribution of a niche group of similarly specialized Deltaproteobacteria, including at sulfidic sites in the Atlantic Ocean, Gulf of Mexico, Guaymas Basin, and North Sea, as well as in terrestrial and estuarine environments. These findings reveal an important biogeochemical role for specialized Deltaproteobacteria at the interface of the carbon, nitrogen, selenium, and sulfur cycles, with their niche adaptation and ecological success potentially augmented by genetic code expansion.
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Affiliation(s)
- Veronika Kivenson
- Interdepartmental Graduate Program in Marine Science, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Blair G. Paul
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - David L. Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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11
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Valkanas MM, Rosso T, Packard JE, Trun NJ. Limited carbon sources prevent sulfate remediation in circumneutral abandoned mine drainage. FEMS Microbiol Ecol 2021; 97:6070647. [PMID: 33417684 DOI: 10.1093/femsec/fiaa262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/31/2020] [Indexed: 01/04/2023] Open
Abstract
Passive remediation systems (PRS) use both biotic and abiotic processes to precipitate contaminants from abandoned mine drainage (AMD) so that the contaminants do not spread into local watersheds. PRS are efficient at removing heavy metals but sulfate remediation frequently does not occur. To understand the reasons for the lack of sulfate remediation, we studied four PRS that treat circumneutral AMD and one raw mine drainage discharge. Using 16S sequencing analysis, microbial community composition revealed a high relative abundance of bacterial families with sulfur cycling genera. Anaerobic abiotic studies showed that sulfide was quickly geochemically oxidized in the presence of iron hydroxides, leading to a buildup of sulfur intermediates. Supplementation of laboratory grown microbes from the PRS with lactate demonstrated the ability of actively growing microbes to overcome this abiotic sulfide oxidation by increasing the rate of sulfate reduction. Thus, the lack of carbon sources in the PRS contributes to the lack of sulfate remediation. Bacterial community analysis of 16S rRNA gene revealed that while the microbial communities in different parts of the PRS were phylogenetically distinct, the contaminated environments selected for communities that shared similar metabolic capabilities.
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Affiliation(s)
- Michelle M Valkanas
- Department of Biological Sciences, Duquesne University, 256 Mellon Hall, 600 Forbes Ave, Pittsburgh, PA 15282, USA
| | - Taylor Rosso
- Department of Biological Sciences, Duquesne University, 256 Mellon Hall, 600 Forbes Ave, Pittsburgh, PA 15282, USA
| | - Jessica E Packard
- Department of Biological Sciences, Duquesne University, 256 Mellon Hall, 600 Forbes Ave, Pittsburgh, PA 15282, USA
| | - Nancy J Trun
- Department of Biological Sciences, Duquesne University, 256 Mellon Hall, 600 Forbes Ave, Pittsburgh, PA 15282, USA
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12
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Schnaars V, Wöhlbrand L, Scheve S, Hinrichs C, Reinhardt R, Rabus R. Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum. Microb Physiol 2021; 31:1-20. [PMID: 33611323 PMCID: PMC8315694 DOI: 10.1159/000513383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/19/2020] [Indexed: 11/19/2022]
Abstract
The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69-96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.
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Affiliation(s)
- Vanessa Schnaars
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Sabine Scheve
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Hinrichs
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard Reinhardt
- Max-Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany,
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13
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Dutta A, Smith B, Goldman T, Walker L, Streets M, Eden B, Dirmeier R, Bowman JS. Understanding Microbial Community Dynamics in Up-Flow Bioreactors to Improve Mitigation Strategies for Oil Souring. Front Microbiol 2020; 11:585943. [PMID: 33343524 PMCID: PMC7744764 DOI: 10.3389/fmicb.2020.585943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023] Open
Abstract
Oil souring occurs when H2S is generated in oil reservoirs. This not only leads to operational risks and health hazards but also increases the cost of refining crude oil. Sulfate-reducing microorganisms are considered to be the main source of the H2S that leads to oil souring. Substrate competition between nitrate-reducing and sulfate-reducing microorganisms makes biosouring mitigation via the addition of nitrate salts a viable strategy. This study explores the shift in microbial community across different phases of biosouring and mitigation. Anaerobic sand-filled columns wetted with seawater and/or oil were used to initiate the processes of sulfidogenesis, followed by mitigation with nitrate, rebound sulfidogenesis, and rebound control phases (via nitrate and low salinity treatment). Shifts in microbial community structure and function were observed across different phases of seawater and oil setups. Marine bacterial taxa (Marinobacter, Marinobacterium, Thalassolituus, Alteromonas, and Cycloclasticus) were found to be the initial responders to the application of nitrate during mitigation of sulfidogenesis in both seawater- and oil- wetted columns. Autotrophic groups (Sulfurimonas and Desulfatibacillum) were found to be higher in seawater-wetted columns compared to oil-wetted columns, suggesting the potential for autotrophic volatile fatty acid (VFA) production in oil-field aquifers when seawater is introduced. Results indicate that fermentative (such as Bacteroidetes) and oil-degrading bacteria (such as Desulfobacula toluolica) play an important role in generating electron donors in the system, which may sustain biosouring and nitrate reduction. Persistence of certain microorganisms (Desulfobacula) across different phases was observed, which may be due to a shift in metabolic lifestyle of the microorganisms across phases, or zonation based on nutrient availability in the columns. Overall results suggest mitigation strategies for biosouring can be improved by monitoring VFA concentrations and microbial community dynamics in the oil reservoirs during secondary recovery of oil.
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Affiliation(s)
- Avishek Dutta
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
| | - Ben Smith
- BP Upstream Technology, London, United Kingdom
| | | | - Leanne Walker
- Rawwater Engineering Company Ltd., Culcheth, United Kingdom
| | | | - Bob Eden
- Rawwater Engineering Company Ltd., Culcheth, United Kingdom
| | | | - Jeff S. Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
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14
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Heyen S, Scholz-Böttcher BM, Rabus R, Wilkes H. Method development and validation for the quantification of organic acids in microbial samples using anionic exchange solid-phase extraction and gas chromatography-mass spectrometry. Anal Bioanal Chem 2020; 412:7491-7503. [PMID: 32970177 PMCID: PMC7533261 DOI: 10.1007/s00216-020-02883-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 11/07/2022]
Abstract
Organic acids play a key role in central metabolic functions of organisms, are crucial for understanding regulatory processes and are ubiquitous inside the cell. Therefore, quantification of these compounds provides a valuable approach for studying dynamics of metabolic processes, in particular when the organism faces changing environmental conditions. However, the extraction and analysis of organic acids can be challenging and validated methods available in this field are limited. In this study, we developed a method for the extraction and quantification of organic acids from microbial samples based on solid-phase extraction on a strong anionic exchange cartridge and gas chromatographic-mass spectrometric analysis. Full method validation was conducted to determine quality parameters of the new method. Recoveries for 12 of the 15 aromatic and aliphatic acids were between 100 and 111% and detection limits between 3 and 272 ng/mL. The ranges for the regression coefficients and process standard deviations for these compound classes were 0.9874–0.9994 and 0.04–0.69 μg/mL, respectively. Limitations were encountered when targeting aliphatic acids with hydroxy, oxo or enol ester functions. Finally, we demonstrated the applicability of the method on cell extracts of the bacterium Escherichia coli and the dinoflagellate Prorocentrum minimum. Graphical abstract ![]()
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Affiliation(s)
- Simone Heyen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, P.O. Box 2503, 26111, Oldenburg, Germany
| | - Barbara M Scholz-Böttcher
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, P.O. Box 2503, 26111, Oldenburg, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, P.O. Box 2503, 26111, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, P.O. Box 2503, 26111, Oldenburg, Germany.
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15
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Watanabe M, Higashioka Y, Kojima H, Fukui M. Proposal of Desulfosarcina ovata subsp. sediminis subsp. nov., a novel toluene-degrading sulfate-reducing bacterium isolated from tidal flat sediment of Tokyo Bay. Syst Appl Microbiol 2020; 43:126109. [PMID: 32847784 DOI: 10.1016/j.syapm.2020.126109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 11/30/2022]
Abstract
Strain 28bB2TT is a sulfate-reducing bacterium isolated in a previous study, obtained from a p-xylene-degrading enrichment culture. Physiological, phylogenetic and genomic characterizations of strain 28bB2TT were performed to establish the taxonomic status of the strain. Cells of strain 28bB2TT were short oval-shaped (0.8-1.2×1.2-2.7μm), motile, and Gram-negative. For growth, the optimum pH was pH 6.5-7.0 and the optimum temperature was 28-32°C. Strain 28bB2TT oxidized toluene but could not utilize p-xylene. Sulfate and thiosulfate were used as electron acceptors. The G+C content of the genomic DNA was 53.8mol%. The genome consisted of an approximately 8.3 Mb of chromosome and two extrachromosomal elements. On the basis of 16S rRNA gene analysis, strain 28bB2TT was revealed to belong to the genus Desulfosarcina, with high sequence identities to Desulfosarcina ovata oXyS1T (99.5%) and Desulfosarcina cetonica DSM 7267T (98.7%). Results of Average Nucleotide Identity (ANI) calculation and digital DNA-DNA hybridization (dDDH) analysis showed that the strain 28bB2TT should be classified as a subspecies under D. ovata. Based on physiological and phylogenetic data, strain 28bB2TT (=NBRC 106234 =DSM 23484) is proposed as the type strain of a novel species in genus Desulfosarcina, Desulfosarcina ovata subsp. sediminis subsp. nov.
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Affiliation(s)
- Miho Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan; Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | - Yuriko Higashioka
- National Institute of Technology, Kochi College, 200-1 Otsu, Monobe, Nankoku-city, Kochi 783-8508, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Hokkaido, Japan
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16
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Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP. A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols. eLife 2020; 9:e50845. [PMID: 32067637 PMCID: PMC7028382 DOI: 10.7554/elife.50845] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Catechol dehydroxylation is a central chemical transformation in the gut microbial metabolism of plant- and host-derived small molecules. However, the molecular basis for this transformation and its distribution among gut microorganisms are poorly understood. Here, we characterize a molybdenum-dependent enzyme from the human gut bacterium Eggerthella lenta that dehydroxylates catecholamine neurotransmitters. Our findings suggest that this activity enables E. lenta to use dopamine as an electron acceptor. We also identify candidate dehydroxylases that metabolize additional host- and plant-derived catechols. These dehydroxylases belong to a distinct group of largely uncharacterized molybdenum-dependent enzymes that likely mediate primary and secondary metabolism in multiple environments. Finally, we observe catechol dehydroxylation in the gut microbiotas of diverse mammals, confirming the presence of this chemistry in habitats beyond the human gut. These results suggest that the chemical strategies that mediate metabolism and interactions in the human gut are relevant to a broad range of species and habitats.
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Affiliation(s)
- Vayu Maini Rekdal
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Paola Nol Bernadino
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Michael U Luescher
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Sina Kiamehr
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Chip Le
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Jordan E Bisanz
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Peter J Turnbaugh
- Department of Microbiology and ImmunologyUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Elizabeth N Bess
- Department of Chemistry and Molecular BiologyUniversity of California, IrvineIrvineUnited States
- Department of Chemistry and Molecular BiochemistryUniversity of California, IrvineIrvineUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
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17
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Boll M, Geiger R, Junghare M, Schink B. Microbial degradation of phthalates: biochemistry and environmental implications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:3-15. [PMID: 31364812 DOI: 10.1111/1758-2229.12787] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 05/10/2023]
Abstract
The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding PA isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the PA isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three PA CoA thioesters belong to the UbiD enzyme family that harbour a prenylated flavin mononucleotide (FMN) cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of phthaloyl-CoA decarboxylase and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate.
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Affiliation(s)
- Matthias Boll
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Robin Geiger
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Madan Junghare
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
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18
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Vogt MS, Schühle K, Kölzer S, Peschke P, Chowdhury NP, Kleinsorge D, Buckel W, Essen LO, Heider J. Structural and Functional Characterization of an Electron Transfer Flavoprotein Involved in Toluene Degradation in Strictly Anaerobic Bacteria. J Bacteriol 2019; 201:e00326-19. [PMID: 31405915 PMCID: PMC6779460 DOI: 10.1128/jb.00326-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 08/08/2019] [Indexed: 11/20/2022] Open
Abstract
(R)-Benzylsuccinate is the characteristic initial intermediate of anaerobic toluene metabolism, which is formed by a radical-type addition of toluene to fumarate. Its further degradation proceeds by activation to the coenzyme A (CoA)-thioester and β-oxidation involving a specific (R)-2-benzylsuccinyl-CoA dehydrogenase (BbsG) affiliated with the family of acyl-CoA dehydrogenases. In this report, we present the biochemical properties of electron transfer flavoproteins (ETFs) from the strictly anaerobic toluene-degrading species Geobacter metallireducens and Desulfobacula toluolica and the facultatively anaerobic bacterium Aromatoleum aromaticum We determined the X-ray structure of the ETF paralogue involved in toluene metabolism of G. metallireducens, revealing strong overall similarities to previously characterized ETF variants but significantly different structural properties in the hinge regions mediating conformational changes. We also show that all strictly anaerobic toluene degraders utilize one of multiple genome-encoded related ETF paralogues, which constitute a distinct clade of similar sequences in the ETF family, for β-oxidation of benzylsuccinate. In contrast, facultatively anaerobic toluene degraders contain only one ETF species, which is utilized in all β-oxidation pathways. Our phylogenetic analysis of the known sequences of the ETF family suggests that at least 36 different clades can be differentiated, which are defined either by the taxonomic group of the respective host species (e.g., clade P for Proteobacteria) or by functional specialization (e.g., clade T for anaerobic toluene degradation).IMPORTANCE This study documents the involvement of ETF in anaerobic toluene metabolism as the physiological electron acceptor for benzylsuccinyl-CoA dehydrogenase. While toluene-degrading denitrifying proteobacteria use a common ETF species, which is also used for other β-oxidation pathways, obligately anaerobic sulfate- or ferric-iron-reducing bacteria use specialized ETF paralogues for toluene degradation. Based on the structure and sequence conservation of these ETFs, they form a new clade that is only remotely related to the previously characterized members of the ETF family. An exhaustive analysis of the available sequences indicated that the protein family consists of several closely related clades of proven or potential electron-bifurcating ETF species and many deeply branching nonbifurcating clades, which either follow the host phylogeny or are affiliated according to functional criteria.
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Affiliation(s)
| | - Karola Schühle
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Sebastian Kölzer
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Peschke
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | | | - Daniel Kleinsorge
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Wolfgang Buckel
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Germany
| | - Lars-Oliver Essen
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Johann Heider
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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19
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Durante-Rodríguez G, Gutiérrez-Del-Arroyo P, Vélez M, Díaz E, Carmona M. Further Insights into the Architecture of the PN Promoter That Controls the Expression of the bzd Genes in Azoarcus. Genes (Basel) 2019; 10:genes10070489. [PMID: 31252700 PMCID: PMC6678401 DOI: 10.3390/genes10070489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/12/2019] [Accepted: 06/26/2019] [Indexed: 12/01/2022] Open
Abstract
The anaerobic degradation of benzoate in bacteria involves the benzoyl-CoA central pathway. Azoarcus/Aromatoleum strains are a major group of anaerobic benzoate degraders, and the transcriptional regulation of the bzd genes was extensively studied in Azoarcus sp. CIB. In this work, we show that the bzdR regulatory gene and the PN promoter can also be identified upstream of the catabolic bzd operon in all benzoate-degrader Azoarcus/Aromatoleum strains whose genome sequences are currently available. All the PN promoters from Azoarcus/Aromatoleum strains described here show a conserved architecture including three operator regions (ORs), i.e., OR1 to OR3, for binding to the BzdR transcriptional repressor. Here, we demonstrate that, whereas OR1 is sufficient for the BzdR-mediated repression of the PN promoter, the presence of OR2 and OR3 is required for de-repression promoted by the benzoyl-CoA inducer molecule. Our results reveal that BzdR binds to the PN promoter in the form of four dimers, two of them binding to OR1. The BzdR/PN complex formed induces a DNA loop that wraps around the BzdR dimers and generates a superstructure that was observed by atomic force microscopy. This work provides further insights into the existence of a conserved BzdR-dependent mechanism to control the expression of the bzd genes in Azoarcus strains.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Microbial and Plant Biotechnology Department. Centro de Investigaciones Biológicas-CSIC. Ramiro de Maeztu, 9. 28040 Madrid, Spain
| | - Paloma Gutiérrez-Del-Arroyo
- Biocatalysis Department. Institute of Catalysis and Petrochemistry-CSIC. Marie Curie, 2, Cantoblanco. 28049 Madrid, Spain
| | - Marisela Vélez
- Biocatalysis Department. Institute of Catalysis and Petrochemistry-CSIC. Marie Curie, 2, Cantoblanco. 28049 Madrid, Spain
| | - Eduardo Díaz
- Microbial and Plant Biotechnology Department. Centro de Investigaciones Biológicas-CSIC. Ramiro de Maeztu, 9. 28040 Madrid, Spain
| | - Manuel Carmona
- Microbial and Plant Biotechnology Department. Centro de Investigaciones Biológicas-CSIC. Ramiro de Maeztu, 9. 28040 Madrid, Spain.
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20
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Pinnell LJ, Turner JW. Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment. Front Microbiol 2019; 10:1252. [PMID: 31231339 PMCID: PMC6566015 DOI: 10.3389/fmicb.2019.01252] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/20/2019] [Indexed: 11/23/2022] Open
Abstract
Plastic is incredibly abundant in marine environments but little is known about its effects on benthic microbiota and biogeochemical cycling. This study reports the shotgun metagenomic sequencing of biofilms fouling plastic and bioplastic microcosms staged at the sediment–water interface of a coastal lagoon. Community composition analysis revealed that plastic biofilms were indistinguishable in comparison to a ceramic biofilm control. By contrast, bioplastic biofilms were distinct and dominated by sulfate-reducing microorganisms (SRM). Analysis of bioplastic gene pools revealed the enrichment of esterases, depolymerases, adenylyl sulfate reductases (aprBA), and dissimilatory sulfite reductases (dsrAB). The nearly 20-fold enrichment of a phylogenetically diverse polyhydroxybutyrate (PHB) depolymerase suggests this gene was distributed across a mixed microbial assemblage. The metagenomic reconstruction of genomes identified novel species of Desulfovibrio, Desulfobacteraceae, and Desulfobulbaceae among the abundant SRM, and these genomes contained genes integral to both bioplastic degradation and sulfate reduction. Findings indicate that bioplastic promoted a rapid and significant shift in benthic microbial diversity and gene pools, selecting for microbes that participate in bioplastic degradation and sulfate reduction. If plastic pollution is traded for bioplastic pollution and sedimentary inputs are large, the microbial response could unintentionally affect benthic biogeochemical activities through the stimulation of sulfate reducers.
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Affiliation(s)
- Lee J Pinnell
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, United States
| | - Jeffrey W Turner
- Department of Life Sciences, Texas A&M University - Corpus Christi, Corpus Christi, TX, United States
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21
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Liu YF, Qi ZZ, Shou LB, Liu JF, Yang SZ, Gu JD, Mu BZ. Anaerobic hydrocarbon degradation in candidate phylum 'Atribacteria' (JS1) inferred from genomics. ISME JOURNAL 2019; 13:2377-2390. [PMID: 31171858 PMCID: PMC6776118 DOI: 10.1038/s41396-019-0448-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/11/2019] [Accepted: 05/03/2019] [Indexed: 02/06/2023]
Abstract
The hydrocarbon-enriched environments, such as oil reservoirs and oil sands tailings ponds, contain a broad diversity of uncultured microorganisms. Despite being one of the few prokaryotic lineages that is consistently detected in both production water from oil reservoirs and stable hydrocarbon-degrading enrichment cultures originated from oil reservoirs, the physiological and ecological roles of candidate phylum “Atribacteria” (OP9/JS1) are not known in deep subsurface environments. Here, we report the expanded metabolic capabilities of Atribacteria as inferred from genomic reconstructions. Seventeen newly assembled medium-to-high-quality metagenomic assembly genomes (MAGs) were obtained either from co-assembly of two metagenomes from an Alaska North Slope oil reservoir or from previous studies of metagenomes coming from different environments. These MAGs comprise three currently known genus-level lineages and four novel genus-level groups of OP9 and JS1, which expands the genomic coverage of the major lineages within the candidate phylum Atribacteria. Genes involved in anaerobic hydrocarbon degradation were found in seven MAGs associated with hydrocarbon-enriched environments, and suggest that some Atribacteria could ferment short-chain n-alkanes into fatty acid while conserving energy. This study expands predicted metabolic capabilities of Atribacteria (JS1) and suggests that they are mediating a key role in subsurface carbon cycling.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Zhen-Zhen Qi
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Li-Bin Shou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, P.R. China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P.R. China. .,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 200237, Shanghai, P.R. China.
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Geiger RA, Junghare M, Mergelsberg M, Ebenau‐Jehle C, Jesenofsky VJ, Jehmlich N, von Bergen M, Schink B, Boll M. Enzymes involved in phthalate degradation in sulphate‐reducing bacteria. Environ Microbiol 2019; 21:3601-3612. [DOI: 10.1111/1462-2920.14681] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/03/2019] [Accepted: 05/11/2019] [Indexed: 12/31/2022]
Affiliation(s)
| | - Madan Junghare
- Department of Biology, Microbial EcologyUniversity of Konstanz, 78457 Constance Germany
| | - Mario Mergelsberg
- Faculty of Biology–MicrobiologyUniversity of Freiburg, 79104 Freiburg Germany
| | | | | | - Nico Jehmlich
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research UFZ 04318 Leipzig Germany
| | - Martin von Bergen
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research UFZ 04318 Leipzig Germany
- Institute of Biochemistry, Faculty of Life SciencesUniversity of Leipzig Brüderstr. 34, 04103 Leipzig Germany
| | - Bernhard Schink
- Department of Biology, Microbial EcologyUniversity of Konstanz, 78457 Constance Germany
| | - Matthias Boll
- Faculty of Biology–MicrobiologyUniversity of Freiburg, 79104 Freiburg Germany
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Junghare M, Spiteller D, Schink B. Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME JOURNAL 2019; 13:1252-1268. [PMID: 30647456 DOI: 10.1038/s41396-019-0348-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 12/13/2022]
Abstract
Syntrophorhabdus aromaticivorans is a syntrophically fermenting bacterium that can degrade isophthalate (3-carboxybenzoate). It is a xenobiotic compound which has accumulated in the environment for more than 50 years due to its global industrial usage and can cause negative effects on the environment. Isophthalate degradation by the strictly anaerobic S. aromaticivorans was investigated to advance our understanding of the degradation of xenobiotics introduced into nature, and to identify enzymes that might have ecological significance for bioremediation. Differential proteome analysis of isophthalate- vs benzoate-grown cells revealed over 400 differentially expressed proteins of which only four were unique to isophthalate-grown cells. The isophthalate-induced proteins include a phenylacetate:CoA ligase, a UbiD-like decarboxylase, a UbiX-like flavin prenyltransferase, and a hypothetical protein. These proteins are encoded by genes forming a single gene cluster that putatively codes for anaerobic conversion of isophthalate to benzoyl-CoA. Subsequently, benzoyl-CoA is metabolized by the enzymes of the anaerobic benzoate degradation pathway that were identified in the proteomic analysis. In vitro enzyme assays with cell-free extracts of isophthalate-grown cells indicated that isophthalate is activated to isophthalyl-CoA by an ATP-dependent isophthalate:CoA ligase (IPCL), and subsequently decarboxylated to benzoyl-CoA by a UbiD family isophthalyl-CoA decarboxylase (IPCD) that requires a prenylated flavin mononucleotide (prFMN) cofactor supplied by UbiX to effect decarboxylation. Phylogenetic analysis revealed that IPCD is a novel member of the functionally diverse UbiD family (de)carboxylases. Homologs of the IPCD encoding genes are found in several other bacteria, such as aromatic compound-degrading denitrifiers, marine sulfate-reducers, and methanogenic communities in a terephthalate-degrading reactor. These results suggest that metabolic strategies adapted for degradation of isophthalate and other phthalate are conserved between microorganisms that are involved in the anaerobic degradation of environmentally relevant aromatic compounds.
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Affiliation(s)
- Madan Junghare
- Microbial Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
| | - Dieter Spiteller
- Chemical Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Bernhard Schink
- Microbial Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
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Mekala LP, Mohammed M, Chinthalapati S, Chinthalapati VR. Pyomelanin production: Insights into the incomplete aerobic l-phenylalanine catabolism of a photosynthetic bacterium, Rubrivivax benzoatilyticus JA2. Int J Biol Macromol 2018; 126:755-764. [PMID: 30572055 DOI: 10.1016/j.ijbiomac.2018.12.142] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/13/2018] [Accepted: 12/16/2018] [Indexed: 02/06/2023]
Abstract
Rubrivivax benzoatilyticus JA2 is a metabolically versatile bacterium, thrives on a wide array of organic compounds under different growth modes. Though genomic insights revealed the aromatic compound catabolic potential of strain JA2 under anaerobic/aerobic conditions, the studies are largely restricted to anaerobic metabolism. The previous study on phenylalanine metabolism in strain JA2 indicated melanin-like pigment production under aerobic conditions; however, characterization of pigment and its biosynthetic pathway is not explored. The current study aims at the characterization of pigment and elucidation of its biosynthetic pathway. Strain JA2 utilized l-phenylalanine as source of nitrogen under anaerobic/aerobic conditions but not as a carbon source. Strain JA2 produced a brown-pigment under phenylalanine-amended aerobic conditions. Spectroscopic and physicochemical analysis identified the purified brown-pigment as a melanin. Further, the genomic insights revealed the presence of a complete set of genes related to pyomelanin synthesis. Identification of key metabolites l-tyrosine, 4-hydroxyphenylpyruvic acid and homogentisic acid and their respective enzyme activities further supports the pyomelanin synthesis. Moreover, the precursors feeding, pathway specific inhibitor studies confirmed the pyomelanin synthesis in strain JA2. Our study revealed an incomplete catabolism of phenylalanine; absence of ring cleavage gene, homogentisate dioxygenase leading to homogentisate accumulation thereby pyomelanin synthesis in strain JA2.
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Affiliation(s)
- Lakshmi Prasuna Mekala
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Mujahid Mohammed
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Sasikala Chinthalapati
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad 500 085, India
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Blázquez B, Carmona M, Díaz E. Transcriptional Regulation of the Peripheral Pathway for the Anaerobic Catabolism of Toluene and m-Xylene in Azoarcus sp. CIB. Front Microbiol 2018; 9:506. [PMID: 29623071 PMCID: PMC5874301 DOI: 10.3389/fmicb.2018.00506] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/06/2018] [Indexed: 11/17/2022] Open
Abstract
Alkylbenzenes, such as toluene and m-xylene, are an important class of contaminant hydrocarbons that are widespread and tend to accumulate in subsurface anoxic environments. The peripheral pathway for the anaerobic oxidation of toluene in bacteria consists of an initial activation catalyzed by a benzylsuccinate synthase (encoded by bss genes), and a subsequent modified β-oxidation of benzylsuccinate to benzoyl-CoA and succinyl-CoA (encoded by bbs genes). We have shown here that the bss and bbs genes, which are located within an integrative and conjugative element, are essential for anaerobic degradation of toluene but also for m-xylene oxidation in the denitrifying beta-proteobacterium Azoarcus sp. CIB. New insights into the transcriptional organization and regulation of a complete gene cluster for anaerobic catabolism of toluene/m-xylene in a single bacterial strain are presented. The bss and bbs genes are transcriptionally coupled into two large convergent catabolic operons driven by the PbssD and PbbsA promoters, respectively, whose expression is inducible when cells grow anaerobically in toluene or m-xylene. An adjacent tdiSR operon driven by the PtdiS promoter encodes a putative two-component regulatory system. TdiR behaves as a transcriptional activator of the PbssD, PbbsA, and PtdiS promoters, being benzylsuccinate/(3-methyl)benzylsuccinate, rather than toluene/m-xylene, the inducers that may trigger the TdiS-mediated activation of TdiR. In addition to the TdiSR-based specific control, the expression of the bss and bbs genes in Azoarcus sp. CIB is under an overimposed regulation that depends on certain environmental factors, such as the presence/absence of oxygen or the availability of preferred carbon sources (catabolite repression). This work paves the way for future strategies toward the reliable assessment of microbial activity in toluene/m-xylene contaminated environments.
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Affiliation(s)
- Blas Blázquez
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel Carmona
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Harrison BK, Myrbo A, Flood BE, Bailey JV. Abrupt burial imparts persistent changes to the bacterial diversity of turbidite-associated sediment profiles. GEOBIOLOGY 2018; 16:190-202. [PMID: 29350440 DOI: 10.1111/gbi.12271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/09/2017] [Indexed: 06/07/2023]
Abstract
The emplacement of subaqueous gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical and biological signatures of turbidite deposition, the response of bacteria and archaea within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and those attached to allochthonous material must respond to substantially altered environmental conditions and selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine (i) the microbial community response to rapid sedimentation and (ii) the preservation and identification of displaced micro-organisms. We collected Illumina MiSeq sequence libraries across turbidite boundaries at ~26 cm sediment depth in La Jolla Canyon off the coast of California, and at ~50 cm depth in meromictic Twin Lake, Hennepin County, MN. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, both the marine and lacustrine turbidite boundaries are sharply demarcated by the abundance and diversity of Chloroflexi, suggesting a characteristic sensitivity to sediment disturbance history or to differences in organic substrates across turbidite profiles. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the buried La Jolla Canyon sediment-water interface reflect turbidite-induced changes to the geochemical environment. Species-level distinctions within the Deltaproteobacteria clearly conform to the sedimentological boundary, suggesting a continuing impact of genetic inheritance distinguishable from broader trends attributable to selective pressure. Abrupt, <1-cm scale changes in bacterial diversity across the Twin Lake turbidite contact are consistent with previous studies showing that relict DNA signatures attributable to sediment transport may be more easily preserved in low-energy, anoxic environments. This work raises the possibility that deep subsurface microbial communities may inherit variations in microbial diversity from sediment flow and deformation events.
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Affiliation(s)
- B K Harrison
- Department of Earth and Atmospheric Sciences, Central Michigan University, Mt. Pleasant, MI, USA
- Department of Earth Sciences, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - A Myrbo
- LacCore/CSDCO, Limnological Research Center, Department of Earth Sciences, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - B E Flood
- Department of Earth Sciences, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - J V Bailey
- Department of Earth Sciences, University of Minnesota, Twin Cities, Minneapolis, MN, USA
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Espínola F, Dionisi HM, Borglin S, Brislawn CJ, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lozada M. Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. MICROBIAL ECOLOGY 2018; 75:123-139. [PMID: 28702706 DOI: 10.1007/s00248-017-1028-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.
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Affiliation(s)
- Fernando Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Sharon Borglin
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Walter P Mac Cormack
- Instituto Nanobiotec, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, and ARCEx-Research Centre for Arctic Petroleum Exploration, Department of Geosciences, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
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Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes. mBio 2017; 8:mBio.02022-17. [PMID: 29259088 PMCID: PMC5736913 DOI: 10.1128/mbio.02022-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi. The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments and provide evidence for a homacetogenic lifestyle of these abundant marine Chloroflexi. Moreover, genome signature and key metabolic genes indicate an evolutionary relationship between these deep-sea sediment microbes and terrestrial, reductively dehalogenating Dehalococcoides.
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Wöhlbrand L, Feenders C, Nachbaur J, Freund H, Engelen B, Wilkes H, Brumsack HJ, Rabus R. Impact of Extraction Methods on the Detectable Protein Complement of Metaproteomic Analyses of Marine Sediments. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/21/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Lars Wöhlbrand
- General and Molecular Microbiology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Christoph Feenders
- Mathematical Modelling; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Jessica Nachbaur
- General and Molecular Microbiology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Holger Freund
- Geoecology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Bert Engelen
- Paleomicrobiology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Heinz Wilkes
- Organic Geochemistry; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Hans-Jürgen Brumsack
- Microbiogeochemistry; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
| | - Ralf Rabus
- General and Molecular Microbiology; Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University of Oldenburg; Oldenburg Germany
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Schmitt G, Arndt F, Kahnt J, Heider J. Adaptations to a Loss-of-Function Mutation in the Betaproteobacterium Aromatoleum aromaticum: Recruitment of Alternative Enzymes for Anaerobic Phenylalanine Degradation. J Bacteriol 2017; 199:e00383-17. [PMID: 28784814 PMCID: PMC5637171 DOI: 10.1128/jb.00383-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/30/2017] [Indexed: 12/22/2022] Open
Abstract
Anaerobic phenylalanine (Phe) degradation in the betaproteobacterium Aromatoleum aromaticum involves transamination and decarboxylation to phenylacetaldehyde, followed by oxidation to phenylacetate. The latter reaction is catalyzed simultaneously by two enzymes, a highly specific phenylacetaldehyde dehydrogenase (PDH) and a rather unspecific tungsten-dependent aldehyde oxidoreductase (AOR). Attempting to establish increased synthesis of AOR, we constructed a mutant lacking the gene for PDH. This mutant still grew on phenylalanine, exhibiting increased AOR activities on medium containing tungstate. In the absence of tungstate, the mutant showed initially severe growth deficiency, but it resumed growth on Phe after longer incubation times. Moreover, the growth rates of the mutant increased during several reinoculation cycles on either tungstate-proficient or -deficient media, reaching the same values as recorded in wild-type strains. We confirmed AOR as the major alternative enzyme serving Phe degradation under tungstate-supplied conditions and identified and characterized the alternative NAD-dependent aldehyde dehydrogenase AldB taking over the function under tungstate-deficient conditions. Sequence analysis of the respective genes from adapted cultures under either growth condition revealed a mutation in the upstream region of the aor operon and a mutation within the coding region of aldB, which are likely involved in the observed adaptation of the deletion mutant to regain fast growth on Phe.IMPORTANCE The betaproteobacterium Aromatoleum aromaticum degrades many aromatic compounds under denitrifying conditions. One of the steps of phenylalanine degradation is catalyzed by two simultaneously induced enzymes, a NAD(P)-dependent phenylacetaldehyde dehydrogenase and a W-containing aldehyde oxidoreductase. We report here that the latter fully complements a constructed deletion mutant lacking the gene for phenylacetaldehyde dehydrogenase and is overproduced after several reinoculations. Moreover, an alternative NAD-dependent dehydrogenase is recruited to resume growth in tungstate-free medium, which does not allow the production of aldehyde oxidoreductase. This alternative enzyme is overproduced and seems to have acquired a point mutation in the active center. Our research illustrates the flexibility of environmentally important bacteria in adapting their metabolic pathways to new challenges within only a few generations.
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Affiliation(s)
- G Schmitt
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, Marburg, Germany
| | - F Arndt
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, Marburg, Germany
| | - J Kahnt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - J Heider
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
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31
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Dörries M, Wöhlbrand L, Rabus R. Differential proteomic analysis of the metabolic network of the marine sulfate-reducer Desulfobacterium autotrophicum HRM2. Proteomics 2017; 16:2878-2893. [PMID: 27701823 DOI: 10.1002/pmic.201600041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/24/2016] [Accepted: 09/30/2016] [Indexed: 01/30/2023]
Abstract
The marine sulfate-reducing bacterium Desulfobacterium autotrophicum HRM2 belongs to the deltaproteobacterial family Desulfobacteraceae and stands out for its capacity of facultative chemolithoautotrophic growth (next to heterotrophy). Here, proteomics-driven metabolic reconstruction was based on a combination of 2D-DIGE, shotgun proteomics, and analysis of the membrane protein enriched fraction applied to eight different substrate adaptation conditions (seven aliphatic compounds plus H2 /CO2 ). In total, 1344 different proteins were identified (∼27% of the 4947 genome-predicted), from which a complex metabolic network was reconstructed consisting of 136 proteins (124 detected; ∼91%). Peripheral degradation routes for organic substrates feed directly or via the methylmalonyl-CoA pathway into the Wood-Ljungdahl pathway (WLP) for terminal oxidation to CO2 . Chemolithoautotrophic growth apparently involves the periplasmic [Ni/Fe/Se]-containing hydrogenase HysAB (H2 oxidation), the reductively operating WLP (CO2 fixation), and classical gluconeogenesis. Diverse soluble proteins (e.g., Hdr, Etf) probably establish a fine balanced cytoplasmic electron transfer network connecting individual catabolic reactions with the membrane menaquinone pool. In addition, multiple membrane protein complexes (Nqr, Qmo, Qrc, Rnf1, Rnf2, and Tmc) provide ample routes for interacting with the reducing equivalent pool and delivering electrons to dissimilatory sulfate reduction (both localized in the cytoplasm). Overall, this study contributes to the molecular understanding of the habitat-relevant Desulfobacteraceae.
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Affiliation(s)
- Marvin Dörries
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.,Department Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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Backman LRF, Funk MA, Dawson CD, Drennan CL. New tricks for the glycyl radical enzyme family. Crit Rev Biochem Mol Biol 2017; 52:674-695. [PMID: 28901199 DOI: 10.1080/10409238.2017.1373741] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Glycyl radical enzymes (GREs) are important biological catalysts in both strict and facultative anaerobes, playing key roles both in the human microbiota and in the environment. GREs contain a backbone glycyl radical that is post-translationally installed, enabling radical-based mechanisms. GREs function in several metabolic pathways including mixed acid fermentation, ribonucleotide reduction and the anaerobic breakdown of the nutrient choline and the pollutant toluene. By generating a substrate-based radical species within the active site, GREs enable C-C, C-O and C-N bond breaking and formation steps that are otherwise challenging for nonradical enzymes. Identification of previously unknown family members from genomic data and the determination of structures of well-characterized GREs have expanded the scope of GRE-catalyzed reactions as well as defined key features that enable radical catalysis. Here, we review the structures and mechanisms of characterized GREs, classifying members into five categories. We consider the open questions about each of the five GRE classes and evaluate the tools available to interrogate uncharacterized GREs.
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Affiliation(s)
- Lindsey R F Backman
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Michael A Funk
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,b Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Christopher D Dawson
- c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Catherine L Drennan
- a Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA , USA.,c Department of Biology , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Howard Hughes Medical Institute , Massachusetts Institute of Technology , Cambridge , MA , USA
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Michas A, Vestergaard G, Trautwein K, Avramidis P, Hatzinikolaou DG, Vorgias CE, Wilkes H, Rabus R, Schloter M, Schöler A. More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis. MICROBIOME 2017; 5:118. [PMID: 28893308 PMCID: PMC5594585 DOI: 10.1186/s40168-017-0337-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/03/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods. RESULTS Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments. CONCLUSIONS The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.
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Affiliation(s)
- Antonios Michas
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Pavlos Avramidis
- Department of Geology, University of Patras, Panepistimioupoli Patron, 26504 Rio-Patras, Greece
| | - Dimitris G. Hatzinikolaou
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Constantinos E. Vorgias
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Heinz Wilkes
- Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
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Wöhlbrand L, Rabus R, Blasius B, Feenders C. Influence of NanoLC Column and Gradient Length as well as MS/MS Frequency and Sample Complexity on Shotgun Protein Identification of Marine Bacteria. J Mol Microbiol Biotechnol 2017; 27:199-212. [PMID: 28850952 DOI: 10.1159/000478907] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/22/2017] [Indexed: 11/19/2022] Open
Abstract
Protein identification by shotgun proteomics, i.e., nano-liquid chromatography (nanoLC) peptide separation online coupled to electrospray ionization (ESI) mass spectrometry (MS)/MS, is the most widely used gel-free approach in proteome research. While the mass spectrometer accounts for mass accuracy and MS/MS frequency, the nanoLC setup and gradient time influence the number of peptides available for MS analysis, which ultimately determine the number of proteins identifiable. Here, we report on the influence of (i) analytical column length (15, 25, or 50 cm) coupled to (ii) the applied gradient length (120, 240, 360, 480, or 600 min), as well as (iii) MS/MS frequency on peptide/protein identification by shotgun proteomics of (iv) 2 marine bacteria. Longer gradients increased the number of peptides/proteins identified as well as the reproducibility of identification. Furthermore, longer analytical columns strictly enlarge the covered proteome complement. Notably, the proteome complement identified with a short column and applying a long gradient is also covered when using longer columns with shorter gradients. Coverage of the proteome complement further increases with higher MS/MS frequency. Compilation of peptide lists of replicate analyses (same gradient length) improves protein identification, while compilation of analyses with different gradient lengths yields a similar or even higher number of proteins using comparable or even less total analysis time.
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Affiliation(s)
- Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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Strijkstra A, Trautwein K, Roesler S, Feenders C, Danzer D, Riemenschneider U, Blasius B, Rabus R. High performance CCD camera system for digitalisation of 2D DIGE gels. Proteomics 2017; 16:1975-9. [PMID: 27252121 PMCID: PMC5095783 DOI: 10.1002/pmic.201500385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 04/20/2016] [Accepted: 05/31/2016] [Indexed: 12/04/2022]
Abstract
An essential step in 2D DIGE‐based analysis of differential proteome profiles is the accurate and sensitive digitalisation of 2D DIGE gels. The performance progress of commercially available charge‐coupled device (CCD) camera‐based systems combined with light emitting diodes (LED) opens up a new possibility for this type of digitalisation. Here, we assessed the performance of a CCD camera system (Intas Advanced 2D Imager) as alternative to a traditionally employed, high‐end laser scanner system (Typhoon 9400) for digitalisation of differential protein profiles from three different environmental bacteria. Overall, the performance of the CCD camera system was comparable to the laser scanner, as evident from very similar protein abundance changes (irrespective of spot position and volume), as well as from linear range and limit of detection.
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Affiliation(s)
- Annemieke Strijkstra
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.,Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.,Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Stefan Roesler
- Intas Science Imaging Instruments GmbH, Göttingen, Germany
| | - Christoph Feenders
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Daniel Danzer
- Intas Science Imaging Instruments GmbH, Göttingen, Germany
| | | | - Bernd Blasius
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.,Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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Shu C, Xiao K, Yan Q, Sun X. Comparative Analysis of Type IV Pilin in Desulfuromonadales. Front Microbiol 2016; 7:2080. [PMID: 28066394 PMCID: PMC5174107 DOI: 10.3389/fmicb.2016.02080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 12/08/2016] [Indexed: 12/24/2022] Open
Abstract
During anaerobic respiration, the bacteria Geobacter sulfurreducens can transfer electrons to extracellular electron accepters through its pilus. G. sulfurreducens pili have been reported to have metallic-like conductivity that is similar to doped organic semiconductors. To study the characteristics and origin of conductive pilin proteins found in the pilus structure, their genetic, structural, and phylogenetic properties were analyzed. The genetic relationships, and conserved structures and sequences that were obtained were used to predict the evolution of the pilins. Homologous genes that encode conductive pilin were found using PilFind and Cluster. Sequence characteristics and protein tertiary structures were analyzed with MAFFT and QUARK, respectively. The origin of conductive pilins was explored by building a phylogenetic tree. Truncation is a characteristic of conductive pilin. The structures of truncated pilins and their accompanying proteins were found to be similar to the N-terminal and C-terminal ends of full-length pilins respectively. The emergence of the truncated pilins can probably be ascribed to the evolutionary pressure of their extracellular electron transporting function. Genes encoding truncated pilins and proteins similar to the C-terminal of full-length pilins, which contain a group of consecutive anti-parallel beta-sheets, are adjacent in bacterial genomes. According to the genetic, structure, and phylogenetic analyses performed in this study, we inferred that the truncated pilins and their accompanying proteins probably evolved from full-length pilins by gene fission through duplication, degeneration, and separation. These findings provide new insights about the molecular mechanisms involved in long-range electron transport along the conductive pili of Geobacter species.
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Affiliation(s)
| | | | | | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast UniversityNanjing, China
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Wöhlbrand L, Ruppersberg HS, Feenders C, Blasius B, Braun HP, Rabus R. Analysis of membrane-protein complexes of the marine sulfate reducer Desulfobacula toluolica Tol2 by 1D blue native-PAGE complexome profiling and 2D blue native-/SDS-PAGE. Proteomics 2016; 16:973-88. [PMID: 26792001 DOI: 10.1002/pmic.201500360] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/16/2015] [Accepted: 12/30/2015] [Indexed: 02/03/2023]
Abstract
Sulfate-reducing bacteria (SRB) obtain energy from cytoplasmic reduction of sulfate to sulfide involving APS-reductase (AprAB) and dissimilatory sulfite reductase (DsrAB). These enzymes are predicted to obtain electrons from membrane redox complexes, i.e. the quinone-interacting membrane-bound oxidoreductase (QmoABC) and DsrMKJOP complexes. In addition to these conserved complexes, the genomes of SRB encode a large number of other (predicted) membrane redox complexes, the function and actual formation of which is unknown. This study reports the establishment of 1D Blue Native-PAGE complexome profiling and 2D BN-/SDS-PAGE for analysis of the membrane protein complexome of the marine sulfate reducer Desulfobacula toluolica Tol2. Analysis of normalized score profiles of >800 proteins in combination with hierarchical clustering and identification of 2D BN-/SDS-PAGE separated spots demonstrated separation of membrane complexes in their native form, e.g. ATP synthase. In addition to the QmoABC and DsrMKJOP complexes, other complexes were detected that constitute the basic membrane complexome of D. toluolica Tol2, e.g. transport proteins (e.g. sodium/sulfate symporters) or redox complexes involved in Na(+) -based bioenergetics (RnfABCDEG). Notably, size estimation indicates dimer and quadruple formation of the DsrMKJOP complex in vivo. Furthermore, cluster analysis suggests interaction of this complex with a rhodanese-like protein (Tol2_C05230) possibly representing a periplasmic electron transfer partner for DsrMKJOP.
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Affiliation(s)
- Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Hanna S Ruppersberg
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Christoph Feenders
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Bernd Blasius
- Mathematical Modelling, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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Dörries M, Wöhlbrand L, Kube M, Reinhardt R, Rabus R. Genome and catabolic subproteomes of the marine, nutritionally versatile, sulfate-reducing bacterium Desulfococcus multivorans DSM 2059. BMC Genomics 2016; 17:918. [PMID: 27846794 PMCID: PMC5109826 DOI: 10.1186/s12864-016-3236-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) are key players of the carbon- and sulfur-cycles in the sediments of the world's oceans. Habitat relevant SRBs are often members of the Desulfosarcina-Desulfococcus clade belonging to the deltaproteobacterial family of Desulfobacteraceae. Despite this environmental recognition, their molecular (genome-based) physiology and their potential to contribute to organic carbon mineralization as well as to adapt to changing environmental conditions have been scarcely investigated. A metabolically versatile representative of this family is Desulfococcus multivorans that is able to completely oxidize (to CO2) a variety of organic acids, including fatty acids up to C14, as well as aromatic compounds. RESULTS In this study the complete 4.46 Mbp and manually annotated genome of metabolically versatile Desulfococcus multivorans DSM 2059 is presented with particular emphasis on a proteomics-driven metabolic reconstruction. Proteomic profiling covered 17 substrate adaptation conditions (6 aromatic and 11 aliphatic compounds) and comprised 2D DIGE, shotgun proteomics and analysis of the membrane protein-enriched fractions. This comprehensive proteogenomic dataset allowed for reconstructing a metabolic network of degradation pathways and energy metabolism that consists of 170 proteins (154 detected; ~91 % coverage). Peripheral degradation routes feed via central benzoyl-CoA, (modified) β-oxidation or methylmalonyl-CoA pathways into the Wood-Ljungdahl pathway for complete oxidation of acetyl-CoA to CO2. Dissimilatory sulfate reduction is fueled by a complex electron transfer network composed of cytoplasmic components (e.g., electron transfer flavoproteins) and diverse membrane redox complexes (Dsr, Qmo, Hmc, Tmc, Qrc, Nuo and Rnf). Overall, a high degree of substrate-specific formation of catabolic enzymes was observed, while most complexes involved in electron transfer appeared to be constitutively formed. CONCLUSIONS A highly dynamic genome structure in combination with substrate-specifically formed catabolic subproteomes and a constitutive subproteome for energy metabolism and electron transfer appears to be a common trait of Desulfobacteraceae members.
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Affiliation(s)
- Marvin Dörries
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Michael Kube
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Waldsieversdorf, Germany
| | | | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Zhou W, Guo W, Zhou H, Chen X. Phenol degradation by Sulfobacillus acidophilus TPY via the meta -pathway. Microbiol Res 2016; 190:37-45. [DOI: 10.1016/j.micres.2016.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 11/30/2022]
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Zamarro MT, Martín-Moldes Z, Díaz E. The ICE XTD of Azoarcus sp. CIB, an integrative and conjugative element with aerobic and anaerobic catabolic properties. Environ Microbiol 2016; 18:5018-5031. [PMID: 27450529 DOI: 10.1111/1462-2920.13465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 11/28/2022]
Abstract
Integrative and conjugative elements (ICE) play a major role in aerobic degradation of aromatic compounds, but they have not yet been shown to be involved in anaerobic degradation. We have characterized here the ICEXTD element which endows to the beta-proteobacterium Azoarcus sp. CIB with the ability to utilize aromatic hydrocarbons. The core region of ICEXTD , which shows a remarkable synteny with that of ICEclc-like elements, allows its own intracellular and intercellular mobility. ICEXTD integrates at the tRNAGly of the host chromosome, but it can also excise to produce a ready to transfer circular form. The adaptation modules of ICEXTD represent a unique combination of gene clusters for aerobic (tod genes) and anaerobic (bss-bbs and mbd genes) degradation of certain aromatic hydrocarbons, e.g., toluene, m-xylene and cumene. Transfer of ICEXTD to other Azoarcus strains, e.g., A. evansii, confers them the ability to degrade aromatic hydrocarbons both aerobically and anaerobically. Interestingly, ICEXTD allows Cupriavidus pinatubonensis, a bacterium unable to degrade anaerobically aromatic compounds, to grow with m-xylene under anoxic conditions. Thus, ICEXTD constitutes the first mobile genetic element able to expand the catabolic abilities of certain bacteria for the removal of aromatic hydrocarbons either in the presence or absence of oxygen.
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Affiliation(s)
- María Teresa Zamarro
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Zaira Martín-Moldes
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Eduardo Díaz
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
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Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DG, Jørgensen BB, Stepanauskas R, Reinhardt R, Schramm A, Loy A, Adrian L. Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling. mBio 2016; 7:e00266-16. [PMID: 27143384 PMCID: PMC4959651 DOI: 10.1128/mbio.00266-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/05/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi The presence of genes encoding dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences were affiliated with the DEH Dsr clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH species. DEH-C11 also harbored genes encoding reductases for arsenate, dimethyl sulfoxide, and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate that this RdhA may not be a terminal reductase. The presence of other genes indicated that nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognized role in sulfur cycling and reveal the potential for expanded catabolic and respiratory functions among subsurface DEH. IMPORTANCE Sediments underlying our oceans are inhabited by microorganisms in cell numbers similar to those estimated to inhabit the oceans. Microorganisms in sediments consist of various diverse and uncharacterized groups that contribute substantially to global biogeochemical cycles. Since most subsurface microorganisms continue to evade cultivation, possibly due to very slow growth, we obtained and analyzed genomic information from a representative of one of the most widespread and abundant, yet uncharacterized bacterial groups of the marine subsurface. We describe several key features that may contribute to their widespread distribution, such as respiratory flexibility and the potential to use oxidized sulfur compounds, which are abundant in marine environments, as electron acceptors. Together, these data provide important information that can be used to assist in designing enrichment strategies or other postgenomic studies, while also improving our understanding of the diversity and distribution of dsrAB genes, which are widely used functional marker genes for sulfur-cycling microbes.
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Affiliation(s)
- Kenneth Wasmund
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Myriel Cooper
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Lars Schreiber
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Karen G Lloyd
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Brett J Baker
- Department of Marine Science, University of Texas-Austin, Marine Science Institute, Port Aransas, Texas, USA
| | - Dorthe G Petersen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | | | | | - Andreas Schramm
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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Jiménez N, Richnow HH, Vogt C, Treude T, Krüger M. Methanogenic Hydrocarbon Degradation: Evidence from Field and Laboratory Studies. J Mol Microbiol Biotechnol 2016; 26:227-42. [PMID: 26959375 DOI: 10.1159/000441679] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microbial transformation of hydrocarbons to methane is an environmentally relevant process taking place in a wide variety of electron acceptor-depleted habitats, from oil reservoirs and coal deposits to contaminated groundwater and deep sediments. Methanogenic hydrocarbon degradation is considered to be a major process in reservoir degradation and one of the main processes responsible for the formation of heavy oil deposits and oil sands. In the absence of external electron acceptors such as oxygen, nitrate, sulfate or Fe(III), fermentation and methanogenesis become the dominant microbial metabolisms. The major end product under these conditions is methane, and the only electron acceptor necessary to sustain the intermediate steps in this process is CO2, which is itself a net product of the overall reaction. We are summarizing the state of the art and recent advances in methanogenic hydrocarbon degradation research. Both the key microbial groups involved as well as metabolic pathways are described, and we discuss the novel insights into methanogenic hydrocarbon-degrading populations studied in laboratory as well as environmental systems enabled by novel cultivation-based and molecular approaches. Their possible implications on energy resources, bioremediation of contaminated sites, deep-biosphere research, and consequences for atmospheric composition and ultimately climate change are also addressed.
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Affiliation(s)
- Núria Jiménez
- Department of Resource Geochemistry, BGR - Federal Institute for Geosciences and Natural Resources, Hannover, Germany
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Musat F, Vogt C, Richnow HH. Carbon and Hydrogen Stable Isotope Fractionation Associated with the Aerobic and Anaerobic Degradation of Saturated and Alkylated Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:211-26. [DOI: 10.1159/000442161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Saturated hydrocarbons (alkanes) and alkylated aromatic hydrocarbons are abundant environmental compounds. Hydrocarbons are primarily removed from the environment by biodegradation, a process usually associated with moderate carbon and significant hydrogen isotope fractionation allowing monitoring of biodegradation processes in the environment. Here, we review the carbon and hydrogen stable isotope fractionation associated with the cleavage of C-H bonds at alkyl chains of hydrocarbons. Propane, <i>n</i>-butane and ethylbenzene were used as model components for alkyl moieties of aliphatic and aromatic hydrocarbons with emphasis on the cleavage of the C-H bond without the involvement of molecular oxygen. The carbon and hydrogen isotope fractionation factors were further used to explore the diagnostic potential for characterizing the mode of bond cleavage under oxic and anoxic conditions. Λ factors, calculated to correlate carbon and hydrogen fractionation, allowed to distinguish between aerobic and anaerobic biodegradation processes in the environment.
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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.
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Affiliation(s)
- Frederick von Netzer
- Helmholtz Zentrum Mx00FC;nchen - German Research Center for Environmental Health, Institute of Groundwater Ecology, Neuherberg, Germany
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Heider J, Szaleniec M, Martins BM, Seyhan D, Buckel W, Golding BT. Structure and Function of Benzylsuccinate Synthase and Related Fumarate-Adding Glycyl Radical Enzymes. J Mol Microbiol Biotechnol 2016; 26:29-44. [PMID: 26959246 DOI: 10.1159/000441656] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The pathway of anaerobic toluene degradation is initiated by a remarkable radical-type enantiospecific addition of the chemically inert methyl group to the double bond of a fumarate cosubstrate to yield (R)-benzylsuccinate as the first intermediate, as catalyzed by the glycyl radical enzyme benzylsuccinate synthase. In recent years, it has become clear that benzylsuccinate synthase is the prototype enzyme of a much larger family of fumarate-adding enzymes, which play important roles in the anaerobic metabolism of further aromatic and even aliphatic hydrocarbons. We present an overview on the biochemical properties of benzylsuccinate synthase, as well as its recently solved structure, and present the results of an initial structure-based modeling study on the reaction mechanism. Moreover, we compare the structure of benzylsuccinate synthase with those predicted for different clades of fumarate-adding enzymes, in particular the paralogous enzymes converting p-cresol, 2-methylnaphthalene or n-alkanes.
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Affiliation(s)
- Johann Heider
- Laboratory of Microbial Biochemistry, LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
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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).
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Affiliation(s)
- Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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47
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Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
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48
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Chaurasia AK, Tremblay PL, Holmes DE, Zhang T. Genetic evidence that the degradation ofpara-cresol byGeobacter metallireducensis catalyzed by the periplasmicpara-cresol methylhydroxylase. FEMS Microbiol Lett 2015; 362:fnv145. [DOI: 10.1093/femsle/fnv145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2015] [Indexed: 11/14/2022] Open
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Funk MA, Marsh ENG, Drennan CL. Substrate-bound structures of benzylsuccinate synthase reveal how toluene is activated in anaerobic hydrocarbon degradation. J Biol Chem 2015. [PMID: 26224635 DOI: 10.1074/jbc.m115.670737] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Various bacteria perform anaerobic degradation of small hydrocarbons as a source of energy and cellular carbon. To activate non-reactive hydrocarbons such as toluene, enzymes conjugate these molecules to fumarate in a radical-catalyzed, C-C bond-forming reaction. We have determined x-ray crystal structures of the glycyl radical enzyme that catalyzes the addition of toluene to fumarate, benzylsuccinate synthase (BSS), in two oligomeric states with fumarate alone or with both substrates. We find that fumarate is secured at the bottom of a long active site cavity with toluene bound directly above it. The two substrates adopt orientations that appear ideal for radical-mediated C-C bond formation; the methyl group of toluene is positioned between fumarate and a cysteine that forms a thiyl radical during catalysis, which is in turn adjacent to the glycine that serves as a radical storage residue. Toluene is held in place by fumarate on one face and tight packing by hydrophobic residues on the other face and sides. These hydrophobic residues appear to become ordered, thus encapsulating toluene, only in the presence of BSSβ, a small protein subunit that forms a tight complex with BSSα, the catalytic subunit. Enzymes related to BSS are able to metabolize a wide range of hydrocarbons through attachment to fumarate. Using our structures as a guide, we have constructed homology models of several of these "X-succinate synthases" and determined conservation patterns that will be useful in understanding the basis for catalysis and specificity in this family of enzymes.
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Affiliation(s)
| | - E Neil G Marsh
- the Department of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Catherine L Drennan
- From the Departments of Chemistry and Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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