1
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Li ZY, Cui YW, Liang HK, Yan HJ, Yang RC. Tetracycline degradation by a mixed culture of halotolerant fungi-bacteria under static magnetic field: Mechanism and antibiotic resistance genes transfer. JOURNAL OF HAZARDOUS MATERIALS 2025; 492:138181. [PMID: 40199074 DOI: 10.1016/j.jhazmat.2025.138181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 03/02/2025] [Accepted: 04/03/2025] [Indexed: 04/10/2025]
Abstract
Efficient antibiotics removal lowers the transmission risk of antibiotic resistance genes (ARGs). However, low efficiency limits the application of biological methods for antibiotics removal. Herein, a mixed culture of halotolerant fungi-bacteria was used for treatment of saline wastewater containing tetracycline (TC). Furthermore, static magnetic field (SMF) was used to increase TC removal. The study examined the effectiveness of SMF in removing antibiotics from saline wastewater and the associated risk of ARGs transmission. The results demonstrated that the application of a 40 mT SMF significantly improved the TC removal efficiency by 37.09 %, compared to the control (SMF=0) The TC was mainly removed through biodegradation and adsorption. In biodegradation, SMF enhanced electron transport system activity, and activities of lignin-degrading enzymes which led to higher TC biodegradation. The activity of lactate dehydrogenase and malondialdehyde decreased, lowering the damage of microbial cell membranes by TC. During the adsorption process, higher generation of extracellular polymeric substances was observed under SMF, which caused an increase in TC removal via adsorption. Microbial community analysis revealed that SMF facilitated the enrichment of TC-degrading microorganisms. Under SMF, vertical gene transfer of ARGs increased, while horizontal gene transfer risk decreased due to a reduction in mobile genetic elements (intl1) abundance. This study demonstrates that SMF is a promising strategy for enhancing TC removal efficiency, providing a basis for improved antibiotic wastewater management.
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Affiliation(s)
- Zhen-Ying Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - You-Wei Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Hui-Kai Liang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Hui-Juan Yan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Rui-Chun Yang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
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2
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Hege D, Gemmecker Y, Clermont L, Aleksic I, Oleksy G, Szaleniec M, Heider J. Genetic manipulation of the betaproteobacterial genera Thauera and Aromatoleum. Methods Enzymol 2025; 714:139-161. [PMID: 40288836 DOI: 10.1016/bs.mie.2025.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2025]
Abstract
Most recombinant proteins are expressed in model host organisms like Escherichia coli. Meanwhile, a significant number of enzymes require complex activation or special cofactors not available from standard hosts. The betaproteobacteria Thauera and Aromatoleum allow access to some of these enzymes, following procedures described in this chapter. The methods described enable transformation and conjugation of vectors into these species as alternate gene expression systems which allow fundamental studies of complex recombinant proteins as well as their biotechnological application.
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Affiliation(s)
- Dominik Hege
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg, Germany
| | - Yvonne Gemmecker
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg, Germany
| | - Lina Clermont
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg, Germany
| | - Ivana Aleksic
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland
| | - Gabriela Oleksy
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg, Germany; Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland.
| | - Johann Heider
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, Marburg, Germany; Synmikro Center Marburg, Marburg, Germany
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3
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Pinel-Cabello M, Wasmund K, Soder-Walz JM, Vega M, Rosell M, Marco-Urrea E. Divergent dual C-H isotopic fractionation pattern during anaerobic biodegradation of toluene within Aromatoleum species under nitrate-reducing conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 361:124823. [PMID: 39197649 DOI: 10.1016/j.envpol.2024.124823] [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: 05/02/2024] [Revised: 07/22/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Toluene is a pollutant frequently detected in contaminated groundwater, mostly due to leakage from underground gasoline storage tanks and pipeline ruptures. Multi-element compound-specific isotope analysis provides a framework to understand transformation processes and design efficient remediation strategies. In this study, we enriched an anaerobic bacterial culture derived from a BTEX-contaminated aquifer that couples toluene and phenol oxidation with nitrate reduction and the concomitant production of carbon dioxide and biomass. The 16S rRNA gene amplicon data indicated that the toluene-degrading consortium was dominated by an Aromatoleum population (87 ± 2 % relative abundance), and metagenome sequencing confirmed that the genome of this Aromatoleum sp. encoded glycyl-radical enzyme benzylsuccinate synthase (BssABC) and phenylphospate synthase (PpsA1BC) homologous genes involved in the first step of toluene and phenol transformation, respectively. Carbon and hydrogen isotopic fractionation were εbulk, C = - 3.5 ± 0.6 ‰ and εrp, H = - 85 ± 11 ‰, respectively, leading to a dual C-H isotope slope of ΛH/C = 26 ± 2. This value fits with a previously reported value for a consortium dominated by an Azoarcus species (ΛH/C = 19 ± 5) but differs from that reported for Aromatoleum aromaticum (ΛH/C = 14 ± 1), both of which grow with toluene under nitrate-reducing conditions. Overall, this suggests the existence of different BssABC enzymes with different mechanistic motifs even within the same Aromatoleum genus.
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Affiliation(s)
- Maria Pinel-Cabello
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra, Spain
| | - Kenneth Wasmund
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Jesica M Soder-Walz
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra, Spain
| | - Maria Vega
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra, Spain
| | - Mònica Rosell
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Hidrogeologia (MAGH), Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), c/ Martí Franquès s/n, 08028, Barcelona, Spain
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra, Spain.
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Gemmecker Y, Winiarska A, Hege D, Kahnt J, Seubert A, Szaleniec M, Heider J. A pH-dependent shift of redox cofactor specificity in a benzyl alcohol dehydrogenase of aromatoleum aromaticum EbN1. Appl Microbiol Biotechnol 2024; 108:410. [PMID: 38976076 PMCID: PMC11231019 DOI: 10.1007/s00253-024-13225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024]
Abstract
We characterise a reversible bacterial zinc-containing benzyl alcohol dehydrogenase (BaDH) accepting either NAD+ or NADP+ as a redox cofactor. Remarkably, its redox cofactor specificity is pH-dependent with the phosphorylated cofactors favored at lower and the dephospho-forms at higher pH. BaDH also shows different steady-state kinetic behavior with the two cofactor forms. From a structural model, the pH-dependent shift may affect the charge of a histidine in the 2'-phosphate-binding pocket of the redox cofactor binding site. The enzyme is phylogenetically affiliated to a new subbranch of the Zn-containing alcohol dehydrogenases, which share this conserved residue. BaDH appears to have some specificity for its substrate, but also turns over many substituted benzyl alcohol and benzaldehyde variants, as well as compounds containing a conjugated C=C double bond with the aldehyde carbonyl group. However, compounds with an sp3-hybridised C next to the alcohol/aldehyde group are not or only weakly turned over. The enzyme appears to contain a Zn in its catalytic site and a mixture of Zn and Fe in its structural metal-binding site. Moreover, we demonstrate the use of BaDH in an enzyme cascade reaction with an acid-reducing tungsten enzyme to reduce benzoate to benzyl alcohol. KEY POINTS: •Zn-containing BaDH has activity with either NAD + or NADP+ at different pH optima. •BaDH converts a broad range of substrates. •BaDH is used in a cascade reaction for the reduction of benzoate to benzyl alcohol.
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Affiliation(s)
- Yvonne Gemmecker
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland
| | - Dominik Hege
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Jörg Kahnt
- Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Seubert
- Faculty of Chemistry, Analytical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.
| | - Johann Heider
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany.
- Center for Synthetic Microbiology, Marburg, Germany.
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5
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Wu Z, Yu X, Ji Y, Liu G, Gao P, Xia L, Li P, Liang B, Freilich S, Gu L, Qiao W, Jiang J. Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132762. [PMID: 37837778 DOI: 10.1016/j.jhazmat.2023.132762] [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: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhan Ji
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xia
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Lifeng Gu
- ChangXing AISHENG Environmental Technology Co., Ltd, Zhejiang 313199, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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6
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Buschen R, Lambertus P, Scheve S, Horst S, Song F, Wöhlbrand L, Neidhardt J, Winklhofer M, Wagner T, Rabus R. Sensitive and selective phenol sensing in denitrifying Aromatoleum aromaticum EbN1 T. Microbiol Spectr 2023; 11:e0210023. [PMID: 37823660 PMCID: PMC10715001 DOI: 10.1128/spectrum.02100-23] [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: 05/19/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Aromatic compounds are globally abundant organic molecules with a multitude of natural and anthropogenic sources, underpinning the relevance of their biodegradation. A. aromaticum EbN1T is a well-studied environmental betaproteobacterium specialized on the anaerobic degradation of aromatic compounds. The here studied responsiveness toward phenol in conjunction with the apparent high ligand selectivity (non-promiscuity) of its PheR sensor and those of the related p-cresol (PcrS) and p-ethylphenol (EtpR) sensors are in accord with the substrate-specificity and biochemical distinctiveness of the associated degradation pathways. Furthermore, the present findings advance our general understanding of the substrate-specific regulation of the strain's remarkable degradation network and of the concentration thresholds below which phenolic compounds become essentially undetectable and as a consequence should escape substantial biodegradation. Furthermore, the findings may inspire biomimetic sensor designs for detecting and quantifying phenolic contaminants in wastewater or environments.
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Affiliation(s)
- Ramona Buschen
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Pia Lambertus
- 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
| | - Simon Horst
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Fei Song
- Human Genetics, Department of Human Medicine, 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
| | - John Neidhardt
- Human Genetics, Department of Human Medicine, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Michael Winklhofer
- Research Center Neurosensory Science, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Sensory Biology of Animals, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Tristan Wagner
- Max Planck Research Group Microbial Metabolism, Max Planck Institute for Marine Microbiology, Bremen, 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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7
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Weber L, Gilat A, Maillot N, Byrne D, Arnoux P, Giudici-Orticoni MT, Méjean V, Ilbert M, Genest O, Rosenzweig R, Dementin S. Bacterial adaptation to cold: Conservation of a short J-domain co-chaperone and its protein partners in environmental proteobacteria. Environ Microbiol 2023; 25:2447-2464. [PMID: 37549929 DOI: 10.1111/1462-2920.16478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Bacterial genomes are a huge reservoir of genes encoding J-domain protein co-chaperones that recruit the molecular chaperone DnaK to assist protein substrates involved in survival, adaptation, or fitness. The atc operon of the aquatic mesophilic bacterium Shewanella oneidensis encodes the proteins AtcJ, AtcA, AtcB, and AtcC, and all of them, except AtcA, are required for growth at low temperatures. AtcJ is a short J-domain protein that interacts with DnaK, but also with AtcC through its 21 amino acid C-terminal domain. This interaction network is critical for cold growth. Here, we show that AtcJ represents a subfamily of short J-domain proteins that (i) are found in several environmental, mostly aquatic, β- or ɣ-proteobacteria and (ii) contain a conserved PX7 W motif in their C-terminal extension. Using a combination of NMR, biochemical and genetic approaches, we show that the hydrophobic nature of the tryptophan of the S. oneidensis AtcJ PX7 W motif determines the strong AtcJ-AtcC interaction essential for cold growth. The AtcJ homologues are encoded by operons containing at least the S. oneidensis atcA, atcB, and atcC homologues. These findings suggest a conserved network of DnaK and Atc proteins necessary for low-temperature growth and, given the variation in the atc operons, possibly for other biological functions.
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Affiliation(s)
- Lana Weber
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Atar Gilat
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nathanael Maillot
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix-Marseille University, French National Center for Scientific Research (CNRS), IMM FR3479, Marseille, France
| | - Pascal Arnoux
- Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM UMR7265), Aix-Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), French National Center for Scientific Research (CNRS), Saint Paul-Lez-Durance, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Vincent Méjean
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Marianne Ilbert
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Olivier Genest
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sébastien Dementin
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
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8
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Reyes-Umana VM, Coates JD. A description of the genus Denitromonas nom. rev.: Denitromonas iodatirespirans sp. nov., a novel iodate-reducing bacterium, and two novel perchlorate-reducing bacteria, Denitromonas halophila and Denitromonas ohlonensis, isolated from San Francisco Bay intertidal mudflats. Microbiol Spectr 2023; 11:e0091523. [PMID: 37772843 PMCID: PMC10581121 DOI: 10.1128/spectrum.00915-23] [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: 03/03/2023] [Accepted: 08/04/2023] [Indexed: 09/30/2023] Open
Abstract
The genus Denitromonas is currently a non-validated taxon that has been identified in several recent publications as members of microbial communities arising from marine environments. Very little is known about the biology of Denitromonas spp., and no pure cultures are presently found in any culture collections. The current epitaph of Denitromonas was given to the organism under the assumption that all members of this genus are denitrifying bacteria. This study performs phenotypic and genomic analyses on three new Denitromonas spp. isolated from tidal mudflats in the San Francisco Bay. We demonstrate that Denitromonas spp. are indeed all facultative denitrifying bacteria that utilize a variety of carbon sources such as acetate, lactate, and succinate. In addition, individual strains also use the esoteric electron acceptors perchlorate, chlorate, and iodate. Both 16S and Rps/Rpl phylogenetic analyses place Denitromonas spp. as a deep branching clade in the family Zoogloeaceae, separate from either Thauera spp., Azoarcus spp., or Aromatoleum spp. Genome sequencing reveals a G + C content ranging from 63.72% to 66.54%, and genome sizes range between 4.39 and 5.18 Mb. Genes for salt tolerance and denitrification are distinguishing features that separate Denitromonas spp. from the closely related Azoarcus and Aromatoleum genera. IMPORTANCE The genus Denitromonas is currently a non-validated taxon that has been identified in several recent publications as members of microbial communities arising from marine environments. Very little is known about the biology of Denitromonas spp., and no pure cultures are presently found in any culture collections. The current epitaph of Denitromonas was given to the organism under the assumption that all members of this genus are denitrifying bacteria. This study performs phenotypic and genomic analyses on three Denitromonas spp., Denitromonas iodatirespirans sp. nov.-a novel iodate-reducing bacterium-and two novel perchlorate-reducing bacteria, Denitromonas halophila and Denitromonas ohlonensis, isolated from San Francisco Bay intertidal mudflats.
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Affiliation(s)
- Victor M. Reyes-Umana
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - John D. Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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9
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Jeong D, Baik MH, Jung EC, Ko MS, Um W, Ryu JH. Potential of indigenous bacteria driven U(VI) reduction under relevant deep geological repository (DGR) conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121674. [PMID: 37085104 DOI: 10.1016/j.envpol.2023.121674] [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: 12/22/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Understanding the biogeochemical U redox processes is crucial for controlling U mobility and toxicity under conditions relevant to deep geological repositories (DGRs). In this study, we examined the microbial reduction of aqueous hexavalent uranium U(VI) [U(VI)aq] by indigenous bacteria in U-contaminated groundwater. Three indigenous bacteria obtained from granitic groundwater at depths of 44-60 m (S1), 92-116 m (S2), and 234-244 m (S3) were used in U(VI)aq bioreduction experiments. The concentration of U(VI)aq was monitored to evaluate its removal efficiency for 24 weeks under anaerobic conditions with the addition of 20 mM sodium acetate. During the anaerobic reaction, U(VI)aq was precipitated in the form of U(IV)-silicate with a particle size >100 nm. The final U(VI)aq removal efficiencies were 37.7%, 43.1%, and 57.8% in S1, S2, and S3 sample, respectively. Incomplete U(VI)aq removal was attributed to the presence of a thermodynamically stable calcium uranyl carbonate complex in the U-contaminated groundwater. High-throughput 16S rRNA gene sequencing analysis revealed the differences in indigenous bacterial communities in response to the depth, which affected to the U(VI)aq removal efficiency. Pseudomonas peli was found to be a common bacterium related to U(VI)aq bioreduction in S1 and S2 samples, while two SRB species, Thermodesulfovibrio yellowstonii and Desulfatirhabdium butyrativorans, played key roles in the bioreduction of U(VI)aq in S3 sample. These results indicate that remediation of U(VI)aq is possible by stimulating the activity of indigenous bacteria in the DGR environment.
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Affiliation(s)
- Dawoon Jeong
- Disposal Safety Evaluation R&D Division, Korea Atomic Energy Research Institute, 111, Daedeok-daero 989 Beon-gil, Yuseong-gu, Daejeon-si, 34057, the Republic of Korea.
| | - Min Hoon Baik
- Disposal Safety Evaluation R&D Division, Korea Atomic Energy Research Institute, 111, Daedeok-daero 989 Beon-gil, Yuseong-gu, Daejeon-si, 34057, the Republic of Korea
| | - Euo Chang Jung
- Nuclear Chemistry Technology Division, Korea Atomic Energy Research Institute, 111, Daedeok-daero 989 Beon-gil, Yuseong-gu, Daejeon-si, 34057, the Republic of Korea
| | - Myoung-Soo Ko
- Department of Energy and Resources Engineering, Kangwon National University, 1, Gangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea
| | - Wooyong Um
- Division of Advanced Nuclear Engineering, Pohang University of Science and Technology, 77, Cheongam-ro, Nam-Gu, Pohang-si, Gyeongsangbuk-do, 37673, Republic of Korea
| | - Ji-Hun Ryu
- Disposal Safety Evaluation R&D Division, Korea Atomic Energy Research Institute, 111, Daedeok-daero 989 Beon-gil, Yuseong-gu, Daejeon-si, 34057, the Republic of Korea.
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10
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Sahoo TP, Kumar MA. Remediation of phthalate acid esters from contaminated environment—Insights on the bioremedial approaches and future perspectives. Heliyon 2023; 9:e14945. [PMID: 37025882 PMCID: PMC10070671 DOI: 10.1016/j.heliyon.2023.e14945] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/17/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Phthalates are well-known emerging pollutants that are toxic to the environment and human health. Phthalates are lipophilic chemicals used as plasticizers in many of the items for improving their material properties. These compounds are not chemically bound and are released to the surroundings directly. Phthalate acid esters (PAEs) are endocrine disruptors and can interfere with hormones, which can cause issues with development and reproduction, thus there is a huge concern over their existence in various ecological surroundings. The purpose of this review is to explore the occurrence, fate, and concentration of phthalates in various environmental matrices. This article also covers the phthalate degradation process, mechanism, and outcomes. Besides the conventional treatment technology, the paper also aims at the recent advancements in various physical, chemical, and biological approaches developed for phthalate degradation. In this paper, a special focus has been given on the diverse microbial entities and their bioremedial mechanisms executes the PAEs removal. Critically, the analyses method for determining intermediate products generated during phthalate biotransformation have been discussed. Concluisvely, the challenges, limitations, knowledge gaps and future opportunities of bioremediation and their significant role in ecology have also been highlighted.
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11
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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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12
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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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13
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Pacheco-Sánchez D, Marín P, Molina-Fuentes Á, Marqués S. Subtle sequence differences between two interacting σ 54 -dependent regulators lead to different activation mechanisms. FEBS J 2022; 289:7582-7604. [PMID: 35816183 PMCID: PMC10084136 DOI: 10.1111/febs.16576] [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: 02/14/2022] [Revised: 06/08/2022] [Accepted: 07/10/2022] [Indexed: 12/13/2022]
Abstract
In the strictly anaerobic nitrate reducing bacterium Aromatoleum anaerobium, degradation of 1,3-dihydroxybenzene (1,3-DHB, resorcinol) is controlled by two bacterial enhancer-binding proteins (bEBPs), RedR1 and RedR2, which regulate the transcription of three σ54 -dependent promoters controlling expression of the pathway. RedR1 and RedR2 are identical over their length except for their N-terminal tail which differ in sequence and length (six and eight residues, respectively), a single change in their N-terminal domain (NTD), and nine non-identical residues in their C-terminal domain (CTD). Their NTD is composed of a GAF and a PAS domain connected by a linker helix. We show that each regulator is controlled by a different mechanism: whilst RedR1 responds to the classical NTD-mediated negative regulation that is released by the presence of its effector, RedR2 activity is constitutive and controlled through interaction with BtdS, an integral membrane subunit of hydroxyhydroquinone dehydrogenase carrying out the second step in 1,3-DHB degradation. BtdS sequesters the RedR2 regulator to the membrane through its NTD, where a four-Ile track in the PAS domain, interrupted by a Thr in RedR1, and the N-terminal tail are involved. The presence of 1,3-DHB, which is metabolized to hydroxybenzoquinone, releases RedR2 from the membrane. Most bEBPs assemble into homohexamers to activate transcription; we show that hetero-oligomer formation between RedR1 and RedR2 is favoured over homo-oligomers. However, either an NTD-truncated version of RedR1 or a full-length RedR2 are capable of promoter activation on their own, suggesting they should assemble into homohexamers in vivo. We show that promoter DNA behaves as an allosteric effector through binding the CTD to control ΔNTD-RedR1 multimerization and activity. Overall, the regulation of the 1,3-DHB anaerobic degradation pathway can be described as a novel mode of bEBP activation and assembly.
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Affiliation(s)
- Daniel Pacheco-Sánchez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Patricia Marín
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Águeda Molina-Fuentes
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Silvia Marqués
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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14
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Lo HY, Martínez-Lavanchy PM, Goris T, Heider J, Boll M, Kaster AK, Müller JA. IncP-type plasmids carrying genes for antibiotic resistance or for aromatic compound degradation are prevalent in sequenced Aromatoleum and Thauera strains. Environ Microbiol 2022; 24:6411-6425. [PMID: 36306376 DOI: 10.1111/1462-2920.16262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/25/2022] [Indexed: 01/12/2023]
Abstract
Self-transferable plasmids of the incompatibility group P-1 (IncP-1) are considered important carriers of genes for antibiotic resistance and other adaptive functions. In the laboratory, these plasmids have a broad host range; however, little is known about their in situ host profile. In this study, we discovered that Thauera aromatica K172T , a facultative denitrifying microorganism capable of degrading various aromatic compounds, contains a plasmid highly similar to the IncP-1 ε archetype pKJK5. The plasmid harbours multiple antibiotic resistance genes and is maintained in strain K172T for at least 1000 generations without selection pressure from antibiotics. In a subsequent search, we found additional nine IncP-type plasmids in a total of 40 sequenced genomes of the closely related genera Aromatoleum and Thauera. Six of these plasmids form a novel IncP-1 subgroup designated θ, four of which carry genes for anaerobic or aerobic degradation of aromatic compounds. Pentanucleotide sequence analyses (k-mer profiling) indicated that Aromatoleum spp. and Thauera spp. are among the most suitable hosts for the θ plasmids. Our results highlight the importance of IncP-1 plasmids for the genetic adaptation of these common facultative denitrifying bacteria and provide novel insights into the in situ host profile of these plasmids.
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Affiliation(s)
- Hao-Yu Lo
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Paula M Martínez-Lavanchy
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Tobias Goris
- Department of Molecular Toxicology, Intestinal Microbiology, German Institute of Human Nutrition, Potsdam-Rehbruecke, Germany
| | - Johann Heider
- Department of Biology, Philipps-Universität Marburg, Germany
| | - Matthias Boll
- Institute of Biology II, Albert-Ludwigs-Universität Freiburg, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Jochen A Müller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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15
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Sanz D, Díaz E. Genetic characterization of the cyclohexane carboxylate degradation pathway in the denitrifying bacterium Aromatoleum sp. CIB. Environ Microbiol 2022; 24:4987-5004. [PMID: 35768954 PMCID: PMC9795900 DOI: 10.1111/1462-2920.16093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/01/2022] [Indexed: 12/30/2022]
Abstract
The alicyclic compound cyclohexane carboxylate (CHC) is anaerobically degraded through a peripheral pathway that converges with the central benzoyl-CoA degradation pathway of aromatic compounds in Rhodopseudomonas palustris (bad pathway) and some strictly anaerobic bacteria. Here we show that in denitrifying bacteria, e.g. Aromatoleum sp. CIB strain, CHC is degraded through a bad-ali pathway similar to that reported in R. palustris but that does not share common intermediates with the benzoyl-CoA degradation pathway (bzd pathway) of this bacterium. The bad-ali genes are also involved in the aerobic degradation of CHC in strain CIB, and orthologous bad-ali clusters have been identified in the genomes of a wide variety of bacteria. Expression of bad-ali genes in strain CIB is under control of the BadR transcriptional repressor, which was shown to recognize CHC-CoA, the first intermediate of the pathway, as effector, and whose operator region (CAAN4 TTG) was conserved in bad-ali clusters from Gram-negative bacteria. The bad-ali and bzd pathways generate pimelyl-CoA and 3-hydroxypimelyl-CoA, respectively, that are metabolized through a common aab pathway whose genetic determinants form a supraoperonic clustering with the bad-ali genes. A synthetic bad-ali-aab catabolic module was engineered and it was shown to confer CHC degradation abilities to different bacterial hosts.
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Affiliation(s)
- David Sanz
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita Salas‐CSICMadridSpain
| | - Eduardo Díaz
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita Salas‐CSICMadridSpain
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16
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Winiarska A, Hege D, Gemmecker Y, Kryściak-Czerwenka J, Seubert A, Heider J, Szaleniec M. Tungsten Enzyme Using Hydrogen as an Electron Donor to Reduce Carboxylic Acids and NAD . ACS Catal 2022;12:8707-8717. [PMID: 35874620 PMCID: PMC9295118 DOI: 10.1021/acscatal.2c02147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Tungsten-dependent
aldehyde oxidoreductases (AORs) catalyze the
oxidation of aldehydes to acids and are the only known enzymes reducing
non-activated acids using electron donors with low redox potentials.
We report here that AOR from Aromatoleum aromaticum (AORAa) catalyzes the reduction of organic
acids not only with low-potential Eu(II) or Ti(III) complexes but
also with H2 as an electron donor. Additionally, AORAa catalyzes the H2-dependent reduction
of NAD+ or benzyl viologen. The rate of H2-dependent
NAD+ reduction equals to 10% of that of aldehyde oxidation,
representing the highest H2 turnover rate observed among
the Mo/W enzymes. As AORAa simultaneously
catalyzes the reduction of acids and NAD+, we designed
a cascade reaction utilizing a NAD(P)H-dependent alcohol dehydrogenase
to reduce organic acids to the corresponding alcohols with H2 as the only reductant. The newly discovered W-hydrogenase side activity
of AORAa may find applications in either
NADH recycling or conversion of carboxylic acids to more useful biochemicals.
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Affiliation(s)
- Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
| | - Dominik Hege
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Yvonne Gemmecker
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Joanna Kryściak-Czerwenka
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
| | - Andreas Seubert
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Johann Heider
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany.,Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
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17
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Becker P, Döhmann A, Wöhlbrand L, Thies D, Hinrichs C, Buschen R, Wünsch D, Neumann-Schaal M, Schomburg D, Winklhofer M, Reinhardt R, Rabus R. Complex and flexible catabolism in Aromatoleum aromaticum pCyN1. Environ Microbiol 2022; 24:3195-3211. [PMID: 35590445 DOI: 10.1111/1462-2920.16074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022]
Abstract
Large quantities of organic matter are continuously deposited, and (a)biotic gradients intersect in the soil-rhizosphere, where biodegradation contributes to the global cycles of elements. The betaproteobacterial genus Aromatoleum comprises cosmopolitan, facultative denitrifying degradation specialists. A. aromaticum pCyN1 stands out for anaerobically decomposing plant-derived monoterpenes in addition to monoaromatic hydrocarbons, polar aromatics and aliphatics. The catabolic network's structure and flexibility in A. aromaticum pCyN1 was studied across 34 growth conditions by superimposing proteome profiles onto the manually annotated 4.37 Mbp genome. Strain pCyN1 employs three fundamentally different enzymes for C-H-bond cleavage at the methyl groups of p-cymene/4-ethyltoluene, toluene and p-cresol, respectively. Regulation of degradation modules displayed substrate specificities ranging from narrow (toluene and cyclohexane carboxylate) via medium-wide (one module shared by p-cymene, 4-ethyltoluene, α-phellandrene, α-terpinene, γ-terpinene and limonene) to broad (central benzoyl-CoA pathway serving 16 aromatic substrates). Remarkably, three variants of ATP-dependent (class I) benzoyl-CoA reductase and four different β-oxidation routes establish a degradation hub that accommodates the substrate diversity. The respiratory system displayed several conspicuous profiles, e.g., the presence of nitrous oxide reductase under oxic and of low-affinity oxidase under anoxic conditions. Overall, nutritional versatility in conjunction with network regulation endow A. aromaticum pCyN1 with broad adaptability. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Patrick Becker
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Annemieke Döhmann
- 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
| | - Daniela Thies
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, 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
| | - Ramona Buschen
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Daniel Wünsch
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolism, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Carolo-Wilhelmina zu Braunschweig, Braunschweig, Germany.,Department of Analytics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Dietmar Schomburg
- Research Group Bacterial Metabolism, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Carolo-Wilhelmina zu Braunschweig, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Carolo-Wilhelmina zu Braunschweig, Braunschweig, Germany
| | - Michael Winklhofer
- Research Center Neurosensory Science, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany.,Sensory Biology of Animals, Institute of Biology and Environmental Sciences (IBU), 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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18
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Reyes-Umana V, Kretschmer J, Coates JD. Isolation of a Dissimilatory Iodate-Reducing Aromatoleum sp. From a Freshwater Creek in the San Francisco Bay Area. Front Microbiol 2022; 12:804181. [PMID: 35111143 PMCID: PMC8801600 DOI: 10.3389/fmicb.2021.804181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/28/2021] [Indexed: 11/26/2022] Open
Abstract
Recent reports of dissimilatory iodate-reducing microorganisms (DIRM) have arisen from studies of bacteria in marine environments. These studies described the physiology and distribution of DIRM while also demonstrating their presence in iodine-rich marine environments. We posited that despite lower iodine concentrations, terrestrial and freshwater ecosystems should also harbor DIRM. We established numerous enrichments from coastal and freshwater environments that actively remove amended iodate. We describe the physiology and genome of a new DIRM isolate, Aromatoleum toluclasticum sp. TC-10, emerging from a freshwater creek microcosm. Like other DIRM, A. toluclasticum sp. TC-10 couples acetate oxidation to iodate reduction with a concomitant increase in the OD600. Our results indicate that A. toluclasticum sp. TC-10 performs dissimilatory iodate reduction (DIR) using the recently described iodate reductase (Idr). We provide further evidence of horizontal gene transfer of the idr genes by demonstrating the lack of Idr in the closely related (99.93% 16S rDNA sequence identity) A. toluclasticum sp. MF63 and describe the heterogeneity of the accessory proteins associated with the iodate reduction island (IRI). These observations provide additional evidence that DIR is a horizontally acquired metabolism with broad environmental distribution beyond exclusively marine environments.
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19
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Huang Z, Liu R, Chen F, Lai Q, Oren A, Shao Z. Nitrogeniibacter aestuarii sp. nov., a Novel Nitrogen-Fixing Bacterium Affiliated to the Family Zoogloeaceae and Phylogeny of the Family Zoogloeaceae Revisited. Front Microbiol 2021; 12:755908. [PMID: 34745064 PMCID: PMC8565577 DOI: 10.3389/fmicb.2021.755908] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/23/2021] [Indexed: 11/13/2022] Open
Abstract
Members of the family Zoogloeaceae within the order Rhodocyclales are found to play vital roles in terrestrial and aquatic ecosystems by participating in biofloc formation in activated sludge, polycyclic aromatic hydrocarbon degradation, and nitrogen metabolism, such as denitrification and nitrogen fixation. Here, two bacterial strains designated H1-1-2AT and ZN11-R3-1 affiliated to the family Zoogloeaceae were isolated from coastal wetland habitats. The 16S rRNA gene sequences of the two strains were 100% identical and had maximum similarity with Nitrogeniibacter mangrovi M9-3-2T of 98.4% and ≤94.5% with other species. Phylogenetic analysis suggested that the two strains belonged to a single species and formed a novel monophyletic branch affiliated to the genus Nitrogeniibacter. The average nucleotide identity (ANI) value and digital DNA-DNA hybridization (dDDH) estimate between the two strains and N. mangrovi M9-3-2T were 78.5–78.7% and 21.4–21.6%, respectively, indicating that the two strains represent a novel species. The genomes of strain H1-1-2AT (complete genome) and ZN11-R3-1 (draft genome) were 4.7Mbp in length encoding ~4,360 functional genes. The DNA G+C content was 62.7%. Nitrogen fixation genes were found in the two strains, which were responsible for the growth on nitrogen-free medium, whereas denitrification genes found in N. mangrovi M9-3-2T were absent in the two strains. The respiratory quinone was ubiquinone-8. The major polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and aminophospholipid. The major fatty acids were summed feature 3 (C16:1ω7c and C16:1ω6c), C16:0, C12:0, and C10:0 3-OH. Based on genomic, phenotypic, and chemotaxonomic characterizations, strains H1-1-2AT and ZN11-R3-1 represent a novel species of the genus Nitrogeniibacter, for which the name Nitrogeniibacter aestuarii sp. nov. is proposed. The type strain is H1-1-2AT (=MCCC 1K04284T=KCTC 82672T), and additional strain is ZN11-R3-1 (=MCCC 1A17971=KCTC 82671). Additionally, phylogenomic analysis of the members of the family Zoogloeaceae including type strains and uncultivated bacteria was performed, using the Genome Taxonomic Database toolkit (GTDB-Tk). Combined with the 16S rRNA gene phylogeny, four novel genera, Parazoarcus gen. nov., Pseudazoarcus gen. nov., Pseudothauera gen. nov., and Cognatazoarcus gen. nov., were proposed. This study provided new insights to the taxonomy of the family Zoogloeaceae.
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Affiliation(s)
- Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China.,Key Laboratory of Inshore Resources Biotechnology (Quanzhou Normal University), Fujian Province University, Quanzhou, China
| | - Renju Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Fenghua Chen
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
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20
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Liao H, Qu M, Hou X, Lin X, Li H, Duan CS, Tian Y. Nitrogeniibacter mangrovi gen. nov., sp. nov., a novel anaerobic and aerobic denitrifying betaproteobacterium and reclassification of Azoarcus pumilus as Aromatoleum pumilum comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34369861 DOI: 10.1099/ijsem.0.004946] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Denitrification is a vital link in the global bio-nitrogen cycle. Here, we isolated a strain (M9-3-2T) that is a novel benzo[a]pyrene (BaP)-tolerant, anaerobic and aerobic denitrifying bacterium from a continuous BaP-enrichment cultured mangrove sediment. In silico comparative genomics and taxonomic analysis clearly revealed that strain M9-3-2T (=MCCC 1K03313T=JCM 32045T) represents a novel species of a novel genus named as Nitrogeniibacter mangrovi gen. nov., sp. nov., belonging to family Zoogloeaceae, order Rhodocyclales. In addition, the species Azoarcus pumilus is transferred into genus Aromatoleum and named Aromatoleum pumilum comb. nov. The predominant respiratory quinone of strain M9-3-2T was ubiquinone-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. In this study, the capacity of strain M9-3-2T to eliminate nitrate was detected under anaerobic and aerobic conditions, and the removal rates of nitrate were 6.1×10-6 µg N/l/h/cell and 3×10-7 µg N/l/h/cell, respectively. Our results suggested that strain M9-3-2T could play an important role in the nitrogen removal regardless of the presence of oxygen in natural or/and man-made ecosystems.
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Affiliation(s)
- Hu Liao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Mingming Qu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xinyue Hou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, PR China
| | - Chen-Song Duan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, PR China
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21
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Wang B, Kuang S, Shao H, Wang L, Wang H. Anaerobic-petroleum degrading bacteria: Diversity and biotechnological applications for improving coastal soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112646. [PMID: 34399124 DOI: 10.1016/j.ecoenv.2021.112646] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Due to the industrial emissions and accidental spills, the critical material for modern industrial society petroleum pollution causes severe ecological damage. The prosperous oil exploitation and transportation causes the recalcitrant, hazardous, and carcinogenic sludge widespread in the coastal wetlands. The costly physicochemical-based remediation remains the secondary and inadequate treatment for the derivatives along with the tailings. Anaerobic microbial petroleum degrading biotechnology has received extensive attention for its cost acceptable, eco-friendly, and fewer health hazards. As a result of the advances in biotechnology and microbiology, the anaerobic oil-degrading bacteria have been well developing to achieve the same remediation effects with lower operating costs. This review summarizes the advantages and potential scenarios of the anaerobic degrading bacteria, such as sulfate-reducing bacteria, denitrifying bacteria, and metal-reducing bacteria in the coastal area decomposing the alkanes, alkenes, aromatic hydrocarbons, polycyclic aromatic, and related derivatives. In the future, a complete theoretical basis of microbiological biotechnology, molecular biology, and electrochemistry is necessary to make efficient and environmental-friendly use of anaerobic degradation bacteria to mineralize oil sludge organic wastes.
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Affiliation(s)
- Bingchen Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Shaoping Kuang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
| | - Hongbo Shao
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China; Institute of Agriculture Resources and Environment, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, PR China; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng 224002, China.
| | - Lei Wang
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Huihui Wang
- College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
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22
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Chen SC, Budhraja R, Adrian L, Calabrese F, Stryhanyuk H, Musat N, Richnow HH, Duan GL, Zhu YG, Musat F. Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses. ISME JOURNAL 2021; 15:3508-3521. [PMID: 34117322 PMCID: PMC8630052 DOI: 10.1038/s41396-021-01022-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/12/2021] [Accepted: 05/21/2021] [Indexed: 11/23/2022]
Abstract
Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used 13C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active cells using single-cell analyses and protein–stable isotope probing. The detection of 13C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. The quantitative role of these microorganisms in pollutant degradation was resolved using single-cell-based uptake measurements. Our strategy advances our understanding of microbially mediated biodegradation processes and has general application potential for elucidating the ecological roles of uncultured microorganisms in their natural habitats.
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Affiliation(s)
- Song-Can Chen
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Rohit Budhraja
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Lorenz Adrian
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, 13355, Berlin, Germany
| | - Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
| | - Gui-Lan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China. .,Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 361021, Xiamen, China.
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany.
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Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments. mSystems 2021; 6:e0035821. [PMID: 34100638 PMCID: PMC8269228 DOI: 10.1128/msystems.00358-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer worldwide, with an annual global production of more than 8 million tons. Because of its improper disposal, endocrine-disrupting DEHP often accumulates in estuarine sediments in industrialized countries at submillimolar levels, resulting in adverse effects on both ecosystems and human beings. The microbial degraders and biodegradation pathways of DEHP in O2-limited estuarine sediments remain elusive. Here, we employed an integrated meta-omics approach to identify the DEHP degradation pathway and major degraders in this ecosystem. Estuarine sediments were treated with DEHP or its derived metabolites, o-phthalic acid and benzoic acid. The rate of DEHP degradation in denitrifying mesocosms was two times slower than that of o-phthalic acid, suggesting that side chain hydrolysis of DEHP is the rate-limiting step of anaerobic DEHP degradation. On the basis of microbial community structures, functional gene expression, and metabolite profile analysis, we proposed that DEHP biodegradation in estuarine sediments is mainly achieved through synergistic networks between denitrifying proteobacteria. Acidovorax and Sedimenticola are the major degraders of DEHP side chains; the resulting o-phthalic acid is mainly degraded by Aestuariibacter through the UbiD-dependent benzoyl coenzyme A (benzoyl-CoA) pathway. We isolated and characterized Acidovorax sp. strain 210-6 and its extracellular hydrolase, which hydrolyzes both alkyl side chains of DEHP. Interestingly, genes encoding DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase and phthaloyl-CoA decarboxylase—key enzymes for side chain hydrolysis and o-phthalic acid degradation, respectively—are flanked by transposases in these proteobacterial genomes, indicating that DEHP degradation capacity is likely transferred horizontally in microbial communities. IMPORTANCE Xenobiotic phthalate esters (PAEs) have been produced on a considerably large scale for only 70 years. The occurrence of endocrine-disrupting di-(2-ethylhexyl) phthalate (DEHP) in environments has raised public concern, and estuarine sediments are major DEHP reservoirs. Our multi-omics analyses indicated that complete DEHP degradation in O2-limited estuarine sediments depends on synergistic microbial networks between diverse denitrifying proteobacteria and uncultured candidates. Our data also suggested that the side chain hydrolysis of DEHP, rather than o-phthalic acid activation, is the rate-limiting step in DEHP biodegradation within O2-limited estuarine sediments. Therefore, deciphering the bacterial ecophysiology and related biochemical mechanisms can help facilitate the practice of bioremediation in O2-limited environments. Furthermore, the DEHP hydrolase genes of active DEHP degraders can be used as molecular markers to monitor environmental DEHP degradation. Finally, future studies on the directed evolution of identified DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase would bring a more catalytically efficient DEHP/MEHP hydrolase into practice.
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Responsiveness of Aromatoleum aromaticum EbN1 T to Lignin-Derived Phenylpropanoids. Appl Environ Microbiol 2021; 87:AEM.03140-20. [PMID: 33741621 DOI: 10.1128/aem.03140-20] [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: 12/23/2020] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
The betaproteobacterial degradation specialist Aromatoleum aromaticum EbN1T utilizes several plant-derived 3-phenylpropanoids coupled to denitrification. In vivo responsiveness of A. aromaticum EbN1T was studied by exposing nonadapted cells to distinct pulses (spanning 100 µM to 0.1 nM) of 3-phenylpropanoate, cinnamate, 3-(4-hydroxyphenyl)propanoate, or p-coumarate. Time-resolved, targeted transcript analyses via quantitative reverse transcription-PCR of four selected 3-phenylpropanoid genes revealed a response threshold of 30 to 50 nM for p-coumarate and 1 to 10 nM for the other three tested 3-phenylpropanoids. At these concentrations, transmembrane effector equilibration is attained by passive diffusion rather than active uptake via the ABC transporter, presumably serving the studied 3-phenylpropanoids as well as benzoate. Highly substrate-specific enzyme formation (EbA5316 to EbA5321 [EbA5316-21]) for the shared peripheral degradation pathway putatively involves the predicted TetR-type transcriptional repressor PprR. Accordingly, relative transcript abundances of ebA5316-21 are lower in succinate- and benzoate-grown wild-type cells than in an unmarked in-frame ΔpprR mutant. In trans-complementation of pprR into the ΔpprR background restored wild-type-like transcript levels. When adapted to p-coumarate, the three genotypes had relative transcript abundances similar to those of ebA5316-21 despite a significantly longer lag phase of the pprR-complemented mutant (∼100-fold higher pprR transcript level than the wild type). Notably, transcript levels of ebA5316-21 were ∼10- to 100-fold higher in p-coumarate- than succinate- or benzoate-adapted cells across all three genotypes. This indicates the additional involvement of an unknown transcriptional regulator. Furthermore, physiological, transcriptional, and (aromatic) acyl-coenzyme A ester intermediate analyses of the wild type and ΔpprR mutant grown with binary substrate mixtures suggest a mode of catabolite repression of superior order to PprR.IMPORTANCE Lignin is a ubiquitous heterobiopolymer built from a suite of 3-phenylpropanoid subunits. It accounts for more than 30% of the global plant dry material, and lignin-related compounds are increasingly released into the environment from anthropogenic sources, i.e., by wastewater effluents from the paper and pulp industry. Hence, following biological or industrial decomplexation of lignin, vast amounts of structurally diverse 3-phenylpropanoids enter terrestrial and aquatic habitats, where they serve as substrates for microbial degradation. This raises the question of what signaling systems environmental bacteria employ to detect these nutritionally attractive compounds and to adjust their catabolism accordingly. Moreover, determining in vivo response thresholds of an anaerobic degradation specialist such as A. aromaticum EbN1T for these aromatic compounds provides insights into the environmental fate of the latter, i.e., when they could escape biodegradation due to too low ambient concentrations.
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Cakić N, Kopke B, Rabus R, Wilkes H. Suspect screening and targeted analysis of acyl coenzyme A thioesters in bacterial cultures using a high-resolution tribrid mass spectrometer. Anal Bioanal Chem 2021; 413:3599-3610. [PMID: 33881564 PMCID: PMC8141488 DOI: 10.1007/s00216-021-03318-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/14/2021] [Accepted: 03/30/2021] [Indexed: 11/20/2022]
Abstract
Analysis of acyl coenzyme A thioesters (acyl-CoAs) is crucial in the investigation of a wide range of biochemical reactions and paves the way to fully understand the concerned metabolic pathways and their superimposed networks. We developed two methods for suspect screening of acyl-CoAs in bacterial cultures using a high-resolution Orbitrap Fusion tribrid mass spectrometer. The methods rely on specific fragmentation patterns of the target compounds, which originate from the coenzyme A moiety. They make use of the formation of the adenosine 3′,5′-diphosphate key fragment (m/z 428.0365) and the neutral loss of the adenosine 3′-phosphate-5′-diphosphate moiety (506.9952) as preselection criteria for the detection of acyl-CoAs. These characteristic ions are generated either by an optimised in-source fragmentation in a full scan Orbitrap measurement or by optimised HCD fragmentation. Additionally, five different filters are included in the design of method. Finally, data-dependent MS/MS experiments on specifically preselected precursor ions are performed. The utility of the methods is demonstrated by analysing cultures of the denitrifying betaproteobacterium “Aromatoleum” sp. strain HxN1 anaerobically grown with hexanoate. We detected 35 acyl-CoAs in total and identified 24 of them by comparison with reference standards, including all 9 acyl-CoA intermediates expected to occur in the degradation pathway of hexanoate. The identification of additional acyl-CoAs provides insight into further metabolic processes occurring in this bacterium. The sensitivity of the method described allows detecting acyl-CoAs present in biological samples in highly variable abundances.
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