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Guo S, Toth CRA, Luo F, Chen X, Xiao J, Edwards EA. Transient Oxygen Exposure Causes Profound and Lasting Changes to a Benzene-Degrading Methanogenic Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13036-13045. [PMID: 36083837 PMCID: PMC9496526 DOI: 10.1021/acs.est.2c02624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
We investigated the impact of oxygen on a strictly anaerobic, methanogenic benzene-degrading enrichment culture derived decades ago from oil-contaminated sediment. The culture includes a benzene fermenter from Deltaproteobacteria candidate clade Sva0485 (referred to as ORM2) and methanogenic archaea. A one-time injection of 0.1 mL air , simulating a small leak into 30 mL batch culture bottle, had no measurable impact on benzene degradation rates, although retrospectively, a tiny enrichment of aerobic taxa was detected. A subsequent 100 times larger injection of air stalled methanogenesis and caused drastic perturbation of the microbial community. A benzene-degrading Pseudomonas became highly enriched and consumed all available oxygen. Anaerobic benzene-degrading ORM2 cell numbers plummeted during this time; re-growth and associated recovery of methanogenic benzene degradation took almost 1 year. These results highlight the oxygen sensitivity of this methanogenic culture and confirm that the mechanism for anaerobic biotransformation of benzene is independent of oxygen, fundamentally different from established aerobic pathways, and is carried out by distinct microbial communities. The study also highlights the importance of including microbial decay in characterizing and modeling mixed microbial communities.
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Affiliation(s)
| | | | | | - Xu Chen
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Johnny Xiao
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
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2
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Shlimon A, Mansurbeg H, Othman R, Head I, Kjeldsen KU, Finster K. Identity and hydrocarbon degradation activity of enriched microorganisms from natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI). Biodegradation 2021; 32:251-271. [PMID: 33782778 DOI: 10.1007/s10532-021-09931-4] [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: 05/26/2020] [Accepted: 02/19/2021] [Indexed: 10/21/2022]
Abstract
A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100-200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C8-C17 alkanes and up to 28% degradation of C18-C33 alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.
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Affiliation(s)
- Adris Shlimon
- Department of Biology, Soran University, Soran, Iraq. .,Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark.
| | - Howri Mansurbeg
- Department of Petroleum Geoscience, Soran University, Soran, Iraq.,Department of Earth and Environmental Sciences, University of Windsor, Windsor, ON, Canada
| | - Rushdy Othman
- Department of Petroleum Geoscience, Soran University, Soran, Iraq
| | - Ian Head
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Kasper U Kjeldsen
- Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
| | - Kai Finster
- Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
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3
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Révész F, Farkas M, Kriszt B, Szoboszlay S, Benedek T, Táncsics A. Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:31130-31142. [PMID: 32474783 PMCID: PMC7392937 DOI: 10.1007/s11356-020-09277-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/12/2020] [Indexed: 04/12/2023]
Abstract
The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.
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Affiliation(s)
- Fruzsina Révész
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - Milán Farkas
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - Balázs Kriszt
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - Sándor Szoboszlay
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - Tibor Benedek
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary.
- Department of Environmental Protection and Safety, Szent István University, Gödöllő, Hungary.
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4
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Solís-González CJ, Loza-Tavera H. Alicycliphilus: current knowledge and potential for bioremediation of xenobiotics. J Appl Microbiol 2019; 126:1643-1656. [PMID: 30661281 DOI: 10.1111/jam.14207] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/28/2018] [Accepted: 01/15/2019] [Indexed: 01/31/2023]
Abstract
Alicycliphilus is a promising candidate for participating in the development of novel xenobiotics bioremediation processes. Members of the Alicycliphilus genus are environmental bacteria mostly found in polluted sites such as landfills and contaminated watercourses, and in sewage sludges from wastewater treatment plants. They exhibit a versatile metabolism and the ability to use oxygen, nitrate and chlorate as terminal electron acceptors, which allow them to biodegrade xenobiotics under oxic or anoxic conditions. Pure cultures of Alicycliphilus strains are able to biodegrade some pollutants such as industrial solvents (acetone, cyclohexanol and N-methylpyrrolidone), aromatic hydrocarbons (benzene, toluene and anthracene), as well as polyurethane varnishes and foams, and they can even transform Cr(VI) to Cr(III). In addition, Alicycliphilus has also been identified in bacterial communities involved in wastewater treatment plants for denitrification, and the degradation of emerging pollutants such as triclosan, nonylphenol, N-heterocyclic aromatic compounds (indole and quinoline), and antibiotics (tetracycline and oxytetracycline). This work summarizes the current knowledge on the Alicycliphilus genus, describing its different metabolic characteristics, focusing on its xenobiotic biodegradation abilities and examining the distinct pathways and molecular bases that sustain them. We also discuss the progress made in genetic manipulation and 'omics' analyses, as well as Alicycliphilus participation in novel bioremediation strategies.
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Affiliation(s)
- C J Solís-González
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - H Loza-Tavera
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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5
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Atashgahi S, Liebensteiner MG, Janssen DB, Smidt H, Stams AJM, Sipkema D. Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds. Front Microbiol 2018; 9:3079. [PMID: 30619161 PMCID: PMC6299022 DOI: 10.3389/fmicb.2018.03079] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022] Open
Abstract
Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Dick B. Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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6
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Atashgahi S, Shetty SA, Smidt H, de Vos WM. Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut. Front Physiol 2018; 9:888. [PMID: 30042695 PMCID: PMC6048469 DOI: 10.3389/fphys.2018.00888] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 06/20/2018] [Indexed: 12/11/2022] Open
Abstract
Humans and their associated microbiomes are exposed to numerous xenobiotics through drugs, dietary components, personal care products as well as environmental chemicals. Most of the reciprocal interactions between the microbiota and xenobiotics, such as halogenated compounds, occur within the human gut harboring diverse and dense microbial communities. Here, we provide an overview of the flux of halogenated compounds in the environment, and diverse exposure routes of human microbiota to these compounds. Subsequently, we review the impact of halogenated compounds in perturbing the structure and function of gut microbiota and host cells. In turn, cultivation-dependent and metagenomic surveys of dehalogenating genes revealed the potential of the gut microbiota to chemically alter halogenated xenobiotics and impact their fate. Finally, we provide an outlook for future research to draw attention and attract interest to study the bidirectional impact of halogenated and other xenobiotic compounds and the gut microbiota.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Sudarshan A Shetty
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands.,Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Helsinki University, Helsinki, Finland
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7
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Influence of Carbon Source on the Efficiency of Nitrogen Removal and Denitrifying Bacteria in Biofilm from Bioelectrochemical SBBRs. WATER 2018. [DOI: 10.3390/w10040393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways. Sci Rep 2018. [PMID: 29540736 PMCID: PMC5852087 DOI: 10.1038/s41598-018-22617-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.
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9
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Gonzalez-Martinez A, Margareto A, Rodriguez-Sanchez A, Pesciaroli C, Diaz-Cruz S, Barcelo D, Vahala R. Linking the Effect of Antibiotics on Partial-Nitritation Biofilters: Performance, Microbial Communities and Microbial Activities. Front Microbiol 2018. [PMID: 29535704 PMCID: PMC5834488 DOI: 10.3389/fmicb.2018.00354] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The emergence and spread of antibiotics resistance in wastewater treatment systems have been pointed as a major environmental health problem. Nevertheless, research about adaptation and antibiotics resistance gain in wastewater treatment systems subjected to antibiotics has not been successfully developed considering bioreactor performance, microbial community dynamics and microbial activity dynamics at the same time. To observe this in autotrophic nitrogen removal systems, a partial-nitritation biofilter was subjected to a continuous loading of antibiotics mix of azithromycin, norfloxacin, trimethoprim, and sulfamethoxazole. The effect of the antibiotics mix over the performance, bacterial communities and bacterial activity in the system was evaluated. The addition of antibiotics caused a drop of ammonium oxidation efficiency (from 50 to 5%) and of biomass concentration in the bioreactor, which was coupled to the loss of ammonium oxidizing bacteria Nitrosomonas in the bacterial community from 40 to 3%. Biomass in the partial nitritation biofilter experienced a sharp decrease of about 80% due to antibiotics loading, but the biomass adapted and experienced a growth by stabilization under antibiotics feeding. During the experiment several bacterial genera appeared, such as Alcaligenes, Paracoccus, and Acidovorax, clearly dominating the bacterial community with >20% relative abundance. The system reached around 30% ammonium oxidation efficiency after adaptation to antibiotics, but no effluent nitrite was found, suggesting that dominant antibiotics-resistant phylotypes could be involved in nitrification–denitrification metabolisms. The activity of ammonium oxidation measured as amoA and hao gene expression dropped a 98.25% and 99.21%, respectively, comparing the system before and after the addition of antibiotics. On the other hand, denitrifying activity increased as observed by higher expression of nir and nos genes (83.14% and 252.54%, respectively). In addition, heterotrophic nitrification cyt c-551 was active only after the antibiotics addition. Resistance to the antibiotics was presumably given by ermF, carA and msrA for azithromycin, mutations of the gyrA and grlB for norfloxacin, and by sul123 genes for sulfamethoxazole. Joined physicochemical and microbiological characterization of the system were used to investigate the effect of the antibiotics over the bioprocess. Despite the antibiotics resistance, activity of Bacteria decreased while the activity of Archaea and Fungi increased.
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Affiliation(s)
| | - Alejandro Margareto
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research, Barcelona, Spain.,Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, Girona, Spain
| | | | | | - Silvia Diaz-Cruz
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research, Barcelona, Spain.,Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Damia Barcelo
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research, Barcelona, Spain.,Catalan Institute for Water Research, Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Riku Vahala
- Department of Built Environment, School of Engineering, Aalto University, Espoo, Finland
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10
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Novel Metabolic Pathway for N-Methylpyrrolidone Degradation in Alicycliphilus sp. Strain BQ1. Appl Environ Microbiol 2017; 84:AEM.02136-17. [PMID: 29030443 DOI: 10.1128/aem.02136-17] [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: 09/27/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022] Open
Abstract
The molecular mechanisms underlying the biodegradation of N-methylpyrrolidone (NMP), a widely used industrial solvent that produces skin irritation in humans and is teratogenic in rats, are unknown. Alicycliphilus sp. strain BQ1 degrades NMP. By studying a transposon-tagged mutant unable to degrade NMP, we identified a six-gene cluster (nmpABCDEF) that is transcribed as a polycistronic mRNA and encodes enzymes involved in NMP biodegradation. nmpA and the transposon-affected gene nmpB encode an N-methylhydantoin amidohydrolase that transforms NMP to γ-N-methylaminobutyric acid; this is metabolized by an amino acid oxidase (NMPC), either by demethylation to produce γ-aminobutyric acid (GABA) or by deamination to produce succinate semialdehyde (SSA). If GABA is produced, the activity of a GABA aminotransferase (GABA-AT), not encoded in the nmp gene cluster, is needed to generate SSA. SSA is transformed by a succinate semialdehyde dehydrogenase (SSDH) (NMPF) to succinate, which enters the Krebs cycle. The abilities to consume NMP and to utilize it for growth were complemented in the transposon-tagged mutant by use of the nmpABCD genes. Similarly, Escherichia coli MG1655, which has two SSDHs but is unable to grow in NMP, acquired these abilities after functional complementation with these genes. In wild-type (wt) BQ1 cells growing in NMP, GABA was not detected, but SSA was present at double the amount found in cells growing in Luria-Bertani medium (LB), suggesting that GABA is not an intermediate in this pathway. Moreover, E. coli GABA-AT deletion mutants complemented with nmpABCD genes retained the ability to grow in NMP, supporting the possibility that γ-N-methylaminobutyric acid is deaminated to SSA instead of being demethylated to GABA.IMPORTANCEN-Methylpyrrolidone is a cyclic amide reported to be biodegradable. However, the metabolic pathway and enzymatic activities for degrading NMP are unknown. By developing molecular biology techniques for Alicycliphilus sp. strain BQ1, an environmental bacterium able to grow in NMP, we identified a six-gene cluster encoding enzymatic activities involved in NMP degradation. These findings set the basis for the study of new enzymatic activities and for the development of biotechnological processes with potential applications in bioremediation.
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11
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Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 2017; 35:845-866. [DOI: 10.1016/j.biotechadv.2017.08.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023]
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12
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Lin W, Sun S, Wu C, Xu P, Ye Z, Zhuang S. Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:14-21. [PMID: 28384499 DOI: 10.1016/j.ecoenv.2017.03.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/18/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
Bio-treatment of flotation wastewater has been proven to be both effective and economical, as a treatment method. Despite this, little is known regarding the effects of toxic organic floatation reagents such as Dianilinodithiophosphoric acid (DDA), on the microbial community performance or dynamics, which are critical to the effective performance of the bio-treatment reactor. A submerged membrane bioreactor (sMBR) was constructed to continuously treat simulated wastewater contaminated with DDA, an organic flotation reagent that is now considered a significant pollutant. The performance of the sMBR system was investigated at different DDA loading concentrations, with assessment of the effects of DDA on the microbial communities within the sMBR, in particular the biodiversity and succession within the microbial community. Results showed that, with increased DDA loadings, the performance of the sMBR was initially negatively affected, but the system adapted efficiently and consistently reached a COD removal rate of up to 80%. Increased DDA loading concentrations had an adverse effect on the activity of both the activated sludge and microbial communities, resulting in a large alteration in microbial dynamics, especially during the start-up stage and the high DDA loading stage. Strains capable of adapting to the presence of DDA, capable of degrading DDA or utilizing its byproducts, were enriched within the sMBR community, such as Zoogloea, Clostridium, Sideroxydans lithotrophicus, Thiobacillus, Thauera amino aromatica and Alicycliphilus denitrificans.
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Affiliation(s)
- Weixiong Lin
- Guangdong Polytechnic of Environmental Protection Engineering,Foshan 528216, China; School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Shuiyu Sun
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Polytechnic of Environmental Protection Engineering,Foshan 528216, China.
| | - Chun Wu
- Guangdong Polytechnic of Environmental Protection Engineering,Foshan 528216, China
| | - Pingting Xu
- Guangdong Polytechnic of Environmental Protection Engineering,Foshan 528216, China
| | - Ziwei Ye
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Shengwei Zhuang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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13
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Hailei W, Ping L, Ying W, Lei L, Jianming Y. Metagenomic insight into the bioaugmentation mechanism of Phanerochaete chrysosporium in an activated sludge system treating coking wastewater. JOURNAL OF HAZARDOUS MATERIALS 2017; 321:820-829. [PMID: 27720470 DOI: 10.1016/j.jhazmat.2016.09.072] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 08/31/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
Phanerochaete chrysosporium was seeded to a sequencing batch reactor treating phenol wastewater. Compared to the contrast reactor (R1), the bioaugmented reactor (R2) exhibits better performance in sludge settling ability, as well as biomass and phenol removal, even though the added fungus is not persistently surviving in the reactor. Bioaugmentation improved bacterial population, growing up to 10,000 times higher than that of eukaryotes. Metagenomic sequencing results show the bioaugmentation finally increases bacterial and eukaryotic richness, but reduces their community diversity. In contrast to R1, bacterial distribution in R2 is more concentrated in Proteobacteria. The relative abundances of filamentous fungi, yeast and microalgae in R2 are all higher than those in R1 at different treatment phases, and two reactors are finally dominated by different protozoan and metazoan. In conclusion, P. chrysosporium improves reactor performances by influencing microbial community structure, and this phenomenon might be attributed to the ecological competition in sludge and toxicity reduction of phenol wastewater. The novelty of this study emphasizes why a species which is not persistently active in bioreactor still plays a crucial role in enhancing reactor performance. Results obtained here impact the conventional criteria for selection of bioaugmentation microbes used in activated sludge systems.
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Affiliation(s)
- Wang Hailei
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China.
| | - Li Ping
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wang Ying
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Liu Lei
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Yao Jianming
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
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14
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Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type. Appl Environ Microbiol 2016; 82:5186-96. [PMID: 27316957 DOI: 10.1128/aem.00916-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED This study was conducted to investigate whether functions encoded in the metagenome could improve our ability to understand the link between microbial community structures and functions in activated sludge. By analyzing data sets from six industrial and six municipal wastewater treatment plants (WWTPs), covering different configurations, operational conditions, and geographic regions, we found that wastewater influent composition was an overriding factor shaping the metagenomic composition of the activated sludge samples. Community GC content profiles were conserved within treatment plants on a time scale of years and between treatment plants with similar influent wastewater types. Interestingly, GC contents of the represented phyla covaried with the average GC contents of the corresponding WWTP metagenome. This suggests that the factors influencing nucleotide composition act similarly across taxa and thus the variation in nucleotide contents is driven by environmental differences between WWTPs. While taxonomic richness and functional richness were correlated, shotgun metagenomics complemented taxon-based analyses in the task of classifying microbial communities involved in wastewater treatment systems. The observed taxonomic dissimilarity between full-scale WWTPs receiving influent types with varied compositions, as well as the inferred taxonomic and functional assignment of recovered genomes from each metagenome, were consistent with underlying differences in the abundance of distinctive sets of functional categories. These conclusions were robust with respect to plant configuration, operational and environmental conditions, and even differences in laboratory protocols. IMPORTANCE This work contributes to the elucidation of drivers of microbial community assembly in wastewater treatment systems. Our results are significant because they provide clear evidence that bacterial communities in WWTPs assemble mainly according to influent wastewater characteristics. Differences in bacterial community structures between WWTPs were consistent with differences in the abundance of distinctive sets of functional categories, which were related to the metabolic potential that would be expected according to the source of the wastewater.
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Identification of Quorum-Sensing Signal Molecules and a Biosynthetic Gene in Alicycliphilus sp. Isolated from Activated Sludge. SENSORS 2016; 16:s16081218. [PMID: 27490553 PMCID: PMC5017383 DOI: 10.3390/s16081218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/19/2016] [Accepted: 07/29/2016] [Indexed: 01/09/2023]
Abstract
Activated sludge is a complicated mixture of various microorganisms that is used to treat sewage and industrial wastewater. Many bacteria produce N-acylhomoserine lactone (AHL) as a quorum-sensing signal molecule to regulate the expression of the exoenzymes used for wastewater treatment. Here, we isolated an AHL-producing bacteria from an activated sludge sample collected from an electronic component factory, which we named Alicycliphilus sp. B1. Clone library analysis revealed that Alicycliphilus was a subdominant genus in this sample. When we screened the activated sludge sample for AHL-producing strains, 12 of 14 the AHL-producing isolates were assigned to the genus Alicycliphilus. A putative AHL-synthase gene, ALISP_0667, was cloned from the genome of B1 and transformed into Escherichia coli DH5α. The AHLs were extracted from the culture supernatants of the B1 strain and E. coli DH5α cells harboring the ALISP_0667 gene and were identified by liquid chromatography-mass spectrometry as N-(3-hydroxydecanoyl)-l-homoserine lactone and N-(3-hydroxydodecanoyl)-l-homoserine lactone. The results of comparative genomic analysis suggested that the quorum-sensing genes in the B1 strain might have been acquired by horizontal gene transfer within activated sludge.
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Visser M, Pieterse MM, Pinkse MWH, Nijsse B, Verhaert PDEM, de Vos WM, Schaap PJ, Stams AJM. Unravelling the one-carbon metabolism of the acetogen Sporomusa strain An4 by genome and proteome analysis. Environ Microbiol 2015; 18:2843-55. [PMID: 26147498 DOI: 10.1111/1462-2920.12973] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/19/2015] [Accepted: 06/26/2015] [Indexed: 01/06/2023]
Abstract
The Sporomusa genus comprises anaerobic spore-forming acetogenic bacteria that stain Gram-negative. Sporomusa species typically grow with one-carbon substrates and N-methylated compounds. In the degradation of these compounds methyltransferases are involved. In addition, Sporomusa species can grow autotrophically with H2 and CO2 , and use a variety of sugars for acetogenic growth. Here we describe a genome analysis of Sporomusa strain An4 and a proteome analysis of cells grown under five different conditions. Comparison of the genomes of Sporomusa strain An4 and Sporomusa ovata strain H1 indicated that An4 is a S. ovata strain. Proteome analysis showed a high abundance of several methyltransferases, predominantly trimethylamine methyltransferases, during growth with betaine, whereas trimethylamine is one of the main end-products of betaine degradation. In methanol degradation methyltransferases are also involved. In methanol-utilizing methanogens, two methyltransferases catalyse methanol conversion, methyltransferase 1 composed of subunits MtaB and MtaC and methyltransferase 2, also called MtaA. The two methyltransferase 1 subunits MtaB and MtaC were highly abundant when strain An4 was grown with methanol. However, instead of MtaA a methyltetrahydrofolate methyltransferase was synthesized. We propose a novel methanol degradation pathway in Sporomusa strain An4 that uses a methyltetrahydrofolate methyltransferase instead of MtaA.
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Affiliation(s)
- Michael Visser
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Mervin M Pieterse
- Department of Biotechnology, Technische Universiteit Delft, Julianalaan 67, 2628 BC, Delft, The Netherlands.,Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Martijn W H Pinkse
- Department of Biotechnology, Technische Universiteit Delft, Julianalaan 67, 2628 BC, Delft, The Netherlands.,Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Peter D E M Verhaert
- Department of Biotechnology, Technische Universiteit Delft, Julianalaan 67, 2628 BC, Delft, The Netherlands.,Netherlands Proteomics Centre, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Department of Veterinary Biosciences, Helsinki University, Helsinki, Finland.,Department of Bacteriology and Immunology, Helsinki University, Helsinki, Finland
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway. Appl Environ Microbiol 2015; 81:6241-52. [PMID: 26150458 DOI: 10.1128/aem.01822-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/26/2015] [Indexed: 11/20/2022] Open
Abstract
In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs.
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Liebensteiner MG, Oosterkamp MJ, Stams AJM. Microbial respiration with chlorine oxyanions: diversity and physiological and biochemical properties of chlorate- and perchlorate-reducing microorganisms. Ann N Y Acad Sci 2015; 1365:59-72. [PMID: 26104311 DOI: 10.1111/nyas.12806] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Chlorine oxyanions are valuable electron acceptors for microorganisms. Recent findings have shed light on the natural formation of chlorine oxyanions in the environment. These suggest a permanent introduction of respective compounds on Earth, long before their anthropogenic manufacture. Microorganisms that are able to grow by the reduction of chlorate and perchlorate are affiliated with phylogenetically diverse lineages, spanning from the Proteobacteria to the Firmicutes and archaeal microorganisms. Microbial reduction of chlorine oxyanions can be found in diverse environments and different environmental conditions (temperature, salinities, pH). It commonly involves the enzymes perchlorate reductase (Pcr) or chlorate reductase (Clr) and chlorite dismutase (Cld). Horizontal gene transfer seems to play an important role for the acquisition of functional genes. Novel and efficient Clds were isolated from microorganisms incapable of growing on chlorine oxyanions. Archaea seem to use a periplasmic Nar-type reductase (pNar) for perchlorate reduction and lack a functional Cld. Chlorite is possibly eliminated by alternative (abiotic) reactions. This was already demonstrated for Archaeoglobus fulgidus, which uses reduced sulfur compounds to detoxify chlorite. A broad biochemical diversity of the trait, its environmental dispersal, and the occurrence of relevant enzymes in diverse lineages may indicate early adaptations of life toward chlorine oxyanions on Earth.
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Affiliation(s)
| | - Margreet J Oosterkamp
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.,Energy Biosciences Institute, University of Illinois, Urbana, Illinois
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.,Department of Biological Engineering, University of Minho, Braga, Portugal
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19
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Mehboob F, Oosterkamp MJ, Koehorst JJ, Farrakh S, Veuskens T, Plugge CM, Boeren S, de Vos WM, Schraa G, Stams AJM, Schaap PJ. Genome and proteome analysis of Pseudomonas chloritidismutans AW-1 T that grows on n-decane with chlorate or oxygen as electron acceptor. Environ Microbiol 2015; 18:3247-3257. [PMID: 25900248 DOI: 10.1111/1462-2920.12880] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/25/2015] [Accepted: 03/05/2015] [Indexed: 01/15/2023]
Abstract
Growth of Pseudomonas chloritidismutans AW-1T on C7 to C12 n-alkanes with oxygen or chlorate as electron acceptor was studied by genome and proteome analysis. Whole genome shotgun sequencing resulted in a 5 Mbp assembled sequence with a G + C content of 62.5%. The automatic annotation identified 4767 protein-encoding genes and a putative function could be assigned to almost 80% of the predicted proteins. The distinct phylogenetic position of P. chloritidismutans AW-1T within the Pseudomonas stutzeri cluster became clear by comparison of average nucleotide identity values of sequenced genomes. Analysis of the proteome of P. chloritidismutans AW-1T showed the versatility of this bacterium to adapt to aerobic and anaerobic growth conditions with acetate or n-decane as substrates. All enzymes involved in the alkane oxidation pathway were identified. An alkane monooxygenase was detected in n-decane-grown cells, but not in acetate-grown cells. The enzyme was found when grown in the presence of oxygen or chlorate, indicating that under both conditions an oxygenase-mediated pathway is employed for alkane degradation. Proteomic and biochemical data also showed that both chlorate reductase and chlorite dismutase are constitutively present, but most abundant under chlorate-reducing conditions.
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Affiliation(s)
- Farrakh Mehboob
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands
| | - Margreet J Oosterkamp
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands
| | - Sumaira Farrakh
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands
| | - Teun Veuskens
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, Wageningen, 6703 HA, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands
| | - Gosse Schraa
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.,Centre of Biological Engineering, University of Minho, Braga, 4710-057, Portugal
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Wageningen, 6703 HB, The Netherlands.
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Liebensteiner MG, Tsesmetzis N, Stams AJM, Lomans BP. Microbial redox processes in deep subsurface environments and the potential application of (per)chlorate in oil reservoirs. Front Microbiol 2014; 5:428. [PMID: 25225493 PMCID: PMC4150442 DOI: 10.3389/fmicb.2014.00428] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 07/29/2014] [Indexed: 12/15/2022] Open
Abstract
The ability of microorganisms to thrive under oxygen-free conditions in subsurface environments relies on the enzymatic reduction of oxidized elements, such as sulfate, ferric iron, or CO2, coupled to the oxidation of inorganic or organic compounds. A broad phylogenetic and functional diversity of microorganisms from subsurface environments has been described using isolation-based and advanced molecular ecological techniques. The physiological groups reviewed here comprise iron-, manganese-, and nitrate-reducing microorganisms. In the context of recent findings also the potential of chlorate and perchlorate [jointly termed (per)chlorate] reduction in oil reservoirs will be discussed. Special attention is given to elevated temperatures that are predominant in the deep subsurface. Microbial reduction of (per)chlorate is a thermodynamically favorable redox process, also at high temperature. However, knowledge about (per)chlorate reduction at elevated temperatures is still scarce and restricted to members of the Firmicutes and the archaeon Archaeoglobus fulgidus. By analyzing the diversity and phylogenetic distribution of functional genes in (meta)genome databases and combining this knowledge with extrapolations to earlier-made physiological observations we speculate on the potential of (per)chlorate reduction in the subsurface and more precisely oil fields. In addition, the application of (per)chlorate for bioremediation, souring control, and microbial enhanced oil recovery are addressed.
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Affiliation(s)
| | | | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; Center of Biological Engineering, University of Minho Braga, Portugal
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Resch V, Jin J, Chen BS, Hanefeld U. Michael hydratase alcohol dehydrogenase or just alcohol dehydrogenase? AMB Express 2014; 4:30. [PMID: 24949265 PMCID: PMC4052635 DOI: 10.1186/s13568-014-0030-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/08/2014] [Indexed: 11/25/2022] Open
Abstract
The Michael hydratase – alcohol dehydrogenase (MhyADH) from Alicycliphilus denitrificans was previously identified as a bi-functional enzyme performing a hydration of α,β-unsaturated ketones and subsequent oxidation of the formed alcohols. The investigations of the bi-functionality were based on a spectrophotometric assay and an activity staining in a native gel of the dehydrogenase. New insights in the recently discovered organocatalytic Michael addition of water led to the conclusion that the previously performed experiments to identify MhyADH as a bi-functional enzyme and their results need to be reconsidered and the reliability of the methodology used needs to be critically evaluated.
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