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Zampolli J, Vezzini D, Brocca S, Di Gennaro P. Insights into the biodegradation of polycaprolactone through genomic analysis of two plastic-degrading Rhodococcus bacteria. Front Microbiol 2024; 14:1284956. [PMID: 38235436 PMCID: PMC10791956 DOI: 10.3389/fmicb.2023.1284956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/17/2023] [Indexed: 01/19/2024] Open
Abstract
Polycaprolactone (PCL) is an aliphatic polyester often utilized as a model to investigate the biodegradation potential of bacteria and the involved catabolic enzymes. This study aims to characterize PCL biodegradative metabolic potential and correlate it to genomic traits of two plastic-degrading bacteria-Rhodococcus erythropolis D4 strain, a new isolate from plastic-rich organic waste treatment plant, and Rhodococcus opacus R7, known for its relevant biodegradative potential on polyethylene and similar compounds. After preliminary screening for bacteria capable of hydrolyzing tributyrin and PCL, the biodegradation of PCL was evaluated in R. erythropolis D4 and R. opacus R7 by measuring their growth and the release of PCL catabolism products up to 42 days. After 7 days, an increase of at least one order of magnitude of cell number was observed. GC-MS analyses of 28-day culture supernatants showed an increase in carboxylic acids in both Rhodococcus cultures. Furthermore, hydrolytic activity (~5 U mg-1) on short/medium-chain p-nitrophenyl esters was detected in their supernatant. Finally, a comparative genome analysis was performed between two Rhodococcus strains. A comparison with genes annotated in reference strains revealed hundreds of gene products putatively related to polyester biodegradation. Based on additional predictive analysis of gene products, gene expression was performed on a smaller group of genes, revealing that exposure to PCL elicits the greatest increase in transcription for a single gene in strain R7 and two genes, including that encoding a putative lipase, in strain D4. This work exhibits a multifaceted experimental approach to exploit the broad potential of Rhodococcus strains in the field of plastic biodegradation.
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Affiliation(s)
| | | | | | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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2
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Reis PCJ, Correa-Garcia S, Tremblay J, Beaulieu-Laliberté A, Muench DG, Ahad JME, Yergeau E, Comte J, Martineau C. Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water. FEMS Microbiol Ecol 2023; 99:fiad153. [PMID: 38012121 PMCID: PMC10710301 DOI: 10.1093/femsec/fiad153] [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: 05/31/2023] [Revised: 10/27/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023] Open
Abstract
Naphthenic acids (NAs) are a complex mixture of organic compounds released during bitumen extraction from mined oil sands that are important contaminants of oil sands process-affected water (OSPW). NAs can be toxic to aquatic organisms and, therefore, are a main target compound for OSPW. The ability of microorganisms to degrade NAs can be exploited for bioremediation of OSPW using constructed wetland treatment systems (CWTS), which represent a possible low energy and low-cost option for scalable in situ NA removal. Recent advances in genomics and analytical chemistry have provided insights into a better understanding of the metabolic pathways and genes involved in NA degradation. Here, we discuss the ecology of microbial NA degradation with a focus on CWTS and summarize the current knowledge related to the metabolic pathways and genes used by microorganisms to degrade NAs. Evidence to date suggests that NAs are mostly degraded aerobically through ring cleavage via the beta-oxidation pathway, which can be combined with other steps such as aromatization, alpha-oxidation, omega-oxidation, or activation as coenzyme A (CoA) thioesters. Anaerobic NA degradation has also been reported via the production of benzoyl-CoA as an intermediate and/or through the involvement of methanogens or nitrate, sulfate, and iron reducers. Furthermore, we discuss how genomic, statistical, and modeling tools can assist in the development of improved bioremediation practices.
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Affiliation(s)
- Paula C J Reis
- Centre Eau Terre Environnement, Institut national de la recherche scientifique, QC, Canada
| | - Sara Correa-Garcia
- Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Québec city, QC G1K 9A9, Canada
| | - Julien Tremblay
- Centre Armand Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Québec city, QC G1K 9A9, Canada
- Energy, Mining and Environment, National Research Council Canada, Montréal, QC H4P 2R2, Canada
| | - Aurélie Beaulieu-Laliberté
- Centre Eau Terre Environnement, Institut national de la recherche scientifique, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Jason M E Ahad
- Geological Survey of Canada, Natural Resources Canada, Québec city, QC G1K 9A9, Canada
| | - Etienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, Montréal, QC H4P 2R2, Canada
| | - Jérôme Comte
- Centre Eau Terre Environnement, Institut national de la recherche scientifique, QC, Canada
- Groupe de recherche interuniversitaire en limnologie (GRIL), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Christine Martineau
- Laurentian Forestry Centre, Natural Resources Canada, Québec city, QC G1V 4C7, Canada
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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: 1.0] [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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Chattopadhyay I, J RB, Usman TMM, Varjani S. Exploring the role of microbial biofilm for industrial effluents treatment. Bioengineered 2022; 13:6420-6440. [PMID: 35227160 PMCID: PMC8974063 DOI: 10.1080/21655979.2022.2044250] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Biofilm formation on biotic or abiotic surfaces is caused by microbial cells of a single or heterogeneous species. Biofilm protects microbes from stressful environmental conditions, toxic action of chemicals, and antimicrobial substances. Quorum sensing (QS) is the generation of autoinducers (AIs) by bacteria in a biofilm to communicate with one other. QS is responsible for the growth of biofilm, synthesis of exopolysaccharides (EPS), and bioremediation of environmental pollutants. EPS is used for wastewater treatment due to its three-dimensional matrix which is composed of proteins, polysaccharides, humic-like substances, and nucleic acids. Autoinducers mediate significantly the degradation of environmental pollutants. Acyl-homoserine lactone (AHL) producing bacteria as well as quorum quenching enzyme or bacteria can effectively improve the performance of wastewater treatment. Biofilms-based reactors due to their economic and ecofriendly nature are used for the treatment of industrial wastewaters. Electrodes coated with electro-active biofilm (EAB) which are obtained from sewage sludge, activated sludge, or industrial and domestic effluents are getting popularity in bioremediation. Microbial fuel cells are involved in wastewater treatment and production of energy from wastewater. Synthetic biological systems such as genome editing by CRISPR-Cas can be used for the advanced bioremediation process through modification of metabolic pathways in quorum sensing within microbial communities. This narrative review discusses the impacts of QS regulatory approaches on biofilm formation, extracellular polymeric substance synthesis, and role of microbial community in bioremediation of pollutants from industrial effluents.
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Affiliation(s)
| | - Rajesh Banu J
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, India
| | - T M Mohamed Usman
- Department of Civil Engineering, PET Engineering College, Vallioor, Tirunelveli, India
| | - Sunita Varjani
- Paryavaran Bhavan, Gujarat Pollution Control Board, Gandhinagar, India
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Identification of a Novel Biosurfactant with Antimicrobial Activity Produced by Rhodococcus opacus R7. Microorganisms 2022; 10:microorganisms10020475. [PMID: 35208929 PMCID: PMC8877126 DOI: 10.3390/microorganisms10020475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/18/2022] Open
Abstract
Rhodococcus members excrete secondary metabolites, especially compounds which act as biosurfactants. In this work, we demonstrated the ability of Rhodococcus opacus R7 to produce a novel bioactive compound belonging to the class of biosurfactants with antimicrobial properties during the growth on naphthalene. Chemical and biochemical analyses of the isolated compound demonstrated that the biosurfactant could be classified as a hydrophobic peptide. The ESI-full mass spectrometry revealed that the isolated biosurfactant showed a molecular weight of 1292 Da and NMR spectra evidenced the composition of the following amino acid residues: Ala, Thr, Asp, Gly, Ser. Surfactant activity of the R. opacus R7 compound was quantified by the critical micelle dilution (CMD) method and the critical micelle concentration (CMC) was estimated around 20 mg L−1 with a corresponding surface tension of 48 mN m−1. Moreover, biological assays demonstrated that R. opacus R7 biosurfactant peptide exhibited antimicrobial activity against Escherichia coli ATCC 29522 and Staphylococcus aureus ATCC 6538 with the minimum inhibition growth concentration (MIC) values of 2.6 mg mL−1 and 1.7 mg mL−1, respectively. In this study for the first time, a hydrophobic peptide with both biosurfactant and antimicrobial activity was isolated from a bacterium belonging to Rhodococcus genus.
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A microbial solution to oil sand pollution: Understanding the microbiomes, metabolic pathways and mechanisms involved in naphthenic acid (NA) biodegradation. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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da Silva TAM, Pereira I, de Aguiar DVA, Dos Santos GF, de Brito TP, de Carvalho RM, Medeiros Junior I, Simas RC, Vaz BG. Direct analysis of naphthenic acids in produced water and crude oil by NH 2-surface-modified wooden-tip electrospray ionization mass spectrometry. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5274-5281. [PMID: 34704566 DOI: 10.1039/d1ay01541a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This work describes the surface coating of wooden toothpicks with amino groups (NH2) for electrospray ionization mass spectrometry (MS) analysis of naphthenic acids (NAs) in produced water samples and crude oil fractions. NH2 was introduced into the cellulosic material through a silanization reaction using aminopropyltriethoxysilane. An NH2-modified toothpick was inserted into the analyte extraction sample and was subsequently used as an electrospray emitter for MS analysis. The extraction conditions were optimized by analyzing NAs (benzoic acid, 1-naphthoic acid, decanoic acid, 3,5-dimethyladamantane-1-carboxylic acid, and 3,5-dimethyladamantane-1-acetic acid) in pure water, and the best condition was using 5 min of extraction time with the samples under agitation. Modified and unmodified wooden toothpicks were compared, and the intensities of all NAs were higher when using the modified substrates than when using the unmodified ones. Limit of detection (LOD), limit of quantification (LOQ), linearity, precision, and recovery were determined by analyzing decanoic acid in seawater samples. The LOD and LOQ were 2 and 5 μg mL-1, respectively, and a linear correlation (R2 = 0.9927) was obtained with concentrations ranging from 5 to 250 μg mL-1. Precision values ranged from 6 to 13% and recoveries from 89 to 106%. The technique was also employed to analyze three produced water samples, in which decanoic acid was semi-quantified, and the concentrations ranged from 10 to 13 μg mL-1. High abundances of acidic compounds of class O2 with DBEs (double bond equivalents) ranging from 1 to 3 and carbon numbers going from 8 to 12 were detected in the produced water samples. The results suggest that the modification of wooden toothpicks with NH2 might offer a significant advancement in the knowledge of cheap substrates that can improve the sensitivity of analysis of NAs in water samples.
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Affiliation(s)
- Thais A M da Silva
- Laboratory of Chromatography and Mass Spectrometry, Institute of Chemistry, Federal University of Goiás, Goiânia, 59078-970, GO, Brazil.
| | - Igor Pereira
- Laboratory of Chromatography and Mass Spectrometry, Institute of Chemistry, Federal University of Goiás, Goiânia, 59078-970, GO, Brazil.
| | - Deborah V A de Aguiar
- Laboratory of Chromatography and Mass Spectrometry, Institute of Chemistry, Federal University of Goiás, Goiânia, 59078-970, GO, Brazil.
| | - Gabriel F Dos Santos
- Laboratory of Chromatography and Mass Spectrometry, Institute of Chemistry, Federal University of Goiás, Goiânia, 59078-970, GO, Brazil.
| | - Talita P de Brito
- Laboratory of Chromatography and Mass Spectrometry, Institute of Chemistry, Federal University of Goiás, Goiânia, 59078-970, GO, Brazil.
| | | | | | - Rosineide C Simas
- Laboratory of Chromatography and Mass Spectrometry, Institute of Chemistry, Federal University of Goiás, Goiânia, 59078-970, GO, Brazil.
| | - Boniek G Vaz
- Laboratory of Chromatography and Mass Spectrometry, Institute of Chemistry, Federal University of Goiás, Goiânia, 59078-970, GO, Brazil.
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Alberts ME, Wong J, Hindle R, Degenhardt D, Krygier R, Turner RJ, Muench DG. Detection of naphthenic acid uptake into root and shoot tissues indicates a direct role for plants in the remediation of oil sands process-affected water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148857. [PMID: 34328940 DOI: 10.1016/j.scitotenv.2021.148857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Bitumen extraction from surface-mined oil sands deposits results in the accumulation of large volumes of oil sands process-affected water (OSPW). Naphthenic acids (NAs) are primary contributors to OSPW toxicity and have been a focal point for the development of OSPW remediation strategies. Phytoremediation is an approach that utilizes plants and their associated microbes to remediate contaminants from soil and groundwater. While previous evidence has indicated a role for phytoremediation in OSPW treatment through the transformation and degradation of NAs, there are no reports that demonstrate the direct uptake of NAs into plant tissue. Using NAs labelled with 14C radioisotopes (14C-NAs) paired with whole-plant autoradiography, we show that NAs representing aliphatic (linear), single-ring, and diamondoid compounds were effectively removed from hydroponic solution and OSPW-treated soil by sandbar willow (Salix interior) and slender wheatgrass (Elymus trachycaulus) and their associated microbiomes. The NA-derived 14C label accumulated in root and shoot tissues of both plant species and was concentrated in vascular tissue and rapidly growing sink tissues, indicating that 14C-NAs or their metabolic derivatives were incorporated into physiological processes within the plants. Slender wheatgrass seedlings grown under axenic (sterile) hydroponic and soil conditions also effectively removed all 14C-NAs, including a highly stable diamondoid NA, demonstrating that plants can directly take up simple and complex NAs without the assistance of microbes. Furthermore, root and shoot tissue fractionation into major biomolecule groups suggests that NA-derived carbon is allocated toward biomolecule synthesis rapidly after NA treatment. These findings provide evidence of plant-mediated uptake of NAs and support a direct role for plants and their associated microbes in the development of future large-scale OSPW phytoremediation strategies.
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Affiliation(s)
- Mitchell E Alberts
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Jeremy Wong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Ralph Hindle
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada; Vogon Laboratory Services Ltd., Cochrane, Alberta, Canada
| | - Dani Degenhardt
- Natural Resources Canada (Canadian Forest Service), Edmonton, Alberta, Canada
| | - Richard Krygier
- Natural Resources Canada (Canadian Forest Service), Edmonton, Alberta, Canada
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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