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Benedek T, Szentgyörgyi F, Szabó I, Farkas M, Duran R, Kriszt B, Táncsics A. Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm. Appl Microbiol Biotechnol 2020; 104:6023-6043. [PMID: 32415320 PMCID: PMC7306034 DOI: 10.1007/s00253-020-10668-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022]
Abstract
In this study, we aimed at determining the impact of naphthalene and different oxygen levels on a biofilm bacterial community originated from a petroleum hydrocarbon-contaminated groundwater. By using cultivation-dependent and cultivation-independent approaches, the enrichment, identification, and isolation of aerobic and oxygen-limited naphthalene degraders was possible. Results indicated that, regardless of the oxygenation conditions, Pseudomonas spp. became the most dominant in the naphthalene-amended selective enrichment cultures. Under low-oxygen conditions, P. veronii/P. extremaustralis lineage affiliating bacteria, and under full aerobic conditions P. laurentiana-related isolates were most probably capable of naphthalene biodegradation. A molecular biological tool has been developed for the detection of naphthalene 1,2-dioxygenase-related 2Fe-2S reductase genes of Gram-negative bacteria. The newly developed COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP-PCR) technique may be used in the monitoring of the natural attenuation capacity of PAH-contaminated sites. A bacterial strain collection with prolific biofilm-producing and effective naphthalene-degrading organisms was established. The obtained strain collection may be applicable in the future for the development of biofilm-based bioremediation systems for the elimination of PAHs from groundwater (e.g., biofilm-based biobarriers).
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Affiliation(s)
- Tibor Benedek
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary.
| | - Flóra Szentgyörgyi
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - István Szabó
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Milán Farkas
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, Pau, France
| | - Balázs Kriszt
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - András Táncsics
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
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Ji L, Fu X, Wang M, Xu C, Chen G, Song F, Guo S, Zhang Q. Enzyme cocktail containing NADH regeneration system for efficient bioremediation of oil sludge contamination. CHEMOSPHERE 2019; 233:132-139. [PMID: 31170583 DOI: 10.1016/j.chemosphere.2019.05.253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Oil sludge is one kind of toxic and persistent contamination to ecology system from petroleum industry. In order to recycle contaminated sands and reduce environmental impacts at a lower operating cost, enzyme cocktail 21/CbFDH including NADH regeneration system for oily sludge bioremediation was constructed for the first time. The intracellular enzymes of oil-degrading strain Acinetobacter calcoaceticus 21 were prepared and the formate dehydrogenase gene Cbfdh from Candida boidinii was cloned and functionally expressed in E.coli BL21 induced by lactose. The activity and stability of CbFDH was enhanced through self-induction medium optimization using Box-Behnken design. The CbFDH activity was 12.2 times increased and was only decreased 3.9% upon storage at 30 °C for 5 d. The CbFDH increased the degradation rate of oil in high concentration. For the sludge with 10% oil (w/w), the degradation rate achieved 35.6% after 12 h using enzyme 21/CbFDH with the protein ratio of 1:4. The results will provide novel perspectives for creation and operation of petroleum-degrading enzymes involving formate dehydrogenase with higher efficiency and lower cost comparing to current microbial strains or consortium.
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Affiliation(s)
- Lei Ji
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, Jinan, 250103, PR China.
| | - Xiaowen Fu
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, Jinan, 250103, PR China
| | - Mutian Wang
- School of Science and Enterprise and Research Centre, Institute of Technology Carlow, Carlow, 00353, Ireland
| | - Chang Xu
- Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, 05405, USA
| | - Guanhong Chen
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, Jinan, 250103, PR China
| | - Fanyong Song
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, Jinan, 250103, PR China
| | - Shuhai Guo
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, Jinan, 250103, PR China
| | - Qiang Zhang
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, Jinan, 250103, PR China.
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Ben Salem F, Ben Said O, Cravo-Laureau C, Mahmoudi E, Bru N, Monperrus M, Duran R. Bacterial community assemblages in sediments under high anthropogenic pressure at Ichkeul Lake/Bizerte Lagoon hydrological system, Tunisia. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:644-656. [PMID: 31185353 DOI: 10.1016/j.envpol.2019.05.146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Bacterial communities inhabiting sediments in coastal areas endure the effect of strong anthropogenic pressure characterized by the presence of multiple contaminants. Understanding the effect of pollutants on the organization of bacterial communities is of paramount importance in order to unravel bacterial assemblages colonizing specific ecological niches. Here, chemical and molecular approaches were combined to investigate the bacterial communities inhabiting the sediments of the Ichkeul Lake/Bizerte Lagoon, a hydrological system under anthropogenic pressure. Although the microbial community of the Ichkeul Lake sediment was different to that of the Bizerte Lagoon, common bacterial genera were identified suggesting a lake-lagoon continuum probably due to the hydrology of the system exchanging waters according to the season. These genera represent bacterial "generalists" maintaining probably general biogeochemical functions. Linear discriminant analysis effect size (LEfSe) showed significant differential abundance distribution of bacterial genera according to the habitat, the pollution type and level. Further, correlation analyses identified specific bacterial genera which abundance was linked with pesticides concentrations in the lake, while in the lagoon the abundance of specific bacterial genera was found linked with the concentrations of PAHs (Polycyclic aromatic hydrocarbons) and organic forms of Sn. As well, bacterial genera which abundance was not correlated with the concentrations of pollutants were identified in both lake and lagoon. These findings represent valuable information, pointing out specific bacterial genera associated with pollutants, which represent assets for developing bacterial tools for the implementation, the management, and monitoring of bioremediation processes to mitigate the effect of pollutants in aquatic ecosystems.
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Affiliation(s)
- Fida Ben Salem
- Laboratoire de Biosurveillance de l'Environment, Faculté des Sciences de Bizerte, Tunisia; MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Olfa Ben Said
- Laboratoire de Biosurveillance de l'Environment, Faculté des Sciences de Bizerte, Tunisia; MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Cristiana Cravo-Laureau
- MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Ezzeddine Mahmoudi
- Laboratoire de Biosurveillance de l'Environment, Faculté des Sciences de Bizerte, Tunisia
| | - Noëlle Bru
- Laboratoire de Mathématiques et de leurs Applications, PAU UMR CNRS 5142, Université de Pau et des Pays de l'Adour, E2S-UPPA, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Mathilde Monperrus
- MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Robert Duran
- MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France.
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Dhote M, Kumar A, Jajoo A, Juwarkar A. Assessment of hydrocarbon degradation potentials in a plant-microbe interaction system with oil sludge contamination: A sustainable solution. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2017; 19:1085-1092. [PMID: 28541720 DOI: 10.1080/15226514.2017.1328388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A pot culture experiment was conducted for 90 days for the evaluation of oil and total petroleum hydrocarbon (TPH) degradation in vegetated and non-vegetated treatments of real-field oil-sludge-contaminated soil. Five different treatments include (T1) control, 2% oil-sludge-contaminated soil; (T2), augmentation of microbial consortium; (T3), Vertiveria zizanioides; (T4), bio-augmentation along with V. zizanioides; and (T5), bio-augmentation with V. zizanioides and bulking agent. During the study, oil reduction, TPH, and degradation of its fractions were determined. Physico-chemical and microbiological parameters of soil were also monitored simultaneously. At the end of the experimental period, oil content (85%) was reduced maximally in bio-augmented rhizospheric treatments (T4 and T5) as compared to control (27%). TPH reduction was observed to be 88 and 89% in bio-augmented rhizospheric soil (T4 and T5 treatments), whereas in non-rhizospheric and control (T2 and T1), TPH reduction was 78 and 37%, respectively. Degradation of aromatic fraction after 90 days in bio-augmented rhizosphere of treatments T4 and T5 was found to 91 and 92%, respectively. In microbial (T2) and Vertiveria treatments (T3), degradation of aromatic fraction was 83 and 68%, respectively. A threefold increase in soil dehydrogenase activity and noticeable changes in organic carbon content and water-holding capacity were also observed which indicated maximum degradation of oil and its fractions in combined treatment of plants and microbes. It is concluded that the plant-microbe soil system helps to restore soil quality and can be used as an effective tool for the remediation of oil-sludge-contaminated sites.
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Affiliation(s)
- Monika Dhote
- a Eco-system Division, National Environmental Engineering Research Institute (NEERI) , Nagpur , India
- b School of Biotechnology , Devi Ahilya University , Indore , India
- c School of Life Sciences , Devi Ahilya University , Indore , India
| | - Anil Kumar
- b School of Biotechnology , Devi Ahilya University , Indore , India
| | - Anjana Jajoo
- c School of Life Sciences , Devi Ahilya University , Indore , India
| | - Asha Juwarkar
- a Eco-system Division, National Environmental Engineering Research Institute (NEERI) , Nagpur , India
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Terrisse F, Cravo-Laureau C, Noël C, Cagnon C, Dumbrell AJ, McGenity TJ, Duran R. Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial Community Reveals Alcanivorax and Cycloclasticus Ecotypes. Front Microbiol 2017; 8:1549. [PMID: 28861063 PMCID: PMC5562018 DOI: 10.3389/fmicb.2017.01549] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/31/2017] [Indexed: 12/26/2022] Open
Abstract
Deciphering the ecology of marine obligate hydrocarbonoclastic bacteria (MOHCB) is of crucial importance for understanding their success in occupying distinct niches in hydrocarbon-contaminated marine environments after oil spills. In marine coastal sediments, MOHCB are particularly subjected to extreme fluctuating conditions due to redox oscillations several times a day as a result of mechanical (tide, waves and currents) and biological (bioturbation) reworking of the sediment. The adaptation of MOHCB to the redox oscillations was investigated by an experimental ecology approach, subjecting a hydrocarbon-degrading microbial community to contrasting oxygenation regimes including permanent anoxic conditions, anoxic/oxic oscillations and permanent oxic conditions. The most ubiquitous MOHCB, Alcanivorax and Cycloclasticus, showed different behaviors, especially under anoxic/oxic oscillation conditions, which were more favorable for Alcanivorax than for Cycloclasticus. The micro-diversity of 16S rRNA gene transcripts from these genera revealed specific ecotypes for different oxygenation conditions and their dynamics. It is likely that such ecotypes allow the colonization of distinct ecological niches that may explain the success of Alcanivorax and Cycloclasticus in hydrocarbon-contaminated coastal sediments during oil-spills.
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Affiliation(s)
- Fanny Terrisse
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Cristiana Cravo-Laureau
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Cyril Noël
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Christine Cagnon
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Alex J Dumbrell
- School of Biological Sciences, University of EssexColchester, United Kingdom
| | - Terry J McGenity
- School of Biological Sciences, University of EssexColchester, United Kingdom
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
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Duran R, Cravo-Laureau C. Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment. FEMS Microbiol Rev 2016; 40:814-830. [PMID: 28201512 PMCID: PMC5091036 DOI: 10.1093/femsre/fuw031] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/28/2015] [Accepted: 07/24/2016] [Indexed: 11/14/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degradation and the biological pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water solubility and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in determining the fate of PAHs in water and sediments, supporting the functioning of biogeochemical cycles and the microbial loop. This review summarises the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecology in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms.
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Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, Pau Cedex, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, Pau Cedex, France
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Wang Y, Wu Y, Wu Z, Tam NFY. Genotypic responses of bacterial community structure to a mixture of wastewater-borne PAHs and PBDEs in constructed mangrove microcosms. JOURNAL OF HAZARDOUS MATERIALS 2015; 298:91-101. [PMID: 26005923 DOI: 10.1016/j.jhazmat.2015.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 05/01/2015] [Accepted: 05/02/2015] [Indexed: 06/04/2023]
Abstract
Mangrove microcosms capable of removing polycyclic aromatic hydrocarbons (PAHs) and polybrominated diphenyl ethers (PBDEs) from wastewater were established under everyday tidal and non-tidal flooding regimes, along with two different mangrove species. Defining how bacterial communities change with pollutants or across treatments will contribute to understanding the microbial ecology of in situ bioremediation systems. A semi-nested PCR-DGGE (denaturing gradient gel electrophoresis) approach was employed, with known genus/species-specific primers targeting the 16S rRNA genes of Sphingomonas and Mycobacterium (related to PAH degradation) and Dehalococcoides (related to PBDE degradation). Results showed that the composition of Mycobacterium- and Dehalococcoides-like populations was critically determined by tidal regime during a medium-term (4-8 months) exposure, while that of Sphingomonas-like population, along with total bacterial community, was more dependent on sediment layer and became prominently affected by tidal regime till the end of 8-month treatment. The effect of plant species was relatively small. Canonical correspondence analysis (CCA) further revealed that Sphingomonas- and Mycobacterium-like populations were significantly associated with phenanthrene and benzo(a)pyrene, respectively, while Dehalococcoides-like population was the only group significantly related to the highest PBDE congener (BDE-209) in the mangrove microcosms.
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Affiliation(s)
- Yafen Wang
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China; School of Environmental Studies, China University of Geosciences, Wuhan, Hubei 430074, China
| | - Yan Wu
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Zhenbin Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Nora Fung-Yee Tam
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
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Duran R, Cuny P, Bonin P, Cravo-Laureau C. Microbial ecology of hydrocarbon-polluted coastal sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15195-15199. [PMID: 26381785 DOI: 10.1007/s11356-015-5373-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
| | - Philippe Cuny
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110, 13288, Marseille, France
| | - Patricia Bonin
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography UM 110, 13288, Marseille, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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Duran R, Bonin P, Jezequel R, Dubosc K, Gassie C, Terrisse F, Abella J, Cagnon C, Militon C, Michotey V, Gilbert F, Cuny P, Cravo-Laureau C. Effect of physical sediments reworking on hydrocarbon degradation and bacterial community structure in marine coastal sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15248-15259. [PMID: 25847440 DOI: 10.1007/s11356-015-4373-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
The present study aimed to examine whether the physical reworking of sediments by harrowing would be suitable for favouring the hydrocarbon degradation in coastal marine sediments. Mudflat sediments were maintained in mesocosms under conditions as closer as possible to those prevailing in natural environments with tidal cycles. Sediments were contaminated with Ural blend crude oil, and in half of them, harrowing treatment was applied in order to mimic physical reworking of surface sediments. Hydrocarbon distribution within the sediment and its removal was followed during 286 days. The harrowing treatment allowed hydrocarbon compounds to penetrate the first 6 cm of the sediments, and biodegradation indexes (such as n-C18/phytane) indicated that biodegradation started 90 days before that observed in untreated control mesocosms. However, the harrowing treatment had a severe impact on benthic organisms reducing drastically the macrofaunal abundance and diversity. In the harrowing-treated mesocosms, the bacterial abundance, determined by 16S rRNA gene Q-PCR, was slightly increased; and terminal restriction fragment length polymorphism (T-RFLP) analyses of 16S rRNA genes showed distinct and specific bacterial community structure. Co-occurrence network and canonical correspondence analyses (CCA) based on T-RFLP data indicated the main correlations between bacterial operational taxonomic units (OTUs) as well as the associations between OTUs and hydrocarbon compound contents further supported by clustered correlation (ClusCor) analysis. The analyses highlighted the OTUs constituting the network structural bases involved in hydrocarbon degradation. Negative correlations indicated the possible shifts in bacterial communities that occurred during the ecological succession.
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Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
- Université de Pau et des Pays de l'Adour, Bâtiment IBEAS, BP 1155, 64013, Pau Cedex, France.
| | - Patricia Bonin
- Aix Marseille Université, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Ronan Jezequel
- Centre de Documentation, de Recherche et d'Expérimentations sur les pollutions accidentelles des Eaux, 715 rue Alain Colas, CS 41836, Brest, France
| | - Karine Dubosc
- Centre de Documentation, de Recherche et d'Expérimentations sur les pollutions accidentelles des Eaux, 715 rue Alain Colas, CS 41836, Brest, France
| | - Claire Gassie
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Fanny Terrisse
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Justine Abella
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Christine Cagnon
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Cecile Militon
- Aix Marseille Université, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Valérie Michotey
- Aix Marseille Université, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Franck Gilbert
- Université de Toulouse; INP, UPS; EcoLab (Laboratoire écologie fonctionnelle et environnement), 118 Route de Narbonne, 31062, Toulouse, France
- CNRS; EcoLab, 31062, Toulouse, France
| | - Philippe Cuny
- Aix Marseille Université, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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Militon C, Jézéquel R, Gilbert F, Corsellis Y, Sylvi L, Cravo-Laureau C, Duran R, Cuny P. Dynamics of bacterial assemblages and removal of polycyclic aromatic hydrocarbons in oil-contaminated coastal marine sediments subjected to contrasted oxygen regimes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15260-15272. [PMID: 25997808 DOI: 10.1007/s11356-015-4510-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
To study the impact of oxygen regimes on the removal of polycylic aromatic hydrocarbons (PAHs) in oil-spill-affected coastal marine sediments, we used a thin-layer incubation method to ensure that the incubated sediment was fully oxic, anoxic, or was influenced by oxic-anoxic switches without sediment stirring. Hydrocarbon content and microbial assemblages were followed during 60 days to determine PAH degradation kinetics and microbial community dynamics according to the oxygenation regimes. The highest PAH removal, with 69 % reduction, was obtained at the end of the experiment under oxic conditions, whereas weaker removals were obtained under oscillating and anoxic conditions (18 and 12 %, respectively). Bacterial community structure during the experiment was determined using a dual 16S rRNA genes/16S rRNA transcripts approach, allowing the characterization of metabolically active bacteria responsible for the functioning of the bacterial community in the contaminated sediment. The shift of the metabolically active bacterial communities showed that the selection of first responders belonged to Pseudomonas spp. and Labrenzia sp. and included an unidentified Deltaproteobacteria-irrespective of the oxygen regime-followed by the selection of late responders adapted to the oxygen regime. A novel unaffiliated phylotype (B38) was highly active during the last stage of the experiment, at which time, the low-molecular-weight (LMW) PAH biodegradation rates were significant for permanent oxic- and oxygen-oscillating conditions, suggesting that this novel phylotype plays an active role during the restoration phase of the studied ecosystem.
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Affiliation(s)
- Cécile Militon
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France.
- Campus de Luminy, case 901, 163 avenue de Luminy, 13288, Marseille Cedex 09, France.
| | - Ronan Jézéquel
- Centre de Documentation, de Recherche et d'Expérimentations sur les pollutions accidentelles des Eaux, 715 rue Alain Colas, CS 41836, 29218, Brest, France
| | - Franck Gilbert
- Université de Toulouse; INP, UPS; EcoLab (Laboratoire écologie fonctionnelle et environnement), 118 Route de Narbonne, 31062, Toulouse, France
- CNRS; EcoLab, 31062, Toulouse, France
| | - Yannick Corsellis
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
| | - Léa Sylvi
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Philippe Cuny
- Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, 13288, Marseille, France
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11
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Faure D, Bonin P, Duran R. Environmental microbiology as a mosaic of explored ecosystems and issues. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13577-13598. [PMID: 26310700 DOI: 10.1007/s11356-015-5164-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/04/2015] [Indexed: 06/04/2023]
Abstract
Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.
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Affiliation(s)
- Denis Faure
- Institut de Biologie Intégrative de la Cellule, CNRS-CEA-Université Paris-Sud, Saclay Plant Sciences, 91198, Gif-sur-Yvette cedex, France,
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12
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Waste lubricating oil removal in a batch reactor by mixed bacterial consortium: a kinetic study. Bioprocess Biosyst Eng 2015; 38:2095-106. [PMID: 26271337 DOI: 10.1007/s00449-015-1449-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
Abstract
The growth kinetics and biodegradation of two waste lubricating oil samples including waste engine oil (WEO) and waste transformer oil (WTO) were studied using pure isolates and mixed culture of Ochrobactrum sp. C1 and Bacillus sp. K1. The mixed culture significantly influenced degradation efficiency of the pure isolates through bioaugmentation process. In particular, the mixed culture was capable of growing on various n-alkanes and polycyclic aromatic hydrocarbons and was able to tolerate unusually high concentrations of waste lubricants (WEO-86.0 g/L and WTO-81.5 g/L). The initial concentration of waste lubricating oils has been varied in the range of 1-10 % (v/v). Under this experimental range, the bacterial growth has been observed to follow Haldane-type kinetics characterizing the presence of substrate inhibition. Haldane model was used to fit the exponential growth data and the following kinetic parameters were obtained: μ max = 0.078 h(-1), K S = 23.101 g/L, K i = 43.844 g/L for WEO; and μ max = 0.044 h(-1), K S = 10.662 g/L, K i = 58.310 g/L for WTO. The values of intrinsic kinetic parameters, like specific growth rate μ max, half saturation constant, K S, inhibition constant, K i and the maximum substrate concentration, S max and growth yield coefficient Y x/s , have been determined using each model hydrocarbon and their mixture as limiting substrate. Relative changes in the values of the kinetic parameters have been correlated to the number of carbon atoms present in n-alkanes. The metabolites from degradation of model hydrocarbon compounds have been identified by GC-MS to elucidate the possible pathway of waste lubricating oil degradation process.
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Liu SH, Zeng GM, Niu QY, Gong JL, Hu XJ, Lu LH, Zhou YY, Hu X, Chen M, Yan M. Effect of Pb(ii) on phenanthrene degradation by new isolated Bacillus sp. P1. RSC Adv 2015. [DOI: 10.1039/c5ra04867b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new strain of bacteria, Bacillus sp. P1, was isolated from compost to degrade PHE in the presence of Pb(ii).
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Mansur AA, Adetutu EM, Kadali KK, Morrison PD, Nurulita Y, Ball AS. Assessing the hydrocarbon degrading potential of indigenous bacteria isolated from crude oil tank bottom sludge and hydrocarbon-contaminated soil of Azzawiya oil refinery, Libya. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:10725-10735. [PMID: 24888608 DOI: 10.1007/s11356-014-3018-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/07/2014] [Indexed: 06/03/2023]
Abstract
The disposal of hazardous crude oil tank bottom sludge (COTBS) represents a significant waste management burden for South Mediterranean countries. Currently, the application of biological systems (bioremediation) for the treatment of COTBS is not widely practiced in these countries. Therefore, this study aims to develop the potential for bioremediation in this region through assessment of the abilities of indigenous hydrocarbonoclastic microorganisms from Libyan Hamada COTBS for the biotreatment of Libyan COTBS-contaminated environments. Bacteria were isolated from COTBS, COTBS-contaminated soil, treated COTBS-contaminated soil, and uncontaminated soil using Bushnell Hass medium amended with Hamada crude oil (1 %) as the main carbon source. Overall, 49 bacterial phenotypes were detected, and their individual abilities to degrade Hamada crude and selected COBTS fractions (naphthalene, phenanthrene, eicosane, octadecane and hexane) were evaluated using MT2 Biolog plates. Analyses using average well colour development showed that ~90 % of bacterial isolates were capable of utilizing representative aromatic fractions compared to 51 % utilization of representative aliphatics. Interestingly, more hydrocarbonoclastic isolates were obtained from treated contaminated soils (42.9 %) than from COTBS (26.5 %) or COTBS-contaminated (30.6 %) and control (0 %) soils. Hierarchical cluster analysis (HCA) separated the isolates into two clusters with microorganisms in cluster 2 being 1.7- to 5-fold better at hydrocarbon degradation than those in cluster 1. Cluster 2 isolates belonged to the putative hydrocarbon-degrading genera; Pseudomonas, Bacillus, Arthrobacter and Brevundimonas with 57 % of these isolates being obtained from treated COTBS-contaminated soil. Overall, this study demonstrates that the potential for PAH degradation exists for the bioremediation of Hamada COTBS-contaminated environments in Libya. This represents the first report on the isolation of hydrocarbonoclastic bacteria from Libyan COTBS and COTBS-contaminated soil.
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Affiliation(s)
- Abdulatif A Mansur
- School of Applied Science, Royal Melbourne Institute of Technology, Melbourne, VIC, 3083, Australia,
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Partovinia A, Naeimpoor F. Comparison of phenanthrene biodegradation by free and immobilized cell systems: formation of hydroxylated compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:5889-5898. [PMID: 24448881 DOI: 10.1007/s11356-014-2516-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 01/02/2014] [Indexed: 06/03/2023]
Abstract
One of the foremost environmental issues having a key role in the feasibility study of polycyclic aromatic hydrocarbons (PAHs) biodegradation is the concern of the toxicity of the formed intermediate metabolites. In this study, biodegradability of phenanthrene (PHE) at initial concentrations of 100-500 ppm and its hydroxylated intermediate metabolites (IMs) in aqueous phase were investigated using free cells (FC) and immobilized cells (IC) in polyvinyl alcohol (PVA) cryogel beads. Results showed that both FC and IC systems were capable of complete PHE biodegradation at initial concentrations lower than 250 ppm after 7 days, though IC system showed a higher PHE removal rate. The maximum IM concentrations observed at initial PHE concentrations of 100 and 250 ppm were 20 and 49 ppm for FC system, whereas 7.4 and 19 ppm were obtained for IC system, respectively, and IMs were finally removed after 7 days. Similarly, at 500 ppm, IC system resulted in higher removal of PHE compared to FC system. However, during the 7-day period for FC system, IMs concentration rose up to 59 ppm, while for IC system, IMs concentration reaches a maximum at day 5 and thereafter it follows a negative rate. It was also shown that resorcinol as an indicator of hydroxylated aromatic metabolites at concentrations of 0-100 ppm can well be biodegraded by free and immobilized cell systems. No prohibition on PHE biodegradation could hence occur due to IMs formation. Additionally, stability of IC system was examined in repeated-batch cultures, showing the effective removal of PHE up to nine reuse cycles.
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Affiliation(s)
- Ali Partovinia
- Biotechnology Research Laboratory, School of Chemical Engineering, Iran University of Science and Technology, P.O. Box 16846-13114, Tehran, Iran
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Vitte I, Duran R, Hernandez-Raquet G, Mounier J, Jézéquel R, Bellet V, Balaguer P, Caumette P, Cravo-Laureau C. Dynamics of metabolically active bacterial communities involved in PAH and toxicity elimination from oil-contaminated sludge during anoxic/oxic oscillations. Appl Microbiol Biotechnol 2012; 97:4199-211. [DOI: 10.1007/s00253-012-4219-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 05/30/2012] [Accepted: 05/31/2012] [Indexed: 10/28/2022]
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McGenity TJ, Folwell BD, McKew BA, Sanni GO. Marine crude-oil biodegradation: a central role for interspecies interactions. AQUATIC BIOSYSTEMS 2012; 8:10. [PMID: 22591596 PMCID: PMC3465203 DOI: 10.1186/2046-9063-8-10] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 04/25/2012] [Indexed: 05/11/2023]
Abstract
The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such "microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons.
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Affiliation(s)
- Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Benjamin D Folwell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
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Cerqueira VS, Hollenbach EB, Maboni F, Vainstein MH, Camargo FAO, do Carmo R Peralba M, Bento FM. Biodegradation potential of oily sludge by pure and mixed bacterial cultures. BIORESOURCE TECHNOLOGY 2011; 102:11003-11010. [PMID: 21993328 DOI: 10.1016/j.biortech.2011.09.074] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/17/2011] [Accepted: 09/18/2011] [Indexed: 05/31/2023]
Abstract
The biodegradation capacity of aliphatic and aromatic hydrocarbons of petrochemical oily sludge in liquid medium by a bacterial consortium and five pure bacterial cultures was analyzed. Three bacteria isolated from petrochemical oily sludge, identified as Stenotrophomonas acidaminiphila, Bacillus megaterium and Bacillus cibi, and two bacteria isolated from a soil contaminated by petrochemical waste, identified as Pseudomonas aeruginosa and Bacillus cereus demonstrated efficiency in oily sludge degradation when cultivated during 40 days. The bacterial consortium demonstrated an excellent oily sludge degradation capacity, reducing 90.7% of the aliphatic fraction and 51.8% of the aromatic fraction, as well as biosurfactant production capacity, achieving 39.4% reduction of surface tension of the culture medium and an emulsifying activity of 55.1%. The results indicated that the bacterial consortium has potential to be applied in bioremediation of petrochemical oily sludge contaminated environments, favoring the reduction of environmental passives and increasing industrial productivity.
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Affiliation(s)
- Vanessa S Cerqueira
- Department of Microbiology, Federal University of Rio Grande do Sul, Sarmento Leite, 500, CEP 90050-170, Porto Alegre, RS, Brazil.
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Role of environmental fluctuations and microbial diversity in degradation of hydrocarbons in contaminated sludge. Res Microbiol 2011; 162:888-95. [DOI: 10.1016/j.resmic.2011.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2010] [Accepted: 03/13/2011] [Indexed: 12/12/2022]
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