“Crude Oil Biodegradation”
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The Hydrocarbon Biodegradation Potential of Faroe-Shetland Channel Bacterioplankton
THE HYDROCARBON BIODEGRADATION POTENTIAL OF FAROE-SHETLAND CHANNEL BACTERIOPLANKTON Angelina G. Angelova Submitted for the degree of Doctor of Philosophy Heriot Watt University School of Engineering and Physical Sciences July 2017 The copyright in this thesis is owned by the author. Any quotation from the thesis or use of any of the information contained in it must acknowledge this thesis as the source of the quotation or information. ABSTRACT The Faroe-Shetland Channel (FSC) is an important gateway for dynamic water exchange between the North Atlantic Ocean and the Nordic Seas. In recent years it has also become a frontier for deep-water oil exploration and petroleum production, which has raised the risk of oil pollution to local ecosystems and adjacent waterways. In order to better understand the factors that influence the biodegradation of spilled petroleum, a prerequisite has been recognized to elucidate the complex dynamics of microbial communities and their relationships to their ecosystem. This research project was a pioneering attempt to investigate the FSC’s microbial community composition, its response and potential to degrade crude oil hydrocarbons under the prevailing regional temperature conditions. Three strategies were used to investigate this. Firstly, high throughput sequencing and 16S rRNA gene-based community profiling techniques were utilized to explore the spatiotemporal patterns of the FSC bacterioplankton. Monitoring proceeded over a period of 2 years and interrogated the multiple water masses flowing through the region producing 2 contrasting water cores: Atlantic (surface) and Nordic (subsurface). Results revealed microbial profiles more distinguishable based on water cores (rather than individual water masses) and seasonal variability patterns within each core. -
Cultivation-Dependent and Cultivation-Independent Characterization of Hydrocarbon-Degrading Bacteria in Guaymas Basin Sediments
ORIGINAL RESEARCH published: 07 July 2015 doi: 10.3389/fmicb.2015.00695 Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments Tony Gutierrez1,2*, Jennifer F. Biddle3, Andreas Teske4 and Michael D. Aitken1 1 Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA, 2 School of Life Sciences, Heriot-Watt University, Edinburgh, UK, 3 College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE, USA, 4 Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Marine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open Edited by: ocean environments. However, there is a paucity of knowledge on the diversity and Peter Dunfield, University of Calgary, Canada function of these organisms in deep-sea sediment. Here we used stable-isotope Reviewed by: probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial Martin Krüger, groups, to investigate polycyclic aromatic hydrocarbon (PAH)-degrading bacteria under Federal Institute for Geosciences 13 and Natural Resources, Germany aerobic conditions in sediments from Guaymas Basin with uniformly labeled [ C]- 13 Casey R. J. Hubert, phenanthrene (PHE). The dominant sequences in clone libraries constructed from C- Newcastle University, UK enriched bacterial DNA (from PHE enrichments) were identified to belong to the genus *Correspondence: Cycloclasticus. We used quantitative PCR primers targeting the 16S rRNA gene of Tony Gutierrez, School of Life Sciences, Heriot-Watt the SIP-identified Cycloclasticus to determine their abundance in sediment incubations University, Edinburgh EH14 4AS, amended with unlabeled PHE and showed substantial increases in gene abundance Scotland, UK [email protected] during the experiments. -
Biotransformation of Medium-Chain Alkanes Using Recombinant P450 Monooxygenase from Alcanivorax Borkumensis SK2 Expressed in Escherichia Coli
Korean J. Chem. Eng., 27(3), 905-909 (2010) DOI: 10.1007/s11814-010-0131-9 RAPID COMMUNICATION Biotransformation of medium-chain alkanes using recombinant P450 monooxygenase from Alcanivorax borkumensis SK2 expressed in Escherichia coli Sang-Ho Baik† Department of Food Science and Human Nutrition, and Research Institute of Human Ecology, Chonbuk National University, Jeonju, Jeonbuk 561-756, Korea (Received 11 May 2009 • accepted 6 September 2009) Abstract−A bioconversion system for medium-chain alkanes was constructed by using a recombinant Escherichia coli whole-cell biocatalyst expressing P450 monooxygenase genes, ferredoxin, and ferredoxin reductase cloned from Alcanivorax borkumensis as an operon. The recombinant E. coli harboring the P450 gene and two related expression component enzymes, ferredoxin and ferredoxin reductase, was constructed in a single vector pET21(a) and successfully expressed in E. coli BL21(DE3) as a soluble form, showing a molecular weight of 53 kDa on 10% SDS-PAGE. When the cell-free extract of E. coli BL21 expressing p450 monooxygenase was subjected to reduced CO difference spectral analysis, a soret band near 450 nm appeared indicating that the cloned P450 was expressed as a functionally active enzyme. The E. coli cells harboring the expressed P450 gene were able to convert n-octane and 1-decene, producing approximately 450 µg/ml of n-octanol and 290 µg/ml of 1,2-epoxydecane, respectively, at pH 7.0 and 30 oC. However, the recombinant E. coli cells were not able to convert the branched alkane, 2,6,10,14-tetramethylpentadecane (C19). Key words: P450 Monooxygenase, Medium-chain Alkane, Esheriachia coli INTRODUCTION (Rd) and Rd reductase, for alkane hydroxylase activity, are thought to be mainly related to the first hydroxylation step of alkanes [7,8]. -
Ex-Situ Biodegradation of Petroleum Hydrocarbons Using Alcanivorax Borkumensis Enzymes
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/322824019 Ex-situ Biodegradation of petroleum hydrocarbons using Alcanivorax borkumensis enzymes Article in Biochemical Engineering Journal · January 2018 DOI: 10.1016/j.bej.2018.01.014 CITATIONS READS 0 26 4 authors, including: Sarra Magdouli Tarek Rouissi Institut National de la Recherche Scientifique Institut National de la Recherche Scientifique 15 PUBLICATIONS 118 CITATIONS 29 PUBLICATIONS 88 CITATIONS SEE PROFILE SEE PROFILE Satinder Kaur Brar Institut National de la Recherche Scientifique 230 PUBLICATIONS 3,462 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: Fate of emerging contaminants in watewater treatment plants View project Occurrence of nano-particles in the environment View project All content following this page was uploaded by Sarra Magdouli on 01 February 2018. The user has requested enhancement of the downloaded file. Accepted Manuscript Title: Ex-situ Biodegradation of petroleum hydrocarbons using Alcanivorax borkumensis enzymes Authors: Tayssir Kadri, Sara Magdouli, Tarek Rouissi, Satinder Kaur Brar PII: S1369-703X(18)30015-9 DOI: https://doi.org/10.1016/j.bej.2018.01.014 Reference: BEJ 6863 To appear in: Biochemical Engineering Journal Received date: 7-9-2017 Revised date: 19-12-2017 Accepted date: 13-1-2018 Please cite this article as: Tayssir Kadri, Sara Magdouli, Tarek Rouissi, Satinder Kaur Brar, Ex-situ Biodegradation of petroleum hydrocarbons using Alcanivorax borkumensis enzymes, Biochemical Engineering Journal https://doi.org/10.1016/j.bej.2018.01.014 This is a PDF file of an unedited manuscript that has been accepted for publication. -
Microbial Communities Responding to Deep-Sea Hydrocarbon Spills Molly C. Redmond1 and David L. Valentine2 1. Department of Biolo
Microbial Communities Responding to Deep-Sea Hydrocarbon Spills Molly C. Redmond1 and David L. Valentine2 1. Department of Biological Sciences, University of North Carolina at Charlotte, [email protected] 2. Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, [email protected] Abstract The 2010 Deepwater Horizon oil spill in the Gulf of Mexico can be considered the world’s first deep-sea hydrocarbon spill. Deep-sea hydrocarbon spills occur in a different setting than surface oil spills and the organisms that respond must be adapted to this low temperature, high pressure environment. The hydrocarbon composition can also be quite different than at the sea surface, with high concentrations of dissolved hydrocarbons, including natural gas, and suspended droplets of petroleum. We discuss the bacteria that may respond to these spills and factors that affect their abundance, based on data collected during the Deepwater Horizon spill and in microcosm experiments in the following years. 1. Introduction When the Deepwater Horizon mobile offshore drilling unit exploded on April 20, 2010 and sank two days later, it caused the world’s first major deep-sea oil spill. Previous well blowouts such as Ixtoc I in the Gulf Mexico in 1979 and Platform A in the Santa Barbara Channel in 1969 also caused significant undersea spills, but the shallower depths of these spills (50-60 m) resulted in most of oil reaching the sea surface. In contrast, the Deepwater Horizon well was 1500 m below the sea surface and ~25% the hydrocarbons emitted remained dissolved or suspended in a deep-sea intrusion layer at depths between 900 and 1300 m (Ryerson et al. -
Degrading Bacteria in Deep‐
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Aberdeen University Research Archive Journal of Applied Microbiology ISSN 1364-5072 ORIGINAL ARTICLE Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel) E. Gontikaki1 , L.D. Potts1, J.A. Anderson2 and U. Witte1 1 School of Biological Sciences, University of Aberdeen, Aberdeen, UK 2 Surface Chemistry and Catalysis Group, Materials and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen, UK Keywords Abstract clone libraries, Faroe-Shetland Channel, hydrocarbon degradation, isolates, marine Aims: The aim of this study was the baseline description of oil-degrading bacteria, oil spill, Oleispira, sediment. sediment bacteria along a depth transect in the Faroe-Shetland Channel (FSC) and the identification of biomarker taxa for the detection of oil contamination Correspondence in FSC sediments. Evangelia Gontikaki and Ursula Witte, School Methods and Results: Oil-degrading sediment bacteria from 135, 500 and of Biological Sciences, University of Aberdeen, 1000 m were enriched in cultures with crude oil as the sole carbon source (at Aberdeen, UK. ° E-mails: [email protected] and 12, 5 and 0 C respectively). The enriched communities were studied using [email protected] culture-dependent and culture-independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. 2017/2412: received 8 December 2017, Bacterial isolates included well-known oil-degrading taxa and several that are revised 16 May 2018 and accepted 18 June reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, 2018 Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at doi:10.1111/jam.14030 genus level particularly between the shallow and the deep, cold-water stations. -
Simulation of Deepwater Horizon Oil Plume Reveals Substrate Specialization Within a Complex Community of Hydrocarbon Degraders
Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders Ping Hua, Eric A. Dubinskya,b, Alexander J. Probstc, Jian Wangd, Christian M. K. Sieberc,e, Lauren M. Toma, Piero R. Gardinalid, Jillian F. Banfieldc, Ronald M. Atlasf, and Gary L. Andersena,b,1 aEcology Department, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; bDepartment of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720; cDepartment of Earth and Planetary Science, University of California, Berkeley, CA 94720; dDepartment of Chemistry and Biochemistry, Florida International University, Miami, FL 33199; eDepartment of Energy, Joint Genome Institute, Walnut Creek, CA 94598; and fDepartment of Biology, University of Louisville, Louisville, KY 40292 Edited by Rita R. Colwell, University of Maryland, College Park, MD, and approved May 30, 2017 (received for review March 1, 2017) The Deepwater Horizon (DWH) accident released an estimated Many studies of the plume samples reported that the structure 4.1 million barrels of oil and 1010 mol of natural gas into the Gulf of the microbial communities shifted as time progressed (3–6, 11– of Mexico, forming deep-sea plumes of dispersed oil droplets and 16). Member(s) of the order Oceanospirillales dominated from dissolved gases that were largely degraded by bacteria. During the May to mid-June, after which their numbers rapidly declined and course of this 3-mo disaster a series of different bacterial taxa were species of Cycloclasticus and Colwellia dominated for the next enriched in succession within deep plumes, but the metabolic capa- several weeks (4, 5, 14). -
Distribution of Pahs and the PAH-Degrading Bacteria in the Deep-Sea
1 Distribution of PAHs and the PAH-degrading bacteria in the deep-sea 2 sediments of the high-latitude Arctic Ocean 3 4 Chunming Dong1¶, Xiuhua Bai1, 4¶, Huafang Sheng2, Liping Jiao3, Hongwei Zhou2 and Zongze 5 Shao1 # 6 1 Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography, State 7 Oceanic Administration, Xiamen, 361005, Fujian, China. 8 2 Department of Environmental Health, School of Public Health and Tropical Medicine, Southern 9 Medical University, Guangzhou, 510515, Guangdong, China. 10 3 Key Laboratory of Global Change and Marine-Atmospheric Chemistry, the Third Institute of 11 Oceanography, State Oceanic Administration, Xiamen, 361005, Fujian, China. 12 4 Life Science College, Xiamen University, Xiamen, 361005, Fujian, China. 13 14 # Corresponding Author: Zongze Shao, Mail address: No.184, 14 Daxue Road, Xiamen 361005, 15 Fujian, China. Phone: 86-592-2195321; E-mail: [email protected]. 16 ¶: Authors contributed equally to this work. 17 18 1 19 Abstract 20 Polycyclic aromatic hydrocarbons (PAHs) are common organic pollutants that can be transferred 21 long distances and tend to accumulate in marine sediments. However, less is known regarding 22 the distribution of PAHs and their natural bioattenuation in the open sea, especially the Arctic 23 Ocean. In this report, sediment samples were collected at four sites from the Chukchi Plateau to 24 the Makarov Basin in the summer of 2010. PAH compositions and total concentrations were 25 examined with GC-MS. The concentrations of 16 EPA-priority PAHs varied from 2.0 to 41.6 ng 26 g-1 dry weight and decreased with sediment depth and movement from the southern to the 27 northern sites. -
Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial
Variation of oxygenation conditions on a hydrocarbonoclastic microbial community reveals Alcanivorax and Cycloclasticus ecotypes Fanny Terrisse, Cristiana Cravo-Laureau, Cyril Noel, Christine Cagnon, A.J. Dumbrell, T.J. Mcgenity, R. Duran To cite this version: Fanny Terrisse, Cristiana Cravo-Laureau, Cyril Noel, Christine Cagnon, A.J. Dumbrell, et al.. Vari- ation of oxygenation conditions on a hydrocarbonoclastic microbial community reveals Alcanivo- rax and Cycloclasticus ecotypes. Frontiers in Microbiology, Frontiers Media, 2017, 8, pp.1549. 10.3389/fmicb.2017.01549. hal-01631803 HAL Id: hal-01631803 https://hal.archives-ouvertes.fr/hal-01631803 Submitted on 30 Nov 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. fmicb-08-01549 August 16, 2017 Time: 11:37 # 1 ORIGINAL RESEARCH published: 16 August 2017 doi: 10.3389/fmicb.2017.01549 Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial Community Reveals Alcanivorax and Cycloclasticus Ecotypes Fanny Terrisse1, Cristiana Cravo-Laureau1, Cyril Noël1, Christine Cagnon1, Alex J. Dumbrell2, Terry J. McGenity2 and Robert Duran1* 1 IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l’Adour, Pau, France, 2 School of Biological Sciences, University of Essex, Colchester, United Kingdom 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. -
Oceanographic Controls of Hydrocarbon Degradation in the Gulf of Mexico
OCEANOGRAPHIC CONTROLS OF HYDROCARBON DEGRADATION IN THE GULF OF MEXICO A Dissertation Presented to The Academic Faculty by Xiaoxu Sun In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Earth and Atmospheric Sciences Georgia Institute of Technology May 2018 COPYRIGHT © 2018 BY XIAOXU SUN OCEANOGRAPHIC CONTROLS OF HYDROCARBON DEGRADATION IN THE GULF OF MEXIC Approved by: Dr. Joel E. Kostka, Advisor Dr. Yuanzhi Tang School of Earth and Atmospheric Sciences School of Earth and Atmospheric Sciences Georgia Institute of Technology Georgia Institute of Technology Dr. Martial Taillefert Dr. David Hollander School of Earth and Atmospheric Sciences College of Marine Sciences Georgia Institute of Technology University of South Florida Dr. Ellery Ingall School of Earth and Atmospheric Sciences Georgia Institute of Technology Date Approved: March 13, 2018 ACKNOWLEDGEMENTS I would like to express my enormous gratitude to my advisor Dr. Joel Kostka for his support through my Ph.D. studies at Georgia Tech. I could not imagine to finish my Ph.D. without his wise guidance and tremendous support. Besides my advisor, I would like to thank all my committee members: Dr. Martial Taillefert, Dr. Ellery Ingall, Dr. Yuanzhi Tang, and Dr. David Hollander for their time and insightful opinions on my thesis. I would also thank all the people that I have collaborated with and the people that helped me in the past 6 years: Dr. Dai Sheng, Dr. Patrick Schwing, Dr. Isabel Romero, Dr. Roger Prince, and the crew members of R/V Weatherbird II and CCCG Amundsen Icebreaker. It was a great pleasure to spend time with my close colleagues: Dr. -
The Transcriptional Response of Prokaryotes to Phytoplanktonderived Dissolved Organic Matter in Seawater
bs_bs_banner Environmental Microbiology (2014) doi:10.1111/1462-2920.12434 The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater Sara Beier,1,2* Adam R. Rivers,3 Mary Ann Moran3 Introduction and Ingrid Obernosterer1,2 Prokaryotes are main processors of marine dissolved 1UPMC University Paris 06, UMR 7621, LOMIC, UMS organic matter (DOM), much of which is derived from 2348, Observatoire Océanologique, Banyuls/mer phytoplankton exudates (Baines and Pace, 1991; Benner, F-66650, France. 2002). Taxonomically distinct phytoplankton species 2CNRS, UMR 7621, LOMIC, Observatoire produce DOM with different chemical composition Océanologique, Banyuls/mer F-66650, France. (Biersmith and Benner, 1998; Sarmento et al., 2013). 3Department of Marine Sciences, University of Georgia, Thus, the question of whether prokaryotic community Athens, GA 30602, USA. composition changes in response to phytoplankton DOM of different origins has been investigated. Outcomes of Summary these studies have differed, however, with some indicat- ing pronounced compositional responses and others only To better understand the functional responses in weak effects (Van Hannen et al., 1999; Lekunberri et al., prokaryotes to dissolved organic matter (DOM), we 2012; Sarmento and Gasol, 2012; Landa et al., 2013b). compared the transcriptional pattern of natural pro- One explanation for these contrasting results could karyotic communities grown in continuous cultures be that both specialist and generalist strategies exist on seawater amended with phytoplankton-derived among prokaryotic taxa (Langenheder et al., 2005; DOM. Metatranscriptomic reads were classified taxo- Gómez-Consarnau et al., 2012; Dinasquet et al., 2013). nomically (by genomic binning) and functionally Depending on the degree of selectivity for specific organic (using Kyoto Encyclopedia of Genes and Genomes), substrates, specialist or generalist behaviour could domi- and the relative gene expression of individual taxa nate a community. -
Membrane Fatty Acid Composition and Cell Surface Hydrophobicity Of
molecules Article Membrane Fatty Acid Composition and Cell Surface Hydrophobicity of Marine Hydrocarbonoclastic Alcanivorax borkumensis SK2 Grown on Diesel, Biodiesel and Rapeseed Oil as Carbon Sources Maria Konieczna 1, Martin Olzog 1, Daniela J. Naether 2, Łukasz Chrzanowski 3 and Hermann J. Heipieper 1,* ID 1 Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr, 15, 04318 Leipzig, Germany; [email protected] (M.K.); [email protected] (M.O.) 2 Department of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str, 9, 60438 Frankfurt, Germany; [email protected] 3 Faculty of Chemical Technology, Poznan University of Technology, 60-965 Poznan, Poland; [email protected] * Correspondence: [email protected]; Tel.: +49-341-2351694 Academic Editors: Carla C. C. R. de Carvalho and Maria José Caramujo Received: 18 May 2018; Accepted: 12 June 2018; Published: 13 June 2018 Abstract: The marine hydrocarbonoclastic bacterium Alcanivorax borkumensis is well known for its ability to successfully degrade various mixtures of n-alkanes occurring in marine oil spills. For effective growth on these compounds, the bacteria possess the unique capability not only to incorporate but also to modify fatty intermediates derived from the alkane degradation pathway. High efficiency of both these processes provides better competitiveness for a single bacteria species among hydrocarbon degraders. To examine the efficiency of A. borkumensis to cope with different sources of fatty acid intermediates, we studied the growth rates and membrane fatty acid patterns of this bacterium cultivated on diesel, biodiesel and rapeseed oil as carbon and energy source. Obtained results revealed significant differences in both parameters depending on growth substrate.