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Oil Biodegradation in Deep Marine Basins

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Part of the book series: Handbook of Hydrocarbon and Lipid Microbiology ((HHLM))

Abstract

Nine important hydrocarbon (oil) basins where offshore petroleum leases have been licensed are compared. These nine basins (Gulf of Mexico, Eastern Mediterranean’s Nile Deep-Sea Fan, Central Mediterranean and the Sirte Basin, North Sea, Caspian Sea, Angola, Trinidad and Tobago, Great Australian Bight, and Brazil’s Amazonian Deep-Sea Basin) are geographically separated and are impacted by very different water masses. The geochemical parameters of these basins are quite distinct, for example, salinities ranging from 39 psu in the Eastern Mediterranean to 12 psu in the Caspian. Additionally, parameters like temperatures of the bottom water are also very distinct, with the temperature in the deep water of the Eastern Mediterranean being between 12 °C and 14 °C and the temperature of the deep water in the North Sea being −2 °C. Each basin represents a unique ecosystem in which distinct microbes may thrive. These distinct environmental parameters may act to constrain the extent of hydrocarbon degradation in these basins. Another potential constraint on hydrocarbon degradation is the extent of natural hydrocarbon seeps in the area. Though many basins have similar if not 16S rRNA identical strains of oil-degrading bacteria, Colwellia psychrerythraea from different basins showed that a mixture of natural selection and neutral evolution has contributed to the divergence of these. Most if not all deep ocean basin microbial communities are dominated by Thaumarchaeota below 200 m. These microaerophilic, ammonium oxidizer, psychrophiles are very adapted to an oligotrophic lifestyle, and though many in this group will degrade oil, they are rapidly outcompeted by other bacteria in oil or high hydrocarbon intrusions, thus the virtual “canary in the coal mine.” Cometabolic biodegradation of oil is well documented but could be an important natural attenuation mechanism for oil in deep marine basins with episodic methane seeps. Microbial community structure can also predict concentrations of oil in deep basins. Many other synergistic effects require more research in environmental systems biology in deep marine basins.

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References

  • Bedborough DR, Blackman RAA, Law RJ (1987) A survey of inputs to the North-Sea resulting from oil and gas developments. Philos Trans R Soc Lond Ser B-Biol Sci 316:495–509

    Article  CAS  Google Scholar 

  • Berger WH, Wefer G, Richter C, Lange CB, Giraudeau J, Hermelin O, Party SS (1998) The Angola-Benguela upwelling system: paleoceanographic synthesis of shipboard results from Leg 175. In: Proceedings of the ocean drilling program, initial reports. 175

    Google Scholar 

  • Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH (2008) Metagenomic signatures of the Peru margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 105:10583–10588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Biddle JF, White JR, Teske AP, House CH (2011) Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes. ISME J 5:1038–1047

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Biju-Duval B, Le Quellec P, Mascle A, Renard V, Valery P (1982) Multibeam bathymetric survey and high resolution seismic investigations on the Barbados Ridge complex (Eastern Caribbean): a key to the knowledge and interpretation of an accretionary wedge. Tectonophysics 86: 275–304

    Article  Google Scholar 

  • Brakstad OG, Daling PS, Faksness LG, Almas IK, Vang SH, Syslak L, Leirvik F (2014) Depletion and biodegradation of hydrocarbons in dispersions and emulsions of the Macondo 252 oil generated in an oil-on-seawater mesocosm flume basin. Mar Pollut Bull 84:125–134

    Article  CAS  PubMed  Google Scholar 

  • Brakstad OG, Nordtug T, Throne-Hoist M (2015) Biodegradation of dispersed Macondo oil in seawater at low temperature and different oil droplet sizes. Mar Pollut Bull 93:144–152

    Article  CAS  PubMed  Google Scholar 

  • Brito EMS, Guyoneaud R, Goñi-Urriza M, Ranchou-Peyruse A, Verbaere A, Crapez MAC, Wasserman JCA, Duran R (2006) Characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in Guanabara Bay, Brazil. Res Microbiol 157:752–762

    Article  CAS  PubMed  Google Scholar 

  • Brown KM (1990) The nature and hydrogeologic significance of mud diapirs and diatremes for accretionary systems. J Geophys Res 95:8969–8982

    Article  Google Scholar 

  • Brown KM, Westbrook GK (1987) The tectonic fabric of the Barbados Ridge accretionary complex. Mar Pet Geol 4:71–81

    Article  Google Scholar 

  • Brown K, Westbrook GK (1988) Mud diapirism and subcretion in the Barbados Ridge accretionary complex: the role of fluids in accretionary processes. Tectonics 7:613–640

    Article  Google Scholar 

  • Campeao ME, Reis L, Leomil L, de Oliveira L, Otsuki K, Gardinali P, Pelz O, Valle R, Thompson FL, Thompson CC (2017) The deep-sea microbial community from the Amazonian basin associated with oil degradation. Front Microbiol 8:13

    Article  Google Scholar 

  • Cardy DLN, Laidler V, Salmond GPC, Murrell JC (1991) Molecular analysis of the methane monooxygenase (MMO) gene cluster of Methylosinus trichosporium OB3b. Mol Microbiol 5:335–342

    Article  CAS  PubMed  Google Scholar 

  • Chekroud Z, Gouda MK, Houhamdi M (2011) Biodegradation of crude oil in marine medium. J Proteomics Bioinformatics 4:231–237

    CAS  Google Scholar 

  • Chicherina OV, Leonov AV, Fashchuk DY (2004) Geographical and ecological characteristics of the Caspian Sea and modern tendencies in the evolution of its ecosystem. Water Resour 31:271–289

    Article  CAS  Google Scholar 

  • Cragg BA, Law KM, Cramp A, Parkes RJ (1997) Bacterial profiles in Amazon Fan sediments, Sites 934 and 940. In: Flood RD, Piper DJW, Klaus A, Peterson LC (eds) Proceedings of ODP, scientific results. Ocean Drilling Program, College Station, pp 565–571

    Google Scholar 

  • Dale T, Rey F, Heimdal BR (1999) Seasonal development of phytoplankton at a high latitude oceanic site. Sarsia 84:419–435

    Article  Google Scholar 

  • Deville E, Battani A, Griboulard R, Guerlais S, Herbin JP, Houzay JP, Muller C, Prinzhofer A (2003) The origin and processes of mud volcanism: new insights from Trinidad. Geol Soc Lond Spec Publ 216:475–490

    Article  CAS  Google Scholar 

  • Deville E, Guerlais S-H, Callec Y, Griboulard R, Huyghe P, Lallemant S, Mascle A, Noble M, Schmitz J (2006) Liquefied vs stratified sediment mobilization processes: insight from the south of the Barbados accretionary prism. Tectonophysics 428:33–47

    Article  Google Scholar 

  • Deville É, Guerlais S-H, Lallemant S, Schneider F (2010) Fluid dynamics and subsurface sediment mobilization processes: an overview from Southeast Caribbean. Basin Res 22:361–379

    Article  Google Scholar 

  • Dubinsky EA, Conrad ME, Chakraborty R, Bill M, Borglin SE, Hollibaugh JT, Mason OU, Piceno YM, Reid FC, Stringfellow WT, Tom LM, Hazen TC, Andersen GL (2013) Succession of hydrocarbon-degrading bacteria in the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico. Environ Sci Technol 47:10860–10867

    Article  CAS  PubMed  Google Scholar 

  • Edwards BR, Reddy CM, Camilli R, Carmichael CA, Longnecker K, Van Mooy BAS (2011) Rapid microbial respiration of oil from the Deepwater horizon spill in offshore surface waters of the Gulf of Mexico. Environ Res Lett 6:9

    Article  Google Scholar 

  • Farag S, Soliman NA (2011) Biodegradation of crude petroleum oil and environmental pollutants by Candida tropicalis strain. Braz Arch Biol Technol 54:821–830

    Article  CAS  Google Scholar 

  • Felden J, Lichtschlag A, Wenzhofer F, de Beer D, Feseker T, Ristova PP, de Lange G, Boetius A (2013) Limitations of microbial hydrocarbon degradation at the Amon mud volcano (Nile deep-sea fan). Biogeosciences 10:3269–3283

    Article  CAS  Google Scholar 

  • Griboulard R, Bobier C, Faugères JC, Vernette G (1991) Clay diapiric structures within the strike-slip margin of the southern leg of the Barbados prism. Tectonophysics 192:383–400

    Article  Google Scholar 

  • Guezennec J, Fiala-Medioni A (1996) Bacterial abundance and diversity in the Barbados trench determined by phospholipid analysis. FEMS Microbiol Ecol 19:83–93

    Article  CAS  Google Scholar 

  • Hazen TC (1997) Bioremediation. In: Amy P, Haldeman D (eds) Microbiology of the terrestrial subsurface. CRC Press, Boca Raton, pp 247–266

    Google Scholar 

  • Hazen TC (2010) Cometabolic bioremediation. In: Timmis KN (ed) Handbook of hydrocarbon microbiology: microbial interactions with hydrocarbons, oils, fats and related hydrophobic substrates and products. Springer, Berlin

    Google Scholar 

  • Hazen TC, Sayler GS (2016) Environmental systems microbiology of contaminated environments. In: Yates M, Nakatsu C, Miller R, Pillai S (eds) Manual of environmental microbiology, 4th edn. ASM Press, Washington, DC, pp 5.1.6-1–5.1.6-10

    Google Scholar 

  • Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D’Haeseleer P, Holman HYN, Osman S, Lu ZM, Van Nostrand JD, Deng Y, Zhou JZ, Mason OU (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330:204–208

    Article  CAS  PubMed  Google Scholar 

  • Hazen TC, Prince RC, Mahmoudi N (2016) Marine oil biodegradation. Environ Sci Technol 50:2121–2129

    Article  CAS  PubMed  Google Scholar 

  • Heijs SK, Laverman AM, Forney LJ, Hardoim PR, van Elsas JD (2008) Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean. FEMS Microbiol Ecol 64:362–377

    Article  CAS  PubMed  Google Scholar 

  • Henry P, Le Pichon X, Lallemant S, Lance S, Martin JB, Foucher J-P, Fiala-MÈdioni A, Rostek F, Guilhaumou N, Pranal V, Castrec M (1996) Fluid flow in and around a mud volcano field seaward of the Barbados accretionary wedge: results from Manon cruise. J Geophys Res 101:20297–20323

    Article  CAS  Google Scholar 

  • IAE (2017) Global oil discoveries and new projects fell to historic lows in 2016

    Google Scholar 

  • Ibraheem IBM (2010) Biodegradability of hydrocarbons by cyanobacteria1. J Phycol 46:818–824

    Article  CAS  Google Scholar 

  • Jones RD, Amador JA (1993) Methane and carbon monoxide production, oxidation, and turnover times in the Caribbean Sea as influenced by the Orinoco River. J Geophys Res 98(C2): 2353–2359

    Article  CAS  Google Scholar 

  • Kimes NE, Callaghan AV, Aktas DF, Smith WL, Sunner J, Golding BT, Drozdowska M, Hazen TC, Suflita JM, Morris PJ (2013) Metagenomic analysis and metabolite profiling of deep-sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill. Front Microbiol 4:17

    Article  Google Scholar 

  • King GM, Kostka JE, Hazen TC, Sobecky PA (2015) Microbial responses to the Deepwater Horizon oil spill: from coastal wetlands to the deep sea. Annu Rev Mar Sci 7(7):377–401

    Article  CAS  Google Scholar 

  • Korshenko A, Gul AG (2005) Pollution of the Caspian Sea. In: Kostianoy AG, Kosarev AN (eds) The Caspian environment, vol 5P. Springer, Berlin/Heidelberg, pp 109–142

    Chapter  Google Scholar 

  • Kuipers B, Witte H, van Noort G, Gonzalez S (2003) Grazing loss-rates in pico- and nanoplankton in the Faroe-Shetland channel and their different relations with prey density. J Sea Res 50:1–9

    Article  Google Scholar 

  • Le Pichon X, Foucher J-P, BoulËgue J, Henry P, Lallemant S, Benedetti M, Avedik F, Mariotti A (1990a) Mud volcano field seaward of the Barbados accretionary complex: a submersible survey. J Geophys Res 95:8931–8943

    Article  Google Scholar 

  • Le Pichon X, Henry P, Lallemant S (1990b) Water flow in the Barbados accretionary complex. J Geophys Res 95:8945–8967

    Article  Google Scholar 

  • Lein AY, Rusanov II, Klyuvitkin AA, Kravchishina MD, Zakharova EE, Veslopolova EF, Makkaveev PN, Ivanov MV (2010) Biogeochemical processes in the water column of the Caspian Sea in November 2008. Dokl Earth Sci 434:1381–1385

    Article  CAS  Google Scholar 

  • Loder MGJ, Kraberg AC, Aberle N, Peters S, Wiltshire KH (2012) Dinoflagellates and ciliates at Helgoland Roads, North Sea. Helgol Mar Res 66:11–23

    Article  Google Scholar 

  • Logan GA, Jones AT, Kennard JM, Ryan GJ, Rollet N (2010) Australian offshore natural hydrocarbon seepage studies, a review and re-evaluation. Mar Pet Geol 27:26–45

    Article  CAS  Google Scholar 

  • Mahmoudi N, Robeson MS 2nd, Castro HF, Fortney JL, Techtmann SM, Joyner DC, Paradis CJ, Pfiffner SM, Hazen TC (2015) Microbial community composition and diversity in Caspian Sea sediments. FEMS Microbiol Ecol 91:1–11

    Article  PubMed  Google Scholar 

  • Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Baelum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK (2014) Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J 8:1464–1475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mastalerz V, de Lange GJ, Dahlmann A (2009) Differential aerobic and anaerobic oxidation of hydrocarbon gases discharged at mud volcanoes in the Nile deep-sea fan. Geochim Cosmochim Acta 73:3849–3863

    Article  CAS  Google Scholar 

  • Moursy AS, El-Abagy MM (1982) Microbial degradation of hydrocarbons in Ismailia canal water. Environ Int 7:423–427

    Article  CAS  Google Scholar 

  • NAS (2003) Oil in the sea III: inputs, fates, and effects. The National Academies Press, Washington, DC

    Google Scholar 

  • Omoregie EO, Niemann H, Mastalerz V, de Lange GJ, Stadnitskaia A, Mascle J, Foucher JP, Boetius A (2009) Microbial methane oxidation and sulfate reduction at cold seeps of the deep Eastern Mediterranean Sea. Mar Geol 261:114–127

    Article  CAS  Google Scholar 

  • Reddy CM, Arey JS, Seewald JS, Sylva SP, Lemkau KL, Nelson RK, Carmichael CA, McIntyre CP, Fenwick J, Ventura GT, Van Mooy BAS, Camilli R (2012) Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill. Proc Natl Acad Sci USA 109:20229–20234

    Article  CAS  PubMed  Google Scholar 

  • Redmond MC, Valentine DL (2012) Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proc Natl Acad Sci USA 109:20292–20297

    Article  CAS  PubMed  Google Scholar 

  • Riegman R, Kraay GW (2001) Phytoplankton community structure derived from HPLC analysis of pigments in the Faroe-Shetland channel during summer 1999: the distribution of taxonomic groups in relation to physical/chemical conditions in the photic zone. J Plankton Res 23:191–205

    Article  CAS  Google Scholar 

  • Rollet N, Logan GA, Kennard JM, O’Brien PE, Jones AT, Sexton M (2006) Characterisation and correlation of active hydrocarbon seepage using geophysical data sets: an example from the tropical, carbonate Yampi Shelf, Northwest Australia. Mar Pet Geol 23:145–164

    Article  Google Scholar 

  • Salmanov MA (2006) Microbiological studies in the Deepwater area of the Southern Caspian Sea. Microbiology 75:206–212

    Article  CAS  Google Scholar 

  • Santas R, Korda A, Tenente A, Buchholz K, Santas P (1999) Mesocosm assays of oil spill bioremediation with oleophilic fertilizers: Inipol, F1 or both? Mar Pollut Bull 38:44–48

    Article  CAS  Google Scholar 

  • Schauer R, Bienhold C, Ramette A, Harder J (2010) Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J 4:159–170

    Article  CAS  PubMed  Google Scholar 

  • Silva A, Oliveira FS, Bernardes D, França F (2009) Bioremediation of marine sediments impacted by petroleum. Appl Biochem Biotechnol 153:58–66

    Article  PubMed  Google Scholar 

  • Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA Jr, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC (2015) Natural bacterial communities serve as quantitative geochemical biosensors. MBio 6:e00326-00315

    Article  Google Scholar 

  • Stackhouse B, Lau MCY, Vishnivetskaya T, Burton N, Wang R, Southworth A, Whyte L, Onstott TC (2017) Atmospheric CH4 oxidation by Arctic permafrost and mineral cryosols as a function of water saturation and temperature. Geobiology 15:94–111

    Article  CAS  PubMed  Google Scholar 

  • Struckmeyer HIM, Wiliams AK, Cowley R, Totterdell JM, Lawrence G, O’Brien GW (2002) Evaluation of hydrocarbon seepage in the Great Australian Bight. AAPEA J 42:371

    Article  Google Scholar 

  • Techtmann SM, Fortney JL, Ayers KA, Joyner DC, Linley TD, Pfiffner SM, Hazen TC (2015) The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth. PLoS One 10:e0120605

    Article  PubMed  PubMed Central  Google Scholar 

  • Techtmann SM, Fitzgerald KS, Stelling SC, Joyner DC, Uttukar SM, Harris AP, Alshibli NK, Brown SD, Hazen TC (2016) Colwellia psychrerythraea strains from distant deep sea basins show adaptation to local conditions. Front Environ Sci 4:33

    Article  Google Scholar 

  • Techtmann SM, Mahmoudi N, Whitt KT, Campa MF, Fortney JL, Joyner DC, Hazen TC (2017) Comparison of thaumarchaeotal populations from four deep sea basins. FEMS Microbiol Ecol 93:10

    Article  Google Scholar 

  • Tissot BP, Welte DH (1984) Petroleum formation and occurrence. Springer, Berlin

    Book  Google Scholar 

  • Valentine DL, Mezic I, Macesic S, Crnjaric-Zic N, Ivic S, Hogan PJ, Fonoberov VA, Loire S (2012) Dynamic autoinoculation and the microbial ecology of a deep water hydrocarbon irruption. Proc Natl Acad Sci USA 109:20286–20291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vezzulli L, Brettar I, Pezzati E, Reid PC, Colwell RR, Hofle MG, Pruzzo C (2012) Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios. ISME J 6:21–30

    Article  PubMed  Google Scholar 

  • Wasmund K, Kurtboke DI, Burns KA, Bourne DG (2009) Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity. FEMS Microbiol Ecol 68:142–151

    Article  CAS  PubMed  Google Scholar 

  • Wenzhofer F, Holby O, Kohls O (2001) Deep penetrating benthic oxygen profiles measured in situ by oxygen optodes. Deep-Sea Res Part I-Oceanogr Res Pap 48:1741–1755

    Article  CAS  Google Scholar 

  • Widdel F, Musat F, Knittel K, Galushko A (2007) Anaerobic degradation of hydrocarbons with sulphate as electron acceptor. In: Barton LL, Hamilton WA (eds) Sulphate-reducing bacteria: environmental and engineered systems. Cambridge University Press, Cambridge, UK

    Google Scholar 

  • Wilkins D, Lauro FM, Williams TJ, Demaere MZ, Brown MV, Hoffman JM, Andrews-Pfannkoch C, McQuaid JB, Riddle MJ, Rintoul SR, Cavicchioli R (2013) Biogeographic partitioning of Southern Ocean microorganisms revealed by metagenomics. Environ Microbiol 15:1318–1333

    Article  CAS  PubMed  Google Scholar 

  • Youssef M, El-Taweel G, El-Naggar A, El-Hawary SE, El-Meleigy M, Ahmed S (2010) Hydrocarbon degrading bacteria as indicator of petroleum pollution in Ismailia Canal, Egypt. World Appl Sci J 8:1226–1233

    CAS  Google Scholar 

  • Zrafi-Nouira I, Guermazi S, Chouari R, Safi NMD, Pelletier E, Bakhrouf A, Saidane-Mosbahi D, Sghir A (2009) Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil. Biodegradation 20:467–486

    Article  CAS  PubMed  Google Scholar 

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Hazen, T.C., Techtmann, S.M. (2018). Oil Biodegradation in Deep Marine Basins. In: Steffan, R. (eds) Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-44535-9_22-1

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