Marine crude-oil biodegradation: a central role for interspecies interactions

Aquatic Biosystems

Terry J McGenity¹  Benjamin D Folwell¹  Boyd A McKew¹  Gbemisola O Sanni¹ 

[1] School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK

关键词: Alcanivorax;    Biogeochemistry;    Microbial interactions;    Bioremediation;    Biodegradation;    Marine microbiology;    Salt marsh;    Crude oil;    Hydrocarbon;   

Others  :  794659
DOI  :  10.1186/2046-9063-8-10

 received in 2012-02-06, accepted in 2012-04-25,  发布年份 2012

【 摘 要 】

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.

【 授权许可】

   
2012 McGenity et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Halpern BS, Walbridge S, Selkoe KA, Kappel CV, Micheli F, D'agrosa C, Bruno JF, Casey KS, Ebert C, Fox HE, Fujita R, Heinemann D, Lenihan HS, Madin EM, Perry MT, Selig ER, Spalding M, Steneck R, Watson R: A global map of human impact on marine ecosystems. Science 2008, 319:948-952.
• [2]National Research Council (NRC): Oil in the Sea III: Inputs, Fates, and Effects. National Academy Press, Washington, D.C; 2003.
• [3]Crone TJ, Tolstoy M: Magnitude of the 2010 Gulf of Mexico oil leak. Science 2010, 330:634.
• [4]ITOPF: Oil Tanker Spill Statistics: 2005. The International Tanker Owners Pollution Federation Ltd, London; 2006.
• [5]de la Huz R, Lastra M, Junoy J, Castellanos C, Vieitez JM: Biological impacts of oil pollution and cleaning in the intertidal zone of exposed sandy beaches: Preliminary study of the ''Prestige'' oil spill. Estuarine Coastal Shelf Sci 2005, 65:19-29.
• [6]Mason C: Biology of Freshwater Pollution. Prentice Hall, Essex; 2002.
• [7]Carls MG, Rice SD, Hose JE: Sensitivity of fish embryos to weathered crude oil: I. Low level exposure during incubation causes malformations, genetic damage, and mortality in larval Pacific herring (Clupea pallasi). Environ Toxicol Chem 1999, 18:481-493.
• [8]Heintz RA: Chronic exposure to polynuclear aromatic hydrocarbons in natal habitats leads to decreased equilibrium size, growth, and stability of pink salmon populations. Integr Environ Assess Manag 2007, 3:351-363.
• [9]Davies JM, Addy JM, Blackman RA, Blanchard JR, Ferbrache JE, Moore DC, Somerville HJ, Whitehead A, Wilkinson T: Environmental effects of the use of oil-based drilling muds in the North Sea. Mar Pollut Bull 1984, 15:363-370.
• [10]Venosa AD, Campo P, Suidan MT: Biodegradability of lingering crude oil 19 years after the Exxon Valdez oil spill. Environ Sci Technol 2010, 44:7613-7621.
• [11]Marshall AG, Rodgers RP: Petroleomics: the next grand challenge for chemical analysis. Accounts of Chemical Research 2004, 37:53-59.
• [12]Harayama S, Kishira H, Kasai Y, Shutsubo K: Petroleum biodegradation in marine environments. J Mol Microbiol Biotechnol 1999, 1:63-70.
• [13]van Hamme JD, Singh A, Ward OP: Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 2003, 67:503-549.
• [14]Suess E: Marine cold seeps. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:187-203.
• [15]Prince RC, Gramain A, McGenity TJ: Prokaryotic hydrocarbon degraders. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:1671-1692.
• [16]Al-Mailem DM, Sorkhoh NA, Al-Awadhi H, Eliyas M, Radwan SS: Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles 2010, 14:321-328.
• [17]Prince RC: Eukaryotic hydrocarbon degraders. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:2065-2078.
• [18]Pérez-Pantoja D, González B, Pieper DH: Aerobic degradation of aromatic hydrocarbons. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:799-837.
• [19]Fuchs G, Boll M, Heider J: Microbial degradation of aromatic compounds - from one strategy to four. Nat Rev Microbiol 2011, 9:803-816.
• [20]Rojo F: Degradation of alkanes by bacteria. Environ Microbiol 2009, 11:2477-2490.
• [21]Kanaly RA, Harayama S: Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria. Microb Biotechnol 2010, 3:136-164.
• [22]Widdel F, Grundmann O: Biochemistry of the anaerobic degradation of non-methane alkanes. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:909-924.
• [23]Tierney M, Young LY: Anaerobic degradation of aromatic hydrocarbons. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:925-934.
• [24]Vogt C, Kleinsteuber S, Richnow H-H: Anaerobic benzene degradation by bacteria. Microb Biotechnol 2011, 4:710-724.
• [25]Zedelius J, Rabus R, Grundmann O, Werner I, Brodkorb D, Schreiber F, Ehrenreich P, Behrends A, Wilkes H, Kube M, Reinhardt R, Widdel F: Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation. Environmental Microbiology Reports 2011, 3:125-135.
• [26]Harayama S, Kasai Y, Hara A: Microbial communities in oil-contaminated seawater. Curr Opin Biotechnol 2004, 15:205-214.
• [27]Head IM, Jones DM, Röling WFM: Marine microorganisms make a meal of oil. Nat Rev Microbiol 2006, 4:173-182.
• [28]Yakimov MM, Timmis KN, Golyshin PN: Obligate oil-degrading marine bacteria. Curr Opin Biotechnol 2007, 18:257-266.
• [29]Coulon F, McKew BA, Osborn AM, McGenity TJ, Timmis KN: Effects of temperature and biostimulation on oil-degrading microbial communities in temperate estuarine waters. Environ Microbiol 2007, 9:177-186.
• [30]McKew BA, Coulon F, Yakimov MM, Denaro R, Genovese M, Smith CJ, Osborn AM, Timmis KN, McGenity TJ: Efficacy of intervention strategies for bioremediation of crude oil in marine systems and effects on indigenous hydrocarbonoclastic bacteria. Environ Microbiol 2007, 9:1562-1571.
• [31]Teramoto M, Suzuki M, Okazaki F, Hatmanti A, Harayama S: Oceanobacter-related bacteria are important for the degradation of petroleum aliphatic hydrocarbons in the tropical marine environment. Microbiology 2009, 155:3362-3370.
• [32]Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, Canion A, Delgardio J, Norton N, Hazen TC, Huettel M: Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill. Appl Environ Microbiol 2011, 77:7962-7974.
• [33]Teira E, Lekunberri I, Gasol JM, Nieto-Cid M, Alvarez-Salgado XA, Figueiras FG: Dynamics of the hydrocarbon-degrading Cycloclasticus bacteria during mesocosmsimulated oil spills. Environ Microbiol 2007, 9:2551-2562.
• [34]McKew BA, Coulon F, Osborn AM, Timmis KN, McGenity TJ: Determining the identity and roles of oil-metabolizing marine bacteria from the Thames estuary, UK. Environ Microbiol 2007, 9:165-176.
• [35]Cui ZS, Lai QL, Dong CM, Shao ZZ: Biodiversity of polycyclic aromatic hydrocarbon-degrading bacteria from deep sea sediments of the Middle Atlantic Ridge. Environ Microbiol 2008, 10:2138-2149.
• [36]Niepceron M, Portet-Koltalo F, Merlin C, Motelay-Massei A, Barray S, Bodilis J: Both Cycloclasticus spp. and Pseudomonas spp. as PAH-degrading bacteria in the Seine estuary (France). FEMS Microbiol Ecol 2010, 71:137-147.
• [37]Yakimov MM, Golyshin PN, Lang S, Moore ERB, Abraham WR, Lunsdorf H, Timmis KN: Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int J Syst Bacteriol 1998, 48:339-348.
• [38]Schneiker SVA, dos Santos PM, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN: Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 2006, 24:997-1004.
• [39]Sabirova JS, Ferrer M, Regenhardt D, Timmis KN, Golyshin PN: Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization. J Bacteriol 2006, 188:3763-3773.
• [40]Sabirova JS, Chernikova TN, Timmis KN, Golyshin PN: Niche-specificity factors of a marine oil-degrading bacterium Alcanivorax borkumensis SK2. FEMS Microbiol Lett 2008, 285:89-96.
• [41]Ron E, Rosenberg E: Acinetobacter and Alkanindiges. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:1800-1803.
• [42]van Beilen JB, Funhoff EG: Alkane hydroxylases involved in microbial alkane degradation. Appl Microbiol Biotechnol 2007, 74:13-21.
• [43]Throne-Holst M, Wentzel A, Ellingsen TE, Kotlar HK, Zotchev SB: Identification of novel genes involved in long-chain n-alkane degradation by Acinetobacter sp. strain DSM 17874. Appl Environ Microbiol 2007, 73:3327-3332.
• [44]Liu CL, Wang WP, Wu YH, Zhou ZW, Lai QL, Shao ZZ: Multiple alkane hydroxylase systems in a marine alkane degrader, Alcanivorax dieselolei B-5. Environ Microbiol 2011, 13:1168-1178.
• [45]Wasmund K, Burns KA, Kurtboke DI, Bourne DG: Novel alkane hydroxylase gene (alkB) diversity in sediments associated with hydrocarbon seeps in the Timor Sea, Australia. Appl Environ Microbiol 2009, 75:7391-7398.
• [46]Wang W-P, Wang L-P, Shao Z: Diversity and abundance of oil-degrading bacteria and alkane hydroxylase (alkB) genes in the subtropical seawater of Xiamen Island. Microb Ecol 2010, 60:429-439.
• [47]Païssé S, Duran R, Coulon F, Goñi-Urriza M: Are alkane hydroxylase genes (alkB) relevant to assess petroleum bioremediation processes in chronically polluted coastal sediments? Appl Microbiol Biotechnol 2011, 92:835-844.
• [48]Golyshin PN, Ferrer M, Chernikova TN, Golyshina OV, Yakimov MM: Oleispira. In In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:1755-1763.
• [49]Teramoto M, Ohuchi M, Hatmanti A, Darmayati Y, Widyastuti Y, Harayama S, Fukunaga Y: Oleibacter marinus gen. nov., sp. nov., a bacterium that degrades petroleum aliphatic hydrocarbons in a tropical marine environment. Int J Syst Evol Microbiol 2011, 61:375-380.
• [50]Golyshin PN, Chernikova TN, Abraham WR, Lunsdorf H, Timmis KN, Yakimov MM: Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int J Syst Evol Microbiol 2002, 52:901-911.
• [51]Lanfranconi MP, Bosch R, Nogales B: Short-term changes in the composition of active marine bacterial assemblages in response to diesel oil pollution. Microb Biotechnol 2010, 3:607-621.
• [52]Coulon F, Chronoupolou P-M, Fahy A, Païssé S, Goñi-Urriza MS, Peperzak L, Acuña-Alvarez L, McKew BA, Brussard C, Underwood GJC, Timmis KN, Duran R, McGenity TJ: Central role of dynamic tidal biofilms dominated by aerobic hydrocarbonoclastic bacteria and diatoms in the biodegradation of hydrocarbons in coastal mudflats. Appl Environ Microbiol 2012, 78:3638-3648.
• [53]Buchanan A, Gonzalez JM: Roseobacter. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:1336-1343.
• [54]Gerdes B, Brinkmeyer R, Dieckmann G, Helmke E: Influence of crude oil on changes in bacterial communities in Arctic sea-ice. FEMS Microbiol Ecol 2005, 53:129-139.
• [55]Yu SH, Ke L, Wong YS, Ta NFY: Degradation of polycyclic aromatic hydrocarbons by a bacterial consortium enriched from mangrove sediments. Environ Int 2005, 31:149-154.
• [56]Duran R: Marinobacter. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:1725-1735.
• [57]Vila J, Nieto JM, Mertens J, Springael D, Grifoll M: Microbial community structure of a heavy fuel oil-degrading marine consortium: linking microbial dynamics with polycyclic aromatic hydrocarbon utilization. FEMS Microbiol Ecol 2010, 73:349-362.
• [58]Melcher RJ, Apitz SE, Hemmingsen BB: Impact of irradiation and polycyclic aromatic hydrocarbon spiking on microbial populations in marine sediment for future aging and biodegradability studies. Appl Environ Microbiol 2002, 68:2858-2868.
• [59]Gutierrez T, Nichols PD, Whitman WB, Aitken MD: Porticoccus hydrocarbonoclasticus sp. nov., an aromatic hydrocarbon-degrading bacterium identified in laboratory cultures of marine phytoplankton. Appl Environ Microbiol 2012, 78:628-637.
• [60]Gauthier E, Déziel E, Villemur R, Juteau P, Lépine F, Beaudet R: Initial characterization of new bacteria degrading high-molecular weight polycyclic aromatic hydrocarbons isolated from a 2-year enrichment in a two-liquid-phase culture system. J Appl Microbiol 2003, 94:301-311.
• [61]Hilyard EJ, Jones-Meehan JM, Spargo BJ, Hill RT: Enrichment, isolation and phylogenetic identification of polycyclic aromatic hydrocarbon-degrading bacteria from Elizabeth River sediments. Appl Environ Microbiol 2008, 74:1176-1182.
• [62]Edlund A, Jansson JK: Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phananthrene-enriched polluted Baltic Sea sediments. FEMS Microbiol Ecol 2008, 65:513-525.
• [63]Gutierrez T, Singleton DR, Aitken MD, Semple KT: Stable isotope probing of an algal bloom to identify uncultivated members of the Rhodobacteraceae associated with low-molecular-weight polycyclic aromatic hydrocarbon degradation. Appl Environ Microbiol 2011, 77:7856-7860.
• [64]Kaeberlein T, Lewis K, Epstein SS: Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 2002, 296:1127-1129.
• [65]McGenity TJ, Gramain A: Cutivation of halophilic hydrocarbon degraders. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:3847-3854.
• [66]Calvo C, Martínez-Checa F, Toledo FL, Porcel J, Quesada E: Characteristics of bioemulsifiers synthesized in crude oil media by Halomonas eurihalina and their effectiveness in the isolation of bacteria able to grow in the presence of hydrocarbons. Appl Microbiol Biotechnol 2002, 60:347-351.
• [67]Zubkov MV, Mary I, Woodward EMS, Warwick PE, Fuchs BM, Scanlan DJ, Burkill PH: Microbial control of phosphate in the nutrient-depleted North Atlantic subtropical gyre. Environ Microbiol 2007, 9:2079-2089.
• [68]Suttle CA: Marine viruses - major players in the global ecosystem. Nat Rev Microbiol 2007, 5:801-812.
• [69]Grossart HP: Ecological consequences of bacterioplankton lifestyles: changes in concepts are needed. Environmental Microbiology Reports 2010, 2:706-714.
• [70]Fuhrman JA: Microbial community structure and its functional implications. Nature 2009, 459:193-199.
• [71]Azam F, Malfatti F: Microbial structuring of marine ecosystems. Nat Rev Microbiol 2007, 5:782-791.
• [72]Grossart HP, Levold F, Allgaier M, Simon M, Brinkhoff T: Marine diatom species harbour distinct bacterial communities. Environ Microbiol 2005, 7:860-873.
• [73]Carman KR, Dobbs FC: Epibiotic microorganisms on copepods and other aquatic crustaceans. Microscope Research Technique 1997, 37:116-135.
• [74]Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Welch DB, Martiny JB, Sogin M, Boetius A, Ramette A: Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS One 2011, 6:e24570.
• [75]Duran R, Goñi-Urriza MS: Impact of pollution on microbial mats. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:2339-2348.
• [76]Shank EA, Kolter R: New developments in microbial interspecies signaling. Curr Opin Microbiol 2009, 12:205-214.
• [77]Mashburn-Warren LM, Whiteley M: Special delivery: vesicle trafficking in prokaryotes. Mol Microbiol 2006, 61:839-846.
• [78]Dubey GP, Ben-Yehuda S: Intercellular nanotubes mediate bacterial communication. Cell 2011, 144:590-600.
• [79]Diggle SP: Microbial communication and virulence: lessons from evolutionary theory. Microbiology 2010, 156:3503-3512.
• [80]Yakimov MM, Denaro R, Genovese M, Cappello S, D’Auria G, Chernikova TN, Timmis KN, Golyshin PN, Giuliano L: Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. Environ Microbiol 2005, 7:1426-1441.
• [81]Kanoh K, Adachi K, Katsuta A, Shizuri Y: Structural determination and proposed biosynthesis of alcanivorone, a novel alpha-pyrone produced by Alcanivorax jadensis. Journal of Antibiotics (Tokyo) 2008, 61:70-74.
• [82]Hara A, Syutsubo K, Harayama S: Alcanivorax which prevails in oil-contaminated seawater exhibits broad substrate specificity for alkane degradation. Environ Microbiol 2003, 5:746-753.
• [83]Wang BJ, Lai QL, Cui ZS, Tan TF, Shao ZZ: A pyrene-degrading consortium from deep-sea sediment of the West Pacific and its key member Cycloclasticus sp P1. Environ Microbiol 2008, 10:1948-1963.
• [84]Luo YR, Tian Y, Huang X, Yan CL, Hong HS, Lin GH, Zheng TL: Analysis of community structure of a microbial consortium capable of degrading benzo[a]pyrene by DGGE. Mar Pollut Bull 2009, 58:1159-1163.
• [85]de Lorenzo V: Systems biology approaches to bioremediation. Curr Opin Biotechnol 2008, 19:579-89.
• [86]de Lorenzo V, Fraile S, Jiménez JI: Emerging systems and synthetic biology approaches to hydrocarbon biotechnology. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:1411-1435.
• [87]Pelz O, Tesar M, Wittich RM, Moore ERB, Timmis KN, Abraham WR: Towards elucidation of microbial community metabolic pathways: unravelling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry. Environ Microbiol 1999, 1:167-174.
• [88]López Z, Vila J, Ortega-Calvo JJ, Grifoll M: Simultaneous biodegradation of creosote-polycyclic aromatic hydrocarbons by a pyrene-degrading Mycobacterium. Appl Microbiol Biotechnol 2008, 78:165-172.
• [89]Wintermute EH, Silver PA: Emergent cooperation in microbial metabolism. Mol Syst Biol 2010, 6:407.
• [90]Bobadilla Fazzini RAB, Preto MJ, Quintas ACP, Bielecka A, Timmis KN, dos Santos VAPM: Consortia modulation of the stress response: proteomic analysis of single strain versus mixed culture. Environ Microbiol 2010, 12:2436-2449.
• [91]Cerniglia CE, Sutherland JB: Degradation of polycyclic aromatic hydrocarbons by fungi. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:2080-2110.
• [92]Chen SH, Aitken MD: Salicylate stimulates the degradation of high molecular weight polycyclic aromatic hydrocarbons by Pseudomonas saccharophila P15. Environ Sci Technol 1999, 33:435-439.
• [93]da Silva M, Esposito E, Joanna D, Canhos V, Cerniglia C: Metabolism of aromatic hydrocarbons by the filamentous fungus Cyclothyrium sp. Chemosphere 2004, 57:943-952.
• [94]Prenafeta-Boldú FX, Summerbell R, de Hoog GS: Fungi growing on aromatic hydrocarbons: biotechnology's unexpected encounter with biohazard? FEMS Microbiol Rev 2006, 30:109-130.
• [95]Harms H, Schlosser D, Wick LY: Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nat Rev Microbiol 2011, 9:177-192.
• [96]Johnsen A, Wick L, Harms H: Principles of microbial PAH-degradation in soil. Environ Pollut 2005, 133:71-84.
• [97]Kotterman M, Vis E, Field J: Successive mineralization and detoxification of benzo[a]pyrene by the white rot fungus Bjerkandera sp. strain BOS55 and indigenous microflora. Appl Environ Microbiol 1998, 64:2853-2858.
• [98]Boonchan S, Britz ML, Stanley GA: Degradation and mineralization of high-molecular-weight polycyclic aromatic hydrocarbons by defined fungal-bacterial cocultures. Appl Environ Microbiol 2000, 66:1007-1019.
• [99]Haritash AK, Kaushik CP: Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): A review. J Hazard Mater 2009, 169:1-15.
• [100]Kazunga C, Aitken M: Products from the incomplete metabolism of pyrene by polycyclic aromatic hydrocarbon-degrading bacteria. Appl Environ Microbiol 2000, 66:4598-4598.
• [101]Allen MA, Goh F, Burns BP, Neilan BA: Bacterial, archaeal and eukaryotic diversity of smooth and pustular microbial mat communities in the hypersaline lagoon of Shark Bay. Geobiology 2009, 7:82-96.
• [102]Valentin L, Feijoo G, Moreira MT, Lema JM: Biodegradationof polycyclic aromatic hydrocarbon in forest and salt marsh soils by white rot fungi. IntBiodeter Biodegr 2006, 58:15-21.
• [103]Frey-Klett P, Burlinson P, Deveau A, Barret M, Tarkka M, Sarniguet A: Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists. Microbiol Mol Biol Rev 2011, 75:583-609.
• [104]Furuno S, Pazolt K, Rabe C, Neu TR, Harms H, Wick LY: Fungal mycelia allow chemotactic dispersal of polycyclic aromatic hydrocarbon-degrading bacteria in water-unsaturated systems. Environ Microbiol 2010, 12:1391-1398.
• [105]Woolgar PJ, Jones KC: Studies on the dissolution of polycyclic aromatic hydrocarbons from contaminated materials using a novel dialysis tubing experimental method. Environ Sci Technol 1999, 33:2118-2126.
• [106]Semple KT, Doick CJ, Wick LY, Harms H: Microbial interactions with organic contaminants in soil: Definitions, processes and measurement. Environ Pollut 2007, 150:166-176.
• [107]Bastiaens L, Springael D, Wattiau P, Harms H, de Wachter R, Verachtert H, Diels L: Isolation of adherent polycyclic aromatic hydrocarbon (PAH)-degrading bacteria using PAH-sorbing carriers. Appl Environ Microbiol 2000, 66:1834-1843.
• [108]Harms H, Smith KEC, Wick LY: Microorganism-hydrophobic compound interactions. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:1479-1490.
• [109]Guerin WF, Boyd SA: Differential bioavailability of soil-sorbed naphthalene to two bacterial species. Appl Environ Microbiol 1992, 58:1142-1152.
• [110]Wick LY, Wattiau P, Harms H: Influence of the growth substrate on the mycolic acid profiles of mycobacteria. Environ Microbiol 2002, 4:612-616.
• [111]Rodrigues AC, Wuertz S, Brito AG, Melo LF: Fluorene and phenanthrene uptake by Pseudomonas putida ATCC 17514: Kinetics and physiological aspects. Biotechnol Bioeng 2005, 90:281-289.
• [112]Vaysse PJ, Sivadon P, Goulas P, Grimaud R: Cells dispersed from Marinobacter hydrocarbonoclasticus SP17 biofilm exhibit a specific protein profile associated with a higher ability to reinitiate biofilm development at the hexadecane-water interface. Environ Microbiol 2011, 13:737-746.
• [113]Wouters K, Maes E, Spitz J-A, Roeffaers MBJ, Wattiau P, Hofkens J, Springael D: A non-invasive fluorescent staining procedure allows Confocal Laser Scanning Microscopy based imaging of Mycobacterium in multispecies biofilms colonizing and degrading Polycyclic Aromatic Hydrocarbons. J Microbiol Methods 2010, 83:317-325.
• [114]Pacwa-Plociniczak M, Plaza GA, Piotrowska-Seget Z, Cameotra SS: Environmental applications of biosurfactants: recent advances. Int J Mol Sci 2011, 12:633-654.
• [115]Perfumo A, Smyth TJP, Marchant R, Banat IM: Production and roles of biosurfactants and bioemulsifiers in accessing hydrophobic substrates. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:1501-1512.
• [116]Kanaly RA, Harayama S, Watanabe K: Rhodanobacter sp. strain BPC1 in a benzo[a]pyrene-mineralizing microbial consortium. Appl Environ Microbiol 2002, 68:5826-5833.
• [117]Iwabuchi N, Sunairi M, Urai M, Itoh C, Anzai H, Nakajima M, Harayama S: Extracellular polysaccharides of Rhodococcus rhodochrous S-2 stimulate the degradation of aromatic components in crude oil by indigenous marine bacteria. Appl Environ Microbiol 2002, 68:2337-2343.
• [118]Abalos A, Viñas M, Sabaté J, Manresa MA, Solanas AM: Enhanced biodegradation of Casablanca crude oil by a microbial consortium in presence of a rhamnolipid produced by Pseudomonas aeruginosa AT10. Biodegradation 2004, 15:249-260.
• [119]Shin KH, Ahn Y, Kim KW: Toxic effect of biosurfactant addition on the biodegradation of phenanthrene. Environ Toxicol Chem 2005, 24:2768-2774.
• [120]Rambeloarisoa E, Rontani JF, Giusti G, Duvnjak Z, Bertrand JC: Degradation of crude oil by a mixed population of bacteria isolated from sea-surface foams. Mar Biol 1984, 83:69-81.
• [121]Chaerun SK, Tazaki K, Asada R, Kogure K: Interaction between clay minerals and hydrocarbon-utilizing indigenous microorganisms in high concentrations of heavy oil: implications for bioremediation. Clay Minerals 2005, 40:105-114.
• [122]Vacca DJ, Bleam WF, Hickey WJ: Isolation of soil bacteria adapted to degrade humic acid-sorbed phenanthrene. Appl Environ Microbiol 2005, 71:3797-3805.
• [123]Shin WS, Pardue JH, Jackson WA: Oxygen demand and sulfate reduction in petroleum hydrocarbon contaminated salt marsh soils. Water Res 2000, 34:1345-1353.
• [124]Widdel F, Knittel K, Galushko A: Anaerobic hydrocarbon-degrading microorganisms: an overview. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:1997-2021.
• [125]Gray ND, Sherry A, Grant RJ, Rowan AK, Hubert CRJ, Callbeck CM, Aitken CM, Jones DM, Adams JJ, Larter SR, Head IM: The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes. Environ Microbiol 2011, 13:2957-2975.
• [126]Zengler K, Richnow H, Rosselló-Mora R, Michaelis W, Widdel F: Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 1999, 401:266-269.
• [127]Walker CB, He Z, Yang ZK, Ringbauer JA, He Q, Zhou J, Voordouw G, Wall JD, Arkin AP, Hazen TC, Stolyar S, Stahl DA: The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol 2009, 191:5793-5801.
• [128]Ficker M, Krastel K, Orlicky S, Edwards E: Molecular characterization of a toluene-degrading methanogenic consortium. Appl Environ Microbiol 1999, 65:5576-5585.
• [129]McInerney MJ, Sieber JR, Gunsalus RP: Syntrophy in anaerobic global carbon cycles. Curr Opin Biotechnol 2009, 20:623-632.
• [130]Yerushalmi L, Lascourreges JF, Rhofir C, Guiot SR: Detection of intermediate metabolites of benzene biodegradation under microaerophilic conditions. Biodegradation 2001, 12:379-391.
• [131]Wimpenny JWT, Abdollahi H: Growth of mixed cultures of Paracoccus denitrificans and Desulfovibrio desulfuricans in homogeneous and in heterogeneous culture systems. Microb Ecol 1991, 22:1-13.
• [132]Gerritse J, Gottschal JC: Two-membered mixed cultures of methanogenic and aerobic bacteria in O2-limited chemostats. J Gen Microbiol 1993, 139:1853-1860.
• [133]Aburto A, Fahy A, Coulon F, Lethbridge G, Timmis KN, Ball AS, McGenity TJ: Mixed aerobic and anaerobic microbial communities in benzene-contaminated groundwaters. J Appl Microbiol 2009, 16:317-328.
• [134]Chayabutra C, Ju L-K: Degradation of n-hexadecane and its metabolites by Pseudomonas aeruginosa under microaerobic and anaerobic denitrifying conditions. Appl Environ Microbiol 2000, 66:493-498.
• [135]Vitte I, Duran R, Jézéquel R, Caumette P, Cravo-Laureau C: Effect of oxic/anoxic switches on bacterial communities and PAH biodegradation in an oil-contaminated sludge. Environ Sci Pollut Res 2011, 18:1022-1032.
• [136]Rocchetti L, Beolchini F, Ciani M, Dell'Anno A: Improvement of bioremediation performance for the degradation of petroleum hydrocarbons in contaminated sediments. Appl Environm Soil Sci 2011, 2011:319657.
• [137]Cravo-Laureau C, Hernandez-Raquet G, Vitte I, Jézéquel R, Bellet V, Godon J-J, Caumette P, Balaguer P, Duran R: Role of environmental fluctuations and microbial diversity in degradation of hydrocarbons in contaminated sludge. Res Microbiol 2011, 162:888-895.
• [138]Field CB, Behrenfeld MJ, Randerson JT, Falkowski P: Primary production of the biosphere: Integrating terrestrial and oceanic components. Science 1998, 281:237-240.
• [139]Biegala IC, Kennaway G, Alverca E, Lennon JF, Vaulot D, Simon N: Identification of bacteria associated with dinoflagellates (Dinophyceae) Alexandrium spp. using tyramide signal amplification-fluorescent in situ hybridization and confocal microscopy. J Phycol 2002, 38:404-411.
• [140]Armbrust EV: The life of diatoms in the world's oceans. Nature 2009, 459:185-192.
• [141]Crump BC, Armbrust EV, Baross JA: Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean. Appl Environ Microbiol 1999, 65:3192-3204.
• [142]Cottrell M, Kirchman D: Natural assemblages of marine proteobacteria and membersof the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl Environ Microbiol 2000, 66:1692-1697.
• [143]Allgaier M, Riebesell U, Vogt M, Thyrhaug R, Grossart HP: Coupling of heterotrophic bacteria to phytoplankton bloom development at different pCO2 levels: a mesocosm study. Biogeosciences 2008, 5:1007-1022.
• [144]Jasti S, Sieracki ME, Poulton NJ, Giewat MW, Rooney-Varga JN: Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton. Appl Environ Microbiol 2005, 71:3483-3494.
• [145]Sapp M, Schwaderer AS, Wiltshire KH, Hoppe HG, Gerdts G, Wichels A: Species-specific bacterial communities in the phycosphere of microalgae? Microb Ecol 2007, 53:683-699.
• [146]Hube AE, Heyduck-Söller B, Fischer U: Phylogenetic classification of heterotrophic bacteria associated with filamentous marine cyanobacteria in culture. Syst Appl Microbiol 2009, 32:256-265.
• [147]Cole JJ: Interactions between bacteria and algae in aquatic ecosystems. Annu Rev Ecol Evol Syst 1982, 13:291-314.
• [148]Rivas MO, Vargas P, Riquelme CE: Interactions of Botryococcus braunii cultures with bacterial biofilms. Microb Ecol 2010, 60:628-635.
• [149]Bell WH, Lang JM, Mitchell R: Selective stimulation of marine bacteria by algal extracellular products. Limnol Oceanogr 1974, 19:833-839.
• [150]Amin SA, Green DH, Hart MC, Küpper FC, Sunda WG, Carrano CJ: Photolysis of iron-siderophore chelates promotes bacterial-algal mutualism. Proc Natl Acad Sci U S A 2009, 106:17071-17076.
• [151]Hopkinson BM, Roe K, Barbeau KA: Heme uptake by Microscilla marina and evidence for heme uptake systems in the genomes of diverse marine bacteria. Appl Environ Microbiol 2008, 74:6263-6270.
• [152]Croft MT, Lawrence AD, Raux-Deery E, Warren MJ, Smith AG: Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 2005, 438:90-93.
• [153]Mouget JL, Dakhama A, Lavoie MC, Delanoue J: Algal growth enhancement by bacteria - is consumption of photosynthetic oxygen involved. FEMS Microbiol Ecol 1995, 18:35-43.
• [154]Huenken M, Harder J, Kirst GO: Epiphytic bacteria on the Antarctic ice diatom Amphiprora kufferathii Manguin cleave hydrogen peroxide produced during algal photosynthesis. Plant Biology 2008, 10:519-526.
• [155]Villareal TA: Laboratory culture and preliminary characterization of the nitrogen-fixing Rhizosolenia-Richelia symbiosis. Mar Ecol 1990, 11:117-132.
• [156]Kneip C, Lockhart P, Voß CMaier U-G: Nitrogen fixation in eukaryotes - new models for symbiosis. BMC Evol Biol 2007, 7:55. BioMed Central Full Text
• [157]Moisander PH, Beinart RA, Voss M, Zehr JP: Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon. ISME J 2008, 2:954-967.
• [158]Matsuo Y, Imagawa H, Nishizawa M, Shizuri Y: Isolation of an algal morphogenesis inducer from a marine bacterium. Science 2005, 307:1598.
• [159]Bruckner CG, Bahulikar R, Rahalkar M, Schink B, Kroth PG: Bacteria associated with benthic diatoms from Lake Constance: phylogeny and influences on diatom growth and secretion of extracellular polymeric substances. Appl Environ Microbiol 2008, 74:7740-7749.
• [160]Gärdes A, Iversen MH, Grossart HP, Passow U, Ullrich MS: Diatom-associated bacteria are required for aggregation of Thalassiosira weissflogii. ISME J 2011, 5:436-445.
• [161]Bolch CJS, Subramanian TA, Green DH: The toxic dinoflagellate Gymnodinium catenatum (dinophyceae) requires marine bacteria for growth. J Phycol 2011, 47:1009-1022.
• [162]Bruckner CG, Rehm C, Grossart HP, Kroth PG: Growth and release of extracellular organic compounds by benthic diatoms depend on interactions with bacteria. Environ Microbiol 2011, 13:1052-1063.
• [163]Kujawinski EB: The impact of microbial metabolism on marine dissolved organic matter. Annu Rev Marine Sci 2011, 3:567-599.
• [164]González J, Figueiras FG, Aranguren-Gassis M, Crespo BG, Fernández E, Morán XAG, Nieto-Cid M: Effect of a simulated oil spill on natural assemblages of marine phytoplankton enclosed in microcosms. Estuar Coastal Shelf Sci 2009, 83:265-276.
• [165]Al-Hasan RH, Khanafer M, Eliyas M, Radwan SS: Hydrocarbon accumulation by picocyanobacteria from the Arabian Gulf. J Appl Microbiol 2001, 91:533-540.
• [166]Benthien M, Wieland A, de Oteyza T, Grimalt J, Kühl M: Oil-contamination effects on a hypersaline microbial mat community (Camargue, France) as studied with microsensors and geochemical analysis. Ophelia 2004, 58:135-150.
• [167]Abed RM, Al-Thukair A, de Beer D: Bacterial diversity of a cyanobacterial mat degrading petroleum compounds at elevated salinities and temperatures. FEMS Microbiol Ecol 2006, 57:290-301.
• [168]Cohen Y: Bioremediation of oil by marine microbial mats. Int Microbiol 2002, 5:189-193.
• [169]van Bleijswijk J, Muyzer G: Genetic diversity of oxygenic phototrophs in microbial mats exposed to different levels of oil pollution. Ophelia 2004, 58:157-164.
• [170]Païssé S, Coulon F, Goñi-Urriza M, Peperzak L, McGenity TJ, Duran R: Structure of bacterial communities along a hydrocarbon contamination gradient in a coastal sediment. FEMS Microbiol Ecol 2008, 66:295-305.
• [171]Cerniglia CE, Van Baalen C, Gibson DT: Metabolism of naphthalene by the cyanobacterium Oscillatoria sp., strain JCM. J Gen Microbiol 1980, 116:485-594.
• [172]Cerniglia CE, Gibson DT, Van Baalen C: Oxidation of naphthalene by cyanobacteria and microalgae. J Gen Microbiol 1980, 116:495-500.
• [173]Semple KT, Cain RB, Schmidt S: Biodegradation of aromatic compounds by microalgae. FEMS Microbiol Lett 1999, 170:291-300.
• [174]Todd SJ, Cain RB, Schmidt S: Biotransformation of naphthalene and diaryl ethers by green microalgae. Biodegradation 2002, 13:229-238.
• [175]Al-Hasan RH, Sorkhoh NA, Al Bader D, Radwan SS: Utilization of hydrocarbons by cyanobacteria from microbial mats on oily coasts of the Gulf. Appl Microbiol Biotechnol 1994, 41:615-619.
• [176]Lei AP, Wong YS, Tam NFY: Removal of pyrene by different microalgal species. Water Sci Technol 2002, 46:195-201.
• [177]Abed RMM, Köster J: The direct role of aerobic heterotrophic bacteria associated with cyanobacteria in the degradation of oil compounds. Int Biodeterior Biodegrad 2005, 55:29-37.
• [178]Raghukumar C, Vipparty V, David JJ, Chandramohan D: Degradation of crude oil by marine cyanobacteria. Appl Microbiol Biotechnol 2001, 57:433-436.
• [179]de Oteyza TG, Grimalt JO, Diestra E, Sole A, Esteve I: Changes in the composition of polar and apolar crude oil fractions under the action of Microcoleus consortia. Appl Microbiol Biotechnol 2004, 66:226-232.
• [180]Abed RMM, Safi NMD, Koster J, de Beer D, El-Nahhal Y, Rullkotter J, Garcia-Pichel F: Microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds. Appl Environ Microbiol 2002, 68:1674-1683.
• [181]Sánchez O, Diestra , Esteve I, Mas J: Molecular characterization of an oil-degrading cyanobacterial consortium. Microb Ecol 2005, 50:580-588.
• [182]Chaillan F, Gugger M, Sailot A, Coute A, Oudot J: Role of cyanobacteria in the biodegradation of crude oil by a tropical cyanobacterial mat. Chemosphere 2006, 62:1574-1582.
• [183]Ghasemi Y, Rasoul-Amini S, Fotooh-Abadi E: The biotransformation, biodegradation, and bioremediation of organic compounds by microalgae. J Phycol 2011, 47:969-980.
• [184]Chisti Y: Biodiesel from microalgae. Biotechnology Advances. 2007, 25:294-306.
• [185]Schirmer A, Rude MA, Li XZ, Popova E, del Cardayre SB: Microbial biosynthesis of alkanes. Science 2010, 329:559-562.
• [186]Shaw SL, Gantt B, Meskhidze N: Production and emissions of marine isoprene and monoterpenes: a review. Advances in Meteorology 2010.
• [187]Exton DA, Steinke M, Suggett DJ, McGenity TJ: Spatial and temporal variability of biogenic isoprene emissions from a temperate estuary. Global Biogeochem CyclesIn press
• [188]Acuña Alvarez L, Exton DA, Timmis KN, Suggett DJ, McGenity TJ: Characterization of marine isoprene-degrading communities. Environ Microbiol 2009, 11:3280-3291.
• [189]Green DH, Llewellyn LE, Negri AP, Blackburn SI, Bolch CJS: Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum. FEMS Microbiol Ecol 2004, 47:345-357.
• [190]Radwan S, Mahmoud H, Khanafer M, Al-Habib A, Al-Hasan R: Identities of epilithic hydrocarbon-utilizing diazotrophic bacteria from the Arabian Gulf coasts, and their potential for oil bioremediation without nitrogen supplementation. Microb Ecol 2010, 60:354-363.
• [191]Binark N, Guven KC, Gezgin T, Unlu S: Oil pollution of marine algae. Bull Environ Contam Toxicol 2000, 64:866-872.
• [192]Kowalewska G: Phytoplankton-the main factor responsible for transport of polynuclear aromatic hydrocarbons from water to sediments in the Southern Baltic ecosystem. ICES J Mar Sci 1999, 56:219-222.
• [193]Geng HF, Belas R: Molecular mechanisms underlying Roseobacter-phytoplankton symbioses. Curr Opin Biotechnol 2010, 21:332-338.
• [194]Abed RMM: Interaction between cyanobacteria and aerobic heterotrophic bacteria in the degradation of hydrocarbons. Int Biodeterior Biodegrad 2010, 64:58-64.
• [195]Warshawsky D, LaDow K, Schneider J: Enhanced degradation of benzo[a]pyrene by Mycobacterium sp. in conjunction with green alga. Chemosphere 2007, 69:500-506.
• [196]Tang X, He LY, Tao XQ, Dang Z, Guo CL, Lu GN, Yi XY: Construction of an artificial microalgal-bacterial consortium that efficiently degrades crude oil. J Hazard Mater 2010, 181:1158-1162.
• [197]Hofmann T, Hanlon ARM, Taylor JD, Ball AS, Osborn AM, Underwood GJC: Dynamics and compositional changes in extracellular carbohydrates in estuarine sediments during degradation. Mar Ecol Prog Ser 2009, 379:45-58.
• [198]Carmichael LM, Pfaender FK: The effect of inorganic and organic supplements on the microbial degradation of phenanthrene and pyrene in soils. Biodegradation 1997, 8:1-13.
• [199]Wick LY, Pasche N, Bernasconi SM, Pelz O, Harms H: Characterization of multiple substrate utilization by anthracene-degrading Mycobacterium frederiksbergense LB501T. Appl Environ Microbiol 2003, 69:6133-6142.
• [200]Teng Y, Luo YM, Ping LF, Zou DX, Li ZA, Christie P: Effects of soil amendment with different carbon sources and other factors on the bioremediation of an aged PAH-contaminated soil. Biodegradation 2010, 21:167-178.
• [201]Sher D, Thompson JW, Kashtan N, Croal L, Chisholm CW: Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria. ISME J 2011, 5:1125-1132.
• [202]Head IM, Swannell RP: Bioremediation of petroleum hydrocarbon contaminants in marine habitats. Curr Opin Biotechnol 1999, 10:234-239.
• [203]Knowles R, Wishart C: Nitrogen-fixation in Arctic marine sediments - effect of oil and hydrocarbon factions. Environ Pollut 1977, 13:133-149.
• [204]Musat F, Harder J, Widdel F: Study of nitrogen fixation in microbial communities of oil-contaminated marine sediment microcosms. Environ Microbiol 2006, 8:1834-1843.
• [205]Thomson AD, Webb KL: The effect of chronic oil pollution on salt-marsh nitrogen fixation (acetylene reduction). Estuaries 1984, 7:2-11.
• [206]Toccalino PL, Johnson RL, Boone DR: Nitrogen limitation and nitrogen-fixation during alkane biodegradation in a sandy soil. Appl Environ Microbiol 1993, 59:2977-2983.
• [207]Taketani RG, dos Santos HF, van Elsas JD, Rosado AS: Characterisation of the effect of a simulated hydrocarbon spill on diazotrophs in mangrove sediment mesocosm. Antonie Van Leeuwenhoek 2009, 96:343-354.
• [208]do Carmo FL, dos Santos HF, Martins EF, van Elsas JD, Rosado AS, Peixoto RS: Bacterial structure and characterization of plant growth promoting and oil degrading bacteria from the rhizospheres of mangrove plants. J Microbiol 2011, 49:535-543.
• [209]Stoeck T, Edgcomb V: Role of protists in microbial interactions with hydrocarbons. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:2423-2434.
• [210]Gertler C, Näther DJ, Gerdts G, Malpass MC, Golyshin PN: A mesocosm study of the changes in marine flagellate and ciliate communities in a crude oil bioremediation trial. Microb Ecol 2010, 60:180-191.
• [211]Dalby AP, Kormas KA, Christaki U, Karayanni H: Cosmopolitan heterotrophic microeukaryotes are active bacterial grazers in experimental oil-polluted systems. Environ Microbiol 2008, 10:47-56.
• [212]Tso SF, Taghon GL: Protozoan grazing increases mineralization of naphthalene in marine sediment. Microb Ecol 2006, 51:460-469.
• [213]Mattison RG, Harayama S: The predatory soil flagellate Heteromita globosa stimulates toluene biodegradation by a Pseudomonas sp. FEMS Microbiol Lett 2001, 194:39-45.
• [214]Rogerson A, Berger J: Enhancement of the microbial degradation of crude petroleum by the ciliate Colpidium colpoda. J Gen Appl Microbiol 1983, 29:41-50.
• [215]Näslund J, Nascimento FJA, Gunnarsson JS: Meiofauna reduces bacterial mineralization of naphthalene in marine sediment. ISME J 2010, 4:1421-1430.
• [216]Carman KR, Bianchi TS, Kloep F: Influence of grazing and nitrogen on benthic algal blooms in diesel fuel-contaminated saltmarsh sediments. Environ Sci Technol 2000, 34:107-111.
• [217]Fleeger JW, Carman KR, Nisbet RM: Indirect effects of contaminants in aquatic ecosystems. Sci Total Environ 2003, 317:207-233.
• [218]Gertler C, Gerdts G, Timmis KN, Golyshin PN: Microbial consortia in mesocosm bioremediation trial using oil sorbents, slow-release fertilizer and bioaugmentation. FEMS Microbiol Ecol 2009, 69:288-300.
• [219]Cappello S, Denaro R, Genovese M, Giuliano L, Yakimov MM: Predominant growth of Alcanivorax during experiments on “oil spill bioremediation”in mesocosms. Microbiol Res 2007, 162:185-190.
• [220]Cochran PK, Kellogg CA, Paul JH: Prophage induction of indigenous marine lysogenic bacteria by environmental pollutants. Mar Ecol Prog Ser 1998, 164:125-133.
• [221]Rosenberg E, Bittan-Banin G, Sharon G, Shon A, Hershko G, Levy I, Ron EZ: The phage- driven microbial loop in petroleum bioremediation. Microb Biotechnol 2010, 3:467-472.
• [222]Lu Z-M, Deng Y, Van Nostrand JD, He Z-L, Voordeckers J, Zhou A-F, Lee YJ, Mason OU, Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D'haeseleer P, Hazen TC, Zhou J-Z: Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J 2012, 6:451-460.
• [223]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 HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU: Deep-sea oil plume enriches indigenous oil- degrading bacteria. Science 2010, 330:204-208.
• [224]Herrick JB, Stuart-Keil KG, Ghiorse WC, Madsen EL: Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site. Appl Environ Microbiol 1997, 63:2330-2337.
• [225]Top EM, Springael D, Boon N: Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters. FEMS Microbiol Ecol 2002, 42:199-208.
• [226]Cuny P, Miralles G, Cornet-Barthaux V, Acquaviva M, Stora G, Grossi V, Gilbert F: Influence of bioturbation by the polychaete Nereis diversicolor on the structure of bacterial communities in oil contaminated coastal sediments. Mar Pollut Bull 2007, 54:452-459.
• [227]Gilbert F, Stora G, Desrosiers G, Deflandre B, Bertrand J, Poggiale J, Gagne J: Alteration and release of aliphatic compounds by the polychaete Nereis virens (Sars) experimentally fed with hydrocarbons. J Exp Mar Biol Ecol 2001, 256:199-213.
• [228]Grossi V, Massias D, Stora G, Bertrand JC: Burial, exportation and degradation of acyclic petroleum hydrocarbons following a simulated oil spill in bioturbated Mediterranean coastal sediments. Chemosphere 2002, 48:947-954.
• [229]Hickman ZA, Reid BJ: Earthworm assisted bioremediation of organic contaminants. Environ Int 2008, 34:1072-1081.
• [230]International Maritime Organization: Bioremediation in marine oil spills: guidance document for decision making and implementation of bioremediation in marine oil spills. IMO Publishing, London; 2004.
• [231]Lin Q, Mendelssohn IA: Determining tolerance limits for restoration and phytoremediation with Spartina patens in crude oil-contaminated sediment in greenhouse. Archiv Agrony Soil Sci 2008, 54:681-690.
• [232]Ramos JL, Duque E, van Dillewjin P, Daniels C, Krell T, Espinosa-Urgel M, Ramos-González M-I, Rodríguez S, Matilla M, Wittich R, Segura A: Removal of hydrocarbons and other related chemicals via the rhizosphere of plants. In Handbook of Hydrocarbon and Lipid Microbiology. Edited by Timmis KN, McGenity TJ, Meer JR, Lorenzo V. Springer, Berlin Heidelberg; 2010:2575-2581.
• [233]Gallego JLR, Garcia-Martinez MJ, Llamas JF, Belloch C, Pelaez AI, Sanchez J: Biodegradation of oil tank bottom sludge using microbial consortia. Biodegradation 2007, 18:269-281.
• [234]Jacques RJS, Okeke BC, Bento FM, Teixeira AS, Peralba MCR, Camargo FAO: Microbial consortium bioaugmentation of polycyclic aromatic hydrocarbons in contaminated soil. Bioresour Technol 2008, 99:2637-2643.
• [235]Munoz R, Guieysse B: Algal-bacterial processes for the treatment of hazardous contaminants: a review. Water Res 2006, 40:2799-2815.
• [236]Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, Wagner M: Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 2007, 9:1878-1889.
• [237]Finzi-Hart JA, Pett-Ridge J, Weber PK, Popa R, Fallon SJ, Gunderson T, Hutcheon ID, Nealson KH, Capone DG: Fixation and fate of C and N in the cyanobacterium Trichodesmium using nanometer-scale secondary ion mass spectrometry. Proc Natl Acad Sci USA 2009, 106:6345-6350.
• [238]Orphan VJ: Methods for unveiling cryptic microbial partnerships in nature. Curr Opin Microbiol 2009, 12:231-237.
• [239]Klitgord N, Segre D: Ecosystems biology of microbial metabolism. Curr Opin Biotechnol 2011, 22:541-546.