Skip to main content

Introduction: Mesocosms and Microcosms

  • Protocol
  • First Online:
Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

Mesocosms and microcosms provide an experimentally tractable way to study environmental processes under close to natural conditions while maintaining some control over gross physical processes. They also allow contaminants to be constrained for appropriate collection and disposal at the end of the experiment. This overview provides an extensive catalog of the literature on mesocosms and microcosms that have been used to study microbial responses to hydrocarbons; it should be a useful introduction for researchers entering the field.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Reilly TJ (1999) The use of mesocosms in marine oil spill ecological research and development. Pure Appl Chem 71:153–160

    Article  CAS  Google Scholar 

  2. Fahy A, McKew B (2010) Microcosms. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 3524–3527

    Google Scholar 

  3. Wagner D, Potsdam P (2010) Microcosm experiments for simulation of freeze-thaw cycles and studying methane dynamics in permafrost-affected soils. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 3454–3460

    Google Scholar 

  4. Kästner M, Richnow HH (2010) In situ microcosm studies to characterize microbial processes in the field. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 3503–3511

    Chapter  Google Scholar 

  5. Macedo AJ, Abraham WR (2010) Microcosms for biofilm analysis on hydrophobic substrates – a multiple approach to study biodiversity, metabolic activity and biofilm structure and dynamic. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 3543–3551

    Chapter  Google Scholar 

  6. Macedo AJ, Abraham WR (2010) Microcosms for biofilm analysis on hydrophobic substrates – a multiple approach to study biodiversity, metabolic activity and biofilm structure and dynamic. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 3543–3551

    Chapter  Google Scholar 

  7. Cappello S, Yakimov MM (2010) Mesocosms for oil spill simulation. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 3513–3521

    Chapter  Google Scholar 

  8. Lindstrom JE, Prince RC, Clark JC, Grossman MJ, Yeager TR, Braddock JF, Brown EJ (1991) Microbial populations and hydrocarbon biodegradation potentials in fertilized shoreline sediments affected by the T/V Exxon Valdez oil spill. Appl Environ Microbiol 57:2514–2522

    CAS  PubMed  PubMed Central  Google Scholar 

  9. OECD (2014) Guidelines for the testing of chemicals, section 3: degradation and accumulation. http://www.oecd-ilibrary.org/environment/oecd-guidelines-for-the-testing-of-chemicals-section-3-degradation-and-accumulation_2074577x

  10. ISO (2014) http://www.iso.org/iso/about.htm

  11. ASTM International (2014) http://www.astm.org/

  12. van Leeuwen CJ, Vermeire TG, Vermeire T (eds) (2007) Risk assessment of chemicals: an introduction. Springer, Berlin

    Google Scholar 

  13. Delille D, Basseres A, Dessommes A, Rosiers C (1998) Influence of daylight on potential biodegradation of diesel and crude oil in Antarctic seawater. Mar Environ Res 45:249–258

    Article  CAS  Google Scholar 

  14. Delille D, Basseres A, Dessommes A (1998) Effectiveness of bioremediation for oil-polluted Antarctic seawater. Polar Biol 19:237–241

    Article  Google Scholar 

  15. Siron R, Pelletier E, Brochu C (1995) Environmental factors influencing the biodegradation of petroleum hydrocarbons in cold seawater. Arch Environ Contam Toxicol 28:406–416

    Article  CAS  Google Scholar 

  16. Delille D, Basseres A, Dessommes A (1997) Seasonal variation of bacteria in sea ice contaminated by diesel fuel and dispersed crude oil. Microbial Ecol 33:97–105

    Article  CAS  Google Scholar 

  17. Lee K, Li Z, Robinson B, Kepkay PE, Blouin M, Doyon B (2011) Field trials of in-situ oil spill countermeasures in ice-infested waters. In: International oil spill conference proceedings (IOSC), vol 2011, paper 160. American Petroleum Institute, Washington

    Google Scholar 

  18. Schwarz JR, Walker JD, Colwell RR (1974) Deep-sea bacteria: growth and utilization of hydrocarbons at ambient and in situ pressure. Appl Microbiol 28:982–986

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Vanderhorst JR, Bean RM, Moore LJ, Wilkinson P, Gibson CI, Blaylock JW (1977) Effects of a continuous low-level No. 2 fuel dispersion on laboratory-held intertidal colonies. In: 1977 international oil spill conference. American Petroleum Institute, Washington, pp 557–561

    Google Scholar 

  20. Gamble JC, Davies JM, Hay SJ, Dow FK (1987) Mesocosm experiments on the effects of produced water discharges from offshore oil platforms in the northern North Sea. Sarsia 72:383–386

    Article  Google Scholar 

  21. Padrós J, Pelletier E, Siron R, Delille D (1999) Fate of a new silicone-based oil-treating agent and its effects on marine microbial communities. Environ Toxicol Chem 18:819–827

    Article  Google Scholar 

  22. Jézéquel R, Merlin FX, Lee K (1999) The influence of microorganisms on oil-mineral fine interactions in low-energy coastal environment. In: International oil spill conference, vol 1999, no. 1. American Petroleum Institute, Washington, pp 771–775

    Google Scholar 

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

    Article  CAS  Google Scholar 

  24. Mercurio P, Burns KA, Negri A (2004) Testing the ecotoxicology of vegetable versus mineral based lubricating oils: 1. Degradation rates using tropical marine microbes. Environ Pollut 129:165–173

    Article  CAS  PubMed  Google Scholar 

  25. McKew BA, Coulon F, Yakimov MM, Denaro R, Genovese M, Smith CJ, Osborn AM, Timmis KN, McGenity TJ (2007) Efficacy of intervention strategies for bioremediation of crude oil in marine systems and effects on indigenous hydrocarbonoclastic bacteria. Environ Microbiol 9:1562–1571

    Article  CAS  PubMed  Google Scholar 

  26. Cappello S, Denaro R, Genovese M, Giuliano L, Yakimov MM (2007) Predominant growth of Alcanivorax during experiments on “oil spill bioremediation” in mesocosms. Microbiol Res 162:185–190

    Article  CAS  PubMed  Google Scholar 

  27. Nikolopoulou M, Kalogerakis N (2008) Enhanced bioremediation of crude oil utilizing lipophilic fertilizers combined with biosurfactants and molasses. Mar Pollut Bull 56:1855–1861

    Article  CAS  PubMed  Google Scholar 

  28. Gertler C, Gerdts G, Timmis KN, Golyshin PN (2009) Microbial consortia in mesocosm bioremediation trial using oil sorbents, slow-release fertilizer and bioaugmentation. FEMS Microbiol Ecol 69:288–300

    Article  CAS  PubMed  Google Scholar 

  29. Vila J, Nieto JM, Mertens J, Springael D, Grifoll M (2010) Microbial community structure of a heavy fuel oil-degrading marine consortium: linking microbial dynamics with polycyclic aromatic hydrocarbon utilization. FEMS Microbiol Ecol 73:349–362

    CAS  PubMed  Google Scholar 

  30. Kadali KK, Simons KL, Sheppard PJ, Ball AS (2012) Mineralisation of weathered crude oil by a hydrocarbonoclastic consortia in marine mesocosms. Water Air Soil Pollut 223:4283–4295

    Article  CAS  Google Scholar 

  31. Sauret C, Christaki U, Moutsaki P, Hatzianestis I, Gogou A, Ghiglione JF (2012) Influence of pollution history on the response of coastal bacterial and nanoeukaryote communities to crude oil and biostimulation assays. Mar Environ Res 79:70–78

    Article  CAS  PubMed  Google Scholar 

  32. Gertler C, Näther DJ, Cappello S, Gerdts G, Quilliam RS, Yakimov MY, Golyshin PN (2012) Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study. FEMS Microbiol Ecol 81:520–536

    Article  CAS  PubMed  Google Scholar 

  33. Hassanshahian M, Emtiazi G, Caruso G, Cappello S (2013) Bioremediation (bioaugmentation/biostimulation) trials of oil polluted seawater: a mesocosm simulation study. Mar Environ Res 95:28–38

    Article  PubMed  CAS  Google Scholar 

  34. Hinga KR, Pilson MEQ, Lee RF, Farrington JW, Tjessem K, Davis AC (1980) Biogeochemistry of benzanthracene in an enclosed marine ecosystem. Environ Sci Technol 14:1136–1143

    Article  CAS  Google Scholar 

  35. Prince RC, McFarlin KM, Butler JD, Febbo EJ, Wang FCY, Nedwed TJ (2013) The primary biodegradation of dispersed crude oil in the sea. Chemosphere 90:521–526

    Article  CAS  PubMed  Google Scholar 

  36. Yamada M, Takada H, Toyoda K, Yoshida A, Shibata A, Nomura H, Wada M, Nishimura M, Okamoto K, Ohwada K (2003) Study on the fate of petroleum-derived polycyclic aromatic hydrocarbons (PAHs) and the effect of chemical dispersant using an enclosed ecosystem, mesocosm. Mar Pollut Bull 47:105–113

    Article  CAS  PubMed  Google Scholar 

  37. Yakimov MM, Gentile G, Bruni V, Cappello S, D’Auria C, Golyshin PN, Giuliano L (2004) Crude oil-induced structural shift of coastal bacterial communities of rod bay (Terra Nova Bay, Ross Sea, Antarctica) and characterization of cultured cold-adapted hydrocarbonoclastic bacteria. FEMS Microbiol Ecol 49:419–432

    Article  CAS  PubMed  Google Scholar 

  38. Teira E, Lekunberri I, Gasol JM, Nieto-Cid M, Álvarez-Salgado XA, Figueiras FG (2007) Dynamics of the hydrocarbon-degrading Cycloclasticus bacteria during mesocosm-simulated oil spills. Environ Microbiol 9:2551–2562

    Article  CAS  PubMed  Google Scholar 

  39. González J, Figueiras FG, Aranguren-Gassis M, Crespo BG, Fernández E, Morán XAG, Nieto-Cid M (2009) Effect of a simulated oil spill on natural assemblages of marine phytoplankton enclosed in microcosms. Estuar Coast Shelf Sci 83:265–276

    Article  CAS  Google Scholar 

  40. Jung SW, Park JS, Kown OY, Kang JH, Shim WJ, Kim YO (2010) Effects of crude oil on marine microbial communities in short term outdoor microcosms. J Microbiol 48:594–600

    Article  CAS  PubMed  Google Scholar 

  41. Joo C, Shim WJ, Kim GB, Ha SY, Kim M, An JG, Kim E, Kim B, Jung SW, Kim YO, Yim UH (2013) Mesocosm study on weathering characteristics of Iranian Heavy crude oil with and without dispersants. J Hazard Mater 248:37–46

    Article  PubMed  CAS  Google Scholar 

  42. Brakstad OG, Daling PS, Faksness LG, Almås 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 

  43. Suni S, Koskinen K, Kauppi S, Hannula E, Ryynänen T, Aalto A, Jäänheimo J, Ikävalko J, Romantschuk M (2007) Removal by sorption and in situ biodegradation of oil spills limits damage to marine biota: a laboratory simulation. AMBIO 36:173–179

    Article  CAS  PubMed  Google Scholar 

  44. Gilde K, Pinckney JL (2012) Sublethal effects of crude oil on the community structure of estuarine phytoplankton. Estuaries Coast 35:853–861

    Article  CAS  Google Scholar 

  45. Elmgren R, Frithsen JB (1982) The use of experimental ecosystems for evaluating the environmental impact of pollutants: a comparison of an oil spill in the Baltic Sea and two long-term, low-level oil addition experiments in mesocosms. In: Grice GD, Reeve MR (eds) Marine mesocosms. Springer, New York, pp 153–165

    Chapter  Google Scholar 

  46. Gray JS (1987) Oil pollution studies of the Solbergstrand mesocosms. Philos Trans R Soc B 316:641–654

    Article  Google Scholar 

  47. Maki H, Sasaki T, Sasaki E, Ishihara M, Goto M, Harayama S (1999) Use of wastewater sludge for the amendment of crude oil bioremediation in meso-scale beach simulating tanks. Environ Technol 20:625–632

    Article  CAS  Google Scholar 

  48. Wang H, Wang C, Lin M, Sun X, Wang C, Hu X (1999) Phylogenetic diversity of bacterial communities associated with bioremediation of crude oil in microcosms. Int Biodeterior Biodegradation 85:400–406

    Article  CAS  Google Scholar 

  49. Pardue MJ, Castle JW, Rodgers JH, Huddleston GM (2014) Treatment of oil and grease in produced water by a pilot-scale constructed wetland system using biogeochemical processes. Chemosphere 103:67–73

    Article  CAS  PubMed  Google Scholar 

  50. Gardner WS, Lee RF, Tenore KR, Smith LW (1979) Degradation of selected polycyclic aromatic hydrocarbons in coastal sediments: importance of microbes and polychaete worms. Water Air Soil Pollut 11:339–347

    Article  CAS  Google Scholar 

  51. Oh YS, Sim DS, Kim SJ (2001) Effects of nutrients on crude oil biodegradation in the upper intertidal zone. Mar Pollut Bull 42:1367–1372

    Article  CAS  PubMed  Google Scholar 

  52. Del’Arco JP, De França FP (2001) Influence of oil contamination levels on hydrocarbon biodegradation in sandy sediment. Environ Pollut 112:515–519

    Article  PubMed  Google Scholar 

  53. Röling WFM, Milner MG, Jones DM, Lee K, Daniel F, Swannell RJP, Head IM (2002) Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Appl Environ Microbiol 68:5537–5548

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  54. Wrenn BA, Sarnecki KL, Kohar ES, Lee K, Venosa AD (2006) Effects of nutrient source and supply on crude oil biodegradation in continuous-flow beach microcosms. J Environ Eng 132:75–84

    Article  CAS  Google Scholar 

  55. Mohajeri L, Aziz HA, Isa MH, Zahed MA (2010) A statistical experiment design approach for optimizing biodegradation of weathered crude oil in coastal sediments. Bioresour Technol 101:893–900

    Article  CAS  PubMed  Google Scholar 

  56. Nikolopoulou M, Pasadakis MN, Norf H, Kalogerakis N (2013) Enhanced ex situ bioremediation of crude oil contaminated beach sand by supplementation with nutrients and rhamnolipids. Mar Pollut Bull 77:37–44

    Article  CAS  PubMed  Google Scholar 

  57. Pontes J, Mucha AP, Santos H, Reis I, Bordalo A, Basto M, Bernabeu A, Almeida CMR (2013) Potential of bioremediation for buried oil removal in beaches after an oil spill. Mar Pollut Bull 76:258–265

    Article  CAS  PubMed  Google Scholar 

  58. Reis I, Almeida CMR, Magalhães CM, Cochofel J, Guedes P, Basto MCP, Bordalo AA, Mucha AP (2014) Bioremediation potential of microorganisms from a sandy beach affected by a major oil spill. Environ Sci Pollut Res 21:3634–3645

    Article  CAS  Google Scholar 

  59. Singh AK, Sherry A, Gray ND, Jones DM, Bowler BFJ, Head IM (2014) Kinetic parameters for nutrient enhanced crude oil biodegradation in intertidal marine sediments. Front Microbiol 5:120

    Article  Google Scholar 

  60. Genovese M, Crisafi F, Denaro R, Cappello S, Russo D, Calogero R, Santisi S, Catalfamo M, Modica A, Smedile F, Genovese L, Golyshin PN, Giuliano L, Yakimov MM (2014) Effective bioremediation strategy for rapid in situ cleanup of anoxic marine sediments in mesocosm oil spill simulation. Front Microbiol 5:162

    Article  PubMed  PubMed Central  Google Scholar 

  61. Lin Q, Mendelssohn IA (1998) The combined effects of phytoremediation and biostimulation in enhancing habitat restoration and oil degradation of petroleum contaminated wetlands. Ecol Eng 10:263–274

    Article  Google Scholar 

  62. Dowty RA, Shaffer GP, Hester MW, Childers GW, Campo FM, Greene MC (2001) Phytoremediation of small-scale oil spills in fresh marsh environments: a mesocosm simulation. Mar Environ Res 52:195–211

    Article  CAS  PubMed  Google Scholar 

  63. Lin Q, Mendelssohn IA, Carney K, Bryner NP, Walton WD (2002) Salt marsh recovery and oil spill remediation after in-situ burning: effects of water depth and burn duration. Environ Sci Technol 36:576–581

    Article  CAS  PubMed  Google Scholar 

  64. Wright AL, Weaver RW (2004) Fertilization and bioaugmentation for oil biodegradation in salt marsh mesocosms. Water Air Soil Pollut 156:229–240

    Article  CAS  Google Scholar 

  65. Horel A, Bernard RJ, Mortazavi B (2014) Impact of crude oil exposure on nitrogen cycling in a previously impacted Juncus roemerianus salt marsh in the northern Gulf of Mexico. Environ Sci Pollut Res 21:6982–6993

    Article  CAS  Google Scholar 

  66. Lindstrom JE, Prince RC, Clark JC, Grossman MJ, Yeager TR, Braddock JF, Brown EJ (1991) Microbial populations and hydrocarbon biodegradation potentials in fertilized shoreline sediments affected by the T/V Exxon Valdez oil spill. Appl Environ Microbiol 57:2514–2522

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Venosa AD, Haines JR, Nisamaneepong W, Govind R, Pradhan S, Siddique B (1992) Efficacy of commercial products in enhancing oil biodegradation in closed laboratory reactors. J Ind Microbiol 10:13–23

    Article  CAS  Google Scholar 

  68. Xu R, Obbard JP (2003) Effect of nutrient amendments on indigenous hydrocarbon biodegradation in oil-contaminated beach sediments. J Environ Qual 32:1234–1243

    Article  CAS  PubMed  Google Scholar 

  69. Venosa AD, Campo P, Suidan MT (2010) Biodegradability of lingering crude oil 19 years after the Exxon Valdez oil spill. Environ Sci Technol 44:7613–7621

    Article  CAS  PubMed  Google Scholar 

  70. Coulon F, Chronopoulou PM, Fahy A, Païssé S, Goñi-Urriza M, Peperzak L, Alvarez LA, McKew BA, Brussaard CPD, Underwood GJC, Timmis KN, Duran R, McGenity TJ (2012) Central role of dynamic tidal biofilms dominated by aerobic hydrocarbonoclastic bacteria and diatoms in the biodegradation of hydrocarbons in coastal mudflats. Appl Environ Microbiol 78:3638–3648

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Chronopoulou PM, Fahy A, Coulon F, Païssé S, Goñi-Urriza M, Peperzak L, Acuña Alvarez L, McKew BA, Lawson T, Timmis KN, Duran R, Underwood GJC, McGenity TJ (2013) Impact of a simulated oil spill on benthic phototrophs and nitrogen-fixing bacteria in mudflat mesocosms. Environ Microbiol 15:242–252

    Article  CAS  PubMed  Google Scholar 

  72. Louati H, Ben Said O, Soltani A, Got P, Cravo-Laureau C, Duran R, Aissa P, Pringault O, Mahmoudi E (2014) Biostimulation as an attractive technique to reduce phenanthrene toxicity for meiofauna and bacteria in lagoon sediment. Environ Sci Pollut Res 21:3670–3679

    Article  CAS  Google Scholar 

  73. Coates JD, Anderson RT, Woodward JC, Phillips EJP, Lovley DR (1996) Anaerobic hydrocarbon degradation in petroleum-contaminated harbor sediments under sulfate-reducing and artificially imposed iron-reducing conditions. Environ Sci Technol 30:2784–2789

    Article  CAS  Google Scholar 

  74. Rocchetti L, Beolchini F, Ciani M, Dell’Anno A (2011) Improvement of bioremediation performance for the degradation of petroleum hydrocarbons in contaminated sediments. Appl Environ Soil Sci. doi:10.1155/2011/319657

    Google Scholar 

  75. Dell’Anno A, Beolchini F, Rocchetti L, Luna GM, Danovaro R (2012) High bacterial biodiversity increases degradation performance of hydrocarbons during bioremediation of contaminated harbor marine sediments. Environ Pollut 167:85–92

    Article  PubMed  CAS  Google Scholar 

  76. Al-Mailem DM, Eliyas M, Radwan S (2014) Enhanced bioremediation of oil-polluted, hypersaline, coastal areas in Kuwait via vitamin-fertilization. Environ Sci Pollut Res 21:3386–3394

    Article  CAS  Google Scholar 

  77. Margesin R, Hämmerle M, Tscherko D (2007) Microbial activity and community composition during bioremediation of diesel-oil-contaminated soil: effects of hydrocarbon concentration, fertilizers, and incubation time. Microbial Ecol 53:259–269

    Article  CAS  Google Scholar 

  78. Couto MNPFS, Monteiro E, Vasconcelos MTSD (2010) Mesocosm trials of bioremediation of contaminated soil of a petroleum refinery: comparison of natural attenuation, biostimulation and bioaugmentation. Environ Sci Pollut Res 17:1339–1346

    Article  CAS  Google Scholar 

  79. Alvarez VM, Marques JM, Korenblum E, Seldin L (2011) Comparative bioremediation of crude oil-amended tropical soil microcosms by natural attenuation, bioaugmentation, or bioenrichment. Appl Environ Soil Sci 156320

    Google Scholar 

  80. Moldes AB, Paradelo R, Rubinos D, Devesa-Rey R, Cruz JM, Barral MT (2011) Ex situ treatment of hydrocarbon-contaminated soil using biosurfactants from Lactobacillus pentosus. J Agric Food Chem 59:9443–9447

    Article  CAS  PubMed  Google Scholar 

  81. Winquist E, Björklöf K, Schultz E, Räsänen M, Salonen K, Anasonye F, Cajthaml T, Steffen KT, Jørgensen KS, Tuomela M (2014) Bioremediation of PAH-contaminated soil with fungi – from laboratory to field scale. Int Biodeterior Biodegradation 86:238–247

    Article  CAS  Google Scholar 

  82. Couto MNPFS, Basto MCRP, Vasconcelos MTSD (2011) Suitability of different salt marsh plants for petroleum hydrocarbons remediation. Chemosphere 84:1052–1057

    Article  CAS  PubMed  Google Scholar 

  83. Bramley-Alves J, Wasley J, King CK, Powell S, Robinson SA (2014) Phytoremediation of hydrocarbon contaminants in subantarctic soils: an effective management option. J Environ Manage 142:60–69

    Article  CAS  PubMed  Google Scholar 

  84. Kauppi S, Romantschuk M, Strömmer R, Sinkkonen A (2012) Natural attenuation is enhanced in previously contaminated and coniferous forest soils. Environ Sci Pollut Res 19:53–63

    Article  CAS  Google Scholar 

  85. Aislabie JM, McLeod M, Fraser R (1998) Potential for biodegradation of hydrocarbons in soil from the Ross Dependency, Antarctica. Appl Microbiol Biotechnol 49:210–214

    Article  CAS  Google Scholar 

  86. Ferguson SH, Franzmann PD, Snape I, Revill AT, Trefry MG, Zappia LR (2003) Effects of temperature on mineralisation of petroleum in contaminated Antarctic terrestrial sediments. Chemosphere 52:975–987

    Article  CAS  PubMed  Google Scholar 

  87. Delille D, Coulon F (2008) Comparative mesocosm study of biostimulation efficiency in two different oil-amended sub-Antarctic soils. Microbial Ecol 56:243–252

    Article  Google Scholar 

  88. Vázquez S, Nogales B, Ruberto L, Hernández E, Christie-Oleza J, Lo Balbo A, Bosch R, Lalucat J, Mac Cormack W (2009) Bacterial community dynamics during bioremediation of diesel oil-contaminated Antarctic soil. Microb Ecol 57:598–610

    Article  PubMed  CAS  Google Scholar 

  89. Braddock JF, Ruth ML, Catterall PH, Walworth JL, McCarthy KA (1997) Enhancement and inhibition of microbial activity in hydrocarbon-contaminated arctic soils: implications for nutrient-amended bioremediation. Environ Sci Technol 31:2078–2084

    Article  CAS  Google Scholar 

  90. Whyte LG, Bourbonnière L, Bellerose C, Greer CW (1999) Bioremediation assessment of hydrocarbon-contaminated soils from the high Arctic. Bioremediat J 3:69–80

    Article  CAS  Google Scholar 

  91. Coulon F, Pelletier E, Gourhant L, Delille D (2005) Effects of nutrient and temperature on degradation of petroleum hydrocarbons in contaminated sub-Antarctic soil. Chemosphere 58:1439–1448

    Article  CAS  PubMed  Google Scholar 

  92. Chang W, Whyte L, Ghoshal S (2011) Comparison of the effects of variable site temperatures and constant incubation temperatures on the biodegradation of petroleum hydrocarbons in pilot-scale experiments with field-aged contaminated soils from a cold regions site. Chemosphere 82:872–878

    Article  CAS  PubMed  Google Scholar 

  93. Walworth J, Harvey P, Snape I (2013) Low temperature soil petroleum hydrocarbon degradation at various oxygen levels. Cold Reg Sci Technol 96:117–121

    Article  Google Scholar 

  94. Ke L, Wang WQ, Wong TWY, Wong YS, Tam NFY (2003) Removal of pyrene from contaminated sediments by mangrove microcosms. Chemosphere 51:25–34

    Article  CAS  PubMed  Google Scholar 

  95. Yu SH, Ke L, Wong YS, Tam NFY (2005) Degradation of polycyclic aromatic hydrocarbons by a bacterial consortium enriched from mangrove sediments. Environ Internat 31:149–154

    Article  CAS  Google Scholar 

  96. Bayer DM, Chagas-Spinelli ACO, Gavazza S, Florencio L, Kato MT (2013) Natural attenuation and biosurfactant-stimulated bioremediation of estuarine sediments contaminated with diesel oil. Appl Biochem Biotechnol 171:173–188

    Article  CAS  PubMed  Google Scholar 

  97. Taketani RG, Franco NO, Rosado AS, van Elsas JD (2010) Microbial community response to a simulated hydrocarbon spill in mangrove sediments. J Microbiol 48:7–15

    Article  PubMed  Google Scholar 

  98. Embar K, Forgacs C, Sivan A (2006) The role of indigenous bacterial and fungal soil populations in the biodegradation of crude oil in a desert soil. Biodegradation 17:369–377

    Article  CAS  PubMed  Google Scholar 

  99. Cho BH, Chino H, Tsuji H, Kunito T, Nagaoka K, Otsuka S, Yamashita K, Matsumoto S, Oyaizu H (1997) Laboratory-scale bioremediation of oil-contaminated soil of Kuwait with soil amendment materials. Chemosphere 35:1599–1611

    Article  CAS  PubMed  Google Scholar 

  100. Radwan SS, Sorkhoh NA, El-Nemr IM, El-Desouky AF (1997) A feasibility study on seeding as a bioremediation practice for the oily Kuwaiti desert. J Appl Microbiol 83:353–358

    Article  Google Scholar 

  101. Hess A, Höhener P, Hunkeler D, Zeyer J (1996) Bioremediation of a diesel fuel contaminated aquifer: simulation studies in laboratory aquifer columns. J Contam Hydrol 23:329–345

    Article  CAS  Google Scholar 

  102. Zoller U, Rubin H (2001) Feasibility of in situ NAPL-contaminated aquifer bioremediation by biodegradable nutrient–surfactant mix. J Environ Sci Health A 36:1451–1471

    Article  CAS  Google Scholar 

  103. Hendrickx B, Dejonghe W, Boënne W, Brennerova M, Cernik M, Lederer T, Bucheli-Witschel M, Bastiaens L, Verstraete W, Top EM, Diels L, Springael D (2005) Dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an in situ mesocosm study. Appl Environ Microbiol 71:3815–3825

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Painter R, Byl T, Sharpe L, Kheder A, Harris J (2011) The role of attached and free-living bacteria in biodegradation in karst aquifers. Water 3:1139–1148

    Article  CAS  Google Scholar 

  105. Bushnell LD, Haas HF (1941) The utilization of certain hydrocarbons by microorganisms. J Bacteriol 41:653–673

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Randall DJ, Tsui TKN (2002) Ammonia toxicity in fish. Mar Pollut Bull 45:17–23

    Article  CAS  PubMed  Google Scholar 

  107. Johnson KS, Coletti LJ, Jannasch HW, Sakamoto CM, Swift DD, Riser SC (2013) Long-term nitrate measurements in the ocean using the in situ ultraviolet spectrophotometer: sensor integration into the APEX Profiling Float. J Atmos Oceanic Tech 30:1854–1866

    Article  Google Scholar 

  108. Boufadel MC, Reeser P, Suidan MT, Wrenn BA, Cheng J, Du X, Huang TL, Venosa AD (1999) Optimal nitrate concentration for the biodegradation of n-heptadecane in a variably-saturated sand column. Environ Technol 20:191–199

    Article  CAS  Google Scholar 

  109. Prince RC, Atlas RM (2005) Bioremediation of marine oil spills. In: Atlas RM, Philp JC (eds) Bioremediation: applied microbial solutions for real-world environmental cleanup. ASM, Washington DC, pp 269–292

    Chapter  Google Scholar 

  110. Galand PE, Casamayor EO, Kirchman DL, Lovejoy C (2009) Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci U S A 106:22427–22432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Sul WJ, Oliver TA, Ducklow HW, Amaral-Zettler LA, Sogin ML (2013) Marine bacteria exhibit a bipolar distribution. Proc Natl Acad Sci U S A 110:2342–2347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Hugoni M, Taib N, Debroas D, Domaizon I, Dufournel IJ, Bronner G, Salter I, Agogué H, Mary I, Galand PE (2013) Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proc Natl Acad Sci U S A 110:6004–6009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth J, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437

    Article  CAS  PubMed  Google Scholar 

  114. Lennon JT, Jones SE (2011) Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 9:119–130

    Article  CAS  PubMed  Google Scholar 

  115. Sauret C, Séverin T, Vétion G, Guigue C, Goutx M, Pujo-Pay M, Conan P, Fagervold SK, Ghiglione JF (2014) ‘Rare biosphere’ bacteria as key phenanthrene degraders in coastal seawaters. Environ Pollut 194:246–253

    Article  CAS  PubMed  Google Scholar 

  116. De Wit R, Bouvier T (2006) ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Environ Microbiol 8:755–758

    Article  PubMed  Google Scholar 

  117. Venosa AD, Holder EL (2007) Biodegradability of dispersed crude oil at two different temperatures. Mar Pollut Bull 54:545–553

    Article  CAS  PubMed  Google Scholar 

  118. Zahed MA, Aziz HA, Isa MH, Mohajeri L, Mohajeri S, Kutty SRM (2011) Kinetic modeling and half-life study on bioremediation of crude oil dispersed by Corexit 9500. J Hazard Mater 185:1027–1031

    Article  CAS  PubMed  Google Scholar 

  119. McFarlin KM, Prince RC, Perkins R, Leigh MB (2014) Biodegradation of oil dispersed with corexit 9500 in Arctic seawater. PLoS One 9(1):e84297

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  120. Rosenberg E, Legmann R, Kushmaro A, Taube R, Adler E, Ron EZ (1992) Petroleum bioremediation; a multiphase problem. Biodegradation 3:337–350

    Article  CAS  Google Scholar 

  121. Bragg JR, Prince RC, Harner EJ, Atlas RM (1994) Effectiveness of bioremediation for the Exxon Valdez oil spill. Nature 368:413–418

    Article  CAS  Google Scholar 

  122. Lee K, Nedwed T, Prince RC, Palandro D (2013) Lab tests on the biodegradation of chemically dispersed oil should consider the rapid dilution that occurs at sea. Mar Pollut Bull 73:314–318

    Article  CAS  PubMed  Google Scholar 

  123. Borden RC, Daniel RA, LeBrun LE, Davis CW (1997) Intrinsic biodegradation of MTBE and BTEX in a gasoline-contaminated aquifer. Water Resour Res 33:1105–1115

    Article  CAS  Google Scholar 

  124. European Maritime Safety Agency (2010) Inventory of national policies regarding the use of oil spill dispersants in the EU. http://emsa.europa.eu/publications/guidelines-manuals-and-inventories.html

  125. Weir SM, Wooten KJ, Smith PN, Salice CJ (2014) Phthalate ester leachates in aquatic mesocosms: implications for ecotoxicity studies of endocrine disrupting compounds. Chemosphere 103:44–50

    Article  CAS  PubMed  Google Scholar 

  126. Prince RC, Elmendorf DL, Lute JR, Hsu CS, Haith CE, Senius JD, Dechert GJ, Douglas GS, Butler EL (1994) 17α(H),21β(H)-hopane as a conserved internal marker for estimating the biodegradation of crude oil. Environ Sci Technol 28:142–145

    Article  CAS  PubMed  Google Scholar 

  127. Douglas GS, Hardenstine JH, Liu B, Uhler AD (2012) Laboratory and field verification of a method to estimate the extent of petroleum biodegradation in soil. Environ Sci Technol 46:8279–8287

    Article  CAS  PubMed  Google Scholar 

  128. Yang C, Wang Z, Liu Y, Yang Z, Li Y, Shah K, Zhang G, Landriault M, Hollebone B, Brown C, Lambert P, Liub Z, Tianet S (2013) Aromatic steroids in crude oils and petroleum products and their applications in forensic oil spill identification. Environ Forensics 14:278–293

    Article  CAS  Google Scholar 

  129. Wang Z, Yang C, Fingas M, Hollebone B, Peng X, Hansen AB, Christensen JH (2005) Characterization, weathering, and application of sesquiterpanes to source identification of spilled lighter petroleum products. Environ Sci Technol 39:8700–8707

    Article  CAS  PubMed  Google Scholar 

  130. Prince RC, Haitmanek C, Lee CC (2008) The primary aerobic biodegradation of biodiesel B20. Chemosphere 71:1446–1451

    Article  CAS  PubMed  Google Scholar 

  131. DMZ (2013) Cultivation of anaerobes. http://www.dsmz.de/fileadmin/Bereiche/Microbiology/Dateien/Kultivierungshinweise/englAnaerob.pdf

  132. USACE (2003) Safety and health aspects of HTRW remediation technologies. http://140.194.76.129/publications/eng-manuals/em1110–1–4007/toc.htm

  133. Kreft AM, Millison KC (2001) Elements of a successful ergonomics program in a research laboratory. Chem Health Saf 8:14–18

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Roger C. Prince .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer-Verlag Berlin Heidelberg

About this protocol

Cite this protocol

Prince, R.C. (2015). Introduction: Mesocosms and Microcosms. In: McGenity, T., Timmis, K., Nogales , B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_173

Download citation

  • DOI: https://doi.org/10.1007/8623_2015_173

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-53107-5

  • Online ISBN: 978-3-662-53108-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics