Environmental Systems Biology Approach to Bioremediation

  • Terry C. HazenEmail author
Part of the Advances in Environmental Microbiology book series (AEM, volume 6)


Pollution is everywhere. Microbes are also everywhere, and many have the ability to degrade environmental contaminants. Understanding how these microbial communities work to degrade environmental contaminants will enable us to use these microbes to clean up the pollution. Understanding, monitoring, and controlling the environment with biological processes, i.e., an environmental systems biology approach to bioremediation, answer the need which is everywhere. By using an environmental systems approach to bioremediation, we make sure we know of any “fatal flaws” in the approach, get a much better handle on life-cycle cost analysis, and can grade an engineered solution into a natural attenuation solution. The whole is greater than the sum of its parts. By using an environmental systems biology approach to bioremediation and cross-linkage of systems at all levels providing multiple lines of evidence involving environmental observations, laboratory testing, microcosm simulations, hypothesis refinement, field testing and validation, and multiple iterations of this circle, we will be able to make new theories and paradigms for bioremediation of contaminated environments.


Pollution Bioremediation GeoChip 16S rRNA Microbial ecology PhyloChip Phospholipid fatty acids Stable-isotope probes Field test plan 


Compliance with Ethical Standards

Conflict of Interest

Terry C. Hazen declares that he has no conflict of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by the author.


  1. Atlas RM, Hazen TC (2011) Oil biodegradation and bioremediation: a tale of the two worst spills in US history. Environ Sci Technol 45(16):6709–6715. CrossRefPubMedPubMedCentralGoogle Scholar
  2. Baelum J, Borglin S, Chakraborty R et al (2012) Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol 14(9):2405–2416. CrossRefPubMedGoogle Scholar
  3. Borden RC, Bedient PB (1986) Transport of dissolved hydrocarbons influenced by reaeration and oxygen limited biodegradation 1. Theoretical development. Water Resour Res 22:1973–1982CrossRefGoogle Scholar
  4. Borglin SE, Hazen TC, Oldenburg CM et al (2004) Comparison of aerobic and anaerobic biotreatment of municipal solid waste. J Air Waste Manage Assoc 54(7):815–822CrossRefGoogle Scholar
  5. Borglin S, Joyner D, DeAngelis KM et al (2012) Application of phenotypic microarrays to environmental microbiology. Curr Opin Biotechnol 23(1):41–48. CrossRefPubMedGoogle Scholar
  6. Chardin B, Dolla A, Chaspoul F et al (2002) Bioremediation of chromate: thermodynamic analysis of the effects of Cr(VI) on sulfate-reducing bacteria. Appl Environ Microbiol 60(3):352–360. CrossRefGoogle Scholar
  7. Chiang CY, Salanitro JP, Chai EY, Colthart JD, Klein CL (1989) Aerobic biodegradation of benzene, toluene, and xylene in sandy aquifer, and data analysis and computer modeling. Ground Water 27:823–834CrossRefGoogle Scholar
  8. Choi NC, Choi JW, Kim SB et al (2009) Two-dimensional modelling of benzene transport and biodegradation in a laboratory-scale aquifer. Environ Technol 30(1):53–62CrossRefGoogle Scholar
  9. de Lorenzo V, Marliere P, Sole R (2016) Bioremediation at a global scale: from the test tube to planet Earth. Microb Biotechnol 9(5):618–625. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Deutschbauer AM, Chivian D, Arkin AP (2006) Genomics for environmental microbiology. Curr Opin Biotechnol 17(3):229–235. CrossRefPubMedGoogle Scholar
  11. Dybas MJ, Hyndman DW, Heine R et al (2002) Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation. Environ Sci Technol 36(16):3635–3644. CrossRefPubMedGoogle Scholar
  12. Faybishenko B, Hazen TC, Long PE et al (2008) In situ long-term reductive bioimmobilization of Cr(VI) in groundwater using hydrogen release compound. Environ Sci Technol 42(22):8478–8485. CrossRefPubMedGoogle Scholar
  13. GSI_Environmental_Inc (2018) Matrix Diffusion Toolkit®. GSI Environmental Inc. Accessed April 19, 2018
  14. Hazen TC (2010a) Biostimulation. In: Timmis KN (ed) Handbook of hydrocarbon microbiology: microbial interactions with hydrocarbons, oils, fats and related hydrophobic substrates and products. Springer, BerlinGoogle Scholar
  15. Hazen TC (2010b) Cometabolic bioremediation. In: Timmis KN (ed) Handbook of hydrocarbon microbiology: microbial interactions with hydrocarbons, oils, fats and related hydrophobic substrates and products. Springer, BerlinGoogle Scholar
  16. Hazen TC (2010c) In situ groundwater bioremediation. In: Timmis KN (ed) Handbook of hydrocarbon microbiology: microbial interactions with hydrocarbons, oils, fats and related hydrophobic substrates and products. Springer, BerlinGoogle Scholar
  17. 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. CrossRefGoogle Scholar
  18. Hazen TC (2018) In situ: groundwater bioremediation. In: Consequences of microbial interaction with hydrocarbons, oils and lipids: biodegradation and bioremediation. Handbook of hydrocarbon and lipid microbiology series. Springer, Cham, pp 1–18. DOI:
  19. Hazen TC, Lombard KH, Looney BB et al (1994) Summary of in situ bioremediation demonstration (methane biostimulation) via horizontal wells at the Savannah river site integrated demonstration project. In situ remediation: scientific basis for current and future technologies, pts 1 and 2. Battelle Press, ColumbusCrossRefGoogle Scholar
  20. Hazen TC, Tien A, Worsztynowicz A et al. (2003) Biopiles for remediation of petroleum-contaminated soils: a polish case study. In: Sasek V, Glaser J, Baveye P (eds) Proceedings of the NATO advanced research workshop on the utilization of bioremediation to reduce soil contamination: problems and solutions, Prague, Czech Republic, June 14, 2000. NATA Science Series IV: Earth and Environmental Sciences. Kluwer Academic Publishers, pp 229–246Google Scholar
  21. Hazen TC, Stahl DA, Hazen TC et al (2006) Using the stress response to monitor process control: pathways to more effective bioremediation. Curr Opin Biotechnol 17(3):285–290. CrossRefPubMedGoogle Scholar
  22. Hazen TC, Dubinsky EA, DeSantis TZ et al (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330(6001):204–208. CrossRefPubMedGoogle Scholar
  23. Hazen TC, Rocha AM, Techtmann SM (2013) Advances in monitoring environmental microbes. Curr Opin Biotechnol 24(3):526–533. CrossRefPubMedGoogle Scholar
  24. He Z, Zhang P, Wu L et al (2018) Microbial functional genes predict groundwater contamination and ecosystem functioning. MBio 9:e02435–e02417. CrossRefPubMedPubMedCentralGoogle Scholar
  25. Holmes DE, Nevin KP, Lovley DR (2004) In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl Environ Microbiol 70(12):7251–7259. CrossRefPubMedPubMedCentralGoogle Scholar
  26. Jiao YQ, D’Haeseleer P, Dill BD et al (2011) Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. Appl Environ Microbiol 77(15):5230–5237. CrossRefPubMedPubMedCentralGoogle Scholar
  27. Kay E, Lesk VI, Tamaddoni-Nezhad A et al (2010) Systems analysis of bacterial glycomes. Biochem Soc Trans 38:1290–1293. CrossRefPubMedGoogle Scholar
  28. Kircher M, Kelso J (2010) High-throughput DNA sequencing – concepts and limitations. BioEssays 32(6):524–536. CrossRefPubMedGoogle Scholar
  29. Konikow LF, Bredeheoft JD (1978) Computer model of two dimensional solute transport and dispersion in ground water. techniques of water resources investigations of the U.S. Geological Survey: Washington, DCGoogle Scholar
  30. Liu J, Techtmann SM, Woo HL et al (2017) Rapid response of eastern mediterranean deep sea microbial communities to oil. Sci Reports 7:11. CrossRefGoogle Scholar
  31. Lu ZM, Deng Y, Van Nostrand JD et al (2012) Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J 6(2):451–460. CrossRefPubMedGoogle Scholar
  32. Madsen EL (2006) The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr Opin Biotechnol 17(1):92–97CrossRefGoogle Scholar
  33. Pombo SA, Schroth MH, Pelz O, Zeyer J (2002) Tracing microbial activity in a contaminated aquifer at the field scale using C-13-labeling of bacterial fatty acids. Geochim Cosmochim Acta 66(15A):A610–A610Google Scholar
  34. Rifai HS, Bedient PB, Borden RC et al. (1987) BIOPLUME II computer model of two-dimensional contaminant transport under the influence of oxygen limited biodegradation in groundwater user’s manual version 1.0 HoustonGoogle Scholar
  35. Rifai HS, Bedient PB, Wilson JT et al (1988) Biodegradation modeling at an aviation fuel spill. ASCE J Environ Eng 114:1007–1029CrossRefGoogle Scholar
  36. Smith MB, Rocha AM, Smillie CS et al (2015) Natural bacterial communities serve as quantitative geochemical biosensors. MBio 6(3):13. CrossRefGoogle Scholar
  37. Tang YJ, Chakraborty R, Martin HG et al (2007) Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid. Appl Environ Microbiol 73(12):3859–3864. CrossRefPubMedPubMedCentralGoogle Scholar
  38. Thomas T, Gilbert J, Meyer F (2012) Metagenomics – a guide from sampling to data analysis. Microb Inf Exp 2(1):3–3. CrossRefGoogle Scholar
  39. Travis BJ, Rosenberg ND (1997) Modeling in situ bioremediation of TCE at Savannah River: effects of product toxicity and microbial interactions on TCE degradation. Environ Sci Technol 31(11):3093–3102CrossRefGoogle Scholar
  40. Trexler R, Solomon C, Brislawn CJ et al (2014) Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania. Front Microbiol 5:522. CrossRefPubMedPubMedCentralGoogle Scholar
  41. USEPA (2018a) BIOCHLOR®. United States environmental protection agency. Accessed April 19, 2018
  42. USEPA (2018b) BIOSCREEN®. United States environmental protection agency. Accessed April 19, 2018
  43. USEPA (2018c) REMChlor®. United States environmental protection agency. Accessed April 19, 2018
  44. USEPA (2018d) REMFuel®. United States environmental protection agency. Accessed April 19, 2018
  45. Woo HL, Hazen TC, Simmons BA et al (2014) Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils. Syst Appl Microbiol 37(1):60–67. CrossRefPubMedGoogle Scholar
  46. Yan J, Im J, Yang Y et al (2013) Guided cobalamin biosynthesis supports Dehalococcoides mccartyi reductive dechlorination activity. Phil Trans R Soc B Biol Sci 368(1616):10. CrossRefGoogle Scholar
  47. Yao Q, Li Z, Song Y et al (2018) Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil. Nat Ecol Evol 2:1–11. CrossRefGoogle Scholar
  48. Zhang P, Van Nostrand JD, He Z et al (2015) A slow-release substrate stimulates groundwater microbial communities for long-term in situ Cr(VI) reduction. Environ Sci Technol 49(21):12922–12931. CrossRefPubMedGoogle Scholar

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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.University of Tennessee and Oak Ridge National LaboratoryKnoxvilleUSA

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