Abstract
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.
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References
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. https://doi.org/10.1021/es2013227
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. https://doi.org/10.1111/j.1462-2920.2012.02780.x
Borden RC, Bedient PB (1986) Transport of dissolved hydrocarbons influenced by reaeration and oxygen limited biodegradation 1. Theoretical development. Water Resour Res 22:1973–1982
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):815–822
Borglin S, Joyner D, DeAngelis KM et al (2012) Application of phenotypic microarrays to environmental microbiology. Curr Opin Biotechnol 23(1):41–48. https://doi.org/10.1016/j.copbio.2011.12.006
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. https://doi.org/10.1007/s00253-002-1091-8
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 27:823–834
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):53–62
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. https://doi.org/10.1111/1751-7915.12399
Deutschbauer AM, Chivian D, Arkin AP (2006) Genomics for environmental microbiology. Curr Opin Biotechnol 17(3):229–235. https://doi.org/10.1016/j.copbio.2006.04.003
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. https://doi.org/10.1021/es0114557
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. https://doi.org/10.1021/es801383r
GSI_Environmental_Inc (2018) Matrix Diffusion Toolkit®. GSI Environmental Inc. http://www.gsi-net.com/en/software/free-software/matrix-diffusion-toolkit.html. Accessed April 19, 2018
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, Berlin
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, Berlin
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, Berlin
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. https://doi.org/10.1128/9781555818821.ch5.1.6
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: https://doi.org/10.1007/978-3-319-44535-9_11-1
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, Columbus
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 229–246
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. https://doi.org/10.1016/j.copbio.2006.03.004
Hazen TC, Dubinsky EA, DeSantis TZ et al (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330(6001):204–208. https://doi.org/10.1126/science.1195979
Hazen TC, Rocha AM, Techtmann SM (2013) Advances in monitoring environmental microbes. Curr Opin Biotechnol 24(3):526–533. https://doi.org/10.1016/j.copbio.2012.10.020
He Z, Zhang P, Wu L et al (2018) Microbial functional genes predict groundwater contamination and ecosystem functioning. MBio 9:e02435–e02417. https://doi.org/10.1128/mBio.02435-17
Holmes DE, Nevin KP, Lovley DR (2004) In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl Environ Microbiol 70(12):7251–7259. https://doi.org/10.1128/aem.70.12.7251-7259.2004
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. https://doi.org/10.1128/aem.03005-10
Kay E, Lesk VI, Tamaddoni-Nezhad A et al (2010) Systems analysis of bacterial glycomes. Biochem Soc Trans 38:1290–1293. https://doi.org/10.1042/bst0381290
Kircher M, Kelso J (2010) High-throughput DNA sequencing – concepts and limitations. BioEssays 32(6):524–536. https://doi.org/10.1002/bies.200900181
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, DC
Liu J, Techtmann SM, Woo HL et al (2017) Rapid response of eastern mediterranean deep sea microbial communities to oil. Sci Reports 7:11. https://doi.org/10.1038/s41598-017-05958-x
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. https://doi.org/10.1038/ismej.2011.91
Madsen EL (2006) The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr Opin Biotechnol 17(1):92–97
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–A610
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 Houston
Rifai HS, Bedient PB, Wilson JT et al (1988) Biodegradation modeling at an aviation fuel spill. ASCE J Environ Eng 114:1007–1029
Smith MB, Rocha AM, Smillie CS et al (2015) Natural bacterial communities serve as quantitative geochemical biosensors. MBio 6(3):13. https://doi.org/10.1128/mBio.00326-15
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. https://doi.org/10.1128/aem.02986-06
Thomas T, Gilbert J, Meyer F (2012) Metagenomics – a guide from sampling to data analysis. Microb Inf Exp 2(1):3–3. https://doi.org/10.1186/2042-5783-2-3
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):3093–3102
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. https://doi.org/10.3389/fmicb.2014.00522
USEPA (2018a) BIOCHLOR®. United States environmental protection agency. https://www.epa.gov/water-research/biochlor-natural-attenuation-decision-support-system. Accessed April 19, 2018
USEPA (2018b) BIOSCREEN®. United States environmental protection agency. http://www.epa.gov/water-research/bioscreen-natural-attenuation-decision-support-system. Accessed April 19, 2018
USEPA (2018c) REMChlor®. United States environmental protection agency. http://www.epa.gov/water-research/remediation-evaluation-model-chlorinated-solvents-remchlor. Accessed April 19, 2018
USEPA (2018d) REMFuel®. United States environmental protection agency. http://www.epa.gov/water-research/remediation-evaluation-model-fuel-hydrocarbons-remfuel. Accessed April 19, 2018
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. https://doi.org/10.1016/j.syapm.2013.10.001
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. https://doi.org/10.1098/rstb.2012.0320
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. https://doi.org/10.1038/s41559-017-0463-5
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. https://doi.org/10.1021/acs.est.5b00024
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Hazen, T.C. (2019). Environmental Systems Biology Approach to Bioremediation. In: Hurst, C. (eds) Understanding Terrestrial Microbial Communities. Advances in Environmental Microbiology, vol 6. Springer, Cham. https://doi.org/10.1007/978-3-030-10777-2_4
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