Abstract
Bioremediation is a sustainable environmental treatment technology that harnesses the natural metabolic activities of living organisms to remove contaminants within soil, sediment, and water environments. Bioremediation is generally accepted as being a more cost-effective and sustainable remediation strategy when compared to chemical-based or pump-and-treat systems. Bioremediation treatment strategies are traditionally categorized as either biostimulation or bioaugmentation. Biostimulation involves the stimulation of indigenous microorganisms that are capable of degrading contaminants of interest. This treatment approach relies on manipulating site conditions to promote the activity and/or proliferation of microorganisms that are known to metabolize target contaminants of concern in order to overcome rate-limiting metabolic processes. In general, biostimulation involves oxidation-reduction reactions wherein either an electron acceptor (e.g., O2, Fe3+, or SO42−) is added to promote oxidative reduction of a contaminant or an electron donor (e.g., organic substrate) is added to reduce oxidized pollutants.
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References
Gavrilescu M (2009) Emerging processes for soil and groundwater cleanup-potential benefits and risks. Environ Eng Manag J 8(5):1293–1307
Jianlong W, Xiangchun Q, Libo W, Yi Q, Hegemann W (2002) Bioaugmentation as a tool to enhance the removal of refractory compound in coke plant wastewater. Process Biochem 38(5):777–781
EPA (2013). Introduction to in situ bioremdiation of groundwater. Office of Solid Wastew and Emergency Response, EPA/542/R-13-018
Ikuma K, Gunsch CK (2012) Genetic bioaugmentation as an effective method for in situ bioremediation: functionality of catabolic plasmids following conjugal transfers. Bioengineered 3(4):236–241
Ikuma K (2011) The effect of select biological and environmental factors on the horizontal gene transfer and functionality of the TOL plasmid: a case study for genetic bioaugmentation
Ikuma K, Gunsch CK (2013) Functionality of the TOL plasmid under varying environmental conditions following conjugal transfer. Appl Microbiol Biotechnol 97(1):395–408
Vogel TM, McCARTY PL (1985) Biotransformation of tetrachloroethylene to trichloroethylene, dichloroethylene, vinyl chloride, and carbon dioxide under methanogenic conditions. Appl Environ Microbiol 49(5):1080–1083
Chae S-R, Hunt DE, Ikuma K, Yang S, Cho J, Gunsch CK, Liu J, Wiesner MR (2014) Aging of fullerene C 60 nanoparticle suspensions in the presence of microbes. Water Res 65:282–289
Fritsche W, Hofrichter M (2008) Aerobic degradation by microorganisms. In: Biotechnology set, 2nd edn, pp 144–167
Gunsch CK, Kinney KA, Szaniszlo PJ, Whitman CP (2006) Quantification of homogentisate-1, 2-dioxygenase expression in a fungus degrading ethylbenzene. J Microbiol Methods 67(2):257–265
Verce MF, Gunsch CK, Danko AS, Freedman DL (2002) Cometabolism of cis-1, 2-dichloroethene by aerobic cultures grown on vinyl chloride as the primary substrate. Environ Sci Technol 36(10):2171–2177
Bossert I, Young L (1986) Anaerobic oxidation of p-cresol by a denitrifying bacterium. Appl Environ Microbiol 52(5):1117–1122
Gibson D, Koch J, Kallio R (1968) Oxidative degradation of aromatic hydrocarbons by microorganisms. I. Enzymic formation of catechol from benzene. Biochemistry 7(7):2653–2662
Rueter P, Rabus R, Wilkest H, Aeckersberg F, Rainey FA, Jannasch HW, Widdel F (1994) Anaerobic oxidation of hydrocarbons in crude oil by new types of sulphate-reducing bacteria. Nature 372(6505):455
Bouwer EJ, Rittmann BE, McCarty PL (1981) Anaerobic degradation of halogenated 1-and 2-carbon organic compounds. Environ Sci Technol 15(5):596–599
Leahy JG, Colwell RR (1990) Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54(3):305–315
Middeldorp PJ, Luijten ML, Pas BAvd, Eekert MHv, Kengen SW, Schraa G, Stams AJ (1999) Anaerobic microbial reductive dehalogenation of chlorinated ethenes. Biorem J 3(3):151–169
Wang P-C, Mori T, Komori K, Sasatsu M, Toda K, Ohtake H (1989) Isolation and characterization of an Enterobacter cloacae strain that reduces hexavalent chromium under anaerobic conditions. Appl Environ Microbiol 55(7):1665–1669
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K (2016) A new view of the tree of life. Nat Microbiol 1:16048
Comolli LR, Banfield JF (2014) Inter-species interconnections in acid mine drainage microbial communities. Front Microbiol 5:367
Martin MS, Santos IC, Carlton DD Jr, Stigler-Granados P, Hildenbrand ZL, Schug KA (2018) Characterization of bacterial diversity in contaminated groundwater using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Sci Total Environ 622–623:1562–1571
Hemme CL, Green SJ, Rishishwar L, Prakash O, Pettenato A, Chakraborty R, Deutschbauer AM, Van Nostrand JD, Wu L, He Z (2016) Lateral gene transfer in a heavy metal-contaminated-groundwater microbial community. mBio 7(2):e02234-15
Anderson RT, Lovley DR (1997) Ecology and biogeochemistry of in situ groundwater bioremediation. Adv Microb Ecol 15:289–350
Proctor CR, Hammes F (2015) Drinking water microbiology—from measurement to management. Curr Opin Biotechnol 33:87–94
Pinto AJ, Xi C, Raskin L (2012) Bacterial community structure in the drinking water microbiome is governed by filtration processes. Environ Sci Technol 46(16):8851–8859
Kinney CA, Furlong ET, Zaugg SD, Burkhardt MR, Werner SL, Cahill JD, Jorgensen GR (2006) Survey of organic wastewater contaminants in biosolids destined for land application. Environ Sci Technol 40(23):7207–7215
Wu C, Spongberg AL, Witter JD, Fang M, Czajkowski KP (2010) Uptake of pharmaceutical and personal care products by soybean plants from soils applied with biosolids and irrigated with contaminated water. Environ Sci Technol 44(16):6157–6161
Hale RC, La Guardia MJ, Harvey EP, Gaylor MO, Mainor TM, Duff WH (2001) Flame retardants: persistent pollutants in land-applied sludges. Nature 412(6843):140–141
Zhang T, Shao M-F, Ye L (2012) 454 pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J 6(6):1137
Nelson MC, Morrison M, Yu Z (2011) A meta-analysis of the microbial diversity observed in anaerobic digesters. Bioresour Technol 102(4):3730–3739
Li B, Yang Y, Ma L, Ju F, Guo F, Tiedje JM, Zhang T (2015) Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J 9(11):2490
Alito CL, Gunsch CK (2014) Assessing the effects of silver nanoparticles on biological nutrient removal in bench-scale activated sludge sequencing batch reactors. Environ Sci Technol 48(2):970–976
Gwin CA, Lefevre E, Alito CL, Gunsch CK (2018) Microbial community response to silver nanoparticles and Ag+ in nitrifying activated sludge revealed by ion semiconductor sequencing. Sci Total Environ 616:1014–1021
Wang S, Gunsch CK (2011) Effects of selected pharmaceutically active compounds on treatment performance in sequencing batch reactors mimicking wastewater treatment plants operations. Water Res 45(11):3398–3406
Lefevre E, Cooper E, Stapleton HM, Gunsch CK (2016) Characterization and adaptation of anaerobic sludge microbial communities exposed to tetrabromobisphenol A. PLoS One 11(7):e0157622
Munck C, Albertsen M, Telke A, Ellabaan M, Nielsen PH, Sommer MO (2015) Limited dissemination of the wastewater treatment plant core resistome. Nat Commun 6:8452
Worth A, Balls M (2002) Alternative (non-animal) methods for chemicals testing: current status and future prospects a report prepared by ECVAM and the ECVAM Working Group on Chemicals. ATLA-NOTTINGHAM- 30:1–3
EPA (2008), Contaminant candidate list (CCL) and regulatory determination (CCL4), https://www.epa.gov/ccl/chemical-contaminants-ccl-4
Gerhard WA, Choi WS, Houck KM, Stewart JR (2017) Water quality at points-of-use in the Galapagos Islands. Int J Hyg Environ Health 220(2):485–493
Goossens H, Ferech M, Vander Stichele R, Elseviers M, E.P. Group (2005) Outpatient antibiotic use in Europe and association with resistance: a cross-national database study. Lancet 365(9459):579–587
Khachatourians GG (1998) Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria. Can Med Assoc J 159(9):1129–1136
Neuhauser MM, Weinstein RA, Rydman R, Danziger LH, Karam G, Quinn JP (2003) Antibiotic resistance among gram-negative bacilli in US intensive care units: implications for fluoroquinolone use. JAMA 289(7):885–888
Witte W (1998) Medical consequences of antibiotic use in agriculture. Science 279(5353):996–997
Allen HK, Donato J, Wang HH, Cloud-Hansen KA, Davies J, Handelsman J (2010) Call of the wild: antibiotic resistance genes in natural environments. Nat Rev Microbiol 8(4):251–259
Knapp CW, Dolfing J, Ehlert PA, Graham DW (2009) Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environ Sci Technol 44(2):580–587
Pruden A, Pei R, Storteboom H, Carlson KH (2006) Antibiotic resistance genes as emerging contaminants: studies in northern Colorado. Environ Sci Technol 40(23):7445–7450
Chopra I, Roberts M (2001) Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol Biol Rev 65(2):232–260
Livermore DM (1995) Beta-lactamases in laboratory and clinical resistance. Clin Microbiol Rev 8(4):557–584
Jacobs L, Chenia HY (2007) Characterization of integrons and tetracycline resistance determinants in Aeromonas spp. isolated from South African aquaculture systems. Int J Food Microbiol 114(3):295–306
Smalla K, Van Overbeek L, Pukall R, Van Elsas J (1993) Prevalence of nptII and Tn5 in kanamycin-resistant bacteria from different environments. FEMS Microbiol Ecol 13(1):47–58
Srinivasan V, Nam H, Nguyen L, Tamilselvam B, Murinda S, Oliver S (2005) Prevalence of antimicrobial resistance genes in Listeria monocytogenes isolated from dairy farms. Foodborne Pathog Dis 2(3):201–211
Zhu B (2007) Abundance dynamics and sequence variation of neomycin phosphotransferase gene (nptII) homologs in river water. Aquat Microb Ecol 48(2):131–140
Mao D, Yu S, Rysz M, Luo Y, Yang F, Li F, Hou J, Mu Q, Alvarez P (2015) Prevalence and proliferation of antibiotic resistance genes in two municipal wastewater treatment plants. Water Res 85:458–466
Colman BP, Arnaout CL, Anciaux S, Gunsch CK, Hochella MF Jr, Kim B, Lowry GV, McGill BM, Reinsch BC, Richardson CJ (2013) Low concentrations of silver nanoparticles in biosolids cause adverse ecosystem responses under realistic field scenario. PLoS One 8(2):e57189
Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74(3):417–433
Holzem R, Stapleton H, Gunsch C (2014) Determining the ecological impacts of organic contaminants in biosolids using a high-throughput colorimetric denitrification assay: a case study with antimicrobial agents. Environ Sci Technol 48(3):1646–1655
Giger W, Alder AC, Golet EM, Kohler H-PE, McArdell CS, Molnar E, Siegrist H, Suter MJ-F (2003) Occurrence and fate of antibiotics as trace contaminants in wastewaters, sewage sludges, and surface waters. CHIMIA Int J Chem 57(9):485–491
Schwartz T, Kohnen W, Jansen B, Obst U (2003) Detection of antibiotic-resistant bacteria and their resistance genes in wastewater, surface water, and drinking water biofilms. FEMS Microbiol Ecol 43(3):325–335
Xi C, Zhang Y, Marrs CF, Ye W, Simon C, Foxman B, Nriagu J (2009) Prevalence of antibiotic resistance in drinking water treatment and distribution systems. Appl Environ Microbiol 75(17):5714–5718
Zhang X-X, Zhang T, Fang HH (2009) Antibiotic resistance genes in water environment. Appl Microbiol Biotechnol 82(3):397–414
Gardner CM, Gunsch CK (2017) Adsorption capacity of multiple DNA sources to clay minerals and environmental soil matrices less than previously estimated. Chemosphere 175:45–51
Gardner CM, Gwin CA, Gunsch CK (2018) A survey of crop derived transgenes in activated and digester sludges in wastewater treatment plants in the United States. Water Sci Technol 77(7–8):1810–1818
Ma B, Blackshaw RE, Roy J, He T (2011) Investigation on gene transfer from genetically modified corn (Zea mays L.) plants to soil bacteria. J Environ Sci Health B 46(7):590–599
Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. Biomed Res Int 2012:251364
Görg A, Weiss W, Dunn MJ (2004) Current two-dimensional electrophoresis technology for proteomics. Proteomics 4(12):3665–3685
Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422(6928):198
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335
Schloss PD, Larget BR, Handelsman J (2004) Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70(9):5485–5492
Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F (2010) Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc 2010(1):pdb.prot5368
Wang S, Gunsch CK (2011) Effects of selected pharmaceutically active compounds on the ammonia oxidizing bacterium Nitrosomonas europaea. Chemosphere 82(4):565–572
Arnaout CL, Gunsch CK (2012) Impacts of silver nanoparticle coating on the nitrification potential of Nitrosomonas europaea. Environ Sci Technol 46(10):5387–5395
Andrieu C, De Freitas N, Doucet A, Jordan MI (2003) An introduction to MCMC for machine learning. Mach Learn 50(1–2):5–43
Goldberg DE, Holland JH (1988) Genetic algorithms and machine learning. Mach Learn 3(2):95–99
Guzdial M, Kolodner J, Hmelo C, Narayanan H, Carlson D, Rappin N, Hubscher R, Turns J, Newstetter W (1996) Computer support for learning through complex problem solving. Commun ACM 39(4):43–46
Kell DB (2006) Metabolomics, modelling and machine learning in systems biology–towards an understanding of the languages of cells. FEBS J 273(5):873–894
Alivisatos AP, Blaser M, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK (2015) A unified initiative to harness Earth’s microbiomes. Science 350(6260):507–508
Ikuma K, Holzem RM, Gunsch CK (2012) Impacts of organic carbon availability and recipient bacteria characteristics on the potential for TOL plasmid genetic bioaugmentation in soil slurries. Chemosphere 89(2):158–163
Gilbert JA, Jansson JK, Knight R (2014) The Earth Microbiome project: successes and aspirations. BMC Biol 12(1):69
Sheth RU, Cabral V, Chen SP, Wang HH (2016) Manipulating bacterial communities by in situ microbiome engineering. Trends Genet 32(4):189–200
Worley-Morse TO, Zhang L, Gunsch CK (2014) The long-term effects of phage concentration on the inhibition of planktonic bacterial cultures. Environ Sci: Processes Impacts 16(1):81–87
Worley-Morse TO, Deshusses MA, Gunsch CK (2015) Reduction of invasive bacteria in ethanol fermentations using bacteriophages. Biotechnol Bioeng 112(8):1544–1553
Morse TO, Morey SJ, Gunsch CK (2010) Microbial inactivation of Pseudomonas putida and Pichia pastoris using gene silencing. Environ Sci Technol 44(9):3293–3297
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Gardner, C.M., Gunsch, C.K. (2020). Environmental Microbiome Analysis and Manipulation. In: O’Bannon, D. (eds) Women in Water Quality. Women in Engineering and Science. Springer, Cham. https://doi.org/10.1007/978-3-030-17819-2_7
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