Skip to main content

Environmental Microbiome Analysis and Manipulation

  • Chapter
  • First Online:
Women in Water Quality

Part of the book series: Women in Engineering and Science ((WES))

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.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 54.99
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. Gavrilescu M (2009) Emerging processes for soil and groundwater cleanup-potential benefits and risks. Environ Eng Manag J 8(5):1293–1307

    Article  Google Scholar 

  2. 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

    Article  Google Scholar 

  3. EPA (2013). Introduction to in situ bioremdiation of groundwater. Office of Solid Wastew and Emergency Response, EPA/542/R-13-018

    Google Scholar 

  4. 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

    Article  Google Scholar 

  5. 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

    Google Scholar 

  6. Ikuma K, Gunsch CK (2013) Functionality of the TOL plasmid under varying environmental conditions following conjugal transfer. Appl Microbiol Biotechnol 97(1):395–408

    Article  Google Scholar 

  7. 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

    Google Scholar 

  8. 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

    Article  Google Scholar 

  9. Fritsche W, Hofrichter M (2008) Aerobic degradation by microorganisms. In: Biotechnology set, 2nd edn, pp 144–167

    Chapter  Google Scholar 

  10. 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

    Article  Google Scholar 

  11. 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

    Article  Google Scholar 

  12. Bossert I, Young L (1986) Anaerobic oxidation of p-cresol by a denitrifying bacterium. Appl Environ Microbiol 52(5):1117–1122

    Google Scholar 

  13. 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

    Article  Google Scholar 

  14. 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

    Article  Google Scholar 

  15. Bouwer EJ, Rittmann BE, McCarty PL (1981) Anaerobic degradation of halogenated 1-and 2-carbon organic compounds. Environ Sci Technol 15(5):596–599

    Article  Google Scholar 

  16. Leahy JG, Colwell RR (1990) Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54(3):305–315

    Google Scholar 

  17. 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

    Article  Google Scholar 

  18. 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

    Google Scholar 

  19. 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

    Article  Google Scholar 

  20. Comolli LR, Banfield JF (2014) Inter-species interconnections in acid mine drainage microbial communities. Front Microbiol 5:367

    Google Scholar 

  21. 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

    Article  Google Scholar 

  22. 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

    Article  Google Scholar 

  23. Anderson RT, Lovley DR (1997) Ecology and biogeochemistry of in situ groundwater bioremediation. Adv Microb Ecol 15:289–350

    Article  Google Scholar 

  24. Proctor CR, Hammes F (2015) Drinking water microbiology—from measurement to management. Curr Opin Biotechnol 33:87–94

    Article  Google Scholar 

  25. 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

    Article  Google Scholar 

  26. 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

    Article  Google Scholar 

  27. 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

    Article  Google Scholar 

  28. 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

    Article  Google Scholar 

  29. 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

    Article  Google Scholar 

  30. Nelson MC, Morrison M, Yu Z (2011) A meta-analysis of the microbial diversity observed in anaerobic digesters. Bioresour Technol 102(4):3730–3739

    Article  Google Scholar 

  31. 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

    Article  Google Scholar 

  32. 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

    Article  Google Scholar 

  33. 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

    Article  Google Scholar 

  34. 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

    Article  Google Scholar 

  35. 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

    Article  Google Scholar 

  36. 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

    Article  Google Scholar 

  37. 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

    Google Scholar 

  38. EPA (2008), Contaminant candidate list (CCL) and regulatory determination (CCL4), https://www.epa.gov/ccl/chemical-contaminants-ccl-4

  39. 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

    Article  Google Scholar 

  40. 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

    Article  Google Scholar 

  41. Khachatourians GG (1998) Agricultural use of antibiotics and the evolution and transfer of antibiotic-resistant bacteria. Can Med Assoc J 159(9):1129–1136

    Google Scholar 

  42. 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

    Article  Google Scholar 

  43. Witte W (1998) Medical consequences of antibiotic use in agriculture. Science 279(5353):996–997

    Article  Google Scholar 

  44. 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

    Article  Google Scholar 

  45. 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

    Article  Google Scholar 

  46. 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

    Article  Google Scholar 

  47. 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

    Article  Google Scholar 

  48. Livermore DM (1995) Beta-lactamases in laboratory and clinical resistance. Clin Microbiol Rev 8(4):557–584

    Article  Google Scholar 

  49. 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

    Article  Google Scholar 

  50. 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

    Article  Google Scholar 

  51. 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

    Article  Google Scholar 

  52. Zhu B (2007) Abundance dynamics and sequence variation of neomycin phosphotransferase gene (nptII) homologs in river water. Aquat Microb Ecol 48(2):131–140

    Article  MathSciNet  Google Scholar 

  53. 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

    Article  Google Scholar 

  54. 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

    Article  Google Scholar 

  55. Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74(3):417–433

    Article  MathSciNet  Google Scholar 

  56. 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

    Article  Google Scholar 

  57. 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

    Article  Google Scholar 

  58. 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

    Article  Google Scholar 

  59. 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

    Article  Google Scholar 

  60. Zhang X-X, Zhang T, Fang HH (2009) Antibiotic resistance genes in water environment. Appl Microbiol Biotechnol 82(3):397–414

    Article  Google Scholar 

  61. 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

    Article  Google Scholar 

  62. 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

    Article  Google Scholar 

  63. 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

    Article  Google Scholar 

  64. 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

    Google Scholar 

  65. Görg A, Weiss W, Dunn MJ (2004) Current two-dimensional electrophoresis technology for proteomics. Proteomics 4(12):3665–3685

    Article  Google Scholar 

  66. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422(6928):198

    Article  Google Scholar 

  67. 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

    Article  Google Scholar 

  68. 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

    Article  Google Scholar 

  69. 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

    Article  Google Scholar 

  70. Wang S, Gunsch CK (2011) Effects of selected pharmaceutically active compounds on the ammonia oxidizing bacterium Nitrosomonas europaea. Chemosphere 82(4):565–572

    Article  Google Scholar 

  71. Arnaout CL, Gunsch CK (2012) Impacts of silver nanoparticle coating on the nitrification potential of Nitrosomonas europaea. Environ Sci Technol 46(10):5387–5395

    Article  Google Scholar 

  72. Andrieu C, De Freitas N, Doucet A, Jordan MI (2003) An introduction to MCMC for machine learning. Mach Learn 50(1–2):5–43

    Article  MATH  Google Scholar 

  73. Goldberg DE, Holland JH (1988) Genetic algorithms and machine learning. Mach Learn 3(2):95–99

    Article  Google Scholar 

  74. 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

    Article  Google Scholar 

  75. 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

    Article  Google Scholar 

  76. 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

    Article  Google Scholar 

  77. 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

    Article  Google Scholar 

  78. Gilbert JA, Jansson JK, Knight R (2014) The Earth Microbiome project: successes and aspirations. BMC Biol 12(1):69

    Article  Google Scholar 

  79. Sheth RU, Cabral V, Chen SP, Wang HH (2016) Manipulating bacterial communities by in situ microbiome engineering. Trends Genet 32(4):189–200

    Article  Google Scholar 

  80. 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

    Google Scholar 

  81. Worley-Morse TO, Deshusses MA, Gunsch CK (2015) Reduction of invasive bacteria in ethanol fermentations using bacteriophages. Biotechnol Bioeng 112(8):1544–1553

    Article  Google Scholar 

  82. 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

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Claudia K. Gunsch .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

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

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-17819-2_7

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-17818-5

  • Online ISBN: 978-3-030-17819-2

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics