Skip to main content
SpringerLink
Log in
Book cover

Advances in Applied Bioremediation pp 339–353Cite as

Molecular Tools for Monitoring and Validating Bioremediation

  • Chapter
  • First Online:

Part of the book series: Soil Biology ((SOILBIOL,volume 17))

Abstract

Bioremediation is now in a position to take advantage of genomic-driven strategies to analyze, monitor and assess its course by considering multiple micro-organisms with various genomes, expressed transcripts and proteins. High-throughput methodologies, including microarrays, fingerprinting, real-time PCR, metagenomics and metaproteomics, show great promise in our environmental interventions against recalcitrant contaminants such as 2,4,6-trinitrotoluene (TNT) that we have been studying for many years. The emerging genomic and metagenomic methodologies will allow us to promote or restore environmental health in impacted sites, monitor remediation activities, identify key microbial players and processes, and finally compile an intelligent database of genes for targeted use in bioremediation.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
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

Learn about institutional subscriptions

References

  • Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH, Watson D, Brodie EL, Hazen TC, Keller M (2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72:3291–3301

    Article  CAS  Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    CAS  Google Scholar 

  • Ashby MN, Rine J, Mongodin EF, Nelson KE, Dimster-Denk D (2007) Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl Environ Microbiol 73:4532–4542

    Article  CAS  Google Scholar 

  • Barlaan EA, Sugimori M, Furukawa S, Takeuchi K (2005) Profiling and monitoring of microbial populations by denaturing high-performance liquid chromatography. J Microbiol Meth 61:399–412

    Article  CAS  Google Scholar 

  • Binga EK, Lasken RS, Neufeld JD (2008) Mini-review: something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J 2:233–41

    Article  CAS  Google Scholar 

  • Boubakri H, Beuf M, Simonet P, Vogel TM (2006) Development of metagenomic DNA shuffling for the construction of a xenobiotic gene. Gene 375:87–94

    Article  CAS  Google Scholar 

  • Chandler DP, Jarrell AE, Roden ER, Golova J, Chernov B, Schipma MJ, Peacock AD, Long PE (2006) Suspension array analysis of 16S rRNA from Fe- and SO4 2− -reducing bacteria in uranium-contaminated sediments undergoing bioremediation. Appl Environ Microbiol 72:4672–4687

    Article  CAS  Google Scholar 

  • Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P (2005) Metagenomic gene discovery: past, present and future. Trends Biotechnol 23:321–329

    Article  CAS  Google Scholar 

  • Daffonchio D (2005) Molecular tools to track complex microbial populations in polluted environments and during reclamation. In: Fava F, Canepa P (eds) Innovative approaches to the bioremediation of contaminated sites, soil remediation series Nº6. INCA, Venice, Italy (ISBN: 88-88214-33-X)

    Google Scholar 

  • Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3:470–478

    Article  CAS  Google Scholar 

  • Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99:5261–5266

    Article  CAS  Google Scholar 

  • DeLong EF (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3:459–469

    Article  CAS  Google Scholar 

  • DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N-U, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM (2006) Community genomics among stratified microbial assemblages in the ocean’s interior. Science 311:496–503

    Article  CAS  Google Scholar 

  • Deutschbauer AM, Chivian D, Arkin AP (2006) Genomics for environmental microbiology. Curr Opin Biotechnol 17:229–235

    Article  CAS  Google Scholar 

  • El Fantroussi S, Agathos SN (2005) Is bioaugmentation a feasible strategy for pollutant removal and site remediation? Curr Opin Microbiol 8:268–275

    Article  CAS  Google Scholar 

  • El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM, Stahl DA (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 69:2377–2382

    Article  CAS  Google Scholar 

  • Erwin DP, Erickson IK, Delwiche ME, Colwell FS, Strap JL, Crawford RL (2005) Diversity of oxygenase genes from methane- and ammonia-oxidizing bacteria in the Eastern Snake River plain aquifer. Appl Environ Microbiol 71:2016–2025

    Article  CAS  Google Scholar 

  • Eyers L, Agathos SN, El Fantroussi S (2004a) Denaturing gradient gel electrophoresis (DGGE) as a fingerprinting tool for analyzing microbial communities in contaminated environments. In: Spencer JFT, Ragout de Spencer AL (eds) Environmental microbiology — methods and protocols. Humana Press, Totowa, pp 407–417

    Google Scholar 

  • Eyers L, George I, Schuler L, Stenuit B, Agathos SN, El Fantroussi S (2004b) Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Appl Microbiol Biotechnol 66:123–130

    Article  CAS  Google Scholar 

  • Eyers L, Smoot JC, Smoot LM, Bugli C, Urakawa H, McMurry Z, Siripong S, El Fantroussi S, Lambert P, Agathos SN, Stahl DA (2006) Discrimination of shifts in a soil microbial community associated with TNT-contamination using functional ANOVA of 16S rRNA hybridized to oligonucleotide microarrays. Environ Sci Technol 40:5867–5873

    Article  CAS  Google Scholar 

  • Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ. Microbiol 65:4630–4636

    CAS  Google Scholar 

  • Gao H, Yang ZK, Gentry TJ, Wu L, Schadt CW, Zhou J (2007) Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Appl Environ Microbiol 73:563–571

    Article  CAS  Google Scholar 

  • George I, Eyers L, Stenuit B, Agathos SN (2008) Effect of 2,4,6-trinitrotoluene on soil bacterial communities. J Ind Microbiol Biotechnol 35:225–236

    Article  CAS  Google Scholar 

  • Gentry TJ, Wickham GS, Schadt CW, He Z, Zhou J (2006) Microarray applications in microbial ecology research. Microb Ecol 52:159–175

    Article  CAS  Google Scholar 

  • Golyshin PN, Martins Dos Santos VAP, Kaiser O, Ferrer M, Sabirova YS, Lünsdorf H, Chernikova TN, Golyshina OV, Yakimov MM, Pühler A, Timmis KN (2003) Genome sequence completed of Alcanivorax borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems. J Biotechnol 106:215–220

    Article  CAS  Google Scholar 

  • Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305:1457–1462

    Article  CAS  Google Scholar 

  • Handelsman J (2005) Sorting out metagenomes. Nature Biotechnol 23:38–39

    Article  CAS  Google Scholar 

  • Harms G, Layton AC, Dionisi HM, Gregory IR, Garrett VM, Hawkins SA (2003) Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ Sci Technol 37:343–351

    Article  CAS  Google Scholar 

  • He Z, Deng Y, Van Nostrand JD, Wu L, Hemme CL, Liebich J (2007a) GeoChip 3.0: Further development and applications of functional gene arrays (FGAs) for analysis of microbial communities. 107th ASM General Meeting, Toronto, ON, Canada, poster N178.

    Google Scholar 

  • He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC (2007b) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1:67–77

    Article  CAS  Google Scholar 

  • Inglis GD, Kalischuk LD (2004) Direct quantification of Campylobacter jejuni and Campylobacter lanienae in feces of cattle by real-time quantitative PCR. Appl Environ Microbiol 70:2296–2306

    Article  CAS  Google Scholar 

  • Kube M, Beck A, Zinder SH, Kuhl H, Reinhardt R, Adrian L (2005) Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol 23:1269–1273

    Article  CAS  Google Scholar 

  • Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3:510–516

    Article  CAS  Google Scholar 

  • Marsh TL, Saxman P, Cole J, Tiedje J (2000) Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl Environ Microbiol 66:3616–3620

    Article  CAS  Google Scholar 

  • Neufeld JD, Mohn WW, de Lorenzo V (2006) Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. Environ Microbiol 8:126–140

    Article  CAS  Google Scholar 

  • Paerl HW, Steppe TF (2003) Scaling up: the next challenge in environmental microbiology. Environ Microbiol 5:1025–1038

    Article  Google Scholar 

  • Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724–3730

    CAS  Google Scholar 

  • Ram RJ, VerBerkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC (2005) Community proteomics of a natural microbial biofilm. Science 308:1915-1920

    Article  CAS  Google Scholar 

  • Rittmann BE, Hausner M, Löffler F, Love NG, Muyzer G, Okabe S, Oerther DB, Peccia J, Raskin L, Wagner M (2006) A vista for microbial ecology and environmental biotechnology. Environ Sci Technol 40:1096–1103

    Article  Google Scholar 

  • Robertson LA, Steer BA (2004) Recent progress in biocatalyst discovery and optimization. Curr Opin Chem Biol 8:141–149

    Article  CAS  Google Scholar 

  • Scow KM, Hicks KA (2005) Natural attenuation and enhanced bioremediation of organic contaminants in groundwater. Curr Opin Biotechnol 16:246–253

    Article  CAS  Google Scholar 

  • Stenuit B, Eyers L, El Fantroussi S, Agathos SN (2005) Promising strategies for the mineralisation of 2,4,6-trinitrotoluene. Rev Environ Sci Biotechnol 4:39–60

    Article  CAS  Google Scholar 

  • Stenuit B, Eyers L, Rozenberg R, Habib-Jiwan J-L, Agathos SN (2006) Aerobic growth of Escherichia coli on 2,4,6-trinitrotoluene (TNT) as sole nitrogen source and evidence of TNT denitration by whole cells and cell-free extracts. Appl Environ Microbiol 72:7945–7948

    Article  CAS  Google Scholar 

  • Suenaga H, Ohnuki T, Miyazaki K (2007) Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ Microbiol 9:2289–2297

    Article  CAS  Google Scholar 

  • Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630

    CAS  Google Scholar 

  • Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308:554–557

    Article  CAS  Google Scholar 

  • van der Lelie D, Lesaulnier C, McCorkle S, Geets J, Taghavi S, Dunn J (2006) Use of single-point genome signature tags as a universal tagging method for microbial genome surveys. Appl Environ Microbiol 72:2092–2101

    Article  CAS  Google Scholar 

  • Wagner M, Nielsen PH, Loy A, Nielsen JL, Daims H (2006) Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays. Curr Opin Biotechnol 17:83–91

    Article  CAS  Google Scholar 

  • Whitaker RJ, Banfield JF (2006) Population genomics in natural microbial communities. Trends Ecol Evol 21:508–516

    Article  Google Scholar 

  • Wick LM, Rouillard JM, Whittam TS, Gulari E, Tiedje JM, Hashsham SA (2006) On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Res 34:e26

    Article  Google Scholar 

  • Wu L,Thompson DK, Li G, Hurt RA, Tiedje JM, Zhou J (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 67:5780–5790

    Article  CAS  Google Scholar 

  • Wu L, Liu X, Schadt CW, Zhou J (2006) Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 72:4931–4941

    Article  CAS  Google Scholar 

  • Yu C-P, Ahuja R, Sayler GS, Chu K-H (2005) Quantitative molecular assay for fingerprinting microbial communities of wastewater and estrogen-degrading consortia. Appl Environ Microbiol 71:1433–1444

    Article  CAS  Google Scholar 

  • Yu C-P, Chu, K-H (2005) A quantitative assay for linking microbial community function and structure of a naphthalene-degrading microbial consortium. Environ Sci Technol 39:9611–9619

    Article  CAS  Google Scholar 

  • Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:288–294

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Unit of Bioengineering, Faculty of Bioengineering, Agronomy & Environment, Université Catholique de Louvain, Place Croix du Sud 2/19, B-1348, Louvain-la-Neuve, Belgium

    Ben Stenuit, Laurent Eyers, Luc Schuler, Isabelle George & Spiros N. Agathos

Authors
  1. Ben Stenuit
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Laurent Eyers
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Luc Schuler
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Isabelle George
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Spiros N. Agathos
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Spiros N. Agathos .

Editor information

Editors and Affiliations

  1. Dept. Biology, University of Waterloo, University Avenue W. 200, Waterloo, N2L 3G1, Canada

    A. Singh

  2. Fac. Inter-Disciplinary &, University of Delhi, Benito Juarez Road, New Delhi, 110021, India

    Ramesh C. Kuhad

  3. Dept. Biology, University of Waterloo, University Avenue W. 200, Waterloo, N2L 3G1, Canada

    Owen P. Ward

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Stenuit, B., Eyers, L., Schuler, L., George, I., Agathos, S.N. (2009). Molecular Tools for Monitoring and Validating Bioremediation. In: Singh, A., Kuhad, R., Ward, O. (eds) Advances in Applied Bioremediation. Soil Biology, vol 17. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-89621-0_18

Download citation

Publish with us

Policies and ethics

Search

Navigation