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Monitoring Microbial Community Dynamics to Evaluate Bioremediation

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Abstract

Bioremediation can be an effective treatment strategy at contaminated sites when applied appropriately and implemented properly. Thus it is important to have methods that can be used to reliably assess biodegradation potential and ultimately the feasibility and performance of bioremediation as a treatment approach. While an important component of site monitoring, decreasing trends in contaminant concentrations can result from physical processes, do not document that loss is due to biodegradation, and can be difficult to discern in practice. Therefore direct measures of microbes responsible for biodegradation of compounds have been developed. These methods fall into two categories: direct measure of biodegradation functional genes using methods such as quantitative PCR and microarrays and indirect measures in changes in microbial community structure using methods such as PCR-DGGE and T-RFLP when target genes are unknown. This chapter describes the various molecular methods being used and examples where they have been applied for the assessment of environmental samples.

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Abbreviations

BSS:

Benzylsuccinate synthase

BTEX:

Benzene, toluene, ethylbenzene, and xylenes

DCE:

cis-1,2-dichloroethene

DGGE:

Denaturing gradient gel electrophoresis

FGA:

Functional gene array

ISP:

Iron–sulfur protein

MNA:

Monitored natural attenuation

MPN:

Most probable number

NAH:

Naphthalene dioxygenase

PAHs:

Polycyclic aromatic hydrocarbons

PCE:

Tetrachloroethene

PCR:

Polymerase chain reaction

PHE:

Phenol hydroxylase

qPCR:

Quantitative polymerase chain reaction

RMO:

Ring-hydroxylating toluene monooxygenase

RT-PCR:

Reverse transcriptase-polymerase chain reaction

RT-qPCR:

Reverse transcriptase-quantitative polymerase chain reaction

TCE:

Trichloroethene

TOD:

Toluene/benzene dioxygenase

TOL:

Toluene/xylene monooxygenase

T-RFLP:

Terminal-restriction fragment length polymorphism

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Authors and Affiliations

  1. Microbial Insights, 10515 Research Dr., Suite 100, Knoxville, TN, 37932-2536, USA

    Brett R. Baldwin & Dora Ogles

  2. Purdue University, 915 West State Street, West Lafayette, IN, 47907-2054, USA

    Cindy H. Nakatsu

Authors
  1. Brett R. Baldwin
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  2. Dora Ogles
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  3. Cindy H. Nakatsu
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Correspondence to Cindy H. Nakatsu .

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Editors and Affiliations

  1. Biotechnology Research Center, The University of Tokyo, Tokyo, Japan

    Hideaki Nojiri

  2. Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan

    Masataka Tsuda

  3. Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan

    Masao Fukuda

  4. Bioproduction Research Institute, Nat'l Inst of Adv Industr Sci and Tech, Sapporo, Hokkaido, Japan

    Yoichi Kamagata

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Baldwin, B.R., Ogles, D., Nakatsu, C.H. (2014). Monitoring Microbial Community Dynamics to Evaluate Bioremediation. In: Nojiri, H., Tsuda, M., Fukuda, M., Kamagata, Y. (eds) Biodegradative Bacteria. Springer, Tokyo. https://doi.org/10.1007/978-4-431-54520-0_15

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