Microbial transformation of organic chemicals in natural environments: Fate of chemicals and substantiation of microbial involvement through enrichment culturing techniques

Ji Dong Gu*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

8 Scopus citations


Environmental organic pollutants, mostly released through industrial processes, application and accidental spills at high quantities, can be partitioned among several physically distinctive compartments of the sediment including clay minerals, organic matter and biologically active biomass. Among these three, biological processes, including both microbial mediated or non-microbial but organic/enzymatic catalyzed, have been recognized for their roles in transformation and, sometimes completely elimination of organic pollutants in the environment (Bollag and Liu 1990; Dilly et al. 2004). Bioremediation by utilization of selective microbial catalyzed biochemical processes and plants is a very attractive technology in dealing with a wide range of environmental contaminants and in situ cleaning up (Atlas 1995; Kuo and Genthner 1996; Jhanson et al. 1999; Whiteley and Bailey 2000; Yu and Gu 2006, 2007a-d; Yu et al. 2007a,b). At the same time, interactions between organic or inorganic pollutants with organic constituents of the sediments have also been actively studied for a better understanding of the fate of chemicals and the chemical processes and mechanisms involved (Wang et al. 1986; Grossart et al. 2003; Montville and Schaffner 2003; Bakker et al. 2004). Among these, an apparent lack of information is about the contributions by biological transformation and inorganic catalyzed process to the overall elimination of pollutants in the environment (Skipper et al. 1967; Yin et al. 2000; Christensen et al. 2002; Gu et al. 2003a,b; Kleinsteuber et al. 2006). In addition, a large quantities of the literature still show research data on degradation based on comparison between biologically active vs. sterilized system by autoclaving to illustrate and support the biotransformation responsible for elimination of chemicals (Jhanson et al. 1999; Kanaly et al. 2002; Obst et al. 2005). This approach may provide initial information on the fate of chemical pollutants in the simulated environment yielding indication of the biodegradability of the chemical concerned, but further mechanisms of biochemical transformation and/or the identity of the microorganisms involved cannot be revealed from the data obtained. The fundamental information about the biological processes involved and the microorganism acting on the chemicals can only be achieved by further the experimental approach through isolation of the microorganisms and then elucidation of the biochemical pathway (Gu and Berry 1991, 1992; Gu et al. 2005). In this way, fundamental understanding of the chemistry of biotransformation, and both basic microbial physiology and biochemistry can be achieved. In the whole process of investigation of the mechanism, abiotic contribution can be minimized or eliminated completely because the testing system will be depleted with environment constituents derived from the sediment used as an inoculum. Because of the abiotic process participating in biological transformation and similarly biological process in non-biological process. Fate of environmental pollutants should be investigated with the overall view about the transformation by abiotic and biological processes so that the information obtained can be comprehensive for an in-depth understanding of the pollutants in the environment with minimum bias. Because of these, the purpose of this chapter is to provide a discussion about biodegradation study where abiotic processes also play an important role.

Original languageEnglish
Title of host publicationSoil Mineral Microbe-Organic Interactions
Subtitle of host publicationTheories and Applications
PublisherSpringer Berlin Heidelberg
Number of pages24
ISBN (Print)9783540776857
StatePublished - 2008
Externally publishedYes


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