Molecular Methods for the Assessment of Microbial Biofilms in Bioremediation
from: Biofilms in Bioremediation: Current Research and Emerging Technologies (Edited by: Gavin Lear). Caister Academic Press, U.K. (2016) Pages: 105-130.
Advances in molecular methods are providing new insights into the diversity and organisation of biofilm microbial communities as well as the genetic basis of biofilm-mediated contaminant degradation. In the first part of this chapter, we consider the various methods available to inform on the taxonomic and genetic composition of microbial biofilms and to visualise the location of microorganisms genes within complex biofilm communities. Methods directed towards the analysis of functional subsets of these communities, including contaminant degraders are also described. The advantages and disadvantages of a variety of contemporary DNA fingerprinting and sequencing methodologies are each considered. In the second part of this chapter, case studies focusing on the use of molecular techniques in bioremediation assessments are presented. We highlight how the labelling of bacterial taxa with gene specific probes can reveal the complex structural organisation of natural biofilms as well as the impact of pollutants on their composition and organisation. Finally, we detail how the DNA of contaminant-degrading bacteria can be isolated to identify even low abundances of pollutant degrading taxa within diverse and active biofilm communities. The research opportunities provided by modern molecular methods continue to rapidly advance our understanding, and application of, biofilms in bioremediation read more ...