Molecular biological tools for the assessment of hydrocarbon-degrading potential in coastal environments

Abstract

This chapter includes the advances achieved so far in the design and implementation of molecular biological tools (MBTs) for the assessment of hydrocarbon-degrading potential in microbial communities from coastal environments of Patagonia. A brief introduction on the role of hydrocarbon-degrading bacteria in marine environments follows the basic concepts of MBTs, methods, and applications. The review then focuses on studies performed on the Patagonian coast to identify functional biomarker genes associated with hydrocarbon biodegradation, with emphasis on polycyclic aromatic hydrocarbons (PAHs): (a) advances on determining the identity, abundance, and biogeographic distribution of dioxygenase gene variants from known obligate PAH-degrading marine bacteria as well as yet uncultured microorganisms; (b) testing of selected variants in experimental systems; and (c) results of recent metagenomic analyses revealing the genetic context and PAH-degrading capabilities of uncultured microorganisms from Patagonia carrying an ecologically relevant biomarker gene. Alkane biodegradation biomarker genes are also covered, as well as analyses based on phylogenetic biomarker genes. Obligate and specialized hydrocarbon degraders are identified in microbial communities from Patagonia by culture-independent approaches based on the 16S rRNA gene. Last, the design and testing of a community-level ecological indicator based on high-throughput sequencing of the 16S rRNA gene and perspectives on the use of MBTs in coastal regions of Argentinean Patagonia are discussed.