Gene-Targeted Metagenomics Reveals Biogeography of Microbial Biodegradation Capabilities

The field of metagenomics allows us to examine the microbial community in situ with regard to both species and physiogenomic composition.  Gene-targeted metagenomics limits the analysis to specific genes allowing a detailed comparison of a particular metabolic activity by microbes in different ecosystems.  We have been applying this research approach to examine the genetic basis for the biodegradation of different aromatic and aliphatic compounds in soils and sediments from different global locations.  Sampling locations included various aquatic environments in Central Asia, China, Korea, Puerto Rico, and the United States. The sampling locations were influenced by various sources of pollution including industry, oil spills, and other anthropogenic factors. We hypothesized that biodegradative gene populations would cluster based on biogeographical influence with distant sample sites clustering separately from one another and sites within the same environment clustering together.  The extent of pollution exposure, history of the site, and environment type were all expected to have an effect on gene populations.  Cluster dendrograms showed that the biodegradative gene populations recovered by pyrosequencing were diverse, with each sample site having a distinct population.  Overall, clustering of gene fragments was more dependent on location than on the site’s history of environmental contamination.