Until recently, culture-independent analysis of microbial communities has relied on analysis of specific nucleic acid sequences amplified from total genomic DNA extracted from the environment. The advent of high-throughput sequencing has however opened the way to large-scale sequencing of environmental genomic DNA. The advantage of this approach is that it is possible to link phylogenetic marker genes such as small subunit rRNA genes with those that relate to an organism's physiological properties. This has led to the discovery of entirely new metabolic capabilities in uncultured organisms. In addition to the widespread presence of novel light-driven proton pumps already alluded to in a previous section, environmental genomics has also led to the discovery of novel archaea that catalyze the oxidation of ammonia to nitrite, previously a process considered to be solely the domain of a small number of bacterial taxa.
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