Diversity of biogeochemical cycling genes from Puget Sound sediments using DNA microarrays.

Oligonucleotide-based microarray permits the simultaneous analysis of thousands of genes on a single chip, so that a better picture of the interactions among thousands of genes can be investigated at the same time. Our oligo microchips contained 763 50-mer probes that scan the region of different functional genes encoding amoA, pmoA, nirS, nirK, nifH, and dsrAB. These genes code for key enzymes in the ecosystem processes of nitrification, methane oxidation, denitrification, nitrogen fixation and sulfur reduction, respectively. We used these oligochips to characterize the distribution of the above genes from Puget Sound sediments at different depths. The composition and distribution of genes from shallower sediments (depths 00.5 cm, 2.0-2.5 cm, 5.0-5.5 cm, and 25.0-25.5 cm) were highly similar but were different from those collected at deeper depths (depths 50-50.5 cm and 84.0-84.5 cm). The deeper sediments present a different community structure with a markedly lower diversity than the shallower depths. Analysis of positive hybridization signals also revealed presence of genes common to all samples. The majority of these genes were similar to those retrieved from various environments (i.e. soils, groundwater, river water, strotomites, marine sediments, and estuarine sediments). Parallel coordinate display showed that the most dominant functional guilds are those that are involved in nitrogen cycling. Our results also indicated that this technology has potential as a tool in revealing a comprehensive "snapshot" of the functional gene composition in marine sediments, although more work is needed to understand the biological meaning of each detectable hybridization signal.