1377 Environmental Technology, Vol. 27. pp 1377-1389 © Selper Ltd., 2006 DIVERSITY OF BIOGEOCHEMICAL CYCLING GENES FROM PUGET SOUND SEDIMENTS USING DNA MICROARRAYS S.M. TIQUIA, 1 * S. GURCZYNSKI 1 , A. ZHOLI 1 AND A. DEVOL 2 * 1 115F Science Building, Department of Natural Sciences, The University of Michigan, Dearborn, MI 48128, USA 1 Department of Natural Sciences, The University of Michigan, Dearborn, MI 48128, USA 2 School of Oceanography, University of Washington, Seattle, WA 98295, USA (Received 10 April 2006; Accepted 25 July 2006) ABSTRACT 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 0- 0.5 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. Keywords: DNA microarrays, microbial community, marine sediments INTRODUCTION Marine sediments constitute 70% of the total earth surface and play an important role in global cycling of C and nutrients [1]. Organic matter from primary production settles to the sea floor, where a major part is remineralized by microorganisms that colonize the sediments. In these areas, the rates of sedimentary oxygen consumption and denitrification are a function of the overlying water concentrations of oxygen and nitrate, and changes in those concentrations directly affect process rates, and thus global C and N dynamics. Nitrification, denitrification, nitrogen fixation, methane oxidation, and sulfate reduction are important environmental processes in biogeochemistry and global changes. It is clear that microbes play important roles in these processes. A great variety of benthic animals (macrofauna) disturb the texture and chemistry of coastal marine sediments. Bioturbation (mixing of surface sediments by the activity of macrofauna) is pervasive in marine environments. The resulting physical and chemical changes are known to enhance microbial activities and growth rates [2]. Our previous work suggested that the bioturbation of the sediments could be one of the key factors affecting the microbial community structure variation with depth [3-5]. We tested this hypothesis more systematically by examining the structure of the denitrifier community within the mixed zone (bioturbation zone) as well as the unmixed zone (below bioturbation zone) from Western Mexico (oxygen-deficient; tropical environment), Pacific Northwest (oxygenated; temperate environment), and Gulf of Mexico (oxygenated; tropical environment). The denitrifier community structure was highly similar down to 37 cm (mixed zone) in Puget Sound and Washington State continental margin sediments, respectively. On the other hand, deeper sediments, retrieved from the unmixed zone, presented a different community structure with a markedly lower diversity. At present,