Denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary

Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered “generalist” and “specialist” archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 11-29% of the abundant NRE archetypes. Archetypes found in a particular site, “specialists”, were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe2+. A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H2S, respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among denitrifying communities and supports the essential role of individual community members in overall ecosystem function. Two color array (Cy3 and Cy5): 90-mer oligonucleotide probe consisting of 70-mer archetype sequence and a 20-mer reference oligo is printed to the slide. Cy3 fluoresced environmental DNA sequences, within 15% of the 70-mer archetype, and the 20-mer, Cy5 fluoresced complementary reference oligo will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Two replicate arrays were run on duplicate targets.