Community structure of denitrifiers, Bacteria, and Archaea along redox gradients in pacific northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes

Steep vertical gradients of oxidants (O-2 and NO3-) in Puget Sound and Wash ington continental margin sediments indicate that aerobic respiration and d enitrification occur within the top few millimeters to centimeters. To syst ematically explore the underlying communities of denitrifiers, Bacteria, an d Archaea along redox gradients at distant geographic locations, nitrite re ductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymor phism (T-RFLP) analysis, The suitablility of T-RFLP analysis for investigat ing communities of nirS-containing denitrifiers was established by the corr espondence of dominant terminal restriction fragments (T-RFs) of nirS to co mputer-simulated T-RFs of nirS clones. These clones belonged to clusters II , III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H, Devol, and J, M, Tiedje, Appl. Environ, Micr obiol, 66:2096-2104, 2000), T-RFLP analysis of nirS and bacterial rDNA reve aled a high level of functional and phylogenetic diversity, whereas the lev el of diversity of Archaea was lower, A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequ encies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the W ashington margin populations. However, changes in community structure withi n sediment core sections during the transition from aerobic to anaerobic co nditions were minor, Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of pop ulations of similar communities, probably through mixing by marine inverteb rates rather than from the development of distinct communities.