Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities

Coral reefs are globally important marine ecosystems as sites of high biotic diversity. Reef flat sediments are reasonably homogeneous in composition. This substratum is subject to gradients in water motion, grazing pressure and benthic productivity. This study used DNA fingerprinting techniques, automated rRNA intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP) to examine patterns of bacterial assemblage composition within Heron Reef flat sediments, targeting the entire bacterial community (not including Archaea) and nitrogenfixing bacteria. ARISA fingerprints contained between 51 and 148 operational taxonomic units (OTU) per surface sediment sample. The mean whole-community similarity between adjacent sites along a transect from Heron Island to the reef crest was 0.50 +/- 0.03 (mean +/- SE) Whittaker Index (comparison of relative abundances) and 0.46 +/- 0.03 Jaccard Index (presence/absence only). Comparison of sediment community fingerprints to a water column community fingerprint collected above the reef flat at high tide indicated that sediments contained different assemblages to the water column (mean similarity between sediments and water column assemblage = 0.15 +/- 0.01 Jaccard Index); however, assemblage composition did not differ significantly from that expected by random association. Vertical sediment cores showed dissimilarity between surface (0 to 3 cm) and deep (3 to 5 cm) community fingerprints, which was probably related to redox state. Comparison of fingerprints of fecally-derived sediments from the sea cucumber Holothuria atra and surrounding sediments indicated that the impact of metazoan grazing could not be distinguished from ambient small spatial scale variability in sediment assemblage composition. The nifH-TRFLP fingerprints of sediment prokaryotic assemblages (amplified from all samples, but only in sufficient quantities for analysis from 7 locations) indicated the presence of ubiquitous, potentially diverse diazotroph communities, with little assemblage similarity between locations. Our results suggested that while bacterial assemblages (including communities of nitrogen-fixing bacteria) in sediments of a coral reef are diverse, their assemblage composition is not related to grazing pressure but may be influenced by other biotic and abiotic environmental conditions such wave energy and sediment depth.