Coral Reefs

, Volume 28, Issue 1, pp 15–26 | Cite as

Diverse communities of active Bacteria and Archaea along oxygen gradients in coral reef sediments



Microbial communities inhabiting highly permeable sediments of Checker Reef in Kaneohe Bay, Hawaii, were characterized in relation to porewater geochemistry (O2, NO3 , NO2 , NH4 +, phosphate). The physiologically active part of the population, assessed by sequencing cDNA libraries of 16S rRNA amplicons, was very diverse, with an estimated ribotype richness ≥1,380 in anoxic sediment. Quantitative analysis of community structure by rRNA-targeted fluorescence in situ hybridization (FISH) indicated that the archaeal population (9–18%) was dominated by marine Crenarchaeota (5–9%). Planctomycetales were the most abundant group in the oxic and interfacial habitat (17–19%) but were a minority (<5%) in anoxic reef sediment, where γ-Proteobacteria were numerically dominant (18%). Another 9–14% of the microbial benthos belonged to β-Proteobacteria, predominantly within the order Nitrosomonadales, many cultured representatives of which are NH4 + oxidizers. The results of this study contribute to the phylogenetic characterization of benthic microbial communities that are important in organic matter degradation and nutrient recycling in coral reef ecosystems.


Coral reef sediment DIN Microbial community Oxygen 



The authors gratefully acknowledge logistical support by the Friends of Heeia (Kaneohe), who made kayaks available for our sampling excursions. Sean Ogata assisted with TOM analyses and cell counts. We thank Brian Popp for supplying a pure culture of Pseudomonas chlororaphis. The German Research Foundation (DFG) supported A.R. with a research scholarship, and A.K.H. was funded by NSF grants OCE-0327332 and GEO-0311912.


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© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Department of Geology and GeophysicsUniversity of Hawaii at ManoaHonoluluUSA
  2. 2.Department of OceanographyUniversity of Hawaii at ManoaHonoluluUSA
  3. 3.Department of Fisheries and Marine Research, Ministry of AgricultureNatural Resources and the EnvironmentNicosiaCyprus

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