Nitrogen‐cycling bacteria and archaea in the carbonate sediment of a coral reef. Issue 5 (15th July 2013)

• Record Type: Journal Article
• Authors: Rusch, A.; Gaidos, E.
• Is Part Of: Geobiology. Volume 11:Issue 5(2013:Sep.)
• Page Start: 472
• Page End: 484
• Publication Date: 2013-07-15
• Subjects: Geobiology -- Periodicals; Biogeochemistry -- Periodicals; Ecology -- Periodicals; 551
• DOI: 10.1111/gbi.12048
• Languages: English
• ISSNs: 1472-4677

Abstract

<abstract abstract-type="main" id="gbi12048-abs-0001"> <title>Abstract</title> <p>In the coarse‐grained carbonate sediments of coral reefs, advective porewater flow and the respiration of organic matter establish redox zones that are the scene of microbially mediated transformations of N compounds. To investigate the geobiology of N cycling in reef sediments, the benthic microbiota of Checker Reef in Kaneohe Bay, Hawaii, were surveyed for candidate nitrate reducers, ammonifying nitrite reducers, aerobic and anaerobic ammonia oxidizers (anammox) by identifying phylotypes of their key metabolic genes (<italic>napA</italic>, <italic> narG</italic>, <italic> nrfA</italic>, <italic> amoA</italic>) and ribotypes (unique RNA sequences) of anammox‐like 16S rRNA. Putative proteobacteria with the catalytic potential for nitrate reduction were identified in oxic, interfacial and anoxic habitats. The estimated richness of <italic>napA</italic> (≥202 in anoxic sediment) and <italic>narG</italic> (≥373 and ≥441 in oxic and interfacial sediment, respectively) indicates a diverse guild of nitrate reducers. The guild of <italic>nrfA</italic> hosts in interfacial reef sediment was dominated by <italic>Vibrio</italic> species. The identified members of the aerobic ammonium oxidizing guild (<italic>amoA</italic> hosts) were Crenarchaeota or close relatives of Nitrosomonadales. Putative anammox bacteria were detected in the RNA pool of Checker Reef sediment. More than half of these ribotypes show ≥90% identity with homologous sequences of <italic>Scalindua</italic> spp., while no evidence was found for members of the genera <italic>Brocadia</italic> or <italic>Kuenenia</italic>. In addition to exploring the diversity of these four nitrogen‐cycling microbial guilds in coral reef sediments, the abundances of aerobic ammonium oxidizers (<italic>amoA</italic>), nitrite oxidizers (<italic>nxrAB</italic>), ammonifying nitrite reducers (<italic>nrfA</italic>) and denitrifiers (<italic>nosZ</italic>) were estimated using real‐time PCR. Representatives of all targeted guilds were detected, suggesting that most processes of the biogeochemical N cycle can be catalyzed by the benthic microbiota of tropical coral reefs.</p> </abstract>