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Nitrogen‐cycling bacteria and archaea in the carbonate sediment of a coral reef
Author(s) -
Rusch A.,
Gaidos E.
Publication year - 2013
Publication title -
geobiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.859
H-Index - 72
eISSN - 1472-4669
pISSN - 1472-4677
DOI - 10.1111/gbi.12048
Subject(s) - anammox , biology , anoxic waters , firmicutes , ecology , proteobacteria , denitrification , denitrifying bacteria , bacteria , chemistry , 16s ribosomal rna , genetics , organic chemistry , nitrogen
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 C hecker R eef in K aneohe B ay, H awaii, were surveyed for candidate nitrate reducers, ammonifying nitrite reducers, aerobic and anaerobic ammonia oxidizers (anammox) by identifying phylotypes of their key metabolic genes ( napA , narG , nrfA , amoA ) and ribotypes (unique RNA sequences) of anammox‐like 16S r RNA . Putative proteobacteria with the catalytic potential for nitrate reduction were identified in oxic, interfacial and anoxic habitats. The estimated richness of napA (≥202 in anoxic sediment) and narG (≥373 and ≥441 in oxic and interfacial sediment, respectively) indicates a diverse guild of nitrate reducers. The guild of nrfA hosts in interfacial reef sediment was dominated by Vibrio species. The identified members of the aerobic ammonium oxidizing guild ( amoA 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 S calindua spp., while no evidence was found for members of the genera Brocadia or K uenenia . In addition to exploring the diversity of these four nitrogen‐cycling microbial guilds in coral reef sediments, the abundances of aerobic ammonium oxidizers ( amoA ), nitrite oxidizers ( nxrAB ), ammonifying nitrite reducers ( nrfA ) and denitrifiers ( nosZ ) 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.