Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary

• Published in: The ISME Journal 2010-02, Vol.4 (2), p.286-300
• Main Authors: Abell, Guy C J, Revill, Andrew T, Smith, Craig, Bissett, Andrew P, Volkman, John K, Robert, Stanley S
• Format: Article
• Language: English
• Subjects: Ammonia; Ammonia - metabolism; Biomedical and Life Sciences; Chlorophyll; Crenarchaeota - genetics; Crenarchaeota - isolation & purification; Crenarchaeota - metabolism; Denitrification; DNA, Archaeal - genetics; Ecology; Ecosystem; Estuaries; Evolutionary Biology; Geologic Sediments - microbiology; Life Sciences; Microbial activity; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microorganisms; Molecular Sequence Data; Nitrification; Nitrogen; Nitrogen - metabolism; Nutrients; original-article; Queensland; Rivers; Salinity; Seawater - microbiology; Sediments; Statistical analysis; Terrestrial environments
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/ismej.2009.105

Nitrification and denitrification are key steps in nitrogen (N) cycling. The coupling of these processes, which affects the flow of N in ecosystems, requires close interaction of nitrifying and denitrifying microorganisms, both spatially and temporally. The diversity, temporal and spatial variations in the microbial communities affecting these processes was examined, in relation to N cycling, across 12 sites in the Fitzroy river estuary, which is a turbid subtropical estuary in central Queensland. The estuary is a major source of nutrients discharged to the Great Barrier Reef near-shore zone. Measurement of nitrogen fluxes showed an active denitrifying community during all sampling months. Archaeal ammonia monooxygenase ( amoA of AOA, functional marker for nitrification) was significantly more abundant than Betaproteobacterial (β-AOB) amoA . Nitrite reductase genes, functional markers for denitrification, were dominated by nirS and not nirK types at all sites during the year. AOA communities were dominated by the soil/sediment cluster of Crenarchaeota , with sequences found in estuarine sediment, marine and terrestrial environments, whereas nirS sequences were significantly more diverse (where operational taxonomic units were defined at both the threshold of 5% and 15% sequence similarity) and were closely related to sequences originating from estuarine sediments. Terminal-restriction fragment length polymorphism (T-RFLP) analysis revealed that AOA population compositions varied spatially along the estuary, whereas nirS populations changed temporally. Statistical analysis of individual T-RF dominance suggested that salinity and C:N were associated with the community succession of AOA, whereas the nirS -type denitrifier communities were related to salinity and chlorophyll- α in the Fitzroy river estuary.