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

Abstract

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 nearshore 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 (b-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-a in the Fitzroy river estuary.

Nitrifying and denitrifying microbial communities and their relationship to nutrient fluxes and sediment geochemistry in the Derwent Estuary, Tasmania

“…Immediately following thawing, sediment samples were homogenised using a spatula, and DNA was extracted and quantified as previously described (Abell et al 2010). The amoA, nirS and 16S rRNA genes were amplified from DNA extractions using the primers and cycling conditions described in Table S1 in the Supplement at www.…”

“…Standards for qPCR were generated by serial dilutions of known copies of PCR fragments of the respective functional gene generated using M13 PCR from clones generated during the present and previous studies (data not shown). Samples were assayed as previously described (Abell et al 2010) to ensure that there was no significant effect of PCR inhibition on the qPCR data.…”

“…These nitrifiers can be quantified and characterized by analysis of the amoA gene encoding the alpha-subunit of ammonia mono oxygenase. Previous studies have demonstrated that sediment, the primary site of estuarine nitrification, may contain both AOA and AOB, with some estuarine regions dominated by AOB (Mosier & Francis 2008, Santoro et al 2008) and others by AOA (Beman & Francis 2006, Abell et al 2010. The reason for the presence of one group of seemingly functionally equivalent groups over another in the environment is unclear, although it has been suggested that pH (Nicol et al 2008), nitrite (Sahan & Muyzer 2008), sulphide and phosphate (Erguder et al 2009) and salinity (Mosier & Francis 2008) may be important, whilst large variations in salinity, oxygen and hydrological factors may shape the structure of these communities (Stehr et al 1995, Cébron et al 2003, Francis et al 2003, Dang et al 2008, Abell et al 2010, Abell et al 2011.…”

“…Previous studies have demonstrated that nirS is the dominant nitrite reductase in estuarine sediments (Abell et al 2010, Mosier & Francis 2011. Denitrifier community abundance and composition (nirS) have been related to both potential denitrification (Mosier & Francis 2011) and environmental variables including large ranges in salinity and chlorophyll a (chl a) (Abell et al 2010, Mosier & Francis 2011.…”

“…Denitrifier community abundance and composition (nirS) have been related to both potential denitrification (Mosier & Francis 2011) and environmental variables including large ranges in salinity and chlorophyll a (chl a) (Abell et al 2010, Mosier & Francis 2011.…”