Dynamics of nitrogen genes in intertidal sediments of Darwin Harbour and their connection to N-biogeochemistry.

Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N2) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness.

Estuarine benthic habitats provide an important ecosystem service regulating the nitrogen cycle.

Globally, a key ecosystem service provided by sedimentary estuarine habitats is the regulation of nutrient cycles. The nitrogen (N) cycle is driven by complex biogeochemical transformations within these sediments-including nitrogen fixation, denitrification, assimilation and anaerobic ammonia oxidation-mediated by microorganisms. Evaluating ecosystem processes and their functional value is a knowledge gap for the wet-dry tropics and even more limited for macrotidal estuaries. The capacity of these important environments to withstand and assimilate increasing nitrogenous loads as a consequence of accelerating development pressures in tropical Australia is largely unknown. Because of the critical role nitrogen cycling plays in estuarine ecosystems, identifying important habitats that underpin N cycling, particularly denitrification known to mitigate anthropogenic N inputs, is important. Detailed benthic habitat mapping of the Darwin-Bynoe region of northern Australia has provided a rare opportunity to demarcate its key habitats, such as intertidal mudflats, seagrass, mangroves, reef and saltmarsh. Combined with new measurements of benthic nitrogen fluxes, it has been possible for the first time to map these processes and develop a simple integrated functional value for N cycling across key benthic habitats of a tropical macrotidal estuary. Maps generated in this process have provided broadscale identification of the functional importance of habitats with relevance to N removal processes. The role of intertidal sediments in denitrification has been highlighted. Furthermore, the study emphasises connectivity across benthic seascapes, where multiple services are likely to interact, in supporting overall function and ecosystem health. The distillation of composite processes in this mapping format allows resource managers and scientists to communicate outputs visually with a simple classification scheme which could be superimposed with additional data to support environmental assessment and management.