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

Julia Fortune; Jodie van de Kamp; Bronwyn Holmes; Lev Bodrossy; Karen Gibb; Mirjam Kaestli

doi:10.1016/j.marenvres.2024.106500

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

Mar Environ Res. 2024 Apr 12:198:106500. doi: 10.1016/j.marenvres.2024.106500. Online ahead of print.

Authors

Julia Fortune¹, Jodie van de Kamp², Bronwyn Holmes², Lev Bodrossy², Karen Gibb³, Mirjam Kaestli³

Affiliations

¹ Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Environment, Parks and Water Security, Northern Territory Government, Australia. Electronic address: julia.fortune@cdu.edu.au.
² CSIRO Environment, Hobart, TAS, Australia.
³ Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia.

PMID: 38626627
DOI: 10.1016/j.marenvres.2024.106500

Abstract

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.

Keywords: Biogeochemistry; Macrotidal; Microbial N-Genes; N-cycling; Tropical estuary.