An inundation threshold regulates nitrate reduction pathways in mangrove sediments

Estuarine hydrological regimes are increasingly altered by dam operations and extreme climate events, reshaping inundation in intertidal wetlands. However, how inundation regulates nitrate (NO₃^-) fate remains unclear. We conducted an 18-month, elevation-controlled marsh-organ experiment with Avicennia marina-planted and unvegetated sediments across a 0 %-65 % gradient in mean inundation frequency. We combined ¹⁵N isotope tracing and metagenomics to quantify NO₃^- reduction pathways and associated microbial attributes. In unvegetated sediments, increasing inundation reduced the contribution of denitrification (DNF) from 62 % to 48 % and increased dissimilatory nitrate reduction to ammonium (DNRA) from 25 % to 34 %. In planted sediments, NO₃^- reduction shifted nonlinearly at approximately 24 % mean inundation frequency. Below this threshold, DNF dominated, contributing 83 %-87 % of NO₃^- reduction, whereas DNRA contributed only 2 %-6 %. Above the threshold, DNF declined to 45 % at the highest inundation frequencies, while DNRA increased to 42 %-48 %, indicating a shift from nitrogen removal toward retention. This transition coincided with plant failure, more reducing conditions, and changes in microbial community and functional profiles. Plant survival was associated with DNF-related taxa (e.g., Pseudomonas and Flavobacterium), nirK, and oxidative metabolism, whereas plant failure was associated with DNRA-related taxa (e.g., Shewanella and Geobacter), nrfA, and fermentative metabolism. These findings identify a vegetation-dependent inundation threshold beyond which nitrogen removal declines and nitrogen retention increases in mangrove sediments.