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The balance between nitrate respiration pathways, denitrification and dissimilatory nitrate (NO 3 - ) reduction to ammonium (DNRA), determines whether bioavailable nitrogen is removed as N 2 between complete denitrification and DNRA and the microbial communities in salt marsh sediments. Complete denitrification significantly decreased with increasing sulphide, resulting in an increase in the contribution of DNRA to NO 3 - between complete denitrification and DNRA and the microbial communities in salt marsh sediments. Complete denitrification significantly decreased with increasing sulphide, resulting in an increase in the contribution of DNRA to NO 3 - respiration. Alternative fates of NO 3 - became increasingly important at higher sulphide treatments, which could include N 2 O production and/or transport into intracellular vacuoles. Higher 16S transcript diversity was observed in the high sulphide treatment, with clear shifts in composition. Generally, low and no sulphide, coupled with high NO 3 - , favoured the activity of Campylobacterales, Oceanospirillales and Altermonadales, all of which include opportunistic denitrifiers. High ∑sulphide conditions promoted the activity of potential sulphide oxidizing nitrate reducers (Desulfobulbaceae, Acidiferrobacteraceae and Xanthomonadales) and sulphate reducers (Desulfomonadaceae, Desulfobacteraceae). Our study highlights the tight coupling between N and S cycling, and the implications of these dynamics on the fate of bioavailable N in coastal environments susceptible to intermittent saltwater inundation and organic matter enrichment., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Long-term anthropogenic nitrate (NO3−) enrichment is a serious threat to many coastal systems. Nitrate reduction coupled with the oxidation of reduced forms of sulfur is conducted by chemolithoautotrophic microbial populations in a process that decreases nitrogen (N) pollution. However, little is known about the diversity and distribution of microbes capable of carbon fixation within salt marsh sediment and how they respond to long-term NO3− loading. We used genome-resolved metagenomics to characterize the distribution, phylogenetic relationships, and adaptations important to microbial communities within NO3−-enriched sediment. We found NO3− reducing sulfur oxidizers became dominant members of the microbial community throughout the top 25 cm of the sediment following long-term NO3− enrichment. We also found that most of the chemolithoautotrophic genomes recovered contained striking metabolic versatility, including the potential for complete denitrification and evidence of mixotrophy. Phylogenetic reconstruction indicated that similar carbon fixation strategies and metabolic versatility can be found in several phylogenetic groups, but the genomes recovered here represent novel organisms. Our results suggest that the role of chemolithoautotrophy within NO3−-enriched salt marsh sediments may be quantitatively more important for retaining carbon and filtering NO3− than previously indicated and further inquiry is needed to explicitly measure their contribution to carbon turnover and removal of N pollution. [ABSTRACT FROM AUTHOR]