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In response to current threats to salt marshes, there are increasing efforts to restore these vital coastal ecosystems and promote their resilience to global change drivers. Unfortunately, the economic cost associated with assessing the effectiveness of restoration is prohibitive and more information is needed about the trajectory and timing of restoration outcomes to improve restoration practices. Microbial communities provide essential salt marsh functions so assessing the degree to which microbial communities in restored marshes resemble reference marshes can serve as a proxy indicator for the potential return of microbial function. We studied a recently restored marsh located on Cape Cod, MA, USA, by examining shifts in the microbial community and sediment edaphic properties in three habitats of a degraded oligohaline marsh, both before and after restoration of tidal flooding and in comparison with three nearby S. alterniflora reference marshes that never had flow restrictions. We hypothesized that the microbial community would respond rapidly to the restoration and that over time these communities would be indistinguishable from reference marsh communities. We found that soil edaphic characteristics shifted along a trajectory of recovery toward the reference marshes, with increases in salinity and decreases in soil organic matter, percentage of carbon, and percentage of nitrogen. The microbial communities in all three habitats within the restored marsh were different from reference marshes, and both the prokaryotic and fungal communities within P. australis and Typha sp. habitats became more similar to reference marshes (similarities increasing from an average of 5 to 16% for prokaryotes and 3 to 10% for fungi) during the first 2 years after restoration. In that same time period, by contrast, there was no return of the native marsh vegetation. These results suggest that shifts in microbial community structure occur prior to shifts in marsh vegetation and may facilitate the successful revegetation of restored marshes. Understanding the recovery trajectory of marshes during restoration and the role that microbes play in promoting the long-term sustainability of these habitats is essential; these results suggest that microbial communities respond rapidly and in a positive direction to restoration efforts. [ABSTRACT FROM AUTHOR]

Summary: The balance between nitrate respiration pathways, denitrification and dissimilatory nitrate (NO3−) reduction to ammonium (DNRA), determines whether bioavailable nitrogen is removed as N2 gas or recycled as ammonium. Saltwater intrusion and organic matter enrichment may increase sulphate reduction leading to sulphide accumulation. We investigated the effects of sulphide on the partitioning of NO3− 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 NO3− respiration. Alternative fates of NO3− became increasingly important at higher sulphide treatments, which could include N2O 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 NO3−, 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. [ABSTRACT FROM AUTHOR]

High‐throughput sequencing has enabled robust shotgun metagenomic sequencing that informs our understanding of the genetic basis of important biogeochemical processes. Slower to develop, however, are the application of these tools in a controlled experimental framework that pushes the field beyond exploratory analysis toward hypothesis‐driven research. We performed flow‐through reactor experiments to examine how salt marsh sediments from varying depths respond to nitrate addition and linked biogeochemical processes to this underlying genetic foundation. Understanding the mechanistic basis of carbon and nitrogen cycling in salt marsh sediments is critical for predicting how important ecosystem services provided by marshes, including carbon storage and nutrient removal, will respond to global change. Prior to the addition of nitrate, we used metagenomics to examine the functional potential of the sediment microbial community that occurred along a depth gradient, where organic matter reactivity changes due to decomposition. Metagenomic data indicated that genes encoding enzymes involved in respiration, including denitrification, were higher in shallow sediments, and genes indicative of resource limitation were greatest at depth. After 92 d of nitrate enrichment, we measured cumulative increases in dissolved inorganic carbon production, denitrification, and dissimilatory nitrate reduction to ammonium; these rates correlated strongly with genes that encode essential enzymes in these important pathways. Our results highlight the importance of controlled experiments in linking biogeochemical rates to underlying genetic pathways. Furthermore, they indicate the importance of nitrate as an electron acceptor in fueling microbial respiration, which has consequences for carbon and nitrogen cycling and fate in coastal marine systems. [ABSTRACT FROM AUTHOR]