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Sulfur-cycling microbial communities in salt marsh rhizosphere sediments mediate a recycling and detoxification system central to plant productivity. Despite the importance of sulfur-cycling microbes, their biogeographic, phylogenetic, and functional diversity remain poorly understood. Here, we use metagenomic data sets from Massachusetts (MA) and Alabama (AL) salt marshes to examine the distribution and genomic diversity of sulfur-cycling plant-associated microbes. Samples were collected from sediments underSporobolus alterniflorusandSporobolus pumilusin separate MA vegetation zones, and underS. alterniflorusandJuncus roemerianusco-occuring in AL. We grouped metagenomic data by plant species and site and identified 38 MAGs that included pathways for sulfate reduction or sulfur oxidation. Phylogenetic analyses indicated that 29 of the 38 were affiliated with uncultivated lineages. We showed differentiation in the distribution of MAGs between AL and MA, betweenS. alterniflorusandS. pumilusvegetation zones in MA, but no differentiation betweenS. alterniflorusandJ. roemerianusin AL. Pangenomic analyses of eight ubiquitous MAGs also detected site- and vegetation-specific genomic features, including varied sulfur-cycling operons, carbon fixation pathways, fixed single-nucleotide variants, and active diversity-generating retroelements. This genetic diversity, detected at multiple scales, suggests evolutionary relationships affected by distance and local environment, and demonstrates differential microbial capacities for sulfur and carbon cycling in salt marsh sediments.

Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are key for the decomposition of organic matter, and sulfur oxidizers remove toxic sulfide, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity, and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here, we use comparative genomics to overcome these challenges and provide an in-depth characterization of sulfur-cycling microbial diversity in salt marshes. We characterize communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with uncultivated sulfur-cycling lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.

 

Quantifying and characterizing groundwater flow and discharge from barrier islands to coastal waters is crucial for assessing freshwater resources and contaminant transport to the ocean. In this study, we examined the groundwater hydrological response, discharge, and associated nutrient fluxes in Dauphin Island, a barrier island located in the northeastern Gulf of Mexico. We employed radon ( 222 Rn) and radium (Ra) isotopes as tracers to evaluate the temporal and spatial variability of fresh and recirculated submarine groundwater discharge (SGD) in the nearshore waters. The results from a 40-day continuous 222 Rn time series conducted during a rainy season suggest that the coastal area surrounding Dauphin Island was river-dominated in the days after storm events. Groundwater response was detected about 1 week after the precipitation and peak river discharge. During the period when SGD was a factor in the nutrient budget of the coastal area, the total SGD rates were as high as 1.36 m day –1 , or almost three times higher than detected fluxes during the river-dominated period. We found from a three-endmember Ra mixing model that most of the SGD from the barrier island was composed of fresh groundwater. SGD was driven by marine and terrestrial forces, and focused on the southeastern part of the island. We observed spatial variability of nutrients in the subterranean estuary across this part of the island. Reduced nitrogen (i.e., NH 4 + and dissolved organic nitrogen) fluxes dominated the eastern shore with average rates of 4.88 and 5.20 mmol m –2 day –1 , respectively. In contrast, NO 3 – was prevalent along the south-central shore, which has significant tourism developments. The contrasting nutrient dynamics resulted in N- and P-limited coastal water in the different parts of the island. This study emphasizes the importance of understanding groundwater flow and dynamics in barrier islands, particularly those urbanized, prone to storm events, or located near large estuaries. 

Human‐made stormwater control systems are biogeochemical hotspots, but construction and management may result in homogenization of their ecosystem structure. Roadside ditches are a ubiquitous part of the landscape, yet few studies have quantified their biogeochemical potential. We conducted a study to determine (a) nitrate (NO₃⁻) removal potential through rate measurements and (b) microbial community structure using 16S rRNA gene (iTag) sequencing in roadside ditches draining predominantly forested, urban, and agricultural watersheds surrounding Mobile Bay, AL (USA). We found that nitrogen (N) removal rates by denitrification and anammox dominated over N‐retention by dissimilatory nitrate reduction to ammonium, accounting for upwards of 89% of NO₃⁻reduction on average. There were no differences in soil characteristics between land use types, but denitrification potential rates in forested ditches were less than half of those in urban and agricultural ditches, possibly as a result of differences in vegetation management. Microbial alpha and beta diversity were largely homogenous across the three land use types. However, indicator species analysis revealed putative ammonia oxidizers (NitrososphaeraceaeandNitrosomonadaceae), nitrate reducers (Gaiellales), and nitrous oxide reducers (Myxococcales) as significant groups in urban and agricultural ditches. We conclude that land use effects on N‐removal in these constructed drainage networks are mediated through key microbial groups and ditch vegetation management strategies. Further, roadside ditches have significant potential for reactive N removal in the landscape.

 

Marine oil spills are catastrophic events that cause massive damage to ecosystems at all trophic levels. While most of the research has focused on carbon‐degrading microorganisms, the potential impacts of hydrocarbons on microbes responsible for nitrification have received far less attention. Nitrifiers are sensitive to hydrocarbon toxicity: ammonia‐oxidizing bacteria and archaea being 100 and 1000 times more sensitive than typical heterotrophs respectively. Field studies have demonstrated the response of nitrifiers to hydrocarbons is highly variable and the loss of nitrification activity in coastal ecosystems can be restored within 1–2 years, which is much shorter than the typical recovery time of whole ecosystems (e.g., up to 20 years). Since the denitrification process is mainly driven by heterotrophs, which are more resistant to hydrocarbon toxicity than nitrifiers, the inhibition of nitrification may slow down the nitrogen turnover and increase ammonia availability, which supports the growth of oil‐degrading heterotrophs and possibly various phototrophs. A better understanding of the ecological response of nitrification is paramount in predicting impacts of oil spills on the nitrogen cycle under oil spill conditions, and in improving current bioremediation practices.

 

Human activities have led to 1–2% of coastal wetlands lost per year globally, with subsequent losses in ecosystem services such as nutrient filtering and carbon sequestration. Wetland construction is used to mitigate losses of marsh cover and services resulting from human impacts in coastal areas. Though marsh structure can recover relatively quickly (i.e., <10 years) after construction, there are often long‐term lags in the recovery of ecosystem functions in constructed marshes. We conducted a year‐long study comparing seasonal plant productivity, ecosystem respiration (), denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) between two 33‐year‐old constructed marshes (CON‐1, CON‐2) and a nearby natural reference marsh (NAT). We found that CON‐1 and CON‐2 were structurally similar to NAT (i.e., plant aboveground and belowground biomass did not differ). Likewise, gross ecosystem productivity (GEP),, and net ecosystem exchange (NEE) were similar across all marshes. Further, DNRA and denitrification were similar across marshes, with the exception of greater denitrification rates at CON‐2 than at the other two sites. While pore‐water ammonium concentrations were similar across all marshes, organic matter (OM) content, pore‐water phosphate, nitrate + nitrite, and hydrogen sulfide concentrations were greater in NAT than CON‐1 and CON‐2. Collectively, this work suggests that current marsh construction practices could be a suitable tool for recovering plant structure and some ecosystem functions. However, the lag in recovery of pore‐water nutrient stocks and OM content also suggests that some biogeochemical functions may take longer than a few decades to fully recover in constructed marshes.

 

Human activities have decreased global salt marsh surface area with a subsequent loss in the ecosystem functions they provide. The creation of marshes in terrestrial systems has been used to mitigate this loss in marsh cover. Although these constructed marshes may rapidly recover ecosystem structure, biogeochemical processes may be slow to recover. We compared denitrification and dissimilatory nitrate reduction to ammonium (DNRA) rates between a 32‐year‐old excavation‐created salt marsh (CON‐2) and a nearby natural reference salt marsh (NAT) to assess the recovery of ecosystem function. These process rates were measured at 5 cm increments to a depth of 25 cm to assess how plant rooting depth and organic matter accumulation impact N‐cycling. We found that, for both marshes, denitrification and DNRA declined with depth with the highest rates occurring in the top 10 cm. In both systems, N‐retention by DNRA accounted for upwards of 75% of nitrate reduction, but denitrification and DNRA rates were nearly 2× and 3× higher in NAT than CON‐2, respectively. Organic matter was 6× lower in CON‐2, likely due to limited plant belowground biomass production. However, there was no response to glucose additions, suggesting that the microbial functional community, not substrate limitation, limited nitrate reduction recovery. Response ratios showed that denitrification in CON‐2 recovered in surficial sediments where belowground biomass was highest, even though biomass recovery was minimal. This indicates that although recovery of ecosystem function was constrained, it occurred on a faster trajectory than that of ecosystem structure.