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1. Hydrologic history and flooding pulses control iron and sulfur metabolic composition with variable associations to greenhouse gas production in a coastal wetland mesocosm experiment

   https://doi.org/10.1101/2025.03.03.641170  

   Finlay, Colin G; Peralta, Ariane L (March 2025, bioRxiv)

   Coastal wetlands can store carbon by sequestering more carbon through primary production than they release though biogenic greenhouse gas production. The joint effects of saltwater intrusion and sea level rise (SWISLR) and changing precipitation patterns alter sulfate and oxygen availability, challenging estimates of biogenic greenhouse gas emissions. Iron-rich soils have been shown to buffer soil sulfidization by sequestering sulfide into iron-sulfide. But as SWISLR increases soil sulfate concentrations, sulfide produced via sulfate reduction will likely exceed the buffering capacity of soil iron, allowing toxic sulfide levels to accumulate. We used a soil mesocosm approach to examine the influence of hydrology (wet, dry, interim) and plant presence (with or without plants) on wetland soils sourced from different hydrologic histories at a restored coastal wetland. We hypothesized that reducing conditions (i.e., flooded, no plants) impact anaerobic metabolisms similarly, whereas oxidizing conditions (i.e., dry, plant presence) disrupt coupled sulfate reduction and iron reduction. Over eight weeks of hydrologic manipulation, 16S rRNA amplicon sequencing and shotgun metagenomic sequencing were used to characterize microbial communities, while greenhouse gas fluxes, soil redox potential, and physicochemical properties were measured. Results showed that contemporary hydrologic treatment affected assimilatory sulfate reduction gene composition, and hydrologic history influenced dissimilatory sulfate reduction and iron reduction gene composition. Sulfate and iron reduction genes were correlated, and dissimilatory sulfate reduction genes explained variance in methane fluxes. These findings highlight the role of historical hydrology, potential saltwater exposure, and soil iron in shaping microbial responses to future changes in soil moisture and salinity. 

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2. Functional effects of subsidies and stressors on benthic microbial communities along freshwater to marine gradients

   https://doi.org/10.1002/ecy.4427  

   Anderson, Kenneth J; Kominoski, John S; Choi, Chang Jae; Stingl, Ulrich (October 2024, Ecology)

   Abstract Leaf litter in coastal wetlands lays the foundation for carbon storage, and the creation of coastal wetland soils. As climate change alters the biogeochemical conditions and macrophyte composition of coastal wetlands, a better understanding of the interactions between microbial communities, changing chemistry, and leaf litter is required to understand the dynamics of coastal litter breakdown in changing wetlands. Coastal wetlands are dynamic systems with shifting biogeochemical conditions, with both tidal and seasonal redox fluctuations, and marine subsidies to inland habitats. Here, we investigated gene expression associated with various microbial redox pathways to understand how changing conditions are affecting the benthic microbial communities responsible for litter breakdown in coastal wetlands. We performed a reciprocal transplant of leaf litter from four distinct plant species along freshwater‐to‐marine gradients in the Florida Coastal Everglades, tracking changes in environmental and litter biogeochemistry, as well as benthic microbial gene expression associated with varying redox conditions, carbon degradation, and phosphorus acquisition. Early litter breakdown varied primarily by species, with highest breakdown in coastal species, regardless of the site they were at during breakdown, while microbial gene expression showed a strong seasonal relationship between sulfate cycling and salinity, and was not correlated with breakdown rates. The effect of salinity is likely a combination of direct effects, and indirect effects from associated marine subsidies. We found a positive correlation between sulfate uptake and salinity during January with higher freshwater inputs to coastal areas. However, we found a peak of dissimilatory sulfate reduction at intermediate salinity during April when freshwater inputs to coastal sites are lower. The combination of these two results suggests that sulfate acquisition is limiting to microbes when freshwater inputs are high, but that when marine influence increases and sulfate becomes more available, dissimilatory sulfate reduction becomes a key microbial process. As marine influence in coastal wetlands increases with climate change, our study suggests that sulfate dynamics will become increasingly important to microbial communities colonizing decomposing leaf litter. 

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3. Salinity Impacts the Functional mcrA and dsrA Gene Abundances in Everglades Marshes

   https://doi.org/10.3390/microorganisms11051180  

   Jordan, Deidra S.; Kominoski, John; Servais, Shelby; Mills, DeEtta (May 2023, Microorganisms)

   Coastal wetlands, such as the Everglades, are increasingly being exposed to stressors that have the potential to modify their existing ecological processes because of global climate change. Their soil microbiomes include a population of organisms important for biogeochemical cycling, but continual stresses can disturb the community’s composition, causing functional changes. The Everglades feature wetlands with varied salinity levels, implying that they contain microbial communities with a variety of salt tolerances and microbial functions. Therefore, tracking the effects of stresses on these populations in freshwater and brackish marshes is critical. The study addressed this by utilizing next generation sequencing (NGS) to construct a baseline soil microbial community. The carbon and sulfur cycles were studied by sequencing a microbial functional gene involved in each process, the mcrA and dsrA functional genes, respectively. Saline was introduced over two years to observe the taxonomic alterations that occurred after a long-term disturbance such as seawater intrusion. It was observed that saltwater dosing increased sulfite reduction in freshwater peat soils and decreased methylotrophy in brackish peat soils. These findings add to the understanding of microbiomes by demonstrating how changes in soil qualities impact communities both before and after a disturbance such as saltwater intrusion. 

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4. Evaluating Plant-Microbe Associations in Response to Environmental Stressors to Enhance Salt Marsh Restoration

   https://doi.org/10.1007/s12237-026-01730-5  

   Davis, Kai A; McKinney, Mary-Margaret S; Gittman, Rachel K; Peralta, Ariane L (July 2026, Estuaries and Coasts)

   Abstract Despite substantial contributions of ecosystem services, mutualistic plant-microbe associations in wetlands are severely threatened by human activities. Therefore, promoting positive plant-microbe associations underpins coastal wetland restoration, where human stressors and climate change challenge successful outcomes. This study examined how salinity stressors influence plant-microbe relationships, where we hypothesized that the presence of marsh microbes would provide a rescue effect by buffering abiotic stressors and yielding higher plant biomass. We used a whole sediment inocula approach and exposed marsh cordgrass (Sporobolus alterniflorus) plugs to a factorial experiment with three levels of microbiome addition (microbial inocula, autoclaved microbial inocula, no microbe control) and two levels of salinity (< 0.5 psu, 20 psu), replicated ten times. We added marsh-site microbial inocula with autoclaved peat-based greenhouse soil and exposed half the plugs to saltwater (20 psu) and half to freshwater (< 0.5 psu). Results revealed that marsh microbial inocula additions during early plant development may ameliorate salinity stressors. Plants treated with microbial inocula and salinity stress exhibited greater aboveground biomass (P < 0.09) than those under freshwater conditions. With live microbial inocula, the median of aboveground biomass and change in plant height were higher in saltwater compared to freshwater conditions. Change in plant height, belowground biomass, root-to-shoot ratio, soil bacterial diversity H’, and evenness J’ were similar across microbial and salinity treatments. However, salinity (P < 0.001) and microbial treatments (P < 0.001) significantly influenced the bacterial community composition, with distinct assemblages under salinity conditions. This work underscores the need for continued research to develop robust protocols for microbiome stewardship that enhance plant resilience and improve the success of future wetland restoration efforts. 

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5. Saltwater and nutrient legacies reduce net ecosystem carbon storage despite freshwater restoration: insights from experimental wetlands

   https://doi.org/10.1111/rec.13524  

   Lee, Dong Yoon; Kominoski, John S.; Kline, Michael; Robinson, Michelle; Roebling, Suzy (January 2021, Restoration Ecology)

   null (Ed.)

   Net ecosystem carbon balance is a comprehensive assessment of ecosystem function that can test restoration effectiveness. Coastal peatlands are globally important carbon sinks that are vulnerable to carbon loss with saltwater intrusion. It is uncertain how wetland carbon stocks and fluxes change during freshwater restoration following exposure to saltwater and elevated nutrients. We restored freshwater to sawgrass (Cladium jamaicense) peat monoliths from freshwater marshes of the Everglades (Florida, U.S.A.) that had previously been exposed to elevated salinity (approximately9 ppt) and phosphorus (P) loading (1 g P m−2 year−1) in wetland mesocosms. We quantified changes in water and soil physicochemistry, plant and soil carbon and nutrient standing stocks, and net ecosystem productivity during restoration. Added freshwater immediately reduced porewater salinity from >8 to approximately 2 ppt, but elevated porewater dissolved organic carbon persisted. Above- and belowground biomass, leaf P concentrations, and instantaneous rates of gross ecosystem productivity (GEP) and ecosystem respiration (ER) remained elevated from prior added P. Modeled monthly GEP and ER were higher in marshes with saltwater and P legacies, resulting in negative net ecosystem productivities that were up to 12× lower than controls. Leaf litter breakdown rates and litter P concentrations were 2× higher in marshes with legacies of added saltwater and P. Legacies of saltwater and P on carbon loss persisted despite freshwater restoration, but recovery was greatest for freshwater marshes exposed to saltwater alone. Our results suggest that restoration in nutrient-limited freshwater wetlands exposed to saltwater intrusion and nutrient enrichment is a slow process. 

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