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Abstract Abundance-weighted averaging is a simple and common method for estimating taxon preferences (optima) for phosphorus (P) and other environmental drivers of freshwater-ecosystem health. These optima can then be used to develop transfer functions to infer current and/or past environmental conditions of aquatic ecosystems in water-quality assessments and/or paleolimnological studies. However, estimates of species’ environmental preferences are influenced by the sample distribution and length of environmental gradients, which can differ between datasets used to develop and apply a transfer function. Here, we introduce a subsampling method to ensure a uniform and comparable distribution of samples along a P gradient in two similar ecosystems: the Everglades Protection Areas (EPA) and Big Cypress National Preserve (BICY) in South Florida, USA. Diatom optima were estimated for both wetlands using weighted averaging of untransformed and log-transformed periphyton mat total phosphorus (mat TP) values from the original datasets. We compared these estimates to those derived from random subsets of the original datasets. These subsets, referred to as “SUD” datasets, were created to ensure a uniform distribution of mat TP values along the gradient (both untransformed and log-transformed). We found that diatom assemblages in BICY and EPA were similar, dominated by taxa indicating oligotrophic conditions, and strongly influenced by P gradients. However, the original BICY datasets contained more samples with elevated mat TP concentrations than the EPA datasets, introducing a mathematical bias and resulting in a higher abundance of taxa with high mat TP optima in BICY. The weighted averaged mat TP optima of BICY and EPA taxa were positively correlated across all four dataset types, with taxa optima of SUD datasets exhibiting higher correlations than in the original datasets. Equalizing the mat TP sample distribution in the two datasets confirmed consistent mat TP estimates for diatom taxa between the two wetland complexes and improved transfer-function performance. Our findings suggest that diatom environmental preferences may be more reliable across regional scales than previously suggested and support the application of models developed in one region to another nearby region if environmental gradient lengths are equalized and data distribution along gradients is uniform. 

Coastal ecosystems rapidly transform as sea levels rise faster than ecosystems can build elevation through biological processes that accrete organic matter and inorganic sediment. Benthic microbial communities (periphyton) are a crucial driver of sediment accretion in coastal wetlands by forming, trapping, and stabilizing sediments. Inorganic sediments can be either generated in situ by mineral-accreting organisms (e.g., calcium carbonates by periphyton), or materials can be transported from a different origin when sediments become resuspended and displaced, such as during high-wind weather events. In situ-generated sedimentary materials may contribute significantly to elevation gains. This study examines the drivers of coastal periphyton mineral production and whether periphytic diatoms may be used to characterize gradients in these drivers. Periphyton mineral production rates and diatom assemblage composition were measured along three coastal gradients of surface water salinity, conductivity, pH, and periphyton nutrient content in the Biscayne Bay Coastal Wetlands of South Florida. Periphyton mineral production rates ranged from 0.20-0.53 g/m2/d and were greatest at sites with the highest periphyton total carbon and mineral content while lowest at sites with the highest periphyton organic content and total nitrogen and soil depth. Diatom assemblages that sorted consistently along the coastal salinity gradient were reliable indicators of periphyton mineral production, with seven taxa indicating high rates and seven indicating low rates. Diatoms can provide a helpful link between biotic and abiotic processes, indicating where periphyton-driven mineral production contributes most to inorganic carbon cycling and mineral-driven elevation recovery and, hence, to resiliency to sea level rise. 

{"Abstract":["Environmental and diatom data were collected from sites in the Big Cypress National Preserve (BICY) by the South Florida/Caribbean Inventory and Monitoring Network of the National Park Service and from sites in the Everglades Protection Area (EPA) as part of the Monitoring and Assessment Program of the Comprehensive Everglades Restoration Plan. Samples from years 2012, 2013, 2019, 2019, and 2020 are included in this dataset. Environmental data include drier variables that have been found to influence diatom assemblage composition in the greater Everglades ecosystem, including periphyton mat total phosphorus (a proxy for phosphorus in the environment), water column pH, water column conductivity, water depth, days since last dry, and hydroperiod. Diatom data include diatom species composition as percent relative abundances. Code included is pertinent to the methods described in "Robust species optima estimates from non-uniformly sampled environmental gradients" by Solomon et al. 2025, Journal of Paleolimnology."]} 

Abstract Pulses of resource availability along environmental gradients can filter the local and regional distribution of macrophyte and microbial mat communities in wetlands. Wetlands that experience short hydroperiods (i.e., <6 months with standing water) may cause macrophyte and microbial mat competition for water. However, the stress gradient hypothesis predicts that abiotic stress should increase facilitative co‐regulation of producer dynamics. To determine if and how macrophyte and microbial mat biomass covary along a hydrologic gradient, we conducted two observational surveys and a biomass removal experiment in Everglades National Park, FL, USA. In the survey, macrophyte and microbial mat biomass were measured over a two‐year period across nine hydrologically regulated macrophyte community types to determine drivers of biomass and macrophyte–microbial mat interactions along a hydroperiod gradient (3–8 months) using a structural equation model. In the experiment, the effect of hydrology on the interaction between macrophytes and microbial mats was quantified by measuring the effect of bimonthly removal of macrophyte or microbial mat biomass on the biomass of both communities in plots in wetlands with contrasting hydroperiods (3–6 months). Hydrology and biological interactions influenced macrophyte and microbial mat biomass, with stronger interactions observed in the shortest hydroperiod transect sites dominated bySchoenus nigricansandCladium jamaicense. Along the hydrologic gradient, we found direct negative effects of macrophyte biomass on microbial biomass and vice versa, and a significant positive effect of microbial response to flooding duration on macrophyte biomass. Experimental macrophyte removal in shorter‐hydroperiod wetlands resulted in a significant increase in microbial biomass while microbial mat removal reduced biomass of the dominant macrophyteC. jamaicense. The facilitative effect of microbial mats on macrophyte biomass in shorter‐hydroperiod wetlands may be driven by mats prolonging soil moisture retention due to their desiccation‐resistant structure. Stress‐induced facilitation supported the stress gradient hypothesis across the short‐hydrologic gradient, while competitive interactions were also observed. As climate and human drivers continue altering hydrology in aquatic systems, the type and strength of community interactions will continue to shift and alter distributions across the landscape. 

Environmental and periphyton data were collected from transects in the Biscayne Bay Coastal Wetlands (BBCW) during the wet and dry seasons of 2022 to investigate the rate of carbonate sediment production by periphyton. Environmental data include surface water metrics (pH, salinity, conductivity, and water depth) and soil depths. Periphyton data include nutrient, production, and diatom species composition in samples collected from artificial substrates (periphytometers) placed in the field. Data collection for this project is complete, although the South Florida Management District continues to monitor these transects for a larger ongoing BBCW project. 

Water column nutrient concentrations and autotrophy in oligotrophic ecosystems are sensitive to eutrophication and other long-term environmental changes and disturbances. Disturbance can be defined as an event or process that changes the structure and response of an ecosystem to other environmental drivers. The role disturbance plays in regulating ecosystem functions is challenging because the effect of the disturbance can vary in magnitude, duration, and extent spatially and temporally. We measured changes in total nitrogen (TN), dissolved inorganic nutrient (DIN), total phosphorus (TP), soluble reactive phosphorus (SRP), total organic carbon (TOC), and chlorophyll-a (Chl-a) concentrations throughout the Everglades, Florida Bay, and the Florida Keys. This region has been subjected to a variety of natural and anthropogenic disturbances including tropical storms, fires, eutrophication, and rapid increases in water levels from sea-level rise and freshwater restoration. We hypothesized that the rate of change in water quality would be greatest in the coastal ecotone where disturbance frequencies and marine P concentrations are highest, and in freshwater marshes closest to hydrologic changes from restoration. We applied trend analyses on multi-decadal data (1996–2019) collected from 461 locations distributed from inland freshwater Everglades (ridge and slough) to outer marine reefs along the Florida Keys, USA. Total Organic Carbon decreased throughout the study area and was the only parameter with a systematic trend throughout the study area. All other parameters had spatially heterogeneous patterns in long-term trends. Results indicate more variability across a large spatial and temporal extent associated with changes in biogeochemical indicators and water quality conditions. Chemical and biological changes in oligotrophic ecosystems are important indicators of environmental change, and our regional ridge-to-reef assessment revealed ecosystem-specific responses to both long-term environmental changes and disturbance legacies. 

This data package encompasses hydrologic variables, soil depth, hydrologically-regulated macrophyte community types, macrophyte biomass and community structure, and microbial mat biomass that was collected in two observational surveys and one in-situ experimental manipulation in six temporary wetland regions located in the Everglades, FL, USA. The goal of this project was to examine the co-variation in macrophyte and microbial mat biomass along the hydrologic gradient present across wetland regions and to determine the type and strength of interactions occurring between the two communities, which was tested using a biomass (macrophyte or microbial mat) removal experiment. The census observational survey took place at 140 sites from 2003-04-09 to 2004-05-26, which were randomly distributed across the hydrologic gradient present across the six temporary wetland regions. The transect observational survey occurred along six transects and each was deliberately established along the present hydrologic gradient within each region; a total of 254 sites were sampled from 2003-02-19 to 2005-03-04. The experiment took place at three temporary wetland sites with contrasting hydroperiods (3 – 6 months), and four transects were established per site with 24 pairs of control and treatment plots per transect. The removal treatment occurred one year before data collection, and data collection occurred from 2004-06-20 to 2006-11-25. The package includes six datasets, one R code file, and two shape files associated with the R code. Data collection for all datasets is complete. FCE1274_Census_Survey includes hydrologically-regulated macrophyte community type classifications, macrophyte biomass, microbial mat ash-free dry mass, mean soil depth, water depth, mean annual hydroperiod, and vegetation-inferred hydroperiod; each site was sampled once during the survey period and a subset of sites were sampled each year. FCE1274_Transect_Survey includes macrophyte community type classifications, macrophyte biomass, microbial mat ash-free dry mass, mean soil depth, water depth, mean annual hydroperiod, and vegetation-inferred hydroperiod. Each site was sampled once during the survey period; all sites along each transect were sampled before moving to the next transect. FCE1274_Removal_Experiment includes total macrophyte biomass, live macrophyte biomass, dead macrophyte biomass, and live macrophyte stem density within each microbial mat removal control and treatment plot along each transect at all three sites. Microbial mat dry mass, microbial mat ash-free dry mass, microbial mat chlorophyll-a concentration, and microbial mat organic content for each macrophyte removal control and treatment plot along each transect at all three sites are included as well. Data was collected once from each plot during the data collection period, and one pair of macrophyte removal plots and microbial mat removal plots were randomly sampled on a bimonthly basis until all plots had been sampled. FCE1274_Removal_Experiment_Macrophyte_Biomass includes total macrophyte biomass for each macrophyte species found within each microbial mat removal control and treatment plot along each transect at all three sites. Data was collected once from each plot during the data collection period, and one pair of microbial mat removal plots were randomly sampled on a bimonthly basis until all plots had been sampled. FCE1274_Removal_Experiment_Macrophyte_Density includes total macrophyte stem density for each macrophyte species found within each microbial mat removal control and treatment plot along each transect at all three sites. Data was collected once from each plot during the data collection period, and one pair of microbial mat removal plots were randomly sampled on a bimonthly basis until all plots had been sampled. FCE1274_Removal_Experiment_Macrophyte_Codes includes the taxon codes assigned to each macrophyte species identified in the FCE1274_Removal_Experiment_Macrophyte_Biomass and FCE1274_Removal_Experiment_Macrophyte_Density datasets. 

Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. These changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon. 

Phytoplankton assembly dynamics in lakes are highly sensitive to variability in climate drivers and resulting physicochemical changes in lake water columns. As climate change increases the frequency of major precipitation events and droughts, many lakes experience increased inputs of colored dissolved organic carbon (CDOC) and nutrients. How these CDOC-related changes in resources, transparency, and thermal stability affect phytoplankton assemblages, succession, and resilience is understudied, particularly in subtropical lakes. Here, we used time series, multivariate, and trait-based functional redundancy analyses to elucidate the roles of phytoplankton in ecosystem resilience and determine potential drivers of assemblage shifts in a subtropical monomictic lake with fluctuating CDOC inputs (Lake Annie, Highlands County, Florida, USA). We found that phytoplankton assemblages and successional patterns differed between two dark-water states (late 2005–mid-2007, late 2012–2019) bracketing a clear-water state (mid-2007–late 2012), caused by shifting CDOC and nutrient concentrations associated with oscillating groundwater levels. Diatoms (Bacillariophyta), which were dominant during the two dark-water states, nearly disappeared and were replaced by synurophytes during the clear-water state. Assemblages had greater interannual consistency in the dark-water states, while mean functional redundancy decreased in the clear-water state. Seasonal phytoplankton successional changes were also more pronounced and synchronized with seasonal hydrologic shifts in the dark-water states. Multiyear assemblage shifts occurred more quickly in clear-to-dark than dark-to-clear state transitions, suggesting phytoplankton in dark-water states may be more resistant to state transitions or even contribute to dark-water state resilience via feedback loops. 

Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This study provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) together with nutrient concentrations and environmental parameters at 14 sites along two transects covering two distinctly different drainages: the peat-based Shark River Slough (SRS) and marl-based Taylor Slough/Panhandle (TS/Ph). Both bacterial as well as eukaryotic community structures varied significantly along the salinity gradient. Although freshwater communities were relatively similar in both transects, bacterioplankton community composition at the ecotone (where freshwater and marine water mix) differed significantly. The most abundant taxa in the freshwater marshes include heterotrophic Polynucleobacter sp. and potentially phagotrophic cryptomonads of the genus Chilomonas, both of which could be key players in the transfer of detritus-based biomass to higher trophic levels.