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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. 

{"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."]} 

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. 

Abstract Degradation of wetland ecosystems results from loss of hydrologic connectivity, nutrient enrichment, and altered fire regimes, among other factors. It is uncertain how drivers of wetland ecosystem processes and wetland vegetation communities interact in reversing the ecological trajectory from degraded to restored conditions. We analyzed biogeochemical and vegetation data collected in wetlands of the Florida Everglades at the start of (2015) and during (2018 and 2021) the initial stages of rehydration. Our objectives were to analyze the allocation of carbon and nutrients among ecosystem compartments and correlated trajectories of vegetation community change following rehydration, to identify the drivers of change, including fire, and analyze macrophyte species‐specific responses to drivers. We expected to see changes in vegetation toward more hydric communities that would differ based on wetland baseline conditions and the magnitude of the hydrologic change. During the study period, both length of inundation and surface water depth increased throughout wetlands in the region, and four fires occurred, which affected 51% of the sampling locations. We observed biogeochemical shifts in the wetland landscape, driven by both hydrology and fire. Total phosphorus concentrations in soil and flocculent detrital material decreased, while soil carbon:phosphorus and nitrogen:phosphorus mass ratios increased at sites further away from water management infrastructure. Transitions in vegetation communities were driven by an increase in hydroperiods and by the distinct changes in nutrient concentrations or soil stoichiometric ratios in each subregion. The abundance of macrophyte species typical of short‐hydroperiod prairies strongly decreased, while dominant long‐hydroperiod species, such asEleocharis cellulosa, expanded. Fire facilitated the expansion of thickly vegetated plumes of invasiveTyphaat sites close to the water inflow sources. Overall, restored hydrology shifted vegetation community composition toward higher abundance of long‐hydroperiod species within six years. In contrast, removal of invasive vegetation controlled by soil phosphorus concentrations will likely require long‐term and interactive restoration strategies. 

Abstract Long‐term ecological research can resolve effects of disturbance on ecosystem dynamics by capturing the scale of disturbance and interactions with environmental changes. To quantify how disturbances interact with long‐term directional changes (sea‐level rise, freshwater restoration), we studied 17 yr of monthly dissolved organic carbon (DOC), total nitrogen (TN), and phosphorus (TP) concentrations and bacterioplankton productivity across freshwater‐to‐marine estuary gradients exposed to multiple disturbance events (e.g., droughts, fire, hurricanes, and low‐temperature anomalies) and long‐term increases in water levels. By studying two neighboring drainages that differ in hydrologic connectivity, we additionally tested how disturbance legacies are shaped by hydrologic connectivity. We predicted that disturbance events would interact with long‐term increases in water levels in freshwater and marine ecosystems to increase spatiotemporal similarity (i.e., synchrony) of organic matter, nutrients, and microbial activities. Wetlands along the larger, deeper, and tidally influenced Shark River Slough (SRS) drainage had higher and more variable DOC, TN, and TP concentrations than wetlands along the smaller, shallower, tidally restricted Taylor River Slough/Panhandle (TS/Ph) drainage. Along SRS, DOC concentrations declined with proximity to coast, and increased in magnitude and variability following drought and flooding in 2015 and a hurricane in 2017. Along TS/Ph, DOC concentrations varied by site (higher in marine than freshwater wetlands) but not year. In both drainages, increases in TN from upstream freshwater marshes occurred following fire in 2008 and droughts in 2010 and 2015, whereas downstream increases in TP occurred with coastal storm surge from hurricanes in 2005 and 2017. Decreases in DOC:TN and DOC:TP were explained by increased TN and TP. Increases in bacterioplankton productivity occurred throughout both drainages following low‐temperature events (2010 and 2011) and a hurricane (2017). Long‐term TN and TP concentrations and bacterioplankton productivity were correlated (r > 0.5) across a range of sampling distances (1–50 km), indicating spatiotemporal synchrony. DOC concentrations were not synchronized across space or time. Our study advances disturbance ecology theory by illustrating how disturbance events interact with long‐term environmental changes and hydrologic connectivity to determine the magnitude and extent of disturbance legacies. Understanding disturbance legacies will enhance prediction and enable more effective management of rapidly changing ecosystems.