Fig 1.
The sampling area with stars indicating the site locations, triangles the location of the National Weather Service (NWS) [30] monitoring stations in Melbourne (MB), Fort Pierce (FP), and Stuart (ST), and circles the inflow gauge locations [United States Geological Service (USGS) [32] in yellow and the South Florida Water Management District (SFWMD) [31] in red]; the streams or canals associated with these gauges are denoted by blue lines. In Maps A and B black stars are the North Indian River Lagoon (IRL) sites: Merritt Island Causeway (MI), Melbourne Causeway (MC) and the Sebastian Inlet (SI). Blue stars (maps A and C) are the North Central IRL sites: Vero Beach Marina (VM), Barber Bridge (BB), Vero Beach (VB), and Round Island (RI). Red stars (maps A and C) are the South Central IRL sites: Harbor Branch Channel (HB), Linkport (LP), Fort Pierce (FP), and Harbortown Marina (HM). Green stars (maps A and D) are the South IRL sites: Jensen Beach (JB), Manatee Pocket (MP), Jupiter Narrows (JN) and Hobe Sound (HS). Maroon stars (maps A and D) are the St. Lucie Estuary (SLE) sites: North Fork (NF), South Fork (SF), Middle Estuary (ME), and South Fork 2 (ST). This map was created by using a map image from the publicly available Florida Fish and Wildlife Conservation Commission using ArcGIS [33]. GPS coordinates for all study sites and environmental monitoring stations are located in S1 Table.
Fig 2.
Porewater salinity and sediment temperature patterns.
Porewater salinity (PWS) (left) and sediment temperature (right) by Estuary by Sampling Period (A) and by Location (B) for the Indian River Lagoon (IRL) and St. Lucie Estuary (SLE). Bars denote largest and smallest values within 1.5*the interquartile range, middle line is the median, ends of boxes are the first and third quartiles. The letters on top of each boxplot denote the results from the pairwise Dunn test with different letters denoting statistical significance (Benjamini-Hochberg adjusted p values < 0.05). In A the letters show how each of the sampling periods were different within each estuary but do not denote inter-estuary comparisons.
Fig 3.
Bar graph, with error bars denoting standard error, summarizing the average muck characteristics associated with each site. Black bars represent water content. The black dotted line denotes the percentage water content (75% [8]) that a site, if it exceeded all three thresholds, could be considered muck. Percent silt/clay is represented by the dark gray bars with the dark gray dotted line representing the 60% [8] threshold. Total organic matter is represented by the light gray bars with the light gray dotted line representing the 10% [8] threshold.
Fig 4.
Total organic matter by copper.
Point graph showing the relationship between copper (Cu) concentration (μg/g sediment) and total organic matter (TOM) percentage. Each of the 204 samples are represented by a point. Color represents the site with dark blue representing Barber Bridge, bright blue Fort Pierce, red Harbor Branch Channel, purple Harbortown Marina, yellow Hobe Sound, pink Jensen Beach, maroon Jupiter Narrows, dark green Linkport, light blue Manatee Pocket, gold Melbourne Causeway, tan Merritt Island Causeway, dark gray Middle Estuary, light blue North Fork, bright green Round Island, light gray Sebastian Inlet, black South Fork, dark purple South Fork 2, light green Vero Beach, and turquoise Vero Beach Marina. Shape represents the number of muck characteristics with circles representing three muck characteristics, triangles two, squares one, and pluses zero. The blue line at 10% [8] represents the threshold that separates the low TOM (left) from the high TOM (right) sites whereas the red line at 65 μg/g [70] separates the high Cu (above) from the low Cu (below) sites.
Fig 5.
Boxplots of Shannon diversity based by Estuary and Sampling Period (A) and Location (B) categories. IRL stands for Indian River Lagoon and SLE for St. Lucie Estuary. The letters on top of each boxplot denote the results from the pairwise Dunn test with different letters denoting statistical significance (Benjamini-Hochberg adjusted p values < 0.05). In A the letters show how each of the sampling periods were different within each estuary but do not denote inter-estuary comparisons. Bars denote largest and smallest values within 1.5 times the interquartile range, middle line is the median, ends of boxes are the first and third quartiles.
Fig 6.
Prokaryotic community patterns.
Stacked bar graphs showing the phylogenetic orders with a mean prevalence greater than 1% across all samples associated with (A) Indian River Lagoon (IRL) and St. Lucie Estuary (SLE); (B) three muck characteristics and zero muck characteristics samples and (C) high total organic matter/high copper (HiHi) and high total organic matter/low copper (HiLo) samples. TOM stands for total organic matter and Cu stands for copper.
Table 1.
Summarized permutational analysis of variance results.
Fig 7.
Distance-based redundancy analysis.
Distance-based redundancy analysis of the sediment samples with colors representing the amount of copper [high or > 65μg/g [70] (black), low or < 65μg/g (gray)]. The shape shows the number of muck characteristics associated with a sample with circles representing 1–3 characteristics and triangles representing no muck characteristics. A filled shape is an Indian River Lagoon sample and a hollow shape represents a St. Lucie Estuary sample. The results of the distance-based linear models are shown by the lines and their associated environmental parameter and shown in S8 Table.