Interdisciplinary Development of Diagnostic Bioindicators for Healthy and Degraded Reefs and Adjacent Built Habitats

We have applied multiple analyses (microbiome, environmental) to characterize sediments from the Kristin Jacobs Coral Aquatic Preserve (KJCAP) and develop new diagnostic markers in the context of reef disturbance responses. The results follow previous FL DEP projects on Port Everglades Inlet (PEI) bacterial microbiome and heavy metals (HM) analyses. The KJCAP sediment sample collections spans over 160 Km and covers reef depths from 2 – 30 m. We also have generated a spatiotemporal map of sediment bacteria combined with contemporary environmental datasets ranging from Palm Beach to Miami-Dade county. Although not explicitly stated in this project, our data could be linked to concurrent studies of local water quality. The following hypotheses were posed for this project: a) PEI- specific bacteria can be detected in reef sediments associated with inlet exposure; b) PEI-specific microbe signatures will decrease in proportion to the distance from the port(s) and c) specific microbiome signatures will be found associated with specific parameters – e.g. less urbanized reef communities, or concentrations of specific heavy metals. We identify and quantify previously characterized PEI bacteria, we developed new quantitative PCR (qPCR) primers from archived PEI microbial sequences for higher sensitive detections. We amplified four bacterial genes - fucose, epimerase, hexulose and catalase, and then tested on various DNA derived of port or reef origins. PCR products were detectable in PEI control DNAs but not in adjacent reef sediments, indicating too much dilution of PEI bacteria on reef sediments.

Opportunistic sampling of a total of n=253 reef sediments collected as part of the 2022 and 2024 National Coral Reef Monitoring Program (NCRMP) seasons were characterized for their microbial community composition (e.g. “microbiomes”) via bacterial 16S rRNA amplicon sequence variant (ASV) analyses and eukaryotic meiofauna via metabarcoding methods. This is the first systematic survey of microbiomes at various depths (2 – 28 m) spanning from Palm Beach to Miami-Dade county. By comparing distributions of bacteria with earlier Florida Keys microbiome data, several KJCAP sites appear to lack specific, potential beneficial bioindicator rbacteria such as genus Woeseia and Family Pirellulaceae. Conversely have an increased relative abundance of fecal indicator bacteria (E coli/Shigella), Psychrobacter, and eukaryotic water molds at some KJCAP sites. Port-specific bacteria (e.g. Anaerolineaceae, Thiotrichaceae, Desulfobacteraceae) were also detected in the ASVs, but decreased with increasing distance from human-built structures. 

Variation in sediment microbiomes was most strongly influenced by the maximum temperature in the month prior to sample collection, total carbon, nickel, zinc and Selenium concentrations and by latitude. Samples with higher total carbon, primarily southern sites in the Port Everglades and Haulover contributing areas, had a higher relative abundance of Moraxellaceae. Samples which had experienced higher maximum temperatures, particularly those near Boynton, had higher Bacillaceae and Desulfocapsaeae, and samples with diverse microbiomes had experienced moderate maximum temperatures, had lower total carbon, zinc and selenium concentrations, but higher nickel concentration. Higher concentrations of some trace metals (mercury, cadmium, barium etc) appeared nearer to ports and inlets than more remote reefs. Moreover, integrated statistical analyses and environmental modeling suggested a structuring of the KJCAP into “inlet exposure areas (IEAs), which in turn are influenced by their closest southern inlet