Differential Impacts of Land-Based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs

Abstract

Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine the relationships between microbial communities in these matrices and those in reef water and coral tissues. Significant differences in microbial communities were noted among all sample types but varied between sampling areas. Contamination from outfalls was found to be the greatest potential source of LBSP influencing native microbial community structure among all reef samples, although pollution from inlets was also noted. Notably, reef water and coral tissue communities were found to be more greatly impacted by LBSP at southern reefs, which also experienced the most degradation during the course of the study. The results of this study provide new insights into how microbial communities from LBSP can impact coral reefs in southeast Florida and suggest that wastewater outfalls may have a greater influence on the microbial diversity and structure of these reef communities than do contaminants carried in runoff, although the influences of runoff and coastal inlet discharge on coral reefs are still substantial.IMPORTANCE Coral reefs are known to be endangered due to sewage discharge and to runoff of nutrients, pesticides, and other substances associated with anthropogenic activity. Here, we used next-generation sequencing to characterize the microbial communities of potential contaminant sources in order to determine how environmental discharges of microbiota and their genetic material may influence the microbiomes of coral reef communities and coastal receiving waters. Runoff delivered through inlet discharges impacted coral microbial communities, but impacts from oceanic outfalls carrying treated wastewater were greater. Geographic differences in the degree of impact suggest that coral microbiomes may be influenced by the microbiological quality of treated wastewater.

Faecal bacterial communities from Mediterranean loggerhead sea turtles (Caretta caretta)

“…Water samples were collected from tanks (two different tanks) and from the open sea (two samples taken one mile off the coast, at approximately 500 m of distance from each other; 44 0.067 0 N; 12 42.558 0 E) using clean plastic bottles. For the genomic characterization of the microbial biomass present in both seawater and tank water, each sample was processed as previously described (Campbell et al, 2015;Staley et al, 2017). Briefly, 1.5 1 of water was aseptically filtered via vacuum filtration using a 50-mm diameter, 0.45-μm pore-size sterile Durapore membrane filter (Millipore, Boston, MA).…”

DNA Sequencing as a Tool to Monitor Marine Ecological Status

“…The indices were correlated, a promising result with regard to inclusion of prokaryotic assemblages into future assessment programs (Caruso et al, 2016). Furthermore, DNA sequencing approaches are used for public health applications related to human pathogens derived from fecal contamination (Tan et al, 2015;Staley and Sadowsky, 2016) and to investigate the impacts of anthropogenic stressors on the coral microbiome (Ziegler et al, 2016;Staley et al, 2017). Kelly et al (2016) demonstrate that eDNA in seawater can be used not only for biodiversity measurement but also for assessing anthropogenic disturbance in coastal environments.…”

Peer Review #1 of "Oceanographic habitat and the coral microbiomes of urban-impacted reefs (v0.1)"

“…Finally, time series for satellite CI were validated by linear regression vs. in-water turbidity measurements (NTU) done with boat-based casts using a factory-calibrated nephelometer throughout the sampling period (2013-2015) ( Supplementary Fig. S1; Staley et al 2017).…”

“…The 55 16S rRNA amplicon sequences from coral tissue samples (24 P. astreoides and 31 S. siderea) were leveraged from a previous study (Staley et al 2017). The program DADA2 identified a total of 22,451 ASVs and after filtering, 15,201 ASVs remained.…”