McCarthy, Peter J.

The Indian River Lagoon (IRL) FL, USA, is an Estuary of National Significance due to its economic and high biodiversity. Microbial populations are understudied in the IRL despite their numerous ecological services. A two-year, nineteen-site Lagoon-Wide Survey (LWS) was conducted to provide the first 16S rRNA amplicon sequencing data on the microbiome of the sediment in the IRL and determine how the microbiome changed in response to environmental and anthropogenic factors. The most influential variables that explained the variability between microbiomes were porewater salinity, total organic matter (TOM), and copper (Cu). These results correlated with some of the anthropogenic pressures the IRL faces such as freshwater discharges from St. Lucie Estuary (SLE), trace metal contamination, and the accumulation of fine-grained, highly organic sediment known as “IRL muck” (muck). Research then focused on determining the microbial differences between three sets of sample types: sediment from the IRL versus the SLE; sediment that had three muck characteristics versus those with zero; and high TOM sediment that had high Cu versus high TOM sediment that had low Cu. Differentially abundant prokaryotes between sample types were determined with novel indicator analysis techniques. One technique tested the effectiveness of an indicator list to separate samples based upon the product of the sensitivity and specificity of partitioning around medoids clustering in comparison to metadata classifications. The other technique allowed for the tracking of changes in the entire indicator microbiome. These new indicator analysis techniques were created using the original LWS data and tested to determine how sediment microbiomes responded during two opportunistic surveys: dredging of muck from an IRL tributary (Eau Gallie River) and Hurricane Irma. These studies have filled the knowledge gap regarding the unknown microbiome of the IRL and how sediment microbiomes respond to extreme events such as dredging and a hurricane. They also led to the development of new indicator analysis techniques that can be used by to track changes in the entire indicator microbiome.

Vibrio vulnificus is a marine pathogen of human health concern, capable of causing potentially fatal wound infections in a select group of the population. Previous studies have indicated this species’ strong negative correlation with salinity, not typically found above 30 ppt. This study assessed the ability of V. vulnificus to become Viable But Nonculturable in response to elevated salinity (35 ppt) as well as investigated novel methods for confirming their entrance into this state. Results showed a complete loss of culturability in both Environmental and Clinical strains of this bacterium by 9 days after inoculation. Using a High Content Imager, it was determined that these pathogens were not dying (< 10%) in response to the treatment and were partially becoming cocci (≈35%). This study indicates the importance of understanding the impact environmental parameters have on this human pathogen, and what it means for reliably detecting them.

Contamination of recreational waters with fecal waste, indicated by the presence of
enterococci, can have consequences for human and ecosystem health. The difficulty in
determining the extent and origin of fecal pollution in dynamic estuarine systems is
compounded by contributions from sources including septic tanks and agricultural runoff.
This study investigated fecal pollution at five sites with variable hydrological conditions
in the St. Lucie Estuary and Indian River Lagoon. The distribution and occurrence of
enterococci was assessed using traditional cultivation. A human-associated microbial
source tracking assay was validated and applied in these estuaries using qPCR. Results
demonstrated a correlation between enterococci concentrations, rainfall, and salinity. The
human-associated assay was sensitive and specific in the lab; however, human fecal
pollution was not detected in the field even though samples contained high levels of
enterococci. This study highlights the importance of expanding the range of water quality
assessment.

Vibrio bacteria are emerging pathogens responsible for 80,000 illnesses and 100
deaths in the United States each year. Infections are directly linked to the marine
environment and are acquired by consuming contaminated seafood or exposing wounds
during aquatic activities. Florida has the highest national incidence of vibriosis, with 20%
of its cases reported from the Indian River Lagoon region, a popular recreation destination.
This study utilized a combination of cultivation and molecular techniques to investigate
the local distribution of V. vulnificus, V. parahaemolyticus and V. cholerae in this local
waterway. The targeted species were found in an array of samples which may facilitate their
transmission to humans. Overall, these bacteria were abundant in estuarine sediments (Vp:
2,439 CFU/g, Vv: 303 CFU/g, Vc: 176 CFU/g), on the sharp edges of oyster shells (Vp: 82
CFU/cm, Vv: 102 CFU/cm, Vc: 41 CFU/cm), and in the water column (Vp: 3.78 CFU/ml,
Vv: 5.51 CFU/ml, Vc: 2.46 CFU/ml). Vibrio also pose a hazard to recreational anglers as
they were recovered from fish (Vp: 61%, Vv: 55%, Vc: 30%), live bait shrimp (Vp: 80%,
Vv: 37%, Vc: 0%) and hooks (Vp: 32%, Vv: 18%, Vc: 0%). Additionally, a molecular
analysis of the V. vulnificus virulence revealed that the local population was dominated by
disease-causing (vcgC) strains, which may explain why wound-related infections are
common in this region.
Vibrio occurrence varied both spatially and temporally due to their relationship with
salinity and temperature. These bacteria exhibited a strong negative correlation with
salinity, being particularly abundant near freshwater discharge locations. Due to Florida’s
year-round warm climate, these species were found to be permanent members of the local
microbial community. Seasonal peaks in abundance occurred between August and
October, a period which corresponds with the warmest water temperatures as well as
frequent rainfall. Predictive models were constructed based on these parameters to provide
a better understanding of how, when and where Vibrio spp. may be encountered by humans.
This information is important for both water management and healthcare initiatives, with
an overall goal of improving local recreational safety.