The Effects of Nutrient Loading and Coral Contamination on the Reefs of Southeast Florida and the Keys

This topic submitted by Joel P. Thrash ( at 2:15 PM on 6/13/03.

The earth's axis of rotation wobbles like a spinning top. There are two periods (a wobble within a wobble): 19,000 AND 23,000 years. Precession has a profound effect on the earth's climate.

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The Effects of Nutrient Loading and Coral Contamination on the Reefs of Southeast Florida and the Keys

Joel P. Thrash
GLG 513
13 June 2003
Dr. R Hays Cummins

Executive Summary

Serving as the home to the only emergent reefs in the continental United States, the coral communities in southeast Florida and the Keys are a critical national resource. However, current research suggests that these reef communities are becoming increasingly threatened from anthropogenic sources of pollution, namely nutrient loading from improperly treated sewage that continues to leak from groundwater on both sides of the Keys. Some impacts of nutrient loading include excessive algal growth, increasing coral diseases, coral contamination, marine grass and sponge mortality, and decreased living coral cover. This paper will highlight and critically examine the current research that suggests that these problems are the result of nutrient loading from, perhaps, inadequate water resource management. The patterns and evidence for fecal contamination in corals of the Florida Keys are described; additionally, the spread of coral diseases as well as efforts to monitor and mitigate nutrient loading will be discussed.


The Florida Reef Tract is the most widespread living coral reef system in North American waters and the third largest system in the world (Florida Keys NMS). Extending over 600mi2 (1550 km2) across southern Florida and across the Florida Keys archipelago, these reefs were formed roughly 6,000 years ago and consist of a series of ridges and channels that form parallel to the Straits of Florida (USGS, 2002). The reefs comprise a bank reef system of almost continuous reef communities in lines that run parallel to each another. There are several distinct habitats including offshore patch reefs, seagrass beds, back reefs and reef flats, bank or transitional reefs, intermediate reefs, sand and soft bottom deep reefs, outlier reefs, and more (Florida Keys NMS, 2003).
Unfortunately, there are numerous threats to the marine environments in south Florida and the Keys. Past research has shown that there is a decline of healthy corals, an invasion by algae into seagrass beds and reefs, a decline in certain fishries, an increase of coral diseases, and coral bleaching (Porter et al, 2001). Although the cause of these problems, whether natural or anthropogenic, can be debated, research has shown that land use and resource exploitation by humans have taken its toll on the coral communities in the Florida Reef Tract. On average, over three (3) million visitors and 80,000 full time residents inhabit the Florida Keys each year; consequently, there are significant direct and indirect effects from the high levels of use from both residents and tourists (Florida Keys NMS, 2003). For instance, over 19 acres of coral reef habitat has been damaged or destroyed by large ship groundings, and over 30,000 acres of seagrasses have been damaged by boat propellers (USGS, 2002). Direct impacts to resources also result from careless divers, snorkelers standing on coral, improperly placed anchors, and destructive fishing methods.
Without a doubt, the indirect human impacts to the Florida Reef Tract are much more severe than direct impacts, and in terms of management, they are especially more difficult to quantify, regulate, and ultimately mitigate. Although sedimentation is the most widespread problem, nutrient loading of nearshore waters is perhaps the most well documented indirect human impact and most severe impact plaguing several stretches of the Florida Reef Tract, particularly in the Florida Keys National Marine Sanctuary. Thus, management and mitigation efforts to protect coral reefs in the Florida Keys should focus on the elimination of diffuse sources of pollution, particularly nutrient and fecal loadings.

Nutrient Loading

Corals and reef environments are subjected to augmented stress from anthropogenic activities, particularly around heavily populated areas such as the Florida Keys. Researchers from the Florida Keys NMS have noted a loss of diversity in corals and an increase in diseased and damaged corals throughout the NMS; similarly, a recent review of coral disease show that 97% of coral disease in the Caribbean region was documented in reefs moderately to highly impacted by human activity (Lipp et al, 2002). Some of these diseases include black band disease, white pox, coral bleaching, and macroalgal blooms (Porter et al, 2001).
Throughout the United States and in multiple types of aquatic environments, diffuse sources of pollution are believed to be the major cause of degraded water quality (Harvell, 1999). In the Florida Reef Tract, this is very much the case. Several diffuse sources of pollution are thought to be responsible for coral disease and contamination, but the most significant seems to be nutrient loading and nutrient enrichment from improperly treated and mismanaged wastewater.
In the Florida Keys alone there are roughly 200 sewage treatment plants, 22,000 septic tanks, 5,000 cesspools and 139 marinas harboring over 15,000 boats (Shinn et al, 1994). Nutrients, namely nitrate (NO3) and phosphorous (undissolved particulate P), are intimately associated with sewage and carried through the region by more than 700 canals and channels (Shinn et al, 1994). Organic nitrogen, NH4, is carried in groundwater reservoirs and is problematic through seepage of porous limestone (Shinn et al, 1994). Removing nitrogen and phosphorous from wastewater requires a technology that, at present, is lacking from septic tanks and most other sewage treatment facilities in the Keys.
Nutrient enrichment in tropical waters has the most significant effect on reef-building corals such as those found in the Florida Reef Tract (Booth et al, 2001). Specifically inorganic forms of N (nitrate) and P (particulate P) have the greatest effect on coral mortality and reproduction (Booth et al, 2001). The production of viable gametes and successful fertilization has been proven to be greatly reduced by such inorganic forms of nitrogen and phosphorous (Booth et al, 2001). Phosphorous on its own has proven to dramatically reduce fertilization and stimulate the growth of irregular embryos (Booth et al, 2001). Corals exposed to elevated amounts of ammonium produced smaller and fewer eggs and had less testes material compared to unexposed corals (Booth et al, 2001).
Another form of diffuse pollution, organochlorine pesticide residue, also appears to have an adverse effect on corals in the Florida Reef Tract. Organochlorine pesticides are known for their persistence and global occurrence in marine waters (Glynn et al, 1995). High levels of organochlorine residues have been found in the sediments near coral communities in the northern section of the Florida Reef Tract (Glynn et al, 1995). Although these residues are 3-4 orders of magnitude less than a previous study in 1989, detectable amounts of chlordane and endosulphan still exist, likely washed from the Florida mainland. Hurricanes such as Andrew still stir up these polluted sediments and cause mortality in coral communities (Glynn et al, 1995). Organochlorine residuals have been shown to adversely disrupt the animal-algal symbioses in corals and interfere with chemical cues that are responsible for reproduction (Glynn et al., 1995). Certain organochlorine pesticide residues, namely DDT and PCBs, bioaccumulate and magnify through the food chain; however, there is insufficient evidence to suggest that these compounds are present in marine sediments or organisms in south Florida.
Nutrient loading and the spread of coral disease are difficult to correlate and ultimately assign risk. Some work by Porter et al suggests that nutrient loading contributes to the spread of coral disease, but several other factors account for patchy distributions and increases in disease frequency, namely black band disease, from one year to the next (Porter et al, 2001). Algal blooms, which inhibit coral growth, are attributed to nutrient loading (Booth et al, 2001).

Water Resource Management

The impacts from deficient waste treatment systems in the Keys extend beyond disease and contamination of corals; in fact, the impacts of these deficiencies are beginning to adversely effect water resources and ultimately the human health and welfare of all citizens in southern Florida and the Keys. Besides illicit discharges in the Keys themselves, untreated sewage and its associated biological pollutants from the Florida mainland are beginning to show up in water resources in south Florida and the Keys.
Specifically, over 400 MGD/day of sewage and industrial waste are disposed in roughly 1000 Class I Underground Injection Wells (UIC) (Sutherland, 2004). These municipal UIC wells are designed to send municipal and industrial waste into deep underground saline aquifers where confining layers hold the waste and slowly release it to the ocean (Sutherland, 2003). The US EPA is principally responsible for permitting and regulating Class I UIC wells, and just before her resignation in May of 2003, US EPA Director Christine Todd Whitman signed off on permits to allow more UIC wells and make exemptions to the Safe Drinking Water Act (SDWA) in order to assimilate the overwhelming amount of increased waste being generated in south Florida.
Despite the decisions by the US EPA, research is beginning to show that waste from UIC wells are not being contained (Shinn et. al, 1998). Studies by the USGS, EPA, and the Florida Department of Environmental Protection have all shown that waste from these wells are migrating upwards into aquifers that are used for drinking water (Shinn et al, 1998). U.S. Geological Society (USGS) tracer studies of injection wells in the Florida Keys have also shown bacteria, viruses, and nutrient loading from migrating UIC sewage waste are contaminating tourist beaches and destroying the nutrient sensitive fragile coastal reef ecosystem in the Florida Keys National Marine Sanctuary (Shinn et al, 1998).
Groundwater seepage is the chief mode of transport causing contamination in the region. Research has shown that the Pleistocene limestone below and between confining beds is extremely porous and permeable and readily transmits fluids both vertically and horizontally (Shinn, 1998). Along with the groundwater, nutrients and fecal bacteria can seep to the overlying seawater through Holocene reefs and wherever Pleistocene limestone is not covered by Holocene sediment (Shinn et al, 1998). Shinn et al also found that tidal pumping serves both to diffuse, dilute and transmit fluids vertically where not confined by Holocene sediment or diagenetically altered unconformities (Shinn et al, 1998).
Thus, the preliminary studies by the US EPA and their consultants are incorrect because the waste is not confined; conversely, the porous limestone promotes vertical seepage into drinking water resources and reef environments just off the coast of south Florida and in the Keys. Mismanaged water resources are the result, and human health and welfare is may be jeopardized. Unlike non-point sources of nutrient loading, this problem can be solved with appropriate policy making and management strategies. One of the easiest solutions might be to mandate tertiary treatment prior to UIC wells.

Monitoring and Mitigation Control

Coral reefs are among the most threatened ecosystems worldwide. Resource managers urgently need indicators to examine the biological condition of reef environments and relate data acquired through remote sensing, water-quality and benthic-community monitoring to stress responses in reef organisms (Halleck et al, 2003). Many would suggest measuring fecal or nutrient counts as chemical indicators, but these methods are not always precise indicators at the species level. For example, fecal counts do not always show up in surface marine water because of the dilution factor, and fecal counts can only be precisely measured in groundwater to assess the impacts to humans (Shinn et al, 1998).
Hallack et al. (2003) have recently shown that foraminifers are ideal bioindicators in coral reef assessment because they use the FORAM Index (Foraminifers in Reef Assessments and Monitoring) to determine the suitability of benthic environments for communities dominated by algal symbiotic organisms (Hallack et al, 2003). The FORAM Index is based on 30 years of research on reef sediments and reef-dwelling larger foraminifers (Hallack et al, 2003). These shelled protists are ideal indicator organisms because: foraminifers are widely used as environmental and paleo-environmental indicators in many contexts, foraminifers with algal symbionts have similar water-quality requirements to reef-building, zooxanthellate corals foraminifers have relatively short life spans as compared with long-lived colonial corals which can facilitate differentiation between long-term water-quality decline and episodic stress events, and foraminifers are relatively small and abundant, permitting statistically significant sample sizes to be collected quickly and relatively inexpensively, ideally as a component of comprehensive monitoring programs (Halleck et al, 2003).
In the western Atlantic region, where disease and bleaching have profoundly damaged coral communities, the FI can be used to assess whether water quality is sufficient to support
reef recovery even in the absence of significant coral populations. Resource managers should increasingly focus on this form on monitoring to assess impacts to coral communities. Using the information, more informed decisions can be made on regulations and mitigation controls.


Like most environmental problems, there are no easy solutions to relieve the stresses being placed on coral reefs from nutrients or fecal bacteria. However, there are several management tools and policies that could be enacted to help protect coral reefs in southern Florida and the Keys. Some of the easiest and most effective mitigation efforts include requiring tertiary treatment on all sewage, including waste injected through UIC wells and municipal sewage. Cleaning up the numerous cesspits, enforcing illicit discharges, and replacing dysfunctional septic tanks are other management strategies to prevent the onslaught of nutrients currently polluting the oligotrophic habitats needed for coral communities to thrive in the Florida Reef Tract. Available funds should also be used to create a more adequate waste disposal infrastructure such as a wide reaching sewerage system on all islands where populations and usage are significant. Additionally, comprehensive monitoring protocols and sampling regimes need to be created in order to rapidly detect wastewater pollution and, ultimately, to determine risk to coral and reef health, as well as human health.
Perhaps more important than any other control measure, governmental agencies, quasi-governmental firms, non-governmental organizations, and academia need to work together an communicate amongst each other in order to protect these valuable ecosystems.


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Shinn, Eugene A, Ronald S. Reece, Christopher D. Reich. 1994. United States Geological
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Shinn, EA. 1998. Groundwater Seepage in the Florida Keys. USGS: Geologic Division.
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