Once a lush and healthy estuary, the Indian River Lagoon is now an enigmatic death trap. Running along 40 percent of Florida’s Atlantic coast, the lagoon’s brackish waters harbor a mysterious killer that has claimed the lives of hundreds of manatees, pelicans, and dolphins.

Nobody knows why.

In April, NOAA declared the spate of manatee deaths an Unusual Mortality Event, a designation granted when marine mammal deaths or strandings are significantly higher than normal, demand immediate attention, and are the result of a common but unknown cause. Soon, the bottlenose dolphin die-off may be given the same designation.

“We have to hope we can find the answer, because until we do, we don’t know how we can help prevent it in the future,” said Jan Landsberg, a research scientist with the Florida Fish and Wildlife Conservation Commission.

Since last July, 51 dolphins, 111 manatees, and as many as 300 pelicans have perished in the lagoon. The deaths don’t follow an obvious pattern: Manatees are dying so quickly that some still have food in their mouths, while the dolphins and pelicans appear to be starving to death.

South Florida Water Management District )

Investigators don’t know if the die-offs are the work of the same killer, or if by some coincidence, nature has produced three unrelated carcass piles at once. The only clear link so far is the lagoon, a treasured and frail ecosystem that’s home to more than 3,500 species of plants and animals.

Scientists searching for the killer are following a long, branching trail; the story begins years ago, when a prolonged drought and cold snap set the lagoon’s resources toppling like a string of dominoes. Now, a multi-year, $3.7 million protection initiative has been adopted in an attempt to put the brakes on the lagoon’s collapse, and prevent future crashes. But its success depends on scientists uncovering the culprit behind the ecological mayhem.

Imperiled Paradise

Designated an “estuary of national significance” by the EPA in 1990, the Indian River Lagoon system stretches for 156 miles along Florida’s eastern coast. Though less than 6 feet deep on average, the lagoon is stuffed with more species of marine life than any other estuary in the continental United States. Salt marshes, mangrove swamps, oyster reefs, fish nurseries, and one of the densest sea turtle nesting sites in the western hemisphere are some of the ecological stars studding the stretch of coastline. Estimates suggest the barrier island complex brings in more than $3.7 billion each year from citrus farming, fisheries, recreation, and employment.

But there’s a darker side to the Sunshine State’s eastern oasis. Surrounded by developments, the lagoon has, for decades, been the drainage pool for leaking septic tanks, polluted streams, and storm water rich with nutrients from fertilizers. It’s a wind-driven system, and without tides to push the water around and flush it out, segments stagnate and pollutants accumulate.

Running from Ponce de Leon Inlet in the north to Jupiter Inlet in Palm Beach county, the lagoon’s waters flow into canals and through locks, twisting and pooling into three main segments: The Indian River, the Mosquito Lagoon, and the Banana River.

SJRWMD

It’s here, in and around the Banana River that scrapes the shores of Cape Canaveral, that the animals are dying.

The trouble, scientists suggest, began a few years ago when a prolonged drought descended upon the region. Normal evaporation combined with scarce rainfall boosted the lagoon’s salinity; at one point, it was saltier than the ocean – an environment that tipped the normal balance of species and created a shifting, wobbling base for the ecosystem to rest on.

Then, in winter 2010, a cold snap settled in.

Freezing temperatures killed the macroalgae that normally live near the lagoon’s surface. As these seaweeds withered and died, their sequestered nutrients flooded the already nutrient-saturated, saline water, creating a potent soup that would fuel the lagoon’s collapse: A blue-green algae superbloom.

For nine months, beginning in early spring 2011, the northern lagoon’s waters were seasick-green. The bloom intensified through the summer and fall, at one point covering 130,000 acres. Cloudy, phytoplankton-filled waters shaded the lagoon’s floor, depriving its seagrasses of the sunlight they needed for photosynthesis and life, and stealing oxygen from fish.

Eventually, about 60 percent – or 47,000 acres – of the lagoon’s seagrasses died, including most of the seagrass beds in the Banana River. “We’ve used seagrasses since the 1980s to assess the lagoon’s environmental condition,” said Troy Rice, with the St. Johns River Water Management District, and director of the Indian River Lagoon National Estuary program. “They’re considered the primary indicator of the lagoon’s health."

Rice has been studying and tracking the lagoon’s changes in fortune for years. Without those seagrass beds, he says, the estuary lost its ability to buffer environmental insults. Sediments that would normally be trapped by the grasses were left floating; nutrients normally sequestered were free to feed further algal blooms. Invertebrates and fish that lived in the seagrass beds were left homeless, manatees left without their primary, grassy food source.

In the summer of 2012, the lagoon turned the color of paper bags as a brown algal bloom took hold, further shading and choking off any recovering seagrasses.

Save the Manatee Club

Manatees in Distress

SJRWMD )

Manatees started dying in the Banana River last July. First a trickle and then a flood, the die-off reached its peak this spring, when more than 50 manatees were found in March. Since then, it has slowly tapered off. Now, the Florida Fish and Wildlife Conservation Commission, in charge of investigating the manatee deaths, reports that carcasses are retrieved every other week or so. “At least the deaths from this cause are not showing up as frequently,” FWC spokesperson Kevin Baxter said in early June.

So far, the 111 carcasses recovered have provided little information about what’s killing the gentle marine mammals. Other than being dead, the manatees look remarkably normal. Whatever is killing them strikes quickly and without much warning. Biologists haven’t been able to find any suffering manatees – just dead ones – and are missing crucial behavioral observations.

“They’re in good body condition from what we can tell, no other diseases or signs of trauma,” said Martine DeWit, a veterinarian with the FWC who does necropsies on the dead manatees.

It appears the animals are dying from shock and drowning. Some still have food in their mouths – but it’s the wrong kind of food, if you’re a manatee. Instead of sea grass, pathologists are finding macroalgae, mostly Gracilaria, in the manatees’ digestive tracts. This type of seaweed is normally not toxic. But, “on microscopic examination of the tissues, we found some inflammation in the wall of their gastrointestinal system,” DeWit said, noting that the changes were only minor. “Our first thought is it has to be something associated with the algae – something in the sediment, absorbed by the algae, or a compound of the algae itself.”

Searches for signs of infection or toxin exposure have produced nothing. Looking in the lagoon for toxins, such as brevetoxin, saxitoxin, domoic or okadaic acids has also led nowhere. “None of the usual culprits are out there,” Landsberg said. “But then there’s always the unknown ones.”

If an anonymous toxin is on the loose in the Indian River Lagoon, finding out what it is will take time. If microbes or sediments are hitching a ride on macroalgae and killing the manatees, finding out why, and what, will also take time. “It’s not CSI, it doesn’t take an hour,” Landsberg said.

So far, scientists’ best guess is only that the manatee die-off is linked to the loss of seagrass, though the connection isn’t obvious. But even if that manatee mystery is solved, there’s no guarantee the same culprit is responsible for the demise of the lagoon’s other victims.

And Then There Were Dolphins

Starting in February, pelicans in the lagoon began dying. For two months, starving birds fell from the sky, spotting the shores with their skinny, wrecked bodies. But by the time manatee mortalities were at a peak this spring, the pelican die-off had waned.

And then the calls started coming in about dead dolphins.

Hubbs-SeaWorld Research Institute )

As of July 3, 51 dolphins have been pulled from the northern and central parts of the Indian and Banana Rivers. It's the largest dolphin die-off in the Indian River Lagoon system, said Megan Stolen, a biologist with Hubbs-Sea World Research Institute. Stolen is part of the team responding to reports of dolphin carcasses; she says only one suffering dolphin has been found alive, and that he’s doing well in dolphin rehab.

Unlike the manatees, the dolphins Stolen finds are not in good shape. Some carcasses are in pieces and too incomplete to learn anything from; many bear the marks of a puzzling plethora of postmortem shark bites. The ones that are intact are mostly sacs of skin and bones. “About 85 percent of those are emaciated,” Stolen said. “Which is pretty extreme.”

Whether the skinny dolphins are the result of depleted or shifting fish stocks, parasites, toxins, disease, or something that simply makes it hard for them to catch fish, is unknown. What scientists do know is that the number of dolphin mortalities during the first half of a normal year is around 17. With roughly 700 dolphins living in the entire lagoon, this year’s mortality rate is already approaching 10 percent of the population.

If NOAA declares an Unusual Mortality Event, the teams attending to the dolphins will get some help from the federal government, in the form of labs, scientists, and funding. That should help narrow the search for suspects.

“The entire lagoon is changing,” Stolen said. “We’re trying to look at the whole picture.”

But putting that picture together is not only difficult, it may be impossible.

Flickr )

“I think, always, the best approach with these investigations is to start with the most obvious hypothesis first,” Landsberg said. “Since these are all occurring coincidentally, is it coincidental or not?”

The scariest option is that the deaths might be unrelated to one another, and simply the result of a multi-pronged ecological catastrophe. Connecting crashing seagrasses with vegetarian manatees, fish-eating mammals and fish-eating birds is not easy. Complicating the picture is that other seagrass-eating species, such as sea turtles, appear unaffected. Other fish-eating species, such as cormorants and herons, are mostly unperturbed. The bull shark population scavenging the dolphin carcasses doesn’t appear to be in trouble. And though the dolphins and pelicans both eat fish, they’re not necessarily eating the same fish. Feasibly, Landsberg says, a toxin could be involved – but for whatever reason is not working its way evenly through the food web.

“It’s like trying to do this big jigsaw puzzle, looking at all this environmental information,” Landsberg said. “You could spend forever going down all these different rabbit holes and getting nowhere.”

The different teams working on solving the mysteries are still assuming the deaths are linked: Whatever is at large in the lagoon is exacting its effects on very specific populations, in a very specific area – for now.

Molecular Detectives

A new project could help investigators find out if a toxin is harming the Indian River Lagoon manatees. At the University of Florida, veterinarians and scientists are testing the genes and proteins expressed when manatees are exposed to toxins, using blood samples from 12 animals: Four that have been exposed to red tide toxins, and eight animals that live on either of Florida's two coasts. Funded in part by the Save the Manatee Club, the project is still in its pilot stage. The goal is to see if differences between affected and healthy animals carry the biological signature of an immune system responding to toxin exposure – a signature they can then test for in the Lagoon's manatees. "You can, potentially, see changes in the protein levels related to genes turning off or on that are now out of whack," said Mike Walsh, an aquatic animal veterinarian at the University. "Could we back in to the idea that yes, this is a toxin, and we need to figure out what it is?"Uncertain Future

With no clear culprit in sight, scientists, rescuers, and residents of the six counties bordering the estuary are on alert. A brown algal bloom is already coloring the Mosquito Lagoon, appearing earlier than it did last year. Florida newspapers are criticizing the state’s inability to enact tougher environmental regulations and keep Florida’s waterways clean, claiming that “State leaders won't act to stop summer slime" and "Gov. Rick Scott does not seem to care” (estimates place the 2011 algal bloom-related economic losses at somewhere between $230 and $470 million, but Florida's governor vetoed a $2-million grant for the Harbor Branch Oceanographic Institute to study the lagoon), and applauding the Sierra Club for its move to report "Slime Crimes."

"Any issues in the environment that are associated with animals or people affect the other," said Mike Walsh, a a veterinarian at the University of Florida. Walsh and his colleagues are helping with the investigations (see sidebar). "If you have an algal overbloom that kills the seagrass, that affects the fish, affects dolphins, affects manatees – every one of these changes can have substantial long term side effects."

The manatee population in particular is suffering. In addition to the mysterious east coast killer, hundreds of manatees have died from a particularly vicious red tide that settled off the state's southwest coast. Those mass mortality events, plus boating accidents and deaths from natural causes, bring the total manatee deaths this year to 672. That's already higher than five of the last six years, and is more than 10 percent of the state’s manatee population, estimated to be roughly 5,000 animals. In 2007, the U.S. Fish and Wildlife Service recommended upgrading the manatees’ listing from “endangered” to “threatened.” Now, budget cuts have put that move on hold, says U.S. Fish and Wildlife spokesman Chuck Underwood. “This isn’t an indication that we know something about what the recent deaths mean,” he said. “It is strictly budget-related.”

What this year’s grim total means for the manatee population is still unknown, but it might take years for the population to recover.

“It's a huge number, more than any other year at this point in time,” said Patrick Rose, president of the Save the Manatee Club, an aquatic biologist who's studied manatees for decades. Rose suggests the Lagoon could take as long as a decade to recover. "From this point forward, if we do everything right, we're still talking maybe 5-10 years for recovery," he said. "The system is so unstable right now that it's going to have to stabilize, even if it stabilizes in a much worse state."

U.S. Fish and Wildlife Service ).

The lagoon is not without hope, though. Late last year, the St. Johns River Water Management District announced the adoption of a four-year, $3.7 million Indian River Lagoon Protection Initiative. Designed to help heal the ailing estuary, the initiative is still in its early stages. But a multidisciplinary taskforce of scientists is already studying and monitoring the embattled ecosystem, trying to sort out what triggered the blooms in 2011 and 2012.

“The lagoon’s health had been improving, and then out of the blue came this unforeseen superbloom,” said William Tredik, the Indian River Lagoon Protection Initiative’s team leader. “The algal blooms seem to have been the catalyst for a lot of other things, but we don’t have all those links figured out yet.”

Initial work is focusing on the northern lagoon, the killing zone that has been the most besieged by blooms. Then, when the taskforce has a better idea of what ignited the algal explosion, potential solutions will be suggested – ideas that could range from adding drainage canals to transplanting seagrasses to overhauling septic systems.

“It’s a beautiful area down there, just breathtaking when you’re out on the water,” Tredik said. “We want to make it as good as we can.”