florida algae
©Daivd Walters / Miami Herald Staff
Peter Frezza, a biologist with Audubon of Florida's Keys office, measures water clarity on the Twin Key banks. The photo was taken from just below the surface and reveals the water's green tinge as a result of the algae bloom in parts of Florida Bay.

Algae has turned Florida Bay's waters a murky green, threatening the ecosystem below. What's causing the sudden blooms isn't clear.

Only a day earlier, the heart of Florida Bay's world-renowned fishing ground was clear enough to count turtle grass blades six feet down. Now, Pete Frezza stared into water so thick with algae it looked an awful lot like pea soup.

Stick an arm in and you wouldn't see your hand.

''This is really, really bad,'' said Frezza, a biologist with Audubon of Florida and avid Florida Bay fisherman.

Scientists who monitor Florida Bay and anglers who chase tarpon and bonefish in its maze of shallows are bracing for bigger, badder algae blooms in coming months.

It was about this same place and time last year -- Twin Keys basin, several miles west of Islamorada -- where a bloom began that would morph into the largest Florida Bay has endured in more than a decade. When it peaked in August, a milky green stain spread from isolated Everglades creeks to Florida Keys reefs before slowly retreating.

Environmentalists and veteran fishing guides like Tad Burke fear a rerun of the early 1990s, when a string of blooms decimated vast swaths of seagrass beds and sponges.

''The blooms we're seeing now, they're not going away in the winter like they used to,'' said Burke, head of the Florida Keys Fishing Guides Association. "These blooms aren't dying. They're moving around with the wind and blowing back up.''

Scientists and managers of the Florida Keys National Marine Sanctuary and Everglades National Park share the concern and are trying to figure what, if anything, to do. Last year's bloom left significant damage, especially to sponges.

Threat to Sponges

Mark Butler, a biologist at Old Dominion University in Virginia, said areas monitored by his surveys show a ''complete wipeout'' of 22 of 24 sponge species -- including the bay's largest, loggerheads, that can reach the size of tractor tires.

''There are sponges that are older than us, huge loggerheads, that are gone,'' Butler said. 'It will take decades to recover.''

Still, scientists who have been studying the blooms for two decades stress that no one can say for sure if Florida Bay faces another green monster this summer. They're still trying to pinpoint what triggers commonly occuring, normally benign one-cell phytoplankton called synechococcus into raging replication.

''We don't see a smoking gun out there,'' said John Hunt, an administrator with the Florida Fish and Wildlife Research Institute who edited a 2007 compilation of Florida Bay studies and led a meeting of scientists and agencies in March on the blooms.

Nutrients clearly fuel the frenzied growth of synechococcus, but their origin remains as murky as the water. The state report, echoed by many scientists at the meeting, downplays human sources that have long been primary suspects -- the Keys' leaky cesspits, nitrogen or phosphorous pollution from farms and reduced flows from the Everglades.

''We understand a lot more about what is going on than we used to,'' said James Fourqurean, a biology professor at Florida International University who has studied the bay's seagrass since the 1980s. "It's a big system, it's a complicated system. There is not a simple cause-and-effect that plays out across the whole bay.''

Nor is there a clear solution -- though there is wide agreement that fixing the C-111 canal in South Miami-Dade County, which diverts water from the bay, is the first place to start.

Florida Bay, which occupies a 750-square-mile triangle between the Keys and the mangrove coast of the Everglades, may look like one big body of water on a map, but studies show its numerous shallow banks restrict circulation, making it function more like a series of smaller basins. The thinking now is that different spots are sensitive to different factors -- with human pollution possibly playing bigger roles near shore and smaller roles, if any, away from it.

A lingering, three-year-old bloom in Northeast Florida Bay is almost certainly the product of a combination of hurricanes, farm runoff and road work to widen the 18-Mile stretch that pumped organic material and nutrients into surrounding waters.

But as to what set off last year's bloom in the dead center of the bay, Fourqurean said, "the current theory is you get as many opinions as there are scientists.''

High temperatures and salinity seem to be strong indicators, but Twin Keys basin went green last week in relatively cool weather. Nutrients could come from both natural and man-made sources -- rotting Everglades vegetation, underground flows or from runoff from farm and suburbs flowing down from Southwest Florida rivers or something else. Dying sea grass also supply fuel, and synechococcus can tap nutrients locked in bay bottom sediment as well.

Droughts or hurricanes also may make the bay more vulnerable, producing extreme conditions that stress other organisms but let synechococcus thrive. It doesn't help that not many things, aside from sponges, eat the algae.

''Florida Bay has really low nutrient conditions. All it needs is a little bit to bump it over the threshold and you have a big effect,'' said Joe Boyer, associate director of the Southeastern Environmental Research Center at FIU, which monitors coastal quality under a contract with the South Florida Water Management District. "It becomes a self-perpetuating cycle. They essentially feed themselves.''

Unlike red tide, which paralyzes and kills fish, manatees and other sea life, synechococcus does most of its damage to bottom plants and animals that provide food and shelter for everything from juvenile lobster to bonefish.

Lengthy blooms block light vital to seagrass. Dense concentrations choke sponges to death, the sticky algae filling the internal canals with mucous-like ooze, said Butler, who described vase sponges "melting away into white brittle mounds.''

When blooms first appeared in the 1990s, suddenly clouding water that had been clear for decades, many scientists saw it as a symptom of a bay on the verge of ecological collapse. Fourqurean recalls being literally ''physically ill'' at his first encounter.

Resilient Sea Life

He, Hunt and a number of other scientists have tempered the view after watching the bay heal and finding, in bay sediments, evidence of an ancient history of blooms.

''The seagrasses in Florida Bay have so far proved amazingly resilient,'' said Fourqurean. Beds thinned or new species moved in, but most places recovered in a few years. Sponges took longer, six to seven years, and 15 or more for some sensitive vase varieties.

Studies haven't found any significant losses of lobster or fish.

But the bay has lost its gin-clear quality, particularly along the Everglades coast.

''The ecosystem is going to survive,'' Fourqurean said. "What is changing is the relative balance of clear water to turbid water.''

Environmentalists, many anglers and other scientists aren't so optimistic. They see the blooms as just one sign of seriously sick bay -- and a potential economic catastrophe for Keys guides and merchants already hammered by rising fuel prices and a stagnant economy.

Jerry Lorenz, state research director for Audubon, has watched nesting numbers for roseate spoonbills plunge to record lows, which he blames on declining water quality in the bay driving off both the wading birds and small fish they feed on.

''What I saw last year,'' Lorenz said, "scared the bejeebies out of me.''