Brown tide clouding the waters in the eastern end of...

Brown tide clouding the waters in the eastern end of Moriches Bay. (June 27, 2011) Credit: Doug Kuntz

Southampton bayman Ed Warner Jr. was out netting baitfish last month when he noticed a suspiciously dark tint in the waters of western Shinnecock Bay.

It was an early sign of brown tide, the harmful algae that has plagued Long Island bays since 1985, when it nearly wiped out the local bay scallop population. Besides shellfish, high concentrations of the algae also threaten marine plants.

Over the past four weeks, this year's baby bloom has darkened and spread to become what Suffolk health officials said is one of the most intense -- though localized -- brown tides in recent years.

Brown tide has clouded normally clear waters from western Shinnecock Bay to eastern Moriches Bay, with the highest concentrations found off Quogue, in Quantuck Bay.

"Quantuck, it looks like you put 2 ounces of cream in a 20-ounce cup of coffee," said Warner, a Southampton Town trustee. "It's a very, very significant discoloration . . . The bay water is a brownish color, and 10 feet over the ocean water is clear."

Brown tide typically occurs in late spring and early summer, when warming waters spur blooms of a tiny marine organism known as Aureococcus anophagefferens. Some scientists link the uptick of brown tide and other harmful algae blooms in recent decades with human pollution of coastal waters.

Stony Brook University associate professor Chris Gobler says brown tide has an edge over rival microscopic organisms because brown tide's genes allow it to thrive in shallow estuaries.

While not harmful to humans, concentrated brown tide blooms make it harder for bivalves to feed and can kill juvenile clams and scallops. Scientists suspect repeated brown tides in the Great South Bay -- where it last bloomed in 2008 -- are hampering efforts to restore the decimated clam population.

Farther east, it's not yet clear if the blooms have harmed shellfish in the estuaries along the South Shore. Few population surveys have been done here, so estimates are based mostly on anecdotal reports from fishermen.

"This particular area, this now marks the fifth consecutive year of a bloom of over 1 million cells per milliliter," Gobler said.

Research shows hard clams stop feeding when brown tide cell counts reach 35,000 per milliliter of water, and most juvenile shellfish die.

Water samples taken from the affected bays showed cell concentrations that exceeded 2.7 million cells per milliner in Moriches Bay; 2.1 million cells per milliner in Quantuck Bay, according to the Suffolk health department.

"These numbers are the highest they've been in years," Michael Jensen of the department's bureau of marine resources wrote in an email. "The good news is that it seems very localized to those areas."

Brown tide is also bad news for eelgrass, the underwater plants that serve as coastal nurseries for young finfish and shellfish. The blooms turn waters opaque, blocking the light plants need for photosynthesis.

Eelgrass plots in some bays along the eastern South Shore have fared poorly in recent years, Gobler said.

Baymen such as Warner worry that the repeated blooms could retard recent gains in bay scallops, which are making a slow comeback in East End waters. "The juvenile scallops might not survive that brown algae."

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