FAIRHOPE, Ala. — The likely cause of an extensive fish kill seen from Bon Secour to Daphne this spring has been found. Officials with the Alabama Department of Conservation and Natural Resources Marine Resources Division say it was not a widespread viral infection, but rather a fungus, Aphanomyces invadens, that killed thousands of fish along the Eastern Shore.

Some of the weakened or dead fish exhibited Mycobacterium (evidenced by red lesions) on the skin, but nothing unusual in their internal organs.

According to the agency, temperature changes along with a freshwater spike from local and upstate rains temporarily altered the ecosystem in Mobile Bay. More than 7.5 inches of rain fell along the Alabama coast in late March and nearly 3 inches fell one day in April. Flash flooding and heavy runoff were the result of both storms.

The altered conditions, particularly water salinity and pH levels, stressed a number of species, enabling the fungus to attack. Although this is not an uncommon occurrence at certain times of the year (especially with mullet), Kevin Anson, an ADCNR biologist stationed in Gulf Shores, said the scope was unusual.

“It is in the respect we do see fish that have signs of disease, and they can vary from fish to fish and season to season,” he said. “The fish with the red splotches are a little less common.”

Anson pointed out that the lesions were not only more widespread than normal, but also impacted a much greater variety of fish. He said, “The number and species are outside the norm of what we expect to see this time of year, but we do usually see some in the spring and fall.”

The initial tests on fish sent to the Auburn University Department of Fisheries and Allied Aquacultures were inconclusive, and ADCNR officials caution that even this diagnosis is not 100 percent certain.

Six fish have been sampled so far, and three showed signs of Aphanomyces invadens infection, while one was found to have Mycobacterium marinum. Some fish are still being tested.

“Our recommendation is not to eat (diseased fish),” Anson said. “Any fish they catch that look normal should be thoroughly prepared and cooked.”

Anson said it would be a good idea to use a towel or gloves when holding a diseased fish, then be sure to wash your hands afterward with soap and water.

Also, always be careful to avoid cutting or scratching yourself while handling fish, crabs, shrimp or oysters because of the ever-present risk of vibrio vulnificus infection. The harmful, waterborne bacteria can cause serious illness in humans, especially those with a weakened immune system.

Hardhead catfish were the first affected by the fish kill this year. Among the other species found to be impacted by the fungus were spotted sea trout, croaker, flounder, red drum and sheepshead. The stench of rotting fish lining the shoreline was fairly common for a while. That is changing, however.

“The number of phone calls and reports (of diseased fish) here have gone down significantly,” Anson said. “The lab techs indicated that some of the fish were regenerating skin, which means they were beginning to heal. The conditions are returning back to normal. In a few weeks, it will be a memory.”

The fish kill prompted some to remember a similar event in 1995 that spanned the entire Gulf of Mexico. Thousands of catfish washed up on beaches at the time, with Texas taking the brunt of the event.

ADCNR notes that netting can cause small fish kills through bycatch and net injuries anytime, while some fish can be injured by birds or other fish and later become infected by fungus.

To report fish kills, call (251) 968-7576.