When Dr. Jim Haney, a professor of biological science at the University of New Hampshire, first saw the results of cyanobacteria sampling from six of the Island’s coastal ponds, he thought there had been a mistake.

A seasoned zoologist who has spent much of the past two decades researching the impacts of tiny, microscopic cyanobacteria in pond systems, Mr. Haney had never seen results like the ones that were coming from Martha’s Vineyard. The Island’s brackish coastal ponds, such as James Pond, Wintucket Cove in the Edgartown Great Pond and Chilmark Pond, were reporting higher levels of BMAA — a known neurotoxin that can be released from cyanobacteria — than he had recorded in any water system in the region, including highly polluted ponds across the state.

But there was another reason Mr. Haney had never seen results like on the Vineyard before: he had never studied brackish ponds.

“We never tested ponds with high salinities,” Mr. Haney said in a recent followup interview with the Gazette. “That’s one of the reasons when we got those results with the high levels that the first thing we did was go back and test our methods, adding salt to make sure that it wasn’t producing some sort of artifact, because I had some sleepless nights to be very honest with you about that.”

According to Mr. Haney, the Vineyard and its 13 or so unique Great Pond ecosystems are at the forefront of a completely nascent science — one that neither he, nor any marine biologist, has studied in great detail before.

While Mr. Haney has extensive experience sampling freshwater ponds — which are often more frequently used, considered to be dirtier, and thus, more scrutinized from a public health perspective than saltwater ponds — the presence of cyanobacteria, toxins and algae blooms in saltwater pond systems like the Vineyards’ represent an unexplored frontier.

Study was initiated after a man became sick while crabbing in Chilmark Pond. — Ray Ewing

The testing conducted by the University of New Hampshire was initiated earlier this fall by Island health agents and the Martha’s Vineyard Commission after an adult man was sickened while crabbing in Chilmark Pond. Large algae blooms were observed in the pond throughout this summer, prompting its closure to recreation. And last summer, Chilmark health officials said a dog died after drinking water from the pond.

Although often informally known as blue-green algae, cyanobacteria, or microscopic bacteria that live in all water systems on the planet, are actually ancient microorganisms that share traits with algae, such as the ability to perform photosynthesis. In fact, they were the first photosynthetic organisms to evolve on Earth, dating back three billion years, and their presence in Island ponds is a well-documented, healthy part of the ecosystem.

But a dramatic increase in the presence of the bacteria can cause harmful algae blooms, resulting in blue-green discoloration in the water column that often looks like pea soup or spilled paint. Ingestion, or even skin contact with the blooms, can be harmful to humans, causing gastrointestinal symptoms, irritation, liver issues and neurological problems.

Newer branches of science are also trying to determine the impacts of cyanotoxins in the air and the food web, as well as the impacts from invisible picocyanobacteria (which is suspected to emit BMAA). And it is generally agreed that because of warming temperatures in the Northeast and increased nutrient levels in water systems, the frequency of cyanobacteria algal blooms will increase.

In a presentation with the Edgartown Great Pond Foundation, Stony Brook University scientist Dr. Christopher Gobler compared the Island’s pond system to southern Long Island, noting that a dog death there had initiated monitoring back in 2011 and that the years since had seen great improvement in the quantity and impact of algae blooms. He said the Vineyard’s level of microcystins, one of the most commonly-studied harmful toxins emitted from cyanobacteria, were actually far below even the Environmental Protection Agency’s threshold for drinking water.

“Even the highest level that was found in the Martha’s Vineyard water bodies are quite low, relative to the standards,” Mr. Gobler said. “And again, the drinking water standards are based on chronic consumption.”

But the high presence of BMAA — a much less-studied cyanotoxin — in the Island’s saltiest ponds was unexpected. While visible algae blooms, which concentrate cyanotoxins in localized high levels, are easy to see, and thus, easier to avoid, invisible picocyanobacteria present different scientific, and public health, conundrums.

“One of the things that really concerned us, quite candidly, was making sure that the high levels of BMAA was not some sort of a fluke, and whether that translates to high levels of aerosols,” Mr. Haney said. “We have no idea. With BMAA, the science is not that far. So, what we’re asking is, can we identify some possible causes? And because the aerosols represent something that we all share, we want to see if they are present, what their levels are, and could they represent some potential threat.”

Both Mr. Haney and Mr. Gobler felt that it was too early to draw any hard conclusions about the safety of the ponds for recreational use. They agreed that Islanders should always avoid blooms, but cautioned against broader conclusions.

For instance, a bloom in one part of the pond does not mean the entire water supply is toxic. And the lack of a bloom doesn’t mean that the water is non-toxic. Mr. Haney also noted that sampling was preliminary and by no means comprehensive.

But a much more rigorous monitoring program on the Island is now being initiated, with the goal to develop a citizen science aerosol analysis kit, as well as to constantly monitor ponds for algae blooms. And there has been discussion between health agents and the commission about using the shellfish hatchery on Lagoon Pond in Oak Bluffs as an ad hoc testing lab for water toxins — another crucial step according to Dr. Gobler for keeping ponds safe.

Dr. Haney felt that constant data was the only way to appropriately address use of the ponds from a public health perspective, which his lab plans to gather on the Island next summer. And as a scientist, he was enthralled by the possible link between high salinity and high levels of BMAA — a potential new connection he plans to further explore.

“The whole toxin thing is in its infancy,” Mr. Haney said. “And that’s the concern for us. We have to keep an open mind and actually measure what is happening.”