At first glance, the mat spreading underfoot doesn’t say WELCOME. On a cool spring morning, Anne Bernhard scans the wetlands at Barn Island Wildlife Management Area in Stonington, a matted acreage of winter-beaten grasses, bare underbrush and flat pools.

“Most people think this is mucky and yucky,” she says.

She can’t wait to get back in.

Salt marsh. Target of engineers and developers. Breeder of mosquitoes and other biting insects. Besieged by human intrusion and pollution and rising seas.

But take a deeper breath, and never mind the whiff of rotten egg. That’s the salt marsh’s tiniest citizens at work, bacteria turning sulfate from sea water and pollutants into hydrogen sulfide, which other microbes use to build the rich microbial mats around them, which in turn support what a salt marsh does: filter water, repel storms, cradle life.

As hostile as civilization has been to salt marshes, she says, humanity has no stronger ally. This can be heaven on earth. By summer, it will host a vivid fiesta of motion and color.

Coastal Connecticut has some of the most vibrant salt marshes this side of Cape Cod or the Gulf Coast, and only a few people stop to look into them, even with the effusive fronds of the reed Phragmites waving in their faces.

Barn Island, at the end of Palmer Neck Road off U.S. 1, opens from a parking lot past a viewing platform and informative signs to a path leading along a raised dike and into the woods beyond. Public visitors do best keeping to paths like that; Bernhard can tell them tales of sinking thigh-deep in a hidden hole and fending off attacking birds with an unseen nest too near.

To the west, off U.S. 1 down Depot Road in Groton, Bluff Point State Park offers parking and bathrooms and a trail with scenic seaside views that include a host of salt marshes. Bernhard also recommends Waterford Beach, with a seaward trail that leads through a marsh, and farther west, Hammonasset State Park in Madison, featuring one of the state’s largest salt marshes. All offer parking and access for viewing.

In a salt marsh, Bernhard sees a trove of mysteries worth solving and a source of salvation for a world fast wading into global warming and calamity. She sees signs of global warming’s and pollution’s dangers, too, right underfoot.

“Put on your boots,” she says at Barn Island, pushing into a pair of Pro Line shin-high rubber waders. “Let’s go in.” She knows just where to step for the least imprint.

As an associate professor of biology and specialist microbial ecology of estuaries and salt marshes, and as chair of the Biology Department at Connecticut College, Bernhard has spent many hours here, studying and sampling, and she understands, as few do, the impact and importance of salt marshes.

Barn Island is her favorite. Here, as in other marshes, war between colliding forces of nature and humankind is most clearly waged. Carved by farmers cutting out large swaths of salt marsh hay, drained for parking lots and marinas, dredged for construction and highways and vivisected by mosquito-control canals, salt marshes still had a fighting chance. Then nitrogen from fertilizers and sewage started choking them, and sea-levels started to rise. Draining and dredging have been stopped. Stopping pollution and climate change, Bernhard says, will take an even more concerted effort, one that doesn’t look likely.

At first glance, this early in spring, this marsh looks like a landscape painted in pale sepias. Knowing where to look, Bernhard finds life, and color, and promise. That thin circle of white along a small pond? Microbes processing sulfur. These lumps here in a muddy bank? Striped mussels, and maybe a few oysters and clams, helping grasses’ thick roots anchor the soft ground. An egret tiptoes into a shallow pond. A fiddler crab scuttles. A meadow mole stirs some spike-grass.

This salt marsh, like all of them, she says, is a tidal dynamo, a powerhouse of productivity, one of the most fertile in creation. “Come back in summer,” she says, “and it’ll just be bright green, high and wide. And in fall, you’ll see big swaths of bright red pickle weed.”

Watch out, meanwhile, she says, for insects. Wearing long sleeves and repellants with DEET is a prime directive. “In July, mosquitoes are the least of our worries,” she says. “It’s actually the green-heads, these big flies, and they hurt!”

At least one of the most dangerous pests doesn’t worry her out here. Ticks, she says, visit salt marshes about as often as thieves visit the I.R.S. They hate salt.

To Bernhard, salt marshes are far more than tick-repellant. They are redoubtable buffers against storm and flood, reliable sponges soaking up water and filtering pollutants, protectors and providers. They are nurseries for frogs and shellfish and birds, too, osprey and ducks and snowy egret, and for some of the fish, striped bass and bluefish and flounder, brought in on tides to breed and feed, that land on dinner plates and attract anglers and admirers from all over the world.

They are virtual fountains of life.

“Look here,” she says, and lifts a microbial mat to reveal a burst of purple. “These are little sulfur bacteria,” she says, “using the sulfur in the marsh to produce their pigment.” And to help the grasses by gobbling sulfide, which can be toxic to them.

Grasses, she says, are the framework of the marsh. A visitor might admire the dramatically coiffured Phragmites, but they are better off celebrating spikegrass, Distichlis spicata, and salt meadow hay, Spartina patens, and the more hardworking cordgrass, Spartina alterniflora. By summer, she says, the grass around her will stand two to three feet high.

“They send out lots of roots,” she says, “so when you try to dig out part of the marsh it’s a tough, tough job. Over time it forms the peat layers. That’s what we’re standing on.”

Strong as they seem, marshes face grave dangers. R. Scott Warren, a renowned salt marsh ecologist and Bernhard’s mentor and colleague as a professor emeritus at Connecticut College, has helped document two major threats acting together: the accelerating rise of sea-levels and the growing nitrogen pollution of coastal ocean and estuaries.

“We as a civilization have learned how to take nitrogen out of the air and turn it into fertilizer,” Warren says. “We do that, we spread it all over the farms of the Midwest, and it goes into the plants and the animals out there, and then we ship all that nitrogen to the east coast, and we eat it, and we (expel) it, and it ends up in Long Island Sound.”

Laden with too much nitrogen, salt marsh can break down quickly. Penned in by development, by housing and industry, malls and marinas, salt marshes have nowhere to go as seas rise. “It’s hard to find a marsh, especially around here, that hasn’t been messed with,” Bernhard says.

At Barn Island, at least, a visitor can also see evidence of

better interventions, of revival and restoration. Connecticut, for instance, has moved to the forefront of those efforts. As Warren says, “The State of Connecticut is really a model for legal protection of salt marshes. It’s very difficult to get a

permit to fill or dredge or degrade a marsh.”

The state is working on restoration, too. At Barn Island, the state has defined five “impoundment areas,” targets for action and also for cooperation, with forces natural and social. Bernhard has walked into the largest, an expanse spreading from an anchoring creek. She points to a rock where, in her words, “all the birds bust open the shells, the clams and

oysters.” Just beyond trees at the very end, houses stand in

a limiting line.

Warren and Bernhard and their colleagues at Connecticut College have been working out here at Barn Island for decades. Warren finds them to be among his favorite places on earth.

“I’m in love with them,” he says. I find them an aesthetic delight and a biological wonder.”

Barn Island is nearly ideal, he says, in offering a dike so viewers can see the marsh close-up and keep their feet dry, though he would just as soon see it gone. (Restoration has included piercing it with culverts, to allow salt water back in.)

Bluff Point showcases marshes well too, from a wide

footpath climbing to its apex. He’d love to see systems of boardwalks, like those in some large southern marshes, built for researchers and visitors alike. But an educational boardwalk takes money, and so does retrofitting sewage plants to take

out nitrogen.

In the long run, neglecting the marshes hurts everyone. “Nobody pays, and we all pay,” he says.

Beaten through a tough winter, salt marshes carry on their life-giving activity quietly — until the next big storm hits.

Then they stand up like nothing else. People in Louisiana learned what the loss of them meant during Hurricane Katrina, and again after the BP oil spill. Among those still studying the spill’s impacts is Bernhard.

What will happen here if the salt marshes wither?

“Flooding will be the most visible for us,” she explains.

“As you lose the salt marshes, you’re going to have a much worse time with flooding. You’re also going to see more

pollution, so beaches will be closed more often as the marshes shrink and they’re not able to take up all the nutrients. We don’t have a lot of red tides here, but you’ll have other kinds

of algal blooms, some could be harmful, release toxins. Fish kills. ... [People] don’t see the marsh as being directly tied to the fish they eat on their dinner table, but it certainly is.”

Inspiring changes in lifestyle and in leadership from industry and government can start, Bernhard says, with a visit. Come and see the salt marshes, she says. Learn about them. Then let them be.

Science yields a lifetime of surprises for Anne Bernhard

By Tim Norris

Growing up in Houston, Texas, spending summers along the ocean in Galveston, Anne Bernhard stepped into biology through the 'big' door - whales.

“I can't remember not wanting to be a biologist,” she says, “and, more specifically, a marine biologist.” Watching Jacques Cousteau on National Geographic specials, thumbing through the magazine's stories on ocean life, she dreamed of studying the great Cetaceans, eye-to-eye.

Her mother, a history professor, and father, a theater manager and writer and actor, encouraged her.

“They often talked about famous female biologists like Sylvia Earle to inspire me,” she says. “I guess it worked!”

With a bachelor's degree in biology from Texas A&M, Bernhard swung into cancer research at the University of Texas Medical School. “My marine biology professor talked me out of pursuing marine biology as a career,” she says, “because he said there were no jobs and no money in it.” She listened,

but missed the ocean and its life.

Science, though, is bursting with surprises. Wandering like Alice through life's wonderland, sampling this and that, Bernhard shifted into environmental science in the master's program at Western Washington University and from the biggest of living creatures to the smallest: microbes.

“My advisor studied phytoplankton, tiny algae,” she says. “I did a project ... and I thought it was pretty cool, [and] went to do my Ph.D. (at Oregon State) in microbial biology.”

Her new field took her from the Pacific coast and work with the University of Washington in Seattle to the Atlantic and the Marine Biological Laboratory at Woods Hole, Massachusetts, working with Dr. Ivan Valiela, a groundbreaking salt marsh scientist and prolific writer. There, she discovered a place where microscopic bacteria and algae and fungi thrive:

Cape Cod, with its Great Sippewissett Marsh and Plum Island Estuary.

“The marsh is a fabulous place for microbes,” she explains, as well as for researchers.

“Just when you think you've figured out the answer, the organisms, especially the microbes, will always surprise you and do something totally unexpected,” she explains.

Her work led her into what was then the largest marine oil spill in American history, the 1989 grounding of the Exxon-Valdez in Prince William Sound off Alaska. Now, 20 years later, she has returned to studying the effects on microbes of the 2010 BP oil spill along Louisiana's gulf coast.

Small wonder that Bernhard found a big welcome at Connecticut College, where her knowledge and experience fit almost perfectly at the school, a center of wetlands research. And the school fit her.

“There are a lot of hard feelings in science,” she says. “People get scooped. It gets a bit cut-throat, because funding is so hard to get. Here, I have my own little niche. And the support I get from the college is absolutely great.”

Besides her research, she has waded into teaching, as an associate professor; and administration, as chair of the college's Biology Department, and found their headaches and rewards.

“There aren't very many people who get paid to play in the mud,” Bernhard says. “Teaching causes me the most stress, but I get the most enjoyment from it, too, especially when I see a student make a connection with something. I love my research, but if that's all I did, without the students, I wouldn't enjoy it nearly as much.”

Anyone nosing into her office on campus will find her two unconventional roommates, Fred and Wilma. She rescued the African dwarf frogs from a biology lab, thinking they would live a few months. They've shared her office, in a glass tank, for two years.

“I didn't know it was a long-term commitment,” she jokes.

At Connecticut College, Bernhard has worked with and learned from some of the nation's most respected wetlands ecologists, and she is seeing a change in generations. Botanist William A. Niering, long-time director of the Connecticut College Arboretum, died in 1999, and Paul E. Fell, a pioneer in salt marsh restoration, died in 2005. Renowned wetlands scholar and teacher R. Scott Warren, though still active with the college, formally retired in 2007. Robert Askins, an authority on migratory birds, joined the faculty in 1981. What they brought and taught, Bernhard says, is a wider and deeper view, now endangered.

“Some of the older ecologists would train more almost as a sort of naturalist,” she says. “They learned the whole system. Now we tend more to focus on one little tiny piece of it. ... Science has become narrower and narrower. My mentors sort of knew everything about the whole system. I'm trying to get there.”

She visits the marsh at Barn Island with her students, who sometimes insist on flip-flops and tank tops, until they run into muddy wallows and biting flies, and with her loved ones, too. She met her husband, Beto Zuniga, in 1988, when both were research assistants in biochemistry in the University of Texas Medical School. (He works now as a computer technician at Connecticut College and has cultivated a side-career in home-brewing beer). They take walks at Barn Island with their Labrador retrievers, Bailey and Thor. Ironically, Bernhard says, Thor is afraid of thunder. But he loves the marsh almost as much as she does.

“The deeper I dig into how the marsh ecosystem works and how the microbes keep it going, the more questions I have,” she says. “Salt marshes and estuaries are really dynamic systems, because they have this tidal influx, twice a day every day, very salty water to fresh water. The organisms that live there, I've been fascinated by the extreme conditions they adapt to.”

She's done a little adapting, herself. And the surprises keep coming.