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In September the vegetables in the produce section at Whole Foods in Lynnfield are what you’d expect to come out of the ground this time of year—turnips, carrots, cucumbers, and a host of other vegetables. But there’s something about the harvest you couldn’t imagine—some of it comes from a farm that’s two flights of stairs above the produce section itself.

Last year, Whole Foods opened at MarketStreet Lynnfield with a feature unseen at any of the supermarket’s other locations around the country: a 17,000-square-foot rooftop farm that’s yielded more than three tons of organically grown crops since its debut. Beyond its convenience, the rooftop farm demonstrates a savvy approach to growing food in unlikely locations. “Whole Foods Market Lynnfield installed a rooftop garden with the intention of bringing the local, organically grown produce to our customers,” says Vanessa Maykel, a Whole Foods marketing team leader. And after two seasons, the results have been tastier than expected.

When Whole Foods first considered adding a farm onto the roof in Lynnfield, the company got in touch with two businesses in Somerville: Green City Growers, which transforms and maintains urban spaces that become productive food sources, and Recover Green Roofs, a design–build firm specializing in vegetated roofs and rooftop farms. The two businesses have long had a symbiotic working relationship: Back in 2010, they collaborated on a 5,000-square-foot farm on top of a Dorchester restaurant.

That project presaged the built-in place, open-air rooftop farm woven into the fabric of the Whole Foods building in Lynnfield, an enterprise that amplifies the concept behind green rooftops popping up around the world. And while outfitting the MarketStreet building to grow a portion of the supermarket’s produce is a big investment, the payoff is on the plate. “The produce we get is more nutrient dense and fresher than anything else available, because the distance between where it’s grown and where it’s being consumed is really as minimal as it can be,” says Jessie Benhazl, CEO of Green City Growers. Urban farming also makes more locally grown food available in congested regions like eastern Massachusetts, and since rooftop gardens and farms repurpose unused space, there’s no competition for ground-level real estate.

Some 20 feet up in the air, if you ignore the HVAC equipment, the leafy rows growing from the soil inside a 130-by-130-foot perimeter with stainless steel edging look a lot like a conventional farm. “We essentially made a giant planter out of the roof by covering the whole surface,” says Mark Winterer, director of operations for Recover Green Roofs. While weaving a green roof into the fabric of a building’s design before its construction is more direct than retrofitting one already in existence, the considerations remain the same: ensuring the building can handle the loading capacity of the farm, preventing hard-to-fix defects in the waterproofing, incorporating safety features, and mitigating storm water runoff.

They used a roof system manufactured by American Hydrotech, Inc., which provides a barrier for the farm without protruding into the building’s waterproofing. (In fact, Winterer says, waterproofing typically lasts twice as long on buildings equipped with green roofs.) Approximately 324 tons of growing material—a wind-resistant composite of shale, sand, compost, and a soil amendment called biochar—is layered over filter fabric and formed into 10-inch mounds. Because roots can spread out without the constraints of a container, the crops themselves are healthier and drought tolerant. When things do dry out, a smart irrigation system that calculates wind, humidity, temperature, and other environmental factors goes to work. “Luckily, Lynnfield gets about 50 inches of rain each year,” Winterer says.

Near the end of the more-than-year-long design process, a mix-up over a critical calculation called the project’s future into question. “I remember sitting at a huge table with about a dozen architects and engineers trying to tell Whole Foods not to do the rooftop farm,” Winterer says. “But they didn’t falter: Whole Foods challenged them to go outside their comfort zone and find a way to incorporate this new technology into their building design.” Recover Green Roofs adapted the design and began building the rooftop farm with all locally sourced materials in April 2013.

The following Memorial Day weekend, Green City Grow- ers planted its first crops. By the time they put the farm to bed in November, Banhazl’s team collected more than 4,000 pounds—or two tons—of food. This season, they’re on pace to more than double those numbers during their twice-weekly harvests.

The plant varieties on the roof at Whole Foods Lynnfield are determined in collaboration with the produce department. “It’s been a really interesting combination of people’s favorite foods and crops they know will sell well,” Benhazl says. Green City Growers’ horticultural director assembles a crop map by season—crops that autumn yields include kale, radishes, jalapen?os, Italian red peppers, banana peppers, and mint—and uses all-organic fertilizers, pesticides, and growing techniques like succession planting to ensure a healthy, continuous harvest. And without an obligation to grow in large quantities, they’ve experimented with uncommon plantings like purple beans and chocolate mint— “interesting things you don’t usually see in the grocery store,” Benhazl says.

The results have been a resounding success. “Our customers love the fresh, local produce,” says Maykel, “and our team members have enjoyed the learning experience of experimenting with the different crops and learning how we can incorporate them into dishes in our different departments in our store, such as our Rooftop Pizza in the bakery.” Additionally, the roof acts an insulator, reducing heating and cooling costs.

While the food is sold on the premises, its destination goes beyond the produce section: Rooftop vegetables have been key ingredients in Whole Foods’ pizzas and other prepared foods. And this past August, Davio’s Northern Italian Steakhouse held a series of Monday Market Menu four-course prix fixe dinners, prepared with freshly picked ingredients from its MarketStreet neighbor. Before getting started, culinary director Rodney Murillo climbed the stairs to get a glimpse of what he had to work with. “It was incredible,” he says. “You don’t get to see that kind of variety around here. You have people that grow tomatoes and basil, but most of the time, that’s it.”

Each Friday, Murillo received a list of what was coming down from the roof, and he’d spend the weekend devising a menu that often paired fresh fish with the fresh harvest. The first week’s green tomato and cucumber gazpacho topped with Maine lobster set the tone; the swordfish entre?e that followed—served with eggplant, purple and orange carrots, chermoula sauce, and cre?me frai?che—was one of the highlights of the month. “[The Monday Market Menu] was a good thing for us, but it was bad, too. Now we’re spoiled,” Murillo says. “We want anything we can get that’s local, from five or 10 miles away instead of hundreds of miles across the country.”

But distance isn’t the only thing that makes a difference: so does the altitude.;;;