On the other hand, organic greenhouse producers cannot use conventional fertilizer nor pesticides to combat pest outbreaks, which makes their jobs harder. Voiland combats pests by releasing beneficial insects, like wasps that parasitize aphids. And both organic and conventional growers can ward off combat disease with good ventilation and regular inspections.

But that hard work can pay off in the form of much less runoff of pesticides and nutrients. (Studies have found both in water samples taken downstream from conventional seedling production facilities, and some states and counties require greenhouses to take steps to limit such runoff)

Local Plants Might Stave Off Disease

In 2009, an outbreak of late blight, the same pathogen that caused the Irish potato crop failure, spread throughout the Northeast. In infected tomato plants, the leaves become spotted brown, a white fungus grows on plants, and they wither to nothing. In farms and gardens from New York to Maine and beyond, the crop gardeners and cooks look forward to all summer was decimated.

“It was just a devastating year,” says Stephen Reiners, a professor at Cornell and the associate chair of its Department of Horticulture.

While the source of the blight was never pinpointed, the disease, which was referred to by Cornell plant pathologist Meg McGrath as the “bubonic plague for plants,” was found in plants at Lowes, Walmart, Home Depot, and Kmart. Extension agents found the infected plants came primarily from one source: the behemoth Bonnie Plants. In 2011 the company, which declined interview requests, was reported to have over 70 facilities in 40 states.

When one plant is diseased in such a centralized system, it has the potential to spread far and wide. Bonnie has always denied its tomatoes brought the blight, and the source of the outbreak was never formally investigated.

In years following the blight epidemic, Tom Zitter, another plant pathologist at Cornell, regularly inspected Bonnie’s Northeastern facilities, looking for disease. He believes the problem began in southern greenhouses, before plants were shipped north. The disease can spread rapidly in the close quarters of a greenhouse, where tiny plants are grown shoulder-to-shoulder in trays, he says.

After 2009, Zitter believes the company started using fungicides to prevent disease more regularly (which helps prevent disease, but also results in more spraying), and is now disposing of diseased plants properly, which usually involves bagging, burning, or burying diseased plants. Since then, he hasn’t found any problems and he stopped his inspections a couple years ago.

“I think that situation has been resolved,” says Zitter, who added he would still purchase vegetable starts from box stores as long as they looked healthy.

His advice to gardeners: Inspect plants closely, steer clear of any that look sick or diseased, and, if you do spot them, find another place to buy seedlings.

Cornell’s McGrath, who researches late blight, says that small, local greenhouses are not necessarily less likely to harbor disease, but they do offer more transparency–much like local produce farms. And the staff is more likely to be able to tell consumers how a plant was raised and what they do to prevent disease. Local production also prevents a disease, if it does exist in one greenhouse, from spreading too broadly.

“Does it matter who you’re purchasing from, big source versus little source? Not necessarily. It’s more how the plant was raised,” says McGrath. For example, growing ornamentals and vegetables together provides an opportunity for some viruses to spread. She says it’s impossible to eliminate the risk the plant of disease, but asking questions, such as, “Were these seeds tested for pathogens?” can also help.

McGrath tries to grow most of the seedlings for her garden herself, but her second choice would be to buy from a local greenhouse. “I like to support my local industry,” she says.

Photo of Home Dept by Ian Freimuth. Photo of tomato plants by Stephanie Ogburn.