Clean greens are healthy greens.

Or so thought a coalition of farmers, growers and processers in California when, in response to a deadly spinach outbreak of the bacteria Escherichia coli (E. coli), they created a new set of bacteria-minimizing standards for growing and handling leafy greens.

Although the standards were designed to eliminate potential sources of contamination by mandating that crop sites be cleared of vegetation and kept a certain distance from wildlife and natural bodies of water, they have had some unintended consequences—namely, the destruction of habitats, the degradation of soil and the pollution of rivers and streams.

Researchers found that the 2006 regulations, corporate standards enforced through third-party audits, have not only been ineffective at reducing the risk of food-borne illness, but have contributed to a loss of ecological diversity in the Salinas River Valley, an area of California prized for its variety of animal and plant life and the center of production for 70 percent of America’s leafy greens.**

A study, published in the May 6 edition of Frontiers in Ecology and the Environment, measured changes farmers and growers made to the environment between 2005 and 2009. Using satellite images from the National Agriculture Imagery Program, researchers broke the 15,000-hectare study area into ecological communities defined by vegetative type. The greatest amount of habitat loss, they found, occurred in transitional communities, where fast-growing grasses, shrubs and trees depend on constant disturbance for survival.

Researchers discovered that the new farming practices have further de-incentivized growers from farming in ways that take into account the importance of natural systems of resource cycling and plant regeneration. Instead, many have cleared land of native vegetation, erected fences and laid poison to deter the presence of wildlife. As a result of growers’ attempts to control for all potential variables on crop sites, farmed areas have become not only uninhabitable for wildlife but also more vulnerable to climate change.

Study authors say the practices are an overzealous attempt to respond to consumer concerns about foodborne illness. “There is this pressure from consumers and buyers to go above and beyond what’s necessary for clean food,” says ecologist Sasha Gennet, a researcher at The Nature Conservancy and the lead author of the study.

The impact of the regulations on foodborne illness has not yet been proven. Since the 2006 outbreak of E. coli was linked with spinach grown in California, at least 15 more domestic E. coli outbreaks have been reported. More than half included cases reported in California.

Iowa State University landscape ecologist Lisa Schulte Moore says the study carries important implications for the future of farming. As the epicenter for the majority of America’s leafy greens, the Salinas Valley is seen as a model of successful farming practices. If these practices continue, Moore says, other states could begin implementing farming regulations that harm the environment. “As someone who lives in one of the biggest farming states in the country, what I’m worried about is, what is this going to mean for other farmers?”

But growers say their methods are necessary to protect consumers. The 2006 E. coli outbreak, for example, sickened 205 people and cost San Juan Bautista–based company Earthbound Farms over $70 million in damages.* But after an investigation into the source of the outbreak turned up no leads, Will Daniels, the company’s director of farm and food safety, led an overhaul of the entire production line. Thanks to a new system of intensive safety precautions—which includes testing crops for pathogens at all levels of the processing line and distancing crop sites from potential sources of microbial contamination, such as streams or animal habitats—Daniels says consumers can be assured that the product they are buying is safe to eat.

Without knowledge of the cause of bacterial outbreaks, California farmers and growers are going too far in their efforts to ensure crops are grown in virtual isolation from their surrounding environment, says Moore. “The main problem is that there’s this understanding in the community that everything we do to improve food safety is great. But it’s this overzealous attempt to improve upon a good thing that’s really costly for the environment.”

*Correction (May 10, 2013): This sentence was edited after posting. It originally erroneously stated that the 2006 E. coli outbreak killed nearly 300 people; there were three fatalities.

**Correction (May 13, 2013): This sentence has been changed. Originally it incorrectly stated that the system of standards includes the California Leafy Green Products Handler Marketing Agreement (LGMA).