For anyone who cares about scientific integrity, or about agricultural practices and policies with profound consequences for everyday life, it's a disturbing allegation. The potential ramifications extend beyond Lundgren to other scientists who might be discouraged from studying important but politically contentious topics.

“There's a message: If you want to prosper at USDA, don't make waves,” says Jeff Ruch, the executive director of the watchdog group Public Employees for Environmental Responsibility. “When you do what Jonathan is doing, you do so at your own peril.”

On Wednesday, PEER filed a federal whistleblower complaint on Lundgren's behalf. According to his complaint, the suspension was part of a campaign of harassment that started last spring after two incidents. First, Lundgren talked to a journalist about the risks of a new genetic-engineering technique pioneered by the agribusiness-behemoth Monsanto. Then he peer-reviewed a report by the Center for Food Safety that criticized the overuse of neonicotinoids, which are ubiquitous in American agriculture and linked to widespread declines in pollinators.

After that, recounted Lundgren in a document released with his complaint, “improper reprisal, interference, and hindrance of my career began in earnest.” He was told not to speak again to the media about those topics. His human-resources department launched a six-month-long investigation of Lundgren's lab, interviewing his staff and reviewing their emails in a search for misconduct. Some were dismissed.

According to Lundgren, supervisors rejected his research proposals, throwing his grant-seeking efforts—the lifeblood of any lab—into disarray. A trip abroad to give a presentation became a red-tape nightmare; slides in the presentation, he was told, needed to be reviewed by at least seven administrators, none with direct expertise in his research. Under the strain he stepped down as lead scientist on a major project at his facility, the North Central Agricultural Research Laboratory.

Lundgren was even asked to remove his name as co-author from an article, “The causes and unintended consequences of a paradigm shift in corn production practices,” in the journal Environmental Science and Policy. “I believe this action raises a serious question concerning policy neutrality toward scientific inquiry,” wrote his co-author, the economist Scott Fausti of South Dakota State University, in a footnote to the paper.

Of course, it’s not yet clear what actually happened. Maybe Lundgren just didn’t get along with his boss. It happens. Asked for comment, the USDA declined to discuss Lundgren’s case specifically, but said in a statement that “we take the integrity of our scientists seriously and we recognize how critical that is to maintaining widespread confidence in our research among the scientific community, policy-makers, and the general public.”