For Bayer, the cost of buying Monsanto is proving higher than the $66 billion it paid for the U.S. agrochemical company.The German pharmaceutical giant is grappling with a tide negative publicity regarding Monsanto's Roundup weed killer, and getting punished by investors in the bargain.

Two months after completing its purchase of Monsanto, Bayer is looking at a drawn-out legal scrimmage over claims the herbicide produced by U.S.-based Monsanto causes cancer.

Shares of Bayer have slumped this week after Monsanto was hit with a $289 million verdict in favor of a groundskeeper, Dewayne Johnson, dying of cancer who blames Roundup for causing his non-Hodgkin's lymphoma.

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Somewhat higher than the $277 million set aside by Monsanto to pay for the litigation, Friday's federal jury ruling is only the first of thousands of unresolved claims related to the weed killer.

"Bayer believes that the jury's verdict is at odds with the weight of scientific evidence, decades of real world experience and the conclusions of regulators around the world that all confirm glyphosate is safe and does not cause non-Hodgkin's lymphoma," the company stated in an email.

Bayer plans to appeal the ruling, which found Monsanto liable for the groundskeeper's illness and lost wages, as well as for its failure to alert the public to Roundup's risks. Monsanto argues that its product is safe, even as researchers, attorneys and regulators for years debated whether the herbicide causes cancer.

"With another 2,000-plus cases pending, this looks potentially ruinous for Bayer," Bernstein analysts led by Jonas Oxgaard wrote in a client note. Still, "The scientific evidence appears to be on Monsanto's side, and in our view an appeal is likely to reverse the ruling," they added.

Bayer is likely to pull Roundup from gardening uses, according to the investment bank.That could cost the company $200 million in revenue. Bayer is expected to continue selling Roundup to farmers.

The German conglomerate's acquisition of Monsanto made the drugmaker the world's biggest seller of seeds and agricultural chemicals. In use for more than four decades, Roundup's major ingredient is a chemical called glyphosate, now the most widely used herbicide on the planet.

The U.S. Environmental Protection Agency said last year that glyphosate is unlikely to cause cancer in people. By contrast, the World Health Organization labels the chemical as "probably carcinogenic to humans."

Adding fuel to the potential public relations fire for Bayer and Monsanto, an advocacy group on Wednesday released the findings of a study that found glyphosate in a number of popular oats-based cereals and granola bars.

The problems for Bayer aren't limited to Roundup. The Canadian government on Wednesday said it would restrict the outdoor use of certain chemicals linked to the deaths of aquatic insects and bees, including the company's clothianidin pesticide, and could decide later in the year to phase out another Bayer product, imidacloprid. Both belong to a class of pesticides that the European Union has proposed banning.

During an investors' call in late May, Bayer CEO Werner Baumann said buying Monsanto position the company to help farmers worldwide "produce healthy, safe and affordable food in a sustainable manner."

Still, looking to avoid linking its brand to protesters and genetically modified crops, Bayer in June confirmed that it would shelve the Monsanto name, and acknowledged the public's unease with the U.S. company's products.

After falling more than 10 percent on Monday as investors mulled the implications of Friday's verdict, Bayer shares steadied the following day only to slide another nearly 4 percent on Wednesday.