The Human Microbiome Project revealed tens of trillions of microbes residing in and on humans. Now scientists are taking a census of plant microbes—and not just the hundreds of billions found in soils. Distinct microbial communities live inside roots, on leaves and within flowers, and all in all have an estimated three to six orders of magnitude greater genetic diversity than their plant hosts. This second genome, much like the human microbiome, provides plants access to nutrients and helps to suppress disease. Scientists and farmers alike think it represents the next big thing in agriculture.

We are only just beginning to understand the interactions between plants and microorganisms. For instance, Jeff Dangl, a plant immunologist at the University of North Carolina at Chapel Hill, and his colleagues recently found that soil bacteria help to determine the flowering time of a wild plant in the mustard family. The results were published in June in Ecology Letters. And back in 2012, the team was surprised to find an abundance of streptomycetes bacteria living in a plant. Streptomycetes are often used to make antibiotics and may protect plants against infection. What is more, Dangl and others think understanding these intimate relationships is critical for increasing agricultural productivity, especially given rising global demand for food.

Commercial companies think so, too. Within the past two years BASF, Bayer CropScience, Chr. Hansen, Novozymes, Monsanto and numerous start-ups have invested about $2 billion in research and development in the area. Most of them are working on so-called biologicals—living crop aids. For example, Tom Johnson, who recently sold his South Dakota–based company TJ Technologies to Novozymes, developed QuickRoots, a seed coating of bacteria and fungi that spurs root growth.

Microorganisms may also be used to get rid of disease faster than breeding and genetic modification as well as to reduce wasteful applications of fertilizers. Thomas Videbæck, an executive vice president at Novozymes, says the company expects advances in the use of microorganisms to supplement rather than replace traditional methods. “There's not a silver bullet in any one of these technologies,” he says, “but we need to overcome the enormous hurdle of being able to produce twice as much food to feed nine billion people.” Earlier this year Novozymes announced the construction of a facility in North Carolina's Research Triangle Park to develop microbial cocktails that function as pesticides and support plant growth. It and other companies are waiting to see just what the plant microbiome will yield.