Nigel Cattlin/Visuals Unlimited/Corbis

A plant may be rooted in place, but it is never lonely. There are bacteria in, on and near it, munching away on their host, on each other, on compounds in the soil. Amoebae dine on bacteria, nematodes feast on roots, insects devour fruit — with consequences for the chemistry of the soil, the taste of a leaf or the productivity of a crop.

From 30 June to 2 July, more than 200 researchers gathered in Washington DC for the first meeting of the Phytobiomes Initiative, an ambitious proposal to catalogue and characterize a plant’s most intimate associates and their impact on agriculture. By the end of the year, attendees hope to carve out a project that will apply this knowledge in ways that will appeal to funders in industry and government.

“We want to get more money,” says plant pathologist Linda Kinkel at the University of Minnesota in St Paul. “But beyond that, let’s just all try to talk the same language and come up with some shared goals.”

The effects of microbes and insects on plant health have often been studied in pairs — one microbe and one plant. But advances in genetic sequencing have opened up ways to survey entire microbial communities. Meanwhile, engineers and computational biologists have developed better ways to manage large data sets, merge disparate recordings into cohesive models and rapidly collect information on the physiology of every plant in a field. “Historically, we haven’t had the capacity to look at this as a system,” says plant pathologist Jan Leach at Colorado State University in Fort Collins. “Now we need to begin to integrate not just the data about the plant and the plant’s environment, but all the biological components in that system.”

Leach coined the term phytobiome in 2013,at a retreat about food security. She defines the phytobiome broadly, to encompass microbes, insects, nematodes and plants as well as the abiotic factors that influence all these.

Since then, she has visited companies, funding agencies and universities to call for a unifying phytobiomes initiative. She has teamed up with Kellye Eversole, a consultant based in Bethesda, Maryland, and the co-owner of a small family farm in Oklahoma, who has experience working on large agricultural genomics projects, including the US National Plant Genome Initiative. That initiative was launched in 1998 and continues to crank out databases and other tools for analysing plant genomes.

Leach hopes that the Phytobiomes Initiative will leave a similar legacy, but she is mindful that federal funding has tightened considerably since 1998. Still, she notes that the project can build on several emerging trends in agriculture. Industry has shown renewed interest in boosting plant growth by manipulating associated microbes (Nature 504, 199; 2013). Companies and farmers are also investing in ‘precision agriculture’, which uses high-tech monitors to track conditions in a field or even around individual plants, allowing farmers to water and fertilize in exactly the right places.

High-tech future

Eversole foresees a day when tractors will carry dipstick-like gauges that provide a snapshot of the microbial community in the soil. Data from the Phytobiomes Initiative would then help farmers to manipulate that community to their advantage, she says.

But first, the initiative needs to standardize protocols and metrics, the meeting’s attendees determined. Kinkel says that efforts are likely to focus initially on cataloguing microbes and insects and their interactions with different crops and habitats. “We’re where plant biologists were 150 years ago,” she says. “We’re still trying to inventory things.”

Work has already begun along these lines: for example, a group at the International Rice Research Institute in Los Baños in the Philippines is fishing for microbial DNA in data discarded from an effort to sequence the rice genome. The goal is to determine which microbes prefer which strains of the crop.

Kinkel, meanwhile, has begun experimenting with manipulating carbon levels in the soil to alter the microbial population, with the aim of improving plant productivity. “If we can understand better who lives on and within plants, we have the potential to manage them to have healthier, more resilient plants,” she says.

Projects such as these would move faster under an organized, cohesive framework, says Sarah Lebeis, a microbiologist at the University of Tennessee in Knoxville who is studying how plants manipulate microbial communities by secreting antibiotics into the soil. “Right now we’re working as individuals,” she says. “Having an initiative will give us focus and hopefully we’ll progress further, faster, better.”