As a child growing up poor in New York City, Jenny T. Kao-Kniffin, School of Integrative Plant Science, Horticulture, would stare out her bedroom window at the nearby community garden. It was surrounded by a tall fence, and although Kao-Kniffin saw other children inside its grounds, she had no idea how to join them. “I couldn’t figure out how to get a foot in the door, how to even touch the soil or plants,” she remembers.

That experience has stayed with her and contributed to her scientific career. “I chose research as a way to get to nature,” she says. “That led me to soil microbiology and restoration ecology, this idea of taking a degraded ecosystem and turning it into something like a natural, productive ecosystem. I was afraid that other kids could end up like I did, with no opportunity to be in nature, so I wanted to do something about that.”

Kao-Kniffin specifically focuses on the rhizosphere (the soil surrounding the roots of plants) and the microbiome (the bacteria and fungi surrounding plant roots). From her early work in natural ecosystems, she has since pivoted to human-managed ones, including agriculture. In a satisfying turn of events, she is collaborating with graduate student Maria Gannett, PhD ’22 Horticulture, and Antonio DiTommaso, Soil and Crop Sciences, on a project Kao-Kniffin once wanted to carry out as a graduate student herself—back when she was working on prairie ecosystems but for which she was unable to get funding. “I had this idea of modifying the soil environment by adding carbon amendments to establish a microbiome that would facilitate a plant community that was more reflective of prairie ecosystems,” she explains.

Now her graduate student Gannett has obtained a Foundation for Food and Agriculture Research Fellowship to apply the same idea to agriculture. By adding carbon amendments to the soil, the researchers stimulate microbial activity, causing microbes to scavenge and take up more nitrogen and phosphorus from the soil, leaving little for the nitrophilous weeds.

“A plant that needs a lot of nitrogen will be disadvantaged early on,” Kao-Kniffin says. “Studies have shown that some nitrophilous plants need to accumulate nitrogen early in their growth, otherwise they won’t continue to grow well. We wanted to see if we could develop a technique to prime the soil for microbiome mediation of plant competition in agricultural fields.”

The initial data from this past summer’s field experiments confirmed that certain weed species are poor competitors with soil microbes for nitrogen. The researchers were amazed at the results. “It was shocking how well the carbon amendment worked against some of these nitrophilous weeds,” Kao-Kniffin says. They are now preparing for a second season of experiments to assess if carbon amendments cause weed populations to favor more weedy legumes, such as clovers and vetch, that can fix their own nitrogen. So far in the first year, the weeds in the soybean test field decreased, with no negative impact on soybean yield.

“This is a really nice way to take concepts in ecology and bring them over to agriculture,” Kao-Kniffin says. “I think this way of modifying the ecosystem by altering microbiome functions has a lot of potential in the future. We need to get away from this routine of relying on genetically modified crops and their paired herbicides, but instead look more toward applying concepts in ecology and evolutionary biology to manage agricultural systems.”

“This is a really nice way to take concepts in ecology and bring them over to agriculture.”

Looking at the benefits of the microbiome to plant communities, Kao-Kniffin has collaborated for many years on projects that explore directed evolution by selecting for soil microbiomes associated with specific, desired plant traits. The earliest of these studies, with graduate student Kevin Panke-Buisse, PhD ’15 Horticulture—now at the United States Department of Agriculture at the University of Wisconsin, Madison—and other collaborators, caused a stir in the microbiome science community.

In their paper, published in the International Society for Microbial Ecology (ISME) Journal in 2015, the researchers showed that they could alter the flowering time of Arabidopsis thaliana through manipulation of the plant’s soil microbiome. They used the experimental evolution approach of assembling microbiomes associated with flowering time over 10 generations. This placed continuous selection pressure on members of the rhizosphere microbiome associated with either earlier or later flowering times. The later-flowering plants were of particular interest since they also bore greater floral biomass that would presumably lead to bigger seeds or yields—desired traits in agricultural plants.

“That paper has been cited over 240 times.” says Kao-Kniffin. “I was shocked because I thought of it as a highly experimental study using a model plant, Arabidopsis, which is not a crop. We wanted to use something where we could control the host genetics and hone in on the microbiome effect—the collective function of the microbiome altering flowering.” Although the flowering time for Arabidopsis was thought to be abiotic, controlled by physical parameters such as temperature, Kao-Kniffin and her colleagues demonstrated that the microbiome can regulate flowering time as well.

In a follow-up to that earlier research, Kao-Kniffin is now working with graduate student Joshua Garcia, PhD ’21 Horticulture, testing the influence of the microbiome on biomass and seed yield for canola, a crop plant. “For this study, we were able to do what we couldn’t do for the first one, which was sequence the rhizosphere samples across every generation to see what changes over time in the microbiome,” Kao-Kniffin says.

The researchers found that the microbiomes grown under selection for increased plant biomass began to diverge from those that were selected randomly, starting in the sixth generation. “As the generations progressed, the microbiomes in the rhizosphere of the higher-yielding plants exhibited a greater density of interactions among bacteria compared with the controls. This means we not only assembled distinctly different compositions of the microbiome associated with plant yield, but also different community behaviors,” Kao-Kniffin says. “We designed this ecological assembly of the microbiome to modulate the host’s phenotype without genetic engineering. This shows the inherent power of bacteria to collectively shape the development of higher organisms in a short period of time.”

Kao-Kniffin recently turned her attention to urban agriculture. This has led her back to New York City, where she is part of a new project to help city farmers construct clean soil from local materials, including city compost, clean sand from below the polluted city topsoil, and perhaps a dose of microbiome especially created for the purpose. She has come full-circle from the little girl who stared out her bedroom window at the community garden she couldn’t enter.

“This is one of the most rewarding parts of my career,” Kao-Kniffin says. “I always wondered how I could do some of this community garden work, and now I’m actually doing it.”