Have you ever bought a plant, cared for it lovingly, only to have it die on you? Aside from being picky about how much water and light they get, plants need nutrients to survive. Now picture this on a nationwide scale for crop plants. 

Every year in the US, we apply 20 million metric tons of fertilizer to soils to provide nutrients to crop plants. Some of these fertilizers are non-renewable, such as phosphate–– so clearly something needs to be done, and one of the possible solutions lies in the tiniest organisms in the soil. 

You see, in the wild, plants obtain the nutrients they need with the help of microorganisms that interact with their roots, such as fungi. Plants provide the fungi with sugars in exchange for things that are just out of reach in the soil: phosphorous, nitrogen and even water. Healthy plants as we know them don’t grow alone, they get by with a little help from their friends. Crop plants obtain about half of the nutrients they need this way, but if we could increase the plants access to these nutrients, this would greatly reduce our dependence on non-renewable chemical fertilizers and essentially be the next green revolution- so why hasn’t it been done?

Despite the fact that plant’s interactions with beneficial fungi have been studied for decades, there are still big gaps in our knowledge. For instance, why don’t all plants form these interactions? And how does a plant distinguish a beneficial fungus in the soil from a parasitic one? How do the and the plant and fungus communicate chemically? Trying to get a coherent understanding about all of the different players involved in this interaction: the genes, proteins, and chemical signals, it can feel like being lost in a thicket of information. What we need is a map.

My goal is to make a map of what is going on in these roots at the molecular level. And I do mean a map: a 2D representation with the physical locations of the genes expressed at moment in time, overlayed on an image of the root. It works like this: I’d take a slice of root that is colonized by the beneficial fungus, and I lay it on a specially coated slide that captures the mRNA from the plant root. What I end up with is a picture of the root which I can zoom in right down to the molecular level to see where each gene is expressed. That’s spatial transcriptomics.

When you combine my data-rich map with the datasets that others are developing for plant roots, we’ll have a grand altas, with which we’ll be able to chart a course to engineer these interactions to be more efficient, or so that more plants can benefit from these microbes, and not just the ones that have already evolved to. Though you could potentially add this to your dying plant at home, the ultimate goal is global food security: healthier crops with more sustainable fertilization.

I hope that we can look back on this era of big data and say that we mined it for discoveries that constituted the second green revolution, because it can't come a moment too soon.