Farmers are facing a phosphorus crisis. The solution starts with soil.

Overuse of fertilizer has led to phosphorus shortages and water pollution. But farms might not need so much to grow healthy crops.

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A farmer spreads organic fertilizers of bone meal pellets and rock phosphate before planting spinach in the Harmony garden in Golden, Colorado.

On an overcast day, Roger Sylvester-Bradley walks along a hawthorn hedge, collecting a thick rind of mud on his leather boots, before stepping into a gently sloping field of barley.

He stoops to pluck an ankle-high seedling from the ground and examines its healthy mop of fine white roots. Turning them in his hands, he says, “when you see a plant that’s deficient in phosphorus, it doesn’t look like this.”

That’s something of a surprise to Sylvester-Bradley, a crop scientist at ADAS, an agricultural consulting company in Cambridge, England. Phosphorus occurs naturally in soil and is a critical nutrient for plant growth. For centuries, farmers have added extra to their fields to boost harvests, but Sylvester-Bradley and his colleagues are studying ways to produce food using less of it.

The reasons are twofold: First, phosphorus runoff from farms contributes to widespread water pollution. Second, we don’t have phosphorus to waste.

Nearly all of the phosphorus that farmers use today—and that we consume in the food we eat—is mined from a few sources of phosphate rock, mainly in the United States,...

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