Over the millennia that we as humans have been farming, the domestication of various plants has led to bigger crops – but this came at the cost of harming plant microbiomes.

(The genetic material of all the microbes, including bacteria, fungi, protozoa and viruses, that live on and in an organism.) Domesticated plants depend more on fertilizer and other soil amendments than their wild relatives because of this loss of beneficial biomes.

Through the thousands of years of human farming, many cultivated plants lost some ability to interact with the soil microbes that provide necessary nutrients. This resulted in some domesticated plants becoming more dependent on fertilizer – one of the world’s largest sources of nitrogen (N) and phosphorous (P) pollution. So how do growers make crops more productive and sustainable? Researchers are recommending reintroducing genes from wild relatives to restore the ability to interact with useful soil microbes.

“We’re so focused on above ground traits that we’ve been able to massively reshape plants while ignoring a suite of other characteristics and have inadvertently bred plants with degraded capacity to gain benefits from microbes,” said Joel Sachs, a professor of biology at the University of California-Riverside.

Bacteria and fungi in a plant’s microbiome form intimate associations with plant roots that can dramatically improve plant growth. They help break down soil elements like P and N, which are absorbed through the roots. (Microbes receive resources from the plants in a symbiotic relationship as well.) But, when fertilizer or other soil amendments are added, making nutrients freely available, plants tend to have less need to interact with microbes.

Sachs and fellow researcher Stephanie Porter of Washington State University-Vancouver looked over 120 studies of microbial symbiosis in plants and found that many types of domesticated plants weren’t that great at forming symbiotic communities with soil microbes.

Domestication has hidden costs, Sachs concluded. “When plants are selected for a small handful of traits like making a bigger seed or faster growth, you can lose a lot of important traits relating to microbes along the way,” he said. And this evolutionary loss turned into a loss for the environment too. Excess N and P from fertilizer can leach from fields into waterways, which can lead to algae blooms, low oxygen levels and dead zones. Nitrogen oxide from fertilizer can enter the atmosphere and contribute to air pollution. Fossil fuels are consumed to manufacture fertilizers.

In an effort to make agriculture more sustainable, some companies have started pushing nitrogen-fixing bacteria as soil amendments – but Sachs said these amendments don’t work well because some domesticated plants no longer have the ability to interact with those beneficial microbes from the soil.

What Sachs, Porter and other researchers are doing to fix these problems is figuring out which traits have been lost and which useful traits have been maintained in the wild relatives of our domesticated crops. Then they’ll work on breeding the wild and domesticated together to recover those traits. Growers may be seeing more primitive versions of their crops in the coming seasons…and that’s not necessarily a bad thing.