Saturday, March 15, 2025

How do crop domestication and improvement reshape the root system and microbial community?

Higher Education Press

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Credit: Xiaoming HE , Frank HOCHHOLDINGER , Xingping CHEN , Peng YU

Modern agriculture highly depends on the achievements of crop domestication and improvement. While these activities increase yields, they also reduce the genetic diversity of crops. At the same time, as a key organ for plants to absorb nutrients and water, the root system's microbial community is of great significance to plant health and growth. So, what are the impacts of domestication and improvement on crop root functions and related microbial communities?

The research team led by Professor Peng Yu from the University of Bonn in Germany deeply explored this issue. The research was recently published in the journal Frontiers of Agricultural Science and Engineering (DOI: 10.15302/J-FASE-2024593).

The study found that crop domestication and improvement have significantly reshaped the structure and function of root traits and related microbial communities. In terms of root traits, domestication has changed the length and density of lateral roots, the number of radicles, the length of the main root, etc. of crops. Taking maize as an example, during the domestication process, the number of its radicles increased, but the lateral root density decreased, the root hair length shortened, the root diameter decreased, and the specific root length increased. In the subsequent modern improvement process, the lateral root density of maize increased again, the main root length became longer, and the size of cortical cells increased.

The structure and function of the microbial community have also been profoundly affected. During the evolution from wild crops to modern crops, the relative abundances of various microorganisms have changed significantly. For example, the number of arbuscular mycorrhizal fungi decreased during the domestication of maize but was enriched in modern maize hybrids; Pseudomonas is more common in the rhizosphere of maize hybrids. In the evolutionary process of common bean, from wild ancestors to landraces and then to modern varieties, the relative abundances of Chitinophagaceae and Cytophagaceae in the rhizosphere gradually decreased, while those of Nocardioidaceae and Rhizobiaceae gradually increased. These changes in the composition of the microbial community play an important role in aspects such as crop nutrient absorption and immune capacity.

Further exploring the mechanisms, some researchers found that crop domestication and improvement affect the assembly and function of the microbial community through gene regulation, alteration of root structure and function, and characteristics of root exudates. For example, the maize domestication gene teosinte branched1 can regulate root development and change the composition of the rhizosphere microbial community; due to differences in gene expression, the structure and function of the rhizosphere microbial community of hybrid maize are different from those of its parents. During the domestication of wheat, from wild strains to modern varieties, plant defense metabolites, antioxidants, plant hormones, and proteinogenic amino acids in grains increased significantly. And during the domestication process from wild emmer to emmer to durum wheat, the patterns of different metabolites (such as fructose, mannitol, and sorbitol) in the rhizosphere varied depending on the soil type. These changes in root exudates have a profound impact on the microbial communities in the rhizosphere and within the roots.

This study summarizes the current research status of the impacts of crop domestication and improvement on root characteristics and the structure and function of related microbial communities, deeply analyzes the influencing mechanisms, and provides a solid theoretical basis for future breeding work.

Journal

Frontiers of Agricultural Science and Engineering

DOI

10.15302/J-FASE-2024593

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Crop domestication and improvement reshape root traits and the structure and function of their associated microbiome

Study: ‘Sustainable intensification’ on the farm reduces soil nitrate losses, maintains crop yields

University of Illinois at Urbana-Champaign, News Bureau

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U. of I. natural resources and environmental sciences researcher Lowell Gentry and his colleagues found that an intensive three-year crop-rotation system reduced nitrate pollution runoff by 50% without compromising crop yields.
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Credit: Photo by Craig Pessman

CHAMPAIGN, Ill. — A nine-year study comparing a typical two-year corn and soybean rotation with a more intensive three-year rotation involving corn, cereal rye, soybean and winter wheat, found that the three-year system can dramatically reduce nitrogen — an important crop nutrient — in farm runoff without compromising yield.

The new findings are detailed in the journal Frontiers in Environmental Science.

“Subterranean drainage pipes called tiles transport nitrogen, in the form of nitrate, from fields to streams, impairing downstream surface waters,” the scientists wrote. Nitrate runoff from farms pollutes streams and lakes, some of which supply drinking water for nearby communities. Nitrates also are carried down major rivers like the Mississippi to the Gulf of Mexico, contributing to a vast oxygen-starved “dead zone.”

“For maximum crop production we need artificial drainage, in the form of tiles and ditches, across much of Illinois. Unfortunately, nitrate can be lost from the rooting zone with tile water,” said Lowell Gentry, a researcher in natural resources and environmental sciences at the University of Illinois Urbana-Champaign who led the new study with Eric Miller, a grower and landowner in Piatt County, Illinois, where the research was conducted. “Our study was designed to see if a more diverse crop rotation could reduce tile nitrate loss and still be competitive with the conventional system of corn and soybean.”

From 2015 to 2023, the researchers determined crop yield and monitored nitrate loss from tile-drained fields on a working farm. Their “control treatment” consisted of two conventionally managed fields under a corn and soybean rotation. The more intensive three-year crop-rotation system was employed on an adjacent field. This field was planted with corn, followed by a full season of soybeans, then winter wheat. A summer harvest of the wheat was followed by a second crop of soybean the same year, or double-crop soybean. Between corn and soybean, a winter cover crop of cereal rye was grown to protect the soil. The cereal rye was terminated with herbicide prior to soybean planting and allowed to decompose on the soil surface, delivering nutrients to the next crop.

A key difference between the rotational systems was the amount of tillage. The control fields were fully tilled in the fall and spring, but the researchers strip-tilled only a narrow swath of the cornfield in the three-year rotation, minimizing the area tilled to one-third of the total field every third year. “By strip-tilling only about a third of the soil at a time, it takes us nine years to fully till the field,” Gentry said. This enhances soil stability.

Crops like cereal rye and winter wheat are planted in the fall after corn and soybean crops are harvested. These crops keep the soil intact, helping reduce erosion and nutrient runoff, Gentry said. Tilling the soil and leaving it bare for the fall, winter and spring increases soil erosion and boosts the growth of oxygen-loving microbes that consume soil-organic matter, releasing more nitrate.

Growers, policymakers and scientists have spent decades looking for ways to reduce the loss of nitrate from agricultural lands. Some approaches involve using woodchip bioreactors or installing wetlands to capture the runoff. But those approaches mean growers lose the fertilizing power of the nitrate.

“It’s very expensive to make fertilizer, and so I think it’s much more strategic to try and conserve the nitrogen, meaning keep it in the field, don’t let it leave in the first place,” Gentry said. “And that’s what the cereal rye and the winter wheat can do. They suck up enough nitrogen during the fall, winter and spring to lower the soil nitrate level. That reduces the tile nitrate level.”

The researchers saw a 50% reduction in tile nitrate losses in the three-year rotation when compared with the normal rotation. This was accomplished without compromising yields, the team found.

The long-term experiment, made possible with continuous funding from the Illinois Nutrient Research and Education Council, allowed the team to learn some important lessons. One year, wet weather prevented early termination of the cereal rye cover crop, allowing it to grow too tall. The added biomass reduced tile nitrate runoff by 90% — a positive outcome — but the excess rye also undermined soybean productivity, lowering yields by 10% that year. Another year, an early killing freeze of the double-crop soybean reduced crop yield and increased tile nitrate loss the next spring.

Gentry also noticed over time that the conventionally managed fields sometimes held standing water after heavy rains, while the experimental fields did not.

“I think that’s the result of much less tillage in the experimental field, and the fact that earthworms are now abundant in the diverse crop rotation,” he said. “It’s interesting to note that both rotations used a conventional herbicide regime, so we know it’s not the herbicides that kill the worms; it’s the tillage.”

Early indications are that the economics of the two systems are comparable, Gentry said.

“This study is a proof-of-concept that a more diverse rotation can achieve this sustainable intensification, reducing nitrate losses while also improving soil quality. Hopefully, recreating conditions that promote the natural processes of soil generation will improve soil quality and soil health, reversing the decadeslong trend of declining organic matter across our agricultural soils.”

Editor’s note:

To reach Lowell Gentry, email lgentry@illinois.edu.

The paper “A diverse rotation of corn-soybean-winter wheat/double crop soybean with cereal rye after corn reduces tile nitrate loss” is available online.

DOI: 10.3389/fenvs.2025.1506113

Winter wheat.

Credit

Photo by USDA-NRCS

Young soybean plants thrive in the residue of a wheat crop.

Credit

Photo by Tim McCabe, USDA Natural Resources Conservation Service