Novel method to measure root depth may lead to more resilient crops
New approach could lead to faster breeding of plants better able to withstand drought, acquire nitrogen and store carbon deeper in soil
PENN STATE
IMAGE:
ALTHOUGH THIS METHOD OF IDENTIFYING DEEP-ROOTING PLANTS WAS ACCOMPLISHED WITH CORN, SHOWN HERE ON A CLOUDY SUMMER MORNING GROWING AT PENN STATE'S RUSSELL E. LARSON AGRICULTURAL RESEARCH CENTER, IT CAN BE USED WITH ALL PLANTS, THE RESEARCHERS SAID.
view moreCREDIT: PENN STATE
UNIVERSITY PARK, Pa. — As climate change worsens global drought conditions, hindering crop production, the search for ways to capture and store atmospheric carbon causing the phenomenon has intensified. Penn State researchers have developed a new high-tech tool that could spur changes in how crops withstand drought, acquire nitrogen and store carbon deeper in soil.
In findings published in the January issue of Crop Science, they describe a process in which the depth of plant roots can be accurately estimated by scanning leaves with X-ray fluorescence spectroscopy, a process that detects chemical elements in the foliage. The method recognizes that roots take up elements they encounter, depending on the depth they reach, and a correlation exists between chemical elements in the leaves and root depth.
The new technology is the subject of a provisional patent application by Penn State, because it promises to speed up the plant-breeding process, according to research team leader Jonathan Lynch, distinguished professor of plant science in the College of Agricultural Sciences. The ability to measure the depth of plant roots without excavating them is a game-changing technology, he said.
“We've known about the benefits of deeper rooting crops for a long time — they are more drought tolerant and have an enhanced ability to take up nitrogen, which tends to move deep with water — but the problem has been how to measure root depth in the field,” he said. “To breed deeper-rooted crops, you need to look at thousands of plants. Digging them up is expensive and time consuming because some of those roots are down two meters or more. Everybody wants deep-rooted crops — but until now, we didn’t know how to get them.”
An added benefit to deeper-rooting crops, Lynch noted, is that they store carbon in the soil more effectively. And soil is the right place to put carbon, he pointed out, because carbon in the atmosphere is a bad thing — it causes global warming. Carbon in the soil is a good thing — it boosts fertility.
“Having deeper roots means that carbon the plants get from photosynthesis is stored down deeper in the soil when they build roots. And the deeper carbon is put in the soil, the longer it stays in the soil,” he said. “The U.S. Department of Energy estimates that just having deep-rooted crops in America alone could offset years of our total carbon emissions. That’s huge — think about all the acres growing crops in America. If those roots grow just a little bit deeper, then we’re storing massive amounts of carbon deeper in the soil.”
Developing the new method — which the researchers called LEADER (Leaf Element Accumulation from DEep Root) — took six years and involved the collection and analysis of more than 2,000 soil core samples at four research sites across the country, noted Molly Hanlon, a former postdoctoral scholar in Lynch’s research group, who spearheaded the study.
It involved growing a set of 30 genetically distinct lines of corn at Penn State’s Russell E. Larson Agricultural Research Center, the University of Colorado’s Agricultural Research and Education Center, the University of Wisconsin Arlington Agricultural Research Station, and the University of Wisconsin Hancock Agricultural Research Station. The researchers found that they could correctly classify the plots with the longest deep root lengths — deeper than 30 or 40 centimeters — using the LEADER method with high accuracy.
A major tenet of soil science is that biological, physical and chemical properties vary with soil depth, explained Hanlon, now a senior research scientist with Donald Danforth Plant Science Center in St. Louis.
“And plant roots grow through these different soil layers,” she said. “The elements are then transported to the shoot where we can quickly and easily assay the elemental content of leaf tissue using X-ray fluorescence. In this way, the leaves can serve as indicators or sensors of where the roots are in the soil.”
In the study, the researchers were able to accurately estimate root depth by analyzing the foliar accumulation of elements naturally occurring in diverse soils. As an alternative method for assessing root depth, in both field and greenhouse experiments, they injected strontium into the soil at a set depth as a tracer for LEADER analysis. Later, they harvested plants growing nearby and determined that strontium detected in the leaves strongly correlated to the depth of their roots.
Although the LEADER method was accomplished with corn, it offers a wider application, Lynch suggested.
“It shows promise as a tool for measuring root depth in different plant species and soils,” he said. “It made sense to do this research with corn — it’s one of the world’s most important crops, grown extensively as a staple food for humans, livestock feed, as a biofuel and as a starting material in industry. Deeper-rooted corn crops able take up more water and nitrogen under limiting conditions, with increased long-term soil carbon storage would be a major development. But this LEADER method can be used with all plants.”
Kathleen Brown, Penn State professor emeritus of plant stress biology, contributed to the research.
This research was funded by the U.S. Department of Energy ARPA-e and the U.S. Department of Agriculture’s National Institute of Food and Agriculture.
JOURNAL
Crop Science
METHOD OF RESEARCH
Experimental study
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
LEADER (Leaf Element Accumulation from DEep Roots): A nondestructive phenotyping platform to estimate rooting depth in the field
Research team identifies genetic contribution to the composition of the microbiome around maize roots
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MAIZE PLANTS GROWING UNDER DROUGHT STRESS IN THE EXPERIMENT PERFORMED AT THE UNIVERSITY OF BONN.
view moreCREDIT: DR. PENG YU, UNIVERSITY OF BONN
In order for plants to grow, they absorb water and nutrients through their roots. In doing so, they rely on tiny helpers: bacteria and fungi in particular are found in a thin layer around the roots. These microbes also ward off organisms that are harmful to the plant, just as the "microbiome" in the human gut helps determine whether we fall ill or stay healthy.
An international research team led by the University of Bonn and with the participation of the IPK Leibniz Institute has now demonstrated on maize plants that the genetic make-up of the host plant has a significant influence on the composition of the root microbes. "It was shown that the root microbiome is strongly dependent on stress conditions such as nutrient or water deficiency," says Dr. Yong Jiang, one of the first authors of the study and a scientist in IPK's research group “Quantitative Genetics”.
The genetic make-up of different maize varieties varies greatly. Regional varieties are adapted to very different environmental conditions, depending on whether they are grown in the cooler highlands or warmer lowlands of South America. "The centuries-long selection of maize varieties adapted to the local climate led to very different genotypes, which we were able to use for the study," says Dr. Peng Yu, head of the junior research group "Functional Root Biology" at the University of Bonn.
The research team has now analysed 129 maize varieties. These were grown under "normal" conditions and under a lack of phosphorus, nitrogen and water. In addition, the DNA of microbes from 3,168 samples taken from the layer around the roots, which is just a few millimetres thick, was sequenced.
The role of the genetic material in the root was revealed under stress conditions. Nutrient and water deficiency also had an influence on the composition of the microbes. However, under the same stress conditions, differences in the microbiome of the maize varieties were nevertheless revealed. "We have shown that certain maize genes interact with certain bacteria," explains Dr. Peng Yu.
The international research team was even able to use data on the growing conditions at the place of origin of a particular maize variety and its genetic make-up to predict which key organisms occur in the microbiome at the root. Bacteria of the genus Massilia stood out in particular: "It was striking that only a few specimens of these microbes were present when there was a sufficient supply of nitrogen," explains Prof. Dr. Gabriel Schaaf from the Ecophysiology of Plant Nutrition department at INRES and member of the PhenoRob Cluster of Excellence at the University of Bonn. If, on the other hand, nitrogen was scarce, many Massilia were found at the roots. The team then "inoculated" maize roots with this bacterium. This showed that the plants subsequently formed many more lateral roots and thus significantly improved their nutrient and water uptake.
In further investigations, the researchers discovered that the root attracts Massilia bacteria with flavones. This is a plant pigment that stimulates the formation of lateral roots with the help of the bacteria. "However, the prerequisite for this was that the maize plant had a microtubule-binding gene," says Dr. Peng Yu.
"For this study, we also opened up the toolbox of quantitative genetics for microbiome research," explains IPK scientist Dr. Yong Jiang. "We were surprised by the large proportion of the genetic component in the formation of the microbiome." The results can be used by both science and breeding. "They can serve as a basis for investigating further agroecological issues and for developing new maize varieties that are better adapted to climate change based on the genome and microbiome data."
JOURNAL
Nature Plants
ARTICLE TITLE
Heritable microbiome variation is correlated with source environment in locally adapted maize varieties
ARTICLE PUBLICATION DATE
21-Mar-2024
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