In a development that could lead to better ways to protect food crops from disease, Berkeley Lab scientists unraveled the community of soil microbes that protect sugar beets from root fungus. From left, Todd DeSantis, Gary Andersen, and Yvette Piceno in the lab where much of the research was conducted. Several PhyloChips are on the table next to them. Photo: Roy Kaltschmidt, Berkeley Lab Public Affairs
Those vegetables you had for dinner may have once been
protected by an immune system akin to the one that helps you fight disease.
Scientists from the U.S. Department of Energy’s Lawrence Berkeley National
Laboratory (Berkeley Lab) and the Netherland’s Wageningen Univ.
found that plants rely on a complex community of soil microbes to defend
themselves against pathogens, much the way mammals harbor a raft of microbes to
The scientists deciphered, for the first time, the group of
microbes that enables a patch of soil to suppress a plant-killing pathogen.
Previous research on the phenomenon of disease-suppressive soil had identified
one or two pathogen-fighting microbes at work.
But the Berkeley Lab-led team found a complex microbial
network. After analyzing soil from a sugar beet field that had become resistant
to a pathogen that causes root fungus, the scientists found 17 soil microbes
fighting to suppress the pathogen. They also determined that all of the
microbes work together to reduce the incidence of fungal infection. Their
discovery that plants use a tight-knit army of soil microbes for defense could
help scientists develop ways to better protect the world’s food crops from
“Individual organisms have been associated with
disease-suppressive soil before, but we demonstrated that many organisms in
combination are associated with this phenomenon,” says Gary Andersen of Berkeley
Lab’s Earth Sciences Division. He conducted the research with fellow Berkeley
Lab scientists Todd DeSantis and Yvette Piceno, as well as several scientists
from the Netherlands
Univ.’s Jos Raaijmakers.
Their research is published in Science Express.
The Berkeley Lab and Dutch scientists analyzed soil from a
sugar beet field in the Netherlands.
Something in the soil suppressed the presence of the pathogen Rhizoctonia
solani, which causes root fungus in beets, potato, and rice.
New research reveals that it takes a community of soil microbes, not just one or two, to protect crops. The top image is a healthy sugar beet field. The bottom image is a field of sugar beets that is infected with root fungus. Photo: Lawrence Berkeley National Laboratory
The sugar beets’ health followed the typical arc of plants
in disease-suppressive soil: they enjoyed a few good years, then they succumbed
to disease, followed by healthy beets again as pathogen-fighting microbes were
activated and the soil became hostile to R. solani. To return the
favor, the sugar beets funnel about a fifth of their photosynthetically
captured carbon through their roots into the soil to fuel the microbes.
Disease-suppressive soils are quite common, and scientists
have identified some of the microbes involved in this underground immune
system. But they don’t know all of the microbes that participate.
To find out, the scientists used the PhyloChip, which is a
credit-card sized chip that can detect the presence of 59,000 species of
bacteria and archaea in samples of air, water, and soil without the need of
culturing. It was developed at Berkeley Lab to rapidly identify not only the
most common and abundant organisms in an environmental sample, but also very
rare types that are present in extremely small numbers. It does this by
comparing a DNA sequences unique to each bacterial species with over one
million reference DNA targets on the chip. The PhyloChip has shed light on many
environmental mysteries, such as what’s killing coral reefs near Puerto Rico
and what degraded much of the oil from the Gulf of Mexico’s
Deepwater Horizon spill.
In this case, soil samples from the sugar beet field were
modified to exhibit six levels of disease suppression. DNA was isolated from
the samples and sent to Berkeley Lab for analysis. The PhyloChip detected more
than 33,000 bacterial and archaeal species in the samples, with all six having
more or less the same types of bacteria.
But when the scientists looked at the abundance of bacteria
in each sample, they found that each had a unique fingerprint. All of the
samples in which disease was suppressed had a greater abundance of 17 unique
types of bacteria. These included well-known fungal fighters such as
Psuedomonas, Burkholderia, Xanthomonas, and Actinobacteria. In addition, other
types of bacteria that have no demonstrated ability to fight pathogens on their
own were found to act synergistically to suppress plant disease.
Based on this, the scientists believe that an uptick in
several bacterial types is a more important indicator of disease suppression
than the presence of one or two bacteria that are especially good at killing
“We now see that the complex phenomenon of disease
suppression in soils cannot simply be attributed to a single bacterial group,
but is most likely controlled by a community of organisms,” says Andersen.
Their research will help scientists pursue unanswered
questions about disease-suppressive soil: Do plants actively recruit beneficial
soil microorganisms for protection against infection? And if so, how do they do
it? It will also help scientists elucidate the mechanisms by which groups of
soil microbes work together to reduce the incidence of plant disease.