permaculture

[Lawrence London <lfljvenaura@gmail.com>]

https://m.phys.org/news/2018-03-complex-soil-microbes.html

Researchers prove complex connection between plants and what soil microbes
eat
[image: Plants really do feed their friends]
<https://3c1703fe8d.site.internapcdn.net/newman/gfx/news/2018/plantsreally.jpg>
Rhizosphere soil for microbial isolations was collected from the Little
Buck watershed at the University of California Hopland Research and
Extension Center in an area in which Avena barbata are the dominant
vegetation. Credit: Heejung Cho

Researchers at the Department of Energy's Lawrence Berkeley National
Laboratory (Berkeley Lab) and UC Berkeley have discovered that as plants
develop they craft their root microbiome, favoring microbes that consume
very specific metabolites. Their study could help scientists identify ways
to enhance the soil microbiome for improved carbon storage and plant
productivity.

"For more than a century, it's been known that plants influence the makeup
of their soil microbiome, in part through the release of metabolites into
the soil surrounding their roots," said Berkeley Lab postdoctoral
researcher Kateryna Zhalnina, the study's lead author. "Until now, however,
it was not understood whether the contents of this cocktail released by
plants was matched by the feeding preferences of soil microbes
<https://phys.org/tags/soil+microbes/> in a way that would allow plants to
guide the development of their external microbiome."

The study, "Dynamic root <https://phys.org/tags/root/> exudate chemistry
and microbial substrate preferences drive patterns in rhizosphere microbial
community assembly," has just been published in the journal *Nature
Microbiology*. The corresponding authors were Berkeley Lab scientists Trent
Northen and Eoin Brodie.

Microbes within soil improve the ability of plants to absorb nutrients and
resist drought, disease, and pests. They mediate soil carbon conversion,
affecting the amount of carbon stored in soil or released into the
atmosphere as carbon dioxide. The relevance of these functions to
agriculture and climate are being observed like never before.

Just one gram of soil contains tens of thousands of microbial species.
Scientists have long known that plants impact the composition of the soil
microbiome in the area surrounding their roots by sending out chemicals
(metabolites). Prior work by Mary Firestone, Berkeley Lab faculty scientist
and a professor of microbiology at UC Berkeley, had shown that plants were
consistently selecting or suppressing the same types of microbes over time
in the root zone, suggesting some form of synchronization between plant and
microbiome development.

Yet, little research had gone into the relationship between specific
metabolites that plants release and the microbes consuming them. The new
study brought together experts in soil science, microbial and plant
genomics, and metabolomics to explore these potential metabolic
connections. Their study took a close look at the rhizosphere of an annual
grass (Avena barbata) common in California and other Mediterranean
ecosystems.

The Berkeley Lab team felt the time was ripe for doing so. As pressure
mounts for farmers to grow enough healthy crops to meet a burgeoning
population's needs, and for new land management strategies that improve
soil carbon storage to reduce atmospheric CO2 and produce healthy soils,
the soil microbiome is the subject of more in-depth scientific research
than ever before.

The researchers set out to determine the relationship between microbes that
consistently bloomed near the grass roots and the metabolites released by
the plant. Their first step was to collect soil from the University of
California's Hopland Research and Extension Center in northern California.
Brodie, deputy director of Berkeley Lab's Climate and Ecosystem Sciences
Division, and his group used what they knew about the lifestyles of these
soil bacteria to develop specialized microbial growth media to cultivate
hundreds of different bacterial species. They then selected a subset that
either flourished or declined as roots grew through the soil.

This collection of microbes was then sent to the Joint Genome Institute
(JGI), a DOE Office of Science User Facility, where their genomes were
sequenced to provide clues as to why their responses to roots differed.
This analysis suggested that the key to success for microbes that thrived
in the rhizosphere was their diet.
[image: Plants really do feed their friends]
<https://3c1703fe8d.site.internapcdn.net/newman/gfx/news/2018/1-plantsreally.jpg>
Microbes that flourish in the area around plant roots take up specific
organic acids from the root exudates. Credit: Javier Ceja-Navarro

Northen, senior scientist in Berkeley Lab's Environmental Genomics and
System Biology Division, is fascinated by the chemistry of microbiomes, and
his group has developed advanced mass spectrometry-based exometabolomic
approaches to elucidate metabolic interactions between organisms. Zhalnina
and Northen combined their expertise to identify what the more successful
microbes surrounding the roots of the Avena grasses preferred to eat.

Using a hydroponic setup at the JGI, they immersed plants at different
developmental stages in water to stimulate them to exude their metabolites,
then measured the metabolites being released by the plants using mass
spectrometry. Subsequently, the cultivated soil microbes were fed a
cocktail of root metabolites, and the researchers used mass spectrometry to
determine which microbes preferred which metabolites.

They found that the microbes that flourished in the area around plant roots
preferred a diet more rich in organic acids than the less successful
microbes in the community.

"Early in its growth cycle, the plant is putting out a lot of sugars,
'candy', which we find many of the microbes like," Northen said. "As the
plant matures, it releases a more diverse mixture of metabolites, including
phenolic acids. What we discovered is that the microbes that become more
abundant in the rhizosphere are those that can use these aromatic
metabolites."

Brodie describes these phenolic acids as very specific compounds released
by plants throughout their development. Phenolic acids are often associated
with plant defenses or plant-microbe communication. This indicates to
Brodie that as they establish the microbial community within the
rhizosphere, plants could be exuding metabolites like phenolic acids to
help them control the types of microbes thriving around their roots.

"We've thought for a long time that plants are establishing the rhizosphere
best suited to their growth and development," said Brodie. "Because there
are so many different types of microbes in soil, if the plants release just
any chemical it could be detrimental to their health.

"By controlling the types of microbes that thrive around their roots, plants
<https://phys.org/tags/plants/> could be trying to protect themselves from
less friendly pathogens while promoting other microbes that stimulate
nutrient supply."

Zhalnina, Firestone, Northen, and Brodie believe their findings have great
potential to influence additional scientific and applied research. Zhalnina
points out that a lot of research and development is currently underway by
government and industry to harness the power of microbes that improve plant
yield and quality of soil to help meet society's growing demands for a
sustainable food supply.

She said, "It's exciting that we can potentially use the plant's own
chemistry to help nourish beneficial microbes
<https://phys.org/tags/microbes/> within soil. Population growth,
especially, has created a demand for identifying more reliable ways to
manipulate the soil <https://phys.org/tags/soil/> microbiome for beneficial
outcome."

*More information:* Kateryna Zhalnina et al, Dynamic root exudate chemistry
and microbial substrate preferences drive patterns in rhizosphere microbial
community assembly, *Nature Microbiology* (2018). DOI:
10.1038/s41564-018-0129-3 <http://dx.doi.org/10.1038/s41564-018-0129-3>
Kateryna Zhalnina et al. Dynamic root exudate chemistry and microbial
substrate preferences drive patterns in rhizosphere microbial community
assembly, *Nature Microbiology* (2018). DOI: 10.1038/s41564-018-0129-3
<http://dx.doi.org/10.1038/s41564-018-0129-3>

*Provided by:* Lawrence Berkeley National Laboratory


-- 
Lawrence F. London, Jr.
lfljvenaura@gmail.com
https://sites.google.com/site/avantgeared