Building models to predict interactions in plant microbiomes

Date:
July 7, 2023
Source:
ETH Zurich
Summary:
Microbiomes play a key role for plant health and could
make agriculture more sustainable -- but the principles
behind the assembly of their communities have remained largely
unknown. Researchers have shown how bacteria can compete for food,
but also cooperate thanks to differences in metabolism -- resulting
in stably structured communities. Their models can accurately
predict these interactions and can help to design microbiomes for
specific applications in the future.


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FULL STORY ========================================================================== Plants, animals, and humans are all home to numerous microorganisms such
as bacteria and fungi. These form complex communities that have a profound impact on the health of their host. One notable microbiome is that of the
human gut, which helps digest our food and protect us against pathogens.

Plants are also host to microbial communities on their roots and
leaves. These communities can promote growth and keep off harmful
bacteria. Plant microbiomes therefore have the potential to make
agriculture more sustainable. However, we currently only have a
rudimentary understanding of the interspecies interactions that shape
these microbial communities.

Why is it that these communities tend to be populated only by certain
kinds of microbes and not others? "We already knew that leaf microbiomes weren't just some random collections of microbes," says Julia Vorholt, Professor of Microbiology at ETH Zurich. "But the rules that determine how these communities form and what mechanisms shape their makeup remained to
be found." Now, a team of researchers led by Vorholt has identified just
such an organising principle for the bacteria that live on the leaves
of the model plant Arabidopsis thaliana(thale cress). The researchers
have developed a set of models that use the nutrient preferences and
metabolic abilities of individual bacterial strains to predict how these
leaf surface microbes compete or cooperate with each other, thereby
helping us better understand the nature of the resulting microbiome.

The research team's study, which was carried out in collaboration
with colleagues at EPFL, has been published in the latest issue of the
journal Science.

Resource competition leads to distinct interactions As part of a previous
work, Vorholt's group had already shown that the microbial communities
found on plant leaves were remarkably similar. "The consistent composition
of these communities points to an underlying mechanism that controls
how the leaf microbiome is created," Vorholt says.

Martin Scha"fer, a postdoc in Vorholt's group and co-lead author on
the study, explains that "since all bacteria ultimately depend on
organic molecules as food, we asked whether we could predict the way
they interact by knowing which food molecules they can metabolise."
Alan Pacheco, also co-lead author, adds: "in a competitive environment,
food niches could lead to stable coexistence and collaboration, with
the microbes interacting for mutual advantage by exchanging resources."
The guiding question posed by Vorholt and her team is: Can the use the metabolic capabilities of different bacteria to understand how the leaf microbiome takes shape? Carbon profiles reveal resource competition
To answer this question, the researchers began by testing the ability
of more than 200 representative strains of bacteria from Arabidopsis thalianaleaves to grow using 45 different carbon sources. Using these
carbon profiles, they determined that there was extensive overlap between
the strains' food niches.

This indicates that there is fierce competition for resources.

The researchers then used these carbon profiles to build a set of reliable metabolic models for all bacterial strains, and simulated interactions
between more than 17,500 pairs of bacteria. Consistent with the extensive overlap in food niches, the simulations showed a marked dominance of
negative interactions: when competition causes the population of at
least one of the two strains to decrease.

Sidestepping competition through cooperation Despite this prevalence of competition, the metabolic models also predicted positive interactions. A closer analysis revealed that these cooperative interactions can be
traced back to the exchange of organic and amino acids. The study's
authors carried out plant experiments to test the models' predictions
and were able to confirm them to an accuracy of 89 percent.

The accuracy of the models came as a surprise even to the researchers themselves: "The high degree of reliability suggests that our initial assumptions about the importance of metabolic characteristics were
correct," Pacheco says.

Harnessing microbiomes for application "What's great about our models is
that they also work in reverse," Vorholt says, "in that they can be used
to identify mechanisms that trigger certain interaction patterns." This
paves the way for targeted microbiome design, which is a key prerequisite
for downstream applications in agriculture.

Currently, seed companies and agricultural chemical producers use
a process of trial and error to search for microbes that sustainably
support crop protection. The team's findings are therefore relevant not
only for fundamental research, but also for applications in microbiome
design for agriculture.

Vorholt is Co-Director of the Swiss National Centre of Competence
in Research (NCCR) Microbiomes. Her team's current study furthers the
research by a network of 20 groups, whose aim is to understand microbiomes
-- from plants to humans - - so that their vast potential for health, agriculture, and environment can be realised.

This can be achieved by, for example, supplementing unbalanced communities
with the right microbe, removing certain species, or even treating
diseases with combinations of bacteria with special functions. Predictive models will play a key role in this goal.

* RELATED_TOPICS
o Plants_&_Animals
# Microbes_and_More # Bacteria # Agriculture_and_Food #
Endangered_Plants
o Earth_&_Climate
# Sustainability # Weather # Geochemistry # Ecology
* RELATED_TERMS
o Sustainable_agriculture o Climate_model o Forest o Meteorology
o Agroecology o Hydroponics o Tamarix o Vegetation

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provided by ETH_Zurich. Original written by Michael Keller. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Martin Scha"fer, Alan R. Pacheco, Rahel Ku"nzler, Miriam
Bortfeld-Miller,
Christopher M. Field, Evangelia Vayena, Vassily Hatzimanikatis,
Julia A.

Vorholt. Metabolic interaction models recapitulate leaf microbiota
ecology. Science, 2023; 381 (6653) DOI: 10.1126/science.adf5121 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2023/07/230707111638.htm

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