Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - MICRORULES (Structural and Functional Architectures of Multi-Kingdom Microbial Consortia Colonizing Plant Roots)

Teaser

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and microbes interact with each other. In roots of healthy plants, bacteria, fungi and oomycetes coexist and interact, forming physically and metabolically interdependent consortia that...

Summary

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and microbes interact with each other. In roots of healthy plants, bacteria, fungi and oomycetes coexist and interact, forming physically and metabolically interdependent consortia that harbor distinct properties compared to their single components. The importance of microbe-microbe interactions for structuring and stabilizing plant-associated microbial communities has been so far neglected and is a central aspect of the project. One promising experimental approach for understanding organizational principles and functional capabilities of root-associated microbial communities is to reconstitute high-complexity microbial communities in laboratory settings to test general ecological principles that would be otherwise impossible to address by field experiments.

The overall objectives are:
1) Characterize the structure of the A. thaliana root microbiota (bacteria, fungi and oomycetes) at a continental scale and identify the major driving forces governing establishment of complex microbial consortia on plant roots .
2) Obtain deeper insights into the fundamental mechanisms underlying the structure and the functions of complex root-associated microbial communities by i) establishing reference microbial culture collections and ii) reconstructing the root microbiota using synthetic microbial consortia and germ-free plants.
3) Generate extensive microbial genome resources for in-depth metatranscriptome studies of multi-kingdom synthetic communities on germ-free plants and initiate the transition from binary plant-microbe to community-level molecular investigations.
4) Dissect the molecular bases of multitrophic plant-microbe interactions and the cascading consequences on plant health.

Work performed

\"1) Characterize the structure of the A. thaliana root microbiota (bacteria, fungi and oomycetes) at a continental scale and identify the major driving forces governing establishment of complex microbial consortia on plant roots .

We tested whether roots of healthy A. thaliana and sympatric grasses growing in various soils and climatic environments can establish stable associations with bacterial and filamentous eukaryotic communities across a latitudinal gradient in Europe. We already sampled natural A. thaliana populations at the flowering stage at 17 sites along a latitudinal gradient in Europe in three consecutive years (2016, 2017 and 2018). We harvested bulk soil (soil), rhizosphere (RS), rhizoplane (RP), and root endosphere (root) compartments of A. thaliana and sympatric grasses at four sites in Sweden, six in Germany, three in France, one in Italy, and three in Spain, each having distinct environmental and soil characteristics. The data have not been published yet but several important conclusions can be already made:
- The analysis of 5,625 microbial community profiles demonstrated strong geographic structuring of the soil microbiota, but not of the root microbiota. The remarkable structural convergence observed for bacteria in roots of A. thaliana and grasses was explained by the presence of few, but diverse geographically widespread taxa that disproportionately colonize roots across sites.
- The composition of the root microbiota was barely affected by host genotype, but altered by location and soil origin, with filamentous eukaryotes responding extensively to locational change
- Climate differences between sites is a primary force explaining temporal and spatial variation in root-associated filamentous eukaryotic communities.

2) Obtain deeper insights into the fundamental mechanisms underlying the structure and the functions of complex root-associated microbial communities by i) establishing reference microbial culture collections and ii) reconstructing the root microbiota using synthetic microbial consortia and germ-free plants.

Roots of healthy plants are inhabited by soil-derived bacteria, fungi, and oomycetes that have evolved independently in distinct kingdoms of life. How these microorganisms interact and to what extent those interactions affect plant health are poorly understood. We established microbial culture collections for reconstitution experiments using germ-free A. thaliana. Our results demonstrated several important general principles:
- Roots of healthy plants are colonized by multi-kingdom microbial consortia.
- Bacterial Root Commensals shape fungal and oomycetal community structure
- Bacterial Root Commensals protect plants against fungi and oomycetes
- Biocontrol activity of Bacterial Root Commensals is a redundant trait and essential for plant survival

To conclude, by establishing reference microbial culture collections for microbiota reconstitution experiments, we provided community-level evidence that competitive interactions between prokaryotic and eukaryotic root microbiota members are critical for plant host survival and maintenance of host-microbiota balance. This pioneer work has been recently published in the prestigious journal \"\"Cell\"\" (Duran, Thiergart et al. 2018)

3) Generate extensive microbial genome resources for in-depth metatranscriptome studies of multi-kingdom synthetic communities on germ-free plants and initiate the transition from binary plant-microbe to community-level molecular investigations.
We have already generated extensive culture collections of root-associated microbes, especially fungi (588 fungal strains) and a large-scale fungal genome sequencing project has been initiated in collaboration with the JGI (USA) and Dr. Francis Martin (INRA Nancy).
- 121 root-associated fungal endophytes have already been genome-sequenced using PacBio and high quality genomes are currently generated. Comparative genome analysis with saprotrophic, mycorrhiza\"

Final results

The project has already generated a number of important outcomes.

- A major publication in Cell indicates the novelty and originality of the research project (Duran, Thiergart et al. Cell, 2018). Our article has been promoted with a Cell cover image. A press release has been written to disperse the important conclusions of the paper (https://www.mpipz.mpg.de/4713649/pr_hacquard_2018_11), a commentary has been written by our colleagues (https://www.sciencedirect.com/science/article/pii/S167420521930022X?via%3Dihub), and the article is recommended at F1000Prime (https://f1000.com/prime/734323252). Our work, demonstrating the relevance of microbial inter-kingdom interactions for microbial community assembly and plant health, represents an important contribution to the field, beyond plant-microbe interactions.

- We also wrote a review article on the same topic (microbe-microbe interactions and plant health, Hassani et al. Microbiome, 2018) that has been already accessed > 9,000 times and is highly cited (> 25 citations in < 1 year). Therefore, the role of microbe-microbe interactions for community assembly, dynamics, and function is becoming a topic of high interest and our work is contributing to this emerging research field thanks to the support of ERC.

- In the next few months, we expect to publish our continental-scale survey of the A. thaliana root microbiota, which provides important clues regarding variation and stability of the root microbiota across European sites. The profound structural convergence observed for bacteria in roots was unexpected at a continental scale given the large geographical distances between sites, contrasting edaphic characteristics, and distinct microbial communities in the surrounding bulk soil. Our results suggest that at least part of the similarity in bacterial community composition observed in roots of divergent plant species in microbiome studies (i.e. Hacquard et al. 2015) is driven by colonization with few, but phylogenetically diverse and geographically widespread taxa that efficiently colonize plant roots across a broad range of environmental conditions.