Microbial Inventory

(December 16th, 2015) What bacteria grow on Arabidopsis’ roots and leaves? German and Swiss scientists catalogued the plant’s prokaryotic life partners and thus established a new model system to study plant microbiota.

A team of scientists from German and Swiss research institutions led by Julia Vorholt from ETH Zurich and by Paul Schulze-Lefert from the Max Planck Institute for Plant Breeding Research in Cologne have inventoried and cultivated the majority of bacterial species that naturally occur on the leaves and roots of the thale cress Arabidopsis thaliana. These bacterial communities promote the health and growth of their host plants: they protect them against pathogens, mobilise soil nutrients and enhance the plants’ tolerance to abiotic stress.

“Now, we can reconstitute the microbiota under defined laboratory conditions with germ-free plants and synthetic communities. Thus, we can systematically explore microbiota functions, which were proposed already decades ago,” senior author Schulze-Lefert observed. The newly established collection comprises almost 8,000 bacterial isolates from plants originating from Germany, France and Switzerland, that is to say from temperate climates. Bacteria were taxonomically classified by sequencing of 16S rRNA genes.

Surprisingly, most of the bacterial species associated with Arabidopsis roots and leaves can be kept in culture. By inoculating germ-free plants with synthetic communities consisting of pure bacterial isolates, the researchers found that the microorganisms are not restricted to their niche of origin but colonise other plant parts.

In previous studies, similar bacteria had been identified on Arabidopsis leaves and roots, irrespective of the origin of the plants. The newly analysed root and leaf microbiota comprised four bacterial phyla typically associated with Arabidopsis, namely Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The sequenced bacterial genomes are available at www.at-sphere.com. Moreover, the researchers observed extensive taxonomic overlap between the leaf and root microbiota, indicating that soil bacteria colonise not only the roots but also the leaves. Genome analyses of 400 isolates additionally revealed a substantial overlap of functional capabilities in the genomes of leaf- and root-derived culture collections.

To repopulate germ-free Arabidopsis plants, the scientists grew them on a sterilised soil substitute. They inoculated seeds and spray-inoculated leaves of germ-free plants with synthetic microbiomes taken from their culture collections and analysed bacteria after several weeks using 16S rRNA sequencing. The transferred bacteria form assemblies, which are similar to natural microbiota on roots and leaves, but are also capable of ectopic leaf or root colonisation. Leaf microbiota benefit from air- and soil-borne inoculations. Moreover, both genome analyses and recolonisation experiments show that microbiota are also specialised to their respective niche.

“Although intimate associations between any higher eukaryote and microbes have in fact been known for more than a hundred years, technological advances such as next generation sequencing technologies, computer science and high-throughput cultivation systems for microbes have recently transformed this research field,” said Schulze-Lefert. “Microbiota research has become for the first time truly quantitative biology,” he added.

With their new model system, the scientists can explore how the activity of a single microbiota member is retained or abrogated in the context of the plant microbial community. “Furthermore, we can use our model to investigate potential microbiota adaptation on plants from the arctic or from arid regions,” Schulze-Lefert explained. The scientist also wants to find out how microbiota members communicate with each other and with the host plant at the molecular level. “We still do not know how the elaborate innate immune system of plants, which is essential for the protection of plants against microbial pathogens, tolerates the establishment of intimate associations with millions of microbes,” he noted.

Bettina Dupont

Photo: MPI f. Plant Breeding Research/ K. Schläppi

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