The first comprehensive collection of plant bacteria

No organism lives by itself. Not even plants. On their leaves and roots complex communities of various bacterial species can be found. Just as the natural intestinal microbial flora helps humans to digest food and protects them from pathogenic microorganisms, these bacteria are presumably also of great importance for plant growth and plant health.

Scientists at ETH Zurich and the Max Planck Institute for Plant Breeding Research in Cologne have now inventoried and cultivated the majority of the bacterial species that naturally occur on a specific plant species. The researchers carried out their investigation using the thale cress (Arabidopsis thaliana), a plant that serves as a model organism in science. The results of this work have just been published in the journal Nature.

For the first time, the researchers have created a comprehensive collection of the bacterial strains living on this species of plant. They isolated almost 10,000 bacterial strains and selected 432 of these for further study. “We were surprised to find that more than half of the species identified through molecular biology could also be cultivated in the laboratory,” says Daniel Müller, a doctoral student in ETH Professor Julia Vorholt’s group and one of the study’s lead authors. Until now, scientists have assumed that about one percent of naturally occurring micro-organisms are able to grow under laboratory conditions. “We were able to disprove this assumption in our study,” says Müller.

Consistent bacterial colonisation

In their study, the researchers found considerable similarities between the microbial communities living on the leaves and on the roots of the thale cress: of the at least one hundred different species of bacteria living on leaves and roots, almost half are the same. It is possible that the majority of the root and leaf bacteria originate from the exceptionally diverse community of soil bacteria, and that leaves of these annual plants are colonised by micro-organisms as the plant grows out of the ground.

The differences between various locations in Switzerland and Germany where the researchers collected wild plants are also small. “Most of the species present were found at all of the locations. There is a considerable evidence to suggest that preserved mechanisms exist which ensure that certain bacteria can grow on plants and others cannot,” says Julia Vorholt, Professor of Microbiology at ETH Zurich. She led the study alongside with Paul Schulze-Lefert, director at the Max Planck Institute for Plant Breeding Research.

A prerequisite for laboratory experiments

Plant microbiome research is still a relatively young discipline. Researchers’ work has thus far been primarily descriptive in nature. Now that the scientists from Zurich and Cologne have created a collection of bacteria with representative strains, they can go one step further: “Thanks to these bacterial isolates, we can now reproduce natural processes in the laboratory and perform targeted experiments under controlled conditions,” says Müller. For this purpose, the researchers cultivate the bacteria on germ-free plants. In initial recolonisation experiments under controlled laboratory conditions, stable bacterial communities were formed, mimicking the population observed in nature. “The experiments were reproducible. This means that our bacterial strains and our approach are suitable for this type of experiment,” says Vorholt.

In the future, the researchers could use this method to analyse the role of individual bacteria in growth promotion and susceptibility of the host plant to pathogens, for example, or to investigate whether the microbiome changes under conditions of stress such as drought or intense sunshine. It would be hard to carry out experiments of this kind outdoors, because the influence of varying environmental conditions would be too strong.

Microflora assists plants

Scientists have already found indications that plants have better access to nutrients and grow more quickly if they are colonised by certain micro-organisms. There are also indications that pathogens have a harder time to establish themselves on a plant if certain bacteria are present on the plant.

Understanding this natural plant protection, which is maintained by the plants’ microbiome, is a question that has started to interest university researchers in recent years. But they are not alone in their endeavours: seed and pest-control companies are also conducting research in this field, with a view to supplying natural, microbial plant protection products in the future.

ETH Professor Vorholt received an Advanced Grant from the European Research Council (ERC) in June. “Thanks to this support and with our new bacteria collection, our long-term aim is to investigate the interaction between plants and the bacteria living on them,” she says.