Understanding Plants’ Microbiome, the Phytobiome

- Molly Cadle-Davidson

The study of the phytobiome with respect to biologicals is natural – it makes perfect sense. Since about 2000, ABM and a growing number of companies have been studying the microbiome. The phytobiome is the plant equivalent of the human microbiome. It includes the plant itself, the plant’s environment and all micro and macroorganisms living in, on or around the plant.

One reason for studying the phytobiome is so we can understand what causes plant diseases.

Beneficial and pathogenic microbes are present on and in the plant and are part of the phytobiome.

In about 2008, the cost of sequencing individual microbes came way down and people were able for the first time to look all the microbes in a biome. They had the technology to look at it and the computational ability to analyze it. These two key capabilities are important.

What are the microbes doing in the phytobiome? Pathogens are present long before a plant disease starts. There are other triggers that cause them to become pathogenic. This has been established for some time.

Other reasons for studying the phytobiome is that we know that there are beneficial microbes and we are using some of them – like Trichoderma, Bradyrhizobium, and Rhizobium, for example – for biological treatment. These organisms are either bacteria or fungi that we know are symbiotic with the plant and allow or help it to perform better.

There are a few approaches to studying the phytobiome to develop biological seed treatments. One method is to study all of the many organisms that could be in the phytobiome, characterize them bioinformatically and then assemble a consortium that could contain anywhere from two to 50 or more organisms representing the entire native population expected in a natural, productive setting.

To do this, you first have to determine bioinformatically that these are the organisms the plant needs and they will work well with the plant as part of its phytobiome to increase yield or other targeted result.

The approach used by ABM is to start with a seed treatment that contains a few strains of Trichoderma that we know improves plant performance. We have learned that these strains remodel the phytobiome and what is present in the rhizosphere – not the bulk soil – right next to the root.

We are changing it in terms of the organisms that are there and the functional profile of the phytobiome. We are changing the community function of the microbes in the local environment.

This is a very robust approach. When we add our biologicals to rhizosphere we know we are recruiting beneficial organisms and suppressing pathogens so that the plant can perform better with its own genetics as well as perform better with the microbes that are already in the soil.

We hope this is one of the answers to agricultural variability which is a thorn in every farmer’s side.