How are microbial communities in plant roots formed?

The roots of a plant and our guts are the organs primarily responsible for absorbing nutrients that we and the plants need for our survival. Both systems are also hosts of dense microbial communities and it has been suggested that the composition of microbial species in these systems is closely related to both human and plant health.

So,  how can we make sure that plants get colonised with a healthy microbiota? Well, here, it gets a bit trickier. The first thing that we have to figure out is: where do all these microbes come from? And what determines which microbes ends up in the root microbiota?

Looking at our selves it is easy to come up with ways in which we might have come in contact with microbes throughout our life that could have colonised our guts. Whether you were breast-feeding or eating sand from the sand box as a kid, the microbes found their way in. Research has even shown that we all carry a distinct set of microbes in our bodies.

So, what about the plants?

individual treeI would like for you all think about plants, not as a large green mass, or a bouquet of flowers, but as individuals like you and me. Individuals that are born by a parent and raised in a patch of soil.

Often when we study plants, we don’t think about the past. We try to determine what we see in full-grown plants with what surrounds them at the moment. In reality, the fact that two seeds share the same genetic makeup, originated in the same flower, or germinated a millimetre apart does not guarantee that they will host an equivalent root microbiota.

Part of the individual variation will be shaped by the plant’s genetic heritage which affects the architecture of the root system, which chemicals the roots expel into the surrounding soil and which life strategy the plant will take on. Another important source of variation comes from environmental conditions throughout the plant’s life.

Let’s have a look at the plant below and think about what has happened to it throughout its life that could affect which microbes it carries in its roots. Well, it started out as a tiny little seed in the flower of its parent. At this point the microbes it got exposed to were the ones of its parent’s flower. Microbes in the flower could come directly from the air, be dropped off by visiting pollinators or transported up through the xylem of the plant to its reproductive tissues. All these microbes have the potential to coat the seed with a kind of microbial start-up kit.


The next step in the life of the plant was when it flew out of the “nest”. Plant seeds can be dispersed in a large variety of ways on their journey to a good spot to germinate. Some seeds will fly with the wind and others will be eaten together with a fruit and start their life in a pile of poop. The different ways in which seeds are dispersed could present them with distinct communities of microbes before they even start to germinate.

Of course, once the seed starts to germinate in the soil, the microbial inhabitants of the soil will be a huge part of the root microbiota, but let’s not forget that the plant had a life before then, that also could play an important part in shaping its root microbiota.

What I am trying to do in my research is to figure out how important these early life stages are for microbial colonisation in roots and what factors create individual communities of microbes in the plants. If we can understand that, then we might also be able to better figure out how healthy or pathogenic microbial communities in plants are formed. You can read more about it in our latest publication: “The root microbiota, a fingerprint in the soil?”

Read more about microbial community assembly in human systems:

Costello et al. 2012

Gonzalez et al. 2012

Read more about the plant microbiota and plant health:

Berendsen et al. 2012

Bakker et al. 2012


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