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What kind of plant genes allow crops to shape the rhizosphere microbiota?

In my lab we aim to decipher the genetic basis of plant-microbe interactions taking place at the root-soil interface, in the so called “rhizosphere”. Microbes in this environment, collectively referred to as the rhizosphere microbiota, can enhance mineral mobilisation for plant uptake and crop protection, thereby representing a yet untapped resource for sustainable agriculture.

One of the key questions we are trying to answer is what kind of plant genes allow crops to shape the rhizosphere microbiota? We believe this will be a vital piece of information for plant breeders: this will allow them to develop crops capable of engaging with the rhizosphere microbiota in a way that will maintain acceptable yield while preserving natural resources.

Considering that, at least intentionally, modern cultivated varieties have not been selected for “microbiota readiness”, we are confident this research field has a great potential for discoveries both in basic science and translational agriculture. I look forward to engaging with colleagues in Rotterdam to learn more about the opportunities and challenges of genome editing in crop plants, as these are likely to impact our quest for plant genes shaping the microbiota.

Current agricultural practices are not sustainable for much longer; the global world population will increase and effectively agriculture will need to produce more with less inputs. Probiotics or the application of microbial inoculants to field crops has a great potential to reverse this negative trend, owing to the fact they effectively represent an attractive and renewable alternative to synthetic fertilisers and agrochemicals. This will contribute to global food security by offsetting part of the environmental and economic “costs” of agricultural practices.

Many plant varieties may be ready for this. Some others may react negatively to beneficial soil microbes. This is one of the reasons why my lab looks at the plant side of these relationships with an emphasis on how plants can discriminate between the “good” (i.e., beneficial microbes), the “bad” and the “ugly” (i.e., parasitic microbes) in the microbiota.

Investigation into barley and wild-barley microbiota

Our main model for investigation is barley, the fourth most cultivated cereal worldwide. One of the peculiarities of barley is that the wild ancestor of modern barley is still accessible for experimentation. We can cross the wild ancestor with the modern variety using genetic approaches. This is crucial for assessing how plants have been shaped by humans since domestication took place at the dawn of agriculture in the Neolithic. We have done exactly that assessment and discovered that modern plants and wild ancestor host distinct microbiotas.

Owing to the fact that wild barley have evolved in more marginal soil conditions compared to the selected varieties, we can hypothesise that the wild barley microbiota is a richer resource of beneficial functions compared to the modern one. So what happens if we couple a wild microbiota with a modern variety? Can we use wild barley genes to do this?

To address these questions we decided to bring plant genetics and metagenomics under the “same roof”. We have been using microbiota sequencing information, i.e., the presence and abundance of rhizosphere microbes, as a “quantitative plant traits” in a genetic mapping approach aiming at identifying regions of the barley genomes putatively controlling microbial recruitment. This allowed us to identify a relatively limited number of these regions, which geneticists call loci: this for us represented a breakthrough since these loci “contain” the plant genes shaping the microbiota.

Generating isogenic lines to assess microbiota recruitment

We are now generating so-called isogenic lines, which are pairs of modern varieties with a nearly-identical genome with the exception of the loci we consider implicated in microbiota recruitment. These loci will then come in two versions: one set of the isogenic lines will have the modern loci, hence the modern genes, and the other set will have the wild genes. These plants will allow us to test the effect on plant performance of coupling a modern variety with a wild microbiota.

Next, using techniques like genome editing, we could create “new versions” of these genes and test whether they confer a better (or worse) microbiota readiness to cultivated plants. With game-changer approaches, such as speed-breeding, our discoveries have the potential to be translated into new crop varieties in the near future.

We are confident and excited that this experimental approach will bring us a step closer to the deployment of the rhizosphere microbiota for sustainable agriculture.


Davide Bulgarelli is Royal Society of Edinburgh Research Fellow at the University of Dundee. He will be presenting at the upcoming 7th Plant Genomics & Gene Editing Congress: Europe in May.


The 7th Plant Genomics & Gene Editing Congress: Europe has a reputation for delivering exceptional networking and learning experiences for everyone working in plant science. With the event only a few months away, download the agenda and see what is on offer.

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