New biotech promises for agriculture often focus on improving the production of food material by plants. This can be done by gene editing or artificial selection, which humans have been doing for thousands of years. The fattest and tastiest fruits were continuously cultivated for obvious reasons, until we ended up genetically differentiating lineages of the same species, leading to the varieties we consume today. Of course, this is a highly inefficient, labor-intensive process that can only be carried out vertically, that is, from generation to generation, due to the slow life cycles of plants. Although this process can be accelerated by in vitro hybridization of varieties or other genetic improvement techniques, it would be foolish not to evaluate a really interesting strategy such as microbiome editing, because of its simplicity and effectiveness.

The hologenome concept

In terrestrial autotrophic organisms, symbiosis with microorganisms is always necessary. Every organism requires a source of carbon, nitrogen, phosphorus, and energy. Although a plant is a highly efficient organism for capturing all these elements, it is no less true that they use a variety of strategies to achieve this, and many of them depend on a genome outside their own, i.e. the microbiome associated with them. The concept of the hologenome is important for understanding this. It was coined to understand the vertical and horizontal transfer of functions contained in this set of microorganisms, which through co-evolution with the particular multicellular species, allows them to be regular commensalists of its tissues, bringing physiological benefit to both organisms. Therefore, plants, like animals, would have a collection of genes foreign to our genome – they are not present in embryogenesis – accessible through microbial action, as could be the digestion of certain polymers or the uptake of moisture.

Where is the plant microbiome found?

The surface of plants, like our own, is colonized by millions of tiny organisms. We can distinguish between the microbiota associated with the root or found below the soil and the microbiota found above this level.

We are talking about very characteristic communities of organisms, so much so that these environments are called rhizosphere, carposphere (the outside of the fruit), anthosphere (floral environment), or spermosphere (outside of the germinated seed). In the rhizosphere, mycorrhizae – associated with fungi that form three-dimensional networks – are an example of these evolutionary adaptations, allowing access of these structures inside the root, some entering inside plant cells (endomycorrhizae). This, which at first glance might appear to be an infection, is actually a delicate balance between the plant and its symbiont, one providing moisture and mineral salts, while the other carbohydrates and vitamins. Now imagine that this isolated interaction could be magnified by several thousand mutualistic relationships, interacting with each other for a common good. We have the association with rhizobacteria in the well-known Rhizobia, almost alien structures that present a great variety of morphologies. Other bacteria allow the fixation of atmospheric nitrogen to be taken up by the root, etc. This, in short, allows a plant to grow healthily, hinder the entry of pathogens, favor immunity or resilience in the face of dry seasons.

Which of these functions are most interesting?

We can list the most important functions of the plant microbiome, which in general terms are: expanding the metabolic repertoire available to the plant, communication with other living beings through VOCs, leaf longevity, leaf extension – and therefore a higher photosynthetic ratio per plant -, favored immunity and root-shoot ratio.

All these characteristics are recommended for maximized production. Of course, plants normally grow with a specialized microbiome for this, although this depends on the type of crop and how it is exploited. The factors that most affect the microbiota are both biotic and abiotic, such as soil pH, water availability, soil pore size, soil type in general, and the presence of organic matter exudates. Since the usual way of acquiring edaphic microbiota is through recruitment in which exudates and root morphology play fundamental roles. This can be supplemented by active modulation of the microbiome, i.e. inoculation of the optimal microbiome. Experiments carried out in greenhouses are successful, but less so in the natural environment. Hungria et al. found significant differences in corn grain yield increase caused by Azospirillum brasilense inoculation, from 30% to 16%.

Current Research & Start-ups

There are some initiatives that are beginning to understand the potential of designing an optimal microbiome for cultivars. This is basically what they do at Indigo Ag (Symbiota), identifying those specific micro-organisms that contribute most to plant health. Pívot Bio is a company more attuned to the sustainable side of using a suitable microbiome, saving water and other resources.

The Future

This field remains largely unexplored despite much recent evidence of plant health with simple microbial inoculation of the roots. In addition to this, it can have beneficial effects on human health. We will soon see new research that does not aim to achieve a sub-optimal microbiome, but rather to overcome the natural capacity through specific modifications. For example, atmospheric nitrogen uptake capacity is a natural limiting factor in the manufacture of proteins and other essential compounds such as the nitrogenous bases that make up nucleic acids. By synthetically enhancing the action of nitrogenase, an enzyme sensitive to high oxygen tension, we could obtain a strain of diazotrophic bacteria. Over time, the way to inoculate and enhance natural or synthetic characteristics will be perfected.