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Microbiome technologies to transform agribusiness

Microorganism cocktails are researchers' bet to make agriculture more sustainable and competitive

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The current Covid-19 pandemic has reinforced the negative character of microorganisms in the social imagination. Not all beings invisible to the naked eye, however, cause diseases or are synonymous with dirt. In fact, most of them - including viruses, bacteria, fungi and protozoa - are essential for maintaining life on earth. Science has advanced in exploring the biotechnological potential of these beings in several areas, such as medicine, food engineering and agriculture.

It is already known, for example, that microorganisms act directly on plants' access to nutrients such as nitrogen. Without them, plant survival and growth would not be possible. And many researchers believe in this potential to develop technologies that improve the sustainability and efficiency of the agricultural industry.

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Corn plants being tested in a greenhouse

The set of microorganisms and the role they play in an environment is called the microbiome. The concept was explained in published article at the beginning of July in the magazine microbiome by scientists from 28 research institutions around the world. The postdoctoral Rafael Soares de Souza is the only Brazilian to sign the work. His research is carried out in Genomics Research Center Applied to Climate Change (GCCRC) – partnership between Unicamp and Embrapa with support from Fapesp.

The initiative was created by the program Microbiome Support, financed by Horizon 2020, a European Union platform that promotes scientific development for problems considered priorities on the bloc's agenda. This is the case with sustainable food production, considering the almost 200 billion people who will inhabit the planet in 2050, according to UN projections. In this sense, microbiome-based technologies are gaining attention from scientists and industry.

Products developed from microbiome technologies for agriculture are called inoculants. Inoculants are a type of cocktail of microorganisms applied to the seed, soil or directly to the plant and benefit its resistance or development. Souza explains that this type of product has been used in agriculture since the 1960s, but that, in general, they are based on isolated microorganisms, such as nitrogen-fixing bacteria. “Today, with microbiome research, we are able to prove that there is a synergistic effect, that there are specific combinations of microorganisms that give a better characteristic to the plant than inoculants with just one microorganism”, says Souza.

In his line of research at GCCRC, Souza and his colleagues developed an inoculant that brings together the microbiome present in sugarcane and applied it to corn plants. According to the postgraduate, plants with the inoculum showed biomass productivity 20 to 30% higher than those that had not been inoculated with the microorganisms. The experiment was carried out in Luiz Eduardo Magalhães, in Bahia, a region chosen by the researchers due to its history of drought. The idea was to test the inoculant's ability to provide resistance to corn in conditions of water scarcity.

During the researchers' experiment as Plants were also affected by a disease called stunting, caused by the corn leafhopper. “To our surprise, after being affected by the disease, the inoculated plants were doing better than the non-inoculated plants. The inoculum helped the plant tolerate the disease,” he said. The reasons behind this type of resistance are still being investigated by researchers.

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The only Brazilian to sign an article on the microbiome, GCCRC postdoctoral fellow Rafael Soares Souza. In the highlight, LGE researcher Marcelo Falsarella Carazzolle: new technologies with the potential to make ethanol production much cheaper and more sustainable 

Biofuels

The development of microbiome-based technologies in agriculture does not only affect food production. The effective use of these technologies has the potential to reduce the need for water resources and fertilizers, increase production and even make plants more resistant to scarcity conditions, including the effects caused by climate change. In the case of biofuels, this means making manufacturing more sustainable and cheaper, as analyzed by Marcelo Falsarella Carazzolle, technician and researcher at the Genomics and BioEnergy Laboratory (LGE) at Unicamp. “Best of all, there is potential to grow these plants in regions with more nutrient-poor land. This reduces process costs and makes the fuel more competitive. The production of corn ethanol, which has been growing in Brazil, could benefit directly from these advances”, explains Carazzolle.

The researcher highlights the so-called second generation ethanol, a biofuel produced from the biomass of a plant and not just from sugar or vegetable oil, as is the case in the traditional production method. Advances in technology have made it possible to use all biomass, including stems and leaves, to produce ethanol, through a process of converting fibers into sugars. According to Carazzolle, new microbiome-based technologies, combined with the development of this new industry, have the potential to make ethanol production much cheaper and more sustainable.

As an example, he cites the cultivation of sisal (agave sisalana). Brazil is the world's largest producer of the plant, with Bahia responsible for around 90% of this production, according to data from Embrapa. The fiber extracted from the leaves is used to manufacture threads and ropes, which in turn are used in the textile industry. Much of the plant's biomass, however, is discarded and could serve as raw material for the production of second generation ethanol. “There is already a whole chain of producers, people who plant, harvest and process this plant to produce sisal fiber. Only 4% of the leaf is used for fiber, the rest, a large amount of biomass, is discarded. We can use this material to produce ethanol”, explains the researcher.

Some plants are already investing heavily in developing technologies for second-generation ethanol production. In Brazil, there are only two in operation that already have the capacity to produce this type of biofuel: Raízen and GranBio. The second has a facility in Alagoas with the capacity to produce around 100 thousand liters of ethanol daily from different types of biomass. Now, GranBio invests in license the technology for institutions around the world.

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Sisal (Agave sisalana) plantation in Bahia. Photo: Marina Pupke Marone (LGE)

From microbiome to inoculant

To find microorganisms present in plants that are potential raw materials for the construction of inoculants, scientists are investigating Brazilian biodiversity itself. One of the research areas of the Center for Research in Genomics Applied to Climate Change (GCCRC) is the analysis of the microbiome of plants present in rupestrian fields, located mainly in Minas Gerais.

The region, despite representing only 1% of the national territory and having soil poor in nutrients, has around 5 thousand native plants described to date. This indicates a great resistance to environmental stress inherent in these species, which can be explained, in part, by the microorganisms - most of which are completely unknown - present in the plants. “It’s like the tip of an iceberg. Most of it is underwater, we don’t know it yet,” says Souza.

After finding the potential microbiome, a sample of the plant is preserved and taken to the laboratory. Then the work of bioinformatics begins. There are already technologies that are capable of mapping the genome of all organisms present in plants and soil. “It becomes like a broth containing different DNA molecules”, compares Carazzolle, who has experience as a bioinformatician at LGE. The work of bioinformatics is to “separate this broth”, reconstructing the DNA of microorganisms and differentiating which ones are present and in what proportion. Thus, it is possible to direct the development of inoculants from microorganisms that are most essential to the development of the plant or affect its resistance to adversities. Once the inoculants are formed, scientists test them in greenhouses and in the field, measuring whether the expected effects are demonstrated in practice.

"The final product of all this work is a set of microorganisms that can be tested separately and together in the form of a cocktail. You know exactly what each of them is doing and under what conditions they work or don't work. Ultimately, we want to create cocktails of microorganisms that can improve agriculture as a whole”, concludes Carazzolle.

 

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sisal plant

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