Microorganisms can help crops adapt to climate change

The microbiome of plants present in Brazilian rocky fields, environments poor in nutrients and water availability, can store important information for the development of agricultural crops that are more tolerant to climate change. Article published on July 31st in the magazine Scientific data, from the Nature group, presents the first data from the genetic sequencing work of microorganisms associated with plant species in the family Velloziaceae, which develop naturally in rocky fields. The role of these microorganisms identified by the study is still little known but, according to the scientists, the new results could help to decipher the survival strategies of these plants under extreme conditions and advance the adaptation of these mechanisms to species of agricultural interest.

Among the authors of the article are researchers from Embrapa and the State University of Campinas (Unicamp) who work with the Center for Research in Genomics for Climate Change (GCCRC), created in 2017 from a partnership between the two institutions and financed by the Fundação de Support for Research in the State of São Paulo (Fapesp). The Center is an expansion of the Mixed Research Unit in Genomics Applied to Climate Change (UMiP GenClima), an initiative by Embrapa and Unicamp established five years earlier, in 2012, with the objective of developing biotechnological solutions for the adaptation of agricultural crops to future scenarios of high temperatures and water deficiency.

“In rocky fields, plants need to survive long periods of drought, grow in shallow, rocky soils that are still among the poorest in phosphorus in the world. This imposes severe development-limiting conditions on plants. We certainly have a lot to learn from them”, explains Isabel Gerhardt, researcher at Embrapa Informática Agropecuária, one of the authors of the article.

Brazilian rock fields are located on rocky outcrops in the central and eastern regions of Brazil, mainly along the Espinhaço Range. For Embrapa Agricultural Informatics researcher Ricardo Dante, the scientific potential of the biodiversity present in these environments is still little explored. Despite occupying less than 1% of the Brazilian land area, Brazilian rock fields are home to more than five thousand plant species, of which more than 40% are endemic to this ecosystem.

Dante also highlights the approach used in the study, which considered the analysis of all microbial genetic material available in the environment, known as metagenomics. It helps to better understand the plant's interaction with the community of microorganisms present and the responses to situations of drought, heat and nutrient scarcity. “There are already several studies on the ecology and ecophysiology of species from rupestrian fields, but on microbial communities and their relationship with survival in such stressful conditions this is the first time”, explains Rafael Soares Correa de Souza, postdoctoral fellow at GCCRC and Fapesp scholarship holder.

The research evaluated the microbiomes of the species Vellozia epidendroides, which occupy areas of shallow soil, and Barbacenia macrantha, which grows on exposed rocks. In areas close to the Serra do Cipó National Park, in Minas Gerais, samples of roots, stems, leaves and soil were collected from six individuals of each species. After processing for DNA extraction, the material was sent to the Joint Genome Institute (JGI), an important consortium of American laboratories linked to the United States Department of Energy.

Through next-generation sequencing technologies, based on bioinformatics platforms and access to large public databases, it was possible to identify and reveal the number of microorganisms present in the samples. The sequencing generated a total of 192 gigabytes (GB) of data, which is now stored and available for public access on the JGI portal. “We found an absurd amount of fungi that were completely unknown to science,” says Antonio Pedro Camargo, doctoral student at GCCRC, Fapesp scholarship holder and first author of the article. “In the case of soils poor in phosphorus there are no mycorrhizae, therefore, perhaps we are facing an important clue as to how these plants manage to extract phosphorus from the environment”, explains Camargo.

Ricardo Dante highlights the union of efforts and different expertise, from the creation of UMiP GenClima, to achieve results like this aimed at generating new biotechnological assets for sustainable agricultural production. Since 2013, the team led by professor at the Institute of Biology, Paulo Arruda, coordinator of the GCCRC, had been carrying out studies that resulted in the complete mapping of the communities of microorganisms associated with sugarcane cultivation. On behalf of Embrapa, Dante and Isabel Gerhardt have already been studying the genomes of species endemic to the rupestrian fields since 2016, also using a multidimensional approach.

“These results are valuable. Now there is long-term work ahead to characterize the functions performed by these microorganisms identified in the study and their potential contribution to advancing adaptation to stress in agricultural crops of interest”, adds Dante.

The article also has among its authors researchers from the Federal University of Pará (UFPA) and the University of Western Australia. The full article, in English, can be read here.