In the harsh, arid conditions of Chile’s vast Atacama Desert – the driest non-polar desert on the planet – only the most resilient plant life can cling on among the water-parched rocks and sand.
How these plants came to thrive in such a hostile place is of particular interest to scientists hoping to understand how plant life might adapt to changing ecosystems in a warming world. Now, in a new study published today in Proceedings of the National Academy of Sciences, an international team of researchers has identified the smoking gun: key genes that have helped Atacama’s hardy shrubs adapt to their desiccated homelands.
The study was an international collaboration between botanists, microbiologists, ecologists, evolutionary biologists and genomic scientists, headed up by a team of Chilean researchers who established a pioneering “natural laboratory” in the Atacama, where they conducted experiments over a decade to understand how the unforgiving landscape was able to nourish life. They measured climate, soil and plant life at 22 sites across varying elevations and types of vegetation.
The research area is home to a surprising variety of plant species, including grasses, annuals and perennial shrubs, all of which are adapted to manage the region’s aridity, altitude, nutrient-poor soil, and the Sun’s harsh radiation.
The team brought samples 1000 miles (1600km) to their laboratory, where they sequenced the genes expressed in the 32 dominant plant species of the region, as well as the genomes of the microbes living in the Atacama soil that co-exist with the plants.
Critically, they found some plant species developed growth-promoting bacteria near their roots to optimise their uptake of nitrogen – a nutrient they need in order to grow, but which is notoriously sparse in the Atacama.
Then, researchers at New York University (NYU) used an approach called phylogenomics to identify which genes had adapted protein sequences, comparing the 32 Atacama species with 32 genetically similar ‘sister’ species.
“The goal was to use this evolutionary tree based on genome sequences to identify the changes in amino acid sequences encoded in the genes that support the evolution of the Atacama plant adaptation to desert conditions,” says Gloria Coruzzi, co-author of the study and a professor at NYU’s Department of Biology and Center for Genomics and Systems Biology.
“This computationally intense genomic analysis involved comparing 1,686,950 protein sequences across more than 70 species,” adds Gil Eshel, who conducted the analysis using the High Performance Computing Cluster at NYU. “We used the resulting super-matrix of 8,599,764 amino acids for phylogenomic reconstruction of the evolutionary history of the Atacama species.”
The studied found 265 candidate genes whose protein sequences were found across multiple Atacama species. Some of these genes adapted the plants’ ability to respond to light and manage photosynthesis, which may have helped them adapt to the extreme irradiation of these high desert plains. Other genes found are involved in the regulation of stress responses and the management of salt intake and detoxification, which could have adapted the plants to Atacama’s high-stress, low-nutrient environment.
A ‘genetic goldmine’ of precious information
The research is timely, as this week the world’s leaders attempt to negotiate a global approach to climate change at COP26.
“Our study of plants in the Atacama Desert is directly relevant to regions around the world that are becoming increasingly arid, with factors such as drought, extreme temperatures, and salt in water and soil posing a significant threat to global food production,” says Rodrigo Gutiérrez, co-author of the study and a professor in the Department of Molecular Genetics and Microbiology at Pontificia Universidad Católica de Chile.
“Most of the plant species we characterised in this research have not been studied before,” he says. “As some Atacama plants are closely related to staple crops, including grains, legumes, and potatoes, the candidate genes we identified represent a genetic goldmine to engineer more resilient crops, a necessity given the increased desertification of our planet.”