A recent breakthrough in separation techniques now allows scientists to focus more precisely on living microorganisms. An international team, led by Dirk Wagner, Ph.D., from the GFZ German Research Centre for Geosciences in Potsdam, has detailed this method in 'Applied and Environmental Microbiology'. The new approach enables the separation of extracellular (eDNA) from intracellular (iDNA) genetic material, offering better insights into living microbial communities in low-biomass settings, which had been difficult using traditional DNA extraction methods.

Researchers employed this method on soil samples collected from the Atacama Desert, spanning from the Pacific coastline to the Andes foothills. The analysis uncovered a range of active microbial life even in the driest sections. "Understanding the roles of eDNA and iDNA helps in exploring all microbial processes," Wagner noted.

Wagner emphasized the significance of these findings: "Microbes are the pioneers colonizing this kind of environment and preparing the ground for the next succession of life." He added that similar processes could be relevant in newly exposed terrains after natural events like earthquakes or landslides, which present a mineral or rock-based substrate.

Conventional DNA extraction tools often result in a mix of genetic material from living, dormant, and deceased microbes. "If you extract all the DNA, you have DNA from living organisms and also DNA that can represent organisms that just died or that died a long time ago," Wagner explained. This mixture complicates the process of identifying active microbial processes, especially in low-biomass environments, which often yield insufficient high-quality DNA for metagenomic sequencing.

To overcome this, the team developed a technique to filter intact cells and separate them from genetic fragments left by dead cells. The process involved gentle rinsing cycles, and after four rounds, they successfully separated the DNA into the two distinct groups.

When analyzing Atacama Desert soil, the researchers found that Actinobacteria and Proteobacteria were present in both eDNA and iDNA samples. This was expected, Wagner said, because living cells contribute to iDNA as they degrade. "If a community is really active, then a constant turnover is taking place, and that means the two pools should be more similar to each other," he added. Samples from less than five centimeters deep showed that Chloroflexota bacteria were prevalent in the iDNA group.

Wagner plans to advance this research by performing metagenomic sequencing on iDNA samples to gain deeper insights into the active microbial communities. He also intends to apply this method to other extreme environments. By focusing on iDNA, he said, researchers can better understand "the real active part of the community."

Research Report:Inside the Atacama Desert: uncovering the living microbiome of an extreme environment

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