A new method enables scientists to distinguish between external and internal DNA, allowing for the identification of microbes thriving in the harsh conditions of the Atacama Desert.
The Atacama Desert, located along Chile’s Pacific Coast, holds the title of the driest place on Earth, making it largely inhospitable for most forms of life. However, research on its sandy soil has uncovered a variety of microbial communities. Understanding these microorganisms in such extreme habitats presents challenges, particularly when it comes to isolating genetic material from living microbes versus that of deceased ones.
A newly developed separation technique is poised to assist researchers in isolating the living components of these communities. In a recent publication in Applied and Environmental Microbiology, a global team of researchers detailed their innovative method for separating extracellular DNA (eDNA) from intracellular DNA (iDNA). This technique enhances the understanding of microbial life in environments with low biomass, a task that conventional DNA extraction methods could not adequately address, according to Dirk Wagner, Ph.D., a geomicrobiologist at Germany’s GFZ Research Centre for Geosciences in Potsdam, who led the study.
The microbiologists applied this technique to soil samples from the Atacama Desert, collected in a west-to-east line from the coastline to the foothills of the Andes. Their findings showcased a diverse range of living and potentially active microbes in the driest areas. Understanding both eDNA and iDNA, Wagner noted, could provide crucial insights into all microbial activities.
“Microbes are the first to inhabit this type of environment and set the stage for subsequent life forms,” Wagner explained. These processes, he added, are not exclusive to the desert setting. “Such methods can also be relevant for newly formed landscapes resulting from earthquakes or landslides, where similar mineral or rock-based substrates are present.”
Many commercially available DNA extraction tools yield a blend of living, dormant, and deceased microbial cells, Wagner commented. “If you extract all the DNA, it contains both material from living organisms and from those that have recently died or have been dead for a long time.” Metagenomic sequencing of this DNA can identify specific microbes and their functions, but often the quality of the DNA is insufficient in low-biomass settings, which Wagner identified as a common limitation.
To overcome this challenge, Wagner and his team devised a technique that isolates intact cells from a mixture, leaving behind genetic fragments of dead cells, known as eDNA. This process includes multiple gentle rinsing cycles, which, as their lab tests indicated, effectively separated nearly all DNA into the two categories after just four repetitions.
Upon analyzing soil from the Atacama Desert, they detected Actinobacteria and Proteobacteria present in all samples across both eDNA and iDNA groups. This was expected, according to Wagner, as living cells continuously replenish the iDNA pool as they die and decay. “In highly active communities, there’s a constant turnover, meaning the two DNA pools are likely to be more alike,” he noted. Notably, in samples taken from less than 5 centimeters deep, Chloroflexota bacteria were predominantly found within the iDNA group.
Looking ahead, Wagner intends to perform metagenomic sequencing on the iDNA samples to gain more insights into the active microorganisms present and to extend this methodology to samples from other extreme environments. Analyzing iDNA, he stated, will allow for a deeper understanding of the genuinely active segment of the microbial community.
