The extraction of environmental DNA from a 2-million-year-old sample (read more about this in our previous blog here!) represents a groundbreaking achievement in the field of paleo genomics. This record has pushed the boundaries of reconstructing ancient marine and terrestrial ecosystems even further, opening new avenues for scientific inquiry and discovery. The concept of delving into the past, akin to an archaeologist, to study the flora, fauna, and microorganisms that once populated the Earth is undeniably captivating. However, the reality of a scientist's daily routine in an ancient DNA laboratory can differ greatly from what we might anticipate.
Ancient DNA analysis can be challenging due to its degraded nature. When a cell dies, the mechanisms responsible for repairing and protecting DNA stop working. This makes the DNA vulnerable to fragmentation and base modification by environmental factors, resulting in shorter and more damaged DNA samples over time. The degradation processes, however, vary depending on the material of origin and the environmental conditions under which the sample is preserved. With polar deep-ocean and freshwater environments being among the most suitable locations for sedaDNA research because of their favorable conditions for its preservation.
Credit: Marina Buffoli. Warning signs on the door that opens into the aDNA lab of the Protistology and Aqautic Ecology group at Ghent University.
Analyzing fossil DNA can be even more complicated due to the potential for contamination from DNA of other organisms. This includes microbial organisms that colonize decaying organic matter, DNA present in the environment during sampling, and DNA introduced through handling, lab equipment, and reagents. While we have become accustomed to wearing masks in the past two years to avoid contagion by viruses, in the case of fossil DNA, we are the ones who pose a risk as a potential source of contamination by introducing our or any DNA into the lab.
To minimize contamination and preserve ancient DNA samples integrity, all steps involved in the manipulation of samples, DNA extraction, and amplification must be carried out in dedicated laboratory facilities. Ancient DNA labs are typically separate and access regulated. Samples are processed, and DNA extraction and amplification are performed in a pre-PCR room equipped with a laminar flow hood. Post-amplification steps are conducted in a separate post-amplification room.
Credit: Marina Buffoli. Marina fully dressed and ready to start working in the aDNA lab.
To ensure a sterile working environment, personnel should wear a full body suit, including a hood, mask, shoe covers, and double gloves, at all times. Surfaces and equipment must be thoroughly sterilized and cleaned before and after each processing step, and even between samples of the same origin. Despite all these efforts to maintain a sterile environment, some level of contamination in ancient DNA studies is unavoidable. Therefore, it should be closely monitored throughout the entire process by using negative controls.
Credit: Marina Buffoli. Marina processing samples in the aDNA lab.
Although it may seem simple and fast to work in such conditions, the reality is that it is much more time-consuming and demanding. Once inside an ancient DNA laboratory, it takes at least an hour to get dressed appropriately and sterilize all surfaces and equipment before the work of any other ordinary molecular biology lab could start. For example, during DNA extraction the work surfaces need constant cleaning, and opening samples once at time is essential to prevent cross-contamination. As a result, the processing time for a set of 10 samples increases to 5-6 hours, while typically, twice the number of samples can be processed in half of the time. In addition, scientists studying fossil DNA cannot drink or leave the ancient DNA facility unless they remove their full body suit and repeat the dressing process to re-enter.
This concise overview provides only a glimpse into the extensive work conducted within a laboratory dedicated to fossil DNA research. Stay tuned for the upcoming second episode, where we will explore the most accurate techniques for reconstructing entire ecosystems from fossil DNA and examine the challenges that persist in this fascinating field of study.
Written by Marina Buffoli