Some organisms, such as tardigrades, rotifers, and nematodes, can survive harsh conditions by entering a dormant state known as “cryptobiosis.” In 2018, researchers from the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia discovered two roundworms (nematode) species in the Siberian Permafrost. Radiocarbon dating revealed that these nematodes have remained in cryptobiosis since the late Pleistocene, approximately 46,000 years ago. A team of researchers from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, the Center for Systems Biology Dresden (CSBD), and the Institute of Zoology at the University of Cologne in Germany used genome sequencing, assembly, and phylogenetic analysis to identify a previously unknown species of permafrost nematode – the Panagrolaimus kolymaensis. This study showed that Panagrolaimus kolymaensis employs similar biochemical mechanisms to survive desiccation and freezing as a life-cycle stage in the well-known model organism Caenorhabditis elegans.
When Anastasia Shatilovich and her colleagues from the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia successfully revived two frozen individual nematodes from a fossilized burrow in silt deposits in the Siberian permafrost, it was a moment of great excitement. The radiocarbon analysis of plant material from the burrow indicated that these frozen deposits, located 40 meters below the surface, had not thawed since the late Pleistocene, between 45,839 and 47,769 years ago. At the same time, the research group led by Teymuras Kurzchalia at the MPI-CBG was already studying how larval stages of the nematode Caenorhabditis elegans survive extreme conditions. When they learned about the permafrost nematodes, they immediately sought collaboration with Anastasia Shatilovich.
Vamshidhar Gade, a former doctoral student in Teymuras Kurzchalia’s research group, started working with the permafrost nematodes. “The molecular and metabolic pathways these cryptobiotic organisms use and how long they can suspend life are not yet fully understood,” he says. Vamshidhar is currently working at ETH in Zurich, Switzerland.
Collaborating with Eugene Myers, the research group leader at MPI-CBG, the DRESDEN-concept Genome Center, and Michael Hiller’s research group, the Dresden researchers conducted a high-quality genome assembly of one of the permafrost nematodes. Despite having DNA barcoding sequences and microscopic images, identifying whether the permafrost worm was a new species or not proved to be challenging. Philipp Schiffer, a research group leader at the Institute of Zoology and co-lead of the incipient Biodiversity Genomics Center Cologne (BioC2) at the University of Cologne, joined forces with the Dresden researchers to determine the species and analyze its genome with his team. Through phylogenomic analysis, they successfully categorized the roundworm as a new species and named it “Panagrolaimus kolymaensis,” after the Kolyma River region where it was found.
By comparing the genome of Panagrolaimus kolymaensis with that of the model nematode Caenorhabditis elegans, the researchers in Cologne identified shared genes involved in cryptobiosis. Surprisingly, most of the genes responsible for entering cryptobiosis in Caenorhabditis elegans, known as Dauer larvae, were also present in Panagrolaimus kolymaensis. The research team further tested the survival ability of Panagrolaimus kolymaensis and discovered that exposure to mild dehydration prior to freezing helped the worms prepare for cryptobiosis and increased their survival at -80 degrees Celsius. At a biochemical level, both species produced a sugar called trehalose when mildly dehydrated in the lab, potentially enabling them to endure freezing and extreme dehydration. Caenorhabditis elegans larvae also benefitted from this treatment, surviving for 480 days at -80 degrees Celsius without any declines in viability or reproduction after thawing.
Vamshidhar Gade and Temo Kurzhchalia state, “Our experimental findings also demonstrate that Caenorhabditis elegans can remain viable for longer periods in a suspended state than previously known. Overall, our research shows that nematodes have developed mechanisms to preserve life for geological time periods.”
“Our findings are crucial for understanding evolutionary processes because generation times can range from days to millennia. The long-term survival of individuals within a species can lead to the re-emergence of lineages that would otherwise go extinct,” concludes Philipp Schiffer, one of the overseeing authors of the study. Eugene Myers adds, “The highly contiguous genome of P. kolymaensis allows for comparisons with other Panagrolaimus species whose genomes are currently being sequenced by Schiffer’s team and colleagues.” Philipp Schiffer believes that “analyzing genomes to study species’ adaptation to extreme environments will enable us to develop more effective conservation strategies in the face of global warming.” Teymuras Kurzchalia remarks, “This study extends the longest reported cryptobiosis in nematodes by tens of thousands of years.”