Genome Analysis of 46000-year-old roundworms shows that nematodes found in the Siberian Permafrost actually belong to a previously undescribed species, Panagrolaimus kolymaensis.

Unraveling the genetic secrets of a 46,000-year-old roundworm from Siberian permafrost has led to the discovery of a novel species. This international research collaboration has revealed that this newly discovered Pleistocene nematode shares significant survival mechanisms with the modern-day nematode, Caenorhabditis elegans.

Some unique organisms, including tardigrades, rotifers, and nematodes, can survive extremely harsh conditions by entering a dormant state, known as “cryptobiosis.”

In 2018, a team of researchers from Russia’s Institute of Physicochemical and Biological Problems in Soil Science RAS unearthed two cryptobiotic roundworm species from the Siberian permafrost.

Radiocarbon dating suggested these nematodes have remained in this suspended state since the late Pleistocene, approximately 46,000 years ago.

An interdisciplinary team of researchers from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), the Center for Systems Biology Dresden (CSBD), and the Institute of Zoology at the University of Cologne, using a combination of genome sequencing, assembly, and phylogenetic analysis, established that the permafrost nematode belonged to a hitherto unknown species, Panagrolaimus kolymaensis.

Anastasia Shatilovich, from the Russian Institute, played a critical role in reviving two frozen nematodes from a fossilized burrow in the Siberian permafrost. The excitement in the scientific community was palpable as a radiocarbon analysis of plant material from the burrow demonstrated that these deposits, deep beneath the surface, had not thawed since the late Pleistocene.

Concurrently, the research group led by Teymuras Kurzchalia at MPI-CBG, was studying how the larval stages of Caenorhabditis elegans survive extreme conditions.

News of the permafrost nematodes prompted an immediate collaboration between Kurzchalia’s team and Shatilovich.

Vamshidhar Gade, then a doctoral student under Kurzchalia, began studying these ancient, cryptobiotic organisms. He aimed to unravel the molecular and metabolic pathways enabling their long-term suspended life.

The researchers from Dresden undertook a comprehensive genome assembly of one of the permafrost nematodes, in collaboration with Eugene Myers from the MPI-CBG, the DRESDEN-concept Genome Center, and Michael Hiller’s research group.

Despite the availability of DNA barcoding sequences and microscopic images, the task of confirming the permafrost worm as a new species was challenging.

Philipp Schiffer, a biodiversity genomics research expert from the Institute of Zoology, was instrumental in defining the roundworm as a novel species using phylogenomic analysis. In homage to the region from which it originated, the Kolyma River, the nematode was named “Panagrolaimus kolymaensis.”

Comparing the genome of Panagrolaimus kolymaensis with Caenorhabditis elegans revealed genes common to both species, crucial in cryptobiosis. To the researchers’ surprise, the majority of genes necessary for entering cryptobiosis in Caenorhabditis elegans, the so-called Dauer larvae, were also present in Panagrolaimus kolymaensis. Exposure to mild dehydration before freezing, enabling the production of a sugar called trehalose, enhanced the survival mechanisms in both species.

Vamshidhar Gade and Temo Kurzhchalia emphasized the significance of their findings.

“Our experimental findings also show that Caenorhabditis elegans can remain viable for longer periods in a suspended state than previously documented. Overall, our research demonstrates that nematodes have developed mechanisms that allow them to preserve life for geological time periods.”

Philipp Schiffer concluded, “Our findings are essential for understanding evolutionary processes because generation times can range from days to millennia and because the long-term survival of a species’ individuals can result in the re-emergence of lineages that would otherwise have gone extinct.”

Eugene Myers added, “P. kolymaensis’s highly contiguous genome will make it possible to compare this feature to those of other Panagrolaimus species whose genomes are presently being sequenced by Schiffer’s team and colleagues.”

He and his colleagues believe that studying species’ adaptation to extreme environments through genome analysis can lead to improved conservation strategies in light of global warming.

Teymuras Kurzchalia succinctly summed up the significance of the study, “This study extends the longest reported cryptobiosis in nematodes by tens of thousands of years.”

The results of the study were published today in the journal PLOS Genetics.

Source: 10.1371/journal.pgen.1010798

Image Credit: Alexei V. Tchesunov and Anastasia Shatilovich / Institute of Physicochemical and Biological Problems in Soil Science RAS