2023-07-28 21:07:14
German researchers have analyzed the genome of a 46,000-year-old nematode from the Siberian permafrost and have revealed the existence of a new species from the Pleistocene, which shares with the nematode ‘Caenorhabditis elegans’ a set of molecular tools for survival, as published in the journal ‘PLoS Genetics’ magazine. 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 found two species of roundworms (nematodes) in the Siberian permafrost.
Radiocarbon dating indicated that individuals of nematodes have remained in cryptobiosis since the late Pleistocene, around 46,000 years ago. Now, researchers from the Max Planck Institute for 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, all in Germany, used the sequencing, assembly and phylogenetic analysis of the genome and discovered that the permafrost nematode belongs to a previously undescribed species, ‘Panagrolaimus kolymaensis’.
They showed that the biochemical mechanisms used by Panagrolaimus kolymaensis to survive desiccation and freezing under laboratory conditions are similar to those of a life cycle stage of the important biological model Caenorhabditis elegans. When Anastasia Shatilovich of Russia’s RAS Institute of Physicochemical and Biological Problems of Soil Science recovered two frozen individual nematodes from a fossilized burrow in silt deposits in the Siberian permafrost, she and her colleagues were more than excited.
After thawing the worms in the laboratory, a radiocarbon analysis of plant material from the burrow revealed that these icy deposits, 40 meters below the surface, had not thawed since the late Pleistocene, between 45,839 and 47,769 years ago. At the same time, Teymuras Kurzchalia’s research group at MPI-CBG (Teymuras Kurzchalia is now retired) was already addressing the question of how the larval stages of the nematode ‘Caenorhabditis elegans’ survive extreme conditions. When the team learned about the existence of permafrost nematodes, he immediately contacted Anastasia Shatilovich to help.
Vamshidhar Gade, then a PhD student in Teymuras Kurzchalia’s research group, began working with permafrost nematodes. “The molecular and metabolic pathways used by these cryptobiotic organisms and how long they would be able to suspend life are not fully known,” says Vamshidhar, who now works at ETH Zurich, Switzerland. The Dresden researchers performed a high-quality genomic assembly of one of the permafrost nematodes in collaboration with Eugene Myers, Director Emeritus and Research Group Leader of MPI-CBG, the DRESDEN Concept Genome Center, and the research group by Michael Hiller, head of a research group at the time at MPI-CBG and now Professor of Comparative Genomics at LOEWE-TBG and the Senckenberg Society for Nature Research.
Despite having DNA barcode sequences and microscopic photographs, it was difficult to determine whether or not the permafrost worm was a new species. Philipp Schiffer, research group leader at the Institute of Zoology, co-director of the fledgling Cologne Center for Biodiversity Genomics (BioC2) at the University of Cologne and an expert in biodiversity genomics research, joined forces with the Dresden researchers to determine the species and analyze its genome with his team. Thanks to phylogenomic analysis, he and his team were able to define the roundworm as a new species, and the team decided to name it ‘Panagrolaimus kolymaensis’. In recognition of the Kolyma River region from which it originates, the nematode was given the Latin name Kolymaensis.
By comparing the genome of ‘Panagrolaimus kolymaensis’ with that of the model nematode ‘Caenorhabditis elegans’, the Cologne researchers identified genes that both species have in common and that are involved in cryptobiosis. To their surprise, most of the genes needed to enter cryptobiosis in the so-called Dauer larvae of ‘Caenorhabditis elegans’ were also present in ‘Panagrolaimus kolymaensis’. Next, the research team tested the survivability of Panagrolaimus kolymaensis and found that exposure to mild dehydration before freezing helped the worms prepare for cryptobiosis and increased their survival at -80 degrees Celsius.
On a biochemical level, both species produced a sugar called trehalose when slightly dehydrated in the laboratory, possibly allowing them to withstand severe freezing and dehydration. The ‘Caenorhabditis elegans’ larvae also benefited from this treatment, surviving for 480 days at -80 degrees Celsius without suffering any reduction in their viability or reproduction after thawing. According to Vamshidhar Gade and Temo Kurzhchalia, “These experimental results also demonstrate that ‘Caenorhabditis elegans’ can remain viable for longer periods in a suspended state than previously documented.
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