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Tardigrade genetic secrets unveiled

New study resolves difference in previous genetic sequencing; foreign genes play some, but not major, part in extremophile abilities.

A scanning electron microscope image of the tardigrade Ramazzottius varieornatus.
A scanning electron microscope image of the tardigrade Ramazzottius varieornatus.
Kazuharu Arakawa and Hiroki Higashiyama

Tardigrades, the microscopic creatures known as water bears or moss piglets, are well-known not just for being as cute as an extremely small button. They have a deserved reputation as some of the planet’s great survivors: one of the few animals to have survived the Earth’s past five mass extinction events, and the only one we know can survive – for up to 10 days – in the vacuum of space.

Though not all of the 1,200 species of tardigrades are equally extreme survivors, various members of the tribe have proven their ability to cope with temperatures that would freeze other animals solid or boil their insides; with toxic environments including levels of radiation 1,000 times higher than what is safe for humans; and with pressures six times greater than that found at the deepest parts of the ocean.

These abilities have naturally made tardigrades a source of great interest to scientists keen to unlock the genetic secrets of their superior abilities as extremophiles – creatures able to survive extreme environmental challenges.

The latest genome sequencing, led by Yuki Yoshida of Keio University in the northern Japanese city of Tsuruoka, has enabled a better comparison of two different tardigrade species that have been the subjects of two previous studies that came to different conclusions about the source of tardigrade super powers.

The first study, published in 2015, involved a preliminary sequencing of the genome of the tardigrade Hypsibius dujardini by a research team led by Thomas Boothby at the University of North Carolina at Chapel Hill. The second, published in 2016 by a team led by Takuma Hashimoto and Daiki Horikawa of the University of Tokyo, involved a significantly higher-quality sequencing of the species Ramazzottius varieornatus.

The 2015 study speculated a crucial part of the animal’s ability to survive extremes might lie in its ability to acquire foreign genes, through the process known as horizontal gene transfer. This was based on one-sixth of the H. dujardini genome being found to derive from bacteria, plants, fungi and archaea – “a proportion nearly double the proportion of previous known cases of extreme horizontal gene transfer”. The Japanese study, however, found a unremarkable level of foreign genes (1.2% or less) and instead pointed to the abundance of “tardigrade-unique proteins” as the source of the animal’s tolerance, thus making the creature a potential “bountiful source of new protection genes and mechanisms”.

In an effort to reconcile these findings, Yoshida’s team – which included Kazuharu Arakawa of the University of Tokyo, also a co-author of the 2016 paper, and researchers from the University of Edinburgh and the James Hutton Institute in Scotland – resequenced and reassembled the genome of H. dujardini to enable a better comparison of the two species.

Their crucial finding: “Compared to previous estimates, our improved genomes show much reduced levels of horizontal gene transfer into tardigrade genomes, but some of the identified horizontal gene transfer (HGT) genes appear to be involved in anhydrobiosis.” They conclude the results of the 2015 study were affected by contamination.

An immunofluorescent micrograph of Hypsibius dujardini.
An immunofluorescent micrograph of Hypsibius dujardini.
Roland Birke / Getty

The tardigrade’s ability as an extremophile rests on its ability to survive in a dehydrated state known as anhydrobiosis – meaning, literally, life without water. Humans, by comparison, begin to experience dizziness and headaches from a loss of more than 5% of their body water; physical and mental impairment from more than 10%; and death from 15-25%. The tardigrade can shed almost all water, curling up into a protective ball known as a tun and slowing its metabolism to 0.01% of its normal rate – a state of suspended animation known as cryptobiosis. It is from this state that tardigrades have been able to spring back to life after days in space and decades in inhospitable conditions on Earth.

Of the two tardigrade species sequenced, R. varieronatus is the more extreme extremophile; it can form a tun within 30 minutes at 30% relative humidity; H. dujardini requires 48 hours of “preconditioning” at 85% relative humidity and a further 24 hours in 30% relative humidity to enter cryptobiosis with a high chance of survival.

The new study, published in PLOS Biology, identifies several tardigrade-specific gene families that facilitate anhydrobiosis. These include cytosolic abundant heat soluble (CAHS) proteins, secretory abundant heat soluble (SAHS) proteins, late embryogenesis abundant protein mitochondrial (RvLEAM) proteins, mitochondrial abundant heat soluble (MAHS) proteins, and damage suppressor (Dsup) proteins. R. varieronatus also shows a “surprising” loss of genes in stress signaling pathways. “While loss of these pathways would be lethal for a normal organism,” the authors write, “loss of these resistance pathways may be associated with anhydrobiosis.”

A few genes that contribute to anhydrobiosis-related functions appear to have been acquired through horizontal gene transfer, however. One of these is a protein for synthesising trehalose, which is thought to act as a protective gel preventing disruption of internal cell organelles in both plants and animals.

Yet many mysteries remain. One outstanding question – to what is the tardigrade most closely related in the animal kingdom – shows just how unique the animal is. It looks most like an arthropod, with eight appendages, a segmented body and comparable central and peripheral nervous systems. Phylogenomic analyses, however, suggests it is more closely related to nematodes, which are unsegmented, have no lateral appendages and have a simple nervous system. Resolving these “conflicts between morphological and molecular data” will, the new study suggests, be “informative”.

"This is just the start,” says paper co-author Mark Blaxter, of the University of Edinburgh. “With the DNA blueprint we can now find out how tardigrades resist extremes, and perhaps use their special proteins in biotechnology and medical applications."

Tim Wallace is a contributor to Cosmos Magazine
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