Wednesday, 20 November 2013

The Microbes Living 3 Kilometres Beneath Antarctica

Welcome to Lake Vostok; beneath 3,700 metres of Antarctic glacier you can sit back, relax and enjoy unrelenting extremes of cold and heat. If you love crushing pressures, starvation and perpetual darkness, then Lake Vostok is the place for you.
Turns out Lake Vostok is the place for much microbial life. As the glacier creeps along at 3 metres per year, lake water freezes to the bottom, providing us with a historical record of its contents. Parts of this lake have been found to be rich in organic carbon, minerals and, of course, organisms. Average cell concentrations in this ice range from one to hundreds per millimetre, with most viable cells found in the ice formed by glacial movement. Previously, rDNA sequences have yielded the discovery of 18 unique Bacteria and 31 Fungi isolates. Phylogenetically, they resembled known species from deep-sea, sediment, polar and cold environments. This study used ice core samples from Lake Vostok ice formed by glacial movement to provide a more detailed view of Lake Vostok's life using metagenomics and metatranscriptomics.
Ice core sample quartering, melting in sterile conditions and ultracentrifugation provided RNA samples which were then copied in cDNA and followed by subsequent PCR amplification, ligation, chromatography and re-amplification with primer sequences. Finally, sequence analysis provided over 36 million base pairs of data.
3,169 sequences were identified as bacterial, 89% of which matched known database sequences by 97-99%; the taxa identified included the phyla Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria and Bacteroides. Only 2 sequences were from Archaea and they were most similar to deep ocean sediments Archaea.
6% of sequences were of eukaryotic origin; dominated by fungal groups, including one rRNA sequence which had 99% similarity to a known thermal-vent fungus. Other sequences found included those of Daphnia, springtails, rotifers, tardigrades, a deepsea bivalve and a anemone species. Many sequences were highly similar to those from uncultured bacteria from intimate parasitic or symbiotic associations with a range of eukaryotes including lobsters, annelids, salmon disease, fish intestines, bivalve larvae, sea squirts, tubeworms, sponges and Antarctic seaweeds.
The presence of certain metabolic capabilities was determined based on the rRNA sequences found; this diagram summarises the pathways they identified;
Figure 3. Summary of steps in nitrogen metabolism (above) indicated from the metagenomic/metatranscriptomic sequence
identities, as well as types of carbon fixation (lower left) and other functions (lower right) indicated by the sequence data.

Each unique sequence found is likely to represent a novel species or strain; especially of the Cyanobacteria and Proteobacteria, the most abundant groups. Metagenomics and transcriptomics have strongly suggested that Lake Vostok has a diverse community based on nitrogen cycling, symbiosis and high salinity toleration. Surprisingly few sequences originated from psychrophilic microbes, but this could be because there are relatively few psychrophile sequences for comparison in GenBank databases. The higher presence of thermophilic sequences supports the suggestions of other studies that Lake Vostok has hydrothermal activity. Sequences indicating arsenic oxidising bacteria also suggest hydrothermal activity, since arsenic is often present in volcanic activities.
The large representation of nitrogen metabolism in the sequences is probably due to frequent nitrogen gas introduction into the lake by glacial melting and movement. Carbon dioxide fixation was mostly represented by the reductive pentose phosphate cycle, with the TCA cycle in second place.
Lake Vostok was a normal lake 35 million years ago and part of a forest ecosystem and since then the lake has been partially exposed multiple times before it became completely frozen over. This means that life has had a number of opportunities to occupy the lake and this is reflected in the diversity hinted at by metagenomic techniques. Given the recent revelations from the discovery of hydrothermal vent ecosystems and the unlikelihood of contamination with the sequences found, Lake Vostok probably does have novel ecosystem dependent on the metabolism of unusual microbial groups; it will be interesting to see what innovations will have be developed to directly observe Lake Vostok's communities and even more so to know what lessons it will provide; ones which may even be extrapolated to how life elsewhere in the universe might exist, particularly on Europa, one of Jupiter's moons, where parallel conditions to Lake Vostok exist. This study also seems to imply that symbioses seem to become much more fundamental to life in extreme environments, for both host and microbe; this may have implications on our understandings on life's origins and the evolution of microbes into organelles.

Shtarkman YM, Koc¸er ZA, Edgar R, Veerapaneni RS, D’Elia T, et al. (2013) Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of

Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya. PLoS ONE 8(7): e67221. doi:10.1371/journal.pone.0067221


  1. Do you think it likely that there are lobsters, sponger, sea squirts and fish down there, seeing as how they found the sequences of associated symbionts and parasites? Larger animals would not have been captured using the ice core sampling technique, so associated microbes may be the only evidence of them.

    1. Before the discovery of hydrothermal vents, life without sunlight and photosynthesis was thought to be impossible; so I think it is a real possibility. Why else would the sequences from these animals plus their associated symbionts be found in the ice cores; I doubt it was contamination, unless the experimenters had a very exotic lunch that day.