Sequencing than soaking in Hot Spring

There are many volcanoes and earthquakes in Japan, but it is not always a bad thing, they are also responsible for the many hot springs. Most Japanese people love soaking in a hot spring and they believe that this eliminates fatigue and improves health. Hot springs also had a great contribution to biotechnology via the heat resistant DNA polymerase from Thermus aquaticus (Taq) and its derivatives. Not only PCR, but also Sanger sequencing was accelerated by these heat resistant enzymes as we all know well.

Scientists have started to study the genome/transcriptome world in hot springs with NGS technologies. Murakami et al., peformed 16S-rRNA (Sanger sequencing) and meta-transcriptome analysis from small RNA (GS FLX sequencing) of groundwater (up to 1,000 m depth) from Yunohara hot spring, Japan. Their phylogenetic analysis using 16S rRNA showed the classification of 17 species including archaea and eubacteria.  There are only 2 or 3 dominant species in typical cases of other hot springs, but this one is rich in diversity. Furthermore, they found the very unique group “Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN)” which is a small organism/cell with only 200 nm size! Their small RNA analysis identified 64,194 (20,057 nonredundant) cDNA sequences, and they found several novel non coding RNAs which have a very stable secondary structure.

Therefore, hot springs may still be gold mines for useful genes and important biological knowledge of unknown underground ecosystems.

 

 

Jun Onodera (Japan)

About Jun Onodera (Japan)

Jun is balancing expanding NGS technologies and potential recipients.

4 Responses to “Sequencing than soaking in Hot Spring”

  1. Interesting article concerning hot springs. Of course such things like volcanos are natural accurances that typically result in increasing diversity. Although I find it surprising that hot springs typically have only a couple of dominating species. I am curious what led to the increase diversity found through metagenomic studies in Japan.

  2. Jun Onodera (Japan)

    Dear Dr./Mr. Doug, at first I’m grateful to your interesting comment. I’m also wondering why it is rich in diversity in this case. In my imagination, it is thought to be causally related to complex nature of Japanese volcanoes which are consisted by four major earth plates – North American plate, Philippine Sea plate, Eurasian plate, and Pacific plate. This geographical complexity could bring biological one. Again just imagination!

  3. Invaluable commentary – I learned a lot from the points – Does anyone know where I might be able to locate a fillable a form form to fill in ?