Wednesday, April 29, 2015

Genomes from Smokers

We’ve got samples! Now comes the really fun part-- discovering new microbes and finding out how they survive and grow in such extreme environments. We are examining these communities using two different approaches. Many of the microbiologists on board are developing new culturing techniques to get novel Bacteria and Archaea to grow as isolated cultures in a lab. Another approach is to look at the communities using molecular techniques to determine the ecology and biochemical mechanisms of microbes in the environment. One of the most exciting developments in environmental microbiology is the ability to perform genomic analysis of environmental samples, known as metagenomics.
Hydrothermal vent chimneys about to be sampled

Metagenomic analysis of a sample should give us information about who is living at these vents as well as how they survive there, but the process is long and difficult. The method begins with extracting and purifying total DNA from sulfide chimneys. Once we break open the cells, we need to purify the DNA to remove any traces of metals or cell debris which inhibit our future sequencing steps. This purified DNA consists of a mixture of genomes from each microorganism that is living in the sample. We then sequence the fragments using a next-generation sequencer that gives us hundreds of millions of fragments of DNA sequences. We then rebuild the genomes from these small fragments using powerful computer algorithms so we can study them in more detail. Once these genomes are reconstructed, it will help us understand how the genomes of these microbes differ between the different deep-sea vents sites here in the Lau Basin, and help guide our culturing efforts in new directions to try and get these microbes to grow in a test tube. We’ll follow this post with more information about how we grow microbes on the ship. 

Contributed by Rick Davis

Inside view of a hydrothermal sulfide chimney sample from ABE. The yellowish mineral is
chalcopyrite, a copper, sulfide, iron mineral CuFeS2

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