Shedding some light on dark organisms

INTRO: dark organisms defined

Physicists have dark matter.  Biologists have what I like to call dark organisms.  These are the myriad organisms that cannot grow in culture, and thus remain relatively unstudied. Consider that some estimates suggest that only 1 in 1000 bacteria can be successfully grown in the lab right now.  That leaves a lot of work to do to to uncover the literally millions of organisms producing antibiotics, anti-cancer therapeutics, and biofuels of tomorrow.

COAL-BED METHANE: a biological process in need of refinement

Since the 1980's, it's been known that some of the natural gas found in coal deposits came from bacterial organism (Schoell 1980).  Of late, companies like synthetic genomics and Luca technologies have developed chemical mixes that can stimulate the bacteria living in coal deposits and get them to eat more coal and turn it into methane.This is a huge potential source of (relatively) clean energy from coal.

Consider, however, that many extreme organisms converting coal into cleaner methane die when moved from the nutrient-poor depths of a coal mine to the nutrient-rich surface, or to the lab. 

We need to understand and grow the organisms producing our future methane, if we want more of this energy.

A GENETIC LOOPHOLE: why culture the organism, when you can get the sequence anyways?

A recent paper in the Journal of Bacteriology turned me on to a new solution to the problem of studying unculturable bacteria.  Why not just sequence the bacteria where they live?

Now that we have next-generation sequencing technology and the complete sequence of almost every model organism, it is possible to rapidly sequence a small amount of starting DNA collected from the wild.

In this JB paper.  The authors collected about a gallon-and-a-half of water from an offshore oil field, isolated the DNA, and assembled the genome of an entirely new species found growing in that oil field. They compared the DNA sequences they collected to a reference organisms sequence grown in the lab.  when they assembled all of their DNA sequencing data, they found a 1.6 million base sequence representing a new strain of the species Methanococcus maripaludis called X1. 

While the authors found some inconsistencies and point mutations in their data, they suggest these results do not indicate multiple strains in their water, but rather technical errors they were able to sort out manually.  Either way, the data from strain X1 will lend insight into the various genes present in nonculturable strains of this organism.

THE NEXT STEP: using these genes in culture

It's an exciting step to see a new strain of an organism sequenced without culturing it first.  It's a big step forward to shedding light on these dark organisms.  The next step will be when we successfully use the genes from these organisms to produce new antibiotics, therapuetics, and fuels. 

REFERENCES

 Schoell M. 1980. The hydrogen and carbon isotopic composition of methane from natural gases of various
origins. Geochim. Cosmochim. Acta 44:649–61

Wang X, Greenfield P, Li D, Hendry P, Volk H, Sutherland TD. Complete Genome Sequence of a Nonculturable Methanococcus maripaludis Strain Extracted in a Metagenomic Survey of Petroleum Reservoir Fluids. J Bacteriol. 2011 Oct;193(19):5595. PubMed PMID: 21914896.