Microbial Dark Matter - The Uncharted Branches of the Tree of Life
by Carina Brehony, 17th August 2013
Microbes inhabit almost every ecological niche known and are the most plentiful cellular life form on the planet. The human body even contains more microbial cells than human cells. In spite of all that is known there are large gaps in our knowledge of microbial diversity partly due to the fact that sampling is skewed towards culturable organisms. Recent developments such as metagenomics, which samples environmental microbial community gene content, and single-cell genome sequencing (SCGS) are accelerating the identification of new species and even new phyla. A recent study published in Nature (Rinke et al, 2013; doi:10.1038/nature12352) (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12352.html) is seen as a major step forward as it uses the latest in single-cell sequencing technology to shine light into the dark unsampled corners of the microbial world-the so called ‘microbial dark matter’.
The authors collected samples from nine ecologically and geographically diverse locations such as a chemical reactor in Mexico, a lagoon in Greece and from the Gulf of Maine. They performed SCGS and obtained draft genomes for 201 bacteria and archaea that have never been sequenced or cultured. Several novel discoveries imply a more flexible boundary between the archaeal and bacterial domains than was previously thought. These include: sigma factors (involved in transcription) thought to be restricted to bacteria found in some of the archaea; a novel coding for UGA, usually a stop codon but in one bacterial lineage is translated as a the amino acid glycine; another bacterial lineage synthesizes the amino acid purine using an archaeal enzyme. They have proposed several new phyla and as such are adding many new leaves to bare parts of the Tree of Life. With no overstatement the authors themselves say this work “provides a systematic step towards a better understanding of biological evolution on our planet.”
These are very exciting times for microbiology and evolutionary biology!
Figure: Novel metabolic features in dataset.
Figure: Sampling sites and single-cell sequencing workflow.