How many microbes live on Earth?

Jonathan Eisen posted on his twitter an  interesting news on BBC about his most recent publication on Nature ("A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea", Nature 462:1056-1060). First of all, congratulations for the nice work! Since the original BBC article is in Spanish, I have tried to translate it here. You will soon realize that neither English nor Spanish are my first languages; I'll fix the mistakes as they are spotted by someone, and I assume responsibility for the remaining errors.

Scientists from US and Germany presented the first issue of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) that collects all living microorganisms on Earth.

It is expected that the publication - whose details appear on Nature Magazine - help researchers to better understand the several roles played by the microorganisms on this planet. It is estimated that the Earth harbors around one nonillion (1 followed by 30 zeros) microbes and despite around 2000 microorganisms already have their genomes deciphered, a large number remains unexplored. The Encyclopedia is being compiled by the Joint Genome Institute under the US Department of Energy, and the German Collection of Microorganisms and Cell Cultures.

Only single-celled ones

"This is a rich sample of the diversity of microbe genomes" says professor Jonathan Eisen, main author of the investigation. "To rely on a better sampling of the whole tree of life give us a better reference point to predict gene functions" he adds. The encyclopedia includes all prokaryotic organisms of the planet, which means the unicellular organisms. Unlike eukaryote organisms like us, yeast and the fungi, the prokaryotic cells don't have a membrane covering their DNA. This organisms are divided in two large groups: the Bacteria, which include the small minority of pathogens that makes us sick, and the Archaea, which are organisms that can survive in extreme environments like thermal waters. Up until now there have been sequenced around one thousand prokaryotic genomes. Almost all of them are pathogenic organisms.
According to professor Eisen "it has been like tracing a world map and including only three cities". Now the new encyclopedia analyzes the main representatives of the big branches of the prokaryotic family tree and the present study shows 56 genomes of this group. As explained by the scientists, even though it is known that microbes can exchange genes with other species (a process called lateral transfer) their position in the family tree, called phylogeny, is more important when we want to pinpoint where new genes appear and how they spread.

The beginning

"Microbes are mediators in almost all known biological processes of the planet" says professor Eddy Rubin, project leader. "And the sequencing of their genomes have revolutionized our understanding of the diverse roles they play". The information obtained with this first group of 56 organisms, adds the scientist, may help researchers in improving processes like biofuel production, bioremediation (to "clean" contaminated surroundings), and the way by which carbon is sequestered in the environment. According to the investigators, this is just the beginning of the project and they expect to be able to sequence all the diversity of microorganisms on Earth, including the hundreds or maybe thousands of microbe genomes currently unknown.  "The known phylogenetic diversity of Bacteria and Archaea is huge, with hundreds of big lineages and probably millions or hundreds of millions of species" says professor Eisen. "This encyclopedical project is starting from the top - with the big phylogenetic groups - with 100 genomes from all tree. "But we are just scratching the surface in the characterization of Earth's diversity" adds the researcher.

My only dispute in this article is that they lead to the impression that all single-celled organisms are prokaryotes. Yes, they fix that in the next sentence when they mention yeasts - which are (mostly?) unicellular - as eukaryotes, but then (unless my semantic interpretation is wrong) they introduce another misunderstanding since yeasts are fungi. But now I understand how hard it must be to convey concepts like phylogeny or Archaea to a broad audience. And I am not sure if "leader" is the best translation for "director"...