microBIO: A new look at the tree of life in high definition HD

Posted October 17, 2017

Non-cropping microorganisms

appear in the new version of the tree of life The tree of life is one of the most important systems of organization of living organisms in biology. The first attempts to classify organisms into a "tree of life" were based on their physical and metabolic characteristics. With the molecular methods based on the comparison of gene sequences they increased the diversity of the branches of the tree because it was no longer necessary the direct observation of the organisms. So far these comparisons have been limited to one gene, the small subunit of ribosomal RNA (SSU rRNA, small subunit ribosomal RNA). To do this, from a sample of DNA from the organism, the SSU rRNA gene was amplified with specific and universal oligonucleotides (in principle for all organisms), sequenced and compared to the sequences of the same gene from the other organisms . The comparison of the sequences of the SSU rRNA gene shows that life is organized into three evolutionary lines, called domains: Bacteria and i> Archaea (representing prokaryotic cells, ie without a nucleus), and Eukarya (eukaryotic cells, with nucleus). This universal phylogenetic tree revealed two important evolutionary facts: not all prokaryotes are closely related from the evolutionary point of view, and the Archaea domain has a closer relationship to the domain < i> Eukarya than the domain Bacteria.

The universal phylogenetic tree , based on the comparison of the sequences of the SSU rRNA gene.

There are more than 30,500 sequenced genomes of the three domains of life, Bacteria, Arquea and Eukarya (September 2015 data).

> Metagenomics is based on the massive sequencing of all DNA in an environmental sample. The result is hundreds of thousands of sequences of fragments of the genome. Then, new bioinformatic methods allow to link these fragments (like a puzzle) and complete (or almost complete) the sequence of the whole genome of a particular organism. With this technique it is not necessary to isolate the organism, we do not need to cultivate it in the laboratory. It is not even necessary to have a prior reference genome to compare. In addition, this genomic approach provides information about the body's potential metabolism, information that can be used to relate it to other organisms and classify it. Now, a group of Californians (along with some Japanese) have used metagenomic technology to propose a new version of the tree of life in high definition, as if we saw the tree with a higher resolution . And the result is very interesting.

They have built their tree of life using some 2,000 complete genomes obtained from public databases plus other 1,011 new reconstructed genomes from samples of DNA obtained from different environments. These were therefore genomes of uncultivated organisms in the laboratory. DNA samples have been obtained from a number of ecosystems: a shallow aquifer system, deep seafloor of Japan, salt marshes of the Atacama desert, green California grassland, a CO2 rich geyser and even the mouths of a pair of dolphins (as you can see the authors have been having fun at the sampling stage).

microBIO: A new look at the tree of life in high definition HD
microBIO: A new look at the tree of life in high definition HD

This new version of the tree of life has included 3,083 organisms.

The new tree of life in high definition . It includes 92 phyla of Bacteria, 26 of Archaea, and the five supergroups of Eukarya. Lineages are marked with a red dot that do not have an isolated and cultivated representative.

This is the first tree of life published since the development of metagenomic techniques. It has required a total of 3,840 hours of computational work from the CIPRES supercomputer.

In new tree shows that the domain Bacteria , the most diverse. The greatest genetic biodiversity is found among bacteria . Archaea is less abundant and less diverse than Bacteria . The low genetic diversity of Eukarya is expected due to its comparatively recent evolution. The result is also compatible with the idea that eukaryotes evolved as chimeras via endosymbiotic fusions involving both bacteria and archaea. The domain Eukarya includes protists, fungi, plants and animals, and branches from Archaea , specifically the TACK group. These phylogenetic analyzes support the hypothesis that the archaea Lokiarchaeota and Eukarya have the same common ancestor.

Another interesting fact , is that unlike what was thought, the class Proteobacteria of the Bacteria domain, is not a monophyletic group, but has more diverse evolutionary origins.

In short, the inclusion of new genomes of previously unknown microbial lineages has greatly expanded the tree of life. This demonstrates the importance of including genomic data independent of the crop to have a more real image of the tree of life.

A new view of the tree of life . 2016. Hug, L.A. et al. Nature Microbiol. Article number: 16048 (2016). doi: 10.1038 / nmicrobiol.2016.48