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Newfound Bacteria Expand Tree of Life
An anonymous reader writes: It used to be that to find new forms of life, all you had to do was take a walk in the woods. Now it's not so simple. The most conspicuous organisms have long since been cataloged and fixed on the tree of life, and the ones that remain undiscovered don't give themselves up easily. You could spend all day by the same watering hole with the best scientific instruments and come up with nothing. Maybe it's not surprising, then, that when discoveries do occur, they sometimes come in torrents. Find a different way of looking, and novel forms of life appear everywhere. A team of microbiologists based at the University of California, Berkeley, recently figured out one such new way of detecting life. At a stroke, their work expanded the number of known types — or phyla — of bacteria by nearly 50 percent, a dramatic change that indicates just how many forms of life on earth have escaped our notice so far.
Molecular ecologist/Microbiologist here
Actually, evolutionary relationships by DNA similarity as you said work extremely well within all 3 domains of life. Typically we use a highly conserved gene to establish phylogeny- the most common being the small subunit ribosomal RNA gene (16S for Bacteria/Archaea, and 18S for Eukaryotes). This gene is conserved across all domains of life, and essential for the functioning of the ribosome (The little machine that makes proteins). Without it, the ribosome wouldn't form, and you wouldn't be living. Now, to the point of lateral transfer of genes- much of the genetic lineage of a bacterium is from vertical inheritance after replication of a cell- the cell divides, and is most closely related to the parent cell from which it originated. You get genetic drift as errors crop up in the genomes of bacteria, and these errors are propagated from cell to dividing cell. Eventually these errors either become a new functional gene, a silent mutation, or are enough to kill the cell. Alternatively (As you stated) you get new function via horizontal gene transfer. But essential genes (such as the gene that codes for 16S rRNA) are not transferred horizontally, and can be used to establish a meaningful phylogeny of life.
Now the definition of a species within microbial life is somewhat contentious, and is typically established at a cutoff of 97 percent sequence similarity of the 16S/18S rRNA gene that correlates with a number of chemotaxonomic (functional/structural) changes. Otherwise yes, what differentiates an E. coli from E. albertii can be somewhat arbitrary. But using 16S/18S we can make much more meaningful and broad statements about higher taxonomic levels (Genus, Order, etc.). Binning genomes as Dr. Banfield did, and finding conserved marker genes like 16S in these novel genomes to establish phylogeny also allows us to infer functional traits and give at least some insight into what these uncultured microbes are doing.