Sunday marked the passing of Carl Woese, one of the most important figures in microbial ecology in recent decades. In fact that’s a bit of an understatement, his discoveries and the methods he pioneered have profoundly altered our understanding of the diversity of life on Earth. Dr. Woese’s key innovation came at the dawn of the genomic era, when the sequencing of DNA was a laborious process carried out without automation. In those days taxonomy, microbial and otherwise, was deduced from an organism’s physiology and morphology. A new bacterium might be classified for example, based on cell shape, gram stain, and growth conditions. Even in multicellular organisms morphology and growth conditions can be misleading – not everything that flies and breathes air is a bird. In microscopic organisms this almost never works. What scientists needed was a way to use the newly available gene sequences to deduce the evolutionary patterns underlying taxonomy.
For this to work however, they needed to find a slowly evolving gene that is present in all taxonomic groups. Early work focused on the gene for a small structural RNA in the ribosome (ribosomal RNA, or rRNA) called 5S. Ribosomes are present in all cells, and have been since the last universal common ancestor. For various reasons ribosomes don’t evolve very quickly, meaning that the gene sequences coding for their structural components are somewhat similar between distantly related organisms – but they evolve enough that there are differences in the sequences from closely related organisms. 5S sequence comparison worked well enough to show that traditional microbial taxonomy was wrong, but due to the gene’s small size not well enough to resolve a true evolutionary history.
Woese focused on a larger rRNA gene called 16S (18S in eukaryotes), first comparing only a couple of 16S sequences (1972, 1974), then a few more (1975), and finally enough to see the big picture in 1977 . The basic method established by Woese to differentiate organisms based on 16S sequence similarity is still the gold standard for microbial taxonomy today, and the basis for much of the work in our lab. The picture has become more complicated since 1977, we now understand that rRNA sequence similarity is only tangentially related to physiology and to what other genes are contained within an organism’s genome. Since this is often the information we really want, knowing the rRNA sequence (and therefor the “species”) of an organism doesn’t always give us the answers we need.
Had Woese only honed the method of 16S rRNA sequence taxonomy it still would have been an impressive scientific work. He is best known however, for the big picture that he observed in 1977 using 16S sequence comparison; that all life on Earth is distributed among three broad domains – the Bacteria, Archaea, and Eukarya. Only the domain Eukarya contains multicellular life (and all that diversity is compressed into a tiny corner). Under a microscope Bacteria and Archaea are indistinguishable. Without rRNA sequence data we might never have realized that these groups are as different from one another as we are to them.
The classic “Woesian” phylogenetic tree showing the three domains of life. The more distant two branches are, the more distant the evolutionary relationship or organisms on them (and the greater the difference in their 16 or 18S rRNA gene sequences). To give yourself a sense of scale consider how close we are to Zea (corn). I’ve had this tree on my hard drive for a while and I’m still trying to track down a citation. Will update when I find it.
Ultimately what Woese gave us were the tools for a lesson in humility. We can now see that humans, mammals, vertebrates, even all animals and plants are a very minor component of life on Earth, and account for a shockingly small portion of life’s diversity. To quote Woese (via the NY Times):
“It’s clear to me that if you wiped all multicellular life-forms off the face of the earth, microbial life might shift a tiny bit, If microbial life were to disappear, that would be it — instant death for the planet.”
Well said!
