bacteria very long ago, though he could not place a time on the divergence. He had,
to that point, cataloged about 40 species of “bacteria,” and these methanogens were
the only representatives that showed such a divergence. Hori had examined the
sequences of 5S rRNA from many bacteria a year before, but methanogens were not
among those he examined and so he did not observe any deep divergences among
the bacteria he examined (Hori 1976). Woese was fortunate in this respect in having
the laboratory of Ralph Wolfe nearby in his department. Woese had little experience
in growing microbes, and his lab was not set up to cultivate any exotic organisms. It
was only because one of Wolfe’s graduate students, William E. Balch, was interested
in working with Woese that methanogens were among the organisms that he
examined, yet another example of the sometimes serendipitous nature of scientific
discoveries.
Shortly thereafter, George Fox and Woese included two more methanogens in
their analysis, along with yeast, duckweed, and human 18S rRNAs, to show that life
was comprised of three major lineages, or urkingdoms (primary kingdoms), that they
named eubacteria (true bacteria), archaebacteria (suggesting an ancient form of life,
perhaps predating bacteria), and urkaryotes (ancestor of modern eukaryotes) (Woese
1977). This finding upended the commonly held notion that prokaryotes were a
monophylogenetic unit. However, even those, like Stanier, who had thought seriously about it were aware that this notion might not be true.
Later extremely halophilic and thermoacidophilic microbes were found to be
archaebacteria, too (Woese et al. 1978; Magrum et al. 1978). As more sequences
were analyzed, it was found that the archaebacterial lineage was comprised of two
major subdivisions, the thermoacidophiles and a group including the halophiles and
methanogens (Fox et al. 1980). The relationship among the three urkingdoms was
not clear until the sequences of duplicated genes were compared and the root of the
small subunit rRNA tree was found to lie between the bacteria and the combined
archaebacteria and eukaryote lineages (Gogarten et al. 1989; Iwabe et al. 1989). The
two lineages within the archaebacteria were later named the Crenarchaeota
(suggesting the ancestral type of archaebacteria) and Euryarchaeota (denoting their
broad spectrum of ecotypes), respectively (Woese et al. 1990). The three
urkingdoms were now called domains (a taxon above kingdom) and renamed
Eucarya (now Eukarya), Bacteria, and Archaea.
Woese’s work appeared to have finally provided a “natural” classification for not
only microbes but all life. Ribosomal RNA trees have been used as the basis for a
universal tree of life (Maddison et al. 2007; http://tolweb.org/tree/). The tree has
allowed investigators to begin examining the evolution of metabolic and genetic
processes, using it as the basic framework on which to place evolutionary events.
Elucidation of a more solid phylogeny certainly brought the study of microbial
evolution back to being a respectable science.
The validity of the rRNA phylogeny was questioned from the start. Not including
objections to the tree based largely on earlier notions of evolutionary history (Woese
1994; Woese and Goldenfeld 2009; Sapp 2005), the phylogeny was not congruent
with those based on RNA polymerase sequences (Klenk et al. 1993) nor indel
analyses (Lake et al. 2008). Indels are short DNA sequence polymorphisms that
correspond to either the addition or removal of a small number of nucleotide bases.
42
K. M. Noll
to that point, cataloged about 40 species of “bacteria,” and these methanogens were
the only representatives that showed such a divergence. Hori had examined the
sequences of 5S rRNA from many bacteria a year before, but methanogens were not
among those he examined and so he did not observe any deep divergences among
the bacteria he examined (Hori 1976). Woese was fortunate in this respect in having
the laboratory of Ralph Wolfe nearby in his department. Woese had little experience
in growing microbes, and his lab was not set up to cultivate any exotic organisms. It
was only because one of Wolfe’s graduate students, William E. Balch, was interested
in working with Woese that methanogens were among the organisms that he
examined, yet another example of the sometimes serendipitous nature of scientific
discoveries.
Shortly thereafter, George Fox and Woese included two more methanogens in
their analysis, along with yeast, duckweed, and human 18S rRNAs, to show that life
was comprised of three major lineages, or urkingdoms (primary kingdoms), that they
named eubacteria (true bacteria), archaebacteria (suggesting an ancient form of life,
perhaps predating bacteria), and urkaryotes (ancestor of modern eukaryotes) (Woese
1977). This finding upended the commonly held notion that prokaryotes were a
monophylogenetic unit. However, even those, like Stanier, who had thought seriously about it were aware that this notion might not be true.
Later extremely halophilic and thermoacidophilic microbes were found to be
archaebacteria, too (Woese et al. 1978; Magrum et al. 1978). As more sequences
were analyzed, it was found that the archaebacterial lineage was comprised of two
major subdivisions, the thermoacidophiles and a group including the halophiles and
methanogens (Fox et al. 1980). The relationship among the three urkingdoms was
not clear until the sequences of duplicated genes were compared and the root of the
small subunit rRNA tree was found to lie between the bacteria and the combined
archaebacteria and eukaryote lineages (Gogarten et al. 1989; Iwabe et al. 1989). The
two lineages within the archaebacteria were later named the Crenarchaeota
(suggesting the ancestral type of archaebacteria) and Euryarchaeota (denoting their
broad spectrum of ecotypes), respectively (Woese et al. 1990). The three
urkingdoms were now called domains (a taxon above kingdom) and renamed
Eucarya (now Eukarya), Bacteria, and Archaea.
Woese’s work appeared to have finally provided a “natural” classification for not
only microbes but all life. Ribosomal RNA trees have been used as the basis for a
universal tree of life (Maddison et al. 2007; http://tolweb.org/tree/). The tree has
allowed investigators to begin examining the evolution of metabolic and genetic
processes, using it as the basic framework on which to place evolutionary events.
Elucidation of a more solid phylogeny certainly brought the study of microbial
evolution back to being a respectable science.
The validity of the rRNA phylogeny was questioned from the start. Not including
objections to the tree based largely on earlier notions of evolutionary history (Woese
1994; Woese and Goldenfeld 2009; Sapp 2005), the phylogeny was not congruent
with those based on RNA polymerase sequences (Klenk et al. 1993) nor indel
analyses (Lake et al. 2008). Indels are short DNA sequence polymorphisms that
correspond to either the addition or removal of a small number of nucleotide bases.
42
K. M. Noll