Structural elements of ribosomes were used to argue that the crenarchaea are most
closely related to eukarya and so constitute a kingdom, to be called the Eocyta,
separate from the euryarchaeotes (Lake et al. 1984). None of these alternative trees
has been as well supported by subsequent research as the original three-domain tree
of Archaea, Bacteria, and Eukarya.
Ironically, the suggestion by Ambler of interspecies gene transfer in 1979 came to
be accepted, if not for the particular instance cited in that work. When complete
genome sequences of bacteria and archaea became available, evidence of horizontal
or lateral gene transfer was obvious. There had been evidence for this prior to
genome sequencing, but it was largely found in scattered publications about single
genes. Certainly horizontal acquisition was known from studies of gene transfer
processes like conjugation, transduction, and natural DNA uptake, but the evolutionary impact of those processes was not revealed by those studies. Widespread
DNA sharing among distant relatives complicated simple depictions of evolutionary
history as phylogenetic trees. Other depictions were proposed that attempted to
incorporate gene sharing, and these include the New Rings of Life (Lake and
Sinsheimer 2013) and the coral of life (Fournier et al. 2009). The ability to even
make phylogenetic trees is frequently called into question given the impact of gene
sharing (Doolittle and Brunet 2016). Darwin’s hope that “. . .ramifying branches
may well represent the classification of all extinct and living species in groups
subordinate to groups” (Darwin 1959) may ultimately prove fruitless in the case of
microbes. Complicating the effort further, recent discoveries of new organisms
through metagenomic sequencing have revealed new, uncultivated lineages including members of the Archaea that contain genes that make them even more closely
related to those of Eukarya. Consequently, the three-domain view of life may change
to a two-domain view (Doolittle 2020) as Dayhoff’s final studies had suggested
earlier.
2.9 Laboratory Evolution Studies Directly Test Darwinian
Principles
On the Origin of Species was published at the very birth of microbiology as a
discipline. Pasteur was demonstrating that bacteria were the agents of ferments
and not chemical processes. He was also showing that microorganisms did not
spontaneously generate in broths and infusions. He showed the importance of
microbes in the fermentation industries which led the way to the organization of
institutes, companies, and, eventually, academic departments formed to support
these industries. Those applied efforts did not directly utilize Darwin’s insights.
Nor did work directed to the medical and public health aspects of microbiology,
though Darwin was familiar with Koch’s work. It was left to those interested in
microorganisms as living organisms to seek evidence of Darwinian attributes
manifested in the microbial world.
2 Darwin’s Science’s Impact on the Evolution of the Microbiological Sciences
43
closely related to eukarya and so constitute a kingdom, to be called the Eocyta,
separate from the euryarchaeotes (Lake et al. 1984). None of these alternative trees
has been as well supported by subsequent research as the original three-domain tree
of Archaea, Bacteria, and Eukarya.
Ironically, the suggestion by Ambler of interspecies gene transfer in 1979 came to
be accepted, if not for the particular instance cited in that work. When complete
genome sequences of bacteria and archaea became available, evidence of horizontal
or lateral gene transfer was obvious. There had been evidence for this prior to
genome sequencing, but it was largely found in scattered publications about single
genes. Certainly horizontal acquisition was known from studies of gene transfer
processes like conjugation, transduction, and natural DNA uptake, but the evolutionary impact of those processes was not revealed by those studies. Widespread
DNA sharing among distant relatives complicated simple depictions of evolutionary
history as phylogenetic trees. Other depictions were proposed that attempted to
incorporate gene sharing, and these include the New Rings of Life (Lake and
Sinsheimer 2013) and the coral of life (Fournier et al. 2009). The ability to even
make phylogenetic trees is frequently called into question given the impact of gene
sharing (Doolittle and Brunet 2016). Darwin’s hope that “. . .ramifying branches
may well represent the classification of all extinct and living species in groups
subordinate to groups” (Darwin 1959) may ultimately prove fruitless in the case of
microbes. Complicating the effort further, recent discoveries of new organisms
through metagenomic sequencing have revealed new, uncultivated lineages including members of the Archaea that contain genes that make them even more closely
related to those of Eukarya. Consequently, the three-domain view of life may change
to a two-domain view (Doolittle 2020) as Dayhoff’s final studies had suggested
earlier.
2.9 Laboratory Evolution Studies Directly Test Darwinian
Principles
On the Origin of Species was published at the very birth of microbiology as a
discipline. Pasteur was demonstrating that bacteria were the agents of ferments
and not chemical processes. He was also showing that microorganisms did not
spontaneously generate in broths and infusions. He showed the importance of
microbes in the fermentation industries which led the way to the organization of
institutes, companies, and, eventually, academic departments formed to support
these industries. Those applied efforts did not directly utilize Darwin’s insights.
Nor did work directed to the medical and public health aspects of microbiology,
though Darwin was familiar with Koch’s work. It was left to those interested in
microorganisms as living organisms to seek evidence of Darwinian attributes
manifested in the microbial world.
2 Darwin’s Science’s Impact on the Evolution of the Microbiological Sciences
43