I. A Brief History of the Classification of Microbes
First...the players
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Aristotle
Let's start in ancient Greece with Aristotle — in addition to many other
contributions to science, he was the first to articulate a dichotomy
of life, classifying all life as being either plants or animals. This
ancient world view of biology persists today, and misinforms our
perspective in terms of evolution, not to mention the structuring of
scientific research (like botany departments and zoology
departments). It was a few thousand years later that the microscope was
invented, and animal/vegetable/or mineral types of classification
were hardly enough to classifiy the new microorganisms, first
called "animacules." Microbes are often non-descript rods, or
spheres. How then does one classify microbes, particularly when they
don't really look different from one another like plants look
different from animals? More about how to do that later, but on to
more history.
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Carolus Linnaeus
Linnaeus lived in the 18th Century and created the familiar hierarchical
classification scheme of life: kingdom, family, class, order,
family, genus and species. Again, this classification scheme is based on
how organisms looked — essentially their phenotype. Although this
heirarchy within the plant and animal kingdoms was an improvement —
an attempt to standardize classification whose legacy persists today —
there were still no good working definitions of "kingdoms" or
"species" which could apply to microorganisms when they were
discovered. Even today the conception of a species of bacteria is
hard to define, in the same way an animal species is
defined.
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Charles Darwin
We are all probably familiar with Charles Darwin, 19th century
father of natural selection and evolution, but he also called for a
framework or geneology of organisms in order to study evolution.
Darwin helped to develop the concept of a geneology of life with
branching lineages. But we attribute the conception of evolutionary
relationships among organisms with a tree — a geneology — to Ernst
Haeckel at roughly the same time.
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Ernst Haeckel
Ernst Haeckel also worked in the mid-19th century. Haeckel was
the first to coin the term "protist" or "Protista," although his
definition also included the bacteria.
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Haeckel's Tree of Life
Ernst Haeckel is attributed to be the first
to describe the evolutionary relationships among living organisms, a geneology of life, as analogous to a tree. Haeckel, interestingly,
described all living things as falling into not just two kingdoms
(plants and animals), but also a third kingdom for microorgansims — the Protista. There are several other interesting features of this
vision — for example, Haeckel postulated a common origin for all
life (plants, animals and microbes). This is still a common
assumption, but it makes sense with modern molecular evidence as well.
OK, let's fast forward a hundred years or so. How do we classify
microbes today, especially when they have no particular morphology or shape to speak of. Scientists had all but given up on
classifying microbes based on their evolutionary relationships (a
phylogeny) until Carl Woese.
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The Woesian Revolution
Woese based his classification on molecules,
not how organisms look or act. This transition from classification
based on phenotype (taxonomy) to one based on genotype enabled him to
determine the evolutionary relationships (a phylogeny) among bacteria — something other researchers had all but given up on. Woese's work was founded on the principle suggested in 1965 that "molecules are
documents of evolutionary history." Basically, DNA can be thought of
as molecular fossils. At the University of Illinios in the late 1970s, Woese wanted to
determine evolutionary relationships among microorganisms, and in
the process, he and colleagues discovered a huge split in the
"prokaryotes" — as big a genetic difference as that between prokaryotes
and eukaryotes. Woese orignally thought that these were primitive
organisms and so called them the Archaea. Later studies showed that
the Archaea were actually more related to the eukaryotes in many
aspects that to the bacteria. So, rather than five kingdoms of life,
Woese argued for three domains (Eucarya, Archaea, and Bacteria). This
conception of three domains of life and two domains of prokaryotes, rather
than the standard prokaryote/eukaryote dichotomy, really shook up the
study of the evolution of life. So how did Woese arise at this
remarkable conclusion? First he needed a molecule to study from all
organisms — ribosomal RNA (rRNA).
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Why use rRNA?
Ribosomal RNA (rRNA) is an RNA component of
the ribosome, the cellular machine which translates the DNA genetic
code to amino acids, and subsequently, proteins. The rRNA genes are
ubiquitous in all life, being conserved enough to identify, yet
containing enough variabilty to determine evolutionary relationships.
But Woese has had a hard time selling this idea, mostly because
everyone has been trained to view life as prokaryotes/eukaryotes,
plants/animals, or the updated version of that &emdash; the five kingdom
view.
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Five Kingdoms or Three Domains?
In the 1960s, Whittaker added one kingdom (fungi) to Aristotles's
view of life (plants and animals) but still relegated all microbes to
either the Protista (eukaryotic microbes) or the Monera (bacteria).
Something from this figure (and view) should be obvious. Why should
we emphasize macroscopic life over microscopic life? In terms of life
on Earth, we still live in an age of microbes. For the majority of
geologic time, some 3-4 billion years, life has evolved — and at least three
billion has been solely microbial.
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The five-kingdom view is still taught, as
I'm sure many of you know. Carl Woese started a revolution in the
classification of life, much like Copernicus did with his idea that the
Sun doesn't revolve around the Earth. We, as humans, possess a
lot of unique characteristics such as the ability to understand
the world we live in. But we are not the pinnacle of evolution — nothing is. Evolution is about change through time, not about
ranking life based on some criterion. Besides, since the bulk of
genetic diversity of life on Earth is been microbial (note where we
are in Woese's tree), shouldn't they get attention simply for that
reason? If you take nothing else from my talk, stop thinking about
biology in terms of five kingdoms.
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Since Woese's early trees, we've added a lot of sequences as you can see
in the figure to the left. I'd like to switch now from talking about
microbes in general, to specfically eukaryotic microbes (that is,
microbial cells which possess a membrane-bound nucleus and tend to be
unicellular). What's the current picture of eukaryotic
phylogeny?
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The Evolution of the Eukaryotes
As in the prokaryotic world, one can see
from this schematic tree of the eukaryotes (below), that the majority of
eukaryotic life is, in fact, microbial (protists). There is far more
phenotypic and genotypic diversity in all the protist groups combined
than within the plant, animal or fungal kingdoms. How many kingdoms
of eukaryotes are there? This is still largely unknown. If we use the genetic measure, we come up with roughly 70 eukaryotic kingdoms, only some of which are shown here. Further, because of our
bias toward macroscopic life, most of the biology of these protists
is largely unknown. How did the eukaryotes evolve? To understand
that, we need to visualize the early Earth.
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