Marine Sampling Sites
So we've chosen three sites altogether in which to check for previously
undiscovered microbes. Two of the sites are local: Bolinas
Lagoon by Stinson Beach and the Berkeley Aquatic Park. We chose these two sites because the sediment had low oxygen levels.
Freshwater Sampling
Another site we've investigated is from a
freshwater lake in Bloomington, Indiana. We chose a freshwater site
in addition to the marine sites because they tend to have different
types of protists than marine environments.
So what have we found? Well, lots of types of protists. I've got
plenty of trees, which I'll spare you, but below are some of the
types of organisms we've found. I suppose if we were on their scale,
they truly would be Creatures from the Black Lagoon. These are some
examples of perhaps the most interesting eukaryotic microbes we've
found, especially in the context of the evolution of
eukaryotes.
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Outside the "Crown"
Many of the protists we've found are not closely related to any known
group of protists. The "crown" refers to the most recent "big bang"
in eukaryote evolution — where it seems a lot of groups of organisms
evolved quickly, including our animal ancestors. Several of the new
environmental sequences are deep in the tree, suggesting that they
might have retained some characteristics of the ancestral eukaryotes.
We think we've found about eight new kingdoms of eukaryotes in just
three environments by just hunting for their DNA. Not bad for a
teaspoon of stinky mud. These pictures are of Giardia (top left),
Trichomonas (top middle), a slime mold (bottom left), Euglena (bottom
middle) and several amitochondriate amoebae (top and bottom
right).
New Kingdoms of Eukaryotes
Here's a comparison of trees with and
without the new groups of eukaryotes. You'll note both the placement
of the new branches (the mode or pattern of evolution) and the
length of the branches (the rate or tempo of evolution).
Models and Sampling Bias
I think it's obvious that we need to
reconsider our knowledge of extant eukaryotic microbes, those
unseen and ungrown, living today all around us. Adding the few we've
discovered into the tree, it really changes the picture of evolution.
And in coming years, the picture will likely change a lot more.
What's more, we can use our knowledge of the rRNA sequence as a tag
to help identify them if we try to grow them — which would be
worthwhile.
Conclusions
In understanding the history of life on
Earth, it is first important to understand our own misconceptions.
So, I've spoken about our own biases and misconceptions in evolution,
life without oxygen, unicellular eukaryotes as opposed to plants and
animals, and how to know organisms without first having to grow
them, and lastly how to find new eukaryotic kingdoms in your own
backyard...
So, it's off to find new microbes — where should we look next?
Boiling Hot Springs!
We're thinking that eukaryotes might have adapted to other extreme
environments other than those without oxygen. Maybe somewhere like
this hot spring in Yellowstone National Park pictured at the left.
Aside from being anoxic, the early Earth was also much warmer than
today. The current idea is that Bacteria and Archaea arose during
these hotter times. Why not eukaryotes?
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