BIOL 1010 Introduction
to Biology: The
Evolution and Diversity
of Life. Spring 2011
Sections A & B
Steve Thompson: [email protected]
http://www.bioinfo4u.net
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Monday, February 14, 2011
They're everywhere, including
the most extreme places!
Archaea inhabit all environments on earth, but
not only that, some of these places are downright
totally inhospitable. So, even though we’ve
looked at this a bit before, we’re going to survey
just what these places are really like — from
open ocean, to stinking cesspools; from salt flats,
to boiling vats of acid; from Antarctic ice floes,
to the hottest places on earth — all are nice,
cozy homes to different types of Archaea.
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Monday, February 14, 2011
The journal articles just keep coming . . . some
examples from August and September 2009 alone!
A nested PCR approach for improved recovery
of archaeal 16S rRNA gene fragments from
freshwater samples
Elisabeth W. Vissers 1 , Paul L.E. Bodelier 1 , Gerard Muyzer 1,2 &
Hendrikus J. Laanbroek 1,3
A glimpse under the rim – the
composition of microbial biofilm
communities in domestic toilets
M. Egert, I. Schmidt, K. Bussey and R. Breves
Microbial diversity and community structure of a highly active
anaerobic methane-oxidizing sulfate-reducing enrichment
G. Christian Jagersma, 1 Roel J. W. Meulepas, 2 Ineke Heikamp-de Jong, 1 Jarno Gieteling, 2 Adam
Klimiuk, 3 Stefan Schouten, 3 Jaap S. Sinninghe Damsté, 3 Piet N. L. Lens 2 and Alfons J. M. Stams 1 *
Archaeal rRNA diversity
and methane production
in deep boreal peat
Anuliina Putkinen 1 , Heli Juottonen 1 ,
Sari Juutinen 2 , Eeva-Stiina Tuittila 2 ,
Hannu Fritze 3 & Kim Yrjälä 1
Archaea in the Gulf of Aqaba
Danny Ionescu 1,2 , Sigrid Penno 1,6 , Maya Haimovich 1 ,
Branko Rihtman 1 , Aram Goodwin 3 , Daniel Schwartz 4 ,
Lena Hazanov 5,6 , Mark Chernihovsky 1,6 , Anton F. Post
1,6 & Aharon Oren 1
Linking phylogenetic and functional diversity to nutrient
spiraling in microbial mats from Lower Kane Cave (USA)
Annette Summers Engel1, Daniela B Meisinger2, Megan L Porter3, Robert A Payn4,
Michael Schmid5, Libby A Stern6, K H Schleifer2 and Natuschka M Lee2
Prevalence and molecular diversity of Archaea in subgingival pockets of periodontitis patients
C. L. Li 1 , D. L. Liu 1 , Y. T. Jiang 2 , Y. B. Zhou 1 , M. Z. Zhang 2 , W. Jiang 2 , B. Liu 2 , J. P. Liang 2
Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin
Erwan G. Roussel, 1* †‡ Anne-Laure Sauvadet, 1‡ Carine Chaduteau, 2 Yves Fouquet, 2 Jean-Luc Charlou, 2 Daniel Prieur 1 and Marie-Anne Cambon Bonavita 1
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Monday, February 14, 2011
It’s become a ‘cottage industry,’
but the ‘classics’ remain.
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Monday, February 14, 2011
And a great overview by Norm
Pace (Carl Woese’s colleague).
Science 2 May 1997: Vol. 276. no. 5313, pp. 734 - 740
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Monday, February 14, 2011
Here’s a nicely done, but silent, slide show of some
of these critters and some of those places.
http://www.youtube.com/watch?v=ix3-n2o1GHo
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Monday, February 14, 2011
And another over view of just the
sort of critters we’re talking about.
http://www.mindbites.com/lesson/4256-biology-the-archaea or
an excerpt at http://www.youtube.com/watch?v=lidGsTUyFSk
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Monday, February 14, 2011
OK, let’s look at some of these environments. Let’s start with
the open ocean, not inhospitable, but totally unexplored.
Here’s what Craig Venter did there: http://fora.t v/2008/02/25/
Joining_3_5_Billion_Years_of_Microbial_Invention#Craig_Venter_
on_the_Sorcerer_II_Expedition
What an amazing time! Wish I could have been on his trip.
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Monday, February 14, 2011
And they quickly colonize soil.
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Monday, February 14, 2011
And nasty, stinky places?
Just one stinky example from ruminants (also in termites):
http://www.youtube.com/watch?v=IrpKD5L626c
But they live in most oxygen poor temperate environments
like swamps, marshes, dumps, and sewage treatment facilities
— everywhere “swamp gas,” i.e. methane is produced!
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Monday, February 14, 2011
And not just methane, ammonia too.
Chris Francis collects
surface sediments at
Elkhorn Slough, a
small estuary that
drains into Monterey
Bay. The samples will
be analyzed in his lab
to determine the
diversity and
activity of ammoniaoxidizing Archaea.
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Monday, February 14, 2011
Here’s a really acidic place
they like in a mine tailing.
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Monday, February 14, 2011
The halophiles of the group like it
really salty.
Salt pools, where the salt concentration can be greater than
1.5 M, would seem to be highly inhospitable environments
for life. Yet certain halophilic Archaea, such as Haloferax
mediterranei, possess biochemical adaptations that enable
them to thrive under these harsh conditions.
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Monday, February 14, 2011
A lot of them like it really hot!
Thermophilic
Archaea can
thrive in habitats
as harsh as a
volcanic vent.
Here, Archaea
form an orange
mat surrounded by
yellow sulfurous
deposits.
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Monday, February 14, 2011
And what about really, really hot, hot springs?
http://science.discovery.com/videos/100-greatest-discoveriesshorts-yellowstones-undergro.html and
http://news.nationalgeographic.com/news/2007/05/070524yellowstone-video.html We’ll check this one out.
Amazing Archaeal diversity!
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Monday, February 14, 2011
Hydrothermal vents are the
‘glamour child’ of this field.
Respectively so, since many
evolutionary biologists suspect that
they mimic the conditions of the very
first life forming conditions on earth!
We NEED to study them, and they are
REALLY, REALLY cool (but not cold at
all).
Just what the heck are they?
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Monday, February 14, 2011
Here’s what hydrothermal vents
are, from WHOI.
http://www.youtube.com/watch?v=rFHtVRKoaUM
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Monday, February 14, 2011
Here’s Bill Nye’s, perspective
on “100 Greatest . . .”
http://science.discovery.com/videos/100-greatest-discoveries-shortshydrothermal-vents.html 18
Monday, February 14, 2011
And the opposite — the
coldest places on earth.
Journal of Bacteriology, December 2004,
8508-8515, Vol. 186, No. 24
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Monday, February 14, 2011
Here’s a recent review:
Nature Reviews Microbiology 4, 331-343 (May 2006)
“Cold-adapted Archaea” by Ricardo Cavicchioli1
Many Archaea are extremophiles. They thrive at high
temperatures, at high pressure and in concentrated acidic
environments. Nevertheless, the largest proportion and
greatest diversity of archaea exist in cold environments.
Most of the Earth's biosphere is cold, and archaea represent
a significant fraction of the biomass. Although
psychrophilic Archaea have long been the neglected
majority, the study of these microorganisms is beginning
to come of age. This review casts a spotlight on the
ecology, adaptation biology and unique science that is being
realized from studies on cold-adapted archaea.
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Monday, February 14, 2011
OK, now let’s talk about the
exam over Section I.
As I mentioned previously, we don’t have
time in class to hand them all back here, so
after class, and any time you can find me in
my office, I’ll give you your Scantron sheet
and the question/answer sheet.
Remember, the final is comprehensive, and
worth 40% of your grade, so I suggest you
take reviewing what you got wrong very
seriously! The final is built directly off the
old exams.
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Monday, February 14, 2011
Here are the distributions; first 1010A.
This is actually quite
encouraging!
Mean: 68.6%
High: 93.0%
Low: 32.0%
Especially, for
your first exam.
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Monday, February 14, 2011
And even better (at least for B’s) in 1010B:
Mean: 66.0%
High: 92.0%
Low: 24.0%
With a
bimodal
distribution.
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Monday, February 14, 2011
And most everybody did poorly on these concepts.
In the statistical analysis of experimental results:
A. More variation in the data means that the results are more likely due to the
manipulation of the variable
B. Less variation in the data means that the results are more likely due to the
manipulation of the variable
C. The smaller the data sample size, the more robust the analysis will be
D. Statistics provide absolute confidence of outcome
___________ describes the geologic history of the earth as erratic, accentuated
by periods of huge changes.
A. Punctuated equilibrium
B. Uniformitarianism
C. Catastrophism
D. Gradualism
The relationship bet ween sickle cell disease and malaria is an example of
A. Balancing selection (balanced polymorphism)
B. Stabilizing (purifying) negative selection
C. Disruptive (diversifying) positive selection
D. Directional positive selection
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Monday, February 14, 2011
Which of the following statements is not true regarding the Wright-Fisher
population model?
A. It is another null model
B. It requires a population to be changing in size over time
C. Permutations from the model can be used determine parameters such as
migration rates
D. It models the effects of genetic drift on the time it takes a population to
coalesce to a single lineage
Which of the following phenomenon cannot result in the biodiversity seen in largescale adaptive radiations?
A. The catastrophic die-off of most members of an ecosystem leaving lots of
empty niches (bottleneck event)
B. The introduction of a few individuals to a new, isolated, diverse environment
(founder effect)
C. Extensive, repeated migrations in and out of an environment
D. Strong natural selection forces acting on novel adaptations
In the overall tree of life, by far the most genetic and metabolic diversity, and
largest number of species are:
A. In the Plantae and Anamalia kingdoms
B. In the Bacteria and Archaea domains
C. In the Eukarya domain
D. In the Insecta class
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Monday, February 14, 2011
Bird, pterosaur, and bat wings are not this; all are ______________ to insect wings.
A. Parsimonious
B. Homologous
C. Analogous
D. Vestigial
Which of the following statements is true regarding ‘primordial soup’ prebiotic,
origin of life, simulations?
A. Experimental conditions usually require the absence of radiation, methane,
ammonia, and water
B. Results have included the production of amino acids and nucleotides
C. Experimental conditions usually require the presence of oxygen
D. Results have included the production of a living cell
Which of the following statements is not true regarding the endosymbiotic theory?
A. Some ancient cell engulfed other ancient cells, which became Eukaryotic
mitochondria and chloroplasts
B. Chloroplasts have their own DNA very similar to photosynthetic [Cyano]
bacterial DNA
C. Mitochondria have their own DNA very similar to aerobic [Proteo]bacterial
DNA
D. Bacteria have mitochondria and chloroplasts from an endosymbiotic event
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Monday, February 14, 2011
The biggest mass extinction on Earth ended the Permian about 250 million years
ago; what were the results?
A. More than 99% of all life on Earth went extinct
B. Lots of empty niches resulted in the adaptive radiation of the mammals
C. Lots of empty niches resulted in the adaptive radiation of the dinosaurs
D. Lots of empty niches allowed for the evolution of the ancestors of both
dinosaurs and mammals
The evolution of Ardipithecus ramidus‘s unique locomotory mode and canine
dentition, may relate to:
A. Migration
B. Genetic drift
C. Sexual selection
D. Convergent evolution
What did you fill in on the left /top end of the computerized answer sheet?
A. Nothing!
B. The wrong VSU student ID!
C. Only the printed number, no bubbles!
D. My VSU student ID, printed and bubbled in
Most, not all, of you got this, but several of you did not do it!
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Monday, February 14, 2011
Next time . . .
We explore the other
domain of non-nucleated,
unicellular organisms more
fully — the Bacteria.
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Monday, February 14, 2011