Transcript All eucaryotes are - University of Colorado Boulder

Into the Natural Microbial World
Norman Pace
MCD Biology
University of Colorado, Boulder
[email protected]
Dedicated to Carl Woese
Outline
•
The molecular Tree of Life - new perspective on
microbial diversity.
•
From phylotype to phenotype: A Yellowstone example.
•
Expansion of the Big Tree: A mapping project.
•
We need to heed what the Tree says about biological
organization -- our textbooks (mostly) get it wrong!
Haeckel, 1866
Making Sense of Sequences:
Molecular Phylogeny
1. Align sequences so that “homologous” residues
are juxtaposed.
2. Count the number of differences between pairs of
sequences; this is some measure of “evolutionary
distance” that separates the organisms.
3. Calculate the “tree”, the relatedness map, that most
accurately represents all the pairwise differences.
Carl Woese
Photo by Jason Lindsey,
U. Ill. Alumni Magazine
You are here -->
Some Lessons from the Big Tree:
- Three main relatedness groups, Eucarya,
Bacteria, Archaea.
- Origin is on the bacterial line of descent:
Eucarya and Archaea are related to the
exclusion of Bacteria.
- Chloroplasts and mitochondria are of
bacterial origin.
- The eucaryal nuclear line is as old as the
archaeal line; the procaryote-eucaryote
model for biological organization was wrong!
- Sequences are identifiers of
organisms - you don’t need to culture
to identify!!
Who’s in here?
What are they doing for a living?
From phylotype to phenotype A Yellowstone story
Carrine Blank
Phil Hugenholtz
Sample Analysis:
Sample --> DNA --> PCR --> RFLP --> Sequence
Anna-Louise
Reysenbach
Universal Libraries Composite
Alpha-Proteobacteria
2%
Bacteria; Novel
Delta-Proteobacteria
Group
Archaea
2%
5%
2%
Thermodesulfobacter
ia
2%
Thermotogales; EM3
2%
Thermus /
Deinococcus
5%
Aquificales:
Hydrogenobaculum
1%
Aquificales:
Hydrogenothermus
2%
Aquificales;
Hydrogenobacter
77%
John Spear
We do need cultures -But not mindless cultivation:
If you want to do microbial ecology by culture,
you have to do what microbiologists have always avoided
------
• Before you start, determine what you are trying to culture.
• Note that most biomass out there is autotrophic.
• Study mixed cultures - much microbial life is syntrophic.
• Minimize O2 - Most microbial diversity (probably) is suboxic.
Guerrero Negro halite-gypsum-life
Photo by John Spear
John Spear
Jeff Walker
We are embedded in a microbial world !
Dan Frank
Kirk Harris
Time for Change: a public
service message
Time for Change: a public
service message
The fundamental issues in any scientific discipline:
ORDER - Organization and relationships
e.g. the periodic table for chemists
e.g. phylogenetic relationships for biologists
CHANGE - How things evolve
e.g. the Hertsprung-Russell star series
e.g. biochemical mechanisms
e.g. the Tree of Life
The public service message:
A Big Lesson from the Big Tree The “Procaryote/Eucaryote” Concept:
Procaryote --> Eucaryote
is an incorrect model for large-scale
biological organization and evolution.
Haeckel, 1866
“Procaryote” means
“non-eucaryote,” nothing more.
Not being something
not a scientifically
is
valid concept or name.
Procaryote/Eucaryote: The Model
(Chatton, 1937)
1. All eucaryotes are “of a kind,” specifically
related to one another.
2. All procaryotes are “of a kind,” related to one
another to the exclusion of eucaryotes.
3. There are two forms of cellular organization
and function.
4. Procaryotes (Haeckel’s “monera”) are simpler than eucaryotes.
5. Procaryotes gave rise to (more advanced) eucaryotes.
Procaryote/Eucaryote: The Test
1. All eucaryotes are “of a kind,” specifically
related to one another.
True
Procaryote/Eucaryote: The Test
1. All eucaryotes are “of a kind,” specifically
related to one another.
True
2. All procaryotes are “of a kind,” related to
the exclusion of eucaryotes.
False
Procaryote/Eucaryote: The Test
1. All eucaryotes are “of a kind,” specifically
related to one another.
True
2. All procaryotes are “of a kind,” related to
the exclusion of eucaryotes.
False
3. There are two forms of cellular organization.and function.
?
Procaryote/Eucaryote: The Test
1. All eucaryotes are “of a kind,” specifically
related to one another.
True
2. All procaryotes are “of a kind,” related to
the exclusion of eucaryotes.
False
3. There are two forms of cellular organization.and function.
?
4. Procaryotes (Haeckel’s “monera”) are simpler than eucaryotes.
NA
Procaryote/Eucaryote: The Test
1. All eucaryotes are “of a kind,” specifically
related to one another.
True
2. All procaryotes are “of a kind,” related to
the exclusion of eucaryotes.
False
3. There are two forms of cellular organization.and function.
?
4. Procaryotes (Haeckel’s “monera”) are simpler than eucaryotes.
5. Procaryotes gave rise to (more advanced) eucaryotes.
False
NA
What does it matter if we call them “procaryotes?”
“Procaryote” is scientifically unjustified, invented and
accepted to fill a gap in knowledge.
The name has false implication in deep evolutionary
matters.
The false understanding of “procaryote” quenches
legitimate inquiry.
It teaches our students false concepts at the most
fundamental level: Order in Biology.
What else to call them??
If you mean “the little stuff out there,”
try “microbes/microbial” There’s a bunch of
little/weird (to us) eucaryotes out there, too!
If you are talking functional or evolutionary
issues, you need to be more precise than
“procaryote.”
To students the concept is in the language;
thus, in the language is the understanding.
Thanks! to :
Carl Woese
David Stahl
David Lane
Gary Olsen
Bernadette Pace
Mitchell Sogin
Steve Giovannoni
Kate Field
Tom Schmidt
Elizabeth Raff
Rudy Raff
Michael Ghiselin
Sean Turner
Ed DeLong
Dan Distel
Tineke Burger-Wiersma
Gene Wickham
Peter Eden
Jim Brown
Annick Wilmotte
(Micrograph: a hypersaline microbial mat
Photo by Ruth Ley)
Art Harrison
Anna-Louise
Reysenbach
Lori Giver
Esther Angert
Sue Barns
Matt Jeffries
Phil Hugenholtz
Brett Goebel
Austin Brooks
Marissa Ehringer
Karen Hershberger
Scott Dawson
Diana Northup
Chris Pitulle
Mike Tanner
Jose de la Torre
Mike Dojka
Eric Lyons
George Spiegelman
Kirk Harris
Dan Frank
John Spear
Hazel Barton
Scott Kelley
Alicia Berger
Jeffrey Walker
Carrine Blank
Ruth Ley
Lars Angenent
Ulrike Theisen
Alli St. Amand
Mary Ann DeGroote
Tina Salmassi
Josh Wilcox
Dominic Papineau
Andrew Dalby
Chuck Robertson
Laura Baumgartner
Leah Feazel
Kimberly Ross
Piret Koll
Mari Rodriguez
Thanks to NIH, NSF, DOE, ONR, NASA
for $upport over the years