Into the Natural Microbial World

Norman PaceMCD Biology

University of Colorado, Bouldernrpace@colorado.edu

Dedicated to Carl Woese

• 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!

Outline

Haeckel, 1866

Making Sense of Sequences: Molecular Phylogeny

1. Align sequences so that “homologous” residuesare 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 WoesePhoto by Jason Lindsey,U. Ill. Alumni Magazine

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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 cultureto identify!!

Who’s in here?What are they doing for a living?

From phylotype to phenotype - A Yellowstone story

Carrine Blank

Phil Hugenholtz

Sample --> DNA --> PCR --> RFLP --> Sequence

Sample Analysis:

Anna-LouiseReysenbach

Universal Libraries Composite

Thermus / Deinococcus

5%

Thermodesulfobacteria

2%

Thermotogales; EM32%

Bacteria; Novel Group

5%

Delta-Proteobacteria2%

Alpha-Proteobacteria2%

Archaea2%

Aquificales: Hydrogenothermus

2%

Aquificales: Hydrogenobaculum

1%

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-lifePhoto 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 relationshipse.g. the periodic table for chemistse.g. phylogenetic relationships for biologists

CHANGE - How things evolvee.g. the Hertsprung-Russell star seriese.g. biochemical mechanismse.g. the Tree of Life

A Big Lesson from the Big Tree -

The “Procaryote/Eucaryote” Concept:

Procaryote --> Eucaryote

is an incorrect model for large-scale

biological organization and evolution.

The public service message:

Haeckel, 1866

“Procaryote” means“non-eucaryote,” nothing more.

Not being something is

not a scientificallyvalid 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 organizationand 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. NA

5. Procaryotes gave rise to (more advanced) eucaryotes.

False

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 evolutionaryissues, you need to be more precise than

“procaryote.”

To students the concept is in the language;

thus, in the language is the understanding.

Carl WoeseDavid StahlDavid LaneGary Olsen

Bernadette PaceMitchell Sogin

Steve GiovannoniKate Field

Tom SchmidtElizabeth Raff

Rudy RaffMichael Ghiselin

Sean TurnerEd DeLongDan Distel

Tineke Burger-Wiersma

Gene WickhamPeter EdenJim Brown

Annick Wilmotte

Art HarrisonAnna-Louise Reysenbach

Lori GiverEsther Angert

Sue BarnsMatt Jeffries

Phil HugenholtzBrett Goebel

Austin BrooksMarissa Ehringer

Karen HershbergerScott DawsonDiana NorthupChris PitulleMike Tanner

Jose de la TorreMike DojkaEric Lyons

George SpiegelmanKirk HarrisDan Frank

John SpearHazel BartonScott KelleyAlicia Berger

Jeffrey WalkerCarrine Blank

Ruth LeyLars AngenentUlrike TheisenAlli St. Amand

Mary Ann DeGroote

Tina SalmassiJosh Wilcox

Dominic PapineauAndrew Dalby

Chuck RobertsonLaura Baumgartner

Leah FeazelKimberly Ross

Piret KollMari Rodriguez

(Micrograph: a hypersaline microbial mat Thanks to NIH, NSF, DOE, ONR, NASA Photo by Ruth Ley) for $upport over the years

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