Into the Natural Microbial World Norman Pace MCD Biology University of Colorado, Boulder 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” 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

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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 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 --> DNA --> PCR --> RFLP --> Sequence Sample Analysis:

Anna-Louise Reysenbach

Universal Libraries Composite 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 O 2 - 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

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

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 scientifically 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. 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 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.

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