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Prokaryotic diversity

We’re covered in germs: Lets design for that. http://www.ted.com/talks/jessica_green_good_germs_make_healthy_buildings.html

Learning outcomes Be able to compare and contrast archaea, bacteria and eukarya Explain the evolutionary relationships between these three domains of life and the most recent evidence for it. Identify the major divisions of bacteria and archaea and describe the broad characteristics of each Explain why we cannot do this for every division Determine which traits (if any) can be used reliably to determine the relationships between microorganisms

How we use evolutionary relationships to discover the diversity of life And why we don’t even know about most of it

Early work on prokaryotic diversity Describe Isolate Study

Great plate-count anomaly

Molecular methods for diversity

How and why we infer relationships among species

We can do the same analysis with DNA Each nucleotide is a ‘character’. ATTCCGCTACTCCTTGAGA ATTACGCTACTCCATGAGA

Phylogenetic analysis process

From Alignment to Tree Pairwise Distance (Divergence) Matrix (1) (2) (3) (4) 7 10 17 (1, 2) (3) (4) 10 17 ((1, 2), 3) (4) 17

Understanding A tree TIP BRANCH NODE (1) (2) (3) (4)

Understanding A tree (1) (2) (3) (4) (1) (2) (3) (4) Time Time (1) (2) (3) (4) Time (1) (2) (3) (4) Time (1) (2) (3) (4) http://guestblog.scientopia.org/wp-content/uploads/sites/35/2012/07/Fred2a.gif

Understanding A tree (1) A. Who is Species (1) most closely related to? B. Who is Species (3) most closely related to? C. Species (4) is more closely related to Species (3) than it is to Species (2). True/False? (2) (3) (4)

Understanding A tree (1) (2) (3) (4) Is this the same tree? (2) (1)

Understanding A tree (1) (2) (3) (4) Is this the same tree? How about this? (3) (1) (2) (4) (2) (1) (3) (4)

Which sequences should we look at in microbiology? Goal: To determine how a particular trait has evolved Goal: To determine evolutionary relationships between distantly related groups (i.e. bacteria domains vs archaea domains) Goal: To identify a bacteria or archaea that you just cultured

Archaea and eukarya are more closely related Comparing Phenotype Sequences Lokiarchaea

Archaea / eukarya / bacteria Cell wall Cell membrane Chromosome Gene organization Cell structures

Eukarya/archaea similarities Gene expression machinery: Sigma factors and transcription factors Organization of DNA within the cell

Competing hypotheses for euk/arch TA Williams, et al. Nature 504, 231-236 (2013) doi:10.1038/nature12779

Support for two domains Archaeal links in the origin of eukaryotes. TA Williams, et al. Nature 504, 231-236 (2013) doi:10.1038/nature12779

Lokiarchaeota: the missing link

Prok diversity Scavenger hunt Work in groups to answer the questions in your handouts. Use the discussion thread on canvas and the pictures displayed on the phylogenetic tree

regroup Based on what you found in the scavenger hunt, if you had to use one phenotype alone to determine the taxonomy of your isolate, what would you choose, if anything? Why? Going back to the TED talk, what do you think we can learn by characterizing environments at the phyla or division level? Lists of favorite traits – wacky and scary