Prokaryotes, , Reconstructing the , of living things

Endosymbiosis • Systematists study evolutionary relationships Ch 28 & 29 •Look for shared derived (=different from ancestor) traits to group • Evidence used: morphology, 26 February 2009 development, and molecular data (especially DNA sequences) ECOL 182R UofA K. E. Bonine 1 2

Why can’t we figure it out perfectly? • More distant history is obscured by

more changes trypanosomes • Among oldest lineages of and in particular, lots of “lateral transfer.” Makes it difficult to infer relationships from phylogeny of red blood cells single .

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Early Diversity of Bacteria & Archaea

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1 What are microbes? can be divided into 3 domains • Only a minority make us sick •Robert Koch, Germ Theory of Disease • In ordinary English, might be anything small 3.8bya –bacteria 1.5bya –yeast –protists – •Prokaryotes = bacteria + archaea • In science, classify by evolutionary • Prokaryote was ancestral and only form for relationships… 7 billions of years 8

Eukarya Scheme has been revised before:

Haeckel (1894) Whittaker (1959) Woese (1977) Woese (1990) Three kingdoms Five kingdoms Six kingdoms Three domains

Eubacteria Bacteria (prokaryotes) Protista Archaebacteria Archaea

Protista Protista Fungi Fungi Plantae Eukarya are Prokaryotes monophyletic, Plantae Plantae Animalia Animalia Animalia paraphyleticparaphyletic, polyphyletic? 9 modified from Wikipedia 10

Shared by all 3 domains Unique to Prokaryotes • Circular • Glycolysis (use to get ATP) • Genes organized into • Semiconservative DNA replication: (2 strands •NO in double helix, during replication each – nucleus: of mRNA into daughter gets one strand from parent, begins before transcription of DNA into other is new) mRNA is complete • DNA encodes polypeptides – • Polypeptides produced by transcription and – translation according to genetic code – [Genes can still get moved around in •Plasma membranes and other ways, both within and between . The latter is . Antibiotic 11 resistance can spread in this way.] 12

2 Divide by (26-02) Prokaryotes are everywhere

• All around us and in us, too: • Way more bacteria + archaea on your skin & in your intestinal tract than “you” cells – WE ARE 28 •> 3x10 in (vs. visible stars in ) • Some survive extreme heat, alkalinity, enteritidis saltiness 360x real speed: • Bottom of the sea replicate in 30 min. • Rocks more than 2km into ’s solid crust http://life8eiml.sinauer.com/Videos/Video-26-02.mpg

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What do they look like? Predominantly unicellular • Many prokaryotes (and some other microbes) lay down a gel-like substance on a surface.This matrix traps others, forming a . • Biofilms can make bacteria difficult to kill. spheres curved/spiral may form a film that rods is impermeable to antibiotics, for example. /cocci / • Dental plaque is a biofilm may be found singly or in 2D/3D chains/plates/blocks ≠ multicellular: each cell is viable independently 15 16

Most common bacterial motion is via Bioluminescence flagella • Some bacteria make light Fibril of flagellin • Useful for getting into a new fish gut! protein, plus a hook and basal body

Rotates about its base

Different from eukaryotic , 17 which beats 18

3 differences seen by Gram stain Exploiting unique bacterial features

•Peptidoglycancell walls unique to bacteria: not found in or Gram-positive bacteria: dense cell wall archaea •Many antibiotics disrupt cell-wall synthesis • This affects only bacteria, and has little or no effect on eukaryotic cells

Gram-negative bacteria: thin peptidoglycan layer, behind outer membrane 19 20

Morphology gives only limited view of Bioremediation? bacterial diversity Hydrogen Production?

Huge diversity in metabolic pathways -Clean up oil spills, toxins – oxygen tolerance -Produce chemicals we find useful – source – carbon source Enrichment Cultures – nitrogen and sulfur grow microbes under variable conditions and see which thrive 21 22

6 nutritional categories (energy, carbon) 6 nutritional categories (energy, carbon) 1. Photoautotrophs 5. Chemoorganoautotrophs

energy from light, carbon from CO2 energy from other organisms, carbon from CO2 2. Photoheterotrophs energy from light, C from other organisms 6. Chemoorganoheterotrophs 3. Chemolithotrophs energy and carbon from other organisms energy from oxidizing inorganic substances – most known prokaryotes, all , fungi,

carbon from CO2 many protists some bacteria, many archaea 4. Chemolithotrophic 3 ways to get energy x 2 ways to get carbon energy from oxidizing inorganic substances = 6 nutritional (metabolic) categories carbon from other organisms 23 24

4 Prokaryotic Metabolic Variety Evolution of Photosynthesis Carbon in 6 Metabolic Categories Energy Source Source

Photoautotrophs light CO2 Photoheterotrophs light other organisms

Chemolithotrophs oxidizing inorganic substances CO2 Chemolithotrophic heterotrophs oxidizing inorganic substances other organisms

Chemoorganoautotrophs other organisms CO2 Chemoorganoheterotrophs other organisms other organisms

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Figure 27.11 Cyanobacteria (Part 2) OXYGEN None in atmosphere for first 2.3 billion years

Cyanobacteria evolved photosynthesis (oxygenic): (ATP + water + oxygen)

Aerobic more efficient than anaerobic 27 28


• Early earth had little free oxygen

(O2) • 2.5 bya prokaryotes evolved ability to + - split 2H2O -> 4H +O2 +4e

• Electrons used to reduce CO2 and make organic compounds.

Stealing electrons capturing light energy producing high energy compounds •O2 was a waste product.

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5 Figure 8.13 The Calvin-Benson Cycle

= Base of Global Then make glucose (and other sugars) … 31 32

Oxygen-generating cyanobacteria form rocklike structures called Oxygen

• Oxygen was poison when it first appeared

• Organisms evolved not just to tolerate oxygen, but to thrive

• Aerobic metabolism faster and more efficient

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Increasing oxygen in atmosphere

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6 Aerobic vs anaerobic metabolism Nitrogen and sulfur metabolism 1. Oxygen is toxic to obligate anaerobes Some bacteria use oxidized inorganic ions, 2. Facultative anaerobes can shift such as nitrate, nitrite or sulfate between anaerobic metabolism (such –Denitrifiers as fermentation) and the aerobic mode –Nitrogen fixers (). –Nitrifiers 3. Aerotolerant anaerobes don’t use – Sulfur-based metabolism oxygen, but aren’t damaged by it 4. Obligate aerobes cannot survive without oxygen 37 38

Prokaryotes are important in can’t use elemental element cycling nitrogen (N2) • Plants depend on prokaryotic nitrogen-fixers • Denitrifiers prevent accumulation of toxic levels of nitrogen in lakes and

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Nitrogen fixers

•Convert atmospheric N2 gas into ammonia by means of the following reaction:

N2 + 6 H  2 NH3 • All organisms require fixed nitrogen

(not N2) for their , nucleic acids, and other nitrogen-containing We use sugars as electron donor and compounds oxygen as electron acceptor when making • Only archaea and bacteria, including energy (=Cellular Respiration) some cyanobacteria, can fix nitrogen Prokaryotes Variable! 41 42

7 Sulfur-based metabolism Archaea stave off global warming

• 10 trillion tons of methane lying deep under the ocean floor Some photoautotrophic bacteria and •Archaeaat the bottom of the seas chemolithotrophic archaea use H2S as an metabolize this methane as it rises electron donor instead of H2O • Otherwise global warming would be extreme

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Prokaryotes live on and in A very few bacteria are other organisms •Endotoxins • Mitochondria and are – e.g. Salmonella and Escherichia descendents of free-living bacteria – released when bacteria die or lyse (burst) • Plants and bacteria form cooperative – from the outer membrane nitrogen-fixing nodules on roots of Gram-negative bacteria – usually cause fever, vomiting, diarrhea • Ruminants depend on prokaryotes to digest cellulose • – e.g. tetanus, botulism, cholera, plague, anthrax • Humans use vitamins produced by our intestinal bacteria – released by living, multiplying bacteria – can be highly toxic, even fatal without fever 45 46

Diversity of prokaryotes Diversity of prokaryotes

• We will discuss 6 of bacteria and 2 of archaea •More are known • More still are uncharacterized: can be 2 6 hard to culture in lab •PCRallows sequencing of unculturable organisms • Phylogeny based primarily on DNA

47 sequence: other traits can evolve rapidly 48

8 1. 2. Cyanobacteria -“purple bacteria” - ancestor of • “blue-green” bacteria mitochondria • photoautotrophs -Some fix • transformed Earth with O nitrogen 2 (Rhizobium) • many fix nitrogen - E. coli • ancestor of chloroplasts - Some cycle nitrogen and sulfur

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3. Spirochetes Spirochetes

•Gram-negative •motile • chemoheterotrophic • some are human parasites •cause syphilis and Lyme disease

51 Axial filaments produce corkscrew-like motion52

4. Chlamydias 5.

•extremely small: 0.2-1.5 µm diameter •mostly Gram-positive •Gram-negative cocci • some produce dormant to • can only live as parasites wait out bad e.g heat, cold, drought •cause – replicate DNA and encapsulate one copy in a tough cell wall – sexually transmitted disease – eye infections (especially trachoma) – parent cell breaks down, releasing – some forms pneumonia – some endospores can be reactivated after more than a thousand years of dormancy

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9 Firmicutes Staphylococcus is a firmicute


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Mycoplasmas are firmicutes 6. often w/ branching filaments

- no cell walls tuberculosis is an - smallest actinomycete known cellular Most of our organisms antibiotics come - very little from actinomycetes e.g. Streptomyces DNA

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1. Archaea •We don’t know much • None are human pathogens -Most are •Most live in extreme environments: thermophilic and temperature, salinity, oxygen acidophilic concentration, or pH - Sulfolobus live in •Have distinctive lipids in their membranes hot sulfur springs, • Look at 2 groups die of cold at 131°F – Crenarchaeota –

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10 2. Euryarchaeota Some Euryarchaeota are - very salty environments •Some are , producing CH 4 -most from CO 2 organisms “dry” to • Responsible for 80-90% atmospheric death methane, often from belching cows -contain pink carotenoids - live in •CH4 is potent greenhouse gas commercial evaporating 61 ponds 62