Classifying Life: Old Scheme

emphasized difference between prokaryotes (bacteria) and eukaryotes (cells with nuclei)

all eukaryotes that weren’t plants, fungi or animals got lumped into the catch-all group “protists”

KingdomMonera(all prokaryotes)

KingdomProtista

Kingdom Kingdom KingdomFungi Plantae Animalia

Whittaker’s “5 Kingdom” system

the Tree of Life has 3 domains

This classification scheme emphasizes differences between 3 main groups, based on their phylogeny –

BACTERIA ARCHAEA EUKARYA

Archaea - also called “extreme-ophiles,” lovers of extreme conditions

- have chemically distinct plasma membranes

- have ribosomes similar to ours

Bacteria- oldest fossils (3.4 billion yr) = bacteria

- live in more O2 -rich, “normal” environments

- cell walls contain a unique material, peptidoglycan

- include many disease-causing pathogens

2 domains of prokaryotes

Bacteria on the head of a pin

Campbell & Reece 2002

Prokaryote Characteristics

Small cells, typically 1-5 m

- more bacteria live in your gut than the # of cells in your whole body

.

protein

see page 567 in text for a full comparison of the 3 domains of life

Prokaryote Characteristics

No organelles inside cell, no nucleus; move with tail-like flagellum

Circular chromosome with fewer genes than eukaryotes (3,200 genes in E. coli, versus ~35,000 in humans)

Small circles of DNA termed plasmids, encoding antibiotic resistance

Cell

Prokaryote ReproductionAsexual reproduction makes 2 exact copies (clones) of original cell

- bacteria can divide every 20 min to 3 hr

Genetic diversity is promoted by several mechanisms:

a) trading plasmids among cells (temporary)

b) exchanging portions of the chromosome during conjugation, when DNA is sent down a hollowtube (pilus) connecting 2 cells

followed by recombination, the permanent movement of genesonto a new chromosome

sex pilus

They are highly abundant in number, and live everywhere

- half of all carbon and 90% of nitrogen + phosphorus found in life is contained in prokaryotes

They have amazingly diverse metabolisms

- bacteria catalyze chemical transformations that affect our atmosphere and global carbon and nitrogen cycles, which in turn affect all life

-

Some bacteria are pathogens that can make people sick

Why care about prokaryotes?

Understanding MetabolismLife is all about getting energy in some form from your environment, and transforming it into another form your cells can use

In chemical systems, energy is stored in bonds between hydrogen and other elements (holding hydrogens means you’re reduced)

Energy can be released by getting H and its electrons off, handing them to some acceptor like oxygen (O2) which is electron-hungry - donor loses its electrons gets oxidized

2 H2O 4 H· + O2 2 H2O light

electron donor,gets oxidized light energy gets

stored in ATP by cellular enzymes

Understanding Metabolism

Photosynthesis:

CO2 + H2O CH2O + O2

ripping H’s and theirelectrons away from oxygenis super hard; requires energy from light

light

[1] CO2 is reduced to sugar, which has energy stored in it for later

[2] the gas CO2 has been fixed, meaning converted to a larger solid molecule (out of thin air!) used for building cell walls

[3] the gas O2 is released as a waste product

Understanding Metabolism

Respiration:

CO2 + H2O CH2O + O2

ripping H’s and their electrons away from carbon just requires oxygen –and the right cellular machinery to achieve a controlled burn !

[1] sugar is oxidized to release its stored energy

[2] the gas CO2 is released into the atmosphere

Metabolic diversity - Prokaryotes

Carbon source (building blocks)

Autotrophy Heterotrophyfix CO2 -C-C-C- eat things for -C-C-C-

light + H2O

organicmolecules(sugar)

reducedinorganicmolecules(CH4,H2S

Energysource

cyanobacteria

BeggiatoaNitrosomonas

Clostridium E. coli

Heliobacter

Metabolic diversity - Eukaryotes

Carbon source (building blocks)

Autotrophy Heterotrophyfix CO2 -C-C-C- eat things for -C-C-C-

light + H2O

organicmolecules(sugar)

reducedinorganicmolecules(CH4,H2S

Energysource

protists, plants(photosynthesis)

protists, animals, fungi(respiration)

Chemo- versus photo-autotrophy

Cyanobacteria CO2 + H2O CH2O + O2

Sulfur bacteria CO2 + H2S CH2O + S2

general formula for sugar

light

Photo-autotrophy:

Light is used to “pump up” low energy electrons from water or hydrogen sulfide, rip them off, then jam them onto carbon

Chemo- versus photo-autotrophy

Cyanobacteria CO2 + H2O CH2O + O2

Sulfur bacteria CO2 + H2S CH2O + S2

light

Chemo-autotrophy:

Requires reduced inorganic compounds, which are normally absent in oxygen-rich environments (why?...)

Electrons in the H-S bond require less energy to remove

Produces a different waste product

Global nutrient cyclesBecause bacterial metabolisms are so diverse, almost any compound can act as fuel or food for some prokaryote

- accounts for their ecological diversity....

One species’ waste product can be the (a) energy source, or (b) electron acceptor, for another species

[1] Critical for cycling nutrients through different molecular forms

Denitrificationby bacteria +archaea

Nitrificationby bacteria

Decompositionby bacteria,archaea, fungi

Nitrificationby bacteria

Fixation by bacteria + archaea

Microbial EcosystemsOne species’ waste product can be the (a) energy source, or (b) electron acceptor, for another species

[2] “food chain” of species can co-exist by not competing for same resources (i.e., not using the same molecule as food)

Different photo-autotrophs even catch different wavelengths of light so they are not in competition

Important principle of ecology: species in direct competition cannot co-exist for long, because one will out-compete the other

Microbial EcosystemsTo think about when setting up your Winogradsky columns in lab:

- What compounds are fuel (electron donors) and which ones act as electron acceptors, becoming waste products?

- How do multiple bacterial species co-exist? What resources does each use?

Genetically, closer to eukaryotes than Domain Bacteria is

“Extremophiles” live in environments that are inhospitable to most life

May yield clues to early life on earth, or life on other planets (?)

Halophiles – common in extremely salty environments (e.g deserts, hot springs)

Thermophiles – Occur in very hot environments (some >100ºC) (e.g. hot springs, undersea vents)

Anaerobes – occur in environments lacking oxygen (e.g. methanogens in the termite hindgut, cow gut)

Domain Archaea

Thermophiles color the surface of this Nevada desert hot spring

Campbell & Reece 2005

Pyrococcus furiosus, source of polymerase used in PCR

Halophiles color the water of salt evaporation ponds in San Francisco Bay

Campbell & Reece 2005

Anaerobes – live in anaerobic (= anoxic, lacking oxygen) environments (cow gut, termite hindgut)

4 H2 + CO2 CH4 + 2 H2Omethane

oxidizedcarbon

reducedcarbon

some Archaea can use oddchemicals like hydrogen gasas fuel

electrons are transferred to oxygen, releasing energy

produces methane, a potentgreenhouse gas

in the ’90s, we discovered that tiny Archaea are very abundant throughout the world’s oceans (100,000 cells per mL of seawater)

Comprised a third of the bacterio-plankton in the Antarctic

- constitute a huge fraction of the biomass in the cold, deep waters of world’s oceans

- many cannot be grown in the lab, and are known only from environmental DNA sequences

Not so extreme?..

DeLong et al., 1994, High abundance of Archaea in Antarctic marine picoplankton. Nature 371:695-7

Prokaryote Phylogeny

last commonancestor of allmembers of Domain Bacteria

All proteobacteria are related to each other (they all shared one common ancestor)

Most bacterial phylogenies (= family trees) are based on comparing the DNA base sequence of a ribosomal RNA gene called 16S

-

Tend to grow in aerobic (oxygen-containing), less extreme environments

Cells surrounded by a cell wall made of material called peptidoglycan, a mixture of peptides (short chains of amino acids) and sugars all cross-linked together to make strong sheets

Have structurally distinct ribosomes, complexes of protein and RNA that carry out protein synthesis in the cell

Have special enzymes to deal with copying the DNA of their circular chromosomes

Domain Bacteria

Antibiotic TargetsAntibiotics target these differences between our eukaryotic cells, and the prokaryotic cells of pathogenic bacteria, to block...

(1) Cell wall biosynthesis – penicillin, vancomycin - block synthesis of peptidoglycan cell wall, without which cells pop when saltiness of surrounding fluid changes

(2) Protein synthesis – erythromycin, tetracycline, streptomycin - jam the bacterial ribosome

(3) DNA replication – Cipro - inhibit enzyme that uncoils DNA after replication of the circular bacterial chromosome

-

Cells stained with purple dye, washed, then stained with red dye

- the peptidoglycan wall traps the purple dye in Gram-positives

- the outer membrane repels the purple dye, but gets stained red

cellwall

plasma membrane plasma membrane

cellwall

Gram-positive Gram-negative- outer membrane covers peptidoglycan wall

- no membrane covering peptidoglycan wall

Bacterial cell wall composition

cellwall

plasma membrane plasma membrane

cellwall

Gram-positive Gram-negative- outer membrane covers peptidoglycan wall

- no membrane covering peptidoglycan wall

Actinobacteria - many chain-forming soil bacteria

- soil bacterium Streptomyces is source of 500 antibiotics

- a few pathogens: tuberculosis, leprosy

Firmicutes - many dangerous pathogens, some of which form resting spores

Bacillus anthracis (anthrax) Clostridium botulinum (botulism) Staphylococcus sp. (staph) Streptococcus sp. (strep)

Two Gram-positive groups

Antibiotic Resistance APPEARANCE

DRUG INTRODUCTION OF RESISTANCE

Penicillin 1943 1946

Streptomycin 1945 1959

Tetracycline 1948 1953

Erythromycin 1952 1988

Vancomycin 1956 1988

Methicillin 1960 1961

Ampicillin 1961 1973

Cephalosporins 1964 late 1960’s

Antibiotic ResistanceAntibiotics were introduced as therapeutic agents against bacterial disease starting in 1943

- Major classes of antibiotics attained widespread use by 1960’s

Infectious bacteria still a major health concern, especially in hospitals

- Post-operation infections by Staphylococcus aureus remain a critical problem for surgery patients

In 1952, most Staph infections succumbed to penicillin

- By late 1960’s, Staph was resistant; next treated with methicillin

- By 1980’s, methicillin-resistance was widespread

- In 1990’s, vancomycin became “drug of last resort”

- vancomycin resistance is common in bacteria other than Staph…

and resistant Staph reported in late 90’s

Ecology of drug resistance

Most antibiotics are natural products isolated from other microbes

- Fungi (penicillins)

- Soil bacteria of genus Streptomyces (erythromycin, streptomycin, tetracycline, vancomycin)

Only 1 class of antibiotic is totally synthetic (Ciprofloxacin)

Antibiotics are an ancient weapon used in chemical warfare between microbes; resistance is a natural defense

Over-use of antibiotics = selection favoring resistant individuals - nukes their competition

- resistance genes accumulate on plasmids, get swapped by bacteria like baseball cards

Cyanobacteria

- photo-autotrophs responsible for our O2-rich atmosphere

- fill the surface waters of the oceans

CO2 + H2O CH2O + O2

Share an ancestor with chloroplastsNitrogen-fixers

N2 reduced organic gas nitrogen compounds

Filamentous: form chains of cells

Alpha proteobacteria Includes Rhizobium which colonizes plant roots and fixes N2 which helps plants to grow

Share an ancestor with mitochondria of eukaryotes!

Beta proteobacteriaIncludes Nitrosomas; aids nitrogen cycling in soil

Ammonium nitrite NH4

+ NO2-

Proteobacteria

Gamma proteobacteriaSalmonella spp. (food poisoning)Vibrio cholerae (cholera)Escherichia coli (human intestinal fauna)

Include Chromatium spp., “sulfur bacteria”CO2 + 2H2S CH2O + H2O + 2S

Epsilon proteobacteriaMostly pathogenic

Campylobacter sp. (blood poisoning)

Helicobacter sp. (stomach ulcers)

yellow sulfur granules

Proteobacteria

Chlamydia

- Gram-negative pathogens- parasites that live only inside host cells- cause blindness, STD’s

Spirochaetes- free-living or pathogenic- swim by spiraling through fluid

Treponema pallidum (syphilis)

Borrelia burgdorferi (Lyme’s disease)