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” Kingdom Monera (all prokaryotes) Kingdom Protista Kingdom Kingdom Kingdom Fungi 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 O 2 -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 Reproduction Asexual 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 hollow tube (pilus) connecting 2 cells  followed by recombination, the permanent movement of genes onto a new chromosome sex pilus

They are highly abundant in number, and live everywhere - h alf 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 Metabolism Life 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 (O 2 ) which is electron-hungry - donor loses its electrons  gets oxidized 2 H 2 O 4 H · + O 2 2 H 2 O light electron donor, gets oxidized light energy gets stored in ATP by cellular enzymes

Understanding Metabolism Photosynthesis: CO 2 + H 2 O CH 2 O + O 2 ripping H’s and their electrons away from oxygen is super hard; requires energy from light light [1] CO 2 is reduced to sugar, which has energy stored in it for later [2] the gas CO 2 has been fixed, meaning converted to a larger solid molecule (out of thin air!) used for building cell walls [3] the gas O 2 is released as a waste product

Understanding Metabolism Respiration: CO 2 + H 2 O CH 2 O + O 2 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 CO 2 is released into the atmosphere

Metabolic diversity - Prokaryotes Carbon source (building blocks) AutotrophyHeterotrophy fix CO 2  -C-C-C-eat things for -C-C-C- light + H 2 O organic molecules (sugar) reduced inorganic molecules (CH 4,H 2 S Energy source cyanobacteria BeggiatoaNitrosomonas ClostridiumE. coli Heliobacter

Metabolic diversity - Eukaryotes Carbon source (building blocks) AutotrophyHeterotrophy fix CO 2  -C-C-C-eat things for -C-C-C- light + H 2 O organic molecules (sugar) reduced inorganic molecules (CH 4,H 2 S Energy source protists, plants (photosynthesis) protists, animals, fungi (respiration)

Chemo- versus photo-autotrophy Cyanobacteria CO 2 + H 2 O CH 2 O + O 2 Sulfur bacteria CO 2 + H 2 S CH 2 O + S 2 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 CO 2 + H 2 O CH 2 O + O 2 Sulfur bacteria CO 2 + H 2 S CH 2 O + S 2 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 cycles Because 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

Denitrification by bacteria + archaea Nitrification by bacteria Decomposition by bacteria, archaea, fungi Nitrification by bacteria Fixation by bacteria + archaea

Microbial Ecosystems One 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 Ecosystems To 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 H 2 + CO 2 CH H 2 O methane oxidized carbon reduced carbon some Archaea can use odd chemicals like hydrogen gas as fuel electrons are transferred to oxygen, releasing energy produces methane, a potent greenhouse 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 common ancestor of all members 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 Targets Antibiotics 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 cell wall plasma membrane cell wall Gram-positiveGram-negative - outer membrane covers peptidoglycan wall - no membrane covering peptidoglycan wall Bacterial cell wall composition

cell wall plasma membrane cell wall Gram-positiveGram-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 DRUGINTRODUCTIONOF RESISTANCE Penicillin Streptomycin Tetracycline Erythromycin Vancomycin Methicillin Ampicillin Cephalosporins1964late 1960’s

Antibiotic Resistance Antibiotics were introduced as therapeutic agents against bacterial disease starting in 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 O 2 -rich atmosphere - fill the surface waters of the oceans CO 2 + H 2 O  CH 2 O + O 2 Share an ancestor with chloroplasts Nitrogen-fixers N 2  reduced organic gas nitrogen compounds Filamentous: f orm chains of cells

Alpha proteobacteria Includes Rhizobium which colonizes plant roots and fixes N 2 which helps plants to grow Share an ancestor with mitochondria of eukaryotes! Beta proteobacteria Includes Nitrosomas; aids nitrogen cycling in soil Ammonium  nitrite NH 4 + NO 2 - Proteobacteria

Gamma proteobacteria Salmonella spp. (food poisoning) Vibrio cholerae (cholera) Escherichia coli (human intestinal fauna) Include Chromatium spp., “sulfur bacteria” CO 2 + 2H 2 S  CH 2 O + H 2 O + 2S Epsilon proteobacteria Mostly 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)