TaxonomyThe modern science of taxonomy began in

the mid 18th cent.founded by Carolus Linnaeus

Taxonomy: Identifying, naming and classifying of organisms.

Systematics: Science dealing with the relationship of organisms to one another.

Phylogeny: The evolutionary history of an organism and its relationship to other species.

Phylogenetic tree

Cladistics Phylogenetic tree is constructed using traits

that have been inherited from a common ancestor.

Organisms related by descent are called a clade.Derived characters: Jaws

LungsAmniotic membraneHairNo tailBipedal

Phylogenetic Tree from Cladistics Sequence of branching implies order that new traits evolved Most likely hypothesis based on existing evidence

Traditional TaxonomyDomain (Super kingdom)KingdomPhylumClassOrderFamilyGenusSpecies

Kings Play Chess On Fat Guys Stomachs

Binomial SystemLinnaeus proposed a two name Latin system

for classification.Genus: A group of very similar organisms

related by common descent from a recent ancestor and sharing similar physical traits.

Species: A specific kind of organism in a genus. A group within a genus that share the same set of structural traits and can successfully interbreed with one another.

Genus and species are italicized with genus capitalized.

Canis familiaris

Domain: EukaryotaKingdom: AnimaliaPhylum:ChordataClass: MammaliaOrder: CarnivoraFamily: CanidaeGenus: CanisSpecies: familiarisCommon name: Dog

Pandinus imperator

Classifying organisms:Linnaeus: 2 kingdom- Plantae and Animalia

Whittaker: 5 kingdom- Monera, Protista, Fungi, Plantae and Animalia

Woese: 6 kingdom- Bacteria, Archaea, Protista, Fungi, Plantae and Animalia

Woese (1996): 3 domain- Bacteria, Archaea and Eukarya

Chapter 16

Organismal DomainsProkaryotes Eukaryotes1-5 um in size10X’s more biomassWider range of

environmentsGreater diversitySingle, circular

chromosomeBest known as bacteria

Disease causing agents are pathogens

Can live without the other

10-100 um in sizeMembrane bound

nucleus and organellesDNA arranged on

multiple chromosomesCan’t live without

prokaryotes

Prokaryotic ShapeCocci

Spherical and occur in chains or clusters

E.g. streptococcus and staphylococci

BacilliRod shaped and occur

singularly, in pairs, or chains

E.g. soil organismsVarious shapes

Vibrios resemble commasSpirilla are short, rigid

helical shapesSpirochetes are longer,

more flexible

Prokaryote External StructureCell wall

Bacteria can be gram (+) or gram (-) (+) simple walls with thicker peptidoglycan (sugar

polymer) (-) more complex walls with less peptidoglycan

Lipids and carbs too that make them more threatening, toxic, and resistant to antibiotics

CapsuleSticky polysaccharides or proteins to adhere to

substratesPili

Hairlike appendages for adhesion

Prokaryote Structure

Prokaryotic StructureMotility

Flagella Naked protein structure w/o microtubules that moves in a

propeller-like motionReproduction and adaptation

Divide by binary fission Speed varies from hours to minutes Limited by nutrients, competition, predation, and waste build up

Internal OrganizationSmall genetic rings that aid in resistance called plasmidsSmaller ribosomesWide range of methods to obtain nutrients

Prokaryotic NourishmentBiofilms

Surface coating colonies of prokaryotes

Can be 1 or more species

E.g. dental plaque, UTI’s, or sewer treatment

ArchaeaLive where other organisms can’t surviveExtreme halophiles

Salt environmentsE.g Great Salt Lake, Dead Sea, or sewater evaporating

pondsExtreme thermophiles

Very hot waterE.g ocean vents, or acidic conditions

MethanogensAnaerobic environments with methane as a waste

productE.g. swamps and GI tracts of animals

Bacterial Types9 groups

Proteobacteria Gram negative

Gram positiveChlamydiasSpirochetesCyanobacteria

ProteobacteriaAlpha (α)

Live in root nodules to fix atmospheric nitrogenForeign DNA carriers into crop plant genomes

Gamma (γ)PhotosyntheticInhabit animal intestines

E.g Salmonella, Vibrio cholerae, and Escheria coliDelta (δ)

Slime secreting myxobacteriaCan form fruiting bodies for selves when food is

scarceAttacks other bacteria

ActinomycetesGram Positive BacteriaForm colonies of branched chains of cells or are

solitaryFound in the soil

Streptomycin cultured by pharmaceutical companies,

Bacillus anthracis Form endospores, cell within a cell that dehydrates and

lies dormant till more favorable conditions existStaphylococcus and streptococcusMycoplasmas

Lack cell walls Tiniest of all known cells

Other Bacterial PhylaChlamydias

Live inside eukaryotesCommon cause of blindness (developing

countries) and most common STD (United States)Spirochetes

Spiral through environments by rotating internal filaments

E.g Treponema pallidum (syphilis) and Borrelia burgdorferi (Lyme disease)

CyanobacteriaOxygen-generating photosynthesis (only bacteria)Food for freshwater and marine ecosystems

Bacterial PoisonsExotoxins are proteins secreted by bacteria

Can exist in the bacteria Clostridium tetani produces muscle spasms (lockjaw) Staphylococcus aureus common on skin and in nasal passages

Produces several types causing varying problemsAcquired from genetic transfer between species

E. coli benign resident of intestines Acquires genes that produce harmful effects

Endotoxins are components of gram (-) outer membranesReleased when cell dies or digested by defensive cellCause same general symptoms

Neisseria meningitidis (bacterial meningitis) and Salmonella (typhoid fever)

Disease ControlImprovements in sanitation

Water treatment and sewer systemsAntibiotic development

Increase in bacterial resistanceEducation

Importance of seeking treatmentPrevention

Biological weapons

Biological WeaponsInhalation anthrax (Bacillus anthracis)

Manufacture endospores to disperse into air Once in lungs they multiply and produce exotoxins

Antibiotics kill the bacteria but can’t eradicate from body

Pnemonic plague (Y. pestis)Airborne as lung tissue is coughed up

Botulinum exotoxin (C. botulinum)Deadliest poison on earthBlocks transmission of nerve signals for muscle

contractionLimited availability of antitoxin

BioremediationUse of organisms to remove pollutantsProkaryotic decomposers major force in sewage

treatmentSolid sludge from filters added to anaerobe

colonies Transformed into use for fertilizer or landfill

Liquid waste over biofilms remove organic material Released into bodies of water

Oil spill and mining site clean up

ProtistsStructure

Membrane bound nucleus with chromosomesOther organelles characteristic of eukaryotesFlagella and cilia in a 9+2 microtubule arrangementUnicellular (most)

Most found anywhere there’s waterSeveral arose from secondary endosymbiosis

Symbiosis is a close association between 2 or more species

Endosymbiont is a species that lives within another species

DiplomonadsHeterotrophicPossibly most ancient lineageNo DNA or electron transport chainAnaerobicE.g Giardia intestinalis

Parasite which derives nutrition from living hosts that are injured by it

Waterbourne parasite often ingested from fecal contaminated water

Parabasalids

HeterotrophicSome energy anaerobicallyE.g Trichomonas vaginalisTravels through reproductive tract

Males and females can be affected, but male symptoms less common

Metronidazole only treatment currentlyResistance is increasing

EuglenozoansCrystalline rod inside the flagellaCan be heterotrophs, photoautotrophs, and

pathogenic parasitesE.g Trypanosoma

Causes sleeping sicknessSpread by African tsetse fly

E.g EuglenaCommon in pond water

AlveolatesMembrane-enclosed sacs below the plasma

membraneStabilize cell surface or regulate and ion content

DinoflagellatesMarine and fresh phytoplanktonRed tide blooms, toxins kill fish and can affect humans

Ciliates2 types of nuclei, 1 for daily activities and 1 for

reproduction E.g Paramecium or Stentor

ApicomplexansParasites of animals

E.g Plasmodium which causes malaria

AmoebozoansMove and feed by lobe shaped

pseudopodia, temporaryextensions of the cell

Parasitic amoebasCause dysentery

Slime moldsOrganisms found in moist, decaying matterSpread under favorable conditions, form spore

producing structures under less favorable ones Plasmodium, single multinucleated mass of cytoplasm Cellular slime molds, solitary until food is scarce

Foraminiferans and RadiolariansMove and feed by thread like psuedopodiaForams

Marine and fresh water organismsHave porous shells of CaCO3 called tests

Psudopodia extend through

RadiolariansMarineInternal shell of silica and outer test

StramenopilesMultiple ‘hairy’ flagella and a single ‘smooth’

flagellumWater molds

Decompose dead plants and animalsCan be parasitic (Ireland potato famine)

DiatomsGlassy cell wall of silicaFresh and marine organisms

Brown algaeAutotrophicCommonly called seaweed