BIOL 305 — Lab Notes

Taxonomy and Keying

10–100mil species on earth today
classification of humans
- Domain – Eukarya
  - Organisms with a nucleus in each cell enclosing the genetic material, as well as additional membrane-bound organelles, including mitochondria; cells averaging about 100 micrometers in diameter. May be unicellular, filamentous, colonial, or multicellular.
- Kingdom - Animalia
  - Multicellular organisms requiring complex organic substances for food; food usually ingested.
- Phylum - Chordata
  - Animals with notochord, dorsal hollow nerve chord, pharyngeal “gill” pouches in pharynx (similar to the throat area in human embryos) at some stage of life cycle.
- Class - Mammalia
  - Young nourished by milk glands, skin with hair, body cavity divided by a muscular diaphragm, red blood cells without nuclei, three ear bones, high body temperature.
- Order - Primates
  - Tree dwellers or their descendants, usually with fingers and flat nails, sense of smell reduced.
- Family - Hominidae
  - Flat face, eyes forward, color vision, upright, bipedal locomotion.
- Genus - Homo
  - Large brain, speech, long childhood
- Species - Homo sapiens
  - Prominent chin, high forehead, sparse body hair.
Dichotomous keys:
- couplets: series of choices for two alternatives
- must be appropriately matched to area or taxon
- making keys:
  - examine similarities/differences in characteristics
  - must be dichotomous, not trichotomous
  - don’t use vague statements; quantity and detail
  - make couplets refer to differences in the same characteristic
  - begin couplet choices with the same word
  - use obvious characteristics
  - use positive statements/include them

Nomenclature and Domains

Introduction:

It is important to understand that classification schemes reflect the views of those that constructed them, and that the answers about relationships continue to be uncovered. […] The point is that our system is not perfect, but becomes continually refined as we learn more about the living things and how they are related. A classification scheme allows us to find and frame the questions that we need to answer.

first attempt at nomenclature: 1700, Carl von Linne/Carolus Linnaeus
- hierarchal classification
- kingdom, family, species
systematics
phylogenetic relationships and dna sequencing
1950s: Robert Whittaker
- broad classification for all forms until 21st century
- Monera kingdom for prokaryotes
- Protista
late 20th: Carl Woese
- microbiological discovery of bacteria and archaea
- rRNA sequencing
- three domain system: Archaea, Bacteria, Eukarya
- phased out kingdom level
protists are a “group”

Three Domains

all life has cells bound by a cell membrane and filled with cytoplasm, DNA
- prokaryotes lack a nucleus, eukaryotes have one
- “true” nucleus

Bacteria

most ancient group of organisms; ancestral organism
- 4 billion years ago, likely living off of hydrogen in hot environments
- fossil evidence of cyanobacteria stromatolite colonies goes back 3.7 million years
- LUCA
  - 4.543 bya planet; fossils can be observed at 3.7mya in microbial mats on W. Greenland rocks
  - only took 400my for unicellular life to exist
  - 355 genes connected; likely a small unicellular organism with ring-shaped DNA
  - living on hydrogen in undersea vents; “warm little pond”
- bacterial symbionts
30 phyla known to be growable as lab cultures
Gram stains based on cell wall composition
- Gram-positive: stains purple, thick peptidoglycan cell wall
- Gram-negative: stains pink, thin peptidoglycan cell wall
- Acid-fast: stains pink, thin cell wall with a thick wax layer
- Cyanobacteria: gram-negative composition, but with a thick cell wall (gram-positive) and green chlorophyll
no cell membrane with a phospholipid bilayer
spores that can remain dormant for years
unicellular, prokaryotic, peptidoglycan
a small percentage of bacterial species are pathogenic
- Streptococcus pneumoniae: bacterial pneumonia, bronchitis, strep throat; high contagion
- Staphylococcus aureus: wound infections, impetigo skin infection
- Escherichia coli: opportunistic digestive infections if external
- Mycobacterium tuberculosis
various forms are autotrophic cyanobacteria
- photosynthetic
- heterocystic: heterocysts perform nitrogen fixation
- present and living for the first 2 million years; waste products created a partial oxygen atmosphere
all habitats/lives: soil, water, hot springs, frozen lakes, symbiosis on all levels including parasitism
- 100t bacterial cells in human host; 10 bacterial cells for each of body cells
small; 40 billion bacterial cells in a gram of soil
- biomass exceeds that of plants/animals on Earth
examples: gram-positive and gram-negative bacteria, cyanobacteria, ancestral mitochondria and chloroplasts
- Streptococcus lactis

Archaea

extremely tiny, uniceullar, prokaryotic organisms
no peptidoglycan or fatty acids
cell membrane contains Isoprene chains and a backwards glycerol
no spores
includes various that live in diverse, extreme environments:
- methanogenic: wetlands, rice fields, mammalian gut/mouth
  - outgassing
  - up to 25% global methane emissions
  - some can consume methane; found in deep-sea sediments
- halophilic: salt-loving, halide environments, extremophile; salt evaporation ponds in Bay Area
  - Halobacterium
- thermoacidophiles: heat and acid loving extremophile; boiling hot springs, hydrothermal vents
some may be in normal environments; soil, skin, symbiotic relationships with other cells
no pathogenic archaea

Eukarya

Protists

protozoa: animal-like unicellular organisms without a cell wall
- majority motile via flagella, cilia, pseudopodia (amoeboid)
- free-living in aquatic habitats and soil fauna, or parasitic (Plasmodium, malaria)
- grazers, decomposers, predators, parasites
- Paramecium
slime-molds: fungus-like
- amoeboid cells without cell walls
- free-living in soils; decomposers
- resemble molds with spore-producing structures (sporangia)
  - water mold filaments
- plasmodial slime molds begin as unicellular amoebae and fuse into plasmodium
  - reproductive structure of stalk with ball of spores
algae: plant-like, with chloroplasts/chlorophyll
- diverse: microscopic unicellular filamentous/colonial organisms and macroscopic seaweeds and kelps
- photosynthetic, aquatic, autotrophic organisms
- free-living
- Prototheca: does not photosynthesize; detritivores that feed on dead/decaying organic materials (infectious)
- dinoflagellates causing paralytic shellfish poisoning: produce neurotoxins
  - neurotoxins can concentrate in shellfish during red tides
- Euglena, Spirogyra

Fungi

multicellular except for yeasts
heterotrophic decomposers
- secrete enzymes that allow to feed on nutrients
cell walls are made from chitin
unicellular yeast and multicellular mycelia forms: threadlike structures
- fleshy fungi produce large reproductive structures in mycelial form: mushrooms, puffballs, earthstars, shelf fungi or conks, morels, and truffles
- molds: “microscopic” mycelial fungi with smaller spore-producing structures
Saccharomyces cerevisiae, Penicillium, Rhizopus

Plantae

autotrophic via chlorophyll/chloroplasts
mostly conduct/transport via vascular tissues
- not mosses and liverworts (external absorption)
- spore reproduction or seeds

Animalia

no cell walls or chloroplasts
heterotrophic
multicellular
some soft-bodied (cnidaria)
some have exoskeletons; most (chordates) have internal skeletons
“vinegar eels”: invertebrate roundworm (found in “scoby”)
hydra, insects

Plants

conifers — seeds are enveloped in cones — Coniferophyta
- vs. Anthophyta
spores: unicellular haploid like sperm/egg
- sorus is full of sporangium and indusium that produce spores
origin of plants: Paleozoic period
- 450mya
- early vascular tissue 400mya
- seeded soon after
- flowering plants 150-130mya; dinosaur age

Bryophytes

Bryophyta
- moss
- damp, shaded areas
- one-cell thick leaves
- branched or unbranched stems
- few cm tall
- absorb nutrients through leaves
- rhizoids at “root”; seta “stem” connecting gametophyte to sporophyte capsules
Hepatica
- liverworts
- flat, lobed leaves
- unicellular rhizoids in leaves
- no distinct stem
- less than 10cm long
- gemma cups with gemmae used in reproduction

Seedless Vascular Plants

Pterophyta
- ferns
- sori: reproductive sections
  - sporangia sacs
- rhizomes (horizontal stems)
- fronded leaves; undersides have sori
- pinnae and stipe pinnate leaves
Sphenophyta
- horsetails/horsetail brush/scouring brush
- underground creeping rhizomes
- jointed, hollow stems; vegetative and spore-producing
- embedded with tiny pieces of silica; sand and glass-like
- spores produce cones at the ends of horsetail stems
- leaves sheath nodes
Lycophyta + Psilophyta

Gymnosperms

conifers: pines (Pinus), larch (Larix), firs (Abies), hemlocks (Tsuga), false-hemlocks/Douglas firs (Pseudotsuga)
cycads: fern trees
- “Old World” areas
Ginkgo: G. biloba
Genetophytes: ephedra and welwitschia
- Mormon tea
- South Africa

Pinaceae

conifers
- most well-known
- pinecones
  - seeds develop in closed pines
  - bracks, spines, and wind wings; allows to bounce away from mother tree to find sperm
- male and female cones
  - female produce seeds: spiral, winged scales
  - male produce pollen
family of pines
- includes pines, cedars, spruces, and hemlocks
monoecious
woody, spiraled cones without stalks; cones point backwards
twisted, needle-like leaves in bundles or pinnate, compound

Cupressaceae

junipers, cypress, redwoods, cedars
- Sequoia sempervirens: tallest trees (379ft)
  - sempervirens → “always green”
- Sequoiadendron giganteum: largest trees (26ft/8M diameter)
- Pinus longaeva (Ancient Bristlecone Pine): oldest trees (5,066 yrs)
- Western Cypress, Incense Cedar, Junipers, and Arbor Vitae
- Dawn Redwood
redwoods formerly in Taxodiaceae family
mostly monoecious; some are dioecious
woody, leathery, or berry-like cones with tiny seeds
- 100,000 seeds = 1 pound
- “seed fruits”
needle and scale-like leaves
grow erect and low to ground (prostrate) or large, giant trees
evergreen scale-like/awl-shaped leaves or needle-like
globe-shaped woody/fleshy cones
redwood adaptations
- thick, fire-resistant bark
- insulation from soil allows for “stump sprout”
  - basal burl buds on soil line sprout new shoots
  - “rings” of redwood trees formed from central parent death

Taxaceae

yews and nutmegs
- Taxus brevifolia
  - southernmost limit of Calaveras
  - extract anti-cancer drug taxol from bark
- Torreya californica
mostly dioecious; some are monoecious
red, fruitlike droops/arils protect seeds
needle-like spiral pinnate whorled leaves

Ginkgoaceae

ornamental male plants; female produce seedless fruit
fan-shaped leaves with notches
fleshy seeds on ends of branches
gymnosperms but not conifers
terminal malodorous ovules
male reproductive parts resemble catkins in pine
single species in China; widely cultivated for oil, timber, and food

Ephedraceae

ephedra
- Ephedra viridis: “Mormon tea”
dioecious
needle-like, stem-like leaves; small and brown
branched shrubs and jointed twigs
green, photosynthetic stems
generally small structures

Angiosperms

one of the most diverse groups of plants on earth while also the newest plant group in evolution: 200 mya and dominating around 100mya
flowers depict type of pollination
- wind pollinators → small flowers with extruding organs
- animal pollinators → colorful/UV petals, produce nectar or odors
alternate anatomical names for the perianth section
- petal: corolla
- sepal: calyx
receptacle and peduncle (pedicel)
ovule inside the ovary; seeds
the ovary may be placed in the flower superior or inferior to the attachment sites of the petals and sepals (nodes)
- hypogynous: superior
- perigynous: semi-inferior
- epigynous: inferior
radial and bilateral symmetry
- regular, actinomorphic: radial
- irregular, zygomorphic: bilateral
  - defined as symmetrical along a medial cut that passes through the central axis
perfect flowers are bisexual; imperfect are unisexual
- as such, all monoecious plants are plants that only have one type of flower which is perfect, or both sexes of imperfect flowers; plants with only one set of imperfect flowers are dioecious and only have one or the other set of sexual organs
- monoecious: corn, squash, melons, pumpkins, Easter lily, pea, dandelions, roses, Cucurbita, begonias
- dioecious: strawberries, gourds, Bradford pears, date palms
petals may be separate or fused together on the receptacle

Fabaceae

pea family
- 3rd largest plant family in the world
- herbs, shrubs, vines, and trees
irregular eudicots with organs in 5’s
- bilaterally symmetric
- banner: the large, topmost petal
- wings: sets of 2, found on the sides
- keel: a petal fused from 2 petals found at the bottom, enclosing the stamen and pistil
alternate, compound leaves
monoecious, with distinct perfect flowers and fruits
- fruit is a legume or a dry pod
terminal leaflet is replaced by a tendril
examples: redbuds (Cercis sp.), lupines (Lupinus sp.), peanuts

Brassicaceae

mustard family
- herbs and small shrubs
- typically annuals or perennials
flowers are in the shape of an urn or a Maltese cross
eudicots with organs in 4’s
- 6 stamens: 2 are inferior to the remaining 4
perfect flowers with superior ovaries
- fruits are made from two-part capsules, ie mustard siliques
alternate, simple leaves
- sometimes fronded
examples: mustard (Brassica rapa), radish (Raphanus sativus), broccoli, brussel sprouts, cabbage, cauliflower, kale, sea rocket

Asteraceae

sunflower family
- herbs and small trees
- typically annuals or perennials
eudicots made of many small, radial flowers (composite)
- ray flowers: the larger “petals” with one flattened, fused corolla/ligule
- disk flowers: the central “head” with a round, tubular corolla and many smaller petals
- composite with many layers of bracts
specialized fruit known as an achene
inferior ovaries
alternate, simple leaves
examples: sunflowers, daisies, chrysanthemums, ragweeds, asters, thistles (artichokes), tidy tips (Layia fremontii)
- 21,000+ species
- largest family of eudicots worldwide
- largest family in California

Lamiaceae

mint family
- herbs and shrubs
eudicots with organs in 4 and 5’s
- 5 fused irregular petals
  - 2 up, 3 down
  - two-lipped
- 4 stamens
- 5 fused sepals
- 2-4 nutlets contained in mature seed capsule
bilaterally symmetric flowers
square stems
opposite leaves
strong, aromatic, mint odor from leaves and vegetative growth
examples: sage (Salvia sp.), rosemary, thyme, mint, Horehound, Self Heal

Poaceae

grass family
- large economic importance: produce supermarket grains
- thousands of sp.
monocots
- linear leaves
specialized wind-pollination flowers; spikelets with glume
single-seeded fruit; the seed is fused onto the fruit wall
examples: oat, barley, wheat, rye, rice, corn, needlegrass, saltgrass

Rosaceae

rose family
- herbs, shrubs, trees
eudicots with radially symmetric organs in 5’s
- separate flowers
- many stamens and many arrangements of pistil(s)
- all parts are joined on a short tube
fruits are achenes, pomes, drupes, rose hips
alternate, compound, toothed leaves with stipules
prickly stems
examples: roses (Rosa sp.), apples, Himalaya berry (Rubus armeniacus), cherries, strawberries, blackberries

Iridaceae

iris family
- greatest diversity found in South Africa
- notable CA plants: Douglas iris, blue-eyed grass
monocots with radially symmetric organs in 3’s
- 3 sepals, petals, and stamens
- petaloid petals
- colorful sepals
- anther and a stigma lip
fruits are capsules
inferior ovaries
basal, equitant leaves with leaf sheaths and folded-over leaves
examples: irises (Iris sp.), blue-eyed grass, gladiolus, freesia

Ericaceae

heath family
- trees, shrubs
- perennials
eudicots with bisexual, fused organs
- vase or urn-shaped flowers
- stamens are x2, with holes and slits on the anthers to release pollen
fruits are capsules, berries, or drupes
examples: blueberries, cranberries, azaleas/rhododendrons (Rhododendron sp.), manzanita (Arcostaphylos sp.), madrones (Arbutus sp.)