BIOL110

Evolution, biodiversity, systems, info flow, energy / matter transf., structure / function relationships

Apply process of science, communicate science, apply quantitative reasoning to bio questions, connect themes wiology @all org levels +tie in other fields

Microbial biodiversity and the role of orgs. in soil

personal experience

Obs / question > research > hypothesis > experiment > analysis > report conclusions

doesnt involve experiment, data already exists (ex. number of people w / autism)

Developed anthrax / rabies vaccines + pasteurisation

Came up w / Kochs postulates and found causative agent behind tuberculosis

4 postulates developed in the 19th century to establish a causative relationship between a microbe and a disease.The postulates require that 1) the microorganism must be found in all infected organisms, 2) it can be isolated and grown in pure culture, 3) the cultured microorganism causes the same disease when introduced to a healthy organism, and 4) the microorganism can be reisolated from the infected experimental host and confirmed to be the same.

Chesnut mushrooms

Basidomycota

White threadlike structures

Mycelium

Water and nutrients

Agrocybe

Baseline / untreated group OR factors to be kept same to avoid affecting experiment

Dont always work for organisms that can't be cultured, or diseases which can have some healthy hosts/super spreaders

Virus transmitted by mosquitos

Philedelphia

The slave trade, and rich philledelphians fled to germantown

<1%

Microrganisms

<1%

anywhere life is possible

About 4.6 billion years

3.5 billion years ago (prokaryotes)

Cyanobacteria put oxygen in the atmosphere through oxygenetic photosynthesis about 2.5 billion years ago

1.5 billion years ago

Light microscope (see small), electron microscope (see SUPER small), biochemical and physiological teqniques, nucleic acid and protien sequencing

Fungi, protists, bacteria, archea

Viruses, viroids, satelites, prions

flagella
plasmid
pili - sticky
70s ribosomes
cytoplasm
cell membrane
cell wall
capsule

Eukaryote much larger, has endomembrane system, has nucleus mitochondria chloroplasts

CO2, light, H2O

CO2, Inorg molecule, Inorganic molecule

Org molecule, light, org molecule

Org molecule, org molecule, org molecule

Purplereen non sulfer bacteria

bacteria, archea, eukarya

plantae, animalia, fungi, protista

NO

YES VERY

temp optima are the temperatures organisms can live and grow in
ex. hyperthermohiles dont grow below 68 degs celcius

Only organisms that live in a given optima can live there, narrowing options

Yes. Ex. obligate aerobes will die without oxygen, while obligate anerobes will die with oxygen

clostridium

YESSS

NO

oxygenic photosynthesis

anoxygenic

oxygenic photosynthesis requires photosystem II

NO diff pigments absorb diff wavelengths

diff orgs have diff pigments and thus absorb diff wavelengths of light for energy (layers in ground)

Phylum ascomycota
perithecia with asci and ascospores
grown on Potato dextrose agar

lyme disease

1-5microns by 1 micron

bacteria MUCH larger

circle

clump of circles

line of circles

bacillus

spiral, fixed

spiral, motile

Borrelia burgdorferi

gram stain
grow on agre
microscopes
agre that changes color depending on pH
metabolismiochem based methods
differential broths

1 billion approx

wash and dilute

Interesting repro structure Apothecium "cup shape"
has asci and ascospores just like perithecia

agre that changes color depending on org growing on it

ex rapid strep test, or rapid covid test

ecology
dna sequencing

Nitrogen cycle
plant and human diseaseq

nitrogen to ammonium

nodules on legumes

anthrax, tetanus, gangrene

archea cell wall lack peptidoglycan, has unusual membrane lipids, none are known pathogens

methanogens, extremophiles, non extreme

thermophiles (heat), halophiles (salt), pH tollerant, pressure tollerant

heterotrophs - consume by exuding enzymes and absorbing nutrients
eukaryotes
ecologically diverse
agent of plant and human disease

Decomposes (recycle nutrients)
symbiotic w/plants (mycorrhizae)
pathogens (human/plant disease) - esp devastating to plants

in/around plant roots

bioremediation, food products like cheese, food processing, fermentation*

antibodies

rapid strep, covid tests

N2 > NH4 (+)

nitrogen gas to ammonium

legumes

when bacteria live in nodules on plants - symbiotic relationship

fire blight, slippery skin

tetanus, gangrene, anthrax, botulism - many can affect animals

Archaea

methanogens, extremophiles, non-extreme archea

they exude enzymes, absorb nutrients

chemoheterotrophs

eukaryotes

they can be decomposers, mychroizae (symbiotes), or pathogens

food processing
fermentation
pharmacutical
bioremediation
food - can be farmed

fermentation
vaginal yeast infections
other yeast infections
thrush - oral yeast infection common in babies

Slender fillaments called hyphae

crosswalls called septa

mycellium

an above ground reproductive structure

spores

spores can be either sexual or asexual, and can be any shape

parathecium

no

chytridiomycota
zygomycota
glomeromycota
ascomycota
basidiomycota

Secret 6th option: "Deuteromycetes"

zygomycota

glomeromycota

Basidiomycota

ascomycota

basidiomycota

ASK

yes

zygomycota

look like a tree, hyphea grow INTO root cells, part of glomeromycota

looks like tree

basidiomycota

chron smut or wheat stem rust

amanita
boletes

yes

ecto

variety

powdery mildew

truffles

yep

ECTO

ECTOOO

has asci with ascospores, part of ascomycota

Sordaria fimicola

a mixture of solids liquids and gasses

5%

25%

interaction of:
climate
living organisms
topography
parent material

temp and rainfall, water can freeze in cracks, expanding the crack

vegetration, roots break rocks etc.

elevation, slope

the minerals being broken up are the ones that end up in soil

45% mineral particles
25% air
25% water
5% organic matter

45%

25%

25%

5%

80% humus
10% roots
10% organism

80%

10%

10%

texture - particle size
density - weight and volume
pore size - small or lrg
structure - presence or absence of aggregates

by particle size

mass over volume

small or large

presence or absence of soil aggregates

clay, less than .002mm
silt, .002mm to .05mm,
Sand, 0.05mm to 2.0mm

O- organic layer
A- topsoil
E - Eluciation layer
B - subsoil
C - Parent rock
R- bedrock

organic layer - humus

Topsoil - minerals with humus

eluviation layer - leached minerals and org matter

Subsoil - deposited minerals and metal salts

semi altered parent material

bedrock - unaltered parent material

mineral soil

sedimentary
metamorphic
igneous

metamorphic rock

igneous rock

sedimentary

carbon from organic matter

mostly oxygen and silicon atoms (O and Si)
Quartz is SiO2
Lots of Aluminum atoms as well (Al)
Minerals that dominate are silicates and aluminosilicates

plants
metabolism
decomposition
humus
mineralization

silt, sand, clay

a combination of all three: silt, clay, and sand

sand has a relatively low surface area compared to clay which has a relatively high surface area

90-700 thousand

about 9 trillion

layer silicate clays are ordered crystalline sheets of Si, Al, Mg or Fe
Layers should have a neutral charge

isomorphous substitution causes permenant charge (Si4+ replanced w Al3+ = -1)
pH can lead to a variable charge (hydroxyl (OH) groups can add or release H+)

cation exchange capacity
pH

holding and release of cations by clay and humus (clay and humus have weak negative charge)

H+, K+, Al3+, Mg2+, Ca2+,

plants need the cations because theyre nutritious, but if soil cant hold them they leech away and plants dont get em

1.2 quintillion

cation exchange capacitty

Sand very low, clay medium, humus very high

1 acid
7 neutral
14 basic

6-8

5.5 to 8

they drop in pH naturally

lack available nutrients
toxic ions (ex. Al)
reduced microrganism activity

add lime (CaCO3)

pH change resistance

higher

phosphorous defficiency

low pH make phosphorous unavailabke to plants

iron defficiency

high pH make iron unavailable to plants

soil organic matter

every org compound ion soil (ex. humus, a stable degraded form of soil)

5%

80%

humus - 80%
biosolids (sewage sludge)
animal manure
microrganisms
animals
plant residues from agro and nat ecosyustem
other orgs

no, there's a limit to how often biosolids can be used because of the toxins in the sewage sludge

Soil aeration
-Many microbes need O2 as do roots of plants
-Soil lacking O2 is anoxic (anaerobic)
Soil water
-Limits microbial activity
-Gas exchange and chemical reactions
Soil temperature
-Influences microbial growth
-Greatest swings at soil surface