Topic 6 Soil BIO 346

soil

• on land terrestrial environment

• recycling system

• root growth for plants

• nutrient uptake

• skin of the earth

soil vs dirt

• soil is mixture of all: mineral and organic solids, gases, liquids, living organisms

• dirt is soil out of place, in new space, removed

parent material

• geological or organic precursors

• deposited on top of rock

• deposits from aquatic systems

• rivers and marine sediments, glaciers

• wind or plant matter

factors affecting formation of soil

1. parent material

2. climate

3. biota

4. topography

5. time

climate

• changes activity and dryness

• precipitation and temp

biota

• plants

• microorganisms

• animals and humans

  • rearranging soil, gardens

topography

• slope and landscape position

• flat area will stay in that place

• slope will cause erosion from wind and rain

• more soil build up in valley

• upland vs wetland

time

• how long parent material has been exposed to soil formation

• weathering time

• waiting for glacier to melt (very slow)

Lichen pioneering organisms

• no soil on rock yet

• fix CO2 with light energy

• feeds archaea, fungi, bacteria

• spongy layer on rock (holds water)

• CO2 dissolved in water makes carbonic acid and degrades rock

• freeze thaw and makes cracks (expanding water)

Bare rock stage

• lichen grow on rock

• consume CO2 and fix N2

• generate organic C

• feed organic heterotrophs

• generate carbonic acid and organic acids

• minerals dissolve rock

freeze thaw

• water in rocks expand from freezing

• cracks form

Slope topography

• weathering material

• soil does not build up

• washed down to erosion into valley

• trees and grass can maintain soil

A horizon

• top soil layer

• rich in OM (HUMUS)

• darkest

• highest bio activity

B horizon

• subsoil

• less OM

• accumulation of minerals and clay

C horizon

• parent material

• bottom layer made from weathered rock

• little bio activity

• closest to bedrock

P/E ratio

precipitation (input) and evaporation (output)

water in vs water out

P/E > 1

• wet conditions

• more water coming than leaving

• downward water movement (leaching)

• nutrients washed out

P/E = 1

• balanced equal water in and out

• no net movement

• nutrients stay

P/E < 1

• dry conditions

• more water leaving than entering

• upward water movement

• water evaporates and salt left behind

soil particles

• less than 2 mm diameter

sand

• 2mm —> 0.05 mm

• big and drains water fast

• low surface area

slit

0.05 mm → 0.002 mm

• feels like flour

• medium surface area

clay

< 0.002 mm

• tiny holds water

• high surface area

loam

• mixture of sand, slit, clay

• adds up to 100

what has the highest cation exchange capactiy (CEC)

clay

• due to high surface area

what has the highest water holding capacity (WHC)

• clay (slow drainage)

• slow permeability

rapid permeability and lowest surface area

• water flows through fast

• sand

• big pores

organic matter breakdown easiest to hardest

sugar → protein → cellulose → hemicellulose → lignin

What does decomposition produce?

CO₂, NH₃, and microbial biomass

“Which persists longest in soil?”

lignin

humus

• final stable organic matter in soil

• carbon that resisted degradation

• gives soil dark colour - dark and MOST nutrient rich

humin

complex of fulvic and humic acid strongly bound to mineral material

• largest and most stable

humic acids

• medium size

• aromatic rings

• cyclic nitrogen forms

• complex condensed polypeptides

fulvic acid

• higher oxygen to carbon ratio

• breaks down faster

• smallest mol

soil microbiota - aerated soils

• O2 present

bacteria and fungi dominate

low O2 soil

bacteria and archaea dominate

who has highest biomass but low numbers

who is most numerous but low biomass

virus (massive outnumber)

What are macroaggregates made of?

Sand, silt, roots, fungal hyphae, bacteria, and polysaccharides

What are microaggregates made of?

clay and OM

what stabilizes soil structure

• fungal hyphae and roots

• tiny long thin threat like filaments that holds soil together = hyphae

alkaline high pH

many species higher diversity

• more microbes survive, less stressful

similar communities

acidic

fewer species

• only specialized species survive

different communities

where is diversity highest

alkaline

where is variability between sites highest

acidic

climate change

increases microbial activity and carbon cycling

short term

more carbon in

• soil still gains

• increase plant growth and microbial activity

long term

more carbon out

• more CO2 in atmosphere

• soil gets depleted

Which nitrogen form is most oxidized?

Nitrate (NO₃⁻)

Which nitrogen form is most reduced?

Ammonia (NH₃)

Which forms are electron acceptors?

Oxidized forms (e.g., NO₃⁻)

Which forms are electron donors?

Reduced forms (e.g., NH₃) ammonia

What organisms carry out most nitrogen redox reactions?

prokaryotes

nitrification

makes usable nitrate for plants

• needs oxygen

• makes nitrate

denitrification

• reduction of nitrate to produce nitrogen gas

• anaerobic conditions

• removes nitrogen from soil (loss)

DNRA

• No3 → NH3

• keeps nitrogen in system

• competes with denitification

ammonia oxiadtion

• nitrification part 1

• Nh3 → NO2

• 35 moles NH3 to fix 1 CO2

• G = - 66

• aerobic

• chemolithoautotrophs

nitrosomonas

• best studied genus

nitrosospira

dominant genus in many soils

nitrite oxidation

• NO2 → NO3

• NOB

• aerobic

• produces even less energy than step 1

• very slow process

commamox

• complete one step nitrification

clay and humus

negative charge

cation

• sticks

• attracts to soil

NH4

ammonium stays in soil

anion

• repel soil

• move w water

NO3

nitrate leaches out

AOA

• dominante neutral alkaline soil

• in agricultural soil

• increase nitrification

AOB

• dominate acidic soil

• higher ammonia oxidation

• adapt to stress

mRNA amoA

amoA = gene for ammonia oxidation enxyme

high AOA mRNA

achera actively nitrfying

high AOB mRNA

bacteria activgely nitrifying

intermediates of nitrification

• hydroxylamines

• nitroxyl

leaky systems

• NO nitric oxide

• N2O nitrous oxide

nitric oxide

NO

air pollution

nitrious oxide

N2O

greenhouse gas

ozone pollution

fertilizer

• farmers add nitrogen

• NH2 ammonium fertilizer

• loss of fertilizer nitrogen

• so famers use nitrifiation inhib

acetylene

• blocks final step of denitrification

• No2 builds up and we measure this

low SOM

• + well drained

• minimal loss of nitrogen

high SOM

poor drain

• high nitrogen loss

nitrogen fixation

• most energticallt expensive

• convers inert N2 to bioavailable NH3