AnnouncementsAnnouncements• HandoutsHandouts

• Wagener Wagener et al.et al. article “Rivers and article “Rivers and Soils…”Soils…”

• Questions: written assignment due in Questions: written assignment due in your section this week (Oct. 7your section this week (Oct. 7thth or 8 or 8thth))

• Writing guidelines will help you with the Writing guidelines will help you with the assignmentassignment

• You can get all of these online: You can get all of these online: www.es.ucsb.edu/classes/envs100/www.es.ucsb.edu/classes/envs100/

• Lecture notes onlineLecture notes online

Summary from Friday…Summary from Friday…• Biology controls the flow of energy Biology controls the flow of energy

between organismsbetween organisms• Plant and animal Plant and animal allocationallocation of energy of energy• Endotherms vs. ectotherms and the Endotherms vs. ectotherms and the

energy available in a food chainenergy available in a food chain• Limits on Primary ProductivityLimits on Primary Productivity

• LightLight• TemperatureTemperature• NutrientsNutrients

Two-minute QuizTwo-minute QuizImagine that you are a limnologist. Imagine that you are a limnologist. (What is a limnologist?)(What is a limnologist?)

Two-minute QuizTwo-minute QuizImagine that you are a limnologist. Imagine that you are a limnologist. (What is a limnologist?) You are doing (What is a limnologist?) You are doing your research at Zaca Lake in Santa your research at Zaca Lake in Santa Barbara County. Barbara County.

Two-minute QuizTwo-minute QuizImagine that you are a limnologist. (What is Imagine that you are a limnologist. (What is a limnologist?) You are doing your research a limnologist?) You are doing your research at Zaca Lake in Santa Barbara County. at Zaca Lake in Santa Barbara County.

You make measurements of phytoplankton You make measurements of phytoplankton and macrophyte biomass over the course of and macrophyte biomass over the course of the year as part of a calculation of the net the year as part of a calculation of the net uptake of COuptake of CO22 by the lake. by the lake.

Which of the following occurrences could Which of the following occurrences could influence plant biomass in the lake? How? influence plant biomass in the lake? How?

1.1. The watershed surrounding Zaca The watershed surrounding Zaca Lake burns.Lake burns.

2.2. El Niño weather patterns cause a El Niño weather patterns cause a drop in the mean air temperatures drop in the mean air temperatures in Santa Barbara County during the in Santa Barbara County during the winter months.winter months.

3.3. Mount Saint Helens erupts.Mount Saint Helens erupts.4.4. A dirt road surrounding the lake is A dirt road surrounding the lake is

paved.paved.5.5. A group of anglers successfully A group of anglers successfully

lobby to stock the lake with more lobby to stock the lake with more fish. fish.

Global Nitrogen CycleGlobal Nitrogen Cycle

Human Human activitiesactivities

Internal Internal cyclingcycling

Fixation by Fixation by lightninglightning

Biological Biological fixationfixation

River flow

River flow

Long-term Long-term burialburial

Denitri-Denitri-ficationfication

Internal Internal cyclingcycling

DenitrificatioDenitrificationn

Biological Biological fixationfixation

N depositionN deposition

Global Nitrogen CycleGlobal Nitrogen Cycle

Human Human activitiesactivities

Fixation by Fixation by lightninglightning

Biological Biological fixationfixation

River flow

River flow

Long-term Long-term burialburial

Denitri-Denitri-ficationfication

Internal Internal cyclingcycling

DenitrificatioDenitrificationn

Biological Biological fixationfixation

N depositionN deposition

Human activity:Human activity:

More fixation, more N emissionsMore fixation, more N emissions

Cycle becomes more “open”Cycle becomes more “open”

Internal Internal cyclingcycling

Plant-Microbe MutualismsPlant-Microbe Mutualisms

• RhizobiumRhizobium• Nitrogen fixationNitrogen fixation

• NN22 NH NH44++

• Mycorrhizal fungiMycorrhizal fungi• Fungal hyphae take up Fungal hyphae take up

nutrients nutrients used by used by plantplant

• Photosynthate from Photosynthate from plants plants used by fungi used by fungi

Mycorrhizal FungiMycorrhizal Fungi

• Increase volume of soil exploited by plantsIncrease volume of soil exploited by plants• Absorbing length increased by 2-3 orders of Absorbing length increased by 2-3 orders of

magnitudemagnitude

• 80% of angiosperms, all gymnosperms, some 80% of angiosperms, all gymnosperms, some fernsferns

• 4-20% of GPP from plant goes to fungus4-20% of GPP from plant goes to fungus• Can enhance both N and P uptakeCan enhance both N and P uptake• Mining of P only Mining of P only induces N limitation induces N limitation• Orchids depend on mycorrhizae for carbon as Orchids depend on mycorrhizae for carbon as

well as nutrientswell as nutrients

What controls nutrient What controls nutrient availability to plants?availability to plants?

• DecompositionDecomposition

NH4+

NO3-

organic N

The physical and chemical breakdown The physical and chemical breakdown of dead organic matterof dead organic matter

• Decomposition is crucial because it:Decomposition is crucial because it:• Provides energy for microbial growthProvides energy for microbial growth• Releases nutrients for plant uptakeReleases nutrients for plant uptake• Influences ecosystem carbon storage Influences ecosystem carbon storage

and therefore climateand therefore climate

DecompositionDecomposition

FungiFungi• Most decomposition in aerobic Most decomposition in aerobic

environmentsenvironments• 60-90% of microbial biomass in forests60-90% of microbial biomass in forests• 50% of microbial biomass in grasslands50% of microbial biomass in grasslands

• Broad enzymatic capabilityBroad enzymatic capability• Cell walls (lignin, cellulose, hemicellulose)Cell walls (lignin, cellulose, hemicellulose)• Cell contents (proteins, sugars, lipids)Cell contents (proteins, sugars, lipids)

• Can transport metabolites through hyphaeCan transport metabolites through hyphae• Surface litter (import nitrogen from soil)Surface litter (import nitrogen from soil)• Wood degraders (import nitrogen from soil)Wood degraders (import nitrogen from soil)• Mycorrhizae (trade carbohydrates for nutrients)Mycorrhizae (trade carbohydrates for nutrients)

A fungus among us:A fungus among us:

Laetiporus gilbertsoniiLaetiporus gilbertsonii

““chicken of the chicken of the woods”woods”

• Often grows on Often grows on eucalyptus stumpseucalyptus stumps

• Massive fruiting at Massive fruiting at the end of the dry the end of the dry seasonseason

AnnouncementsAnnouncements• HandoutsHandouts

• Wagener Wagener et al.et al. article “Rivers and article “Rivers and Soils…”Soils…”

• Questions: written assignment due in Questions: written assignment due in your section this week (Oct. 7your section this week (Oct. 7thth or 8 or 8thth))

• Writing guidelines will help you with the Writing guidelines will help you with the assignmentassignment

• You can get all of these online: You can get all of these online: www.es.ucsb.edu/classes/envs100/www.es.ucsb.edu/classes/envs100/

• Lecture notes onlineLecture notes online

Summary from MondaySummary from Monday• Global Nitrogen CycleGlobal Nitrogen Cycle

• Without humans, cycling Without humans, cycling withinwithin a system dominates a system dominates• Human impacts make a system more “open”Human impacts make a system more “open”

Summary from MondaySummary from Monday• Global Nitrogen CycleGlobal Nitrogen Cycle

• Without humans, cycling Without humans, cycling withinwithin a system a system dominatesdominates

• Human impacts make a system more “open”Human impacts make a system more “open”• Plant-microbe MutualismsPlant-microbe Mutualisms

• Mycorrhizae: very common, fungus gives nutrients Mycorrhizae: very common, fungus gives nutrients to plant in exchange for carbonto plant in exchange for carbon

• Nitrogen-fixers: plant roots make nodules, bacteria Nitrogen-fixers: plant roots make nodules, bacteria give N to plant in exchange for carbongive N to plant in exchange for carbon

Summary from MondaySummary from Monday• Global Nitrogen CycleGlobal Nitrogen Cycle

• Without humans, cycling Without humans, cycling withinwithin a system a system dominatesdominates

• Human impacts make a system more “open”Human impacts make a system more “open”• Plant-microbe MutualismsPlant-microbe Mutualisms

• Mycorrhizae: very common, fungus gives Mycorrhizae: very common, fungus gives nutrients to plant in exchange for carbonnutrients to plant in exchange for carbon

• Nitrogen-fixers: plant roots make nodules, Nitrogen-fixers: plant roots make nodules, bacteria give N to plant in exchange for carbonbacteria give N to plant in exchange for carbon

• Decomposition: breakdown of organic matterDecomposition: breakdown of organic matter• Who does it? Macrofauna, mesofauna, Who does it? Macrofauna, mesofauna,

microfaunamicrofauna•FungusFungus

Two-minute QuizTwo-minute Quiz• You are hunting for truffles (the You are hunting for truffles (the

yummy underground fruiting body of a yummy underground fruiting body of a fungus) in the forest with your trusty fungus) in the forest with your trusty pig. Where are you most likely to find pig. Where are you most likely to find them and why?them and why?a) In a forest gap where there a) In a forest gap where there

is a grassy meadow is a grassy meadow

b) Near the base of a treeb) Near the base of a tree

c) Near a rocky outcrop where c) Near a rocky outcrop where the soils are thin and there is the soils are thin and there is not much vegetation not much vegetation

Can fungi photosynthesize?Can fungi photosynthesize?• All fungi are All fungi are heterotrophsheterotrophs

• they they cannotcannot photosynthesize and gather photosynthesize and gather energy from the sunenergy from the sun

• they must take carbon from dead organic they must take carbon from dead organic mattermatter

• Some fungi are green, but Some fungi are green, but they do not they do not photosynthesizephotosynthesize

Main Players in Main Players in DecompositionDecomposition

Macrofauna (greater than 2 mm): Macrofauna (greater than 2 mm): ecosystem engineers, turn soil overecosystem engineers, turn soil over

• earthwormsearthworms• termitestermites

Mesofauna (0.1-2 mm): Mesofauna (0.1-2 mm): fragment litter, injest litter covered with fragment litter, injest litter covered with

microfaunamicrofauna• collembolacollembola

Microfauna (less than 0.1 mm): Microfauna (less than 0.1 mm): main decomposers, larger ones prey on main decomposers, larger ones prey on

bacteriabacteria • nematodesnematodes• amoebasamoebas• fungifungi• bacteriabacteria

How does it decomposition How does it decomposition work?work?

• smaller molecules can get engulfed smaller molecules can get engulfed completely (phagocytosis)completely (phagocytosis)

• larger molecules must be broken larger molecules must be broken down down outsideoutside of the decomposer’s of the decomposer’s bodybody• hyphae are small!hyphae are small!• bacteria are even smaller!!bacteria are even smaller!!

• bacteria and fungus produce bacteria and fungus produce exoenzymesexoenzymes to break things down to break things down

FungiFungi

• Why are there so many in forests?Why are there so many in forests?• fungi specialize in breaking down woodfungi specialize in breaking down wood

high Chigh C

high Nhigh NNN

CC

hyphaehyphae

fruiting fruiting bodiesbodies

BacteriaBacteria• Grow rapidlyGrow rapidly• Specialize on labile substratesSpecialize on labile substrates• Some bacteria function anaerobicallySome bacteria function anaerobically• Dependent on diffusionDependent on diffusion• Spatial specialistsSpatial specialists

• Rhizosphere, macropores, interior of Rhizosphere, macropores, interior of aggregatesaggregates

• Biofilms on particle surfacesBiofilms on particle surfaces• Chemical specialistsChemical specialists

• Different bacteria produce different Different bacteria produce different enzymes (consortia)enzymes (consortia)

Why do Decomposers Decompose Why do Decomposers Decompose Stuff?Stuff?

• Decomposition does release nutrients Decomposition does release nutrients into the soil, into the soil, BUT…BUT…

• Decomposers don’t care that they are Decomposers don’t care that they are performing an “ecosystem process”performing an “ecosystem process”

• Decomposers need C and nutrients Decomposers need C and nutrients too!too!

• They get energy (C) and nutrients They get energy (C) and nutrients from breaking down organic matterfrom breaking down organic matter

What controls decomposition?What controls decomposition?

• ClimateClimate • QuantityQuantity of dead of dead materialmaterial

(also known as (also known as “substrate”)“substrate”)

• QualityQuality of substrate of substrate• SizeSize• Bond StrengthBond Strength• RegularityRegularity• ToxicityToxicity• Nutrient ContentNutrient Content

Substrate QualitySubstrate Quality

1. Size of molecule1. Size of molecule• Large molecules must be broken down Large molecules must be broken down

outside of cellsoutside of cells• ExoenzymesExoenzymes

2. Bond Strength2. Bond Strength• Peptide bonds compared to aromatic Peptide bonds compared to aromatic

ringsrings• peptide bondspeptide bonds are easy to break are easy to break• aromatic rings have double bonds & are aromatic rings have double bonds & are

strongerstronger

• The same amount of nitrogen:The same amount of nitrogen:• fresh litter is high in proteinfresh litter is high in protein• older organic matter in soil has aromatic older organic matter in soil has aromatic

ringsrings

Substrate QualitySubstrate Quality

3. Regularity of structure3. Regularity of structure• Cellulose has a regular structureCellulose has a regular structure

• Lignin has an irregular structureLignin has an irregular structure4. Toxicity4. Toxicity

• Toxins protect plants from herbivory & Toxins protect plants from herbivory & pathogenspathogens

• May also affect decomposers May also affect decomposers 5. Nutrient content5. Nutrient content

• Nutrients are essential for microbial growthNutrients are essential for microbial growth

Substrate QualitySubstrate Quality

Predictors of Decomposition Predictors of Decomposition RateRate

• C:N ratioC:N ratio• Index of ratio of cytoplasm to cell wallsIndex of ratio of cytoplasm to cell walls• Measure of nitrogen concentrationMeasure of nitrogen concentration• Directly affects decomposition ONLY in Directly affects decomposition ONLY in

presence of labile Cpresence of labile C

• Lignin:N ratio (this is a better Lignin:N ratio (this is a better predictor)predictor)• Integrated measure of N concentration Integrated measure of N concentration

and substrate size/complexityand substrate size/complexity

• Office hours on Monday:Office hours on Monday:• Look for Kevin in my office (Girvetz Look for Kevin in my office (Girvetz

2307)2307)

• Online fun!Online fun!

AnnouncementsAnnouncements

• HowHow decomposition occurs decomposition occurs• microbes exude exoenzymes that attack microbes exude exoenzymes that attack

substratesubstrate

• BacteriaBacteria• small, grow quickly, spatial specializationsmall, grow quickly, spatial specialization• chemical specializationchemical specialization

Summary from WednesdaySummary from Wednesday

cellulose

cellulose

fragment

glucose

1 2

more recalcitrant

more labile

• WhyWhy decomposition occurs decomposition occurs• microbes don’t care that they are performing microbes don’t care that they are performing

an “ecosystem service”, they just need an “ecosystem service”, they just need energy and nutrientsenergy and nutrients

• Controls on decompositionControls on decomposition• ClimateClimate• Quantity of substrateQuantity of substrate• Quality of substrateQuality of substrate

• size of moleculesize of molecule• bond strengthbond strength

Summary from WednesdaySummary from Wednesday

• regularity of structureregularity of structure• toxicitytoxicity• nutrient contentnutrient content

SoilsSoils

• "We know more about the movement "We know more about the movement of celestial bodies than about the soil of celestial bodies than about the soil underfoot." underfoot." - - Leonardo Da Vinci, circa 1500'sLeonardo Da Vinci, circa 1500's

SoilsSoils

• "Be it deep or shallow, red or black, "Be it deep or shallow, red or black, sand or clay, the soil is the link sand or clay, the soil is the link between the rock core of the earth between the rock core of the earth and the living things on its surface. It and the living things on its surface. It is the foothold for the plants we is the foothold for the plants we grow. Therein lies the main reason grow. Therein lies the main reason for our interest in soils." for our interest in soils." - - Roy W. Simonson, Roy W. Simonson, USDA Yearbook of USDA Yearbook of Agriculture, 1957Agriculture, 1957

What is Soil?What is Soil?

• Natural body comprised of solids, liquids, & Natural body comprised of solids, liquids, & gases gases

• On the surface of the land On the surface of the land • Has one or both of the following: Has one or both of the following:

• horizonshorizons• the ability to support rooted plants the ability to support rooted plants

• Upper limit:Upper limit:• boundary between soil and air, shallow water, boundary between soil and air, shallow water,

live plants, or plant materials that have not live plants, or plant materials that have not begun to decomposebegun to decompose

• Lower limit:Lower limit:• bedrock or 200mbedrock or 200m

losses

additions

translocations transformation

s

Soil Formation FactorsSoil Formation Factors

Cl.O.R.P.T.H.Cl.O.R.P.T.H.• ClimateClimate• OrganismsOrganisms• ReliefRelief• Parent materialParent material• TimeTime• Human activityHuman activity

Biome:

A large climatic region where plants are similar to each other