Midterm 2 Material Flashcards
What are the three things soil microbes are important for?
- Nutrient cycling
- Pathogenesis/disease
- Chemical breakdown and carbon transformation (decomposition)
What is a key morphological trait of fungi?
Filamentous growth
What are the advantages of being filamentous fungi?
They have a large surface area, are able to degrade wood and complex carbon (because filaments can go into wood fibers and pull them apart by growing into them), can move things from one place to another, and can wrap around/tie things
What are the disadvantages to being filamentous fungi?
-Are sensitive to disturbance (they break easy)
- Taking samples causes them to die
- Need more resources as bigger
What is a mycorrhizal association?
is a symbiotic structure formed by a fungus plus a plant
Can plants refuse a mycorrhizal association?
Yes plants can refuse association if it’s not energetically useful for the plant- when the plant isn’t under stress and has lots of P and N it doesn’t associate
What is the difference between acquisition of phosphate by mycorrhizal roots versus just regular roots?
Regular roots have depletion zone in which the root will take up phosphate, mycorrhizal roots extend past this depletion zone which then takes up phosphate outside of zone- makes it more efficient
Can phosphours move to plants? Can nitrogen?
no and yes
What are the benefits/disadvantages of being small as bacteria?
are resilient to physical disturbance
have better surface area to volume ratio
have small energy requirement
less predation
can form biofilms on things
Can hide
stuck where they are
smaller than things they try to eat sometimes (ie humic substances)
Can bacteria hide in soil?
yes, can be hidden by clay
How bacteria get nutrients?
Bacteria need water to be running through to bring them nutrients as they can’t actively go get them
Why are bacteria a lot more abundant in tillaged soils?
Because fungi get killed off due to the tillage which leaves more bacteria relatively
Why are fungi a lot more abundant in forested soils?
Because forest ecosystems are very acidic and fungi are acid tolerant, also because forests provide a lot of wood and stuff that fungi feed on.
Are bacteria diverse?
yes taxonomically and functionally, involve both bacteria and archae
What is bioremediation?
is the study of looking at how bacteria break up pollutants
What are antibiotics?
is when organisms (bacteria or fungi)put out chemical signals to kill eachother, bacteria make antifungal and fungi make antibacterial, they both also develop resistance so it’s constant evolution
What 3 functions can bacteria do?
nitrogen cycle
phosphorus cycle
carbon cycle
What three things prevent decomposition?
climate (environmental protection)
Soil texture/mineralogy (Physical Protection)
Composition and structure of the SOM (Chemical protection)
What is the definition of decomposition?
the physical an chemical breakdown of chemical compounds, moving them along a continuum from fresh to humidified
Why is decomposition important?
Because it takes nutrients that are unavailable and make them available again
Releases gases (CO2) back to atmosphere
lets us see regeneration after disturbance
removes dead biomass
Puts co2 back in atmosphere
What are the two pathways of decomposition?
physical and chemical
What consists of the physical pathway of degradation?
leaching and fragmentation
What consists of the chemical pathway of degredation?
mineralization
for ex ammonification
How do we measure degradation?
you collect litter, dry it, weigh it into bags, dry and weigh contents of bags and calc the loss of mass and plot results
What do degradation plots look like?
Look at mass loss over time, usually is an exponential decline
What does the eqn of degradation look like? What’s k?
ln Lt/L0 = -kt
k is a constant obtained from the exponential model of specific plants
What species is the fastest to decompose? What species is the slowest to decompose?
Acer Saccharum
Betula populifolia
What way do we quantify k from an exponential curve?
K= litterfall (how much litter there is)/ litter pool (amount of litter that falls down)
The larger the k the faster the what?
degradation
What is the effect of temperature and water on soil OM?
As ppt increases and temp increases the percent of organic matter in soil plateaus, ORGANIC MATTER DECREASES at higher temps and higher water amounts
Is there an optimal temp for soil decomposition to happen? Why?
yes, because too cold decomposition slows down and too hot decomposition slows down.
Feb 9 lec
Feb 12 lecture
As the C:N ratio increases what happens to the decomposition rate? Why?
It decreases, this is because microbes don’t have the energy to break down products as they become nitrogen limited which they need for their metabolic processes
What important element is usually limiting ecosystems?
nitrogen
Why is nitrogen important for life (plants)?
Because it’s a major substance in plants next to water, is a building block of life, is in chlorpphyll, cytochromes, alkaloids and many vitamins
and plays roles in metabolism, growth, reproduction, and heredity
Why is nitrogen important for life (cellular wise)?
because it’s a crucial apart of amino acids, fatty acids, sugar residues, and nucelobases
How does nitrogen limit ecosystems?
It needs to be fixed into systems and limits primary productivity in most terrestrial ecosystems
What are the three forms of nitrogen in the atmosphere?
Gaseous form
-Di-nitrogen
-Traces gases
Organic:
- Biomass components (amino acids, nucleic acids)
-SOM
Inorganic
-Ammonium
-Nitrate
-Nitrite
What are the differences between ammonium, nitrate, and nitrite?
Ammonium and nitrate- both have positive charges , ammonium more acidic and leaches readily
Nitrite- is smaller type, very reactive
Nitrate needs to get reduced to ammonia to be taken in biochemical pathways
What are the inputs of nitrogen (naturally)?
N2 fixation (biotic, abiotic)
Atmospheric deposition (wet and dry)
Fertilization
erosion
What are the outputs of nitrogen?
Biomass removal
Erosion
Volatilization
Leaching/infiltration
Why are terrestrial system usually limited by N?
Because N2 in it’s gaseous form is triple bonded, requires a lot of energy to break the bond so decomposers can fix it and use it for plants
In what ways can nitrogen be fixed?
abiotic and biotic
What are the abiotic ways nitrogen can get fixed?
Atmospheric- thunder and electric discharge cooks N2 into nitrate
Industrial
What are the biotic ways nitrogen can get fixed?
through free-living organisms- aerobic bacteria, anaerobic bacteria, and blue green algae
or symbiotic organisms- such as stem nodules and stem nodules
How does the symbiosis between legumes and rhizobia work?
legumes feed co2 to rhizobia to provide energy for the bacteria to fix nitrogen as it doesn’t have to use the energy to fix carbon
How do rhizobium nodules get created?
the bacteria makes nodules in plants roots, the nodules are anaerobic as nitrogen needs to be reduced to be fixed
Why are nodules pink?
has hemoglobin that scavenges oxygen and prevents it from interfering with N fixation
Why does atmospheric N deposition change over time?
Because of industrialization (get more nitrogen deposition in areas with higher industry)
the haber-Bosch process (an artificial way to make nitrogen)
Livestock production
How does the haber-bosch process work?
Nitrogen from the air and hydrogen from natural gas in a 1:3 ratio gets pressures and cooled to make ammonia. The unreacted gases get recycled.
What are the consequences of nitrogen deposition?
lake/stream acidification/eutrophication
decreased plant biodiversity
changes in soil nutrient cycling
How does nitrogen deposition affect the fungal community structures?
when nitrogen deposition is low there’s more decomposition genes expressed so fungal biomass and richness increases. When the deposition is high, fungal biomass and richness decreases and stress genes are more expressed. More symbiosis is found when N deposition low and primarily saprotrophic when N deposition high.
Why does nitrogen addition decrease fungal decomp activity?
Because fungi will just use free energy that rather using their own energy to break down lignin to get nitrogen
Feb 14 lec
What is the environmental response of added N in detritus and soil mass?
Lower decomposition, high soil carbon pool, lower N mineralization
What is the environmental response of added nitrogen in plant biomass N?
higher productivity
higher tissue nitrogen
Higher N cycling
Higher herbivory
species change- exmaple less symbiosis
What is the environmental response to adding nitrogen interms of leaching losses?
higher soil acidification
higher plant mortality
What are the four types of nitrogen transformations?
Organic to inorganic (Nucleotide to ammonia)
inorganic to organic (ammonia to amino acid)
oxidized to reduced (No3- to NH4)
reduced to oxidized (NH4+ to No3-_
What are the 6 types of nitrogen transformations?
Fixation/Immobilization
* Mineralization
* Volatilization
* Nitrification
* Denitrification
* Conversion
to trace gasses
Explain what fixation/immobilization is for nitrogen gasses?
fixation- getting nitrogen from atmosphere into plant material
Immobilized- taken into plants from soil solution
Explain what mineralization is?
Is the release of an ion from it’s biotic form
What is volatilization (in terms of N)?
gasses escape from soil
What is nitrification?
is a process of oxidizing ammonia, fungi and bacteria do this, make ammonia to nitrite to nitrate
Why is nitrification two steps long?
because diff organisms do each part, AOB and NOB
What is denitrification?
when you reduce nitrate to nitrogen- is an anaerobic process
What three things (sources of energy) do bacteria need?
energy source, carbon source, and electron source- these all feed into creating the macromolecules organisms need
What is the oxidation-reduction potential?
tendency of a substance to grain or lose electrons
Why do things grow slowly in very redoxed environments?
because there is very very little energy in reduced environments
Why does oxygen act as an electron sink when it’s present?
Because it pulls electrons towards itself, creating aerobic processes
What is a hole in the pipe model?
Under stress nitrification and denitrification become imperfect so we get byproducts (n trace gasses) that are partially reduced/oxidized, important to see whether trace gasses will be made depending on the stress on the microbes
Who controls the process of nitrogen transformation?
Three diff processes
three diff processes
a) microbes take up nitrogen from organic matter, create soluble nutrients, this is then taken up by plants (passive)
b) fungal hyphae and mychorrizae get’s organic matter (active)
c) the plants exudes organic acids which will exchange with nutrients present in soil through CEC
Can bacteria store nitrogen?
No
Why do microorganisms ever release their nitrogen?
Because there’s excess nitrogen in the soil system (bacteria can’t store the nitrogen)
if the microorganisms are starving- will degrade their own enzymes and proteins to get carbon but release nitrogen associated with it (mineralize it)
or they get eaten and the stuff that ate them releases ammonium
How do plants get nitrogen?
will either manipulate microbes in rhizosphere, passively waiting for it, or actively take up organic monomers (for ex amino acids)
What is the rhizosphere?
is area around plant root
How do plants manipulate microbes in rhizosphere? What is this effect called?
the root exudes carbon and as it grows it puts out further carbon, the bacterial biomass increases and then bacteria get nitrogen form surrounding SOM, then as the root goes past the bacteria poplns the bacteria gets starved and root hairs that grow later take up the nitrogen they exude
- called the priming effect
Can plants only take up nitrogen through bacterial help? What does the recent science say?
No, plants can take up nitrogen through depolymerization of soil organic matter creating monomers that plants can take up.
Where does phosphorus come from?
weathering rocks, not from atmosphere
How does phosphorus return back to the system?
through geological upheaval
What processes does phosphorus go through?
adsorption (phosphorus binds to soil particles)
desorption (phosphorus bound to soil particles is released)
precipitation
dissolution
weathering
Feb 16 lec
What is the simpson’s index? What does it tell us? What does it not tell us?
quantifies diversity, larger numbers means more diversity, allows us to compare ecosystems
This doesn’t tell us the different function of various species or who is there, can’t say the rate of turnover, relationships between them, whether the organisms are invasive or native
What three things are the cause of diversity according to the biodiversity ecosystem functioning research?
competition- more competition means you need to find more ways to get resources
stress- more stress means higher diversity
disturbance- low disturbance results in it being too stable, high disturbance results in it being very unstable
Why does competition, stress, and disturbance cause diversity?
Because of the need to explore niches
What is a keystone species?
A keystone species is a plant or animal that plays a unique and critical role in the way an ecosystem functions- w out them the ecosystem would not be the same or cease to exist
What are the five diff types of keystone species?
Predators
Prey
Ecosystem Enginners
Mutualists
Producers
What is an example of a keystone species that is being affected by climate change?
Hawaiian native birds
Why are Hawaiian native birds being forced upwards?
because air temperatures rising is causing the mosquito zones to expand which remove the native birds refuge as they can kill them (via malaria)
Why are mosquito numbers increasing?
Due to increasing amounts of feral pigs, feral pigs knock down trees and destroy vegetation creating perfect ecosystem for baby mosquitos to thrive.
What are the four categories of ecosystem services?
cultural, supporting, regulating, and provisioning
Week 7 trophic dynamics
What are the two trophic categories?
Autotrophs and heterotrophs
What are autotrophs?
producers
What are heterotrophs?
consumers don’t make their own energy
What are the 4 levels of heterotrophs?
herbivores
carnivores
detritivores
microbivores
In a plant based trophic system how is it structured?
Has a one way flow of energy, energy goes from net primary producers up through each trophic level- herbivore, carnivores, secondary carnivores, with respiration coming off each step- and any energy (uneaten food, feces) goes into SOM
How is a detritus based trophic system structure?
is based on dead organic matter, is most of the energy transfer to the ecosystem
Bacteria and fungi break down SOM, any loss in each level of the system goes back to the SOM. A detritus trophic system is not one way as partially broken down things get recycled again to be broken down
Within each change of level in a trophic system do we lose or gain energy?
lose energy
What determines how much energy we’ll lose in each trophic level?
the food quality, how much each trophic level contributes
What are the two ways energy flow can be regulated in trophic systems?
by the availability of producers or by prey
Do trophic levels vary temporally and spatially?
yes
Is all primary production consumed? Where does the unconsumed go?
No, certain structures are not digestible- goes to detritus
What is a bottom-up controls?
the availability of food is limited by base trophic level (primary producers) and therefore upper trophic levels production are limited
What pattern in organisms and biomass do we see?
organisms being herbivores and biomass being plants
As plant biomass increases we see much more herbivore biomass, however even at similar values of biomass there can be variation in herbivory
Why is it that there can be variation in herbivory at the same plant biomass?
Because some biomass is not available for animals to eat (plants can physically and chemically defend themselves)
What three things effect the resource allocation of plants to growth or defense? How?
Genetics- can have genetic capability to allocate resources
environment- the environments might have low fertility so plants can allocate more towards defense
season- the times of year matter for what they allocate energy too
Provide an example of a plant allocating resources towards defense for them not to be eaten? Can this be affected seasonally?
The more leaves a plant has the lower the amount of tanins are and vice versa. This is because we have to prioritize growth or defense, this makes sense as if there’s more foliage the need for defense is small. This can be affected seasonally.
In low soil fertility what happens to growth? Plant defense? decompostion?
growth decreases, so plant defense increases, so fewer herbivores break down leaves which leads to slower decomposition- leads to low soil fertility
In high soil fertility what happens to growth? Plant defense? Decomposition?
We see rapid growth, low plant defense, and so they get eaten at higher rates which then leads to rapid decomp and also returns nutrients passing by decomp
What is a top-down control?
The consumption by predators alters the abundance of organisms that feed on plants, see more primary production- this is called a trophic cascade
When there’s odd numbers of trophic levels what happens?
makes a green world - more primary production
When there’s even numbers of trophic levels what happens?
even ones lead to decreased primary production
What is a biomass pyramid? What does it tell us?
is the plant biomass shape that gets reduced each trophic level
What is the difference between aquatic ecosystem biomass pyramids and terrestrial biomass pyramids?
We give more biomass to primary producers (ie trees), in aquatic ecosystems the phytoplankton are very small- don’t have to allocate energy to structure, see inversion
What is the difference between aquatic ecosystem energy flow pyramids and terrestrial energy flow pyramids?
aquatic ecosystems have less loss of energy in each system because they don’t need to allocate energy to supports such as woody trees etc, water holds everything up
How does body size and generation time differ between aquatic and terrestrial systems?
in terrestrial- have big body size with long generation times, herbivores and carnivores are smaller than the primary producers
In aquatic- primary producers are small, don’t live long time, herbivores and carnivores get larger and have large gen times
Why do animals require more N and P than plants?
Because they have growth events, nitrogen plays big role in making lactate for ex
Do organisms take nutrients preferentially? why?
Yes, so animals can meet their nutritional needs
What has more variation in nutrients, animals or plants?
plants
What is the benefit of pooping over decomposing?
is a faster way to return nutrients to ecosystems
How can caribous be selective in the nutrients they take?
caribou can eat lichen during times where they need nutrients to support things like staying warm in cool environment, but in spring they need high level of nitrogen and shift food preferences then to vascular plants
What ratio do terrestrial plant species usually need of N:P?
12-13
In plants do we see a 1-1 ratio of nutrients in plants versus soil? How do plants adjust to this?
No, No, boreal vegetation is nitrogen limited and oil soils are phosphorus limited
Why do we see low N:P ratio in animals that are rapidly growing? What about ones with structural components?
because they have phosphorus rich ribosomes, also because bones require more phosphorus
N deficient plants increase the rate of what and reduce the rate of what?
N deficient plants increase the rate of nitrogen uptake and reduce the rate of phosphorus uptake
Is trophic effiency pretty low or high?
low at 5-20%
What are the three components of trophic efficiency?
consumption
assimilation
production
What is the formula of trophic efficency?
is the efficiency of consumption, assimilation, and production which equals productionn/productionn-1
What’s the formula for trophic consumption?
is the amount ingested over production by the lower trophic level (n-1)
Where is consumption efficiency higher? Where is it lower?
Is lower in terrestrial system compared to aquatic, see low consumption efficiencies in places with woody structures
What are the four factors that determine ingestion?
time available for eating
time spent looking for food
proportion of food eaten
rate of consumption
What is assimilation efficiency?
is the proportion of food ingested that entered the blood stream, is food assimilated/food ingested
What has higher assimilation efficiency? Carnivores or herbivores?
Carnivores, as herbivores tend to eat things with structural compounds (such as cell wall and cytoplasm) which aren’t as digestible
How do cows get nutrition from grass?
they spend energy eating it and spend energy breaking it down via bacteria
What is production efficiency?
is the proportion of assimilated energy converted to growth and reproduction , so production over assimilated energy
How is production efficiency determined?
by metabolism, for hoeotherms theres a high demand of metabolism so you gte lower production efficencies than poikilotherms
In homeotherms does production efficiency increase or decrease with decreasing body size? Why?
decreases due to surface area volume ratio, larger ratios cause production efficiency to decrease with decreasing body size
In poikilotherms, does production efficiency decrease with increasing body size?
yes
Does production efficiency decrease with age?
yes, as less energy is dedicated to growth/reproduction
What is stoichiometry?
is the balance of nutrients needed to grow and reproduce, tells us what the organism needs and it’s specific needs, also tells us how organism may eat and what will be available for it
Do plants preferentially take up different isotopes?
yes, if we look at ratio of light and heavy isotopes we can determine the range of prey items they might have and helps us build trophic systems also helps with extinct organisms. Can find ratio in the animals bones.
describe slide 21 in week 7 notes
What is the definition of phenology?
the seasonal timing of life history events
What is phenological mismatch?
when consumer and resource seasonality are mismatched
What can phenology affect?
can be impacted through climate change which effects resource availability, composition, and range shifts
can affect biomass/and or nutrients
Week 8
What are functional traits?
Characteristics of organisms that influence growth, reproduction or survival are response traits.
Wat are effect traits?
species traits that affect nutrient supply, microclimate, trophic cascades, or disturbance
What is grimes ecological classification framework?
it groups traits into three categories, competitive, stress tolerant, and ruderal.
When stres sincrease sress tolerant traits are favoured, when distrubance increases bisturanbce traits, and when competiton increases than competitive traits
Feb 9 lecture stuff
Why is the percent organic matter over precipitation plot lacking?
It tells as at high water content and and low temps is degrades fast and high water content results in more carbon which plateaus quickley during higher temperatures but it doesn’t tell us the relationship between temperature, water, or carbon
What are the four phases of degradation?
Phase 1- Lag
Phase 2- Fragmentation, leaching, microbial mineralization
Phase 3- Microbial mineralization, further fragmentation
Phase 4- Stable phase, lignin degradation
How does fragmentation work as a physical way of degradation?
freeze/thaw cycles and animal activities break detritus into smaller pieces, these pieces have a higher surface area and therefore increase their rate of decomp
What is the effect of biota on degradation?
when microbes present degrade faster, when mesofauna present degrade even faster
How does degradation change depending on the size of your mesh bag?
if the holes in the bag are large get more faster degradation than small (larger surface area)
How does litter quality affect the rate of degradation?
It affects the rate of degradation as certain types of litter degrade faster than others and hold differing utilization efficiencies.
Litter quality dependent on the size of the molecule, structure of the molecules, enzyme location, and enzyme type determines the rate of degradation
How do bacteria prevent enzyme loss?
bacteria anchor on end of the enzyme in their membranes so the enzyme doesn’t diffuse away, also grow in a biofilm to slow down enzyme movement
How do bacteria work together to degrade stuff?
they assemble into a consortium, a group of organisms that share the cost of enzyme production and then one of them makes the enzyme- biofilms sometimes might incase them
What are the three enzymes used to decompose cellulose?
endocellulase
exocellulase
glycosidase
How do microbes outcompete other microbes for nutrients?
they specialize and exploit niches
What is brown rot versus white rot?
brown rot-is the rapid depolymerization of cellulose and low weight compounds rapidly diffuse into plant cell wall
White rot- is the gradual thinning of the plant cell wall because enzymes are too large to penetrate it
Why do organisms degrade nasty carbon?
because ir provides a competitive advantage
because they need to get past it to get nitrogen (lignin tends to forma cage around proteins and hemicellulose that contain N)
or by accident
What is cometabolism?
is the accidental break down of SOM by an extracellular enzyme in the environment, doesn’t provide benefit
