biogeochemistry exam 2

lets get this shit

life- what do we need?

• materials (C,H,N,O,P,S)

• energy to build ATP

photosynthesis

* autotrophs, a.k.a self feeders

chlorophyll (light reaction)

calvin benson cycle

• evolved over 2 billions years ago (cyanobacteria

• no super efficient but hasn’t really changed since its evolution

• drastically change O2 atmosphere concentration

oxic respiration

• autotrophs & heterotrophs

• oxidation process → releases CO2

• 1 glucose = 38 ATP 4 metabolic processes

(gycolosis-cytosol)

(krebs-mitochondria)

primary production

* amount of plant produced over time

(mass/area/time : gm-2d-1)

biomass

* total amount of plant material at a point in time (gm^2)

gross primary production (GPP)

* all CO2 fixed into organic matter of plant (over a period of time)

net primary production (NPP)

* rate of organic matter available for other uses beyond supporting energy cost (respiration) of primary producers

NPP=GPP-Ra

* Ra - autotrophic respiration

Re=Ra+Rh

• Re - ecosystem respiration

• Rh - heterotrophic respiration (microbes)

net ecosystem production (NEP)

NEP=GPP-Re

• can be positive or negative

• only CO2

(just know) NECB

• overall ecosystem C balance from all sources and sinks (physical biological)

• anthropogenic

• other forms of C

net ecosystem exchange (NEE)

* exchange of CO2 b/w ecosystem and atmosphere

net ecosystem production (NEP)

• ≈ NEE

• NEP=GPP-Ra-Rh or NEP=NPP-Rh

NEP=NPP-Rh

• NPP : C that is stored in plants and what they “provide” to the ecosystem

  • litter inputs

  • herbivory

  • very little NPP escapes decomposition and is stored in ecosystem

• Rh is closely correlated w/ NPP because NPP is the input(quantity quality)

• Rh : what is transpired by heterotrophs in the ecosystem

  • heterotrophic respiration

  • largest avenues of C loss from an ecosystem

  • decomposer microbes and their predator account for most Rh

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decomposition definition

* physical and chemical breakdown of detritus
* detritus : dead plant, animal, and microbial material

organic material (OM)

• dead plant material leaf root system litter

• animal bodies & residues

The three phases of decomposition ???

phase 1: leaching

phase 2: fragmentation

phase 3: chemical alteration

1\.) leaching

• physical process by which mineral ions and small water soluble compound dissolve in water (forms dissolved organic matter (DOM))

  • absorbed by organisms

  • react w minerals in soil

  • exported from system

• RAPID (if h2o present..CLEOOOOO NOORRR ;( )

• (mostly) labile : compounds easily broken down

  • le suga

  • la animo acids

2\.) fragmentation

• larger pieces of organic matter broken into smaller pieces by soil/animals they eat and create surfaces for microbe colonization

  • INCREASE SURFACE AND MASS

• mix into soil and return OM to soil as fecal pellets and respire CO2 (Rh)

• INCREASE portion of litter that is accessible to microbial attack

• pierce protective barriers (cuticle, bark, skin, exoskeleton o_O)

• INCREASE FRAG/ INCREASE DECOMP

• feeding activity of animals

3\.) chemical alteration

• chemical changes that occur to OM

  • primarily by heterotrophic microbes

• OM → (mineralization) → CO2

  • (inorganic) mineral

  • nutrients

  • water

• OM → (transformation) → complex organic compounds OM soil mineral complexes

  • recalcitrant : resist further microbe breakdown

evolutionary forces that shape decomposition

* those that maximize growth, survival, and reproduction of soil organisms

decomposition

• feeding activity of soil animals

• heterotrophic microbes

• OCCURS TO MEET THE ENERGETIC AND NUTRITIONAL DEMANDS OF DECOMPOSER ORGANISMS

OM → (mineralization) → CO2

• (inorganic) mineral

• nutrients

• water

• important in c-cycle bc of carbon balance

  • heterotrophic respiration → Re = Rh + Ra

• the release of nutrients that are tied up in OM is essential for maintaining productivity and nutrient cycle

  • rate of decay is a control over productivity

organic carbon storage

• climate mitigation

• plant nutrition

• can persist for a long time

  • controls biological activity

  • physical and chemical ____???

controls over decomp. change w time

• senescence : deteriorate w time

• bacteria and fungi already colonized while on plant

decomposition rate

rate that mass is lost over time

d/dt = e^-Kt

• d/dt : change in quantity over time

• K : decomposition rate constant

• units: time ^-1

• (negative exponential model)

what influences K?

• of intrinsic (litter quality) factors

• of extrinsic (environmental and biological) factors

mean residence time (MRT)

• time required to decompose under steady state conditions

• 2 ways to measure

  • measure mass loss over time and fit curve to estimate K, then MRT = 1/K

  • MRT = litter pool/ litter fall so K = litter fall/ litter pool

litter pool/mass of litter in the area →

g litter m^-2 / g C m^-2

litter fall

litter traps to catch leaves stems and root ingrowth cores

microorganisms

microbes

fungi

• relatively larger standing stalk

• turnover time: weeks

• filamentous hyphae

• reproduce sexually/asexually by sporulation

• breakdown of all classes of plant molecules

bacteria/archea

• small standing stock

• 1-10 days

• single cell

• large surface : volume (rapidly absorb substrate)

• reproduce by cell division

• can grow and divide quickly

Fungi + bacteria? (the perfect 2???)

• both can secrete extracellular enzymes to break down OM

• partially degraded OM + enzymes + microbial biomass on and within the OM makes it more palatable for other decomposers

slay

rate of decay and amount of OM remaining is controlled by

• substrate quality

• microbial community

  • players, biomass, activity, nutrients

• environment

  • moisture, temp

substrate quality

* litter quality
* size of molecules
* large molecules cannot pass through membranes
* types of chemical bonds
* ester bonds vs aromatic rings
* regularity of structures
* lignin has highly irregular structure
* no specific enzyme.. so broken down slowly by nonspecific enzymes
* toxicity
* phenolics kill or reduce activity of microbe
* nutrient concentrations
* nutrients (N,P) are required by microbes to produce new microbial biomass

NPP = GPP-Ra

• support biomass and activity of decomposers

• some OM persists storage

• plant biomass dies

  • litter then goes through

    • mineralization

    • transformation

    • leaching

litter inputs → decomposition products

• nutrients enter

• climate/environment (aid w decomp??)

  • temp

  • moisture

  • oxygen

temperature in decomp

• INCREASE TEMP = INCREASE RATE OF REACTION

• decomposer organisms have a thermal tolerance range and optimum

  • acclimate and adapt overtime

• in general

  • INCREASE TEMP = INCREASE DECOMP

  • highest in warm moist condition if oxygen is available

moisture in decomp

• water facilitates the diffusion of substrate nutrients to microbe and waste products away from microbes

• INCREASE MOISTURE = INCREASE DECOMP

  • until soil becomes so waterlogged that aerobic conditions inhibit decomposition

oxygen in decomp

• terminal electron acceptors in oxic respiration

• anerobic metabolism e- acceptors (NO3^- & SO4^2-)

• less energetically favorable than oxic respiration

• LOW O2 → results in lower microbial biomass; DECREASES DECOMP

• LOW O2 → limits macroinvertebrate; DECREASES FRAGMENTATION AVAILABLITY in the ecosystem will part determine the quality of litter and microbial biomass/activity

nutrients in decomp

* the effects of nutrients on decomp are largely indirect and mediated by C quality of the substrate

biological stoichiometry

• living things need a certain ratio of carbon to build their bodys and offspring

  • nutrients (C:N ; C:P)

• high C:N (low N) - decay slower (general pattern)

• low C:N (high N) - generally decay quickly

microbial population growth

look at the powerpoint stuff. check lecture 13

* the one with green boxes

microbial pop growth STARVED FOR N

• substrate N limited

• not enough N to meet/sustain microbe population and activity growth

• ABSORBS (NH4+) from ecosystem

  • N IMMOBILIZATION

microbial pop growth STARVED FOR C

GAGA OOOO EEH

• microbial growth is often C limited

• need to decompose the OM to meet energy demands of decomposer if substrate has SURPLUS N for microbial needs

• RELEASE N to the ecosystem

  • N MINERALIZATION

take a step back, g. consider what dictates substrate quality and C:N

• C → structural

• N,P → physiology

  • photosynthesis

plant economics spectrum (PES)

• ecological traits are functionally coordinated and adapt along environmental gradients

• a way to conceptually organize trade-offs between resource acquisition and conservation

PES plant

• LES : leaf economic spectrum

• WES : wood economic spectrum

• RES : root economic spectrum

investing strategy→ RESOURCE RICH ENVIRONMENT

• resource acquisition

• traits that promote fast C acquisition

  • photosynthesis

• large leaves

• high nutrient content

  • N&P

• fast growing (not structurally complex)

• low tissue longevity (low density)

decomposition (tissue quality)

• low C:N (high N)

• not structurally complex

• faster rate of decay

investing strategy→ RESOURCE POOR ENVIRONMENT

• resource conservation

• traits that promote conservation of tissues

  • lower productivity

• smaller, denser

• structurally complex (cellulose lignin gurl)

• well protected tissues

• lower nutrient concentration

• long tissue longevity

decomposition (tissue quality)

• high C:N (low N)

• complex and defended (jealous tbh..)

• slower rate of decay

fresh litter inputs → flux rate → decomposition products

• inputs → nutrients

• climate/environment

  • temp, moisture, O2

• decomposer → community activity and pop size and composition determines decomp rate and extent

• INTERCONNECTED

  • each component must be thought of within the entire context

2 questions idek she if answered… lmk ;-;

1. what kind of litter is being produced

2. does the environment support high or low microbial biomass and activity

part of lecture 13 notes :)

major reservoir (nitrogen-cycle)

• atmosphere N(triple bond)N

• N2 nonreactive

reactive N (n-cycle)

• inorganic reduced

  • NH3 : ammonia

  • NH4+ : ammonium

• inorganic oxidized

  • NO3- : nitrate

  • N2O : nitrous oxide

• organic

  • DON

    • urea

    • amines

    • amino acids

new inputs to ecosystem (n-cycle)

• N fixation

• N deposition (not focused in class)

losses from ecosystem (n-cycle)

• denitrification

• leaching

• fire → volatilization N

• biomass removal

internal cycling (n-cycle)

• mineralization

• immobilization

• nitrification

• plant uptake

pools and fluxes W/IN ecosystem

• inputs (N-fixation) and losses (denit, leaching) are relatively small in comparison to the internal cycling

  • mineralization

  • immobilization

  • nitrification

  • plant uptake

• vast majority of nutrients that support GPP are recycled in the ecosystem

  • recycled N supports approx. 90% annual plant demand

N mineralization & immobilization

• balance is a critical regulator of N availability for GPP

• (1) N absorbed by plants used by plant to build plant body and for its physiology eventually plant tissues die → litter

  • DOM contains C, N, P

• (2) microbes break down organic matter during this process dissolved organic matter is released through action of exoenzymes

  • also called dissolved organic nitrogen DON

• microbes absorb it and use the C to meet their energy needs and also use the C and N to build new microbial biomass

microbes require a certain ratio of C:N (10:1) STARVED FOR N

• if DON is N poor (high C:N) the microbe must take NH4+ from the environment to meet its needs

• N IMMOBILIZATION

  • N is taken into the microbes body and others cannot use it until the microbe secretes it → enzyme or dies and decomposes

• ex. N poor → sawdust

microbes require a certain ratio of C:N (10:1) STARVED FOR C

• is DON is N rich (low C:N) and the microbe has a surplus of N after its needs are met then it releases NH4+ to the environment

• N MINERALIZATION

  • keeps eating (yum) to get C and releases N

• ex. N rich → manure

mineralization vs immobilization, which one occurs?

general rules

• C:N 25:1 or lower : mineralization

• C:N > 25:1 : immobilization

within the soil profile usually both are happening simultaneously and the balance between them regulates the size of the soluble N pool

• must also consider if the environment supports high microbial activity and pop growth bc the carbon status of the microbes is what is driving the decomposition

  • → magnifies the effects if substrate quality (C:N) on the rates of immobilization vs mineralization

• C:N → determines mineralization vs immobilization

• climate → effect rate

nitrification

• NO3^-

  • nitrate can be taken up by the plants and microbes but must then be reduced to NH4+ so more energetically expensive

  • negative charge so less likely to stick to soil particles (generally have a neg. charge) than NH4+ cation

  • nitrification rate is key for controlling magnitude leaching loss

• find nitrification in places that support HIGH N MINERALIZATION (tropic) or places w added NH4+ fertilizer

  • agriculture

NH4+ amount and availability determine rate and amount of nitrification

• bc nitrification substrates (NH4+, NO2-) are not rich in energy

• nitrifiers grow slow and compete poorly for NH4+ against plants and microbes immobilizing N competition regulates nitrification rates

external source of soluble reactive N

• nitrogen fixation : N2 → NH3

  • N-FIX LIMITED TO WARM, HIGH LIGHT ENVIRONMENTS W/ ENOUGH P

• enzyme : nitrogenase

  • denatured by oxygen so nitrogen fixation requires a low or no oxygen environment (anaerobic)

• N-fixing microbes : bacteria

  • free-living or form symbiotic relationship w/ plants

• very energetically demanding to fix N can use up to 25% of GPP

• only competitively advantageous in low N systems bc if reactive N is available it is energetically cheap to take it up and other microbes would outcompete the comparatively slow growing N-fixers or plants would not feed N-fixers to get N they would simply take it up from the environment

• enzymatic reaction so INCREASE in WARMER TEMPERATURE

why does N limitation exist is organisms can fix it? what constrains N fixation?

• energy availability

  • need HIGH productivity to fuel it

  • HIGH light

  • WARM temps (tropics)

  • not shade but sunny

    • overstory or disturbed open canopy

• other nutrients available = P

  • require a lot of ATP

• N-FIX LIMITED TO WARM, HIGH LIGHT ENVIRONMENTS W/ ENOUGH P

pathways of N loss

• denitrification : NO3- → NO2- → NO → N2O →N2

  • form of anerobic respiration - heterotrophic bacteria

    • bacteria facultative anaerobes <- normally respire O2 but in absence use N-oxides

• ONLY OCCURS IF OXYGEN IS ABSENT

  • 3 conditions required

    • low oxygen

    • high nitrate concentrations

    • supply organic carbon

• NO3- <- product of nitrification

  • bc anaerobic process conditions that favor denit often limit supply NO3- nitrification aerobic

• HIGH DENIT - wetlands w/ aerobic zone or lateral supply of NO3- rice paddies, periodic flooding/draining

• need organic matter to fuel anerobic respiration

  • DECREASE OM = DECREASE DENIT

other pathways of N loss

• leaching of dissolved organic nitrogen (DON) or NO3- nitrate

• often large fluxes after disturbance when there is reduced uptake NO3, NH4 → NO3

• occurs when fertilizer application exceeds plants and microbial demands

• fire volatilizes N

  • the amount lost and forms (NO-, N2, NH3) depends on the temperature of the fire

phosphorus (P)

• essential for all organism

  • DNA, RNA, ATP & phospholipids that form cell membranes

• limits or colimits primary production in many ecosystem both terrestrial and aquatic (lakes, streams, oceans)

  • especially tropical forest and freshwater ecosystems

• P - rarely found in elemental form

  • orthophosphates (basic→acidic)

    • PO4^-3 (pH 14)

    • HPO4^-2 (pH 10)

    • H2PO4- (pH 5)

      • pH 5, 10 → primary forms taken up by the plants

    • H3PO4 (pH 0)

    • PH3 - phosphines

      • gas form extremelly rare

        • negligible atmospheric component

  • Porg - organic P <- living or dead plant/animal/microbe biomass

    • dissolved forms and particulates (porg & orthophosphates)

  • Procks

weathering

* break down of primary (rocks) minerals over time
* jESUS CHrIST mARIE! THeyRE miNERalS! (bb moment lol)

P cycle

• one of the slowest biogeochemical cycles on earth

  • boooo

• atmosphere does not PLAY.. a significant role since P-compounds are solid (not gas)

• they can dissolve in water or be in particulate form

• main P source to the oceans is runoff from river

  • 15 (looks like 1.5 on her notes tho.. idk hard to see lmk) Mt dissolved P

  • 20 Mt suspended particulate P

• Prock weathering non-reversable

• background levels in an ecosystem depends on the parent material

  • parent material: what rocks are made of

    • controls the amount of P in the rock to begin with

weathering controlled by BOTH biological and physical aspects

* weathering rates INCREASE WITH
* INCREASE TEMPERATURE
* INCREASE PRECIPITATION
* INCREASE SLOPE
* INCREASE VEGETATION

shorter cycle w in the geologic P cycle

• P can cycle 100,000 + years before reaching the bottom of the ocean

• only a small component enters the “fast” cycle

  • most remain bound up in rocks

    • aww :c

mineralization and immobilization (p-cycle)

• inputs: OM

• output: H2PO4-

• soil microbes

• rate and amount immobilized or released depends on

  • environment (moisture, temp)

  • C:P of substrate (litter)

    • 300:1 immobilization

    • <200:1 mineralization

adsorption and desorption (p-cycle)

• fast and reversible

• P from soil solution is attached/bound to the surface of soil particles adsorption

• the reverse desorption

• clay surfaces or Fe and Al oxide (+ charges) depends on soil type

  • INCREASE CLAY or INCREASE Fe & Al oxides then

  • INCREASE P will be unavailable bc bounded/absorbed

• oxisols → soil order → highly weathered tropics dominant colloid are Fe, Al oxides

precipitation and dissolution (p-cycle)

• precipitation: process by which metal ions (Al3+, Fe3+) (Ca 2+ - calcarous soil) react w phosphate ions in the soil solution to form minerals such as Al-, Fe-, Ca-, phosphate

• slow involves a permanent change into metal phosphate but metal phosphate can release phosphate back upon dissolution

  • dissolution : release rate slow - form of weathering of a secondary mineral

P uptake by plant

• assimilation

• available P moves through soil by diffusion

• take up mostly HPO4^2- and H2PO4- <- pH dependent

form symbiotic relationship w/ mycorrhizal fungi

(but we already knew that bc we’re girl bosses su)

• long filamentous hyphae

• INCREASE ROOT SURFACE which INCREASES the PROBABLILITY of encountering P

• appox. 80% terrestrial plants form mycorrhizal symbiosis

  • critical step in the evolution of land plants

fixed P pool ⇔ active P pool ⇔ solution P

• 3 pools exist in equilibrium w each other

• fixed P pool → primary mineral

• active P pool → absorbed, secondary mineral, organic matter-P

factors that influence P availability

• clay content (absorption)

• soil minerology [Fe, Al] (absorption)

• soil pH

  • high pH Ca+

  • low pH Al- , Fe-

• organic matter

  • mineralized → release P

  • competes for absorption sites

phosphates in cleaning products

• prevent Ca and Mg ions from binding w soap

• banned in 17 states

• NOT TEXAS (who wouldve though tho)

• EPA sets voluntary limits

aquatic ecosystem

• P often limits primary production

• if you add P → stimulate rapid growth of phytoplankton and algae

• FW & estates coast w carbonate sediments or co-limited N and P

algal blooms (shallow aquatic environment)

• shades out benthic primary producers leading to sediment resuspension switching system to an alternate stable state

  • phytoplankton dominated

• can be toxic depending on community composition of algae

  • harmful algae blooms

  • red tide

• can create dead zones

  • INCREASE ALGAL GROWTH which sink and decompose but aerobic respiration of decomposers takes O2 out of water column

  • hypoxic zones

    • cannot sustain many organisms

human alternation of global P cycle

* humans → mine P approx. 23 Tg (10^12g)/ year
* spread it all around
* fertilizers, livestock feed, trade livestock move food crops
* INCREASE CONSUMPTION of P → approx. 3% annually
* INCREASE POPULATION
* meat

humans effing up (p-cycle)

* we release lot of P from rocks (concentrated) @ a rate that exceeds new P rock formation

5 countries hold approx. 85% of P in minable deposits

• morocco (#1)

• china (#2)

• south africa

• algeria

• syria

will we run out of P?

• no known substitues

• estimated peak of production

  • 2030

• BUT recent discovery “new” reserves pushes this date back a few decades

_> i needa see the source for that bc w ohio i be trippin

push for sustainable management to →

protect aquatic environments, promote food security