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Nitrogen assimilation. Plant Physiol Biotech, Biol 3470 Feb. 28, 2006 Lecture 12 Chapter 8. Nitrogen: an essential element. . Fourth most common element Proteins, NAs, PGRs, chlorophyll,… Bioavailable forms: nitrate ( NO 3 - ) and ammonia ( NH 4 + )

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Nitrogen assimilation

Nitrogen assimilation

Plant Physiol Biotech, Biol 3470

Feb. 28, 2006

Lecture 12

Chapter 8

Nitrogen an essential element
Nitrogen: an essential element

  • Fourth most common element

    • Proteins, NAs, PGRs, chlorophyll,…

  • Bioavailable forms: nitrate (NO3-)

    and ammonia (NH4+)

  • Paradox:limiting in environment for growth but plenty available in atmosphere as N2

    • Biologically unavailable!

    • Need prokaryotes to help with this…

The n cycle circulates n in the biosphere
The N cycle circulates N in the biosphere

  • 3 major N pools:

    • atmosphere, soil, biomass

  • plants convert inorganic soil N to organic N (amino acids, NAs, etc.)

  • Organic N moves up the chain to animals (they eat plants!)

  • Returns to soil in animal waste and decomposition after death

Nitrification by bacteria


or mineralization

by prokaryotes and fungi

Organic N pools

Fig 8.1

Essential n cycle processes include ammonification nitrification and denitrification
Essential N cycle processes include ammonification, nitrification and denitrification

  • Ammonification by prokaryotes and fungi returns N to soil: organic N  ammonia (NH4+)

  • Make ammonia biologically available by its sequential oxidization to nitrite and nitrate by soil bacteria during nitrification

  • Plants must compete for nitrate with soil bacteria that reduce NO3- to N2: denitrification

    • 93 to 130 Mt / year back to atmosphere

N fixation reduces n 2 to nh 4
N fixation reduces N nitrification and denitrification2 to NH4+

  • Soil N pool loses N to atmosphere but regains N through action of fixing bacteria

  • N2 NH4+ does not happen spontaneously: highly endergonic = very energetically costly

    Where does the biologically available soil N come from?

  • 10% of N fixed into N oxides: lightning, UV, air pollution

  • 30% via industrial N fixation: make N using fossil fuels via Haver-Bosch process at high T and pressure

  • 60% via biological N fixation by microorganisms: poorly understood but extremely valuable process

Only prokaryotes are nitrogen fixers
Only prokaryotes are nitrogen-fixers nitrification and denitrification

  • Need dinitrogenase (a/k/a nitrogenase) to fix/reduce N2 directly to ammonia

  • Can be free living or symbionts, photosynthetic or heterotrophic bacteria or cyanobacteria

  • All need low/zero O2andhigh C levels: high energy requirement for N fixation slows growth

  • Symbiotic relationship involves metabolic integration between specific bacterial (microsymbiont) and plant (host) species

  • This usually results in forming nodules on the roots/stem

  • This is seen between Rhizobia (bacteria) and legumes (plant)

Fig. 8.2

Only a small number of economically important plants can fix their own organic n
Only a small number of economically important plants can fix their own organic N

Alfalfa (Medicago sativa)

  • These are legumes

    • “Pea family” (Fabaceae): lupin, clover, alfalfa, field beans and peas

  • Note that the top 5 crops cannot fix N and are reliant on fertilizer for high yields

  • This ability evolved over a long period of time and involves both plant and bacterial genes

  • Engineering this trait into modern crops is thus very difficult but economically desirable

  • Rhizobia exist as biovars that restrict the legume species with whom they can establish symbiotic relationships

Rhizobia multiply and infect multiple plant cells within the developing nodule
Rhizobia multiply and infect multiple plant cells within the developing nodule

  • Bacteria continuously multiply during infection

  • Infection complete when bacteria released into host cells by budding off plasma membrane of infection thread

  • Nodule keeps growing via nodule meristem (rapidly dividing cells)

  • Bacteria multiply and infect new plant cells

  • Establish vascular connections with plant: photoassimilate (C) in, fixed N (ammonia, AAs) out

  • When they start fixing N2 for the plant they are called bacteroids



Fig. 8.3

Fig. 8.5

Oxygen inhibits dinitrogenase
Oxygen inhibits dinitrogenase developing nodule

  • Irreversibly denatures both constituent proteins

  • But need cellular respiration to make ATP!

  • Strategies

  • Free living bacteria maintain an anaerobic lifestyle or only fix N2 when under anaerobisis

  • Cyanobacteria structurally isolate nitrogen fixing cells (heterocysts): thick walls, high respiratory capacity limits O2 levels, lack PSII and thus can’t evolve O2

Fig. 8.8

  • Nodules restrict O2 to an O2-binding protein, leghemoglobin

    • Synthesized by host, present in bacteroid infected host cells

    • Keeps respiration high while sequestering O2 from dinitrogenase

Key metabolic step is conversion of fixed ammonia to organic n
Key metabolic step is conversion of fixed ammonia to organic N

  • Most plants can assimilate either NO3- or ammonia

  • Recall that nitrifying bacteria scavenge and convert ammonia to NO3-

    • too bad, NH4+ is the preferred form (already reduced for incorporation into organic molecules)

  • N assimilation is energetically expensive: 2 to 15% of plant’s energy production

  • Let’s examine assimilation of N from these two molecules

N assimilation is reliant on a steady supply of C !!

Fig. 8.7

Nitrogen assimilation is a series of reactions that coordinate c and n metabolism
Nitrogen assimilation is a series of reactions that coordinate C and N metabolism


Biologically unavailable!


(via nitrification by bacteria or fertilizer)




Nitrate reductase

+ nitrite reductase

ADP + Pi



Biologically available but toxic!


(C skeleton from ______ )

  • inhibits N2ase

  • Uncouples ATP synthesis from e- transport

  • Thus, plants use the Glu synthase cycle to rapidly assimilate N into organic molecules

Glutamate synthase cycle


ADP + Pi + NAD+



For export to N sinks

Where does the fixed n go
Where does the fixed N go? coordinate C and N metabolism

  • Primarily exported via xylem: monitor by radiolabeling and examining xylem exudate

  • Temperate legumes export asparagine

  • Asparagine is 2 steps away from Glu and Gln siphoned from glutamate synthase cycle



Glu + OAA  αKG + Asp

Gln + Asp  Glu + Asn

Exported from Glu synthase cycle



Siphoned from Glu synthase cycle


  • Making N into an exportable form consumes ~20% of C allocated to N fixation

  • Want to export organic N with as little C attached as possible (low C:N ratio)

  • Asparagine: 2

No3 is assimilated by nitrate nitrite reductase
NO3- is assimilated by nitrate/nitrite reductase coordinate C and N metabolism

  • Uptake of nitrate is an energy-dependent process involving a specific transporter protein (like for most inorganic elements!)

  • Some of this carrier is constitutive but most is inducibleupon exposure to NO3- (inhibited by exposure to protein synthesis inhibitors)

  • Can store NO3- in vacuole, assimilate directly in roots, or translocate in xylem to leaves (sinks) for assimilation there

    Nitrate reductase activity coordinates N and C assimilation

  • Its complex regulation includes mechanisms of:

    • light and substrate which implies a requirement for photosynthetic energy (e.g., reducing power to supply e-)

    • phytochrome

    • reversible phosphorylation by a protein kinase/phosphatase

N uptake rate varies with plant age
N uptake rate varies with plant age coordinate C and N metabolism

  • Highest during early rapid growth phase

  • N uptake declines as plant enters reproductive phase

  • Assimilated N directed towards young, developing leaves

  • Leaves reach their maximum N content just before full maturity

  • Then leaves become net N exporters even though they continue to import N

    • a/k/a N cycling

  • Developing seeds are strong N sinks: requirement cannot be met by soil uptake alone

  • Steal (reallocate) N from mature leaves

Fig. 8.12

Metabolic consequences of n cycling
Metabolic consequences of N cycling coordinate C and N metabolism

  • Most soluble leaf N is tied up in one protein: __________ !

  • This protein is thus an N storage protein

  • Plants mobilize N to storage in seeds, which may reduce photosynthetic capacity

  • In legumes, a lowered C assimilation rate reduces the capacity for N assimilation

    • Major limiting factor for seed yield in legumes

  • Perennials (e.g., trees) mobilize leaf N (rubisco, chlorophyll) in the autumn and store it in the roots as storage protein

    • N is too precious to discard with leaves!

Agricultural productivity is directly dependent on bioavailable n
Agricultural productivity is directly dependent on bioavailable N

… which depends on soil pH, temp., O2, H2O

  • Influence activity of microorganisms responsible for N assimilation

  • N is removed with the crop each year!

  • Farmers want to maximize productivity: most crops linearly increase yield with N applied until the critical concentration is reached

Fig. 8.13

N fertilizers are costly
N fertilizers are costly bioavailable N

  • Energetically: 1.5 kg oil per kg fixed N

    • 1/3 of energy cost of a crop of maize is N fertilizer

  • Financially for farmers

  • Without added N, yield on a plot eventually declines to a stable, base level

    Natural ecosystems are also N limited

  • 2/3 contribution from N fixers, 1/3 from atmosphere (deposition of NxOs)

  • Most N retained in forest canopy or degraded from litter and

    • Leached into the soil, or

    • Degraded by bacteria, fungi etc.

  • Finally convert organic N to inorganic N (NO3-, NH4+) via mineralization(e.g., ammonification)

  • Accompanied by immobilization: retention and use of N by decomposing organisms

  • Net mineralization (mineralized N minus immobilized N) is available to plants

Rate of natural nitrification varies with environmental conditions
Rate of natural nitrification varies with environmental conditions

  • Nitrification by bacteria = rate of adding N to soil bioavailable pool (as NO3-, NH4+)

  • Varies with temperature, pH, moisture, oxygen

  • Needs a lot of O2 because this process is energy dependent

  • Nitrification is likely a significant source of bioavailable N; difficult to show because plants keep soil N levels low!

  • Stored N in perennials helps plants overcome low soil NO3- levels