nitrogen fixation. nitrogen fixation the growth of all organisms depend on the availability of...

NITROGEN FIXATION

Nitrogen Fixation

• The growth of all organisms depend on the availability of Nitrogen (e.g. amino acids)

• Nitrogen in the form of Dinitrogen (N2) makes up 80% of the air we breathe but is essentially inert due to the triple bond (NN)

• In order for nitrogen to be used for growth it must be "fixed" (combined) in the form of ammonium (NH4) or nitrate (NO3) ions.

Nitrogen Fixation

• The nitrogen molecule (N2) is quite inert. To break it apart so that its atoms can combine with other atoms requires the input of substantial amounts of energy.

• Three processes are responsible for most of the nitrogen fixation in the biosphere:

• atmospheric fixation

• biological fixation • industrial fixation

Industrial Fixation

• Under great pressure, at a temperature of 600oC, and with the use of a catalyst, atmospheric nitrogen and hydrogen (usually derived from natural gas or petroleum) can be combined to form ammonia (NH3).

• Ammonia can be used directly as fertilizer, but most of its is further processed to urea and ammonium nitrate (NH4NO3).

Haber-Bosch

3CH4 + 6H2O --> 3CO2 + 12H2

4N2+12H2 --> 8NH3 (high T,press)

Changing Nitrogen Cycle

Humans have doubled the N fixation rates

over natural levels

Nitrogen Fixation Process

Energetics• NN• Haber-Bosch (100-200 atm, 400-500°C,

8,000 kcal kg-1 N)• Nitrogenase (4,000 kcal kg-1 N)

Biological Fixation

The ability to fix nitrogen is found only in certain bacteria.

Some live in a symbiotic relationship with plants of the legume family (e.g., soybeans, alfalfa).

Some establish symbiotic relationships with plants other than legumes (e.g., alders).

Some nitrogen-fixing bacteria live free in the soil. Nitrogen-fixing cyanobacteria are essential to

maintaining the fertility of semi-aquatic environments like rice paddies.

Biological Fixation cont.

• Biological nitrogen fixation requires a complex set of enzymes and a huge expenditure of ATP.

• Although the first stable product of the process is ammonia, this is quickly incorporated into protein and other organic nitrogen compounds.

• Scientist estimate that biological fixation globally adds approximately 140 million metric tons of nitrogen to ecosystems every year.

Some nitrogen fixing organisms

• Free living aerobic bacteriao Azotobactero Beijerinckiao Klebsiellao Cyanobacteria (lichens)

• Free living anaerobic bacteriao Clostridiumo Desulfovibrioo Purple sulphur bacteriao Purple non-sulphur bacteriao Green sulphur bacteria

• Free living associative bacteriao Azospirillum

• Symbiontso Rhizobium (legumes)o Frankia (alden trees)

Some nitrogen fixing organisms

Estimated Average Rates of Biological N2 Fixation

40-3001-1501-50

50-15050

Actinorhizal plant symbioses with FrankiaAlnusHippophaëCeanothusCoriariaCasuarina

50-100100-600

Leguminous plant symbioses with rhizobiaGrain legumes (Glycine, Vigna, Lespedeza, Phaseolus)Pasture legumes (Trifolium, Medicago, Lupinus)

10-20300

40-80

Cyanobacterial associationsGunnera AzollaLichens

5-25Grass-Bacteria associative symbioses

Azospirillum

250.3

0.1-0.5

Free-living microorganismsCyanobacteria Azotobacter Clostridium pasteurianum

N2 fixed (kg ha-1 y-1)Organism or system

Rank of Biological Nitrogen Fixation

0.1 - 25Free- living

5 - 25Rhizosphere associations

10 - 300Cyanobacteria- moss

50 - 600Rhizobium-legume

Nitrogen Fixation (kg N/ha/year)

N2 fixing system

Nitrogen Fixation

• All nitrogen fixing bacteria use highly conserved enzyme complex called Nitrogenase

• Nitrogenase is composed of of two subunits: an iron-sulfur protein and a molybdenum-iron-sulfur protein

• Aerobic organisms face special challenges to nitrogen fixation because nitrogenase is inactivated when oxygen reacts with the iron component of the proteins

Nitrogenase

FeMo Cofactor

N2 + 8H+

2NH3 + H2

8e-

4C2H2 + 8H+ 4C2H2

DinitrogenaseDinitrogenasereductase

Fd(red)

Fd(ox)

nMgATP

nMgADP + nPi

N2 + 8H+ + 8e- + 16 MgATP 2NH3 + H2 + 16MgADP

Nitrogenase

Genetics of Nitrogenase

Dinitrogenase reductaseDinitrogenaseRegulatory, activator of most nif and fix genesFeMo cofactor biosynthesisFeMo cofactor biosynthesisUnknownElectron transferRegulatoryRegulatory, two-component sensor/effectorElectron transferTransmembrane complex

nifHnifDKnifAnifBnifENnifSfixABCXfixKfixLJfixNOQPfixGHIS

Properties and functionGene

Types of Biological Nitrogen Fixation

Free-living (asymbiotic)• Cyanobacteria• Azotobacter

Associative• Rhizosphere–Azospirillum• Lichens–cyanobacteria• Leaf nodules

Symbiotic• Legume-rhizobia• Actinorhizal-Frankia

Free-living N2 Fixation

Energy• 20-120 g C used to fix 1 g N

Combined Nitrogen• nif genes tightly regulated• Inhibited at low NH4

+ and NO3- (1 μg g-1 soil, 300 μM)

Oxygen• Avoidance (anaerobes)• Microaerophilly• Respiratory protection• Specialized cells (heterocysts, vesicles)• Spatial/temporal separation• Conformational protection

Heterocyst

Associative N2 Fixation

• Phyllosphere or rhizosphere (tropical grasses)• Azosprillum, Acetobacter• 1 to 10% of rhizosphere population• Some establish within root• Same energy and oxygen limitations as free-

living• Acetobacter diazotrophicus lives in internal

tissue of sugar cane, grows in 30% sucrose, can reach populations of 106 to 107 cells g-1 tissue, and fix 100 to 150 kg N ha-1 y-1

Phototrophic N2-fixing Associations

• Lichens–cyanobacteria and fungi• Mosses and liverworts–some have associated

cyanobacteria• Azolla-Anabaena (Nostoc)–cyanobacteria in

stem of water fern Gunnera-Nostoc–cyanobacteria in stem nodule of dicot Cycas-Nostoc–cyanobacteria in roots of gymnosperm

Azolla pinnata (left) 1cm. Anabaena from crushed leaves Of Azolla.

Simbiosis Anabaena-Azolla

Frankia and Actinorhizal Plants

• Actinomycetes (Gram +, filamentous); septate hyphae; spores in sporangia; thick-walled vesicles

Frankia vesicles showing thick walls that confer protection from oxygen. Bars are 100 nm.

Alder and the other woody hosts of Frankia are typical pioneer species that invade nutrient-poor soils. These plants benefit from the nitrogen-fixing association, while supplying the bacterial symbiont with photosynthetic products.

Actinorhizal Plant Hosts

DatiscaDatiscaceae

CoriariaCoriariaceae

Cercocarpus, Chamaebatia, Cowania, Dryas, Purshia

Rosaceae

Ceanothus, Colletia, Discaria, Kentrothamnus, Retanilla, Talguenea, Trevoa

Rhamnaceae

Elaeagnus, Hippophaë, ShepherdiaElaeagnaceae

Comptonia, MyricaMyricaceae

Allocasuarina, Casuarina, Ceuthostoma, Gymnostoma

Casuarinaceae

AlnusBetulaceae

GeneraFamily

Legume-Rhizobium Symbiosis

• The subfamilies of legumes (Caesalpinioideae, Mimosoideae, Papilionoideae), 700 genera, and 19,700 species of legumes

• Only about 15% of the species have been evaluated for nodulation

• Rhizobiumo Gram -, rodo Most studied symbiotic N2-fixing bacteriao Now subdivided into several generao Many genes known that are involved in nodulation (nod, nol,

noe genes)

Taxonomy of Rhizobia

Aeschynomene (stem nodule)spp.Photorhizobium

Galega (goat’s rue), Leucaenagalegae[Rhizobium]

Lotus (trefoil)Astragalus (milkvetch)Cicer (chickpea)

Cicer (chickpea)

lotihuakuiiciceritianshanensemediterraneum

‘Meso rhizobium’

Sesbania (stem nodule)caulinodansAzorhizobium

Glycine (soybean)Glycine (soybean)Glycine (soybean)

japonicumelkaniiliaoningense

Bradyrhizobium

Melilotus (sweetclover), Medicago (alfalfa), TrigonellaGlycine (soybean)Sesbania Sesbania, Acacia

melilotifrediisaheliteranga

Sinorhizobium

Trifolium (clovers)Pisum (peas), Vicia (field beans), Lens (lentils), LathyrusPhaseolus (bean)Phaseolus (bean), LeucaenaPhaseolus (bean)

leguminosarum bv. trifolii“ bv. viciae“ bv. phaseolitropicietli

Rhizobium

Host plantSpeciesGenus

Rhizobium Root Nodules

The picture above shows a clover root nodule. Available from [Internet]

Rhizobium Root Nodules

A few legumes (such as Sesbania rostrata) have stem nodules as well as root nodules. Stem nodules (arrows) are capable of photosynthesis as well as nitrogen fixation.

Formation of a Root Nodule

Nodulation in Legumes

Infection Process

• Attachment• Root hair curling• Localized cell wall

degradation• Infection thread• Cortical cell

differentiation• Rhizobia released into

cytoplasm• Bacterioid

differentiation (symbiosome formation)

• Induction of nodulins

Role of Root Exudates

General• Amino sugars, sugars

Specific• Flavones (luteolin), isoflavones

(genistein), flavanones, chalcones

• Inducers/repressors of nod genes

• Vary by plant species• Responsiveness varies by

rhizobia species

nod Gene Expression

Commonnod

genes

Nod factor–LCO(lipo-chitin

oligosaccharide)

Nodule Metabolism

Oxygen metabolism• Variable diffusion barrier• Leghemoglobin

Nitrogen metabolism• NH3 diffuses to cytosol• Assimilation by GOGAT• Conversion to organic-N

for transportCarbon metabolism• Sucrose converted to

dicarboxylic acids• Functioning TCA in

bacteroids• C stored in nodules as

starch

• Anaerobic jar

Anaerobic Culture Methods

• Anaerobic chamber

Anaerobic Culture Methods

• Encourages growth of desired microbe• Assume a soil sample contains a few

phenol-degrading bacteria and thousands of other bacteriao Inoculate phenol-containing culture medium with

the soil and incubateo Transfer 1 ml to another flask of the phenol

medium and incubateo Transfer 1 ml to another flask of the phenol

medium and incubateo Only phenol-metabolizing bacteria will be

growing

Enrichment Media

• Suppress unwanted microbes and encourage desired microbes.

Selective Media

Streak Plate

• After incubation, count colonies on plates that have 25-250 colonies (CFUs)

Plate Count