Nitrogen assimilation is the formation of organic nitrogen compounds like amino acids from inorganic nitrogen compounds present in the environment. Organisms like plants, fungi and certain bacteria that cannot fix nitrogen gas (N2) depend on the ability to assimilate nitrate or ammonia for their needs. Other organisms, like animals, depend entirely on organic nitrogen from their food.

1. Nitrogen assimilation
Nitrogen assimilation is the formation of organic nitro-
gen compounds like amino acids from inorganic nitrogen
compounds present in the environment. Organisms like
plants, fungi and certain bacteria that cannot fix nitro-
gen gas (N2) depend on the ability to assimilate nitrate or
ammonia for their needs. Other organisms, like animals,
depend entirely on organic nitrogen from their food.
1 Nitrogen assimilation in plants
Plants absorb nitrogen from the soil in the form of nitrate
(NO3
−
) and ammonium (NH4
+
). In aerobic soils where
nitrification can occur, nitrate is usually the predominant
form of available nitrogen that is absorbed.[1][2]
However
this need not always be the case as ammonia can pre-
dominate in grasslands[3]
and in flooded, anaerobic soils
like rice paddies.[4]
Plant roots themselves can affect the
abundance of various forms of nitrogen by changing the
pH and secreting organic compounds or oxygen.[5]
This
influences microbial activities like the inter-conversion of
various nitrogen species, the release of ammonia from or-
ganic matter in the soil and the fixation of nitrogen by
non-nodule-forming bacteria.
Ammonium ions are absorbed by the plant via ammonia
transporters. Nitrate is taken up by several nitrate
transporters that use a proton gradient to power the
transport.[6][7]
Nitrogen is transported from the root to
the shoot via the xylem in the form of nitrate, dissolved
ammonia and amino acids. Usually[8]
(but not always[9]
)
most of the nitrate reduction is carried out in the shoots
while the roots reduce only a small fraction of the ab-
sorbed nitrate to ammonia. Ammonia (both absorbed
and synthesized) is incorporated into amino acids via the
glutamine synthetase-glutamate synthase (GS-GOGAT)
pathway.[10]
While nearly all[11]
the ammonia in the root
is usually incorporated into amino acids at the root itself,
plants may transport significant amounts of ammonium
ions in the xylem to be fixed in the shoots.[12]
This may
help avoid the transport of organic compounds down to
the roots just to carry the nitrogen back as amino acids.
Nitrate reduction is carried out in two steps. Nitrate is
first reduced to nitrite (NO2
−
) in the cytosol by nitrate
reductase using NADH or NADPH.[7]
Nitrite is then re-
duced to ammonia in the chloroplasts (plastids in roots)
by a ferredoxin dependent nitrite reductase. In photosyn-
thesizing tissues, it uses an isoform of ferredoxin (Fd1)
that is reduced by PSI while in the root it uses a form of
ferredoxin (Fd3) that has a less negative midpoint poten-
tial and can be reduced easily by NADPH.[13]
In non pho-
tosynthesizing tissues, NADPH is generated by glycolysis
and the pentose phosphate pathway.
In the chloroplasts,[14]
glutamine synthetase incorpo-
rates this ammonia as the amide group of glutamine us-
ing glutamate as a substrate. Glutamate synthase (Fd-
GOGAT and NADH-GOGAT) transfer the amide group
onto an 2-oxoglutarate molecule producing two gluta-
mates. Further transaminations are carried out make
other amino acids (most commonly aspargine) from glu-
tamine. While the enzyme glutamate dehydrogenase
(GDH) does not play a direct role in the assimilation,
it protects the mitochondrial functions during periods
of high nitrogen metabolism and takes part in nitrogen
remobilization.[15]
1.1 pH and Ionic balance during nitrogen
assimilation
Every nitrate ion reduced to ammonia produces one OH−
ion. To maintain a pH balance, the plant must either
excrete it into the surrounding medium or neutralize it
with organic acids. This results in the medium around the
plants roots becoming alkaline when they take up nitrate.
To maintain ionic balance, every NO3
−
taken into the root
must be accompanied by either the uptake of a cation or
the excretion of an anion. Plants like tomatoes take up
metal ions like K+
, Na+
, Ca2+
and Mg2+
to exactly match
every nitrate taken up and store these as the salts of or-
ganic acids like malate and oxalate.[16]
Other plants like
the soybean balance most of their NO3
−
intake with the
excretion of OH−
or HCO3
−
.[17]
Plants that reduce nitrates in the shoots and excrete alkali
from their roots need to transport the alkali in an inert
form from the shoots to the roots. To achieve this they
synthesize malic acid in the leaves from neutral precur-
sors like carbohydrates. The potassium ions brought to
the leaves along with the nitrate in the xylem are then
sent along with the malate to the roots via the phloem. In
the roots, the malate is consumed. When malate is con-
verted back to malic acid prior to use, an OH−
is released
and excreted. (RCOO−
+ H2O -> RCOOH +OH−
) The
potassium ions are then recirculated up the xylem with
fresh nitrate. Thus the plants avoid having to absorb and
store excess salts and also transport the OH−
.[18]
Plants like castor reduce a lot of nitrate in the root itself,
and excrete the resulting base. Some of the base produced
in the shoots is transported to the roots as salts of organic
1

2. 2 2 REFERENCES
NO3-
RCOO-
RCOOH
K+
K+
Vacoule
RCOO-
K+
RCOO-
RCOOH
NH3
Amino
Acids
NO3-
NH3
Amino
Acids
NO3- K+
Shoot
Root
Tomato
Castor
Soybean
Different plants use different pathways to different levels. Toma-
toes take in a lot of K+
and accumulate salts in their vacuoles,
castor reduces nitrate in the roots to a large extent and excretes the
resulting alkali. Soy bean plants moves a large amount of malate
to the roots where they convert it to alkali while the potassium is
recirculated.
acids while a small amount of the carboxylates are just
stored in the shoot itself.[19]
2 References
[1] Xu, G.; Fan, X.; Miller, A. J. (2012). “Plant Nitro-
gen Assimilation and Use Efficiency”. Annual Review
of Plant Biology. 63: 153–182. doi:10.1146/annurev-
arplant-042811-105532. PMID 22224450.
[2] Nadelhoffer, KnuteJ.; JohnD. Aber; JerryM. Melillo
(1984-10-01). “Seasonal patterns of ammonium and ni-
trate uptake in nine temperate forest ecosystems”. Plant
and Soil. 80 (3): 321–335. doi:10.1007/BF02140039.
ISSN 0032-079X.
[3] Jackson, L. E.; Schimel, J. P.; Firestone, M. K.
(1989). “Short-term partitioning of ammonium and ni-
trate between plants and microbes in an annual grass-
land”. Soil Biology and Biochemistry. 21 (3): 409–415.
doi:10.1016/0038-0717(89)90152-1.
[4] Ishii, S.; Ikeda, S.; Minamisawa, K.; Senoo, K.
(2011). “Nitrogen cycling in rice paddy environ-
ments: Past achievements and future challenges”. Mi-
crobes and environments / JSME. 26 (4): 282–292.
doi:10.1264/jsme2.me11293. PMID 22008507.
[5] Li, Y. L. N.; Fan, X. R.; Shen, Q. R. (2007). “The re-
lationship between rhizosphere nitrification and nitrogen-
use efficiency in rice plants”. Plant, Cell & Environment.
31 (1): 73–85. doi:10.1111/j.1365-3040.2007.01737.x.
PMID 17944815.
[6] Sorgonà, A.; Lupini, A.; Mercati, F.; Di Dio, L.; Sun-
seri, F.; Abenavoli, M. R. (2011). “Nitrate uptake along
the maize primary root: An integrated physiological and
molecular approach”. Plant, Cell & Environment. 34 (7):
1127–1140. doi:10.1111/j.1365-3040.2011.02311.x.
[7] Tischner, R. (2000). “Nitrate uptake and reduction
in higher and lower plants”. Plant, Cell and Envi-
ronment. 23 (10): 1005–1024. doi:10.1046/j.1365-
3040.2000.00595.x.
[8] Scheurwater, I.; Koren, M.; Lambers, H.; Atkin, O. K.
(2002). “The contribution of roots and shoots to whole
plant nitrate reduction in fast- and slow-growing grass
species”. Journal of Experimental Botany. 53 (374):
1635–1642. doi:10.1093/jxb/erf008. PMID 12096102.
[9] Stewart, G. R.; Popp, M.; Holzapfel, I.; Stewart, J.
A.; Dickie-Eskew, A. N. N. (1986). “Localization
of Nitrate Reduction in Ferns and Its Relationship to
Environment and Physiological Characteristics”. New
Phytologist. 104 (3): 373–384. doi:10.1111/j.1469-
8137.1986.tb02905.x.
[10] Masclaux-Daubresse, C.; Reisdorf-Cren, M.; Pageau, K.;
Lelandais, M.; Grandjean, O.; Kronenberger, J.; Val-
adier, M. H.; Feraud, M.; Jouglet, T.; Suzuki, A. (2006).
“Glutamine Synthetase-Glutamate Synthase Pathway and
Glutamate Dehydrogenase Play Distinct Roles in the
Sink-Source Nitrogen Cycle in Tobacco”. Plant Physi-
ology. 140 (2): 444–456. doi:10.1104/pp.105.071910.
PMC 1361315 . PMID 16407450.
[11] Kiyomiya, S.; Nakanishi, H.; Uchida, H.; Tsuji, A.;
Nishiyama, S.; Futatsubashi, M.; Tsukada, H.; Ishioka,
N. S.; Watanabe, S.; Ito, T.; Mizuniwa, C.; Osa, A.;
Matsuhashi, S.; Hashimoto, S.; Sekine, T.; Mori, S.
(2001). “Real time visualization of 13N-translocation
in rice under different environmental conditions using
positron emitting Ttacer imaging system”. Plant Physi-
ology. 125 (4): 1743–1753. doi:10.1104/pp.125.4.1743.
PMC 88831 . PMID 11299355.
[12] Schjoerring, J. K.; Husted, S.; Mäck, G.; Mattsson, M.
(2002). “The regulation of ammonium translocation in
plants”. Journal of Experimental Botany. 53 (370): 883–
890. doi:10.1093/jexbot/53.370.883. PMID 11912231.

3. 3
[13] Hanke, G. T.; Kimata-Ariga, Y.; Taniguchi, I.; Hase, T.
(2004). “A Post Genomic Characterization of Arabidop-
sis Ferredoxins”. Plant Physiology. 134 (1): 255–264.
doi:10.1104/pp.103.032755. PMC 316305 . PMID
14684843.
[14] Tcherkez, G.; Hodges, M. (2007). “How stable iso-
topes may help to elucidate primary nitrogen metabolism
and its interaction with (photo)respiration in C3 leaves”.
Journal of Experimental Botany. 59 (7): 1685–1693.
doi:10.1093/jxb/erm115. PMID 17646207.
[15] Lea, P. J.; Miflin, B. J. (2003). “Glutamate synthase and
the synthesis of glutamate in plants”. Plant Physiology and
Biochemistry. 41 (6–7): 555–564. doi:10.1016/S0981-
9428(03)00060-3.
[16] Kirkby, Ernest A.; Alistair H. Knight (1977-09-01).
“Influence of the Level of Nitrate Nutrition on Ion Up-
take and Assimilation, Organic Acid Accumulation, and
Cation-Anion Balance in Whole Tomato Plants”. Plant
Physiology. 60 (3): 349–353. doi:10.1104/pp.60.3.349.
ISSN 0032-0889. Retrieved 2013-02-19.
[17] Touraine, Bruno; Nicole Grignon; Claude Grignon (1988-
11-01). “Charge Balance in NO3−-Fed Soybean Estima-
tion of K+ and Carboxylate Recirculation”. Plant Physi-
ology. 88 (3): 605–612. doi:10.1104/pp.88.3.605. ISSN
0032-0889. Retrieved 2013-02-23.
[18] Touraine, Bruno; Bertrand Muller; Claude Grignon
(1992-07-01). “Effect of Phloem-Translocated
Malate on NO3− Uptake by Roots of Intact Soy-
bean Plants”. Plant Physiology. 99 (3): 1118–1123.
doi:10.1104/pp.99.3.1118. ISSN 0032-0889. Retrieved
2013-02-19.
[19] Allen, Susan; J. A. Raven (1987-04-01). “Intracellular pH
Regulation in Ricinus communis Grown with Ammonium
or Nitrate as N Source: The Role of Long Distance Trans-
port”. Journal of Experimental Botany. 38 (4): 580–596.
doi:10.1093/jxb/38.4.580. ISSN 0022-0957. Retrieved
2013-02-23.

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