10. NITROGEN TURNOVER
Nitrogen – very important component of all
and esp. of microbial cells (amino acids,
proteins, nucleic acids,)
10.1. Ammonification
= the main mineralization reaction in Ncycling, very typical especially in soils
 Organic N-substances
NH3, NH4+
 Main substances for ammonification:
amino acids, proteins, nucleic acids, urea,
chitin, uric acid, peptidoglycan…
 Aerobic and anaerobic
 Psychrophils, mesophils, thermophils
 Ammonification is significantly influenced
by C:N ratio:
25 : 1 – OK for microorganisms – they
have enough energy sources and
nutrients (C + N)
< 25 : 1 - Surplus of nitrogen – high
production of NH3
< 25 : 1 – Shortage of nitrogen in
decomposable material, slow breakdown
of substances, N from other sources will
be used (soil solution); result =
immobilization - flow of N into
microbial cells
 The use of NH4+
- source of N for biosynthesis
(microorganisms prefer often NH4+to
NO3-, ± plants)
- source of energy through nitrification
- volatisation
- sorption on soil clays and organic
matter
- component of soil exchange complex
- leaching (underground and surface
water
 Protein ammonification
The most important ammonification
Protein hydrolysis to amino acids
Amino acids deamination
NH3
Aerobic products - NH3, CO2…. (Bacillus,
Pseudomonas…)
Anaerobic products - NH3, CO2, H2S,
scatol, indol, mercaptans….
(Clostridium…)
10.2. Autotrophic nitrification
Aerobic oxidation of NH3 in two steps
Chemolithotrophic autotrophs
Source of energy for nitrifying bacteria
Conditions: aeration, pH (opt. 6.6 – 8.0),
moisture, temperature
Nitrification = index of soil fertility
 Nitritation
NH4+ + O2
NO2- + H2O (+E)
Nitrosomonas, Nitrosococcus, Nitrosocystis
 Nitratation
NO2- + O2
NO3- (+E)
(Nitrobacter, Nitrococcus)
 Significance of nitrification
Source of energy for nitrifying bacteria
NO3- - main source of N for plants
NO3- is used in denitrification
NO3- is less stable in soil (anion), the result
- high losses of N
Leaching into underground water –
limitation for its use as a drinking
water
Leaching into surface water – it could
resulted in eutrophisation = developing
of algae, the biomass decomposition
using O2
Shortage of O2 for higher
organisms
Nitrification in farm yard manure is
undesirable – it can result in nitrogen
losses
10.3. Heterotrophic nitrification
Heterotrophic bacteria and fungi convert
organic N-substances directly to NO3- – the
rate is 4times slower than autotrophic
nitrification
RNH2 RNHOH RNO
RNO3 NO3-3
-1
+1
+3
+5
Typical for acidic environment
Bacteria: Arthrobacter, Mycobacterium
Fungi:Aspergillus,Penicillium, Cladosporium
10.4. Denitrification
= microbial reduction of NO3- in anaerobic
conditions
 Dissimilative denitrification
NO3-
NO2-
NO
N 2O
N2
= alternative respiration chain in which O
from nitrates is an acceptor of H+
- for denitrifiers the source of energy
- mostly heterotrophic bacteria, strong
dependence on C availability
- denitrifying genera: Pseudomonas,
Alcaligenes, Bacillus, Thiobacillus,
Rhizobium, Paracoccus
- conditions: -O2, N oxides (NO3-) as
oxidant, organic substances or HS- or
NH4- as reductant
- agriculturally undesirable soil process –
loss of nitrogen
- environmentally: when the N-oxides
are produced = undesirable process –
changes in atmosphere (green-houses
gasses)
 Assimilative denitrification
= anaerobic respiration
NO3- + H+
NH4+ + H2O (+E)
- for denitrifiers the source of energy
- if surplus of NO3- process positive,
NH4+ more stabile in the soil
- the use of NH4+ - see ammonification
10.5. N2 fixation
very important process returning N2 to soil
 Total inputs – (kg. year-1) (Paul, Clark,
1996):
N2 fixation
175 000
Fertilizers
85 000
Lightning
20 000
Anthropogenic
40 000
Total
320 000
 Legumes
140 kg.ha-1.y-1
Rice
Meadows
Other cultivated crops
Forest
30 kg.ha1.y-1
15 kg.ha-1.y-1
5 kg.ha-1.y-1
10 kg.ha-1.y-1
 Nitrogenase reduce N2 in strictly
anaerobic conditions
N2 HN=NH
H2N-NH2
2 NH3 2NH4+
High need for energy (ATP)
 Diazotrophs include: organotrophs,
phototrophic sulphur bacteria,
cyanobacteria
 Soil free living bacteria: Clostridium,
Azotobacter
 Associative bacteria: Azospirillum
 Symbiotic bacteria: Frankia (fixation in
vesicle); Rhizobium, Bradyrhizobium etc.
(fixation with bacteroids)
 Clostridium
G+ spore forming straight anaerobic
bacterium
Source of energy – different organic Csubstances (from simple to complex)
Present also in lower pH (> 5)
Fixation approx. 5 kg.ha-1.y-1
Presence: several soils
 Azotobacter
G- non-sporulating pleiomorphic
aerobic bacterium (cocci – rods)
Source of energy – simple organic Csubstances
Present in neutral soils, pH close to 7
Need for P, Ca, K…
Fixation approx. 5 - 10 kg.ha-1.y-1
Presence: in high quality soils
 Symbiotic fixation
Attributed to several plants
Most important in legumes (700 genera
with 14000 species)
Frankia and group of rhizobia
(Rhizobium, Bradyrhizobium ….)
 Rhizobium (nodule forming bacteria)
G- pleiomorphic rods (straight in soil and in
laboratory media, branched in root nodules
= bacteroids)
N2 fixation occurs only in the roots if the
content of soil nitrogen is low (organic Nsubstances, NH4+, NO3-)
O2 control with leghemoglobin
High demand for energy:
N2+6e-+12ATP+8H- = 2NH3+12ADP+12Pi
NH3 (NH4+) is incorporated into organic
forms (amino acids) in the associated
plant cells
Process is genetically coded:
Nif-genes: nitrogenase
Nod-genes: nodulation
Process of nodulation
- attachment on the root (specific lectins)
- infection of root hairs
- rhizobia moving through root
- forming plant peribacteroid membrane
(fixation is carried on by specialized
cells)
- rhizobia change into bacteroids
- nitrogen fixation (plant is giving sugars,
rhizobia NH3) = “pure symbiosis”
- destroying of old nodules, lyses of cells,
mineralization
Level of fixation:
(0) – 50 – 150 (800) kg.ha-1.y-1
Inoculation
To improve N2 fixation seeds could be
inoculated before sowing
Rhizobia are specific for nearly each
plant genera
10.6. Immobilisation
 Inorganic substances are used in
biosynthesis to produce organic substances
as a component of living cells (result = cell
growing, cell division)
Inorganic
Organic
Demand for energy
 Examples:
NH4+
Amino acids
SO42-
Methionine (amino acid)
H2PO4- + ADP
CO2
Proteins
ATP
Glucose
 Influence of biogenic elements ratio
(optimum):
C:N
25 : 1
C:P
100 : 1
C:S
400 : 1
 Very typical process for soil – flow of
elements from soil solution into microbial
cells
 Significance for soil
Positive – when nutrients are in surplus,
leaching is avoided, the nutrients are
“stored” in microbial cells, their death
and mineralization return nutrients into
soil
Negative – when there are not enough
nutrients in soil, the competition
appears between plants a
microorganisms