13. SOIL MICROBIOLOGY
13.1. INTRODUCTION
 Soil main roles
(1) medium for plant growth
(2) water controlling in the hydrologic
system
(3) nature’s recycling system
(4) habitats for living organisms
(5) an engineering medium in humanbuild ecosystems
 Soil definition
Natural body formed from “parent
material” as a result of chemical,
physical and biological processes;
regularly it is divided into horizontal
layers – soil horizons
 Soil volume composition
(1) 45 % mineral component
(2)
5 % organic component (in CR
mostly 1-3 (6) %)
(3) 50% pores (20-30 % water, 20-30 %
air, optimum 30 % water)
 Soil organic matter (SOM)
Only 1-6 %, but crucial significance for
soil properties. Composition:
(1) living organisms (= soil biomass);
microorganisms, zooedafon, living
roots
(2) remains of plants, animals and
microorganisms
(3) remains in decomposition
(4) humus
(Soil = main reservoir of microbes)
 Humus
(1) black (brown) organic part of SOM
(2) very complex
(3) resistant to microbial decomposition
(half time of decomposition from tens
to thousands years; plant residues
weeks or months)
(4) narrow C:N ratio (10-12 : 1); for plant
material very often more than 60 : 1
(5) important for soil structure, water
holding capacity, nutrient stability…..
= soil fertility
 Soil mineral constituents
Huge diversity in the size and composition
(1) stones, gravel … (> 2 mm)
(2) sand (2 – 0.05 mm)
(3) silt (0.05 – 0.002 mm)
(4) clay (< 0.002)
The proportion of particles = soil texture
(sandy loam, silty clay…)
Soil structure – the possibility of soil
particles to form aggregates
 Soil (water) solution
Regularly soil solution contains small but
significant quantities of soluble inorganic
compounds = nutrients for plants and
microorganisms
Important concentration of H+ and OHions (pH)
 Soil air
Soil air differs from atmospheric – great
variability, high moisture, the content of
CO2 higher than O2 (may be 5-10 %)
13.2. MAIN SOIL MICROORGANISM
GROUPS
 General composition (Brady, Weil 1999)
Number/g
kg/ha
Bacteria
108-109
400-5000
Actinomyces 107-108
400-5000
Fungi
105-106
1000-15000
Algae
104-105
10-500
Protozoa
104-105
20-200
Nematodes
10 –102
10-150
Mites
1-10
5-150
Collembola
1-10
5-150
Earthworms
100-1500
Other fauna
10-100
(Usually the total biomass of
microorganisms = 5000 – 13000 kg/ha)
 C-source
Heterotrophs – use of organic C –
substances (mostly saprophytes)
Autotrophs – use of CO2
Mixotrophs - use of CO2 together with
organic C – substances
Zymogenic – decay of plant residues
 Source of energy
Chemotrophs – energy from chemical
substances decomposition
Phototrophs – use of light energy
 Source of electrons, H+
Organotrophs – organic substances
Litotrophs – inorganic substances
 Combinations of the descriptions
Chemoorganotrophic heterotrophs
Chemolitotrophic autotrophs
Photolitotrophic autotrophs
 Physiological (metabolic) groups
Defined according the activities in
metabolic processes:
C-cycling - amylolytic, cellulolytic, butyric
bacteria, (lactic acid bacteria, propionic
bacteria)....
N-cycling – ammonifying b., nitrifying b.
etc.
P-cycling – P-solubilizing bacteria…..
 Important genera (examples):
Non-sporulating rods: Pseudomonas,
Mycobacterium, Arthrobacter, Rhizobium
Spore-forming bacteria – Bacillus,
Clostridium
Cocci – Staphylococcus, Micrococcus…
Actinomyces – Streptomyces, Nocardia
Fungi – Mucor, Aspergillus, Penicillium,
Trichoderma, Fusarium…
13.3. RELATIONSHIP AMONG
MICRORGANISMS AND PLANTS
 Spermosphere
Microorganisms living on the surface of
seeds (sometimes problematic – esp.
fungi)
 Phytosphere
Microorganisms living on the surface of
above ground parts of plants (up to
108/g)
Mainly proteolytic – Pseudomonas up to
90 %
Other components: fungi, spore-forming
bacteria (Clostridium, Bacillus), lactic
acid bacteria…
 Rhizosphere
Ecological niche – surface and close
surroundings of plant roots
Microflora is influenced by root
exudates (source of simple nutrients)
Rhizosphere effect = the change of
microflora:
(1) low diversity (non-sporulating rods
prevail);
(2) the higher population /2-1000
times/ than in root-free soil (ratio
R/S)
 Mycorrhizae
Symbiotic association between a fungus
and plant root, sometimes obligatory
Significance:
(1) for plant: better water and
nutrients supply
(2) for fungus: source of C-substances
(3) root fungi activity in mineralisation
Vesicular-arbuscural mycorrhizae
(VAM), fungus is present into root
cells forming vesicules and arbuscules
13.4.SOIL MICROORGANISM
FUNCTIONS
13.4.1. SOIL FORMATION (SF)
Factors influencing soil formation:
(1) parent materials
(2) climate
(3) biota
(4) topography
(5) time
SF starts with rock (parent material)
weathering – physical, chemical biological (breakdown, synthesis,
disintegration, decomposition)
Physical – influence of temperature, water
(ice), wind, plants, animals….
Chemical – water (hydrolysis), oxygen
and esp. organic and inorganic acids
originated by biological activities
(H2CO3, H2SO4, HNO3, oxalic acid…..)
Important role of autothrophs during SF
= synthesis of organic substances
Synthesis of humus substances
Role of living organisms:
(1) biological weathering
(2) organic matter accumulation
(3) profile mixing
(4) nutrient stability
(5) aggregate formation (stability)
13.4.2. CARBON CYCLING
13.4.3. NITROGEN CYCLING
13.4.4. PHOSPHORUS CYCLING
13.4.5. SULPHUR CYCLING
13.4.6. MINERALISATION
Organic substances
Inorganic subst.
= one of main function of microorganisms,
usually it starts with hydrolysis
= source of nutrients for plants, microbes..
Examples for soil:
 Carbon substances
(cellulose, hemicellulose, pectin, lignin,
organic acids…)
Aerobic respiration
Org. C-substances CO2 + H2O + E
Butyric fermentation (anaerobic)
Org. C-substances
CO2 + acids
(butyric, acetic…) + alcohols +
H2 + e
(Non complete mineralisation)
 Nitrogen cycling
(proteins, amino acids, urea, nucleic
acids, chitin…)
Ammonification (both aerobic and
anaerobic)
Org. N-substances
NH4+ + others
 Phosphorus cycling
(ATP, nucleic acids, phosphoproteins,
phytates…)
Org. P-substances
H2PO4-, HPO42-,
PO43 Sulphur cycling
(methionine, cystine, organic ester
sulphates…)
Org. S-substances
H2S (anaerobic)
Org. S-substances
SO42 Priming effect
= the higher level (speed) of
mineralisation after amendment of
easily mineralisable substances to
slowly mineralisable substances
Significance:
- decomposition of complex substances
- detoxification of xenobiotics
13.4.7. HUMIFICATION
= process of humus formation (synthesis)
from organic material
Humus = complex of amorphous and
colloidal substances; dark colour;
narrow ratio of C : N (10-12 : 1); very
low level of degradability (half time of
mineralisation - from tens to thousands
years)
Conditions for humification:
(1) source of organic matter
(2) external conditions
(3) microflora
 Source of organic matter (OM)
OM = source both of components for
humus synthesis and energy
OM with short half time of
mineralisation = source of energy
(simple substances – root exudates, the
finest roots…)
OM with medium or long half time of
mineralization = source of humus
components + source of energy (plant
residues, farmyard manure, compost)
Decomposition
Rapid
Energy Components
Good
Bad
Sugars, starches
Crude proteins
Hemicellulose
Cellulose
Fats, waxes
Lignin, phenolics
Very slow
Bad
Good
Decomposition of organic residues
100%= mineralisation (CO2) 60-80 %
biomass
6-8 %
non-humus sub.
6-8 %
humus
10-30 %
Three phases of humus synthesis
(1) breakdown of water soluble
substances – mostly energy
production
(2) breakdown of insoluble substances,
production of intermediates
(3) physical and chemical phase –
condensation and polymerisation,
stable humus is produced
 External conditions for humus synthesis
Temperature
generally 20°-65°C, optimum 30° –
45°C,
with growing temperature the speed is
growing but mineralisation is also
higher (lower humus production)
high temperature is important for
destruction of pathogens and weed
seeds
Aeration
higher aeration stimulates
mineralisation; humus production is
lower but high quality; optimum =
combination of aerobic (dominant)
and anaerobic conditions
Water
optimum humidity for soil – 60% of
maximum water holding capacity
optimum humidity for composting –
approx. 65 relative %
pH
optimum 7 (6 – 7) for high quality of
humus
Other factors
climate, erosion, exposition, parent
material…
 Microflora
Synthesis of humus = responsibility of
soil microorganisms
There are not special microorganisms
responsible only for humification –
this is the activity of complex soil
microflora
The process starts with bacteria very
quickly followed by fungi and is
completed with actinomyces
Two main microbial phases:
(1) bacterio-fungi phase
(2) actinomycetal phase
HUMUS
 Components:
Fulvic acids – yellow, lower stability,
half time of mineralisation (2) 10 –
200 years
Humic acids – dark (brown, black),
high stability, half time of
mineralisation 800 – 4000 years
Humins – very stable, biologically less
activity, half time of mineralisation
> 4000 years
 Significance:
Physical properties (structure - pores,
water capacity…)
Chemical properties (sorption of
nutrients, cation exchange capacity,
pH – buffering…)
Biological properties (improving
conditions for soil biota)
13.4.8. IMMOBILISATION
= anabolic process needing energy
Inorganic subst. Organic substances
in living organisms
Result = growing microbial biomass
 Examples:
NH4+
Amino acids (Proteins)
NO3- ( NH4+)
Amino acids
(Proteins)
SO42cystine (-SH)
H2PO4phospho-organic subst.
 Influence of carbon content; nearly all
N, S, P is immobilized if
C:N
>40:1
C:S
>(200) 400:1
C:P
>100:1
 Significance:
Positive – nutrients are “stored” in soil,
less probability of leaching and
erosion losses
Negative – competition between plants
and microorganisms, organic subst.
cannot be used by plants
13.4.9. SOIL SICKNESS
Usually result of monocultures, exp. some
plants – apple tree, lucerne, some
vegetables…..
Less sensitive – cereals esp. corn (maize)
Signs:
Shortage of some nutrients
Higher pathogen incidence
Decreasing microbial diversity
Changes in decomposition activity
Some metabolites are increasing
Result = worse soil biological quality, bad
plant growth, decreasing yield of
agricultural plants
Solution:
Plant diversity
Agriculture – plant rotation
Organic fertilizing
Soil improving – pH, watering…
13.4.10.
DETOXICATION
Growing significance last decades with the
higher environment pollution (the higher
use of xenobiotics).
Detoxification = natural activity of soil
microorganisms, three levels:
(1) main metabolic pathway (pollutant =
source of nutrients or/and energy)
(2) secondary utilization, (pollutant =
secondary source of nutrients or/and
energy)
(3) co-metabolism (individual molecules of
pollutant are metabolised, importance
for microorganisms is very limited
Biodegradability is defined by “half-time
of decomposition”
Chlorinated hydrocarbons 2-5y
Triazine herbicides
1-2y
Urea herbicides
2-10mo
Organophosphate insect.
1-12wk
Carbamate insecticides
1-8wk
Variants of detoxification
(decontamination, bioremediation):
“in situ” – for low level of soil
contamination, improving by
optimisation of soil properties (pH,
content of water and nutrients,
aeration, cultivation…)
“ex situ” – for higher level of soil
contamination,
(1) soil removing
(2) dilution with non-contaminated
material
(3) nutrient level (ratio C:N:P)
improvement
(4) pH
(5) inoculation
(6) processes management (aeration,
watering…
“ex situ” detoxification variants:
land-farming
bed reactor
bioventing etc.
Microorganisms active in
decontamination:
Achromobacter
Alcaligenes
Arthrobacter
Pseudomonas
Trichoderma
Aspergillus
Penicillium
13.4.11.
SELFCLEANING
= result of soil homeostasis = self
regulation
= antagonistic relations between
autochthonous and alochthonous soil
microflora
Contaminated microorganisms are
eliminated by usual typical soil
microorganisms
Principles:
- nutrient competition
- space competition
Significance – positive process, “soil
health” esp. elimination of pathogens
(both plant and animal)
Stimulation:
- crop diversity, crop rotation
- external conditions regulation (pH,
aeration, water content, nutrient
content…)