Markéta Marečková
e-mail: sagova@vurv.cz
Microorganisms in soil
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Soil structure and its
Soil ecosystem
Trophic relationships
Key processes
Estimation, models and evaluation
Soil is the most complex environment
Ecosystem
Abiotic
Structure
Biotic
Function
Soil ecosystem
dominated by
•bedrock
•darkness
heterotropic
organisms
predation
porous mixture
of solids, liquids
and gases
•plant nutrition
•decomposition of
OM
Methods of study
Abiotic factors
Solids
Porous material of solids, liquids and gases
Bedrock : e.g. limestone,dolomite (neutral to alkaline), silicate (acidic)
Determines the basic soil pH.
Humus: Humic acids are aromatic and aliphatic remains of lignin, aminoacids
and sugars.
Humus is a product of decomposition, microbial or chemical. Humus is usually
acid and is negatively charged.
Clay particles: large surface, together with humus influence ion exchange.
Negatively charged.
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Adsorbtion afinity: Al 3+ > Ca 2+ = Mg 2+ > K+ = NH3+ >Na+
Maier et al., 2000
Abiotic soil components
sand
mineral
particles
silt
pores
mineral
particles
organic matter
gravel
pores
mineral
particles
organic matter
pores
Struktura půdy
oživení porů
Velikost porů,
odpovídající procesy a organismy.
Na velikostní úrovni jílových částic (μm)
se vyskytují pouze bakterie a houbová
vlákna. Na úrovni prachu (0.063 mm) a
písku (2 mm) se vyskytují kořenové
vlášení, kořeny, prvoci, hlístice.
Meier et al., 2002
Abiotic factors
Water, liquids
Water is the main limiting factor in soil
water content is correlated to organic
matter content
Pore size:
macropores > 0.08 mm, gravitation water, plants
mesopores 0.08 -0.03 mm,capillary water
micropores 0.03-0.005 mm,inside agregates,
bacteria
ultramicropores 0.005-0.0001mm,inside clay
particles
cryptopores < 0.0001mm, too small even for
macromolecules
Maier et al., 2000
Abiotic soil components
Free and bound water
Water potential: force necessary for movement of a certain amount
of water under a given pressure and material
Adhesion (binding force to solid surfaces – matrix potential, Ψm)
Binding to ions (osmotic potencial, ΨS)
Gravitation force (gravitation potencial, Ψg)
Reaches negative values because it is compared to free water. Given in
pressure units.
surface forces, Ψm, - 31 až – 10000 atm
capillary forces, ΨS -0.1 až -30 atm
gravitation forces, Ψg 0 až -0.5 atm
Maier et al., 2000
Soil structure
examples of characteristics
pH
vodivost
Ca
Mg
Al
Fe
humus
% organic
μS
mg/kg
mg/kg
mg/kg
mg/kg
%
%
Alpilles
7.54
256
5900
184
3.0
1.0
2.3
16.1
Bozi Dar
3.27
47
1290
106
5.3
1.4
40.6
95.7
Devin
7.87
200
6210
163
3.0
1.0
1.4
12.0
Kotyz
7.52
310
7600
191
3.0
1.2
3.7
26.6
Meluzina
5.03
86
2700
137
10.4
2.5
18.5
7.6
Nechranice
6.08
64
3470
618
3.0
1.0
7.2
11.6
Oblik
7.9
200
6090
307
3.0
1.0
0.5
21.5
Podyji
5.55
75
2010
404
4.1
2.9
3.2
10.2
Rynholec
6.31
53
2840
83
6.5
1.0
0.1
7.2
Saline Giraud
8.12
21350
3150
67
3.0
1.0
0.0
3.3
slanisko Nesyt
7.97
537
3390
1250
3.0
1.0
0.5
6.6
Srbsko
7.65
141
4740
141
3.0
1.0
0.5
8.2
Slepici vrch
4.57
24
100
29
3.0
1.0
0.7
1.5
Trebon
4.01
80
1160
289
3.4
4.4
3.8
9.1
Soil structure and life niches
Habitat of microorganisms: variable in space and time
(obydlí)
stratified by physical and chemical forces and important
nutrients– C, organické látky, 02, N, P, S
microhabitat
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soil particles
rhizosphere
air bubbles
sufaces of
organisms
life form
active cells, spores, fillaments,
collonies, biofilms
Living forms
Viruses,
phages
Living forms
Diversity of viruses in various soils
•Comparison of agricultural, forest and
alpine soils.
•Highest diversity (Simpson index) was
found in forest soils
•The highest percentage of viruses were
bacteriophages
Living forms
Bacteria
Proteobacteria: pseudomonads, myxobacteria, rhizobia
Acidobacteria
Actinobacteria: streptomycets, corynebacteria
Verrucomicrobia
Firmicutes: bacilli, clostridia, laktobacilli
Planctomycetes
Chondromyces
109 cells and thousands of species per gram soil. Culivativable part is only from tenths to
Aerobic dominate the anaerobic in regular soil several times.
Spatial variability is enourmous.
Streptomyces
Myxococcus
Bacillus
Living forms
Algae and Fungi
Molds
Blue
greens
Nostoc
Algae
Cryptomonas
Aspergillus
Blue green algae and algae live only in top several cm of soil. They often make a
crust or a biofilm and they are adapted to very dry environment even deserts.
Living forms
Protozoa
Amoebas
Acanthamoeba
Heterotrophic flagellates
Paranema
Living forms
Cilliates
Euplotes, Stylonychia
Nemathods
Living forms
Mites
Springtails
Orchesella
Živé složky půdy
Oligochaetes
Lumbricullus variegatus
Mammals
Microtus arvalis
structure
Soil horizons
In soil, organic and anorganic material is layered to soil horizons. They are created by
plant litter and water from rain and groundwater.
Abundance and biomass of soil populations
structure
Distribution by source
Resources occur in soil mostly at aggregates of different sizes. E.g. in upper soil
there are larger pieces of OM than in the lower soil. Bacteria aggregate as site of
sources.
Scale analysis (A) Distribution of soil patches
colonized by bacteria in a two-dimensional grid
with an indication of the four sizes of microsamples
used. (B) Same distribution after the test for the
presence of bacteria. The black and white
elementary units represent positive and negative
results, respectively. (C) Corresponding curves
obtained after sampling, showing the percentages
of positive microsamples as a function of the four
microsample sizes. Different types of distribution
of bacteria are shown in rows a, b, and c.
Grundmann et al.2004
terminal fragment lenght
structure
Inhabiting pore according to its size
T-RFLP profiles
in three fractions
of differently
treated soils
Sessitch et al.2001
Example: The highest number of bacteria phylotypes occurred in the clay fraction.
Protection from predation. Fertilization does not change this relationship. Also highest
diversity in the smaller pores – association with particles is stronger than the nutrient
exchange
structure
Organic matter sources
Organic matter
main factor influencing productivity of soil environment. ovlivňuje:
•plant nutrition
•community composition
•water content
•agregate stability
•erosion control
„Hot spots“ sites of highest mircorbial activity.
90% of activity goes on in 10% of soil volume.
E.g. rhizosphere and burries of animals
The main source of OM is the higher plants. One part of plants is quickly mineralized
to CO2, phosphates, sulfates, nitrates etc. and used by other organisms. the other
part is decomposed only partly and makes up humus. The ration of both
components differes between sites, the most important factors being pH and
moisture. Clay component and humus are the source of soil fertility. Both processes
mineralization and humification are driven by bacteria and fungi. Bacteria and fungi
add to humus also by their bodies which make a biomass of 40-200 g m-2.
structure
Nutrition
DOC
DON
NH4+
NO3-
Example
Relationships between contents of
C, N, bacteria and fungi in soil at
5 diffrent sites (beech, pine,
meadow, organic field, convention
field at 5 and 25 oC.
Sites differ by:
fungi abundance but not that of
bacteria
Fungi quantity correlated with C and
negatively with N. Bacteria correlate
with temperature.
DOC dissolved organic carbon,
DON dissolved organic nitrogen
bacteria
fungi
function
Rate of soil processes
Example
mineralization
All processes are faster at
higher temperature.
Respiration is similar at
all sites.
Mineralization N,
imobilization C
and nitrification are the
highest in a meadow and
smalest in a forest
imobilization N
nitrification
structure
Nutrient consumption
Soil bacteria according to the K-r
selection
K organisms: slow metabolism, consumption of
nutrients from small amoutns of poorly available
sources, large genomes, filamentous forms,
adaptation to harsh conditions (cold, deserts), stay
at sites
Streptomyces, Micromonospora,
Streptosporangium (podřády), myxobakterie
r organisms: fast growing, fast reactions to a
new source, consumption of available sources
at good living conditions, coccal forms, fast
growth, tolerate stress
Burkholderia, Xanthomonas, Agrobacterium,
entherobakterie
structure
C content in soil by source
arable land
meadow
forest
subtropical forest
alpine meadow
microbial C
ug/g
70 - 720
250 - 1080
420 - 980
2670
470
1120
420 - 1770
800 - 1670
1670
330 - 1090
200 - 790
1000 - 2750
total C
%
1.0 - 3.8
3.0 - 6.0
2.5 - 5.5
2.9
2
1.9
0.9 - 2.6
1.2 - 6.0
2.1
0.9 - 1.8
0.7 - 1.3
1.7 - 2.8
Examples of organic C content and microbial C content. In meadow ecosystems
microbial content is higher.
processes
Trophic pyramid
•Soil trophic pyramid is not well known
•Dominating process is decompostion
Predation influences dynamics of the
energy exchange processes
•The best methods to describe are isotope
probing
•Limitation by C except in the rhizosphere
(and by water as at all terrestrial
ecosystems)
predators II
predators I
PP
secundary decomposers
primary decomposers
nutrition
predators I
decomposers, PP
chemolithotrophie
shredded litter,
microorganisms
litter
Trophic relationships
in soil environment
natural meadow ecosystem
wheat monoculture
Agroecosystem is simplified,
no mycorhiza, N2 fixation, limited
nematods and increasing
effect of cilliates
processes
Trophic processes
Two basic types of food webs:
Plant community
Bacterial food web is more typical for high
pH , higher N, and lower soil moisture.
Typical of fast overturn. Predators are
protozoa and nematods. It is controlled by
nutrients (bottom up).
Fungal – oposite, controlled by predation
(top down)
exudates
litter
bacteria
protists
fungal
Food web in rhizosphere is fast.
Production and biomass are several times
higher than in the litter web. Interactions
between plants, bacteria and protozoa are
called a microbial loop. In this community,
predators effectively control bacterial
growth but the effect of secondary
predators is low. Nutrients cycle locally and
are not spread around. Plants give up to 40
% of assimilated carbon to rhizosphere
microorganisms.
energetic canal
based on exudates
based on litter
bacterial
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Carbon and other nutrients
Basic flows of energy and nutrients in soil ecosystems
procesess
Trophic relationships
Trophic relationships
Example:
A field with convention farming
(full) and a field with organic
farming (dashed) were followed
during a year.
Biomass of bacteria and fungi
correlated with temperature.
Maximum of bacterial biomass
was reached in relationship to
soil moisture. This
demonstrates limitation with
water in a soil community.
Bacterivorous nematods were
highest in winter, which shows
high tolerance to T and
avoiding of predators.
Bloem et al., 1994
Function of organisms by body size organismů
predation
predation
predation
grazing
substrate processing
Energy flow
pore formation
litter fragmentation
bioturbation
Habitat formation
Trophic interactions are fast while habitat formation is a long term process
function
Primary production
Chemolithotrophy
Fixace CO2
Energie: oxidace železa, amonných solí, sirníků, síry, kovů, dusitanů
Zastoupení autotrophů podle qPCR
Jourdan et al., 2005
Zastoupení autotrofů v průběhu tří let
Bernhart et al., 2007
Predation
Predation in soil: consumption of heterotrophic organisms with detritus
the main cause of bacterial mortality in soil
soil predators:
bakterivorous: protozoa, nematods, and bacterial predators
phtophagous: mites, springtails
•no cyclic relationships
•high redundancy causes high stability,
•many prey species
•fast nutrient cycle, mineralization
Maier et al., 2000
Function
predation
Escape from predation:
attachement to soil, small pores,
pathogenicity, antibiosis, filaments, biofilm.
Protection from digestion:
release of toxines, intracellular parazitism
Salinas et al., 2007
funkce
Predation
Consumption rate of bactria by prozoa.
5000 bacterial cells per min
800 kg of bacteria per ha per year
Movement of protozoa in soil: flagellates 2-4 cm,
amoebas 3-6 cm, cilliates 1-2 cm
Example:
Correlation between the number of protozoa
and bacteria at different sites in Danmark.
The regular relationship on the figure
demonstrates the possibility of bacteria
control by protozoa at those sites.
Ekelund et al., 2001
Mutualisms of three species
Pisum sativum - Streptomyces lydicus – Rhizobium sp.
Streptomyces lydicus collonizes rhizosphere:
increases the number of nodules i.e. supports infections by nitrogen fixing
Rhizobium sp.,increases the nodule surface, supports growth of rhizobia
mostly by supplying Fe and other nutrients
Fe, other nutrients?
Pisum
sativum
exudates, O2?
S. lydicus
N source ?
N source
nutrients
Rhizobium sp.
Fe, other nutrients
Tokala et al., Appl. Environ. Microbiol. 68, 2161-2171, 2002.
Nodes with a streptomycetes Nodes without streptomycetes
Nodes with streptomycetes have a large surface,
which enables better nutrient utilization
Tokala et al., Appl. Environ. Microbiol. 68, 2161-2171
function
Limitations of microbial processes
Limitation
Microorgansims are limited by specific requirements to moisture and temperature.
They have limited or no capability to move.
Microorganisms are dependent on dispersion by other organisms.
Everything is everywhere but the environment selects.
Adaptation
Microorganisms are adapted to utilization of any organic substrate.
Dispose of often large genomes, which contains pathways expresed under
different conditions.
Microorganisms grow quickly in the lab but very slowly in nature, one generation
between 6 and 18 months, they are waiting for the ideal conditions to come.
V laboratoři rostou velmi rychle, ale v přírodě je obrat mezi 6 a 18 měsíci.
function
Limitations of microbial processes
Horizontal relationships – competition, comensalism, antibiosis
Not well studies.
Comensalisms occurs in C utilization. Cooperation in utilization of recalcitrant forms
or in anaerobic conditions.
Example: „Disease supressive soils“
Use of antibiosis in agriculture. Disease suppressive soils are known for
suppression of a specific pathogen, fungi, bacteria or nemathods. The
most well known is disease suppression of take all wheat disease cause
by mold Gauemanomyces graminis by antibiotics produced by
pseudomonads.
Disease suppressive soils
example Tievaliopsis basicola
microarray for identification of 1500 bacterial genera
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Conducive
Suppressive
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conducive
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Inoculated
Not inoculated
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20%
Inoculated
Not inoculated
suppressive
11%
differences in composition of communities in disease suppressive
and conducive soils
Kyselkova et al.,
ISME 2009
Biodegradation
Microorganisms oxidating carbohydrates:
bacteria, molds, yeasts, bluegreen algae, algae
Only aerobic process
dependence on temperature, pH and sources of anorganic nutrients
Xenobiotics: (pesticids, polychlorinated bifenyls, explosives, tints,
chlorinated solvents etc.)
some are structurally related to natural compounds – slow
degradation by existing enzymes
degradation of completely foreign compounds takes much longer,
degradation pathways must be developed
Genomes of microorganisms – what is necessary
Glass et al.: Essential genes of a minimal bacterium
PNAS 2006;103;425-430
„minimal bacteria“ - Mycoplasma genitalium
482 protein coding genes, since 2002 Nanoarchaeum equitans, 491 kb)
→ 382 from the total of 482 genes of M.genitalium are essential
Genomes of microorganisms – what is necessary
Haggblom et al.
Degradation of MTBE, methyl tert-butyl ether
One bacteria in 109 which can degrade it. Took 5 years to find it using
enrichment cultivation.
Biodegradation of oil
Bacteria aggregate in high numbers at the edge between water and organic
phase, or are present directly inside the organic phase
Biodegradation of oil
Functional metagenomic profiling of nine biomes
15 milion od sequences were evaluated
divided by metabolisms and functions
9 bioms: underground, saline, sea,
coral, freshwater, fish,
terrestrial animals, microbial,
and moskyto
Sekvence divided also by the origin
to viral and microbial
Nature 452, April 2008
Separation of sequences by
canonic ordination analysis
mikrobiální
Microbial and viral set differes
significantly
Processes dominating for
microorganisms:
cell wall building, sulfur, signalization,
movement, respiration, building
of proteins
Viral processes:
membrane transport, potassium,
phosphorus, cell division, DNA,
virulence, sekundary metabolites,
fatty acids
virový
Climatic changes in relationship to soil microorganisms