Transcript The Microbial Ecosystem

Microbial Life in Soil
Prof. dr. ir. Willy Vestraete
Dr. ir. Tom Van de Wiele
Laboratory of Microbial Ecology and Technology
(LabMET)
Faculty of Bioengineering
Ghent University
LabMET.Ugent.be
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Laboratory of
Microbial Ecology and Technology
Topics of Discussion
The microbial ecosystem in the soil
The most common bacterial soil processes
The microbial growth
The simulation of the microbial transport in the soil
The bioavailability of contaminants
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Laboratory of
Microbial Ecology and Technology
Topics of Discussion
The microbial ecosystem in the soil
The most common bacterial soil processes
The microbial growth
The simulation of the microbial transport in the soil
The bioavailability of contaminants
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Laboratory of
Microbial Ecology and Technology
1. The Microbial Ecosystem

Ecological importance of soil:
– The production of biomass (food,…)
– The natural biotope for:
• Micro-organisms
• The plant-communities
• The animal world
– To filter or to buffer soil contaminants:
• By retaining, transforming, neutralizing…
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Laboratory of
Microbial Ecology and Technology
1. The Microbial Ecosystem

The interactions between soil and soil-biotic
communities
climate
geological substrate;
mother material
vegetation
and soil biota
topography
soil properties
and soil profile
time
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Laboratory of
Microbial Ecology and Technology
1. The Microbial Ecosystem
“The soil represents a set of physicalchemical conditions in which life
develops in all diversity.”
 Life: complex communities with ten
thousand different species of microorganisms:

– Bacteria
– Fungi
– Protozoa
Micro-aggregates
and macro-organisms
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Laboratory of
Microbial Ecology and Technology
1. The Microbial Ecosystem

The soil biodiversity:
Group
Number of species
Density
Micro-organisms
35.000
105-108/g
Nematodes
7.000
104-105/g
Protozoa
5.000
-
Insects
60.000
-
Mites
30.000
-
Grubs
3.500
-
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Laboratory of
Microbial Ecology and Technology
1. The Microbial Ecosystem

The microbial biodiversity:
– 35.000 different species
– 105-108 per gram soil
– Great diversity of ‘genetic capacity’ and
‘biological know-how’
– Participant of a ‘food-web’ in the soil, that
develops and grows in complexity until a
maximally efficient filling in of the soil
functions is obtained
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Laboratory of
Microbial Ecology and Technology
1. The Microbial Ecosystem

Soil-profile and micro-organisms:
micro-organisms contribute to the profile-development by
increasing the solubility of the organic and inorganic material
A0
A1: much humus
A2: less humus
B1: humus
B2: iron
Mother-material
Deposition of organic material
Elution of anorganic and organic compounds
from the upper layer
Depositon of compounds
cm depth
Horizon
Bacteria
Fungi
3-8
A1
7800
119
20-25
A2
1800
50
65-75
B1
10
6
135-145
B2
1
3
Podzol: number of propagules x 103/g
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Laboratory of
Microbial Ecology and Technology
Topics of Discussion
The microbial ecosystem in the soil
The most common bacterial soil processes
The microbial growth
The simulation of the microbial transport in the soil
The bioavailability of contaminants
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Soil bacteria are nutritionally exigent, more
than one half of the bacteria requires one or
more growth factors
Requirements
% of the soil bacteria
a. Minerals + Organic C-Source
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b. a + Amino-acids
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c. a + b + Vitamins
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d. a + b + c + Soil-extract
40
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Organo-heterotrophic bacteria:
building organic cell-compounds out of
organic material
Bacillus: amino-acids
Clostridium: carbohydrates + amino-acids

Chemo-lithotrophic bacteria (autotrophic):
building organic cell-compounds out of
chemical reactions with anorganic material
Nitrosomonas: NH4+ + 3/2 O2  NO2- + 2H+ + H2O
Nitrobacter: NO2- + 1/2 O2  NO3-
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Microbial respiration: oxygen or other
compounds act as hydrogen(=electron)acceptor
– Aerobic: O2
– Facultative aerobic: O2, NO3– Facultative anaerobic: O2, NO3-, organic
acceptors
– Anaerobic: Fe3+, Mn4+, SO42-, CO2, organic
acceptors

Aerobic conditions: Eh > 0, anaerobic
or anoxic conditions: Eh < 0
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Laboratory of
Microbial Ecology and Technology
STANDARD REDUCTION POTENTIALS
substrate
Aerobic
conditions O2
Anaerobic Fe3+
conditions
NO3-
SO42CO2
product
H+ e0.82 V
H2O
0.77 V
Fe2+
0.74 V
N2
-0.23 V
H2S
-0.24 V
CH4
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

The degradation of organic compounds:
– Happens through selective enzymes and
delivers energy for the microbial
metabolism: metabolic degradation
– Happens fortuitously by non selective
enzymes and delivers no energy for the
metabolism: cometabolic degradation

Reaction kinetics:
metabolic > cometabolic
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Degradation of biotic organic material:
If favorable conditions are present, every
compound will be degraded by the microorganisms, in a quick (DT50: hours-days) or
slow way (DT50: months-years), e.g.
– Cellulose (Cellovibrio, Aspergillus, Streptomyces)
(DT50-aerobically: 3-4-5 months)
– Lignin (Basidiomycetes)
(DT50-aerobically: 0,5-1y)
– Hydrocarbons e.g. aromatic compounds (Bacillus)
(DT50-aerobically-monomers: 0,5-1 month)
(DT50-anaerobically-polymers: months-years)
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Example: Aerobic cleavage of the aromatic ring of
catechol by oxygenase enzymes
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Degradation of xenobiotic organic material:
If favorable conditions are present, some
compounds will be degraded, other ones are
recalcitrant.
 The more a xenobiotic compound resembles
a biotic one, so much the more it will be
recognized by microbial enzymes and be
transformed
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Degradation pathways
for the pesticide
parathion
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Rules of thumb to judge the biodegradability of an
unknown aliphatic chemical compound
– The C2-C18 chain length is optimal
– CC > C=C > C-C
– The more branched, the less the biodegradability
>
>
– Substitution with –OH or –COOH is positive
– Substitution with –Cl, –NO2, –SO3H is negative
– The more substituents, the stronger the positive or
negative effect
– The closer the substituents towards the active group, the
greater its influence
O
Cl
OH
Cl
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Rules of thumb to judge the biodegradability of an
unknown aromatic chemical compound
– Substitution: see aliphatic compounds
– Para isomers are more biodegradable than ortho, resp. meta
OH
OH
OH
isomers.
Cl
>
>
Cl
Cl
– Poly aromatic compounds are difficult to degrade, e.g.
benzopyrenes
Naphtalene
Benzo[a]pyrene
Pyrene
Recalcitrance
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Laboratory of
Microbial Ecology and Technology
2. Bacterial Soil Processes

Environmental factors:
– A higher microbial diversity increases the
degradation-capacity by proto-coöperation
– Water-content: optimal ca. 20%
– Temperature: factor 1,5-2 for 10°C
– Sorption: through sorption processes,
compounds are no longer bio-available
(see below), e.g. straws slows down the
degradation of atrazin.
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Laboratory of
Microbial Ecology and Technology
Topics of Discussion
The microbial ecosystem in the soil
The most common bacterial soil processes
The microbial growth
The simulation of the microbial transport in the soil
The bioavailability of contaminants
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Laboratory of
Microbial Ecology and Technology
3. Microbial Growth

Growth: increase in the number of cells
 Essential: any given cell has finite life span in
nature  species maintains only as result of
continued growth of the population
 Useful in designing methods to control microbial
growth
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Laboratory of
Microbial Ecology and Technology
3. Microbial growth
☞ Time required for complete growth cycle is highly
variable and dependent on nutritional,
environmental and genetic factors
Time
Total number
of E. coli cells
0u00
0u20
0u40
1u00
1u20
1u40
2u00
2u20
2u40
3u00
3u20
3u40
4u00
…
7u00
1
2
4
8
16
32
64
128
256
512
1024
2048
4096
…
2097152
20
21
22
23
24
2n
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Laboratory of
Microbial Ecology and Technology
3. Microbial growth

Bacterial growth: cells divide into two new cells by
binary fission
Bacillus subtilis
Dividing streptococci
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Laboratory of
Microbial Ecology and Technology
3. Microbial growth
☞ Bacterial population growth: typical growth curve
500
400
300
200
100
0
☞ Growth rate: change in cell number or cell
mass per unit time
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Laboratory of
Microbial Ecology and Technology
Substrate (mg/l)
Log10 viable organisms/ml
600
3. Microbial Growth

Most information available resulting from
controlled laboratory studies using pure cultures of
micro-organisms
☞ Compare the complexity of growth in a flask and
growth in a soil environment. Although we understand
growth in a flask quite well, we stil cannot always
predict growth in the environment!
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Laboratory of
Microbial Ecology and Technology
Topics of Discussion
The microbial ecosystem in the soil
The most common bacterial soil processes
The microbial growth
The simulation of the microbial transport in the soil
The bioavailability of contaminants
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Laboratory of
Microbial Ecology and Technology
4. Microbial transport in the soil

The knowledge about bacterial
transport in soil is required:
– To protect groundwater sources from
microbial contamination
– To estimate the influence of rainfall on
microbial transport in soil
– To design sustainable and safe in situ
bioremediation techniques
(Can the contact between micro-organisms
and the contaminants be realized?)
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Laboratory of
Microbial Ecology and Technology
4. Microbial transport in the soil

Determined by:
– Dispersion (no straight path by diffusion (concentration
gradient and Brownian movement) and mechanical mixing)
– Advection (transport of non-reactive components at a rate equal
to the average velocity of the percolating water)
– Sorption (a part of the bacteria will be sorbed onto the soil
particles)
– Retention (a part of the bacteria will be retained in the pores in
the soil)
– Microbial die-off

Modeling this transport requires interdisciplinary
research (microbiology + hydrogeology)
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Laboratory of
Microbial Ecology and Technology
4. Microbial transport in the soil

Example: The modelling of the evolution of the concentration
of the anaerobic micro-organism Desulfitobacterium
dichloroeliminans strain DCA1 and the contaminant 1,2dichloroethane in an in situ bioaugmentation strategy by
MOCBAC-3D (Prof. L. Lebbe and K. Smith, UGent)
Concentration of Desulfitobacterium dichloroeliminans strain DCA1
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Laboratory of
Microbial Ecology and Technology
4. Microbial transport in the soil

Example: The modelling of the evolution of the concentration
of the anaerobic micro-organism Desulfitobacterium
dichloroeliminans strain DCA1 and the contaminant 1,2dichloroethane in an in situ bioaugmentation strategy by
MOCBAC-3D (Prof. L. Lebbe and K. Smith, UGent)
Concentration of the contaminant 1,2-DCA
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Laboratory of
Microbial Ecology and Technology
Topics of Discussion
The microbial ecosystem in the soil
The most common bacterial soil processes
The microbial growth
The simulation of the microbial transport in the soil
The bioavailability of contaminants
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Laboratory of
Microbial Ecology and Technology
5. Bio-availability




Definition: the fraction of the total concentration of a
contaminant that will be taken up by the microorganisms out of the environment
Generally: the bio-availability to the micro-organisms
is directly dependent on the solubility of the
contaminant in the aqueous phase
Affecting processes: diffusion of the contaminant in
the boundary layer, the macro-pores and the micropores, physico-chemical interactions with the particle
surface and the desorption velocity of the
contaminant out of the sediment which is strongly
dependent on the particle size and particle density
Consequence: The degradation efficiency of a
contaminant will be reduced as much as
the mass transfer is limited to the micro-organism
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Laboratory of
Microbial Ecology and Technology
5. Bio-availability

Processes of bio-availability
Biological membrane
Bound
Contaminant
Dissociation
Absorbed
contaminant in
micro-organism
Association
Place of
biological
response
Free
Contaminant
Partitioning and interaction
of the contaminant with
different phases
Passive or facilitated
diffusion or active transport
of the contaminant
through the membrane
to the micro-organism
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Assimilation, dissimilation and
accumulation of the contaminant
with specific reaction kinetics
Laboratory of
Microbial Ecology and Technology
3. Bio-availability
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Laboratory of
Microbial Ecology and Technology
5. Bio-availability

Significance of bio-availability:
– The mass transfer limits the bio-availability
– The endpoint of bioremediation must be
related to the matrix
– The concentration of a contaminant in a
specific soil must be recalculated to the
concentration in a ‘standard soil’ to
evaluate the contamination extent
– Important for legislation: the line must be
drawn, but where? (high ‘grey-value’)
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Laboratory of
Microbial Ecology and Technology
Take-home message

Great diversity in the ecosystem of the soil

Micro-organisms participate in
biogeochemical processes and are able to
biodegrade a variety of biotic and xenobiotic
compounds

Knowledge about the transport of microorganisms in soil is required for safely
designing clean-up strategies

Bio-availability is determined by the masstransfer of compounds to the microorganisms, so the endpoint of bioremediation
is not absolute
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Laboratory of
Microbial Ecology and Technology