microbial life in soil
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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. Topics of Discussion. The microbial ecosystem in the soil - PowerPoint PPT PresentationTRANSCRIPT
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1 Laboratory of Microbial Ecology and Technology
Microbial Life in Microbial Life in SoilSoil
Prof. dr. ir. Willy VestraeteDr. ir. Tom Van de Wiele
Laboratory of Microbial Ecology and Technology (LabMET)
Faculty of BioengineeringGhent UniversityLabMET.Ugent.be
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Topics of DiscussionTopics 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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Topics of DiscussionTopics 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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1.1. The Microbial EcosystemThe 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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1.1. The Microbial EcosystemThe Microbial Ecosystem The interactions between soil and soil-biotic
communities
climategeological substrate;
mother material topography
vegetationand soil biota
soil propertiesand soil profile
time
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1.1. The Microbial EcosystemThe Microbial Ecosystem“The soil represents a set of physical-
chemical conditions in which life develops in all diversity.”
Life: complex communities with ten thousand different species of micro-organisms:– Bacteria– Fungi– Protozoa
and macro-organisms
Micro-aggregates
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1.1. The Microbial EcosystemThe 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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1.1. The Microbial EcosystemThe 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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1.1. The Microbial EcosystemThe Microbial Ecosystem Soil-profile and micro-organisms:
micro-organisms contribute to the profile-development by increasing the solubility of the organic and inorganic material
A0A1: much humusA2: less humusB1: humusB2: ironMother-material
Deposition of organic materialElution 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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Topics of DiscussionTopics 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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2.2. Bacterial Soil ProcessesBacterial 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 15
b. a + Amino-acids 15
c. a + b + Vitamins 30
d. a + b + c + Soil-extract 40
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2.2. Bacterial Soil ProcessesBacterial Soil Processes Organo-heterotrophic bacteria:
building organic cell-compounds out of organic materialBacillus: amino-acidsClostridium: carbohydrates + amino-acids
Chemo-lithotrophic bacteria (autotrophic):building organic cell-compounds out of chemical reactions with anorganic materialNitrosomonas: NH4
+ + 3/2 O2 NO2- + 2H+ + H2O
Nitrobacter: NO2- + 1/2 O2 NO3
-
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2.2. Bacterial Soil ProcessesBacterial Soil ProcessesMicrobial 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+, SO4
2-, CO2, organic acceptors
Aerobic conditions: Eh > 0, anaerobic or anoxic conditions: Eh < 0
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STANDARD REDUCTION POTENTIALS
substrate product
e-H+
O2
Fe3+
SO42-
CO2
NO3-
H2OAerobic conditions
Anaerobic conditions
0.82 V
Fe2+0.77 V
N20.74 V
H2S-0.23 V
CH4-0.24 V
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2.2. Bacterial Soil ProcessesBacterial Soil ProcessesThe 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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2.2. Bacterial Soil ProcessesBacterial Soil Processes Degradation of biotic organic material:
If favorable conditions are present, every compound will be degraded by the micro-organisms, 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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2.2. Bacterial Soil ProcessesBacterial Soil Processes Example: Aerobic cleavage of the aromatic ring of
catechol by oxygenase enzymes
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2.2. Bacterial Soil ProcessesBacterial 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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2.2. Bacterial Soil ProcessesBacterial Soil Processes Degradation pathways
for the pesticide parathion
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2.2. Bacterial Soil ProcessesBacterial Soil Processes Rules of thumb to judge the biodegradability of an
unknown aliphatic chemical compound– The C2-C18 chain length is optimal– CC > 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
> >
OH
O
Cl
Cl
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2.2. Bacterial Soil ProcessesBacterial 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
isomers.
– Poly aromatic compounds are difficult to degrade, e.g. benzopyrenes
OH
Cl
OH OH
Cl
Cl
> >
Naphtalene Pyrene Benzo[a]pyrene
Recalcitrance
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2.2. Bacterial Soil ProcessesBacterial 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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Topics of DiscussionTopics 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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3.3. Microbial GrowthMicrobial 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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3.3. Microbial growthMicrobial growth ☞ Time required for complete growth cycle is highly variable and dependent on nutritional, environmental and genetic factors
20
21
22
23
24
2n
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
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3.3. Microbial growthMicrobial growth Bacterial growth: cells divide into two new cells by
binary fission
Bacillus subtilis
Dividing streptococci
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Log
10 v
iab
le o
rgan
ism
s/m
l
3.3. Microbial growthMicrobial growth
☞ Bacterial population growth: typical growth curve
☞ Growth rate: change in cell number or cell mass per unit time
0
400
300
200
100
600
500
Su
bst
rate
(m
g/l)
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3.3. Microbial GrowthMicrobial 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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Topics of DiscussionTopics 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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4.4. Microbial transport in the soilMicrobial 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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4.4. Microbial transport in the soilMicrobial 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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4.4. Microbial transport in the soilMicrobial 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 1,2-dichloroethane 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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4.4. Microbial transport in the soilMicrobial 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 1,2-dichloroethane 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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Topics of DiscussionTopics 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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5.5. Bio-availabilityBio-availability Definition: the fraction of the total concentration of a
contaminant that will be taken up by the micro-organisms 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 micro-pores, 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 asthe mass transfer is limited to the micro-organism
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5.5. Bio-availabilityBio-availability Processes of bio-availability
Biological membrane
BoundContaminant
FreeContaminant
AssociationDissociationAbsorbed
contaminant inmicro-organism
Place ofbiologicalresponse
Partitioning and interactionof the contaminant with
different phases
Passive or facilitateddiffusion or active transport
of the contaminantthrough the membraneto the micro-organism
Assimilation, dissimilation and accumulation of the contaminant with specific reaction kinetics
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3.3. Bio-availabilityBio-availability
resistance of matrix against diffusion
organic matter clay sand water
106
104
102
100
10-2
102
104
106
108
1010
copiotrophs
oligotrophs
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5.5. Bio-availabilityBio-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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Take-home messageTake-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 micro-organisms in soil is required for safely designing clean-up strategies
Bio-availability is determined by the mass-transfer of compounds to the micro-organisms, so the endpoint of bioremediation is not absolute