microbial life in soil

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


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


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…


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


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


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 -


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


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


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


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

-


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


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


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


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)


2.2. Bacterial Soil ProcessesBacterial Soil Processes Example: Aerobic cleavage of the aromatic ring of

catechol by oxygenase enzymes


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


2.2. Bacterial Soil ProcessesBacterial Soil Processes Degradation pathways

for the pesticide parathion


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


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


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.


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


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


3.3. Microbial growthMicrobial growth Bacterial growth: cells divide into two new cells by

binary fission

Bacillus subtilis

Dividing streptococci


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)


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!


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?)


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)


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


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


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


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


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


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’)


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

microbial life in soil

Documents

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microbial life

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organic cell

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aminoacids clostridium

different species105