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Terrestrialhabitats

Microbial Ecology

http://commtechlab.msu.edu/sites/dlc-me/zoo/index.html

About 30 % of the Earth is covered byterrestric habitats

Climate is dominating factor

Land is no continuum; there are manygeographic barriers (separation of the continents)

Water availability often limiting factor

Quick changes of temperature, extremesmore pronounced in the air (gaseous)

Pronounced circulation of air (provision of oxygen)

Soils represent most important source foressential nutrients nitrogen (N), phosphorus (P) und iron (Fe)

Terrestrial habitats

2

Importance of soil

Soil as a ressource

Production in agriculture and forestry,

filter for groundwater

Global loss of soil via

Sealing, housing, errosion

Additional environmental hazards via

Actual contaminations and polluted areas

Protection of soil in Germany is regulated in:

Bundes-Bodenschutzgesetz (BBodSchG, 06.02.1998)

Aim: Sustaining or restoring the soil function

„Hierzu sind schädliche Bodenveränderungen vorsorglich abzuwehren,

bzw. der Boden und Altlasten sowie dadurch verursachte Gewässer-

verunreinigungen zu sanieren.“

Importance of microorganisms for soil fertility

Decomposition of organic matter:

Supply of plant-available nutrients

Stabilisation of soil aggregates by microbial exudates:

Enhancement of : plant's ability to propagate roots through the soil,

filter capacity, water storage capacity

Anthropogenic influences (farming, fertilization, plant protection)

Should have no negative impact on microbial communities

3

Soil horizons

O-horizon: organic layersundecomposted plant material

A-horizon: humic upper layerdark in color, growing plants,highest numbers and activities of microorganisms

B-horizon: mineralic layerslittle organic matter, input fromA-horizon, microbial activitystill detectable

C-horizon: soilbase above bedrockgererally low microbial activities,terrestrial subsurface

Abb

.: B

rock

, 19

97 (

verä

nder

t)

Structure of soil particles

O2 concentrations in soil particles

Abb.: B

rock, 1997

Micro habitats

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Degradation of organic matter in soil

Composting Formation of humic acids

Abb.: Fritsche, 1998

Interaction with plantsRhizosphere & phyllosphere

Degradation of organic matter in soilSaprophytic microorganisms

Adaptation to changing conditionsSporeformers in soil

Examples for terrestrial microorganisms

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• Lichen: Symbiosis between algae and fungi

• Mycorrhizae (‘Wurzel-Pilz‘): Symbiosis between plants and fungi

• Root nodule (Wurzelknöllchen): Symbiosis between legumes and nitrogen-fixing bacteria

Microbial interaction with plants

• Eukaryotes: Nucleus and cell wall

• Chitin represnts main component of the cell wall

• Chemoorganotrophic, require in general low nutrient conditions

• Often parasitic or saprophytic

• Tolerate extreme temperatures, low pH conditions, low water availability

• Ubiquitous by spreading of spores

Fungi - Important microorganisms in soil

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• Ascomyceten (Neurospora, Saccharomyces)Soil, live on plant litter

• Basidiomyceten (zB. Knollenblätterpilz, Champignon)Soil, live on plant litter

• Zygomyceten (Rhizopus = gemeiner Brotschimmel)Soil, live on plant litter

• Oomyceten (Allomyces)Aquatic

• Deuteromyceten (zB. Penicillium, Aspergillus, Candida)Soil, plant material, cadaver and surfaces of animals

Classification of fungi

Ascomycetes (filamentous fungi)

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Basidiomycetes (Formation of fruiting bodies)

Myxomycetes (Plasmodium)

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• Symbiosis of plant roots and fungi

• Hypothesis: All terrestrial plants live mycorrhizal

• Ectomycorrhizae - Endomycorrhizae

• Fungi benefit from release of organic substances by the plant

• Plant benefit from increased surface and protection again other plants

Mycorrhizae

Typical ectomycorrhizal root of a pine with Thelophora terrestris(fungi)

• Symbiosis between legumes and certain, mainly Gram-negative bacteria

• Happen in many agricultural important plant like soybean, bean und pea

• Fixation of N2 in special nodules connected to the roots

• Selcetion advantage by growth on nutrient poor soil

• Hots plants and bacteria synthesize together O2-binding leghemoglobin (red colour)

Root nodules (Wurzelknöllchen):Symbiosis between plants and N2-fixing bacteria

Root nodules of a soybean (Bradyrhizobium japonicum)

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Only performed by prokaryotes

Occurs in free-living or symbiotic-associated microorganisms

Reduction of N2 to ammonium (utilized for anabolism)

Requires high amount of energy (Cleavage of a triple-bonds)

Catalyzed by the enzyme-complex Nitrogenase

Oxygen changes( irreversible) function of Dinitrogenase-Reductase

Different protection mechanisms to prevent O2-Inactivation:a) Rapid removing of O2 by high respiration ratesb) Slimeformation (eg. Azotobacter)c) Specific cells/compartements (eg. Cyanobakterien)

Ecological advantage: Growth in environments with low or no nitrogen source

Fixation of elemental nitrogen gas (N2)

Infection of roots by Rhizobiumand formation of nodules

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AcetobacterSugarcane

FrankiaAlder (Alnus)

Other plants

RhizobiumClover

RhizobiumPea

Rhizobium, Bradyrhizobium

Soy bean, bean

BacteriaLegumes

Symbiosis between plants and N2-fixing bacteria

Influence of root nodules on the growth yield of agricultural plants (soybean)

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Endospores in soil microorganisms

Differentiated cells that forms within a vegatative cell

Resistant to heat, dryness, radiation and harsh chemical

Represent ideal form for spreading by wind, water or excrements

Endosporeformers: Bacillus (aerobic) and Clostridium (anaerobic)

Remain dormant for extremely long time periods (250 millions of years? Halophilic bacteria from salt crystals)

Contain many specific layers which do not occur in vegetative cells

Characteristic compound:Dipicolinic acid

Ca-Dipicolinic acid -complex reduces water content with in the endospore + stabilizing function

Endospores(Bacillus megaterium)

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Own work

Dissertation:

Entwicklung und Anwendung von Methoden zur Differenzierung von

Funktionen und Strukturen bakterieller Populationen des Bodens

Biologische Bundesanstalt für Land- und Forstwirtschaft, Institut für Biochemie und Pflanzenvirologie, 1998

Structure Community composition (TGGE)

Function Kind and intensity of metabolic activity (BIOLOG)

Fingerprinting microbial communities

Top-down approach advantageous:

Differentiation of complex habitats

High number of samples

Investigating successions

Application of molecular protocols

No cultivation bias

Detection of not-yet cultured organisms

1 Negative controle

5 Polymers

28 Carbohydrates

2 Esters

24 Fatty acids

1 Bromated compound

3 Amides

20 Aminoacids

1 Aromates

3 Nucleosides

3 Amines

2 Alcohols

3 Phosphorylated compounds

Composition of a BIOLOG microtiter-plate

A

H

G

F

E

D

C

1

B

2 3 4 5 6 7 8 9 10 11 12

95 C-sources:

Principle (originally):Assessment of substrate utilization spectra of different bacterial pure cultures

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Differently treated soils

Attemts to classify the investigated effects

Classicalmicrobiological

methods

Structure Function

Strategy to analyze external effects on the soil microflora

Extraction of micobial cells

Analysis of metabolic patterns

Principle component analysisTest statistics

Identification of Carbon sources

Incubation in BIOLOG-platesTemperature Gradient Gel Electrophoresis

Extraction of nucleic acids

PCR / RT-PCRof 16S rDNA/rRNA

fragments (app. 450 bp)

Analysis of TGGE-patterns

Quantitative comparizonCluster analysis

Identification of TGGE bands

OD-values

< 0,000,00 - 0,020,02 - 0,040,04 - 0,060,06 - 0,080,08 - 0,10> 0,10

Microbial populations of differently farmed fields

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Principle component analysis of BIOLOG patterns

Rott field 93

Rott field 94

Test field

1 year of rotting

Autumn 1994

Autumn 1995Spring 1994

1. PC

2. P

C

0

1

2

3

4

5

-2 0 2 4 6 8

Rott fields Test fields

Test field ‘94 Rott field ‘94Rott field ‘93

1/2 1 1 1/2 2 1/2 1Rotting years

Spring Autumn Spring Autumn Spring Autumn Spring Autumn

Comparizon of TGGE patterns over longer time-intervals

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VR 93 2 years rotting

Test field

Rott field ‘93

0,860,78

0,66

0,73

0,660,73

0,75

0,850,68

0,720,66

0,67

0,51

0,600,56

0,38

0,85

Spring

Autumn

11/2 year rotting

1/2 yearrotting

1 year rotting

1 yearrotting

2 yearerotting

Test field

Rott field ‘93

Rott field ‘93

Rott field ‘93

Rott field ‘94

Rott field ‘94

Rott field ‘93

Rott field ‘94Rott field ‘93

Clusteranalysis of TGGE-profiles

What are poluted areas?

Old depositions

Inoperative landfills

Properties, where waste was treated,

stored or dumped

Harmful soil contaminations

Inhibit soil function

Cause dangers, severe disadvantages or annoyance

to single persons or general public

Old treatment sites

Properties of inoperative plants

Properties where hazardous substances

were handled and caused soil contamination

Toxic waste and bioremediation

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Strategies for soil remediation

Methods

Physico chemical

Thermic

Biological

Treatments

In-Situ-treatmentwithout excavation

Ex-Situ-treatmentafter excavation

On-Site-treatment Off-Site-treatment

Washing of soil

Burning of soil

Bioremediation

Waste water

Dead soil

Biologically active soil

Ex-Situ remediation

Supporting microbial activities

Aeration and nutrient supply

Comparable to composting

Abb.: Fritsche, 1998

Protection of environment

Enclosed containments (tents, ...)

Cleaning of air and water

Enhancing the bioavailability of polutants

Homogenisation (mechanically)

Disaggregation or suspension of the soil

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Example for In-Situ treatments

Abb.: Waschke, 1999

Abb.: Fritsche, 1998

„Superbugs“ – The solution?

Advantage

Directed construction of specialists

High utilization-rates in bioreactors

Disadvantage

Risk? Release of GEMs!

Labstrains often die in wilderness

So far, no techncal applicationfor „Superbugs“

Abb.: Fritsche, 1998