microbial ecology - uol. de · microbial interaction with plants • eukaryotes: nucleus and cell...
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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
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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
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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