Pseudomurin
Das Pseudopeptidoglycan oder Pseudomurein ist eine Substanz, die bei Archaeen als Zellwand auftritt. Es handelt sich um ein Polysaccharid, an das kurze Aminosäureketten gebunden sind.
Nitrogen assimilation
Nitrogen assimilation is the process by which inorganic nitrogen compounds are used to form organic nitrogen compounds such as amino acids, amides, etc. Plants and other organisms, which cannot utilise nitrogen molecules directly, depend on the absorption of nitrogen as nitrates or ammonia.
nitrogen immobilization
The nitrogen immobilization is the quantity of nitrogen taken more quickly by the soil microorganisms and use for their activity or for their composition. These quantity of nitrogen is immobilized. A part will be liberated at the dead of the microorganism.
The Eddy Covariance Method
Eddy covariance is a micro-meteorological method that is currently popular to directly observe the exchanges of gas, energy, and momentum between ecosystems and the atmosphere.
Per measurement interval
- vertical wind speed
- horizontal wind speed
- gas concentration
measurement
The dynamic chamber method
Chamber flux 50-100 m3 h-1: generated by pump and directed through the chamber
Homogeneous mixture of the gas in the chamber
Quasi-continous measurement of CO2-concentrations at entrance and exit of chamber
Continous long-term measurements possible: daily and seasonal patterns can get reconstructed
The static chamber method
1. Installation of closed chamber: bottom part is often a ring covering the height of the vegetation on top of which the closed chamber gets installed
2. Gas samples will be taken in regular time intervalls and the accumulation of CO2 inside the chamber will be quantified
Universal biomolecule function
→ DNA is encoding the genetic information
→ RNA is transfering the genetic information
→ proteins are the functional machineries encoded by the above information
→ Metabolites are formed by the proteins and cover a wide spectrum of functions
The microbial anabolism
→ Many pathways are reversible, i.e. they can either be used to transfer an organic compound taken up towards glycolysis & TCA, or they can reversibly be used to synthetisize a certain compound needed by the cell for anabolism
→ Often one single enzyme is different between forward and reverse pathway and then the „reverse“ (i.e. anabolic) enzyme requires energy for catalyzing the reaction, e.g. Glykolyse <→ Gluconeogenese
→ Nearly all organisms can produce the basic compounds of life (the essential molecules);
DOC
dissolved organic carbon (part of dissolved organic matter)
→ Definition by size: must pass a 0.45 μm filter paper
negative DOC functions
After leaching or surface losses, the DOC has rather negative functions
1) nutrient source for microbes → Eutrophication of water bodies
2) co-allocation of nutrients into ecosystem compartments, where it causes eutrophication → nutrient loss from the ecosystem
3) transport of heavy metals and pollutants into the water body
Weathering
Breakdown of rocks through:
Water, rain, ice
Chemicals
Temperature shifts
Biota
Erosion
Removal of weathered rocks by :
Wind
Gravity
(Biota)
Exfoliation
Als Exfoliation wird in der Geologie die Ablösung kugelschaliger Körper vom darunter liegenden Felskörper bezeichnet, welche durch Druckentlastung bei emporgestiegenen Tiefengesteinen zustande kommt. Dadurch können Gesteinskuppen in Form von Kugelkalotten entstehen, die in manchen Regionen die Landschaft prägen.
Abrasion
Küstenerosion beziehungsweise (geologische) Abrasion ist die allmählich fortschreitende Veränderung von (Meeres-)Küsten aufgrund von Erosion durch Gezeiten, Wellen und Wettereinflüssen wie Wind, Regen und Temperaturunterschiede, Naturereignisse wie Hurrikane oder Erdbeben, aber auch durch Einwirkungen auf die Umwelt, etwa aufgrund der Schädigung der obersten Bodenschichten durch menschlichen Einfluss oder die Klimaerwärmung
Frost-wedging
Chemical weathering reactions
Oxidation
Hydration
Hydrolysis
Reduction/mineral dissolution
Animal-Assisted Rock weathering
Borrowing for home and passage making and thereby movement of rocks from below to above-ground exposing the rock to weathering forces. Expansion of fissures through mobility.
Urine/excrements/mucus moisten rocks, seep into cracks and provide reactants and water for (bio)chemical weathering.
Bore into rocks for protection either by scraping away the grains or secreting acid to dissolve the rock.
Plant-Assisted Rock weathering
Growth in joints & cracks, which pries rock apart in order to find moisture, nutrients, and hold.
Excretion of organic and inorganic compounds for nutrient
scavenging:
Creation of a humid microenvironment
Acidification dissolves rocks along edges and crack
Chelation of nutritional elements from rock parent material
Lichen-Assisted Rock weathering
Fungi:
excrete acids and chelators
dissolve rock minerals
release of nutrients
benefit for algae
Algae:
Photosynthesis: CO2 orgC
orgC used by fungi for growth
Archeae
• Morphologically similar to bacteria
• Prokaryotic cell type
• Separate classification1977
• Differences in cell wall and enzymes
Slime Mold
• Used to be classified fungi
• Fruiting bodies
• Single cell life stage
Protozoa
• free-living/parasitic
• Historically called "one-celled animals“
• animal-like (motility/ predation/ no cell wall)
Cell wall:
What is its function?
• protecting the cell from osmotic and mechanical stress
• gives rigidity / defines the cellular structure
• high plasticity and permeable
• mediates relationships with environment (adhesins and receptors)
Cell wall: Archeae
• wide variety of cell wall types
• adapted to hostile environment
• Some archaea lack a cell wall
S-layer (surface layer)
• Found in most archeae
• part of cell wall
• Achored to cell membrane
• made of protein / glycoprotein
protein sheath
• lattice structure similar to S-layer
pseudomurein
• similar to peptidoglycan
Methanochondroitin
• similar to chondroitin (connective tissue animalia)
Cell wall: Fungi
Proteins (20–50%) – NB interaction environment
• Most glycoproteins (associated with polysaccharides)
• maintenance of shape
• adhesion processes
• absorption of molecules
• signal transmission…
Glucan (50-60%) – NB rigidity
• most important structural component
• Provide rigidity
• Link proteins and chitin
Chitin (1-20%) – NB anchor
• polymers in the extracellular space
• Structure and anchor
Membrane transport systems: Simple diffusion (passive)
• Small hydrohobic molecules
• O2, CO2, N2
• Small uncharged molecules
• H2O, urea, glycerol
Membrane transport systems: Facilitated diffusion (passive)
• Larger uncharged molecules
• Requires integral proteins
• Glucose/ sucrose
Membrane transport systems: Active transport
• Require ATP
• Against concentration gradient
• Charged molecules
• Na+, K+, Cl-…(Still quite small)
Extracellular enzymes: polymers
Release exoenzymes into the environment (or stay attached to the cell wall)
• cleave the bondings of polymers
• Substrate specific (eg. cellulase, proteinase)
• Monomers can be taken up into cell
• Endoenzymes break up further
Active movement: Special machinery
Flagellum (“whip”)
pili
Cilia (eyelash)
Pseudopd (“false feet”)
• Locomotion and sensory organelle
• Propeller motion
Prokaryote
• Made of flagellin (protein)
• No ATP needed (bacteria)
→ energy from proton-motive force
Eukaryote
• Made of tubulin (protein)
• ATP needed
Pili
Locomotion and conjugation
• Only prokaryotes
• Attach and pull (twitching)
• Only eukaryotes
• Beating motion
• amoeba
• lobelike appendages
• anchor to a solid surface and pull themselves forward
Microbial navigation systems
+/-stumulus:
messenger protein transduces the signal from the receptors to the flagella change direction of rotation from default CCW to CW = tumbling
Classification: O2 requirement/ tolerance:
Obligate aerobes
• Electrons shuttled along electron transport chain
• Series of redox reactions
• final electron acceptor is oxygen
Facultative anaerobe
• depends on the environment
• O2 present – aerobic respiration
• O2 not present – anaerobic respiration
Obligate anaerobes
• final electron acceptors other than O2
• Eg. Nitrate (NO-3) or sulphate (SO2-4)
• anaerobic respiration
• variable tolerance to O2
Copiotroph
an organism found in environments rich in nutrients, particularly carbon. They are the opposite to oligotrophs, which survive in much lower carbon concentrations.
• Nutrient rich environments with fluctuations
• Heavily fertilized soils
• Bacteria
• r-strategists
Oligotroph
ein Organismus, der in einer Umgebung leben kann, die sehr wenig Nährstoffe bietet. Sie können Copiotrophen gegenübergestellt werden, die nährstoffreiche Umgebungen bevorzugen.
• Nutrient poor environments
• Access recalcitrant SOM
• Fungi
• K-strategists
C cycle
Removing CO2 from the atmosphere
• Autotrophs!
• C and energy from inorganic sources
• Some is stored in biomass (C pool)
C into the soil:
• root exudates (labile)
• Organic matter (litter / animal/ microbial)
Soil organic matter (large C pool):
• Sequestration/ stabilisation
• Decomposed by microbes (recycling)
Returning C to the atmosphere
• Autotrophic respiration
• Heterotrophic respiration
• Microbial respiration
C cycle: Abiotic Factors
Nutrient availability
• Esp. N and P availability
• N important in photosynthesis
• Limit microbial biomass formation
Soil moisture
• Plant and microbial activity
• Accessibility of SOM
↑ Temp = ↑ microbial activity
↑ organic carbon decomposition
↑ CO2 released by respiration
↑ CO2 = ↑ photosynthesis
↑ root exudates and labile C pool
C cycle: Budget
Balance determines whether:
Ecosystem is a C sink or source
C sink:
• ↑ CO2 removed from atmosphere
→ photosynthesis
• ↑ C stored underground
→ Anabolic processes
→ C into biomass
→ Especially cell walls (persistent)
Microbial necromass (entombing)
C source:
• More C lost from system (respiration)
• More catabolic reactions
• More CO2 into the atmosphere
N-fixation
• Specialised microbes (rhizobia)
• Aerobes
• Nitrogenase enzyme (O2 labile)
• Cost 16ATP per mol N
N mineralisation
• Fungi and some bacteria
• extracellular enzymes
• Break down OM
nitrification
• 2 oxidation reactions
• Gain energy
• Under oxic conditions
• Bacteria and archeae
denitrification
• Anaerobic respiration
• Nitrite/nitrous oxides as terminal
electron acceptors
• Facultative anaerobes
• Eg. waterlogged soils when ↑N
• Many groups of bacteria and archeae
• Some fungi
DNRA
• Dissimilatory nitrate reduction to ammonia
is the result of anaerobic respiration by chemoorganoheterotrophic microbes using nitrate (NO3−) as an electron acceptor for respiration.[1][2] In anaerobic conditions microbes which undertake DNRA oxidise organic matter and use nitrate (rather than oxygen) as an electron acceptor, reducing it to nitrite, and then to ammonium
• respiration in anoxic environments in which nitrate is present
functional redundancy
different species can replace same functions
Nitrification
Unter Nitrifikation versteht man die bakterielle Umwandlung von Ammonium (NH4+) über das Zwischenprodukt Nitrit (NO2-) zu Nitrat (NO3−). Dies geschieht beispielsweise durch Bakterien in landwirtschaftlich genutzten Böden.
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