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82 Cards in this Set
- Front
- Back
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Responses to high temperature
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acclimation: heat shock response
- chaperonins refold proteins correctly - proteases degrade irreversibly damaged proteins adaptation: thermophily (Topt ≥ 45 °C) hyperthermophily (Topt ≥ 80 °C) highest known growth temperature: 122 °C (Methanopyrus kandleri) |
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Adaptations to low temperature
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challenge: membrane rigidity
adaptation: short-chain and/or unsaturated fatty acids |
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Adaptations to low temperature
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challenge: rigidity of proteins
adaptations: mostly hydrophilic amino acids, flexible secondary and tertiary structure |
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Adaptations to high temperature
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challenge: photopigments not stable at T > 73 °C
adaptation: chemotrophy |
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Adaptations to high temperature
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challenge: membrane stability
adaptation: saturated fatty acids (Bacteria) lipid monolayer (Archaea) |
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Adaptations to high temperature
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challenge: protein stability
adaptations: hydrophobic interior, ionic surface, stronger tertiary structure |
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Adaptations to high temperature
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challenge: DNA and RNA stability
adaptations: high GC content, positive supercoils, histones (Archaea), stabilizing solutes |
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Responses to low temperature
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acclimation: psychrotolerance
- dormancy - endospore formation  adaptation: psychrophily (Tmin ≤ 0 °C and Tmax < 20 °C) |
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Adaptation to low temperature
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challenge: freezing cytoplasm adaptation: cryoprotectants
(glycerol, sugars, antifreeze proteins) |
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Microbes and UV-VIS radiation
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exploitation of radiation:
- photosynthesis - signal acclimation of phototrophs to low irradiance: - more pigments and light-harvesting complexes - less proteins for electron transfer and CO2 fixation responses to high irradiance: - avoidance (motile organisms) - carotenoids, mycosporin-like amino acids (MAAs) - antioxidants, repair systems |
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Ionizing radiation
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sources:
- radionuclides - cosmic radiation - X rays, CAT scans, radiotherapy |
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Reactive oxygen species
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Fenton reaction: H2O2 + Fe2+ → Fe3+ + OH ‒ + OH·
hydroxyl radical: most reactive, but short-lived removal of harmful oxygen species: - superoxide dismutase: O2‒ → H2O2 - catalase, peroxidase: H2O2 → H2O |
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Strategies of radiotolerance
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polyploid genomes → homologous recombination (after double-strand break)
DNA and protein repair systems ROS formation catalyzed by Mn2+ yields less harmful products than Fenton (Fe2+ catalyzed) reaction |
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Microbes in magnetic fields
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magnetotaxis: orientation towards microoxic habitat??
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Microbes in flow fields
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rheotaxis: cell drift perpendicular to water flow
helical flagella experience shear-induced lift, while cell body experiences drag → torque |
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Microbial interactions with oxygen
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O2 production (oxygenic photosynthesis)
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Microbial interactions with nutrients
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availability of C, N and P sources:
oligotrophic, mesotrophic, eutrophic |
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Starvation strategies
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NH3 limitation → activation of N2 fixation system
low concentration of amino acids → reduce translation |
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Sulfur redox cycle
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sulfate:
- seawater (28 mM) - sulfate minerals (gypsum) sulfide: - hydrothermal fluids - sulfide minerals (pyrite) |
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Microbial guilds in the S cycle
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phototrophic Sred oxidizers
(purple S bacteria, green S bacteria) chemolithotrophic Sred oxidizers chemolithotrophic Sox reducers chemoheterotrophic Sox reducers |
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Purple sulfur bacteria
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photosynthesis with electron donor H2S or S2O32-
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Green sulfur bacteria (Chlorobi)
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photosynthesis with electron donor H2S → S0 → SO42-
S deposited outside cell photoheterotrophy photoautotrophy: steps of citric acid cycle in reverse chlorosomes: rich in BChl c, d or e attached to cell membrane (BChl a) |
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Chemolithotrophic S oxidation
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H2S → S0 → S2O32– → SO42–
electron acceptors: O2, Fe(III), NO3– Proteobacteria, Aquificae Archaea: Acidianus, Sulfolobus, Sulfurococcus |
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Microbial reduction of Sox
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electron acceptors: SO42–, SO32–, S2O32– or S (→ H2S)
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Microbial guilds in the Fe cycle
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Microbial reduction of Fe(III)
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Fe(III) insoluble at pH > 4 → extracellular e‒ acceptor
nanowires: Geobacter sp. electron shuttle (humic acids, plant exudates): Shewanella sp. |
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Microbial oxidation of Fe(II)
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Fe(II) oxidizers often acidophiles:
- Acidothiobacillus ferrooxidans (autotroph, pH = 1-3) - Ferroplasma sp. (autotroph, pH = 0-2, no cell wall) Ferroplasma acidarmanus: - intracellular pH = 6 → H+ influx → ATP production - H+ influx neutralized by electrons from Fe(II) oxidation Fe(II) oxidizers at oxic-anoxic interfaces: - quick to compete with abiotic reaction - Galionella ferruginea phototrophic Fe(II) oxidizers: - Chlorobium ferrooxidans, Rhodopseudomonas palustris |
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Intracellular functions of Fe
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Fe necessary for:
- cytochromes - iron-sulfur proteins - enzymes (catalase, peroxidase, oxygenases, nitrogenase) - magnetosomes Fe harmful as catalyst of the Fenton reaction: H2O2 +Fe2+ →Fe3+ +OH– +HO• few species can replace Fe2+ by Mn2+ |
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Regulation of intracellular Fe
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ferric uptake regulator (Fur): regulatory protein binding Fe
Fe scarce: - Bfr not needed; anti-bfr prevents translation of bfr RNA - expression of genes that enhance Fe uptake - secretion of siderophores Fe abundant: Fur binds Fe - Fur+Fe repress transcription of anti-bfr → Bfr production - Fur+Fe repress operons that are active under Fe limitation gene/operon: anti-bfr, genes for enhanced Fe uptake repressor: Fur protein corepressor: Fe |
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Methanogenic habitats
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anoxic sediments of lakes and wetlands
paddy fields animal digestive tracts (rumen, cecum,...) geothermal and hydrothermal environments landfills, anoxic wastewater treatment reactors |
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Microbial methanogenesis
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strictly anaerobic
special coenzymes: - C1 carriers: methanofuran, CoM, F430 - electron carriers: F420, CoB 3 pathways: - reduction of CO2 - reduction of methyl groups - cleavage of acetate |
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Methanogenic Archaea
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CO2 +4H2 →CH4+2H2O alternative substrates: CO, formate
CH3OH + H2 → CH4 + H2O alternative substrates: small molecules with -CH3 group CH3COOH → CH4 + CO2 alternative substrate: pyruvate |
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Aerobic methane oxidation
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2CH4 +O2 →2CH3OH→H-CHO→H-COOH→CO2 H-CHO → assimilation
key enzyme: methane monooxygenase (Mmo) (competitor substrate: NH3) stacked internal membranes contain Mmo |
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Anaerobic methane oxidation
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electron acceptor: SO42–, NO2–
reverse methanogenesis ?? key enzyme: methyl-CoM reductase slow growing consortia of methanotrophs and sulfate reducers |
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Single-species methane cycle ?
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Lost City Methanosarcina (LCMS):
hypothesis: differentiation of biofilm population → methanogenic ecotype, methanotrophic ecotype potentially syntrophic interaction between these ecotypes |
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Competition
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Intraspecific competition
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carrying capacity K: maximum number of individuals that an environment will sustainably support
K is a measure of intraspecific competition strong predation eliminates competitors (N << K) |
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Interspecific competition
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competition coefficient αjk : per-cell effect of species j on the population growth of species k
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Competitive exclusion
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Georgyi Gause (1934): species with the same ecological niche cannot coexist in stable
equilibrium competition experiments with Paramecium species |
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Niche differentiation
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character displacement: differential use of resources
microhabitat differentiation: - temporal separation (day- vs. night-active, fluctuating supply of resource,...) - spatial separation (heterogeneous habitat) environmental change (over time or space) promotes coexistence → high species richness |
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Competition - example
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probiotic treatment:
use of harmless bacteria to outcompete pathogens |
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Predation
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consumption of a living organism (prey) by another (predator) [not saprotrophy/detritivory]
predation reduces competition between prey Lotka-Volterra model of predation |
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Predatory bacteria
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predators: Bdellovibrio sp., Bacterivorax sp.
(small, highly motile) prey: various gram-negative bacteria |
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Microbial predation mechanisms
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phagocytosis (unicellular eukaryotes)
prey cell invasion (Bdellovibrio sp.) secretion of antibiotics and hydrolytic exoenzymes (Streptomyces coelicolor) ---- rather mechanism of interference competition?? wolfpack predation (Myxococcus xanthus): prey colony invasion, followed by cooperative cell killing and lysis |
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Parasitism
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interaction in which an organism (parasite) obtains resources from another (host), causing harm but not immediate death
examples: - Nanoarchaeum equitans (host: Ignicoccus sp.) - bacterial pathogens - parasitic protozoa (Plasmodium spp., Toxoplasma spp.) |
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Viruses
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bacteriophages: parasites on microbial hosts
typically narrow host spectrum → density-dependent mortality → viruses affect evenness of community defense mechanisms of bacterial/archaeal hosts: - restriction endonucleases, modification of own DNA - CRISPR: memory bank of formerly encountered viruses → recognition and destruction of viral DNA/RNA |
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Marine viruses
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- Viruses are important, dynamic and diverse components of the marine environment.
- Virally mediated bacterial death creates more dissolved organic matter for bacterial consumption and increases the cycling rates of C and nutrients in the marine environment. - Horizontal gene transfer by viruses is an important mechanism of gene exchange in the marine environment. |
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Symbioses
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mutualism:
interaction of organisms to their mutual benefit syntrophy: metabolic mutualism symbiosis: mutualism with close physical association of partners examples: - lichen (fungus and phototroph) - mycorrhiza (fungus and plant root) - N2-fixing bacteria and legume roots - microbes and ruminants - microbes and hydrothermal vent fauna interference competition: alga suppresses coral by - toxins - anoxia - transmission of coral pathogens - promotion of detrimental microbes |
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Microbe-microbe interactions
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++ mutualism:...
[examples: metabolic networks, syntrophy, symbiosis] |
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Syntrophy
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inter-species cooperation that leads to the degradation of a substance that neither partner could degrade alone
commonly: transfer of H2 from fermenting organism to H2-consuming microorganism maybe: transfer of CH4 from methanogen to methanotroph syntrophic electron transfer → electric current |
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Syntrophic H2 transfer
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(secondary) fermentation by itself is endergonic, but
removal of product H2 affects reaction constant K |
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Syntrophic electron transfer
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extracellular electron transfer via redox shuttles
or nanowires (conductive pili) |
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Methanotrophic symbiosis
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syntrophic consortia catalyzing anaerobic CH4 oxidation
[consortium: highly structured association with coordinated cell division] |
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Phototrophic symbiosis
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phototrophic bacterial consortia
"Chlorochromatium aggregatum": - motile chemotrophic β-proteobacterium, ~ 16 epibiontic green sulfur bacteria - contact layer: periplasmic tubules, no chlorosomes - epibionts interconnected by filaments |
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Lichen
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symbiosis of fungus and oxygenic phototroph
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Allelopathy
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interference competition by release of compounds that kill or inhibit potential competitors
weapons of microbial warfare: - antibiotics - lytic agents, reactive oxygen species [predation?] - siderophores [exploitation competition?] - signal compounds (altering the behavior of competitors or predators) - degradation of competitors' signal compounds |
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Allelopathy - examples
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colonies of Streptomyces sp. inhibit growth of Staphylococcus aureus
supernatant of Burkholderia thailandensis culture inhibits growth of Bacillus subtilis lawn |
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Quorum sensing
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regulatory system that coordinates gene expression in response to population density, using cell-to-cell communication by signaling molecules (autoinducers) chemically diverse signal compounds
- examples: acylhomoserine lactones (AHLs), oligopeptides antibiotics – signals or inhibitors? effect may depend on concentration and/or recipient |
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Quorum sensing
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processes coordinated by quorum sensing:
- light emission in luminescent bacteria (Aliivibrio fischeri) - biofilm formation (Pseudomonas aeruginosa) - production of virulence factors (Staphylococcus aureus) - capability of DNA uptake (Bacillus subtilis) |
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Quorum sensing or allelopathy?
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Paenibacillus dendritiformis:
nutrient limitation → secretion of serine protease |
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Microbe - plant interactions
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competition for light, CO2, nutrients
symbioses: - mycorrhizae - diazotrophs in rhizosphere - diazotrophs in root nodules - diazotrophs in phyllosphere parasitism: microbial pathogens of plants and algae mutualism: phytoprotective microbes |
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Mycorrhizae
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symbioses of plant roots and fungi
ectomycorrhiza: fungus froms sheath around tree root endomycorrhiza: fungal mycelium embedded in root tissue (occurs in >80 % of plant species) large surface area of mycelium improves nutrient uptake |
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Rhizosphere symbioses
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rhizosphere (Hiltner 1904):
region of soil directly influenced by plant roots |
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Rhizosphere symbioses
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plant root exudates benefit rhizosphere microbes:
- nutrition (amino acids, sugars, vitamins, tannins,...) - inhibition of competitors (antimicrobial exudates) |
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Root nodule symbioses
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agriculturally important legumes (soy, beans, clover,...)
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Phyllosphere symbioses
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ecto- and endosymbioses with plant stems and leaves
pigmented yeasts and bacteria on leaves → UV protection endophytic fungi in grasses → protection from herbivores N2-fixing lichens on tree bark N2-fixing cyanobacterium Anabaena azollae in leaf cavities of water fern Azolla (frequent inhabitant of rice paddies) |
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Microbial plant pathogens
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fungal infections of plants and algae
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Microbes protecting plants
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chemotaxis of protective microbes:
- attractants: organic acids, amino acids, sugars - quick response by flagellated bacteria (Azospirillum) antimicrobial root exudates → competitive advantage to resistant colonists protective bacteria - outcompete pathogens for resources (for example, by releasing high-affinity siderophores) - release antibiotics - degrade virulence factors - degrade quorum sensing signals of pathogens - induce systemic resistance of the plant |
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Phytoprotective microbes
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protein of Bacillus thuringiensis converted to endotoxin during digestion by larvae of moths,
flies and beetles → microbial insecticide application of B. thuringiensis spores on plants |
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Predation of animals on microbes
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grazing by protozoa:
- density-independent reduction of bacterial abundance - recycling of carbon and nutrients (microbial loop) - protective strategies predation by metazoa: - biofilms on rocks (scraped off) or sand grains (deposit feeding) - filter feeding (by gills, tentacles,...) on microbial plankton - microbes associated with food (detritus, slime, faeces) - human consumption of yogurt, blue cheese, salami etc. |
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Predation of fungi on animals
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adhesive hyphae, often forming loops or rings
→ nematode trap → hyphae penetrate into trapped nematode, release enzymes → digestion of prey examples: Arthrobotrys sp., Dactylella sp.) |
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Predation of fungi on animals
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fungus (Pleurotus sp.) releases paralyzing toxin
→ hyphae invade paralyzed nematode, release enzymes → digestion of prey |
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Microbial gardening
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directed external cultivation of microbes for later consumption; typically fungus and N2- fixing bacteria
benefits for gardener (ants, termites, bark beetles): - protein-rich food source - microbial cellulases benefit for microbe (fungus): - supply of detritus - dispersal - competitive advantage of preemptive colonization |
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Interactions in microbial gardens
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coculture of fungus with antibiotic-producing bacteria
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Microbes and ruminants
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rumen symbionts:
Bacteria, Archaea, Fungi, anaerobic protists 1010 – 1011 cells (g content)-1 microbial hydrolysis of cellulose, fermentation of glucose benefits for ruminant animal: - fermentation products (fatty acids) - microbially produced amino acids and vitamins - microbial cells as high-protein food source |
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Microbes and termites
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microbial symbionts in termite hindgut: - cellulolytic protozoa or bacteria
- fermenting bacteria - acetogenic bacteria - methanogenic archaea |
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Intestinal microbes of humans
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1013 – 1014 microbial cells inhabit gastrointestinal tract
composition of gut microflora depends on: - resources (diet) - conditions (pH, O2, host enzymes, medication) - interactions with other inhabitants microbial contributions: - synthesis of vitamins - gas production (CO2, CH4, H2) - hydrolysis of indigestible polysaccharides - participation in steroid metabolism |
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Endozoic chemolithotrophs
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hydrothermal vent fauna: tubeworms, clams, mussels
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Endozoic chemolithotrophs
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microbial consortia in gutless oligochaetes: - γ-proteobacteria: chemosynthesis of Corg,
oxidation of H2S - δ-proteobacteria: sulfate reduction |
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Microbial lanterns
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hosts: cephalopods, fish, tunicates (nocturnal or deep sea)
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Endozoic phototrophs
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endosymbiont terminology by color:
- zooxanthellae (yellow or brown algae, dinoflagellates) - zoochlorellae (green algae) - cyanellae (cyanobacteria) hosts: molluscs, corals, sponges, sea urchins,.... mutual exchange of nutrients and organic compounds phototaxis of host → phototroph optimally exposed to light |
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Parasitic protozoa
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Toxoplasma gondii (toxoplasmosis)
Entamoeba histolytica (amoebic dysentery) |
