Explain the terms Microbiota and Microbiome
Microbiota: microbial cells harbored by each organism
Microbiome: genomes of the microbiota (now accessible due to the advances in sequencing technologies)
Explain why soil cannot be easily colonized by living organisms
no easy mineral availability —> 25.8% silicon
kations are enclosed in silicate matrix
negatively charged ions (NO3-, Cl-) are easily washed out
several ions like phosphate, iron, sulfate and Ca2+ form insoluble complexes
Explain how plants get access to minerals in soil
plants acidify the soil to make kations become available through ion exchange principle
but still: negatively charged ions are easily washed out & phosphate, iron, sulfate and Ca2+ form insoluble complexes
roots secrete organic compounds to get access to minerals (chelates)
beneficial bacteria like rizobacteria live in symbiosis with the plants providing iron, nitrogen etc.
How do roots get access to phosphate without bacteria?
Phosphate usually occurs bound insoluble to calcium (Ca3(PO4)2)
roots secrete organanic acids (like Citramalic acid)
chelation of calcium ions by citramalic acid releases phosphate
How do roots get access to iron without bacteria?
roots secrete phenolics of the coumarin family to chelate iron
different strategies for iron uptake in dicots and monocots:
dicots: reduction of insoluble Fe3+ to soluble Fe2+, chelation of iron with coumarins, then uptake via transporter system
monocots: chelation with siderophores (e.g. mugineic acid), uptake via transporters, THEN reduction of insoluble Fe3+ to soluble Fe2+
1. Which lifestyles can root-colonizing microbes have?
Symbionts/Mutualist
Commensals
Pathogens
What are different compartments of the rhizosphere and how can you experimentally determine the microbiota of each tissue?
(ecto)rhizosphere (outside/surrounding roots)
rhizoplane (directly on root surface)
endo(rhizo)sphere (between root cells)
different compartments differ in their composition of operational taxonomic units (OTUs), but both are very high in Proteobacteria
experiment:
2. In which ways do rhizobacteria support root function?
Bacteria perform phosphate assimilation from surroundings, provide more phosphate for roots
3. Which factors can be responsible for “community shifts” in the rhizosphere?
Plant gives nutrients that support symbiont growth (sugars, mucilage)
Plant secretes inhibitors (DIMBOA) that are toxic to some microbia
4. Many soil bacteria cannot be cultivated in the lab. How can you determine their abundance in biological samples? Name two methods.
for both: extraction of DNA from rhizosphere
sequencing of 16S rDNA —> operational taxonomic units (OTUs)
single strand conformation polymorphism (SSCP) analysis —> microarray analysis (PhyloChip with 16S rRNA sequences)
Explain SSCP (Single-Strand conformation polymorphsm analysis
What are differences between bacteria found in rhizosphere and bulk soil
bacteria in rhizosphere: fast-growing, predominatly culturable, amino acid-requiring, microaerohpilic, gram negative rods (e.g. Pseudomonas)
bacteria in bulk soil: gram positive rods/dwarf cocci, nonculturable (e.g. Arthrobacter)
What are characteristics of rhizobacteria?
- Chemotaxis
• Motility of the flagellum
• Ability to attach to the root surface through
polysaccharides and surface proteins
• Metabolic acitivity, general fitness and stress
tolerance
• Competence for biofilm formation
—> high competence of colonizing rhizosphere
How are biofilms formed and why are they important?
Biofilm = well-organized community with numerous specialized functions
formation triggered by root exudates (step by step see picture)
benefits:
protection against desiccation (through exopolysaccharides)
synthesis of anti-fungal/microbial compounds
consortial metabolism
horizontal gene transfer
slow growth under starvation conditions -> beneficial against antibiotics
synthesis of virulence factors in case of pathogens to overwhelm defense response of host
5. Which soil bacterium is associated with suppressing “take-all disease“ in wheat? How can it suppress disease?
“Take-all disease” is caused by the root-infecting fungus Gaeumannomyces graminis var. tritici
DAPG is produced by Pseudomonas strains which inhibits the growth of the fungus.
After several monocultured live cycles the growth of the pathogenic fungus in entirely inhibited due to the beneficial Pseudomonas strains
6. What are the functions of the maize secondary metabolite DIMBOA?
Dimboa (produced in maize) is a selective antimicrobial compound that is beneficial for rizobacteria and leads to chemotaxis of certain strains.
Pseudomonas putida (a beneficial microbe) shows chemotaxis
7. What is the function of chelating compounds in root exudates?
Uptaking of ionic component of the soil. Chelating leads to the formation of metallo complex which leads to the uptake of anions (positive charged) essential ions to make it accesable for the plants.
Siderophores
Coumarines
8. Plant roots deposit organic material not only through root exudates but also by……
9. Name a bacterial compound that indicates high population densities.
Biofilm formation is triggered by root exudates
Cells of biofilm secrete adhesive extracellular polymeric substances
Bacteria are quorum sensing, by sensing a signal molecule above a certain threshold, biofilm formation gets encourages.
Molecule:
And: Myo-inositol
How do commensals exade the plant immune system?
Altered PAMPs (eg flg22)
acidification of rhizosphere supresses PAMP triggering
extracellular effectors supress PAMP triggering
What are the differences between SAR and ISR (=induced systemic resistance)?
SAR is triggered by microbes via SA and the expression of PR genes
ISR is rhizobacteria mediated (e.g. Pseudomonas), SA independent, JA/ET dependent
both SAR and ISR are dependent on NPR1
10. ISR (=induced systemic resistance) leads to the priming of JA/ET-dependent defense genes and not of SA-dependent defense genes. Plot the expected PR1 and PDF1.2 expression levels after Psm infection of naïve plants and ISR plants (4 samples).
11. Specific plant growth promoting Pseudomonads produce auxin only in the presence of a certain amino acid which can occur in the root exudates. Which amino acid might be important for this process? What experiment showed this?
Trp (precursor of auxin)
Experiment: auxin producing pseudomonas leads to increased root surface area
12. Recently transcription of a ß-glucosidase gene has been found to be induced in roots treated with ISR-inducing Pseudomonas WCS417 strain (=ISR inducer). Constitutive expression of this gene led to constitutive ISR. How might such an enzyme contribute to ISR?
Production of scopolin due to induction of transcription factor by Pseudomonas
The ß-glucosidase (BGLU42) catalyzes further reactions
It might produce the mobile signal needed for ISR
Transferaufgabe: Which hormones and proteins influence SAR and ISR?
SAR: SA, NPR1 are required
ISR: ET, JA-Ile, ETR1 (Ethylene receptor) are required
What is MYB72 and what does it do?
MYB72= transcription factor
It links ISR and iron deficiency response
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