Lecture 25: Competition in the Rhizosphere

Question 1

What is the rhizosphere?

Answer 1

Soil surrounding the roots

Question 2

Whats the rhizoplane?

Answer 2

the surface of the roots

Question 3

What is the endosphere?

Answer 3

the interstitial space between cells of the roots

Question 4

What are the different interactions between different organisms united by surrounding soil?

Answer 4

Soil is the environment for interaction between:
1. Pathogens
a. Harmful to plant
2. The plant(s)
3. Biocontrol PGPRs
a. Symbiotes: integrates, sometimes
irreversible relationships
b. Commensals: independent colonisers;
don’t really add or take away anything

Question 5

What are root exudates?

Answer 5

1. Amino acids
2. Organic acids
3. Putrescine
4. Sugars
5. Vitamins etc

Plants secrete 20% of the fixed carbon they produce into the soil. This allows for a high biomass in the rhizosphere, causing bacteria to chemotax to the roots.

Plants do this to feed the bacteria

Question 6

What happens when bacteria chemotax to the exudates from the roots

Answer 6

1. attach and form a microcolony
2. Colony enlarges, forming a
   exopolysaccharide biofilm around it

Question 7

How is rhizosphere colonisation possible?

Answer 7

1. Various forms of attachment and motility
   systems in different bacteria
2. EPS (exopolysaccharides) and fimbriae
   a. Allow bacteria to attach to surfaces
3. Flagella - allow chemotaxis
4. Type 4 pili - allow bacteria to move
   around on the rhizoplane

Question 8

How can bacteria behave hostile to each other?

Answer 8

Through enzyme secretory pathways

1. Type 2: secrete toxins to kill fungi, insects
   and other bacteria
2. Type 3: effectors

Question 9

What are the different enzymes and their functions secreted by bacteria?

Answer 9

1. Chitinases
   a. Prod. by certain Pseudomonas spp.
   b. Hydrolyse fungal cell (by
   hydrolysing chitin) walls - biocontrol
2. Pectate lyase
   a. Digest plant material (e.g., potatoes)
   b. allows bacteria to live off decaying
   material
3. AHL Lactonases
   a. Degrade QS molecules (what
   bacteria to know their position and
   surrounding bacterial population
   b. Interferes with Quorum sensing of
   other bacteria - changing their
   behaviour
4. Bacteriocins
   a. Diverse, narrow-spectrum
   proteinaceous toxins
   b. Allows bacteria to kill each other to
   fight for rhizosphere space
   c. There is often immunity genes
   against these

Question 10

How can secretion systems create virulence and cytotoxicity?

Answer 10

Type 3 secretory effectors

Affects the plant/fungal cells; e.g., by toying with their immune system

Question 11

What are the different plant pathogenesis

Answer 11

1. Erwinia amylovora - cause fire blight
2. Xanthomonas campestris - cause
   black rot/leaf spot
   a. excessive secretion of type 2 enzymes
3. Steptomyces scabies (common scab)
   a. plant immune system trying to fight
   off bacteria

Question 12

Why are plants able to survive the different pathogensis’ caused by bacteria?

Answer 12

Biocontrol PGPR bacteria

1. Suppress pathogenic plant bacteria
2. Contribute to:
   a. biofertilisation
   b. root growth stimulation
   c. Plant stress control
   d. Pathogen antagonism

Question 13

What are the different ways biocontrol PGPR bacteria contribute to plant growth promotion and biocontrol?

Answer 13

1. Biofertilisation
   a. Plants need various things. E.g.,
   nitrogen, phosphorus, etc. which
   they may not be very good at
   acquiring themselves
   b. Rhizobium - ‘symbiotic’ nitrogen
   fixation
   c. Azospirillum, Azotobacter -
   free-living N2 fixers (nitrogen
   bio-fertilisers)
   d. Phosphate solubilisation - inorganic
   phosphate to organic acids
2. Root growth stimulation
3. Plant stress control
4. Pathogen antagonism

Question 14

How do bacteria encourage plant growth?

Answer 14

1. Hormones
2. Auxins - plant growth hormones,
   promote growth and development
   a. Indole-3-acetic acid (IAA)
3. Bigger plant = more exudate!!!!
4. Azotobacter, Pseudomonas sp.
   a. Encode genes for production and
   degradation of IAA
   b. also produce other plant growth
   factors - “Gibberellins” and “Cytokinins”

Question 15

How do volatiles and cofactors affect plant growth

Answer 15

1. Bacillus, Enterobacter, certain
   Pseudomonas sp
   a. Prod enzymes for synthesis of “2-3-
   butanediol acetoin” (plant growth
   promoting metabolites)
   b. (“Volatile”)
2. Pyrroloquinoline quinone (PQQ)
   a. Antioxidant
   b. Antifungal activity
   c. ISR induction
   d. (“Cofactor”)

Question 16

How do ACC deaminase control plant stress responses?

Answer 16

“Aminocyclopropane-1-carboxylic acid” (ACC) ethylene precursor

1. Stress -> ethylene production
2. = Inhibition of root elongation,
   accelerated abscission, aging and
   senescence
3. ACC deaminase turns the ACC into
   NH3 and alpha-ketobutyrate
4. ACC deaminase protects against:
   a. Polyaromatic hydrocarbons
   b. Phytopathogenic bacteria
   c. Heavy metals (e.g., Ca2+, Ni2+)
   d. Drought
   e. Salt

Question 17

How do the biocontrol molecules produced by Pseudomonas aid pathogen antagonism

Answer 17

1. Siderophores
   a. Pyoverdin
   b. Pyochelin
2. Phenazines
   a. Phenazine-1-carboxylate
   b. Phenazin-1-carboxamide
   c. Pyocyanin
3. Antibiotics
   a. Hydrogen cyanide
   b. 2-4-DAPG
   c. Pyoluteorin
   d. Pyrrolnitrin
4. Cyclic lipopeptides
   a. Viscosinamide

Question 18

What do siderophores do?

Answer 18

1. Produce by many bacteria
2. Iron/other metal-binding small (500-
   1000Da) molecules
3. Facilitate metal ion scavenging
4. Once secreted, bind to a metal, and then
   is re-up-taken by a different bacteria
5. E.g., Pyoverdin:
   a. Fe3+ scavenger
   b. Can inhibit pathogen growth via iron
   limitation
6. E.g., Pyochelin
   a. Weak Fe3+, strong Cu2+ & Zn2+
   chelator
   b. Can function as antifungal antibiotic

Question 19

What do cyclic lipopeptides do?

Answer 19

1. Function as powerful surfactants
2. Antibiotic activity due to membrane
   solubilisation
3. Allow bacteria to move across plant
   surface
4. Without these genes (when KO) they
   dont move

Question 20

What do phenazines do?

Answer 20

E.g., Pyocyanin & Phenazine-1-carboxamide

1. Inhibit electron transport in pathogenic
   species
2. Catalyse formation of hydroxyl radicals in
   combination with ferripyochein - damage
   lipids and other molecules
3. Contribute to oxygen shuttling in
   microoxic environments
4. May contribute to iron mobilization in soil

Question 21

there are many antibiotic properties

Question 22

What is iChip

Answer 22

Raises percentage of culturable soil bacteria from <1% to ~50%

1. Bacteria can get in but not out and then
   be cultured on soil

Question 23

How is the rhizosphere diverse?

Answer 23

> 30,000 different species of bacteria
Even the same species can have HUGE diversity between them
Do different things previously discussed

Question 24

What are Arbuscular mycorrhizal fungi (AMF)

Answer 24

Symbiosis of plants with AMF occur in more than 90% of plant species

For the plant:

1. improved phosphate uptake
2. improved nitrogen uptake

For the fungus:
1. Carbon - hexose sugars

Question 25

What do nematodes and other insects do?

Answer 25

1. Nematodes:
   a. eat roots, organic matter, and bacteria
   b. can be beneficial, pathogen, or neutral
2. Insects and worms:
   a. eat plants, roots, organic matter, other
   insects
   b. can be beneficial, pathogenic, or
   neutral