WK - Plant Microbiomes Below Ground I

Question 1

What is the Rhizosphere? (2)

Answer 1

• The zone of soil tightly attached to plant roots.
• Influenced by root exudates and inhabited by diverse microorganisms.

Question 2

What is the Rhizoplane? (2)

Answer 2

• The surface of the root itself.
• Where microorganisms are physically attached.

Question 3

What is the Endosphere? (2)

Answer 3

• The interior of the root.
• Home to endophytic microorganisms living within root tissues, often in symbiotic relationships.

Question 4

What is Rhizosphere Filtering? (2)

Answer 4

• Root exudates attract and select microbes suited to this nutrient-rich soil zone.
• Filters for microbes capable of utilizing carbon compounds and nutrients from roots.

Question 5

What is Rhizoplane Filtering? (2)

Answer 5

• Only microbes that can attach to the root surface thrive here.
• Selection favors microbes with attachment mechanisms (e.g., biofilms).

Question 6

What is Endosphere Filtering? (2)

Answer 6

• The most selective zone; microbes must penetrate root tissues.
• Endophytes that can evade plant defenses and form symbiotic relationships are favored.

Question 7

What is the significance of the Rhizosphere? (4)

Answer 7

• Coined by German agronomist Hiltner in 1904.
• Region of soil tightly attached to roots, around 2mm thick, with many gradients.
• Important interface between plant and environment for nutrient uptake.
• Some plants release up to 40% of their photosynthetic carbon through roots as rhizodeposits and exudates.

Question 8

What do Rhizodeposits include (5) and what are they?

Answer 8

• Sloughed-off root cap
• Border cells
• Mucilage
• Exudates
• Enzymes

Organic materials released from roots into the soil.

Question 9

What are other forms of carbon exchange related to Rhizodeposits? (3)

Answer 9

• Volatiles
• Symbioses
• Cell death

Question 10

What are the properties and functions (6) of Mucilage in exudation?

Answer 10

Properties: High molecular weight; actively secreted.

Functions:

• Lubricates growing roots.
  Reduces desiccation.
• Promotes soil aggregation, affecting water and oxygen flow.
• Assists in defense by trapping microbial spores.
• Serves as a carbohydrate source for some microbes.
• Certain roots (e.g., crown roots) can house nitrogen-fixing microbes.

Question 11

What are the characteristics of Exudates (3)

Answer 11

• Consist of a highly diverse array of low molecular weight carbon compounds.
• Composition changes with plant life stage, nutrition, stress, time of day, and environmental conditions.
• Main types include organic acids, amino acids, proteins, sugars, and phenolics (free and lignin-bound).

Question 12

What are 3 functions of exudates?

Answer 12

• Aid in nutrient acquisition.
• Provide defense (antagonism/allelopathy).
• Attract beneficial microbes.

Question 13

What are the unique aspects of root exudates and their impact on the microbiome? (3)

Answer 13

• Each plant has a unique chemical fingerprint in its root exudates.
• Plant genotype affects exudate composition, influencing all microbiome compartments, especially the rhizosphere.
• High microbial diversity in the rhizosphere is supported by resource partitioning, allowing many microbes to coexist by utilizing different exudate compounds.

Question 14

What are the components of defense exudates in plants? (6)

Answer 14

• Mucilage.
• Phytoalexins and phytoanticipins.
• Benzoxazinoids (phytoanticipins).
• Phenolics (including flavonoids and phenylpropanoids).
• Terpenoids
• Border cells (as part of rhizodeposits).

Question 15

What is (2)chemotaxis in relation to microbial attraction?

Answer 15

• Microbes are attracted to carbon compounds.
• They can actively move toward (or away from) chemical gradients.

Question 16

What are the key functions of the rhizosphere? (5)

Answer 16

1) Nutrient Uptake: Enhances the availability and absorption of water and essential nutrients.

2) Soil Structure Improvement: Contributes to soil aggregation and stability through root exudates.

3) Microbial Activity: Supports diverse microbial communities that aid in nutrient cycling and organic matter decomposition.

4) Pathogen Suppression: Promotes beneficial microorganisms that inhibit harmful pathogens.

5) Plant Growth Promotion: Facilitates plant growth through the production of growth-promoting substances by rhizobacteria.

Question 17

What are some methods for studying Exudates? (2)

Answer 17

• In-situ analysis
• Chromatogrpahy

Question 18

What are some of the ways that roots can influence the microbiome? (5)

Answer 18

• Roots can alter the oxygen environment.
• Roots can alter the pH.
• Roots can release exudates.
• Roots have sloughed-off cells.
• Roots release mucilage.

Question 19

What are the characteristics and functions of the rhizoplane?

Answer 19

Characteristics:

• Tightly attached microorganisms.
• Acts as a “gate” to the root interior.

Filtering:

• Selects for microbes that can attach to the roots themselves.

Plant Immune System:

• Utilizes pattern recognition receptors (PRR) and microbe-associated molecular patterns (MAMPs).
• Includes flagellin proteins for recognition.

Question 20

What are 4 characteristics of the root endosphere?

Answer 20

• Endophytes
• Microbes colonise within the plant tissues
• Plant immune system - The root endosphere interacts with the plant’s immune system
• More contamination – Plant chloroplasts and mitochondria also carry 16S rRNA genes, indicating microbial presence

Question 21

What are the characteristics of internal microbes and their colonization mechanisms? (3)

Answer 21

Can colonize intercellular and intracellular spaces.

Specialized Genes Needed for Colonization:

• Polymer degrading enzymes (e.g., cellulases and pectinases).
• Secretion systems.

Question 22

What are the types of plant-associated taxa? (4)

Answer 22

Commensals:

• Provide free nutrients to plants.

Plant Growth-Promoting Rhizobacteria (PGPR):

• Umbrella term for bacteria that aid the plant (e.g., nitrogen fixation).

Mycorrhizal Fungi:

• Form symbiotic relationships with plants, enhancing nutrient uptake.

Pathogens:

• Microbes that can harm the plant.

Question 23

What are the microbial effects on plant physiology? (4)

Answer 23

• Alter root structure and architecture.
• Influence plant immune responses.
• Reduce abiotic stress (e.g., drought, salinity).
• Improve plant nutrient status.

Question 24

What are the roles of various plant hormones influenced by microbes? (5)

Answer 24

Indole-3-Acetic Acid (Auxin):

• A growth hormone that promotes root and shoot growth.
• Produced by several bacteria (~80%) and can also be degraded by some.

Jasmonic Acid and Salicylic Acid:

• Crucial hormones for plant immunity and stress signaling.
• Certain microbes can interfere with these signaling pathways.

Ethylene:

• A growth hormone important for stress responses (e.g., drought).
• Some bacteria produce enzymes (e.g., ACC oxidase, ACC deaminase) that modify ethylene levels.

Gibberellins:

• Growth hormones that can also be produced by some microbes.

Nutrient Availability:

• Influence the availability of phosphorus, nitrogen, potassium, and iron.

Question 25

How does Pseudomonas syringae manipulate plant signaling? (3)

Answer 25

Phytotoxin Production:

• Produces coronatine, which mimics jasmonic acid.
• Suppresses salicylic acid defense signaling, weakening the plant’s immune response.

Auxin Production:

• Produces auxin, promoting lateral root formation.
• This manipulation enhances its ability to invade the plant.

Type III Secretion System (T3SS):

• Facilitates the delivery of effector proteins into plant cells.
• Supports the colonization and establishment of the pathogen within the host.

Question 26

What are the methods for collecting the microbiome from different plant compartments? (3)

Answer 26

Rhizosphere:

• Shake roots and then vortex in a solution.

Rhizoplane:

• Use sonication.

Root Endosphere:

• Use the whole root after cleaning.

Scientists collect each compartment in various ways; there is no standardization.