The Root-Soil Interface

Question 1

Structure

Answer 1

1. Rhizo-endosphere
2. Controlling the rhizosphere
3. Microbiome detection, structure and mapping
4. PGPRs
5. Suppressive soils
6. Engineering N2 fixation

Question 2

rhizosphere

Answer 2

• immediately around roots
• hotspots for microbial growth
• decreased diversity compared to soil
• 1-3mm
• rich C supply

Question 3

endosphere

Answer 3

• inside roots
• apoplastic

Question 4

phyllosphere

Answer 4

leaf surface

Question 5

spermosphere

Answer 5

seed surface

Question 6

RAMs

Answer 6

root-associated micro-organisms

Question 7

root exudates

Answer 7

• 5-10% plant photosynthate
• increase soil nutrients

Question 8

soil and root influence

Answer 8

reciprocal

Question 9

where is diversity highest?

Answer 9

rhizoendosphere

Question 10

rhizoplane

Answer 10

• outer root
• strongly influenced by the plant
• under massive selection (> rhizosphere)

Question 11

controlling the rhizosphere

Answer 11

• exudates are key
• huge variety of architecture

Question 12

root architecture

Answer 12

• depths, fibrousness
• tap rooting
• increases diversity of habitats

Question 13

Plants are farming the soil

Answer 13

changing the composition of the microbial community

Question 14

Describe plant farming of the soil

Answer 14

1) root border cells + mucilage slough off to provide lubrication and carbon
2) suicidal epidermal cells release nutrients
3) symbiosis allows the plant to mine phosphorus and nitrogen

Question 15

soils

Answer 15

• oxygen, pH and protease profiles
• spatially heterogeneous

Question 16

roots

Answer 16

• decreased oxygen tension (due to uptake)
• acidification
• enzyme release

Question 17

Describe the relationship between roots, diversity and activity

Answer 17

• closer to the root, microbial diversity decreases, but activity increases

Question 18

rhizoplane culturing

Answer 18

• possible for 60% (need to know the conditions)
• usually rapid growth
• bog soil: 5mo’ generation time on polyaromatic stimulant
• WGS, bioinformatics

Question 19

Attachment and microcolony formation

Answer 19

1) bacterial chemoattraction -> roots (trapped!)
2) initial weak attraction mediated by hydrophobic + electrostatic forces
3) primary attachment mediated by adhesins, flagella, fimbriae and pilli
4) secondary attachment mediated by cellulose root fibrils and species. specific factors
5) microcolonies form mature biofilms by protective exopolysachharide synthesis

Question 20

primary attachment

Answer 20

reversible

Question 21

secondary attachment

Answer 21

irreversible

Question 22

PAMP/LCO perception

Answer 22

• PAMPS, (L)COs perceived by receptor heteroduplices; some shared between nodulation, mycorrhization (common symbiosis signals), and PTI
• LCO and C4 suppress PAMP receptor stimulation
• rapid endocytic takeover

Question 23

Arabidopsis root-inhabiting microbiota

Answer 23

• OTUs
• rhizoplane: distinctive
• soil and rhizosphere: shared

Question 24

OTUs

Answer 24

• operational taxonomic units
• track differences in soil fractions
• binned to >97% identity

Question 25

RAB

Answer 25

- increased actinobacteria and proteobacteria - form community

Question 26

microbiome detection

Answer 26

- Oxford Nanopore - PCR - ERIC - Meta'Omics - restriction fragment length polymorphism: not used anymore

Question 27

Oxford Nanopore

Answer 27

- look for highly conserved vs variable regions - sequence counts correlate with organismal abundance

Question 28

PCR

Answer 28

- take a known gene region and restriction-digest it - generates a band pattern for organism/community profile

Question 29

ERIC

Answer 29

- Enterobacterial Repetitive Intergenic Consensus - spacer regions using a particular set of primers - NB only certain primers work for certain groups

Question 30

Meta'Omics

Answer 30

- metagenomics - metaproteomics - metatranscriptomics - covariance of long read sequences establishes communities

Question 31

Microbiome structure

Answer 31

- OTUs - ASVs - lots of these techniques taken form marine biology

Question 32

ASVs

Answer 32

Amplicon sequence variants

Question 33

Bray-Curtis dissimilarity

Answer 33

- Cij samples in common @ sites Si, Sj

Question 34

PCA

Answer 34

- dimensionless - relative

Question 35

Microbiome mapping techniques

Answer 35

- flow cytometry - global mutagenesis

Question 36

flow cytometry

Answer 36

- count fluorescently labelled bacteria via microfluidic devices

Question 37

global mutagenesis

Answer 37

- TnSeq - BcrSeq - used to determine effects of mutation

Question 38

How to map the microbiome

Answer 38

i) make a pool of bacteria with a single mutation (insertions must collectively cover all genes) ii) inoculate plant iii) recover output pool iv) necessary genes: lost

Question 39

PGPR

Answer 39

- plant growth promoting rhizobacteria - selective - synthesise plant hormones (indoles, auxin) - produce ABs, siderophores that antagonise pathogens - ACC decreases plant ethylene - solubilise nutrients (e.g. phytases) - fix N2

Question 40

ACC

Answer 40

- 1-aminoacylcyclopropane 1-carboxylic acid - maintains plant growth

Question 41

siderophores

Answer 41

- Pseudomonas: pyroverdines - Rhizopus arrhizus: rhizoferrin

Question 42

nitrogen fixation by PGPRs

Answer 42

- 13N2 data from Setaria viridis and Herbaspirillum show that nitrogen does reach the plant

Question 43

How do PGPRs survive?

Answer 43

1) SAR 2) ISR

Question 44

SAR

Answer 44

- systemic acquired resistance - shared w/ pathogens - salicylic-acid dependent

Question 45

ISR

Answer 45

- induced systemic resistance - specific to symbionts - jasmonic acid dependent

Question 46

Suppressive soils

Answer 46

- opposite of conducive - proof-of-principle - sugar beet and Rhizoctonia sorzani - build up microbes that inhibit pathogens

Question 47

wheat

Answer 47

- good yield - declines over successive years - yield increases with suppressive soils - suppression is lost in non-ribosomal peptide synthetase mutant - Pseudomonas haplotypes, Actinobacteria

Question 48

Pseudomonads

Answer 48

- produce 2,4-diacetylphloroglucinol - AM - causes suppression

Question 49

Endophytes

Answer 49

- PGPing - e.g. Pseudomonads - fix N2 - supported by vascular high sugar levels

Question 50

Brazilian sugarcane (Gluconacetobacter diazotrophicus)

Answer 50

Herbaspirillium

Question 51

rhizopines

Answer 51

- induce N2 fixation - 3-D-methyl-scyllo-inosamine - scyllo-inosamine - synthesis genes have been artificially transferred from bacteria -> plants

Question 52

Engineering N2 fixation in cereals

Answer 52

novel rhizopine secreted -> rhizosphere

Question 53

Next step for engineering N2 fixation in cereals

Answer 53

transfer nitrogenase into plant mitochondria

Question 54

Control of N2 fixation

Answer 54

- NifA: master regulator - rhizopines