Applied rhizosphere microbiology and partnerships

Landscape soils and surface environments - Week 5 Workshop 2b

Raphael Viscarra Rossel, Lewis Walden

2026-03-18

Overview of Workshop 2b

Moving from rhizosphere concepts to applied rhizosphere microbiology and partnerships


Focus of this session

  • Who are the key microbial players?
  • What C, N, P processes do they drive?
  • How do plants steer their microbiome?

Learning goals

By the end of this session you will be able to:

  • Describe key microbial functional groups in the rhizosphere
  • Link these groups to C, N, and P transformations
  • Explain how plants steer rhizosphere communities with exudates and partnerships
  • Apply this to Banksia, Jarrah, and Acacia systems on the SCP–Scarp

The rhizosphere microbiome (quick recap)

Who lives there?

  • Bacteria and archaea
  • Fungi (mycorrhizal and saprotrophic)
  • Protozoa and nematodes
  • Viruses (phages)

Key features

  • ⬆ abundance and activity than bulk soil

- Community shaped by root exudates and soil conditions

Thinking in functional groups

To understand rhizosphere processes, we need to:

Group microbes by what they do–functions–not just who they are (taxonomy).

  • Functional groups: sets of microbes that perform similar roles in C, N, P cycling

  • Examples: decomposers, mutualists, transformers (nitrifiers, denitrifiers, P-mobilisers), predators, pathogens

Microbial functional groups

  • Decomposers: Bacteria, fungi that break down OM → CO₂ + mineral nutrients

  • Mutualists: Mycorrhizae (P, N foraging),
    N-fixers (rhizobia in nodules)

  • Transformers: Nitrifiers, denitrifiers,
    P-mobilisers (change nutrient forms)

  • Predators: Protozoa, nematodes (graze bacteria/fungi, release NH₄⁺)

  • Pathogens: root-infecting fungi/oomycetes (e.g. Phytophthora)

Video (6.5 minutes) - The soil food web

A rhizosphere-scale mini food web - Energy flow

Energy and Carbon

  • Plants invest 10–40% of photosynthate as root exudates and litter
  • This C fuels microbial growth and activity
  • Microbes respire ➡ CO₂ released back to atmosphere
  • Microbial activity ➡ mineral nutrients released for plant uptake

- Result: Plant C investment drives nutrient availability

A rhizosphere-scale mini food web - Trophic interactions

Trophic steps and the “microbial loop”

  • Level 1: Bacteria and fungi consume C from exudates/litter (decomposers)
  • Level 2: Protozoa and nematodes graze bacteria/fungi (predators)
  • Grazing releases NH₄⁺ locked in microbial biomass (plant-available N)
  • Grazing accelerates microbial turnover ➡ faster nutrient cycling

- Without grazers: N stays immobilised in microbes, unavailable to plants

A rhizosphere-scale mini food web - Outputs

What the rhizosphere produces

  • C output: CO₂ from microbial respiration
    (C loss from system)
  • N output: NH₄⁺ and NO₃⁻ from mineralisation and grazing (plant-available)
  • P output: PO₄³⁻ from mineralisation and
    P-mobilisation (plant-available)
  • These outputs are localised in the rhizosphere (mm–cm scale)

In Week 6: We’ll scale these rhizosphere processes to ecosystem C, N, P budgets

Functional groups and N processes

Decomposers

  • Break down organic N → NH\(_4^+\) (mineralisation)
  • Immobilise N into microbial biomass

Nitrifiers

  • Convert NH\(_4^+\) → NO\(_3^-\) in aerobic zones

Denitrifiers

  • Reduce NO\(_3^-\) → N\(_2\), N\(_2\)O under low O\(_2\)

Predators - Grazers (protozoa, nematodes) release NH\(_4^+\) in waste

Functional groups and P processes

P in soil is strongly bound to minerals or OM. Has low mobility in weathered sands and laterites.

Key groups

  • P-mobilising bacteria and fungi
    • Release organic acids (e.g. citrate, malate)
    • Produce phosphatases (cleave organic P)
  • Mycorrhizae
    • Explore fine pores and microsites
    • Access P beyond the root depletion zone

Quick matching task (5 min) - handout

Match each description to:

  • A functional group
  • A process (e.g. mineralisation, nitrification, denitrification, P mobilisation)

Examples:

  1. Converts NH\(_4^+\) to NO\(_3^-\) in well-aerated soil.
  2. Releases NH\(_4^+\) when grazing on bacteria.
  1. Uses NO\(_3^-\) as an electron acceptor under low O\(_2\), producing N gases.
  2. Releases organic acids to dissolve mineral P near roots.

Plants steering the microbiome

Plants influence which groups dominate via:

Exudate quality

  • Specific sugars, amino acids, organic acids favour specific taxa

Partnerships

  • Mycorrhizae: P (and sometimes N) foraging extensions
  • N-fixers: external N input into the system

Banksia on SCP sands – microbial focus

Challenge: deep, highly weathered quartz sands with extremely low P and N

Key functional groups

  • P-mobilisers activated by cluster root organic acid exudation
  • Mycorrhizal hyphae extend P access in understorey species
  • N-fixing nodules in understorey legumes (e.g. Bossiaea) supply N to the community

Jarrah on laterites – microbial focus

Challenge: Low nutrients, low pH, high Al - demands a multi-layered microbial strategy

Key functional groups

  • Decomposers recycle litter ➝ NH₄⁺ and PO₄³⁻
  • Mycorrhizal networks extend roots beyond depletion zones
  • P-mobilisers release organic acids and phosphatases
  • Acid-tolerant bacteria dominate mineral horizons

Acacia and N-fixation – microbial focus

Where Acacia matters

  • SCP sands – low N, disturbance-prone
  • Post-fire Jarrah – N lost by volatilisation
  • Coastal dunes – early coloniser

N inputs

  • Direct: rhizobia in nodules fix N₂ ➝ NH₄⁺ for the plant/soil
  • Indirect: N-rich litter decomposes ➝ NH₄⁺ for neighbours

Three systems: A, B, C

We compare microbial roles in:

  • System A: SCP Banksia woodland
    • P extremely limiting, low N, deep sand
  • System B: Post-fire Jarrah forest
    • N volatilised, P moderate, disturbance
  • System C: Fertile valley bottom
    • Higher P and N, finer texture

Activity – functional groups by system (10 min, part 1)

In groups

For each system (A, B, C), fill the table on your handout:

System Main limitation(s) Key functional groups
A: Banksia woodland ___________________ ___________________________
B: Post-fire Jarrah ___________________ ___________________________
C: Fertile valley ___________________ ___________________________

Consider:

  • Which nutrients limit growth? (P, N, both)
  • Which functional groups are critical to overcome these limitations?

Activity – functional groups by system (5 mins, part 2)

Same groups

Add a third column:

System Main limitation(s) Key functional groups Plant–microbe strategies
A: _______________ _____________________ ______________________
B: ________________ _____________________ ______________________
C: _______________ _____________________ ______________________

For each system note 1–2 strategies, e.g.:

  • Exudate patterns
  • Mycorrhizal dependence
  • N-fixer presence
  • Litter inputs

When microbes are harmful: Phytophthora dieback

Phytophthora cinnamomi

infects roots of many SW WA species — collapsing the rhizosphere from the inside:

  • Destroys fine roots → shrinks effective root zone
  • Collapses mycorrhizal networks and P-mobilisers
  • Disrupts water and nutrient uptake → canopy dieback
  • Spreads via water and soil disturbance → landscape-scale impacts

Discussion – rhizosphere health and management (5 mins)

In pairs Choose a Banksia or Jarrah site:

  1. How would Phytophthora infection change:
    • Effective root-zone depth?
    • Key microbial functional groups?
  1. What management could:
    • Protect rhizosphere health?
    • Support beneficial functional groups during restoration?

Key takeaways

  • The rhizosphere is a hotspot where microbial functional groups drive local C, N, and P transformations.

  • Plant C investment (10–40% as exudates and litter) fuels a rhizosphere food web that returns mineral N and P to plants and releases CO₂.

  • Predators (protozoa, nematodes) grazing bacteria and fungi form a “microbial loop” that unlocks NH₄⁺ and speeds nutrient cycling.

  • P-mobilising microbes and mycorrhizae are essential for accessing tightly bound P in weathered SCP sands and laterites.

  • Banksia, Jarrah, and Acacia use different plant–microbe partnerships to solve P and N limitation along the SCP–Scarp.

Looking ahead to Week 6

Week 6

  • Embeds these processes in full C, N, and P cycles
  • Examines how management (clearing, fire, fertiliser, restoration) alters:
    • C inputs and turnover
    • N and P availability
    • Long-term soil C storage and resilience

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