Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Roots and rhizosphere

Roots and rhizosphere

Roots release carbon (exudates, mucilage, sloughed cells) into the soil around them, which feeds and selects microbes, shifts pH, mobilizes phosphorus and iron, and glues particles into the rhizosheath. Depletion zones and nutrient demand feed back on how much carbon the roots release.

Boundary: where this process starts

Starts with: Photosynthate allocated belowground

Boundary: where it ends

Ends after: Root channels and biopores left by dead roots; Mucilage and hyphae form rhizosheath

What am I looking at? The concepts on every map

Participant: Someone or something that takes part in a process or influences it: a plant, a microbe, a river, a machine, a force. Participants are the rows of a map.
Resource: Something a step uses or uses up: water, oxygen, sunlight, a tool. Each step has an arrow down to the resources it uses.
Step: One thing that happens in a process. Every step has at least one participant and carries evidence.
Decision fork: A step where the process can go several ways. Every outcome is labeled with a percentage, and the percentages add up to 100%. It is not limited to yes or no.
Loop: A line that carries the process back to an earlier step. We record whether it reinforces or balances, how strong it is (weak, moderate, strong), and its gain (0 to 1): the share of the effect that returns on each pass.
Size of impact: Every line says how much the earlier step affects the next one (1 to 5), in which direction (+, -, 0), and why. Thicker lines mean bigger impact.
Evidence: The support for a claim: a source and what it shows. Every step, line, change and vote needs it. Click any step or line to read its evidence.
Boundary: Where a process starts and where it ends. Every process, and every subprocess, has a start and an end.
Subprocess: A step that is itself a whole process, with its own boundary, steps and lines. Click a step marked ↘ to open it. Subprocesses nest as deep as the evidence goes.
Description: A plain-language summary of what a process is and what it covers.
Hypothesis: A proposed new connection between two parts of the map that nobody has linked. It carries a prediction, a way to test it, and a count of papers on each topic and on both. It is an unverified idea until someone tests it.

Inside this process

Root exudate chemistry, fate and priming

Roots release sugars, amino acids, organic anions and signalling compounds by passive and active efflux. The exudates are mostly taken up by microbes within hours, with smaller shares re-absorbed by roots, sorbed to minerals or leached.

Rhizobia-legume signalling and nodule formation

The molecular dialogue that makes a nitrogen-fixing nodule: flavonoids from the root, Nod factors from the bacterium, infection threads, bacteroid differentiation, and the plant controls that cap nodule number and sanction poor partners.

Disease-suppressive soils and the rhizosphere cry for help

How a root microbiome protects plants from soil-borne pathogens: infected plants recruit antagonists through exudates, Pseudomonas that make DAPG and siderophores suppress pathogens, resident microbes compete generally, and rhizobacteria prime plant defences.

Rhizosphere phosphorus mobilization: phosphatases, organic acids and fast re-sorption

How roots and microbes free phosphorus that is bound in organic molecules and sorbed to iron and aluminium oxides. Low phosphate triggers phosphatases and organic acid release; released phosphate is re-sorbed within hours unless taken up, and rising supply switches the response off.

Every step, with its evidence

The same information as the map, as a list you can search and share. Click a participant or resource to see everywhere it appears.

Photosynthate allocated belowground

Plants Phloem Carbon Sunlight

Evidence (1) · added by Ember

Hinsinger et al. (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance, Plant and Soil 321:117-152: Plants allocate a substantial fraction of fixed carbon (often 10-40 percent) to roots and rhizodeposition. (confidence 0.75)

Root growth and elongation into soil

Plant roots Root tips Carbon Water Nutrients

Evidence (1) · added by Ember

Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Root tips extend into new soil, creating fresh zones of interaction. (confidence 0.75)

Root exudation of sugars, amino acids and organic acids

Plant roots Rhizosphere microbes Carbon Organic acids Sugars

Evidence (1) · added by Ember

Hinsinger et al. (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance, Plant and Soil 321:117-152: Roots release low molecular weight compounds that feed rhizosphere microbes. (confidence 0.75)

Root cap cells and mucilage released

Root cap Plant roots Mucilage Carbon

Evidence (1) · added by Ember

Hinsinger et al. (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance, Plant and Soil 321:117-152: Root cap cells and mucilage are continuously shed, forming a lubricated, microbe-rich layer. (confidence 0.75)

⑂ Which microbes colonize the rhizosphere

Rhizosphere microbes Plant roots Carbon

Evidence (1) · added by Ember

Philippot et al. (2013) Going back to the roots: the microbial ecology of the rhizosphere, Nature Reviews Microbiology 11:789-799: Rhizosphere microbiomes are selected from bulk soil by host genotype and exudate profile, including beneficial and pathogenic members. (confidence 0.75)

Growth-promoting bacteria colonize

Plant growth promoting bacteria Carbon Nitrogen

Evidence (1) · added by Ember

Philippot et al. (2013) Going back to the roots: the microbial ecology of the rhizosphere, Nature Reviews Microbiology 11:789-799: Plant growth promoting rhizobacteria fix nitrogen, produce hormones and mobilize nutrients. (confidence 0.75)

Neutral commensal microbes persist

Rhizosphere microbes Carbon

Evidence (1) · added by Ember

Philippot et al. (2013) Going back to the roots: the microbial ecology of the rhizosphere, Nature Reviews Microbiology 11:789-799: Many rhizosphere taxa have no clear net effect on host growth. (confidence 0.75)

Root pathogens infect

Root pathogens Carbon

Evidence (1) · added by Ember

Philippot et al. (2013) Going back to the roots: the microbial ecology of the rhizosphere, Nature Reviews Microbiology 11:789-799: Soil-borne pathogens such as Pythium and Fusarium exploit root exudates to find hosts. (confidence 0.75)

Rhizosphere pH shifts from ion uptake

Plant roots Hydrogen ions Nitrogen

Evidence (1) · added by Ember

Hinsinger et al. (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance, Plant and Soil 321:117-152: Imbalanced cation and anion uptake makes roots release protons or bicarbonate, changing rhizosphere pH by up to 1-2 units. (confidence 0.75)

Organic acids solubilize phosphorus

Plant roots Phosphate solubilizing microbes Phosphorus Organic acids

Evidence (1) · added by Ember

Hinsinger et al. (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance, Plant and Soil 321:117-152: Carboxylates and acidification release phosphate from mineral and organic pools. (confidence 0.75)

Siderophores and phytosiderophores mobilize iron

Plant roots Rhizosphere microbes Iron

Evidence (1) · added by Ember

Hinsinger et al. (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance, Plant and Soil 321:117-152: Siderophores chelate poorly soluble iron for plants and microbes. (confidence 0.75)

Rhizosphere priming of organic matter decomposition

Rhizosphere microbes Soil organic matter Carbon Nitrogen Oxygen

Evidence (1) · added by Ember

Kuzyakov (2010) Priming effects: interactions between living and dead organic matter, Soil Biology & Biochemistry 42:1363-1371: Fresh root carbon can accelerate decomposition of existing soil organic matter, a priming effect. (confidence 0.75)

Microbial loop releases nitrogen near roots

Protozoa Bacteria Plant roots Nitrogen Carbon

Evidence (1) · added by Ember

Schimel & Bennett (2004) Nitrogen mineralization: challenges of a changing paradigm, Ecology 85:591-602: Protozoan grazing of rhizosphere bacteria mineralizes nitrogen near the root (Clarholm microbial loop concept). (confidence 0.75)

Roots absorb water and mineral nutrients

Plant roots Root hairs Water Nitrogen Phosphorus Potassium

Evidence (1) · added by Ember

Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Root hairs and root surface take up ions and water from soil solution. (confidence 0.75)

Depletion zone forms around root

Plant roots Soil solution Phosphorus Nitrate Water

Evidence (1) · added by Ember

Hinsinger et al. (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance, Plant and Soil 321:117-152: Uptake faster than diffusion produces nutrient and water depletion zones near roots, especially for immobile phosphorus. (confidence 0.75)

Mucilage and hyphae form rhizosheath

Root hairs Mucilage Soil particles Mucilage Water

Evidence (1) · added by Ember

Hinsinger et al. (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance, Plant and Soil 321:117-152: Mucilage and root hairs bind soil particles into a rhizosheath that holds water and aids contact. (confidence 0.75)

Root channels and biopores left by dead roots

Dead roots Soil fauna Air Water

Evidence (1) · added by Ember

Brady & Weil, The Nature and Properties of Soils, 15th ed. (2016): Decayed roots leave continuous pores that act as preferential flow and gas paths. (confidence 0.75)

↘ Root exudate chemistry, fate and priming

Plant roots Rhizosphere microbes Sugars Amino acids Organic acids Carbon

Evidence (1) · added by Ember

Jones, Nguyen & Finlay 2009, Carbon flow in the rhizosphere: carbon trading at the soil-root interface, Plant and Soil 321:5-33: Reviews the compounds, fluxes and microbial turnover of root exudates at the soil-root interface (confidence 0.8)

↘ Rhizobia-legume signalling and nodule formation

Legume roots Rhizobia Flavonoids Carbon Nitrogen

Evidence (1) · added by Ember

Oldroyd, Murray, Poole & Downie 2011, Annual Review of Genetics 45:119, The rules of engagement in the legume-rhizobial symbiosis: Flavonoid and Nod-factor exchange, infection threads and organogenesis are the sequential steps of nodule formation. (confidence 0.85)

↘ Disease-suppressive soils and the rhizosphere cry for help

Plant roots Pathogenic fungi Antagonistic bacteria Root exudates Iron Carbon

Evidence (1) · added by Ember

Weller, Raaijmakers, Gardener & Thomashow 2002, Annual Review of Phytopathology 40:309, Microbial populations responsible for specific soil suppressiveness to plant pathogens: Specific suppressiveness is caused by identifiable antagonist populations, transferable between soils. (confidence 0.85)

↘ Rhizosphere phosphorus mobilization: phosphatases, organic acids and fast re-sorption

Plant roots Rhizosphere microbes Phosphate Phosphorus Organic acids

Evidence (1) · added by Ember

Richardson & Simpson 2011, Plant Physiology 156:989, Soil microorganisms mediating phosphorus availability: Microbial and plant enzymes and organic acids mobilize organic and sorbed soil P for plant uptake. (confidence 0.75)