Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Roots and rhizosphere / Rhizobia-legume signalling and nodule formation
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.
Boundary: where this process starts
Starts with: Legume roots exude flavonoids (luteolin, genistein, daidzein) that activate rhizobial NodD
Boundary: where it ends
Ends after: The nodule fixes Dinitrogen and delivers ammonium-derived amino acids to the plant
Line thickness = size of impact (1 to 5)% on a line = chance a fork takes that branch📄 = pieces of evidence on a stepNegative effectLoops backHypothesisResource used up (arrow into the step)Resource used, not used upResource made or released (arrow out of the step)
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.
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.
Legume roots exude flavonoids (luteolin, genistein, daidzein) that activate rhizobial NodD
Evidence (1) · added by Ember
- Oldroyd, Murray, Poole & Downie 2011, Annual Review of Genetics 45:119: Host flavonoids bind NodD and switch on nod gene expression in the compatible rhizobial species. (confidence 0.85)
Rhizobia secrete Nod factors (lipochitooligosaccharides) that act at nanomolar to picomolar concentration
Evidence (1) · added by Ember
- Denarie, Debelle & Prome 1996, Annual Review of Biochemistry 65:503, Rhizobium lipo-chitooligosaccharide nodulation factors: Nod factors are host-specific signals active on root hairs at about 10^-9 to 10^-12 M. (confidence 0.7)
Root-hair LysM receptor kinases (NFR1 and NFR5 in Lotus) perceive Nod factors and trigger calcium spiking
Evidence (1) · added by Ember
- Radutoiu et al. 2003, Nature 425:585, Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases: Mutants in NFR1 or NFR5 fail to respond to Nod factors and do not nodulate. (confidence 0.85)
An infection thread grows through the root hair into the cortex while cortical cells divide to form the nodule primordium
Evidence (1) · added by Ember
- Oldroyd, Murray, Poole & Downie 2011, Annual Review of Genetics 45:119: Infection thread progression is coordinated with cortical cell division under cytokinin signalling. (confidence 0.8)
Autoregulation of nodulation: shoot-acting CLE peptides and the SUNN/HAR1 receptor kinase cap nodule number
Evidence (1) · added by Ember
- Ferguson et al. 2010, Journal of Integrative Plant Biology 52:61, Molecular analysis of legume nodule development and autoregulation: Mutants of HAR1/SUNN hypernodulate, showing a root-shoot loop limits nodule number. (confidence 0.8)
Rhizobia are released into plant cells and differentiate into nitrogen-fixing bacteroids (in Medicago via NCR peptides, with genome endoreduplication)
Evidence (1) · added by Ember
- Van de Velde et al. 2010, Science 327:1122, Plant peptides govern terminal differentiation of bacteria in symbiosis: Nodule-specific cysteine-rich peptides drive terminal bacteroid differentiation in Medicago. (confidence 0.85)
The nodule fixes Dinitrogen and delivers ammonium-derived amino acids to the plant
Evidence (1) · added by Ember
- Udvardi & Poole 2013, Annual Review of Plant Biology 64:781: Bacteroids import dicarboxylates and export fixed nitrogen across the symbiosome membrane. (confidence 0.85)
Host sanctions: nodules that fix less nitrogen get less oxygen and their rhizobia reproduce about 50% less
Evidence (1) · added by Ember
- Kiers, Rousseau, West & Denison 2003, Nature 425:78, Host sanctions and the legume-rhizobium mutualism: Soybean nodules with N2 fixation prevented (Ar:O2) had about 50% lower rhizobial reproduction. (confidence 0.85)