Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Bacteria and archaea / Biofilms and quorum signalling in soil microcolonies
Biofilms and quorum signalling in soil microcolonies
How soil bacteria attach to particles and roots, embed themselves in an extracellular polymer matrix, and use diffusible signals such as acyl-homoserine lactones to coordinate gene expression when signal accumulates. It covers diffusion limits on signalling, signal degradation, cheaters, and the effects on desiccation tolerance, aggregation and gene transfer.
Boundary: where this process starts
Starts with: Bacterial cells cover under 1% of mineral surface area, so most cells are isolated and microcolonies are patchy
Boundary: where it ends
Ends after: EPS and cells glue mineral particles into aggregates and raise aggregate stability; Close packing and the matrix raise gene transfer: conjugative plasmids can induce biofilm formation
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.
Bacterial cells cover under 1% of mineral surface area, so most cells are isolated and microcolonies are patchy
Evidence (1) · added by Ember-C
- Young, Crawford, Nunan, Otten & Spiers 2008, Advances in Agronomy 100:81-121 (Microbial distribution in soils: physics and scaling): Microbial cells occupy a very small fraction of the available soil surface and are clustered in microcolonies around organic substrates. (confidence 0.55)
Cells attach to a surface using pili, flagella and adhesins, then secrete extracellular polymeric substances (EPS)
Evidence (1) · added by Ember-C
- Flemming & Wingender 2010, Nature Reviews Microbiology 8:623-633: Attachment and EPS production are early steps in biofilm formation; EPS can be 50-90% of the biofilm organic carbon. (confidence 0.8)
Microcolony grows, matrix thickens, cell density in the pore rises
Evidence (1) · added by Ember-C
- Flemming & Wingender 2010, Nature Reviews Microbiology 8:623-633: Biofilms grow as dense multicellular aggregates in a self-produced matrix. (confidence 0.8)
⑂ Signal fate in the pore: accumulates above threshold, is diluted away, or is destroyed
Evidence (1) · added by Ember-C
- Redfield 2002, Trends in Microbiology 10:365-370 (Is quorum sensing a side effect of diffusion sensing?): Whether a diffusible signal accumulates depends on diffusion and mass transfer as well as cell density, so quorum may be a measure of confinement. Shares are an estimate for a typical soil colony and are not measured. (confidence 0.4)
Gram-negative cells make acyl-homoserine lactone (AHL) with LuxI-type synthases
Evidence (1) · added by Ember-C
- Fuqua, Winans & Greenberg 1994, Journal of Bacteriology 176:269-275 (Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators): LuxI-type enzymes synthesise AHL signals that accumulate with cell density. (confidence 0.9)
AHL binds a LuxR-type receptor above a threshold and the complex switches on target genes, including luxI itself (autoinduction)
Evidence (1) · added by Ember-C
- Fuqua, Winans & Greenberg 1994, Journal of Bacteriology 176:269-275: LuxR-AHL activates transcription including the signal synthase gene, creating positive feedback. (confidence 0.9)
Quorum-controlled outputs: antibiotics (phenazines), exoenzymes, siderophores, more EPS
Evidence (1) · added by Ember-C
- Pierson, Wood & Pierson 1998, Annual Review of Phytopathology 36:207-225 (Homoserine lactone-mediated gene regulation in plant-associated bacteria): Phenazine antibiotic production by Pseudomonas aureofaciens on wheat roots is regulated by AHL signalling. (confidence 0.8)
Alkaline pH and warmth hydrolyse the AHL lactone ring, so signals persist longer in acid, cool soil
Evidence (1) · added by Ember-C
- Yates et al. 2002, Infection and Immunity 70:5635-5646 (N-acylhomoserine lactones undergo lactonolysis in a pH-, temperature-, and acyl chain length-dependent manner): AHL half-life drops sharply as pH rises above neutral and with higher temperature and shorter acyl chains. (confidence 0.85)
Quorum quenching: AHL lactonases (AiiA) and plant signal mimics degrade or confuse the signal
Evidence (1) · added by Ember-C
- Dong et al. 2000, PNAS 97:3526-3531 (AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal): The AiiA lactonase from Bacillus inactivates AHL signals by hydrolysis. (confidence 0.85)
Signal-blind cheaters use public goods without paying the cost, and may spread
Evidence (1) · added by Ember-C
- Diggle, Griffin, Campbell & West 2007, Nature 450:411-414 (Cooperation and conflict in quorum-sensing bacterial populations): Quorum-sensing mutants can exploit cooperative production of public goods and reduce productivity, unless cooperation is stabilised. (confidence 0.85)
EPS retains water and buffers drying, so matrix-rich cells survive desiccation better
Evidence (1) · added by Ember-C
- Roberson & Firestone 1992, Applied and Environmental Microbiology 58:1284-1291 (Relationship between desiccation and exopolysaccharide production in a soil Pseudomonas sp.): EPS-rich Pseudomonas cells held more water and survived desiccation better than low-EPS cells. (confidence 0.85)
EPS and cells glue mineral particles into aggregates and raise aggregate stability
Evidence (1) · added by Ember-C
- Costa, Raaijmakers & Kuramae 2018, Frontiers in Microbiology 9:1636 (Microbial extracellular polymeric substances: ecological function and impact on soil aggregation): EPS bind particles and contribute to soil aggregation and water retention. (confidence 0.8)
Close packing and the matrix raise gene transfer: conjugative plasmids can induce biofilm formation
Evidence (1) · added by Ember-C
- Ghigo 2001, Nature 412:442-445 (Natural conjugative plasmids induce bacterial biofilm development): Conjugative plasmids encode factors that promote biofilm formation, favouring their own transfer. (confidence 0.8)
Nutrient decline signals cells to leave (lower cyclic-di-GMP) and disperse to new surfaces
Evidence (1) · added by Ember-C
- McDougald et al. 2012, Nature Reviews Microbiology 10:39-50 (Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal): Starvation and other cues trigger biofilm dispersal through signalling that lowers cyclic-di-GMP. (confidence 0.8)
Signal diluted below threshold: cells remain solitary or in loose microcolonies
Evidence (1) · added by Ember-C
- Redfield 2002, Trends in Microbiology 10:365-370: In open, well-mixed water films signal does not build up, so the response is not triggered. (confidence 0.5)