swarming motility

Deep research

Generated by just research-trait; source: research/traits/morphology/swarming_motility-deep-research-falcon.md

# Swarming Motility: Curation-Focused Research Report for TraitMech Causal Graph

## 1. Trait Scope Summary

**Swarming motility** (traitmech:000062) is a flagella-dependent, multicellular surface motility in which bacteria move rapidly and coordinately across semi-solid surfaces. It is distinguished from other surface motility modes (twitching, sliding, gliding) by its absolute requirement for functional flagella, its collective/multicellular nature, and its typical association with hyperflagellation and secretion of wetting surfactants (partridge2013swarmingflexibleroaming pages 1-2, partridge2022surveyingaswarm pages 5-7). Swarming occurs on semi-solid agar (typically 0.5–1.5% w/v) and requires sufficient surface hydration for flagella-driven propulsion (partridge2013swarmingflexibleroaming pages 2-4, partridge2022surveyingaswarm pages 3-5).

**Boundary cases and distinctions:**
- **Swimming** is individual, liquid-phase flagellar motility; swarming is collective and surface-associated (partridge2022surveyingaswarm pages 5-7).
- **Sliding** is passive, flagella-independent surface spreading driven by colony growth pressure and surfactant secretion (partridge2013swarmingflexibleroaming pages 5-6).
- **Twitching** is type IV pilus–dependent and does not require flagella.
- Species vary in swarming strategy: "robust swarmers" (e.g., *Proteus mirabilis*) display dramatic cell elongation and hyperflagellation on hard agar (≥1.5%), while "temperate swarmers" (e.g., *E. coli*, *Salmonella*) require softer agar (0.5–0.8%) and depend more on surfactant secretion (partridge2013swarmingflexibleroaming pages 4-5, partridge2013swarmingflexibleroaming pages 4-4).

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## 2. Candidate Causal Graph Nodes

The following table groups all proposed nodes by type, with suggested ontology CURIEs and taxon scope.

| Node Label | Node Type | Suggested CURIE | Taxon Scope | Notes |
|---|---|---|---|---|
| FlhDC (FlhD4C2 master regulator complex) | gene/protein complex | label-only candidate | Proteus mirabilis; Enterobacterales; broad Gram-negative flagellar regulon | Class I/master regulator of flagellar gene hierarchy; central to swarmer differentiation and swarming-associated flagellar expression (yang2024unveilingthehidden pages 6-7, lee2015lossofflil pages 1-2) |
| FliA (sigma-28, σ28) | sigma factor protein | GO:0001130 | Broad bacteria; documented in Proteus mirabilis | Flagellar sigma factor activated downstream of FlhDC; drives class III flagellar/chemotaxis genes (yang2024unveilingthehidden pages 6-7, lee2015lossofflil pages 1-2) |
| FlgM | anti-sigma factor protein | label-only candidate | Broad bacteria | Anti-σ28 factor in class II regulon; included in canonical flagellar hierarchy linked to swarming competence (yang2024unveilingthehidden pages 6-7) |
| FliL | motor accessory protein | label-only candidate | Broad bacteria; especially Proteus mirabilis, Pseudomonas aeruginosa | Supports high-torque motor function and surface sensing; implicated in swarming and mechanosensory signaling (lee2015lossofflil pages 12-13, wu2024torquespeedrelationshipof pages 13-15) |
| FliC | flagellin | GO:0009288 | Broad bacteria | Major filament subunit; flagellar output required for swarming; loss perturbs surface sensing programs in P. aeruginosa (kuchma2025geneticanalysisof pages 1-2) |
| MotAB | stator complex | label-only candidate | Broad bacteria; especially Pseudomonas aeruginosa | Proton-driven stator; favors low-load swimming and can repress swarming in P. aeruginosa relative to MotCD (anda2024howp.aeruginosa pages 2-4, anda2024howp.aeruginosa pages 8-10, anda2024howp.aeruginosa pages 1-2) |
| MotCD | stator complex | label-only candidate | Pseudomonas aeruginosa and related dual-stator bacteria | High-load stator critical for swarming on surfaces; deletion abolishes swarming in P. aeruginosa (anda2024howp.aeruginosa pages 2-4, wu2024torquespeedrelationshipof pages 13-15, anda2024howp.aeruginosa pages 1-2) |
| FliG | rotor switch protein | label-only candidate | Broad bacteria; documented in Pseudomonas aeruginosa | Rotor/switch component transmitting stator torque; implicated in flagellar-mediated surface sensing circuitry (kuchma2025geneticanalysisof pages 1-2) |
| RhlA | enzyme | label-only candidate | Pseudomonas aeruginosa | Required for HAA production; key swarming-linked surfactant biosynthesis determinant (deziel2003rhlaisrequired pages 1-2, deziel2003rhlaisrequired pages 8-9) |
| RhlB | rhamnosyltransferase 1 | label-only candidate | Pseudomonas aeruginosa | Catalyzes mono-rhamnolipid synthesis with RhlA-derived substrates; part of rhlAB operon (kohler2000swarmingofpseudomonas pages 3-6, deziel2003rhlaisrequired pages 8-9) |
| RhlC | rhamnosyltransferase 2 | label-only candidate | Pseudomonas aeruginosa | Converts mono-rhamnolipids to dirhamnolipids; quorum-sensing-regulated surfactant pathway member (daniels2004quorumsensingand pages 8-11, deziel2003rhlaisrequired pages 8-9) |
| RhlI | autoinducer synthase | label-only candidate | Pseudomonas aeruginosa | Synthesizes C4-HSL; activates rhl quorum-sensing branch controlling swarming surfactants (daniels2004quorumsensingand pages 8-11, daniels2004quorumsensingand pages 11-12) |
| RhlR | transcriptional regulator | label-only candidate | Pseudomonas aeruginosa | C4-HSL-responsive QS activator controlling rhlAB/rhlC and swarming outputs (daniels2004quorumsensingand pages 8-11, daniels2004quorumsensingand pages 11-12) |
| LasI | autoinducer synthase | label-only candidate | Pseudomonas aeruginosa | Synthesizes 3-oxo-C12-HSL; upstream QS layer influencing swarming via rhl pathway (kohler2000swarmingofpseudomonas pages 3-6, kohler2000swarmingofpseudomonas pages 6-6) |
| LasR | transcriptional regulator | label-only candidate | Pseudomonas aeruginosa | QS activator in las system; las mutants show reduced/delayed swarming (kohler2000swarmingofpseudomonas pages 3-6, daniels2004quorumsensingand pages 8-11, kohler2000swarmingofpseudomonas pages 6-6) |
| SwrA | regulatory protein | label-only candidate | Bacillus subtilis | Swarming activator that cooperates with DegU~P to activate fla/che transcription (mordini2013theroleof pages 5-7, mordini2013theroleof pages 1-2) |
| DegU | response regulator | label-only candidate | Bacillus subtilis | Phosphorylated DegU acts as dual regulator; with SwrA it promotes motility regulon expression (mordini2013theroleof pages 5-7, mordini2013theroleof pages 2-3, mordini2013theroleof pages 9-10) |
| DegS | sensor histidine kinase | label-only candidate | Bacillus subtilis | Phosphorylates DegU, enabling SwrA-DegU~P control of fla/che and swarming (mordini2013theroleof pages 2-3, mordini2013theroleof pages 3-5) |
| DgcO | diguanylate cyclase | label-only candidate | Escherichia coli | Major DGC promoting swarming via colanic acid production; defines c-di-GMP threshold for swarming (hwang2025cdigmpisrequired pages 8-11, hwang2025cdigmpisrequired pages 2-5, hwang2025cdigmpisrequired pages 11-14) |
| DgcM | diguanylate cyclase | label-only candidate | Escherichia coli | Secondary DGC contributing to swarming-associated c-di-GMP signaling (hwang2025cdigmpisrequired pages 8-11, hwang2025cdigmpisrequired pages 11-14) |
| YcgR | c-di-GMP effector / flagellar brake | label-only candidate | Escherichia coli; Salmonella enterica | c-di-GMP receptor that slows/brakes flagellar motor and opposes motility at elevated c-di-GMP (partridge2013swarmingflexibleroaming pages 6-7, liu2022theeffectof pages 1-2) |
| YhjH (PdeH) | phosphodiesterase | label-only candidate | Escherichia coli; Salmonella enterica | Lowers c-di-GMP to preserve flagellar motility/swarming competence (partridge2013swarmingflexibleroaming pages 6-7) |
| SrfA operon (surfactin synthetase) | operon / NRPS system | label-only candidate | Bacillus subtilis | Biosynthetic locus for surfactin, a canonical swarming wetting agent in B. subtilis (partridge2022surveyingaswarm pages 5-7, mordini2013theroleof pages 1-2) |
| WcaJ | glycosyltransferase | label-only candidate | Escherichia coli | Initiates colanic acid biosynthesis; required for CA-dependent swarming in E. coli (hwang2025cdigmpisrequired pages 5-8, hwang2025cdigmpisrequired pages 11-14) |
| c-di-GMP (cyclic di-GMP) | chemical / second messenger | CHEBI:17950 | Broad bacteria | Central signaling molecule balancing swarming versus sessility; low/intermediate levels can support swarming, high levels inhibit motility and favor biofilm (partridge2013swarmingflexibleroaming pages 7-8, hwang2025cdigmpisrequired pages 1-2, liu2022theeffectof pages 1-2) |
| Surfactin | lipopeptide biosurfactant | CHEBI:29375 | Bacillus subtilis | Wetting agent essential or strongly supportive for B. subtilis swarming on standard media (daniels2004quorumsensingand pages 6-7, partridge2022surveyingaswarm pages 5-7) |
| Rhamnolipids | glycolipid biosurfactant | CHEBI:63748 | Pseudomonas aeruginosa | Canonical swarming surfactants; pathway and abundance modulate swarm expansion/patterning (kohler2000swarmingofpseudomonas pages 3-6, caiazza2005rhamnolipidsmodulateswarming pages 5-6) |
| HAAs (3-(3-hydroxyalkanoyloxy)alkanoic acids) | surfactant precursor metabolites | label-only candidate | Pseudomonas aeruginosa | RhlA-derived precursors that can themselves serve as minimal surfactants for swarming (caiazza2005rhamnolipidsmodulateswarming pages 5-6, deziel2003rhlaisrequired pages 1-2) |
| C4-HSL (N-butyryl-L-homoserine lactone) | quorum-sensing autoinducer | CHEBI:78425 | Pseudomonas aeruginosa | Autoinducer produced by RhlI; activates RhlR-dependent surfactant/swarming program (daniels2004quorumsensingand pages 8-11, kohler2000swarmingofpseudomonas pages 6-6) |
| 3-oxo-C12-HSL | quorum-sensing autoinducer | CHEBI:65033 | Pseudomonas aeruginosa | LasI/LasR signal upstream of rhl QS network affecting swarming (kohler2000swarmingofpseudomonas pages 3-6, kohler2000swarmingofpseudomonas pages 6-6) |
| Colanic acid | exopolysaccharide / surfactant | label-only candidate | Escherichia coli | Acts as surfactant and wetting agent enabling E. coli swarming under specific c-di-GMP conditions (hwang2025cdigmpisrequired pages 1-2, hwang2025cdigmpisrequired pages 5-8, hwang2025cdigmpisrequired pages 11-14) |
| PQS (Pseudomonas quinolone signal) | quorum-sensing signal molecule | CHEBI:134179 | Pseudomonas aeruginosa | Links las and rhl systems and can influence swarming-associated regulatory flow (daniels2004quorumsensingand pages 11-12) |
| Serrawettin | biosurfactant | label-only candidate | Serratia marcescens | Serratia wetting agent; useful comparative swarming surfactant node (partridge2022surveyingaswarm pages 5-7) |
| Swarming motility | biological process / trait | GO:0000331 | Broad bacteria | Target trait: flagella-dependent, multicellular surface translocation on semi-solid surfaces (partridge2013swarmingflexibleroaming pages 5-6, partridge2022surveyingaswarm pages 5-7) |
| Hyperflagellation | biological process | label-only candidate | Broad bacteria | Increased flagellar number is a common swarmer-cell adaptation in multiple taxa (partridge2013swarmingflexibleroaming pages 5-6, partridge2022surveyingaswarm pages 5-7) |
| Cell elongation (swarmer differentiation) | biological process | GO:0032989 | Especially Proteus mirabilis; also other robust swarmers | Surface-associated differentiation into elongated swarm cells (daniels2004quorumsensingand pages 6-7, lee2015lossofflil pages 1-2) |
| Surface sensing / mechanosensing | biological process | GO:0009593 | Broad bacteria | Flagellar load/surface contact sensing triggers swarming or biofilm-related responses (kuchma2025geneticanalysisof pages 1-2, lee2015lossofflil pages 12-13) |
| Quorum sensing | biological process | GO:0009372 | Broad bacteria | Cell-density signaling controlling surfactant and other swarm-related outputs (daniels2004quorumsensingand pages 6-7, daniels2004quorumsensingand pages 8-11) |
| Surfactant secretion | biological process | label-only candidate | Broad bacteria | Release of wetting agents such as rhamnolipids/surfactin/serrawettin to reduce surface tension (partridge2022surveyingaswarm pages 5-7, deziel2003rhlaisrequired pages 1-2) |
| Flagellar rotation / motor function | biological process | GO:0001539 | Broad bacteria | Torque generation and switching required for propulsion and surface adaptation (kuchma2025geneticanalysisof pages 1-2, lee2015lossofflil pages 12-13) |

Showing the first 60 of 280 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.