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Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Bacteria and archaea / Actinomycetes: Streptomyces hyphal life cycle, extracellular enzymes and antibiotics

Actinomycetes: Streptomyces hyphal life cycle, extracellular enzymes and antibiotics

The filamentous Gram-positive actinomycetes (mostly Streptomyces) that grow as branching mycelium in soil, degrade chitin and cellulose, make antibiotics and geosmin, and survive drought as spores. It also covers nitrogen-fixing Frankia in actinorhizal nodules.

Boundary: where this process starts

Starts with: Dormant spore germinates in a wet, nutrient-rich pulse and sends out a germ tube

Boundary: where it ends

Ends after: Death and lysis of colonies return amino sugars and cell wall carbon to the soil organic pool; Aerial hyphae produce spore chains; geosmin released attracts springtails that eat and disperse spores

PARTICIPANTSRESOURCESStreptomycesActinobacteriaFrankiaCompetingbacteriaStreptomycessporesOtherparticipantsCarbonWaterNitrogenAntibioticsChitinImpact +3 of 5. Click for details and evidence.moisture pulseImpact 02 of 5. Click for details and evidence.dry spellImpact 02 of 5. Click for details and evidence.genetic repertoireImpact +4 of 5. Click for details and evidence.hypha growsImpact -3 of 5. Click for details and evidence.growth consumes resourcesImpact +3 of 5. Click for details and evidence.45% ↻ balances · moderate · 0.4 still enoughImpact +4 of 5. Click for details and evidence.55% depleted and competitiveImpact +3 of 5. Click for details and evidence.clusters availableImpact +4 of 5. Click for details and evidence.antibiotic releaseImpact -3 of 5. Click for details and evidence.selection for resistanceImpact +2 of 5. Click for details and evidence.↻ reinforces · weak · 0.2 arms race raises pImpact +2 of 5. Click for details and evidence.↻ reinforces · weak · 0.2 competitors cleareImpact +3 of 5. Click for details and evidence.sporulationImpact +2 of 5. Click for details and evidence.spore survivalImpact +2 of 5. Click for details and evidence.colony lysisImpact 01 of 5. Click for details and evidence.symbiotic relativeImpact +2 of 5. Click for details and evidence.nodule turnoverImpact +2 of 5. Click for details and evidence.carbon and N recycledImpact +3 of 5. Click for details and evidence.spores dispersedDormant spore germinates in a wet, nutrient-rich pulse and sends out a germ tube: uses CarbonDormant spore germinates in a wet, nutrient-rich pulse and sends out a germ tube: uses WaterVegetative mycelium grows by tip extension and branching, penetrating particles and secreting hydrolases (chitinase, cellulase, xylanase): uses CarbonVegetative mycelium grows by tip extension and branching, penetrating particles and secreting hydrolases (chitinase, cellulase, xylanase): uses ChitinResource depletion sensed: substrate mycelium partly lyses and the colony switches to aerial hyphae: uses CarbonResource depletion sensed: substrate mycelium partly lyses and the colony switches to aerial hyphae: uses NitrogenSecondary metabolism switches on: antibiotics, siderophores and geosmin made as growth slows: uses CarbonA single genome carries about 20-30 biosynthetic gene clusters (S. coelicolor: 8.67 Mb, 7,825 genes, over 20 clusters): uses CarbonAntibiotics suppress competing bacteria and fungi and at low dose act as signals that alter neighbour gene expression: uses CarbonAntibiotics suppress competing bacteria and fungi and at low dose act as signals that alter neighbour gene expression: uses AntibioticsNeighbours evolve resistance, so antibiotic production and resistance co-escalate: uses AntibioticsGram-positive thick walls and spores allow activity at low water potential, so actinobacteria are enriched in drying soil: uses WaterAerial hyphae produce spore chains; geosmin released attracts springtails that eat and disperse spores: uses WaterDeath and lysis of colonies return amino sugars and cell wall carbon to the soil organic pool: makes CarbonmakesDeath and lysis of colonies return amino sugars and cell wall carbon to the soil organic pool: makes Nitrogenmakesfuels germ tube growthCarbon: fuels germ tube growthtriggers sporegerminationWater: triggers spore germinationacquired through hyphalpenetrationCarbon: acquired through hyphal penetrationdegraded by secretedchitinaseChitin: degraded by secreted chitinasedepletion triggersaerial switchCarbon: depletion triggers aerial switchlysed to releasenutrientsNitrogen: lysed to release nutrientsdiverted to secondarymetabolismCarbon: diverted to secondary metabolismchannelled tobiosynthetic clustersCarbon: channelled to biosynthetic clusterssupports antibioticsynthesisCarbon: supports antibiotic synthesissuppress competingmicrobesAntibiotics: suppress competing microbesco-escalate withresistanceAntibiotics: co-escalate with resistancetolerated at lowpotentialWater: tolerated at low potentialaids spore dispersalWater: aids spore dispersalreturned to soil organicpoolCarbon: returned to soil organic poolreleased from deadcoloniesNitrogen: released from dead coloniesStart: Streptomycesspore meets moistureand nutrientsSTARTStart: Streptomyces spore meets moisture and nutrientsEnd: Spores dispersed,nutrients and secondarymetabolites releasedENDEnd: Spores dispersed, nutrients and secondary metabolites releasedDormant sporegerminates in a wet,nutrient-rich pulse a…📄1Dormant spore germinates in a wet, nutrient-rich pulse and sends out a germ tubeVegetative myceliumgrows by tip extensionand branchin…📄1Vegetative mycelium grows by tip extension and branching, penetrating particles and secreting hydrolases (chitinase, cellulase, xylanase)Resource depletionsensed: substratemycelium partly lys…📄1Resource depletion sensed: substrate mycelium partly lyses and the colony switches to aerial hyphaeSecondary metabolismswitches on:antibiotic…📄1Secondary metabolism switches on: antibiotics, siderophores and geosmin made as growth slowsA single genome carriesabout 20-30biosynthetic ge…📄1A single genome carries about 20-30 biosynthetic gene clusters (S. coelicolor: 8.67 Mb, 7,825 genes, over 20 clusters)Antibiotics suppresscompeting bacteria andfungi and at low do…📄1Antibiotics suppress competing bacteria and fungi and at low dose act as signals that alter neighbour gene expressionNeighbours evolveresistance, soantibiotic producti…👍1📄1Neighbours evolve resistance, so antibiotic production and resistance co-escalateGram-positive thickwalls and spores allowactivity at low wat…📄1Gram-positive thick walls and spores allow activity at low water potential, so actinobacteria are enriched in drying soilAerial hyphae producespore chains; geosminreleased attrac…📄1 ↗1Aerial hyphae produce spore chains; geosmin released attracts springtails that eat and disperse sporesFrankia fixes N2 inactinorhizal nodules(alder, Casuarina…👍2📄1Frankia fixes N2 in actinorhizal nodules (alder, Casuarina), using vesicles with a hopanoid lipid envelope as oxygen barrierDeath and lysis ofcolonies return aminosugars and cell wa…📄1Death and lysis of colonies return amino sugars and cell wall carbon to the soil organic pool
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)
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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.

Dormant spore germinates in a wet, nutrient-rich pulse and sends out a germ tube
Streptomyces sporesWaterCarbon
Evidence (1) · added by Ember-C
  • Flardh & Buttner 2009, Nature Reviews Microbiology 7:36-49: Spores germinate and grow out as hyphae when water and nutrients are available. (confidence 0.85)
Vegetative mycelium grows by tip extension and branching, penetrating particles and secreting hydrolases (chitinase, cellulase, xylanase)
StreptomycesExtracellular enzymesChitinCelluloseCarbon
Evidence (1) · added by Ember-C
  • Chater et al. 2010, FEMS Microbiology Reviews 34:171-198 (The complex extracellular biology of Streptomyces): Streptomyces secretes a large set of hydrolytic enzymes, with up to about 800 predicted secreted proteins in S. coelicolor. (confidence 0.75)
⑂ Resource depletion sensed: substrate mycelium partly lyses and the colony switches to aerial hyphae
StreptomycesSoil solutionCarbonNitrogen
Evidence (1) · added by Ember-C
  • Chater 2006, Philosophical Transactions of the Royal Society B 361:761-768 (Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics): Programmed cell death of the vegetative mycelium releases nutrients that fuel aerial hyphae and sporulation. Shares are an estimate for a typical soil microsite and are not measured. (confidence 0.45)
Secondary metabolism switches on: antibiotics, siderophores and geosmin made as growth slows
StreptomycesCarbonIron
Evidence (1) · added by Ember-C
  • van der Meij et al. 2017, FEMS Microbiology Reviews 41:392-416 (Chemical ecology of antibiotic production by actinomycetes): Antibiotic production is tied to nutrient limitation, competition cues and development. (confidence 0.8)
A single genome carries about 20-30 biosynthetic gene clusters (S. coelicolor: 8.67 Mb, 7,825 genes, over 20 clusters)
Streptomyces coelicolorCarbon
Evidence (1) · added by Ember-C
  • Bentley et al. 2002, Nature 417:141-147 (Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)): 8.67 Mb linear chromosome with 7,825 predicted genes and at least 20 clusters for secondary metabolites. (confidence 0.9)
Antibiotics suppress competing bacteria and fungi and at low dose act as signals that alter neighbour gene expression
StreptomycesCompeting bacteriaSoil fungiCarbonAntibiotics
Evidence (1) · added by Ember-C
  • Raaijmakers & Mazzola 2012, Annual Review of Phytopathology 50:403-424 (Diversity and natural functions of antibiotics produced by beneficial and pathogenic soil bacteria): Soil antibiotics inhibit competitors and, at sub-inhibitory levels, regulate community members. (confidence 0.8)
Neighbours evolve resistance, so antibiotic production and resistance co-escalate
Competing bacteriaStreptomycesAntibiotics
Evidence (1) · added by Ember-C
  • D'Costa et al. 2006, Science 311:374-377 (Sampling the antibiotic resistome): Soil Streptomyces isolates from a collection were multidrug resistant, with resistance to many antibiotics of both natural and synthetic origin. (confidence 0.85)
Gram-positive thick walls and spores allow activity at low water potential, so actinobacteria are enriched in drying soil
ActinobacteriaSoil waterWater
Evidence (1) · added by Ember-C
  • Naylor & Coleman-Derr 2018, Frontiers in Microbiology 9:2223 (Drought stress and root-associated bacterial communities): Actinobacteria (monoderm) are consistently enriched in the roots and soils of drought-stressed plants. (confidence 0.8)
Aerial hyphae produce spore chains; geosmin released attracts springtails that eat and disperse spores
StreptomycesSpringtailsGeosminWater
Evidence (1) · added by Ember-C
  • Becher et al. 2020, Nature Microbiology 5:821-829 (Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal): Geosmin acts as an olfactory cue for Folsomia candida, and springtails carry viable spores in guts and on cuticles. (confidence 0.8)
Frankia fixes N2 in actinorhizal nodules (alder, Casuarina), using vesicles with a hopanoid lipid envelope as oxygen barrier
FrankiaAlderCasuarinaDinitrogenAmmoniumOxygen
Evidence (1) · added by Ember-C
  • Berry et al. 1993, PNAS 90:6091-6094 (Hopanoid lipids compose the Frankia vesicle envelope, presumptive barrier of oxygen diffusion to nitrogenase): Frankia vesicle envelopes are made of hopanoid lipids that restrict O2 diffusion to nitrogenase. (confidence 0.85)
Death and lysis of colonies return amino sugars and cell wall carbon to the soil organic pool
StreptomycesSoil microbesCarbonNitrogen
Evidence (1) · added by Ember-C
  • Chater et al. 2010, FEMS Microbiology Reviews 34:171-198: Programmed lysis recycles colony material, and hyphal necromass is rich in peptidoglycan amino sugars. (confidence 0.6)