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Harvard UniversityFAS Center for Systems Biology
Competition and cooperationin
microbial spatial expansions
Melanie JI MüllerDavid R Nelson, Andrew W Murray
Range expansions• Range expansion = species conquer new territory• Species - expand from where they evolved - migrate in response to environmental change - invade when brought to new territory
Life on surfaces• Microbes grow in a variety of habitats
• Many are surfaces: - leaves, bark, fruits, rocks - animal epithelial surfaces - man-made surfaces
• Different species grow together, can compete, cooperate
Life on surfaces• What is the impact of spatial structure on
- growth patterns? - population dynamics? - species interactions? - evolution?
Grow microbes in the lab
well-mixed population structured population
• shaken liquid culture • colonies on agar surface
12mm2mm
Day 0 Day 6
1mm
1) Mix yellow and blue strains
2) Inoculate drop on agar surface
→ observe pattern3) Colony expands
• Range expansion assay:
Microbial range expansions
Hallatschek & Nelson, Theoret. Pop. Biol. 2008
• Human migration
Neutral range expansions• Yeast migration
1week
Ramachadran et al, PNAS 2005Distance [km] from Addis Ababa, Ethiopia
Outline
• Competition: Spatial growth with selection
• Cooperation: Spatial growth with cooperative interaction
• Basic effects of spatial growth: - spatial demixing - reduced genetic diversity
Spatial growth without and with selection• Yellow and blue with same growth rate
• Yellow grows faster than blue
curved sector boundary
bulge
Homeland yellow:blue 1:1 Homeland yellow:blue 1:500
Sector shape • Assume: - fixed for either blue or yellow - constant radial velocities v1, v2
→ Sector angle = logarithmic spiral
• Theory
2 2
2 1
( ) ( )dr rddrtv v
• Equate time increments:
relative fitness
Spatial versus well-mixed fitness
1.4
1.2
1.0
1.0 1.2 1.4
• Sectors spatial relative fitness = ratio of velocities
• Yeast not motile spatial = well-mixed fitness
fitness in well-mixed culture
fitne
ss o
n pl
ate
• Well-mixed culture relative fitness = ratio of growth rates
Outline
• Competition: Spatial growth with selection
• Cooperation: Spatial growth with cooperative interaction
• Basic effects of spatial growth
Mutualistic yeast• want: yeast cross-feeding
→ (almost) no growth
Leu–Trp+
Leu+Trp–
Mutualistic yeast• How to make yeast secrete an amino acid? → overproduction
chorismate
anthranilate
Trp2
tryptophan
other amino acids
• Tryptophan biosynthesis
…
…
Mutualistic yeast• How to make yeast secrete an amino acid? → overproduction using feedback resistance (FBR)
chorismate
anthranilate
• Tryptophan biosynthesis
…
Trp2FBR
TRYPTOPHAN
other amino acids
…
• Similar feedback-resistance for leucine biosynthesis
Mutualistic yeast• want: yeast cross-feeding
→ robust growth
Leu–TrpFBR
LeuFBRTrp–
Range expansion patterns
1mm
1mm
Mutualism
Range expansion patterns
→ inhibited demixing → spatial demixing1mm1mm
Mutualism No mutualism
Mutualists grow slower (50%)
Mutualist patch size
100μm
L
Spatial expansion demixed patches
Mutualist patch size
Leu diffuses into leu-consumer patch:
leucine diffusion
~ 700 μm
→ Length scale
leucine uptake by cells
100μm
L = 50μm
Spatial expansion demixed patches
Mutualist patch sizeDiffusion of patch boundaries due to cell division pushing
~ 1 μm
100μm
L = 50μm
cell size ~ 5μm → diffusion ~ 25μm2/generation
growth velocity ~ 20μm/generation
~ 50 μm
Patch size
Mutualist patch size
100μm
ξ║
L=ξ┴
growthdirection
Correlation lengths: - in expansion direction: ξ║ = 110 μm- perpendicular: ξ┴ = 52 μm
Theory
diffusion selection genetic drift
• time development with selection:
• What is the selection?
• f = fraction of blue cells x = coordinate along front
2
2
( , ) (1 )( ) (1 ) ( , )2
f x t f f fD s f f f x tt x N
2
2
( , ) ( ) (1 ) ( , )2
f x t f dV f f fD x tt x df N
Intuition: noisy diffusion in potential V(f)
Theory
diffusion selection genetic drift
• dynamics: f = fraction of blue cells, x = coordinate along front2
2
( , ) (1 )( ) (1 ) ( , )2
f x t f f fD s f f f x tt x N
2
2
( , ) ( ) (1 ) ( , )2
f x t f dV f f fD x tt x df N
Intuition: noisy diffusion in potential V(f)
stable fraction f*
• mutualism: growth depends on partner → frequency-dependent selection
f = fraction of blue cells0 1
V(f)
Lots of blue cellsyellow grows faster
Lots of yellow cells blue grows faster
Mutualists expand together
6 : 1 1 : 1 1 : 6Day 0
Day 7, mutualism
100 : 1 1 : 100
1mm
1mm
2mm
Day 7, no mutualism
Mutualists expand together
6 : 1 1 : 1 1 : 6Day 0
Day 7, no mutualism
Day 7, mutualism
100 : 1 1 : 100
1mm
1mm
2mm
…but so is their production/uptake!
Why preferred ratio ~ 1:1?Leu, trp very different…
To expand together – or not
Mutualism→ frequency-dependent selection→ mixing at fraction f*
Small front population size→ genetic drift (noise) → local fixation = demixing
no leu, trp lots of leu, trp
Probe antagonism: vary amino acid concentrations in medium
f = fraction of blue cells0 1
V(f)
f*
To expand together – or not
no leu, trp lots of leu, trp
vary amino acid concentrations
in medium
[leu]
[trp]
Leu+Trp-
Leu-Trp+
[leu]
[trp]
Leu+Trp-
Leu-Trp+
yellow dominates
blue dominates
demixed
mixed
[leu]
[trp]
Leu+Trp-
Leu-Trp+
[leu]
[trp]
Leu+Trp-
Leu-Trp+
mutualism strength
demixing strength ~1/Ne
[leu]
Leu+Trp-
Leu-Trp+Antagonism of mutualism and genetic drift• Phase transition from mixing to demixing (theoretical physics: directed percolation)
• Demixing although mixing would be beneficial
Theoretical phase diagram
Korolev & Nelson, PRL 2011
Benefit for blue
Ben
efit
for y
ello
w
blue wins
• demixing depends on - mutualism strength - symmetry
demix
Mutualism→ inhibited
demixing
yellowwins
• experiment: vary amino acid concentrations
[leu]
[trp]
Leu+Trp-
Leu-Trp+
mutations
Mutants in mutualistic colonies• Mutualistic colonies exhibit 0-5 mutation sectors Average: ca. 1 sector/colony Phenotypic mutation rate 10^-9 - 10^-6 /generation/cell)
• Compare: sector shape for pure selection
The most common mutant
Blue cells from sector+ yellow ancestor
Yellow cells from sector+ blue ancestor
Isolate singlecells
Compare: sector shape for pure selection
Mutants
• blue mutant & yellow ancestor• blue & yellow ancestors
- faster, thin-striped growth with ancestral yellow partner- better at sucking up leucine
up
Dlk c
Characteristic length scale
• Yellow cells behave like ancestor• Blue cells have heritable phenotype:
Conclusions
• Spatial growth with selection: - relative fitness ↔ sector shape - can be used to measure fitness
• Spatial growth with mutualistic interaction: - inhibited spatial demixing - spatial expansion impedes mutualism - mutations change pattern
• Basic effects of spatial growth: - spatial demixing
THEORYDavid Nelson
Oskar HallatschekKirill Korolev
EXPERIMENTAndrew Murray
Beverly NeugeborenDavid van Dyken
Thank you!…for your attention
References•Genetic drift opposes mutualism during spatial population expansion MJI Müller, BI Neugeboren, DR Nelson, AW Murray Proceedings of the National Academy of Sciences 111 (3), 1037-1042, 2014
•Spatial population expansion promotes the evolution of cooperation in an experimental Prisoner’s Dilemma JD Van Dyken, MJI Müller, KML Mack, MM Desai Current Biology 23 (10), 919-923, 2013
•Selective sweeps in growing microbial colonies KS Korolev, MJI Müller, N Karahan, AW Murray, O Hallatschek, ... Physical Biology 9 (2), 026008, 2012
Thank you!…for your attention