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Slide of the Seminar
The importance of fluid mechanics in the microbial world: From the transport of bacteria to the formation
of biofilms
Prof. Roberto Rusconi
ERC Advanced Grant (N. 339032) “NewTURB” (P.I. Prof. Luca Biferale)
Università degli Studi di Roma Tor Vergata C.F. n. 80213750583 – Partita IVA n. 02133971008 - Via della Ricerca Scientifica, 1 – 00133 ROMA
The importance of fluid mechanics in the microbial world:
From the transport of bacteria to the formation of biofilms
Roberto Rusconi
Bacteria within biofilms are up to 1000 times more resistant to antibiotics
Hall-Stoodley et al. Nat. Rev. Microbiol. 2004
Catheters
Implants
Gums
Endocarditis
Lung infections
Urinary infections
The “biofilm” threat
University of Rome Tor Vergata - 29th November 2018
Monds & O’Toole. Trends Microbiol. 2009
Industrial applications
Medical devices
Environment
Biofilms form everywhere and often in the presence of flow
University of Rome Tor Vergata - 29th November 2018
Rusconi & Stocker. Curr. Op. Microbiol. 2015
Guasto, Rusconi & Stocker. Annu. Rev. Fluid Mech. 2012
How does fluid flow affect bacterial swimming dynamics?
Relative flow speed (mm/s)
Shear (s-1)0-10 10
0 0.5-0.5
Bacillus subtilis
1 cm
x
y
H=
750
µm
x
y
z
University of Rome Tor Vergata - 29th November 2018
Flow, t = 15 sFlow, t = 5 s Flow, t = 30 s
Bacterial concentration0.5 1 1.50
No flow
0
-0.3
0.3
y/W
How does fluid flow affect bacterial swimming dynamics?
Dead cells
Flow, t = 30 s
0.5 1 1.50
1 cm
x
y
H=
750
µm
x
y
z
University of Rome Tor Vergata - 29th November 2018
Mean shear S = 1.25 s-1 S = 2.5 s-1 S = 5 s-1 S = 10 s-1 S = 25 s-1 S = 50 s-1
Bac
teria
l con
cent
ratio
n
0.5
1.5
Maximal depletion occurs at intermediate shear
100
B. subtilis – wild typeB. subtilis – smooth swimmerP. aeruginosa
0
0.2
0.4
1 10D
eple
tion
inde
xMean shear rate, S (s-1)
• Rod shape (1µm x 3µm)
• Multiple flagella
• Rod shape (0.5µm x 1.5µm)
• Single flagellum
Bacillus subtilis
Pseudomonas aeruginosa
1
University of Rome Tor Vergata - 29th November 2018
Mean shear S = 1.25 s-1 S = 2.5 s-1 S = 5 s-1 S = 10 s-1 S = 25 s-1 S = 50 s-1
Bac
teria
l con
cent
ratio
n
0.5
1.5
Maximal depletion occurs at intermediate shear
1
University of Rome Tor Vergata - 29th November 2018
x
y
ϕ
V
q Swimming speed, V = 50 µm/s
Rotational diffusion, DR = 1 rad2/s
Aspect ratio, q = 10
Mean shear S = 1.25 s-1 S = 2.5 s-1 S = 5 s-1 S = 10 s-1 S = 25 s-1 S = 50 s-1
Bac
teria
l con
cent
ratio
n
0.5
1.5
Maximal depletion occurs at intermediate shear
1
University of Rome Tor Vergata - 29th November 2018
x
y
ϕ
V
q Swimming speed, V = 50 µm/s
Rotational diffusion, DR = 1 rad2/s
Aspect ratio, q = 10
Experiments Simulations
Mean shear S = 1.25 s-1 S = 2.5 s-1 S = 5 s-1 S = 10 s-1 S = 25 s-1 S = 50 s-1
Bac
teria
l con
cent
ratio
n
0.5
1.5
Maximal depletion occurs at intermediate shear
1
University of Rome Tor Vergata - 29th November 2018
x
y
ϕ
V
q Swimming speed, V = 50 µm/s
Rotational diffusion, DR = 1 rad2/s
Aspect ratio, q = 10
Experiments Simulations Simulations, spheres (q = 1)
Mean shear S = 1.25 s-1 S = 2.5 s-1 S = 5 s-1 S = 10 s-1 S = 25 s-1 S = 50 s-1
Bac
teria
l con
cent
ratio
n
0.5
1.5
Maximal depletion occurs at intermediate shear
1
University of Rome Tor Vergata - 29th November 2018
Swimming speed, V = 50 µm/s
Rotational diffusion, DR = 1 rad2/s
Aspect ratio, q = 10
Experiments
Elongated particle in shear flow
Simulations Simulations, spheres (q = 1)
Elongation and rotational diffusion control bacterial depletion in flow
University of Rome Tor Vergata - 29th November 2018
Rusconi et al. Nat. Phys. 2014
B. subtilis – smooth swimmer
DR = 0
0
-0.3
0.3
y/W
ϕ
0 π/2 π-π/2-π
Zöttl & Stark. EPJE 2013
Tumbling
Swinging
Separatrix
Elongation and rotational diffusion control bacterial depletion in flow
University of Rome Tor Vergata - 29th November 2018
DR = 1 rad2/s
ϕ
0 π/2 π-π/2-π
DR = 1 rad2/s, Experiments
ϕ
0 π/2 π-π/2-π
DR = 0
0
-0.3
0.3
y/W
ϕ
0 π/2 π-π/2-π
WS ~ S-0.5
Rusconi et al. Nat. Phys. 2014
Elongation and rotational diffusion control bacterial depletion in flow
University of Rome Tor Vergata - 29th November 2018
DR = 1 rad2/s, Experiments
ϕ
0 π/2 π-π/2-π
Rusconi et al. Nat. Phys. 2014
Experiments, no flow
Experiments
Fokker-Planck
Elongation and rotational diffusion control bacterial depletion in flow
University of Rome Tor Vergata - 29th November 2018
Dep
letio
n In
dex
Rotational Péclet number, Pe = S/DR
10-3
10-2
10-1
100
10-2 10-1 100 101 102 103
Pe2 S-0.5
Pe<<1Competition between shear-induced alignment and rotational diffusion
Pe>>1Depletion effect is limited by the distance between the separatrices
Rusconi et al. Nat. Phys. 2014
Ezhilan & Saintillan. J. Fluid Mech. 2015
Spatial heterogeneity in suspensions of phytoplankton cells
University of Rome Tor Vergata - 29th November 2018
Spatial heterogeneity in suspensions of phytoplankton cells
University of Rome Tor Vergata - 29th November 2018
10 µm
Spatial heterogeneity in suspensions of phytoplankton cells
University of Rome Tor Vergata - 29th November 2018
10 µm
Spatial heterogeneity in suspensions of phytoplankton cells
University of Rome Tor Vergata - 29th November 2018
10 µm
Barry, Rusconi et al. J. Roc. Soc. Interface 2015
Spatial heterogeneity in suspensions of phytoplankton cells
University of Rome Tor Vergata - 29th November 2018
10 µm
Barry, Rusconi et al. J. Roc. Soc. Interface 2015
Shear suppresses bacterial chemotaxis
1 cm
400 µm
N2 O2 (mM)
Glass
PDMS
1.2
0.1
Mean shear rate, S (s-1)
Che
mot
actic
inde
x
0
1
1 10 100Bac
teria
l con
cent
ratio
n
y/W
0
1
2
0-0.3 0.3
S = 2.5 s-1
S = 10 s-1
S = 25 s-1
S = 50 s-1
No flow
O2
University of Rome Tor Vergata - 29th November 2018
Shear promotes surface attachment
1 cmB
acte
rial s
urfa
ce c
over
age
(%)
Time (s)0 1000 2000 3000
0
0.5
1
1.5
2S = 5 s-1
S = 10 s-1
S = 25 s-1
S = 50 s-1
No flow
S = 100 s-1
P. aeruginosa
Mean shear rate, S (s-1)10010
Sur
face
cov
erag
e ra
tio
1
2
P. aeruginosa
University of Rome Tor Vergata - 29th November 2018
H. Auradou et al., in preparation
Wall shear rate (s-1)
E. coli
Nor
mal
ized
den
sity
Flow velocity Shear rate
Shear induces preferential attachment to corrugated surfaces
University of Rome Tor Vergata - 29th November 2018
Shear induces preferential attachment to corrugated surfaces
ExperimentsE. coli
University of Rome Tor Vergata - 29th November 2018
Shear induces preferential attachment to corrugated surfaces
Experiments
Simulations
E. coli
University of Rome Tor Vergata - 29th November 2018
Shear induces preferential attachment to corrugated surfaces
University of Rome Tor Vergata - 29th November 2018
h= 100 µm
y x
z
Experiments Simulations
Intensity distribution0.51 0
Escherichia coli GFP
q = 8, V = 22 µm/s, DR = 0.5 rad2/s
Shear induces preferential attachment to corrugated surfaces
University of Rome Tor Vergata - 29th November 2018
h= 100 µm
y x
z
Escherichia coli GFP
q = 8, V = 22 µm/s, DR = 0.5 rad2/s
Experiments Simulations
Intensity distribution0.51 0
Shear induces preferential attachment to corrugated surfaces
University of Rome Tor Vergata - 29th November 2018
h= 100 µm
y x
zy(
µm)
15
0
0x (µm)
-15
20 40 60 80 100
V= 22 µm/s
V= 0 µm/s
Simulations
FlowFlow
Radial shear rate, S
r(1/s)
15
30
0
x (µm)0 25 50
FlowFlow
Shear induces preferential attachment to corrugated surfaces
University of Rome Tor Vergata - 29th November 2018
Experiments
Simulations
Motility and flow control bacterial transport and attachment around pillars
University of Rome Tor Vergata - 29th November 2018
50 µm
U (m
m/s)
Sr (1/s)
0.5
1
0
20
40
0
FlowFlow velocity, U
Radial shear rate, Sr
200 µm
100 µm
50 µm
100 µmx
y
z
Motility and flow control bacterial transport and attachment around pillars
University of Rome Tor Vergata - 29th November 2018
50 µmFlow
Flow
Pseudomonas aeruginosa PA14
50µmU=150 µm/s
Motility and flow control bacterial transport and attachment around pillars
University of Rome Tor Vergata - 29th November 2018
y (µ
m)
P. aeruginosa PA14 GFP
45
0
0
-45
45-45x (µm)
Flow 25 µm
Intensity, I (a.u.)25 500
Fluorescent image of cells attached after 6 h of
continuous flow
PA14 wt GFPIntensity,I (a.u.)
5
10
0
PA14 ΔflgE GFP PA14 ΔmotB GFP
Motility and flow control bacterial transport and attachment around pillars
University of Rome Tor Vergata - 29th November 2018
Id0.5
1
0
U= 150 µm/s U= 300 µm/s U= 600 µm/s U= 1000 µm/s
Normalized intensity distribution
Polar distribution
Simulations, ExperimentsFlow
Motility and flow control bacterial transport and attachment around pillars
University of Rome Tor Vergata - 29th November 2018
Flow velocity, U (µm/s)500 1000
Τ𝜎 𝜃
𝜎 𝑢 0.8
1.2
0.4
B
U=
1000
µm
/sU
= 30
0 µm
/s
I/Imax0.51 0
B
C
C
1500
Τ𝜎 𝜃
𝜎 𝑢 0.8
1.2
0.4
Flow velocity, U (µm/s)500 1000 1500
(Τ
𝜎 𝜃𝜎 𝑢) e
xp
( Τ𝜎𝜃 𝜎𝑢) sim
1
0.510.5
Experiments Simulations
1
0.6
1
0.6
Motility and flow control bacterial transport and attachment around pillars
University of Rome Tor Vergata - 29th November 2018
Capture efficiency
η = Particles captured by the collector
Particles in the volume of liquid passing through the projected
area of the collector
Flow, Uη
0.00
1
250
0.00
01
500 750 1000
Flow velocity, U (μm/s)
Motility and flow control bacterial transport and attachment around pillars
University of Rome Tor Vergata - 29th November 2018
Cap
ture
effi
cien
cy, η
1
0.1
10Péclet number, Pe
0.01
Simulations
1 103 105
Non-motile particles
Dcoll = 50 μmDcoll = 100 μmDcoll = 200 μm
Motility and flow control bacterial transport and attachment around pillars
University of Rome Tor Vergata - 29th November 2018
Experiments – P. aeruginosa Simulations
η/D
pill(μ
m-1
)
10-2
I/Dpi
ll(a
.u.)
0.1
1
10 1000100
~Pe-1.1 10-4
10-3
~Pe-1.3
10 1000100Péclet number, Pe Péclet number, Pe
Motility and flow control bacterial transport and attachment around pillars
University of Rome Tor Vergata - 29th November 2018
Flow around corners triggers the formation of streamers
100 µm
Pseudomonas aeruginosa suspension
Confocal z-scan after 8 hours of flow
University of Rome Tor Vergata - 29th November 2018
Flow around corners triggers the formation of streamers
100 µm
100 µm100 µm
100 µm 100 µm
University of Rome Tor Vergata - 29th November 2018
Flow around corners triggers the formation of streamers
100 µm
30 min 60 min 90 min
Bottom surface Mid-plane
100 µm
University of Rome Tor Vergata - 29th November 2018
Streamer formation is independent of bacterial motility
100 µm 100 µm
100 µm 100 µm
University of Rome Tor Vergata - 29th November 2018
Secondary flow drives streamer formation
100 µm
100 µmRusconi et al. J. R. Soc. Interface 2010
University of Rome Tor Vergata - 29th November 2018
Secondary flow drives streamer formation
Rusconi et al. Biophys. J. 2011
100 µmNumerical simulations
Sharper turns
More streamers
University of Rome Tor Vergata - 29th November 2018
Streamers are frequent in natural and artificial systems
Valiei et al. Lab Chip 2012
Drescher et al. PNAS 2013
Porous media
Filtration systems
Marty et al. Biofouling 2012
Medical stents
University of Rome Tor Vergata - 29th November 2018
Summary and acknowledgments
Flow controls the spatial distribution of motile microorganisms
Flow affects the formation and the structure of biofilms
Flow induces preferential attachment of bacteria to surfaces
University of Rome Tor Vergata - 29th November 2018
roberto.rusconi@hunimed.eu
Eleonora Secchi (ETH)Roman Stocker (ETH)
Howard Stone (Princeton)
Jeff Guasto (Tufts)
Sigolene Lecuyer (Lyon)
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