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Bacteriology for Engineers
st
for the 21 Century
Tom Curtis
Newcastle University
Mara, D. D. (1974) Bacteriology for Sanitary Engineers, Churchill Livingstone, Edinburgh
and London, 209 p
“Bacteriology for Engineers [17]
is an excellent reference on the
bacteriology of wastewater ”
– Metcalf and Eddy 1979
– 1974!
• Duncan was 29!
Mara, D. D. (1974) Bacteriology for Sanitary Engineers, Churchill Livingstone, Edinburgh
and London, 209 p
“Engineers put bacteria
to work sewage
treatment systems”
Urbanization
Chapter 14: Waste Treatment 1974
Waste Stabilisation
Ponds
Activated
Sludge
Attached Growth
Anaerobic
Waste Treatment 2011
1910
1899
1914
1930/74
"European and North American practices do not
represent the zenith of scientific treatment, nor
are they the product of a logical and rational and
design process.”
“Rather, treatment practices are the products of
history, a history that started about a 100 years
ago when little was known about the
fundamental physics and chemistry of the
subject and when practically no applicable
microbiology had been discovered."
Feachem, Bradely, Garelick and Mara (1983)
Evolution: 1974
Chapter 2!
Evolution: 2010
Stylised Representation of Carl Woese’s 3 Domain Tree of Life
An Explosion in methods
DGGE LH-PCR
TGGE
CARD-FISH
PCR
SIP
RT-PCR
Microarray
TTGE RNA-SIP
s
Real Time-PCR
T-RFLP Macroarrays
ARISA
RSGP
Clone libraries
MICROLAMP
FISH
MAR-FISH
FISH
Arrays
Pyrosequencin
STARFISH
IS-PCR
g
Explosion in data
• Cost falling
• Moore’s law vs
sequencing
• Efficiency growth
now exceeding
Moore’s law
Economist June 2010
An explosion in hubris
“The ability to routinely write the software
of life will usher in a new era in science,
and with it, new products and applications
such as advanced biofuels, clean water
technology... “
http://www.jcvi.org/cms/research/projects
/first-self-replicating-synthetic-bacterialcell/overview/
The scale of the microbial world
• ~1021 stars in Universe
• ~1030 bacteria in the world
• ~1029 bacteria in the sea
• ~4x1011 Stars in the galaxy
• ~1018 bacteria in a modest
activated sludge plant
• >2.8 billion years of evolution
• Untutored observation is futile
Sample of a map of the million brightest
galaxies within 109 light-years from earth
Species diversity in Activated
Sludge
• 30,000 sequences
from UK AS plants
Derby
8000
– Sequencing noise
removed
• Just to sequence 90%
of diversity in 0.25 ml
requires
– 2-8 MILLION
sequences
7000
Number of Species
• 1000s of species in AS
plants!
Wanlip
6000
5000
4000
3000
2000
1000
0
Lognormal
Inverse
Gaussian
Davenport et al., in prep
The second largest bridge in the
The largest
railway
bridge:1725
Roman
World
Severan
Bridge,
~200 AD
Causey
Arch,Turkey
Built 1725
The Forth railway bridge:1885
• Designed 1882
• Rationally designed and new materials
• Classical structural theory
Engineering without theory is
possible
“avoids risks, but stops the
progress of all improvement”
“Lavish expenditure of material
and labour”
“Failure within a limited number
of years”
“Misdirected ingenuity….vain
pursuit of unworkable
innovations
W M Rankine 1853:
The Harmony of Theory and Practice in
Mechanics
Prof. Civil Engineering Glasgow 1853-82
Vain pursuit of the unworkable
What kind of theory do we need?
• Parsimony,
• Generality,
• Consilience,
• Predictiveness.
– Calibration
Photo by J Harrison /ASU
Wilson, E.O (1998) Consilience, The unity of knowledge Random House, New York.
Good Company
"Simplicity is the ultimate sophistication"
– Leonardo Da Vinci
“KISS: Keep it simple stupid”
– Clarence Johnson, Lockheed
"Very good Tom.....
but it is too f@*%ing complicated”
– Duncan Mara
Ecological Theory
McArthur and Wilson 1965
Tools to predict diversity
Theory of Island Biogeography
McArthur and Wilson 1965
Still too f@%ing complicated
• Island biogeography theory
– Cannot be parameterised
– We do not know
•
•
•
•
How many species there are on an island (S)
How many species in the “source” (ie P)
Immigration rates
Extinction rates
Stochastic assembly of a functional group
Sloan (2006) theory (after Bell/Hubbell)
Sloan’s Stochastic Model
A. Source community q
B. Local community NT
(NT predicted by ASMx)
q
m
m
m
C. Sampling from q into NT
NT
Sloan et al., 2006
Frequency
Immigration rate affects relationship between
frequency and abundance
1
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
0
0.1
0.2
0.3
0.4
0.5
Mean abundance of a species
Ntm = 1
Ntm = 2
Ntm = 10
0.6
Ammonia oxidising bacteria in
activated sludge
1.2
Frequency
1
0.8
0.6
0.4
99%
97%
Model Ntm=11.6
0.2
0
0
0.2
0.4
0.6
Mean Abundance (Pi)
0.8
1
NT = 47.2
The Sea
1.2
Frequency
1
0.8
0.6
Observed
0.4
Model Ntm = 32.7,
m =0.1
0.2
0
0
0.05
0.1
0.15
0.2
0.25
0.3
Mean abundance
With thanks to Ake Hagstrom
Lungs
1
Frequency
0.8
0.6
Neutral Model Ntm = 14.65
0.4
Detection frequency in
the lungs of 24 people
0.2
0
0
0.1
0.2
0.3
Mean Relative abundance (p i )
0.4
We can find m
• m emerges from NTm
• But a sort of fitted parameter
• It has a biological reality..
• The number of immigration events for each birth
Immigration Scales
1
100
10000
1000000
100000000
100000000
0
Immigration (per death/birth)
1
0.1
0.01
0.001
Clone
FISH
0.0001
0.00001
0.000001
0.0000001
DGGE
0.00000001
0.000000001
Individuals
TRFLP
What Scaling Means
• If 1016 individuals, NTm = 10
• Probability of a death being replaced
– from outside 10-15
– by growth 1-10-15
• Immigration
– very rare in mature community
– Very very high in new community
Implications
Engineers
• Dynamics might be
slower than we think
– Even “unsuitable” microbes
may disappear slowly
• Start up crucial
– Practitioners have always
known this
• We should “design” the
seeding process
– Design is not always
intuitive
Ecology and Evolution
• Explains the founder
effects
– (qv babies and teeth)
• Rates of Immigration &
Evolution can be
compared
Dynamics will be crucial
• Neutral dynamics are slow
• We know that taxa vary
• Selective pressure could wipe out neutral
dynamics
Incorporating biological effects
• The Sloan model has an advantage
parameter
– ai
• Can confer advantage or disadvantage
– Over time
– Over community
– Advantage sums to zero
• Σa=0
Criddle/Well’s dataset in Palo Alto
WWTP
OTU 2
0.6
OTU 8
OTU 9
relative abundance amoA
0.5
0.4
0.3
0.2
0.1
0
1
3
5
7
9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51
week number
Criddle et al., 2009
Beta distribution calibration
NTm = 19
m = 6.13e-007
Ofiteru et al., PNAS 2010
Gamma distribution calibration
NTm = 19
θ=4
Ofiteru et al., PNAS 2010
Most abundant AOB
dX   m '  p  X   2a i X 1  X   dt  2 X 1  X dWt
- a = 0 model is totally neutral
R2 = 0.2
Most abundant AOB
dX   m '  p  X   2a i X 1  X   dt  2 X 1  X dWt
Including environmental
factors
a  2.44  0.06  T  0.04  Cr
R2 = 0.39
“if a theory can explain 70% of
the observed phenomena it will
have served its purpose well”
MacArthur and Wilson 1967
Preliminary Application
• Using models to guide
seeding and to predict
dynamics
– EG Low temp
anaerobic digestion
Methanogenic activity- H2/CO2
3
2.5
2
1.5
1
0.5
0
0
5
4oC_H2/CO2
10
8oC_H2/CO2
15
15oC_H2/CO2
The future
Energy use in the UK
water sector
Telephony costs
70
2000
50
40
30
20
10
0
1980
1990
2000
Year
2010
Kwh/Ml of wastewater
Cents/ minute
60
1800
1600
1400
1200
1000
800
600
400
200
0
Landline long distance
State of Working America 2006-2007;
Federal Communications Commission
2003 2004 2005 2006 2007
Average
Best
Worst
• Energy content of wastewater;15-20 Kj/g
COD
– 0.4-0.5 Kwh/person
• Energy demand of Conventional WWT
– 0.2 Kwh/person
Heidrich et al., 2011
Mara, D. D. (1974) Bacteriology for Sanitary Engineers,
Churchill Livingstone, Edinburgh and London, 209 p
“ ‘water bacteriology is
really more than just
the total count’ ”*
Thank you