Bacteriology for Engineers for the 21 st Century
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Transcript of Bacteriology for Engineers for the 21 st Century
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Bacteriology for Engineersfor the 21st Century
Tom CurtisNewcastle University
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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!
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Mara, D. D. (1974) Bacteriology for Sanitary Engineers, Churchill Livingstone, Edinburgh
and London, 209 p
“Engineers put bacteria to work sewage treatment systems”
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Urbanization
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Chapter 14: Waste Treatment 1974
Waste StabilisationPonds
Attached Growth
ActivatedSludge
Anaerobic
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Waste Treatment 2011
1910
1899
1914
1930/74
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"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)
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Evolution: 1974
Chapter 2!
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Evolution: 2010
Stylised Representation of Carl Woese’s 3 Domain Tree of Life
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An Explosion in methods
PCR TTG
E
TGGE
FISH
T-RFLP
STARFISH
MAR-FISH
RT-PCR
MICRO-FISH
Real Time-PCR
DGGECARD-FISH
Clone libraries
Microarrays
RNA-SIPSIP
MacroarraysRSGP
Pyrosequencing
Arrays
LH-PCR
ARISA
LAMP
IS-PCR
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Explosion in data
• Cost falling
• Efficiency growth now exceeding Moore’s law
• Moore’s law vs sequencing
Economist June 2010
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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-bacterial-cell/overview/
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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
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Species diversity in Activated Sludge
• 30,000 sequences from UK AS plants– Sequencing noise
removed
• 1000s of species in AS plants!
• Just to sequence 90% of diversity in 0.25 ml requires– 2-8 MILLION sequences Lognormal Inverse
Gaussian
0
1000
2000
3000
4000
5000
6000
7000
8000Derby Wanlip
Num
ber
of S
peci
es
Davenport et al., in prep
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The largest railway bridge:1725
Causey Arch, Built 1725
The second largest bridge in the Roman World
Severan Bridge, Turkey ~200 AD
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The Forth railway bridge:1885
• Designed 1882 • Rationally designed and new materials• Classical structural theory
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Engineering without theory is possible
W M Rankine 1853: The Harmony of Theory and Practice
in Mechanics Prof. Civil Engineering Glasgow 1853-
82
“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
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Vain pursuit of the unworkable
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What kind of theory do we need?
• Parsimony,
• Generality,
• Consilience,
• Predictiveness. – Calibration
Wilson, E.O (1998) Consilience, The unity of knowledge Random House, New York.
Photo by J Harrison /ASU
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Good Company
“KISS: Keep it simple stupid”
– Clarence Johnson, Lockheed
"Simplicity is the ultimate sophistication"
– Leonardo Da Vinci
"Very good Tom..... but it is too f@*%ing complicated”
– Duncan Mara
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Ecological Theory
McArthur and Wilson 1965
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Tools to predict diversityTheory of Island Biogeography
McArthur and Wilson 1965
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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
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Stochastic assembly of a functional group Sloan (2006) theory (after
Bell/Hubbell)
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Sloan’s Stochastic Model
A. Source community q
B. Local community NT (NT predicted by ASMx)
C. Sampling from q into NT
NT
m
m
mq
Sloan et al., 2006
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Immigration rate affects relationship between frequency and abundance
0 0.1 0.2 0.3 0.4 0.5 0.60
0.10.20.30.40.50.60.70.80.9
1
Ntm = 1 Ntm = 2 Ntm = 10Mean abundance of a species
Freq
uenc
y
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0
0.2
0.4
0.6
0.8
1
1.2
0 0.2 0.4 0.6 0.8 1
Mean Abundance (Pi)
Freq
uenc
y
99%97%Model Ntm=11.6
NT = 47.2
Ammonia oxidising bacteria in activated sludge
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0
0.2
0.4
0.6
0.8
1
1.2
0 0.05 0.1 0.15 0.2 0.25 0.3
Mean abundance
Freq
uenc
y
Observed
Model Ntm = 32.7, m =0.1
The Sea
With thanks to Ake Hagstrom
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0
0.2
0.4
0.6
0.8
1
0 0.1 0.2 0.3 0.4
Mean Relative abundance (p i)
Freq
uenc
y
Neutral Model Ntm = 14.65
Detection frequency inthe lungs of 24 people
Lungs
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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
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Immigration Scales
0.000000001
0.00000001
0.0000001
0.000001
0.00001
0.0001
0.001
0.01
0.1
11 100 10000 1000000 100000000
10000000000
Individuals
Imm
igra
tion
(per
dea
th/b
irth
)
Clone
FISH
DGGE
TRFLP
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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
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ImplicationsEngineers• 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
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Dynamics will be crucial• Neutral dynamics are slow
• We know that taxa vary
• Selective pressure could wipe out neutral dynamics
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Incorporating biological effects• The Sloan model has an advantage
parameter– ai
• Can confer advantage or disadvantage– Over time – Over community– Advantage sums to zero
• Σ a = 0
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Criddle/Well’s dataset in Palo Alto WWTP
0
0.1
0.2
0.3
0.4
0.5
0.6
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 51week number
rela
tive
abun
danc
e amoA
OTU 2 OTU 8 OTU 9
Criddle et al., 2009
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NTm = 19
Beta distribution calibration
m = 6.13e-007
Ofiteru et al., PNAS 2010
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NTm = 19θ = 4
Gamma distribution calibration
Ofiteru et al., PNAS 2010
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' 2 1 2 1i tdX m p X X X dt X X dWa
R2 = 0.2
- a = 0 model is totally neutral
Most abundant AOB
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' 2 1 2 1i tdX m p X X X dt X X dWa
Most abundant AOB
Including environmental factors
2.44 0.06 0.04T Cra
R2 = 0.39
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“if a theory can explain 70% of the observed phenomena it will have served its purpose well”
MacArthur and Wilson 1967
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Preliminary Application• Using models to
guide seeding and to predict dynamics– EG Low temp
anaerobic digestion
0 2 4 6 8 10 12 140
0.5
1
1.5
2
2.5
3
Methanogenic activity- H2/CO2
4oC_H2/CO2 8oC_H2/CO2 15oC_H2/CO2
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The futureTelephony costs Energy use in the
UK water sector
2003 2004 2005 2006 20070
200400600800
100012001400160018002000
Average BestWorst
Kw
h/M
l of
was
tew
ater
1980 1990 2000 20100
10203040506070
Landline long distanceYear
Cen
ts/ m
inut
e
State of Working America 2006-2007; Federal Communications Commission
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• 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
ACTIVATED SLUDGE IS
DEAD
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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’ ”*
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Thank you