Bacteriology for Engineersfor the 21st Century

Tom CurtisNewcastle 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 StabilisationPonds

Attached Growth

ActivatedSludge

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

PCR TTG

E

TGGE

FISH

T-RFLP

STARFISH

MAR-FISH

RT-PCR

MICRO-FISH

Real Time-PCR

DGGECARD-FISH

Clone libraries

Microarrays

RNA-SIP

SIP

MacroarraysRSGP

Pyrosequencing

Arrays

LH-PCR

ARISA

LAMP

IS-PCR

Explosion in data

• Cost falling

• Efficiency growth now exceeding Moore’s law

• Moore’s law vs sequencing

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-bacterial-cell/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– Sequencing noise

removed

• 1000s of species in AS plants!

• Just to sequence 90% of diversity in 0.25 ml requires– 2-8 MILLION

sequencesLognormal Inverse

Gaussian

0

1000

2000

3000

4000

5000

6000

7000

8000Derby Wanlip

Nu

mb

er

of

Sp

eci

es

Davenport et al., in prep

The largest railway bridge:1725

Causey Arch, Built 1725

The second largest bridge in the Roman World

Severan Bridge, Turkey ~200 AD

The Forth railway bridge:1885

• Designed 1882 • Rationally designed and new materials• Classical structural theory

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

Vain pursuit of the unworkable

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

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

Ecological Theory

McArthur and Wilson 1965

Tools to predict diversityTheory 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)

C. Sampling from q into NT

NT

m

m

m

q

Sloan et al., 2006

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

Fre

quen

cy

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

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

Fre

qu

en

cy

Observed

Model Ntm = 32.7, m =0.1

The Sea

With thanks to Ake Hagstrom

0

0.2

0.4

0.6

0.8

1

0 0.1 0.2 0.3 0.4

Mean Relative abundance (p i)

Fre

qu

ency

Neutral Model Ntm = 14.65

Detection frequency inthe lungs of 24 people

Lungs

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

0.000000001

0.00000001

0.0000001

0.000001

0.00001

0.0001

0.001

0.01

0.1

1

1 100 10000 1000000 1000000001000000000

0

Individuals

Imm

igra

tion

(pe

r de

ath/

birt

h)

Clone

FISH

DGGE

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

• Σ a = 0

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 51

week number

rela

tive

ab

un

dan

ce amoA

OTU 2 OTU 8 OTU 9

Criddle et al., 2009

NTm = 19

Beta distribution calibration

m = 6.13e-007

Ofiteru et al., PNAS 2010

NTm = 19θ = 4

Gamma distribution calibration

Ofiteru et al., PNAS 2010

' 2 1 2 1i tdX m p X X X dt X X dW

R2 = 0.2

- a = 0 model is totally neutral

Most abundant AOB

' 2 1 2 1i tdX m p X X X dt X X dW

Most abundant AOB

Including environmental factors

2.44 0.06 0.04T 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

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

The future

Telephony costsEnergy use in the

UK water sector

2003 2004 2005 2006 20070

200400600800

100012001400160018002000

Average BestWorst

Kw

h/M

l of

wast

ew

ate

r 1980 1990 2000 20100

10

20

30

40

50

60

70

Landline long distance

Year

Cen

ts/

min

ute

State of Working America 2006-2007; Federal Communications Commission

• 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

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