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Bacteriology for Engineers for the 21 st Century

Bacteriology for Engineers for the 21 st 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 ”

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Bacteriology for Engineers for the 21 st Century

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  1. Bacteriology for Engineersfor the 21st Century Tom Curtis Newcastle University

  2. 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!

  3. Mara, D. D. (1974) Bacteriology for Sanitary Engineers, Churchill Livingstone, Edinburgh and London, 209 p “Engineers put bacteria to work sewage treatment systems”

  4. Urbanization

  5. Chapter 14: Waste Treatment 1974 Activated Sludge Waste Stabilisation Ponds Attached Growth Anaerobic

  6. Waste Treatment 2011 1914 1910 1899 1930/74

  7. "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) Feachem et al., 1983

  8. Evolution: 1974Chapter 2!

  9. Evolution: 2010 Stylised Representation of Carl Woese’s 3 Domain Tree of Life

  10. An Explosion in methods DGGE LH-PCR TGGE CARD-FISH PCR SIP RT-PCR Microarrays TTGE RNA-SIP Macroarrays Real Time-PCR T-RFLP ARISA RSGP Clone libraries MICRO-FISH LAMP FISH MAR-FISH Arrays Pyrosequencing STARFISH IS-PCR

  11. Explosion in data • Cost falling • Efficiency growth now exceeding Moore’s law • Moore’s law vs sequencing Economist June 2010

  12. 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/

  13. 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

  14. 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 Number of Species Davenport et al., in prep

  15. The largest railway bridge:1725 The second largest bridge in the Roman World Severan Bridge, Turkey ~200 AD Causey Arch, Built 1725

  16. The Forth railway bridge:1885 • Designed 1882 • Rationally designed and new materials • Classical structural theory

  17. 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

  18. Vain pursuit of the unworkable

  19. Photo by J Harrison /ASU 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.

  20. 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

  21. Ecological Theory McArthur and Wilson 1965

  22. Tools to predict diversityTheory of Island Biogeography McArthur and Wilson 1965

  23. 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

  24. Stochastic assembly of a functional group Sloan (2006) theory (after Bell/Hubbell)

  25. Sloan’s Stochastic Model q • Source community q • Local community NT • (NT predicted by ASMx) • Sampling from qinto NT m m m NT Sloan et al., 2006

  26. Immigration rate affects relationship between frequency and abundance

  27. Ammonia oxidising bacteria in activated sludge NT = 47.2

  28. The Sea With thanks to Ake Hagstrom

  29. Lungs

  30. We can find m • memerges from NTm • But a sort of fitted parameter • It has a biological reality.. • The number of immigration events for each birth

  31. Immigration Scales Clone FISH DGGE TRFLP

  32. 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

  33. Implications Engineers Ecology and Evolution Explains the founder effects (qv babies and teeth) Rates of Immigration & Evolution can be compared • 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

  34. Dynamics will be crucial • Neutral dynamics are slow • We know that taxa vary • Selective pressure could wipe out neutral dynamics

  35. 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

  36. Criddle/Well’s dataset in Palo Alto WWTP Criddle et al., 2009

  37. Beta distribution calibration NTm = 19 m = 6.13e-007 Ofiteru et al., PNAS 2010

  38. Gammadistribution calibration NTm = 19 θ = 4 Ofiteru et al., PNAS 2010

  39. Most abundant AOB - a = 0 model is totally neutral R2 = 0.2

  40. Most abundant AOB Including environmental factors R2 = 0.39

  41. “if a theory can explain 70% of the observed phenomena it will have served its purpose well” MacArthur and Wilson 1967

  42. Preliminary Application • Using models to guide seeding and to predict dynamics • EG Low temp anaerobic digestion

  43. The future Energy use in the UK water sector Telephony costs Kwh/Ml of wastewater State of Working America 2006-2007; Federal Communications Commission

  44. Energy content of wastewater;15-20 Kj/g COD • 0.4-0.5 Kwh/person • Energy demand of Conventional WWT • 0.2 Kwh/person ACTIVATED SLUDGE IS DEAD Heidrich et al., 2011

  45. 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’ ”*

  46. Thank you

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