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George Kowalchuk: Combining Large- and Small-Scale Studies to Uncover Soil-Borne Microbial Diversity

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George Kowalchuk's talk at the 1st Earth Microbial Project Meeting in Shenzhen

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George Kowalchuk: Combining Large- and Small-Scale Studies to Uncover Soil-Borne Microbial Diversity

  1. 1. George A. Kowalchuk Nederlands Institute of Ecology (NIOO-KNAW) Dept. Microbial Ecology Wageningen Combining large- and small-scale studies to uncover soil-borne microbial diversity Royal Academy of Arts and Sciences (KNAW) Institute for Ecological Sciences (IEW)
  2. 2. George A. Kowalchuk Nederlands Institute of Ecology (NIOO-KNAW) Dept. Microbial Ecology Wageningen What microbial ecology has to gain from the EMP? Royal Academy of Arts and Sciences (KNAW) Institute for Ecological Sciences (IEW)
  3. 3. hybrid title “ Why the EMP is important, and what we need to keep in mind as we attempt this grand challenge”
  4. 4. <ul><li>Brief introduction to microbial diversity </li></ul><ul><li>Why the EMP? </li></ul><ul><li>Microbial diversity: the need to think big and small </li></ul>Stuff I plan to discuss
  5. 5. Soil-borne microbial diversity <ul><li>Central to the functioning of terrestrial ecosystems e.g. nutrient cycling, plant growth, biodegradation </li></ul><ul><li>Huge numbers: >10 9 cells per gram soil; </li></ul><ul><li>> 10 32 cells on the planet </li></ul>Soil-borne microbial diversity is by far the greatest source of biodiversity on the planet! Estimates = 10 7 – 10 12 species “ it’s basically like, wow, there are way more species than you can imagine…”
  6. 6. Accelerating rate of discovery < 30 years Ernst Haeckel’s tree of life The Evolution of Man (1879) 100 + years
  7. 7. Major fields to be governed by microbial (meta)-genomics <ul><li>Climate change (understanding the problems and the solutions) </li></ul><ul><li>Energy </li></ul><ul><li>Human Health and nutrition (personal genomics) </li></ul><ul><li>Industry and agriculture </li></ul><ul><li>Ecological and evolutionary understanding </li></ul>
  8. 8. Climate change The Netherlands 50 years from now??
  9. 9. Genomics past: history of our planet Let’s go back in time – way back
  10. 10. Climate change The Earth does not support life because it is a nice place to live. It is a nice place to live principally because living organisms, in particular microorganisms, have shaped it to be that way. Microbes are Earth’s principle climate engineers, and the fate of our planet relies on understanding how this works
  11. 11. Energy <ul><li>Production of H 2 </li></ul><ul><li>Biological light harvesting machines (coupled to harvesting H 2 ) </li></ul><ul><li>Biofuel cells </li></ul><ul><li>Artificial cell factories </li></ul>
  12. 12. Human Health and Nutrition Personalized medicine: personalized to you and your sickness Medicine based upon you, your symbionts and your pathogens (or gene expression)
  13. 13. Industry and agriculture <ul><li>Over half of all natural products and enzymes come from soil-borne microbes </li></ul><ul><li>Given that only a small fraction of soil microbes are known, it follows that a wealth of biology is waiting to be utilized </li></ul><ul><li>Need to look are microbes in their natural habitat (importance of interactions) </li></ul><ul><li>Increasing need for sustainable agriculture, relying on microbial partnerships </li></ul>
  14. 14. <ul><li>How many species are there on Earth? </li></ul>Ecological and evolutionary understanding (basic global questions to be addressed by EMP)
  15. 15. <ul><li>How many species are there on Earth? </li></ul><ul><li>What is the global gene pool? </li></ul>Ecological and evolutionary understanding (basic global questions to be addressed by EMP)
  16. 16. <ul><li>How many species are there on Earth? </li></ul><ul><li>What is the global gene pool? </li></ul><ul><li>How do ecosystems function? </li></ul>Ecological and evolutionary understanding (basic global questions to be addressed by EMP)
  17. 17. Ecological and evolutionary understanding (basic global questions to be addressed by EMP) <ul><li>How many species are there on Earth? </li></ul><ul><li>What is the global gene pool? </li></ul><ul><li>How do ecosystems function? </li></ul><ul><li>What are the patterns of microbial diversity and function? </li></ul>
  18. 18. Microbial diversity: the need to think big and small
  19. 19. Microbial diversity: the need to think big and small To date, we have mostly concentrated on scales of convenience as opposed to those of greatest relevance
  20. 20. Microbial diversity: the need to think big and small <ul><li>To date, we have mostly concentrated on scales of convenience as opposed to those of greatest relevance </li></ul><ul><li>Drivers of microbial community organization and activity (perspective of the microbes and their local environment) </li></ul><ul><li>Global patterns of microbial diversity and impact (ecosystem and planetary perspective) </li></ul>
  21. 21. Space log Time log Coverage of traditional approaches in microbial ecology Greatest relevance to microbial organization & activity Greatest relevance to global environ-mental impact The need to think big and small Stepping outside the typical boundaries of microbial ecology
  22. 22. On the big side <ul><li>How are microbial properties linked to large-scale climatic and biogeochemical properties of the planet? </li></ul><ul><li>Global patterns of microbial diversity and biogeography </li></ul><ul><li>(and have humans disrupted these) </li></ul><ul><li>Effects of unlimited dispersal and huge total population sizes </li></ul>
  23. 23. On the big side <ul><li>How are microbial properties linked to large-scale climatic and biogeochemical properties of the planet? </li></ul><ul><li>Global patterns of microbial diversity and biogeography </li></ul><ul><li>(and have humans disrupted these) </li></ul><ul><li>Effects of unlimited dispersal and huge total population sizes </li></ul><ul><li>Is everything everywhere? </li></ul><ul><li>Does microbial diversity fluctuate in time? </li></ul><ul><li>Has microbial diversity been accumulating over time and/or is it being lost? </li></ul>HTP sequencing methods and ancient DNA approaches hold the potential to answer some of these very basic questions of diversity on Earth
  24. 24. Tracking microbial diversity across past climate change events Years
  25. 25. Thinking really small… root 
  26. 26. A Sledge-o-matic approach to microbial ecology Soil sample Sledge-o-matic: It slices , it dices, it even … circumcises But it doesn’t describe in situ microbial communities well
  27. 27. environmental genome sequencing (inter)activities of players may be deduced from all of their individual genome sequences
  28. 28. Are soil-borne microbes living on islands? Charles Darwin   
  29. 29. Soil Microbial Ecology at the Micro-Scale <ul><li>Detailed environmental analysis </li></ul><ul><li>Meta-transcriptomic analysis of soil aggregate classes </li></ul><ul><li>Meta-genomic & community analysis of individual soil aggregates </li></ul><ul><li>3-D mapping of microbial populations </li></ul>Physical Structure - Tomography - ESEM - Activity Micro-habitats - Micro-electrodes - EDX (ESEM) -Metagenomics Microbial Community - Spatial distribution - Phylogeny - Aggregate Micro-colon y Soil Fractions
  30. 30. Use of protein-encoding gene (rpoB) to help examine selection versus neutral patterns of community assembly
  31. 31. Micro-scale patterns of microbial distribution 1 2 3 11 5 17 6 16 12 10 15 13 14 7 4 8 9 18 19 20 +1.0 -1.0 CCA Prin. Comp. #1 = 37.2% CCA Prin. Comp. #2 = 24.1%
  32. 32. Soil Microbial Ecology at the Micro-Scale <ul><li>Detailed environmental analysis </li></ul><ul><li>Meta-transcriptomic analysis of soil aggregate classes </li></ul><ul><li>Meta-genomic & community analysis of individual soil aggregates </li></ul><ul><li>3-D mapping of microbial populations </li></ul>Physical Structure - Tomography - ESEM - Activity Micro-habitats - Micro-electrodes - EDX (ESEM) -Metagenomics Microbial Community - Spatial distribution - Phylogeny - Aggregate Micro-colon y Soil Fractions
  33. 33. Some thoughts as the EMP moves forward <ul><li>Take scale into account – also consider samples with reduced diversity to allow more complete assembly </li></ul>
  34. 34. Some thoughts as the EMP moves forward <ul><li>Take scale into account – also consider samples with reduced diversity to allow more complete assembly </li></ul><ul><li>Special focus to well established experimental sites: i.e. with enhanced meta-data </li></ul>
  35. 35. Some thoughts as the EMP moves forward <ul><li>Take scale into account – also consider samples with reduced diversity to allow more complete assembly </li></ul><ul><li>Special focus to well established experimental sites: i.e. with enhanced meta-data </li></ul><ul><li>Examine samples in time (long-term and short-term) </li></ul>
  36. 36. Some thoughts as the EMP moves forward <ul><li>Take scale into account – also consider samples with reduced diversity to allow more complete assembly </li></ul><ul><li>Special focus to well established experimental sites: i.e. with enhanced meta-data </li></ul><ul><li>Examine samples in time (long-term and short-term) </li></ul><ul><li>Consider the meta-transcriptome </li></ul>
  37. 37. Some thoughts as the EMP moves forward <ul><li>Take scale into account – also consider samples with reduced diversity to allow more complete assembly </li></ul><ul><li>Special focus to well established experimental sites: i.e. with enhanced meta-data </li></ul><ul><li>Examine samples in time (long-term and short-term) </li></ul><ul><li>Consider the meta-transcriptome </li></ul><ul><li>Continue to engage the broad scientific community </li></ul>
  38. 38. Some thoughts as the EMP moves forward <ul><li>Take scale into account – also consider samples with reduced diversity to allow more complete assembly </li></ul><ul><li>Special focus to well established experimental sites: i.e. with enhanced meta-data </li></ul><ul><li>Examine samples in time (long-term and short-term) </li></ul><ul><li>Consider the meta-transcriptome </li></ul><ul><li>Continue to engage the broad scientific community </li></ul><ul><li>Don’t be afraid to hype it up… </li></ul>
  39. 39. Thanks…
  40. 41. Artificial communities in artificial soils (destructive) sampling after 0, 2, 4, 7, 10, and 14 days Inoculation of microcosms Cell enumeration & in situ visualization <ul><li>same matrix potential (-20kPa) </li></ul><ul><li>different vol. water content: 4,99%, 10,91%, and 37,49% </li></ul><ul><li>all pores up to 7.5 um filled with water </li></ul>
  41. 42. (VU-Amsterdam) Erik Verbruggen, Marcel van Heijden, James Weedon, Rien Aerts, Toby Kiers (University of Vienna) Tim Urich, Christa Schleper (O.U. Environ. Genomics) Sanghoon Kang, Zhiang He, Jizhong (Joe) Zhou (BAS) Kevin Newsham, David Pearce, Pete Convey (LBNL-Berkeley) Yvette Piceno, Eoine Brodie, Todd De Santis, Gary Andersen (U of Copenhagen) Eske Willerslev (U. Glasgow) Chris Quince, Bill Sloan (RUG) Rampal Etienne Acknowledgements (NIOO) Barbara Drigo (U. New South Wales; Sydney, Australia), Etienne Yergeau (Biotechnology Research Institute; Montréal), Eiko Kuramae, Remy Hillikens, Anna Kielak (RU Groningen), Matthias de Hollander, Agata Pijl, Hans van Veen, Wietse de Boer, Michiel Vos, Sarah Jennings, Alexandra Wolf, Juliet Huet Latest Impact Factor = 6.397 Covering the breadth of microbial ecology

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