The document discusses the importance of considering both large and small scales when studying soil-borne microbial diversity. It notes that traditional approaches have focused on scales of convenience rather than those most relevant to microbes and their environments. Looking forward, the Earth Microbiome Project needs to examine global patterns and impacts as well as local microbial distributions, activities, and interactions by considering different scales, time points, meta-transcriptomics, and reducing sample diversity.

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. 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. hybrid title “ Why the EMP is important, and what we need to keep in mind as we attempt this grand challenge”

6. Accelerating rate of discovery < 30 years Ernst Haeckel’s tree of life The Evolution of Man (1879) 100 + years

8. Climate change The Netherlands 50 years from now??

9. Genomics past: history of our planet Let’s go back in time – way back

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

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)

18. Microbial diversity: the need to think big and small

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

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

24. Tracking microbial diversity across past climate change events Years

25. Thinking really small… root 

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. environmental genome sequencing (inter)activities of players may be deduced from all of their individual genome sequences

28. Are soil-borne microbes living on islands? Charles Darwin   

30. Use of protein-encoding gene (rpoB) to help examine selection versus neutral patterns of community assembly

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%

39. Thanks…

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