What we think we know about microbes (what our methods tell us to think)

1. What we think we know about microbes(what our methods tell us to think) Paul F. Kemp

2. What does this picture tell us?

3. Life stages: growth, senescence, death • Diversity • Competition for identical resources • Characteristic growth patterns • Resource dependence

4. How about this one?

5. Life stages: growth, senescence, death • Diversity • Competition for identical resources • Characteristic growth patterns • Resource dependence • Recognizable organisms: species • Properties of isolated organisms

6. What do we think we know about this cell?

7. It has: • Shape • Size • Cryptic identity • It might be alive

8. How about these?

9. Diversity of shapes and sizes • Biomass

10. Diversity of shapes and sizes • Biomass Growth • Biomass turnover • Grazing rate to match production rate

11. Diversity of shapes and sizes • Biomass Growth • Biomass turnover • Grazing rate to match production rate Life, growth, death, grazers add up to:

12. Diversity of shapes and sizes • Biomass Growth • Biomass turnover • Grazing rate to match production rate Bacterial “communities” • Producers and consumers • Energy and material transfers Microbial loop Biogeochemical cycles

13. Anonymous communities

14. New insights • Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning • Increase in Bacterial Community Diversity in Subsurface Aquifers Receiving Livestock Wastewater Input • Bacterial community diversity associated with four marine sponges from the South China Sea based on 16S rDNA-DGGE fingerprinting • Stability and Change in Estuarine Biofilm Bacterial Community Diversity

16. If we know who is present… Can we now understand “community”?

17. What is “Community”? • “Community” is not an abundance, or a recognition that there are diverse organisms present, or even a list of who’s present. • “Community” is the relationship among the members of the community.

18. Studying communities Consider the scales at which we sample and study microbial processes to learn about microbial communities. Let’s anthropomorphize to gain some perspective.

19. Microbes are abundant

20. Studying abundant microbes • A typical value for bacterial abundance in coastal seawater is 106 ml-1. • 1 million people occupy an area of ~32,000 km2 in the USA, and ~14,500 km2 in Europe. • What could we learn about people and their environment, using a sampling device that collects 1 million at a time? • Would we understand “community”?

21. The Big Picture • Population size. Over time, net population growth or loss. Perhaps birth and death versus immigration and emigration. • Standing stock of materials and goods. • Over time, infer the net exchange of materials and goods in and out of area. • Sound familiar? We study bacterial populations and economies, not communities.

22. Appropriate Scale • How can we define an appropriate scale for the study of microbial communities? • Let’s consider the spatial dimensions of a bacterial community.

23. Bacterial Scale • 105 -106 ml-1 At 106 ml-1 the average distance between neighboring bacteria in water is ~62 µm, or ~100 cell diameters. At 105 ml-1 the distance increases to ~130 µm, about 200 diameters. • On a human scale, your nearest neighbor would be 200-400 m away.

24. How we think of bacteria

25. The real microbial world

26. Sparse Bacterial Communities • “Abundant” bacterial communities are actually sparsely populated and highly dispersed. They are telecommunities of organisms separated by great distances. • How can organisms interact across great distances?

27. Bacterial Interactions • Communication: information obtained by a cell through the detection of the activity of another cell. • Popular examples of bacterial communication : cell signaling and quorum sensing, bioluminescence, toxicity, swarming behavior.

28. Is communication possible? • For a small molecule, e.g. NH4+, HS-, typical diffusion times are: • 1 cell diameter 0.1 ms • between 2 cells 1 second • 1 cm 9 hours • 10 cm 38 days • 1 cm chain letter 200 seconds • 10 cm chain letter 35 minutes

29. Maybe bacteria aren’t a community… • Do bacteria cooperate enough to make communication possible? • Maybe bacteria are better thought of as individuals who co-exist and happen to use common resources, but rarely interact • Maybe bacteria act as communities only when they are crowded together, e.g. biofilms, or on particles

30. Some important points… • When you listen to experts, keep in mind they are only mostly right. Paradigms are discarded every year. • Don’t get too fond of your favorite ideas. • Important issues and questions are forgotten as paradigms change. • Paradigms are less broad than they look.

31. Important questions? • Is the “community” concept meaningful? • What obligate , interdependent relationships exist among microbes? • Does the microbial loop exist? • Do familiar ecological concepts apply? • Competition, exclusion, coexistence, dependence. Too many species! • Why do inactive microbes persist? • Why do bacteria colonize sinking particles?

32. Model systems • Model systems are models because someone chooses to work on them. • Much of what you will hear in this course will pertain to a specific model system. • The rules change in other model systems.

33. Example: Deep biosphere • Arguably one of the largest biomes on Earth. • Life is dependent on fluid motion; it’s an aquatic environment. • Bacteria known to penetrate to great depth, probably limited by temperature. • Archaea may be present, Eucarya and viruses are unknown.

34. Example: Deep biosphere • Ultraoligotrophic • Unmeasurable growth • No known mechanisms for death • Abiotic energy supplies, e.g. radiolysis of water, thermogenesis of organic compounds • Unknown connectivity to overlying ocean

35. Do the same rules apply to… • Permanently ice covered Antarctic lakes • Terrestrial soils • Aquatic sediments • Deep ocean • Coastal ocean

36. Innovations lead to new insights, new questions… • AO cell counts 1977 (Hobbie et al) • DAPI 1980 (Porter and Feig) • rRNA 1980s (Woese et al) • FISH 1989 (DeLong et al) • Genomics 1972, 1995, 2001 • Pyrosequencing 1996-2000 • ??? 2008