Main points from last lecture

1. 1 • Main points from last lecture • Differences between prokaryotes (Bacteria and Archaea) and eukaryotes • Differences among Bacteria, Archaea, and Eucarya: organelles, cell walls (peptidoglycan in bacteria), lipids (ester vs ether linkage) • Use of small subunit ribosomal RNA as phylogenetic marker (16S rRNA for prokaryotes)

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3. Main points, conti. 4. Dividing up microbes into functional groups source of carbon: autotroph vs. heterotroph source of energy: phototroph vs. chemotroph Chemoorganotroph= heterotroph 5. Eukaryotic microbes in various functional groups: primary producers, grazers, and mixotrophy. 6. Connection between phylogeny (“community structure”) and function (metabolism—what microbes do) is a big question in microbial ecology today. 3

4. Terms you need to learn (if you don’t know already) DNA, protein RNA: mRNA, tRNA, and rRNA Ribosomes (proteins + rRNA) Lipids (ester vs. ether) Organelles: Nucleus, chloroplast, mitochondria 4

5. 20 Big pools & fluxes High biomass Large organic carbon pool ca. 50% of primary production

6. Early emphasis on “net phytoplankton” Big enough to catch with large nets Easily visible and distinguishable by light microscopy (electron microscopy needed for species level identification) 21 What primary producers are in the oceans? What are the main types of phytoplankton?

7. Shape and Size Pigments: many more than in land plants All have chlorophyll a (chl a) used to estimate phytoplankton biomass Anoxygenic photosynthesizing bacteria have bacteriochlorophyll a Many (all?) have “accessory pigments”, which really are main light harvesting pigments These pigments can be used to quantitatively estimate abundance of specific algal groups Identifying features of algae 22

8. Why so many different type of pigments 22A

9. Note “attenuation” (shading) at both ends of the spectrum 22B

10. Very simple guide to photosynthesis Light 23 Accessory PigmentsChlorophyll a H2O O2 Light Reactions ATP and NADH CO2 Dark Reactions CH2O

11. Some important eukaryotic algal groups: large or net phytoplankton 24

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13. Lots of chlorophyll and 14CO2 fixation in <1 um size fraction Epifluorescence counts of auto-fluorescencing cells Cells were too small (ca. 1 um) and without internal structures, i.e. they are bacteria. (But there are some small eukaryotic phytoplankton—poorly understood. 26 Evidence that the oceans have more than just “net phytoplankton”

14. 27 • Coccoid cyanobacteria are abundant and important in the oceans! • 1. Well known in lakes and reservoirs • Importance in oceans discovered in 1980 (Synechococcus) and Prochlorococcus (1986) • Another important cyanobacterium: Trichodesmium

15. 29 Some separate Prochlorococcus from “cyanobacteria” and equate “cyanobacteria” with Synechococcus, but not true Synechococcus and Prochlorococcus are both cyanobacteria and are distantly related

16. Selected papers about marine coccoid cyanobacteria Li, W. K. W. and others 1983. Autotrophic picoplankton in the tropical ocean. Science 219: 292-295. Chisholm, S. W., R. J. Olson, E. R. Zettler, R. Goericke, J. B. Waterbury, and N. A. Welschmeyer. 1988. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334: 340-343. Palenik, B. and others 2003. The genome of a motile marine Synechococcus. Nature 424: 1037-1042. Rocap, G. and others 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047. Waterbury, J. B., S. W. Watson, F. W. Valois, and D. G. Franks. 1986. Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus, p. 71-120. In T. Platt and W. K. W. Li [eds.], Photosynthetic Picoplankton. Department of Fisheries and Oceans. 30

17. Schematic of epifluorescence microscope 31 Excitation light Ocular (10x): emission Dichroic mirror Objective (100X) Stage with sample

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19. 33 Sample is excited by lower wavelength light (say 400 nm) and the emitted light (“emission”) is at a higher wavelength (say 600 nm) Final magnification= 1000X

20. 34 Autofluorescencing cells = autotrophs= phototrophs Must have pigment, with few exceptions Usually chlorophyll, but can excite different pigments with different wavelenghts of light Heterotrophic cells (heterotrophic bacteria) Need to add fluorogenic stain (DAPI and acridine orange) to stain DNA or other cellular material

21. 35 Red color due to fluorescence from chl a

22. 35A

23. 36 PropertySynechococcusProchlorococcus Size 1.0 um 0.7 um Chlorophyll a Yes Modified Chlorophyll b No Yes Phycobilins Yes Less, variable Visible in microscope? Yes Difficult Habitat Widespread Open oceans

24. 37 Biomass in North Pacific Gyre From Campbell et al. 1994 L&O

25. 38 Cells per ml HBACT=heterotrophic Bacteria; Pro=Prochlorococcus; Syn=Synechnococcus; PEUK=picoeukaryotes From Landry and Kirchman, DSR 2002

26. 39 Numbers worth remembering Viruses: 107 ml-1 Heterotrophic Bacteria: 106 ml-1 Cyanobacteria: 105 ml-1 Protists (grazers): 104 ml-1 Large (>3 um) phytoplankton: 103 ml-1

27. 40 In oligotrophic waters, coccoid cyanobacteria account for >90% of Phytoplankton biomass (chlorophyll a) Primary production

28. 41 Global estimates: Roughly 50% of total marine primary production If marine is 50% of total production---> Cyanobacteria account for about 25% of global primary production!!

29. 42 From Madigan et al.“Brock Biology of Microorganisms”

30. 43 Another main type of cyanobacteria: Trichodesmium (formally known as Oscillatoria) Filaments of several cells, common in Sargasso Sea Can form macroscopic tuffs of cells Do NOT have heterocysts More about Tricho and heterocysts when we talk about N2 fixation.

31. Other algae: note the weird and wonderful shapes!

32. Not all algae are “nice”