Successfully reported this slideshow.
Institute of Marine and Coastal Sciences        Why is there so much microbial diversity in                     NJ and Bey...
Overview of the seminar          •Background on how we do oceanography and a           small lecture          •Measurement...
Winch and “A” frame                                   Text                                    TextThursday, March 29, 12
Niskin Bottles to collect water samples at depthThursday, March 29, 12
Floats for     Look at all         equipment     the hard            going over     hats and            the side     safet...
Inside the ship in the science labs. All the space is used.Thursday, March 29, 12
Why study bacteria in the ocean?       ASM workshop--2000Thursday, March 29, 12
How biologists                         understood the                         tree of life in                         1866...
Axhplmnap                         ni yo n sm                          oc i i l                               o e          ...
Electron                         micrograph of                         bacteria                         collected off     ...
Viable counting of bacteria by serial dilution and plate count                                            Microbial Life-’...
Counting the number of viable cells by                    serial dilution and plate count                                 ...
Results of bacterial counts with 6 methods                                     Jannasch & Jones, 1959Thursday, March 29, 12
What is Meant by Molecular Ecology?             Using methodology that identifies specific             molecules in a comple...
What biomolecules can we work with?                              Microbial Life-’02 Perry et al.Thursday, March 29, 12
Traditional Clone and Sequence MethodThursday, March 29, 12
The Ribosomal RNA SSU tree of life       Bacteria                                                                         ...
Problem         Why are there so many bacterial species in              the ocean [or anywhere else] ?                    ...
The solution to the Paradox of the Plankton                                   Hutchinson 1961Thursday, March 29, 12
The solution to the Paradox of the Plankton                                   Hutchinson 1961Thursday, March 29, 12
Stable Co-existence--resource partitioning                                                    Chesson 2000Thursday, March ...
Stable Co-existence--resource partitioning                                                    Chesson 2000Thursday, March ...
Stable Co-existence- [selective predation]                                             Hutchinson 1961                    ...
Interesting question            Do bacteria in the coastal ocean of New             Jersey experience rapidly changing    ...
Interesting question            Do bacteria in the coastal ocean of New             Jersey experience rapidly changing    ...
1           Results from the GRIST Experiment                                   The GRIST study aimed to target the       ...
Almost-diel study times indicated by the 2 orange boxesThursday, March 29, 12
Five approaches using RNA/DNA based                methods to determine activity             1. mRNA analysis             ...
What biomolecules can we work with?                              Microbial Life-’02 Perry et al.Thursday, March 29, 12
Universal Ribosomal rRNA content vs. Growth Rate                  12                    9       RNA/DNA                   ...
What can we predict?Thursday, March 29, 12
How does Terminal Restriction                    Fragment Length Polymorphism work?     Sample                            ...
Signal Strength   Ribosomal RNA fingerprints during the GRIST experiment                                                  T...
4             Incorporation of stable isotopes into              DNA and separation by ultracentrifugation                ...
Semi-conservative replication of DNA                               15N                          generations               ...
Map of Sample SitesThursday, March 29, 12
TRFLP fingerprints of nosZ genes from benzoate     fed slurries from Norfolk and LEO             Signal Strength           ...
Increase in TRFLP peak areas through       time for LEO-15 and Norfolk incubations                               Gallagher...
7                           Orinoco River Plume                                  Puerto Rico                              ...
Enrichment culture/ resource partitioning                                         Wawrik et al., 2005Thursday, March 29, 12
Carbon utilization patterns of bacteria in the plume                          L. Kerkhof, C. Ferraro, L. McGuinness       ...
Nitrogen utilization patterns of bacteria in the plume                          L. Kerkhof, C. Ferraro, L. McGuinness     ...
First Conclusions  1) Ribosome fingerprinting can distinguish active from    resident bacteria.  2) Not every bacterial gro...
Conclusions     A) Whether there is resource partitioning        among bacteria depends on your        environment.     B)...
Upcoming SlideShare
Loading in …5
×

East Coast MARE Ocean Lecture Mar 29, 2012 - Why is there so much microbial diversity in NJ & beyond?

613 views

Published on

East Coast MARE hosted an Ocean Lecture & Educators’ Night for teachers focused on bringing ocean literacy to students in New Jersey. Dr. Lee Kerkhof of Rutgers University presented the scientific lecture on March 29, 2012. For more information visit http://coseenow.net/mare/opportunities-resources/ocean-lecture-educators-night/.

Published in: Education, Technology
  • Be the first to comment

  • Be the first to like this

East Coast MARE Ocean Lecture Mar 29, 2012 - Why is there so much microbial diversity in NJ & beyond?

  1. 1. Institute of Marine and Coastal Sciences Why is there so much microbial diversity in NJ and Beyond? Rutgers University, Lee KerkhofThursday, March 29, 12
  2. 2. Overview of the seminar •Background on how we do oceanography and a small lecture •Measurements of the coast of New Jersey •Assessment of active bacteria in the Orinoco River Plume •Determination of active bacteria in the subsurface Then, I get to revisit these sites again with a different methodologyThursday, March 29, 12
  3. 3. Winch and “A” frame Text TextThursday, March 29, 12
  4. 4. Niskin Bottles to collect water samples at depthThursday, March 29, 12
  5. 5. Floats for Look at all equipment the hard going over hats and the side safety gearThursday, March 29, 12
  6. 6. Inside the ship in the science labs. All the space is used.Thursday, March 29, 12
  7. 7. Why study bacteria in the ocean? ASM workshop--2000Thursday, March 29, 12
  8. 8. How biologists understood the tree of life in 1866. 3 main groups of organisms Based primarily upon morphologyThursday, March 29, 12
  9. 9. Axhplmnap ni yo n sm oc i i l o e Microbial Life-’02 Perry et al.Thursday, March 29, 12
  10. 10. Electron micrograph of bacteria collected off the coast of HawaiiThursday, March 29, 12
  11. 11. Viable counting of bacteria by serial dilution and plate count Microbial Life-’02 Perry et al.Thursday, March 29, 12
  12. 12. Counting the number of viable cells by serial dilution and plate count Microbial Life-’02 Perry et al.Thursday, March 29, 12
  13. 13. Results of bacterial counts with 6 methods Jannasch & Jones, 1959Thursday, March 29, 12
  14. 14. What is Meant by Molecular Ecology? Using methodology that identifies specific molecules in a complex mixture to identify specific groups of microorganisms to address ecological questions Target molecules can be: •Unique pigments or 2o metabolites •Lipids •Proteins •Nucleic AcidsThursday, March 29, 12
  15. 15. What biomolecules can we work with? Microbial Life-’02 Perry et al.Thursday, March 29, 12
  16. 16. Traditional Clone and Sequence MethodThursday, March 29, 12
  17. 17. The Ribosomal RNA SSU tree of life Bacteria Eukarya Proteobacteria Gram-Positive Bacteria Archaea Slime Molds Animals Entamoebae Green Non-Sulfur Bacteria MethanobacteriumHalobacterium Fungi Cyanobacteria Plants Methanococcus Thermoplasma Thermoproteus ThermococcusFlavobacteria Ciliates Sulfolobus Archaeoglobus Methanopyrus Ignicoccus Flagellates Pyrodictium Thermotoga Microsporidia Diplomonads Aquifex Universal AncestorThursday, March 29, 12
  18. 18. Problem Why are there so many bacterial species in the ocean [or anywhere else] ? There should be competitive exclusion, i.e. the best adapted organism out competes all the others. Hardin 1960Thursday, March 29, 12
  19. 19. The solution to the Paradox of the Plankton Hutchinson 1961Thursday, March 29, 12
  20. 20. The solution to the Paradox of the Plankton Hutchinson 1961Thursday, March 29, 12
  21. 21. Stable Co-existence--resource partitioning Chesson 2000Thursday, March 29, 12
  22. 22. Stable Co-existence--resource partitioning Chesson 2000Thursday, March 29, 12
  23. 23. Stable Co-existence- [selective predation] Hutchinson 1961 Chesson 2000Thursday, March 29, 12
  24. 24. Interesting question Do bacteria in the coastal ocean of New Jersey experience rapidly changing patchy niches that could account for microbial diversity?Thursday, March 29, 12
  25. 25. Interesting question Do bacteria in the coastal ocean of New Jersey experience rapidly changing patchy niches that could account for microbial diversity? Test this with activity measurements of bacteria in the water column on a diel cycle.Thursday, March 29, 12
  26. 26. 1 Results from the GRIST Experiment The GRIST study aimed to target the active bacteria in the coastal ocean and assess the relationship between traditional rate measurements and gene-based methodologies for linking processes from the molecular to the global scale. LEO-15Thursday, March 29, 12
  27. 27. Almost-diel study times indicated by the 2 orange boxesThursday, March 29, 12
  28. 28. Five approaches using RNA/DNA based methods to determine activity 1. mRNA analysis 2. MICROFISH analysis 3. BrDU incorporation 4. Ribosome fingerprinting 5. Stable Isotope incorporationThursday, March 29, 12
  29. 29. What biomolecules can we work with? Microbial Life-’02 Perry et al.Thursday, March 29, 12
  30. 30. Universal Ribosomal rRNA content vs. Growth Rate 12 9 RNA/DNA 6 3 0 0.0 0.5 1.0 1.5 2.0 Specific Growth Rate (h-1) Kerkhof and Ward, 1993Thursday, March 29, 12
  31. 31. What can we predict?Thursday, March 29, 12
  32. 32. How does Terminal Restriction Fragment Length Polymorphism work? Sample Size separate on automated sequencer Gene 1 A B Gene 2 Gene 3 Gene 4 Gene n Purify DNA Gene n+ 1 PCR with fluorescent primers Restriction Enzyme Digest Only labeled fragments appear as peaks ABI Software AnalysisThursday, March 29, 12
  33. 33. Signal Strength Ribosomal RNA fingerprints during the GRIST experiment TRFLP Size (in base pairs)Thursday, March 29, 12
  34. 34. 4 Incorporation of stable isotopes into DNA and separation by ultracentrifugation Radajewski et al 2000, Nature 403: 646–649Thursday, March 29, 12
  35. 35. Semi-conservative replication of DNA 15N generations 14N Meselson and Stahl 1958, PNAS 44: 671-–649Thursday, March 29, 12
  36. 36. Map of Sample SitesThursday, March 29, 12
  37. 37. TRFLP fingerprints of nosZ genes from benzoate fed slurries from Norfolk and LEO Signal Strength TRFLP Size (in base pairs) Gallagher et al., 2005 AEM 71:5192-5196Thursday, March 29, 12
  38. 38. Increase in TRFLP peak areas through time for LEO-15 and Norfolk incubations Gallagher et al., 2005 AEM 71:5192-5196Thursday, March 29, 12
  39. 39. 7 Orinoco River Plume Puerto Rico 65o W 60o W Guadalupe Caribbean Basin 15o N Satellite surface Chla St. Lucia 5-10 mg/m3 2-5 mg/m3 0.5-1.5 mg/m3 Venezuela Trinidad Tobago 10o NThursday, March 29, 12
  40. 40. Enrichment culture/ resource partitioning Wawrik et al., 2005Thursday, March 29, 12
  41. 41. Carbon utilization patterns of bacteria in the plume L. Kerkhof, C. Ferraro, L. McGuinness Station 12 13C protein uptake 13C amino acid uptake 13C Pigment uptake 112 bp 85 bp 140 bpThursday, March 29, 12
  42. 42. Nitrogen utilization patterns of bacteria in the plume L. Kerkhof, C. Ferraro, L. McGuinness Far Plume SiteThursday, March 29, 12
  43. 43. First Conclusions 1) Ribosome fingerprinting can distinguish active from resident bacteria. 2) Not every bacterial group is behaving uniformly in the field. But, there are some repeating patterns indicating non-randomness. 3) Roughly 25-50% of the microbial population are not growing in the Mid-Atlantic Bight and the Orinoco River Plume (i.e. DNA signal, no RNA signal). 4) So far, little correlation to measured environmental parameters.Thursday, March 29, 12
  44. 44. Conclusions A) Whether there is resource partitioning among bacteria depends on your environment. B) The role of predation in structuring the community plays a more important role than typically appreciated. C) Elucidating the microbial food web using molecular tools is just in its infancy. There is so much more to learn!Thursday, March 29, 12

×