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Grants List


University of California, San Diego Scripps Institution of Oceanography

Closely interacting microbes as hotspots of biogeochemical activity

To investigate how closely coupled marine microorganisms interact physically and exchange nutrient molecules. By combining new microscopy tools with molecular and isotope techniques, this project aims to advance understanding of the mechanisms that drive biogeochemical cycles in the surface ocean.

Title: Closely interacting microbes as hotspots of biogeochemical activity
Date Awarded: Jun 2011
Amount: $867,414
Term: 38 months
Grant ID: GBMF2758
Funding Area: Science, Marine Microbiology Initiative


Microbes in the ocean are highly abundant (billions per liter of seawater) and diverse. They are able to strongly influence the ocean’s carbon cycle and global climate. Photosynthetic microbes (phytoplankton) remove huge amounts--over 100 billion tons yearly-- of the greenhouse gas carbon dioxide (CO2) from the atmosphere, turning it into their own biomass. Other microbes (“heterotrophs”) manage to strongly compete with animals to use a substantial, but variable, fraction of this biomass, respiring back CO2. We are testing the idea that microbes are so successful in using organic matter and respiring it to CO2 by interacting physically with the phytoplankton to exchange nutrient molecules at the photosynthesis “hotspots” (before the nutrients diffuse away). Use of advanced microscopy tools is helping understand the ecology of the tiny microbes in their minuscule habitats by direct observation of their behavior and interactions--as one would study the ecology and ecosystem influence of fish in the sea or elephants in the forest. This is also opening up the field of microscale ecology.

Bacteria and Archaea interactions with marine primary productivity are a major factor in ecosystem dynamics, upper ocean respiration and regulation of carbon export to the ocean’s interior. Therefore, the nature and strength of metabolic coupling of microbes with primary productivity are critical biogeochemical variables in a changing ocean. Since individual microbes exert their influence on primary productivity at a nanometer to millimeter spatial scale we are studying the microbial interactions at these scales. Our focus is on Cyanobacteria-bacteria interactions as creating biogeochemical hotspots— microscale loci of intense carbon fixation, growth, respiration and nutrient regeneration and nutrient exchange-- in the relatively nutrient poor bulk seawater. Powerful tools for individual cell interrogation and molecular imaging of the microenvironment are now becoming available (including Atomic Force Microscopy and laser confocal microscopy) and we have been applying these techniques to our research. We emphasize individual based ecology—studying individual microbe’s interactions with microbes and materials in its microenvironment.  We stress the power of observation— to “look” at the microbes in a “drop” of seawater as they interact with organic matter, attach with other microbes, grow, respire, kill, die--in short display their biology, ecology and ability to cumulatively shape the biogeochemical state of the ocean.

Read more:

Baudoux, A. C., R. W. Hendrix, G. C. Lander, X. Bailly, S. Podell, C. Paillard, J. E. Johnson, C. S. Potter, B. Carragher, & F. Azam. (2012). Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses. Environ Microbiol, 14(8), 2071-2086. doi: 10.1111/j.1462-2920.2011.02685.x

Collins, D. B., A. P. Ault, R. C. Moffet, M. J. Ruppel, L. A. Cuadra-Rodriguez, T. L. Guasco, C. E. Corrigan, B. E. Pedler, F. Azam, L. I. Aluwihare, T. H. Bertram, G. C. Roberts, V. H. Grassian, & K. A. Prather. (2013). Impact of marine biogeochemistry on the chemical mixing state and cloud forming ability of nascent sea spray aerosol. J Geophys Res Atmos, 118(15), 8553-8565. doi: 10.1002/jgrd.50598

Garren, M., & F. Azam. (2012a). Corals shed bacteria as a potential mechanism of resilience to organic matter enrichment. ISME J, 6(6), 1159-1165. doi: 10.1038/ismej.2011.180

Garren, M., & F. Azam. (2012b). New directions in coral reef microbial ecology. Environ Microbiol, 14(4), 833-844. doi: 10.1111/j.1462-2920.2011.02597.x

Lander, G. C., A. C. Baudoux, F. Azam, C. S. Potter, B. Carragher, & J. E. Johnson. (2012). Capsomer dynamics and stabilization in the T = 12 marine bacteriophage SIO-2 and its procapsid studied by CryoEM. Structure, 20(3), 498-503. doi: 10.1016/j.str.2012.01.007

Pedler, B. E., L. I. Aluwihare, & F. Azam. (2014). Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1401887111

Prather, K. A., T. H. Bertram, V. H. Grassian, G. B. Deane, M. D. Stokes, P. J. DeMott, L. I. Aluwihare, B. P. Palenik, F. Azam, J. H.  Seinfeld, R. C. Moffet, M. J. Molina, C. D. Cappa, F. M. Geiger, G. C. Roberts, L. M. Russell, A. P. Ault, J.  Baltrusaitis, D. B. Collins, C. E. Corrigan, L. A. Cuadra-Rodriguez, C. J. Ebben, S. D. Forestieri, T. L. Guasco, S. P. Hersey, M. J. Kim, W. F. Lambert, R. L. Modini, W. Mui, B. E. Pedler, M. J. Ruppel, O. S. Ryder, N. G. Schoepp, R. C. Sullivan, & D. Zhao. (2013). Bringing the ocean into the laboratory to probe the chemical complexity of sea spray aerosol. Proc Natl Acad Sci U S A, 110(19), 7550-7555. doi: 10.1073/pnas.1300262110

Samo, T. J., B. E. Pedler, G. I. Ball, A. L. Pasulka, A. G. Taylor, L. I. Aluwihare, F. Azam, R. Goericke, & M. R. Landry. (2012). Microbial distribution and activity across a water mass frontal zone in the California Current Ecosystem. J. Plankton Res., 34(9), 802-814. doi: 10.1093/plankt/fbs048