Moore Foundation MMI


The grant to the Scripps Institution of Oceanography supports investigating how heterotrophic bacteria respond to nascent cellular debris and virus particles.  By combining new microscopy tools with molecular and isotope techniques, this project aims to advance understanding of the mechanisms that drive biogeochemical cycling of phytoplankton lysate in the surface ocean.

AFM micrographs of model lysate paticles (E. coli ribosomes) adsorbed onto mica (A) and with marine bacterium SWAT3 (Vibrio sp.) (C and D respectively).

Hypothesis 1: Bacteria cell surfaces have strong, but variable affinity to scavenge nascent subcellular particles released from lysing phytoplankton. The acquired particles serve as microspatially sustained organic matter source in nutritionally dilute and fluctuating bulk environment.

Hypothesis 2:  Cell surface enzymatic hydrolysis rapidly dissipates the captured particles. This enhances bacterial growth rate (and C flow into the microbial loop).

Hypothesis 3: Subcellular particle capture and processing on bacterial surface increases bacterial growth efficiency in the upper ocean--with implications for air-sea CO2 exchange and global climate.   

Project Data
Further information and data can be obtained by contacting Dr. Farooq Azam:

Cellular particles in natural assemblages

In microcosm experiments, we observed a succession of the phytoplankton and bacterial community over the different phases of the bloom, indicating bacteria that may be more likely to capture and utilize subcellular particles when the bloom collapses (e.g. γ-ProteobacteriaPseudomonas spp. and Marinomonas spp. and members of the Bacteroidetes phyla). Imaging showed clustering of bacteria around the phytoplankton cells and evidence of gel matrix formation during this process that may be a strategy to capture subcellular particles.   In further investigations with RuBisCO as a model subcellular particle, we observed an increase in proteinase activity confirming rapid hydrolysis of substrates and the formation of similar bacterial clusters.

Microscale organization during the bloom at 144 hrs. A. AFM image, cells (circled red) embedded in a gel matrix; 
B.  Epifluorescence image of phytoplankton and bacteria cluster, Green: active cells marked by redox-sensor green, and Red: chlorophyll 

(Left) Proteinase activity of a microbial community when exposed to extracellular RuBisCO.  (Right) AFM image of microbial cluster of a community at 24 hrs.

Viral degradation by bacteria

Related to the investigation of the viral degradation by bacteria, the viral attachments to non-host bacteria was investigated by microscopy. We incubated two isolated viruses with four bacteria in artificial seawater and the attachments between them was quantified. The attachment was occurred in every combination of virus and bacteria and the rates were relatively different depending on the combinations. 

Representative image of viral attachments to non-host bacteria observed by epifluorescence microscopy after SYBR Green I staining.  Small dots are viruses and large ellipsoids are bacteria. Arrows indicate the attachments. (Virus: Vibrio phage SIO-2Bacteria: Bacteroidetes BBFL7).

Dinoflagellate Lysate Degradation

Marine bacteria have been shown to rapidly colonize and degrade phytoplankton detritus which plays a significant role in ocean carbon export. Here, we studied the the mechanisms of bacterial colonization and degradation of particulate organic matter, by means of observation of bacterial interactions with dead dinoflagellate (Pyrocystis fusiform) cells at the microscale.

Representative image of a marine bacterium (Vibrio sp. SWAT-3) covered with lysate particles from a dead dinoflagellate (L. polydrum)

Nanoscale Structure of Seawater

AFM micrographs of natural seawater show a variety of complex nanoscale structures that populate the microbial microenvironment and influence microbial behavior.  Microbial association with loose aggregates of particles, detritus and larger structures is frequently observed within seawater.
(Please contact Dr. Azam for addition information about AFM data)

Representative height image of seawater with particle aggregates designated.

AFM micrograph (height image) of marine microbes (blue circles) associated with colloidal particles and larger structures.

    Additional images of individual marine microbes (white arrows) associated with particle aggregates.

Microbes are frequently observed with attached particles (white arrows) on their surface.

An example of microbes associated with larger structures (discarded larvacean house), which is partially covered with colloidal particles.

AFM images of an individual microbe found within diatom lysate material.

Bacterioplankton drawdown of coral mass-spawned organic matter

Article link:

Each year in the Caribbean, coral of the genus Orbicella engage in highly predictable mass-spawning reproductive events. Here, we joined a team from PennState University ( to investigate microbial response to a pulse of spawn derived organic matter using a combination of field and microcosm studies. We show that the total organic carbon (TOC) concentration was elevated to 515 µMC and that 68% of it degraded within just 66 hr. In collaboration with The University of Tokyo (, we also sequence bromodeoxyuridine labeled 16S-rRNA genes to determine the active microbial taxa responding to the event and provide evidence that these active taxa were primarily responsible for the measured TOC degradation. Furthermore, we used Fourier transform ion cyclotron mass spectrometry (FT-ICR-MS) in collaboration with the Alfred Wegener Institute ( to characterize the dissolved organic matter pool and show the presence of three unique molecular formulas to this mass-spawning event. 

Time-lapse imaging of microbial surfaces changes and structure dissolution

AFM time-lapse visualization of the dynamic surfaces of live Pseudoalteromonas sp. TW7 cells.  
Error mode images on the left and corresponding stiffness images on the right.

Time-lapse visualization of the microbial surface changes of an individual Alteromonas sp. ALTSIO cell.  

Height image on the left with processed image visualizing convex bumps on the right.

AFM time-lapse visualization of ALTSIO cells exposed to E. coli ribosomes in solution.

AFM visualization of dissolution of flagella (SWAT-3) on bare mica. 

Previous Grant


The grant to the Scripps Institution of Oceanography supports investigating 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.

 Atomic Force Microscope image of Synechoccocus cell associated with a heterotrophic marine bacterium  

Our overarching hypothesis is that the abundant cyanobacteria-bacteria associations display a range of fundamental adaptive strategies and underlying mechanisms and critically influence the oceanic biogeochemical dynamics and global climate

  1. *Bacteria-cyanobacteria associations are phylogenetically diverse

  1. * Bacteria-cyanobacteria associations involve nutrient exchange between partners

  1. *Bacteria-cyanobacteria associations involve structurally & biochemically specific interactions 

Past Project Data