Dr Natrah's Attachment at Scripps Institution of Oceanography: Week 4

12 MAY 2014
Week 4: 28 April – 2 May 2014
Attachment in the lab of Marine Microbial Ecology under Prof. Dr Farooq Azam
Scripps Institution of Oceanography, San Diego, United States Of America

You definitely can learn a lot of things from a microscope!
Last week, the discussion focused on a microscope producing two-dimensional image (2D). This week, we’ll look at microscopes which can provide three-dimensional images (3D). In Azam’s lab, the Confocal Scanning Laser Microscopy (CSLM) and Atomic Force Microscopy (AFM) are among the examples.
The Confocal Scanning Laser Microscopy (CSLM) is a system where the fluorescent microscope is coupled with laser light beam. Here, different cell sections can be studied through the scanning of different layers with different fluorescence range. The images are then compiled by the microscope to create a 3-D image of the samples.

Among the advantages of using CSLM are 1) the system is non-invasive (will not disrupt the cells); 2) users can study the microscopic world in 3D; 3) clearer image than the conventional fluorescence microscopy and 4) capable of measuring quantitative data such as thickness, area and the volume of cellular structures. In the field of aquatic microbial ecology, the microscope is useful to measure thick samples or aggregates e.g., biofilm enabling the observation of different cells in various layers. These types of microscopes are also used to study specific strains inside animal hosts (e.g., fish) and the structure of cells (e.g., vesicle production in bacterium).

Similar to CLSM, the Atomic Force Microscopy (AFM) also provides 3-D image without the need for sample fixation. The machine enables physicochemical interrogation of living specimens even up to a scale of nanometers. It also provides information on the local properties of the sample such as topography, viscoelasticity, electrical & magnetic forces & chemical bonding.


In Azam’s lab, the microscope has been used to show symbiotic interactions between the pelagic marine bacteria by looking at the surface structure. It has been shown that certain bacteria are intimately associated through pili and gel production in the microenvironment. The researchers also coupled the study with the epifluorescence microscope to know the cell abundance1.

1. Malfatti and Azam (2009) Atomic force microscopy reveals microscale networks and possible symbioses among pelagic marine bacteria. Aquatic Microbial Ecology 58:1-14.


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