More on DNA from Ocean Bacteria

A while back I wrote this post on efforts to sequence the DNA of sea going bacteria. Research in that area has continued and new findings have recently been reported. They are quite fascinating – so much so I am putting off several other posts (one of these days I’ll get that post on the evolution of voltage gated sodium channels written) so I can blog about it (since I have been blogging about bacteria a lot I have been getting this strange compulsion to change the name of my blog to Aetiology Jr. – nah!)
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Each cubic centimeter of seawater is inhabited by thousands of different types of bacteria. In the post I linked to above I talked about attempts to sequence the DNA of species from different depths. The new research took a different approach. What researchers tried to do was sequence the combined DNA of all the microbes in a single sample of seawater (in order to get their samples the researchers had to process over 160 gallons of seawater per sample in order to obtain enough DNA). From Science Daily:

One of the researchers’ overall goals was to determine how the microbes near the surface are different from those that live thousands of meters down. Not surprisingly, in samples from the sunlit waters within about 100 meters of the surface, the researchers found a lot of microbial DNA sequences that were associated with photosynthesis. This means many microbes in these waters were probably using sunlight as a source of energy. Surface samples also contained microbial DNA that was associated with movement and propulsion. This suggests that movement is important for these microbes, perhaps helping them follow chemical gradients or move from food particle to food particle.
In contrast, DNA from microbes in deeper waters suggests many survive by attaching to and breaking down particles of organic material. Such particles continually sink down from the surface waters into the deep sea, providing food for many organisms in the form of ‘marine snow.’

The most interesting result was the finding of large amounts of viral DNA in the samples. Researchers think this viral DNA came from infected bacteria since they excluded free living viruses from their sample. Most of the viral DNA came from near surface waters.
Interesting stuff…

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4 Responses

  1. An ignorant question: How do they exclude living viruses from their sample? The only thing I could think of was that if viruses are smaller than bacteria they could use a filter to let them through and keep the bacteria, but I have no idea if that is right.

  2. The article doesn’t say…

  3. I’m pretty sure I remember that they use filters. I think the process goes something like this: filter out everything that’s too large, filter out everything that’s too small, DNA isolation, DNA sequencing.

  4. RPM is right. They expected that their filters would exclude most virus sized particles. From the science paper:

    Viruses are ubiquitous and abundant components of marine plankton, and influence lateral gene transfer, genetic diversity, and bacterial mortality in the water column (37�40). The large number of viral DNA sequences in our dataset was unexpected (Fig. 5; fig. S12), because we expected planktonic viruses to pass through our collection filters. Previous studies using a similar approach found only minimal contributions from viral sources (19, 40).

    Another thing I found interesting is that in the deeper samples one of the most abundant sequence types found were transposases.

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