James has already homed in on one important part of the discovery: the preponderance and diversity of proteorhodopsins - microbial photopigments that are capable of capturing solar energy in a manner different from photosynthesis. As always, light-sensitive molecules are thought to be tightly connected to the evolution of circadian clocks so I expect to see some research on this in the near future.
The biggest challenge of this kind of research is how to take gobs of goo, i.e., the collective DNA from everything collected in the samples, and figure out which sequence belongs to whom. How many microbes have really been captured in the sample? How do those microbes look like? What can we say about their biochemistry, physiology and behavior? What can we say about their ecology and their evolutionary history? What counts as a 'species' in the asexual world of microbes?
The methods they use to try to start answering those questions are all genomic - other bloggers may be able to better understand and explain the details which involve various sequence alignments and comparisons to known microbial genomes.
What I'd like to see is a more ecological approach: sampling at different places, at different depths and at different times.
Many aquatic organisms, both unicellular and multicellular, are vertical migrants. They may swim up to the surface during the night and sink down to a greater depth during the day (or vice versa). Sampling at two or more different depths at noon and again at midnight and comparing the sequences can separate the genomes - those sequences that always appear together in the sample will belong to the same organism, those that sequester belong to different organisms.
Likewise, some organisms swim up to the surface only once a month during the full moon. Some never do and are always found only at greater depths. There is likely a seasonal change in the community compposition as well.
Of course, it is expected that different species will be found at different parts of different oceans, in rivers and estuaries, in lakes and streams, which can tell us something about the ecology of the organisms in each of these environments.
Finally, repeated sampling over a number of years at the same place, same depth and same time of day/lunar cycle/year will allow us to track the long terms effects of climate change on the aquatic communities.