Or: doing science, one milliliter at a time.
For sampling protists in our geothermal streams we use Sedgewick Rafter cell counters. The “Sedgewick” is a particular type of microscope slide that holds a volume of exactly 1 mL. It has a grid of 20x50mm which allows to identify and count the microorcanisms in the volume under observation. This is a sample of what we see (more or less):
(picture taken from: http://www.flickr.com/photos/microagua/)
At first glance they all may look the same. Then one notices that some are bigger, some smaller, some has a proboscis or a snout, some are elongated, some are funnel-shaped.
Then you begin giving names. Some are easy: Stentor is huge and looks like a funnel, Metopus has a twisted nose and swims spinning. It has a very long and active proboscis? It’s Lacrymaria. Hypotrichs can be trickier: easy to spot as hypotrichs, but a more specific taxonomy would require keeping them still and higher magnifications, while Sedgewicks only allow magnifications up to 100x. Let alone holotrichs, which sometimes look like featureless hairy spheres. It’s even worse with the smaller bugs, the ones below 30 microns. You can only look at the general shape and behaviour, but many times you have to give up and just call them “Small ciliates, unknown”.
It is like being in a wood, trying to identify birds without the use of traps or mist-nets. One can spot the large ones, giving them names, but then there is a profusion of small brown birds that just fly away inbetween the trees, leaving just the time to see something among the shadows and say “oh, there was a bird”. Jack, a friend of mine and passionate birdwatcher, would probably say that I am just not good enough.
Going back to protists: it can be very frustrating, but it is also exciting to see such a high degree of biodiversity in such small volumes, at a spatial scale that is so different from ours and only now I am beginning to understand (that means, I am finally grasping how narrow my understanding is).
Now, after weeks of microscope work, frustration starts prevailing over excitement and doubts grow. Is our taxonomical resolution enough to unravel biodiversity patterns? Is it sensible to characterize the microbial diversity of a stream by studying only few milliliters of its sand and water, or it is just a romantic attempt disguised as science?
Hopefully, a closer look to the data we are collecting will succeed in clearing my doubts and answering some questions.