Seeing the unseen, how do we look at coral-associated microbes?

The first and most important issue is that microbes are everywhere in the ocean.  Like a doctor during surgery, we need to keep any collection equipment very clean so that we are not adding foreign microbes to the coral.  Deep-sea coral samples can be collected by a trawl, dredge, or by a submersible or remotely operated vehicle (ROV).  In many of these cases, multiple corals may be combined in a single container.  This is not acceptable for microbiological studies since one coral’s microbial community could contaminate another’s when they touch.  Similarly, contact with sand or clay from the bottom, other animals, or even seawater from a different depth, could contaminate the coral samples.  The cold-water corals must also be protected against changes in temperature between the sea floor and the surface, since temperature changes could cause a shift in the coral-associated microbial community.  Ideally, coral samples for microbiology should be collected in an insulated container that has separate, sealed compartments for each individual sample.

Classical microbiology is based on the ability to grow microbes on nutrient agar (a semi-solid gel of microbial food).  Growing microbes means you can take them back to the laboratory and study them – identify them based on certain genes, and characterise them by testing their metabolic and biochemical capabilities.  This method is relatively easy and inexpensive.  The downside is that microbes can be picky eaters, so each type of nutrient agar (and there are hundreds) will only grow a small percentage of the microbes that are on the coral.  Some microbes are so finicky, we can’t figure out how to get them to grow at all yet.

The other way we can study microbes (especially the ones that don’t like to grow on agar) is to extract their DNA directly from the coral and then use molecular (genetic) techniques to identify them.  This can be done using targeted fluorescent probes to count certain microbial groups, or by creating libraries of sequences from the coral-associated microbes and then comparing those sequences to a database of sequences from previously described (“known”) microbes.