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Wetlands and Aquatic Research Center - Florida
Cruise Log: 10/10/2008
A Laboratory Microbiologist Goes to Sea
So why, you may ask, did they send a laboratory and/or coastal environmental microbiologist to sea? Pretty simple, really; we're trying to understand everything we can about the environment around the deep water coral mounds in the Gulf of Mexico. Luckily for me, that includes the microbiology associated with the deep water coral Lophelia.
It's about time someone other than a microbiologist understood that microbes rule the world. That's not hyperbole (too much).
First, let's get a bit of a bacterial primer out of the way. Those of you familiar with bacteria; you may want to skip this bit.
Bacteria are tiny. Really tiny. If a human cell were the size of a computer keyboard, the bacteria would be about the size of the Q. Human cells keep their DNA packed in a membrane-bound nucleus, bacteria don't have a nucleus. Human cells have other internal structures, like the endoplasmic retuculum, mitochondria, and Golgi bodies. Bacteria don't have these structures. Basically, we're talking about tiny, fairly simple bags of life.
Nearly everyone is familiar with some of the bacteria that can cause diseases in humans. Bugs like Salmonella and E. coli (food poisoning), Staphylococcus (like MRSA, eek!) and others. But they are not the only bacteria out there. In fact, we couldn't survive without our host of bacteria. Our skin is normally covered with benign Staph, it helps crowd out other bugs that might make us sick. Our guts are full of E. coli and other bacteria that help us break down our food. Most of the time, bacteria are far more helpful than they are harmful, as long as they stay where they are supposed to be. We have somewhere around 10 times more bacterial cells in and on our bodies than we have human cells, and we couldn't live without them.
The environment is full of bacteria, too. They are the most successful type of organism on the planet. There are more bacteria in a small handful of soil than there are people on Earth. The bacteria around (and in) us are collectively far more metabolically diverse than any animal. They'll use just about any available source of energy or carbon. If all you have are some metal compounds and methane, then there are bacteria that can thrive on that.
Because of all that diversity of metabolisms, you can't really understand what is happening in an environment, with all its nutrient recycling and various energy sources and sinks, until you understand at least a little about the bacterial communities that are contributing to that environmental cycling.
That's what I'm here for.
We don't have the tools aboard to do a full microbial community characterization of the Lophelia while at sea. That would require some way to make sure the community didn't get changed by the decrease in pressure and the increase in temperature as it was hauled the 500 meters to the surface. We'd need a Kellogg sampler or something similar to kill and preserve the sample at depth and keep it from getting contaminated by the rest of the water so we could use the DNA once the sample is back in the lab. Ideally, this would be the preferred way to analyze the entire microbial community, but life (and research) is often about compromise.
Rather than DNA analysis of the entire community, we are targeting bacteria and fungi that we can culture, or grow, in the lab. There are some trade-offs to this method. On the one hand, the most we can hope for is about 1 to 10% of the bacterial community; most bacteria are resistant to culture. On the other hand, once we have some bacteria growing, we'll be able to characterize them much more fully than we could with DNA. The DNA sequence will tell us what the bacteria are related to, but not what they are capable of doing, nor how they contribute to the nutrient cycling and energy budget of the environment. Plus, this characterization is the only way to fully describe a new species.
Basically, we're going old-school. When a piece of Lophelia is sampled and brought up by the ROV, I give it a thorough rinse with sterile saline to wash off anything it may have picked up during the ascent. Then, using flame-sterilized tools, I break off a single polyp, place it in a sterile aluminum dish and using a very specialized tool (pictured, being flame sterilized) I smash the heck out of it. I add a little sterile saline so it can be pipetted, then I put a small amount onto a petri dish with nutrient agar. Since the water around the coral is fairly cold, I incubate the dishes in the fridge, to keep the bacteria close to their natural growing temperature.
In a few days, fingers crossed, I'll have lots of bacterial colonies on the five different kinds of agar that I brought. I'll spend the next several months figuring out what kind of bacteria they are, and more interestingly, what they can do and how they fit into the deep water coral environment.
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