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Hunting the Sediment’s Smallest Inhabitants

posted Jul 4, 2012, 3:01 PM by Shannon Casey   [ updated Jul 6, 2012, 8:31 AM ]
Happy Fourth of July from the Melville! So far, we have been in sight of land for the whole cruise, and we are hoping to catch some of the fireworks tonight along the coast. We have even been able to see our home labs at Scripps Institution of Oceanography, and Monday morning brought us directly west of the Scripps Pier for the Oxygen Minimum Zone (OMZ) Team’s first sediment sampling site.

Working with me on sediment processing are two members of my lab at Scripps, graduate student Natalie Millan and visiting undergraduate student Laura Ioca. The three of us have been working to study the bacteria that live in OMZ sediments. Marine sediments support an enormous number of bacteria, on average about 10^9 cells per cubic centimeter. Our work focuses on a large group of bacteria called actinomycetes, which all over the world are almost always found as a part of this sizable sediment bacterial community.

Photo: Kelley Gallagher retrieves a fresh sediment core from the multicorer,
which has just returned from the seafloor.

Photo: Mudcores are taking off the multicorer and immediately stored in a freezer.
Pictured here,  Laura Ioca and Cheif Scientist Christina Frider are taking record of the samples.

Our first job when we collect a sediment core is to split it up in to sections. The top section of a core and the bottom section of a core are likely to be very different environments. The availability of oxygen and nutrients, for example, will usually vary widely, even between very thin layers of the core. By splitting into sections, we can then determine where actinomycetes are found and where they are most active. Splitting the cores, as it turns out, is a challenging and messy business, and it took all three of us working together to get a single core ready to be brought into the lab. Getting to work with the mud, though, seems to me to be the most fun job on the ship, and I don’t think I’m alone in this opinion.

Photo: Kelley and fellow Scripps graduate student Natalie Millan split a
freshly collected mud core into sections for processing in the lab.

There are two ways that we use to look for actinomycetes in a sediment sample. The first is by looking at DNA sequences found in sediments. To do this we purify all of the DNA found in a sediment sample, leaving us with sequences from all of the bacteria found in that sample. By searching this large amount of DNA for sequences specific to actinomycetes, we can learn in which sediment types they are found. One of the most interesting aspects of the actinomycetes is that they dedicate a large amount of energy to the production of small complex molecules, and for the most part the function of these molecules is unknown. We can also search the DNA mixture for genes responsible for making these molecules, so that we learn in what environments they are important.

The second way that we study sediment actinomycetes is by trying to grow them from the samples we collect. We spread a small amount of the sediment, usually less than a gram, on nutrient-filled agar Petri plates. Giving them an unlimited and easy food source allows them to grow to such a density that we can see them, in small blobs called colonies. The resulting plates are usually fascinating to look at, sediment bacteria colonies don’t look like the bland pictures of E. coli you are used to seeing. We sometimes see colonies producing incredible pigments – orange, purple, green, and sometimes even inky black. They also can make some strange shapes. Colonies of a bacterial group called Bacillus grow in threadlike spirals. Some bacteria can move around on a Petri plate in a behavior called swarming. The ones we are looking for, actinomycetes, are leathery and sometimes colorful. After some time, they produce spores that appear as a powdery substance on top of the colonies.

Photo: Kelley and Natalie Millan prepare Petri plates for growing mud cultures.

Once we find some actinomycetes, we move them to a new Petri plate so that they are a pure culture. We can then use these new isolates in lab-based experiments. The small molecules that actinomycetes produce are of such unusual and diverse structures that they can sometimes be developed into new pharmaceuticals. Looking in under-sampled marine environments, like the OMZ, is a good way to find new types of actinomycetes that make some molecules that haven’t been isolated before. Any unusual isolates we find can be screened for production of new anti-cancer agents or antibiotics. So the samples we collect this trip will be used to both learn about the ecology of this important group of bacteria and bring us some new isolates that could produce promising pharmaceuticals. So far we’ve gotten some promising samples to help us towards this goal, and we are looking forward to more collecting the rest of this week.

--Kelley Gallagher, Scripps Graduate Student