Diffuse flow vent with microbial mat (white)
Metagenomics is a powerful set of research tools, as well as a field of study in its own right. The purpose of genomics is to determine the DNA sequence of an organism and deduce its functionality and potential interactions with its environment and neighbors based on that information. It follows, then, that metagenomics is concerned with the DNA sequences of a collection of organisms and the various functions and interactions of the group. In principle, metagenomic studies of the deep sea are no different from metagenomic studies of, say, soil or the human gut. We start with community DNA and perform the same sets of physical manipulations, use the same types of BLAST algorithms, and similar predictive models. But in practice, obtaining the DNA from the deep sea in order to do these “mundane” analyses is a curious challenge.
Deep sea vehicles like Alvin have been essential in collecting organisms from deep sea hydrothermal vents. Since bacteria and archaea form the base of the food web at vent systems, most of the higher organisms maintain intimate relationships with these microbes. For example, the giant tube worm Riftia creates compartments in its body known as symbiosomes in which chemosynthetic bacteria coexist with the worm, providing it with nutrients for life. Many of the vent invertibrates like shrimp or Alvinella worms are coated with bacteria. These organisms provide a substrate on which the bacteria grow, and then feed upon these very bacteria. When such organisms are collected, the specialized microbes can be harvested from their bodies for metagenomic analysis. In addition to these organism associated microbes, Alvin may also collect small pieces of vent material or microbial mats.
TEM images of vent microbes collected using the LVWS. A. Viruses (T = tailed viruses, likely bacteriophages), scale bar = 200 nm; B. bacterium and viruses (B = bacterium), scale bar = 500 nm.
Vent macroinvertibrates: shrimp, mussels (upper right), and tubeworms (lower left) have developed intimate relationships with chemosynthetic bacteria. Collecting these organisms enables us to obtain unique communities of associated microbes.
But if you want to get vent microbes in bulk, particularly viruses, there’s no easy way: you’re just going to have to design a contraption to do it. This requires the brain of an engineer, the patience of a saint, and the heart of a gambler – because like any oceanographic endeavor, once your equipment goes over the side, there’s always the possibility that it’s the last time you’ll see it. This actually happened in 2003 with a piece of equipment (see LVWS) designed to sample viruses from diffuse flow hydrothermal vents
In 2006, a new device designed to collect microbes was deployed: we are calling the Holistic Microbial Sampler. This device consists of a sampling nozzle that can be placed close to diffuse-flow vents, a pump to draw water, several filters, and bags for containing the sampled water. As the water is pumped through the series of filters, microbes of various sizes are trapped and separated. The final filter in the series is a tangential flow filter (TFF), which is used to concentrate viruses from the vent water. When the sampler is brought back aboard, the microbes (including bacteria, archaea, and viruses) can be retrieved, their DNA extracted and sequenced, and any suite of analyses performed. The Holistic Microbial Sampler will be deployed again in October, 2007 – wish us luck!
Holistic Microbial Sampler. The sampling port is deployed by Alvin at a diffuse flow vent. Water is pumped through a series of filers, terminating in a tangential flow filter (TFF) which concentrates viruses from >200 liters of vent water.)