Sequencing the oceans: deciphering life en masse with metagenomics

Image of a archaea named Ferroplasma acidiphilum

It’s a simple idea: provide bacterial cells with the right nutrients and temperature to mimic what they would experience in their native environment – perhaps your gut or respiratory tract, or perhaps the soil – and they will obligingly multiply and give you billions of themselves to pick and probe and experiment with. But this idea, that we can pluck a single bacterial cell from the environment and nurture and cajole it to divide into a visible waxy spot in a Petri dish, or a cloudy swarm in nutrient broth, has its limits.

The reality for microbiologists is far more intriguing, because we actually have no way of culturing a vast majority of the world’s micro-organisms. Microbes that inhabit the oceans are just such recalcitrant malcontents when it comes to traditional laboratory culturing techniques. With 90% of marine life by weight being microbial, the ocean, it seems, is a veritable lolly shop for an oceanic microbiologist – only most of these invisible organisms remain frustratingly elusive to study in the lab.

A recent article in Science, however, proves that just because we can’t grow ‘em, doesn’t mean we can’t know ‘em. Genomics has stepped in to do the heavy lifting that incubators and Petri dishes cannot.

The result? Meet Euryarchaeota: a tiny microbe that has never been cultured in the lab, but whose genome has now been deciphered. Euryarchaeota belongs to the archaea, a group of micro-organisms that were once lumped in with bacteria until scientists discovered their unique evolutionary history and put them in a group all of their own: neither prokaryote (as bacteria are), nor eukaryote (like most other things including plants, animals, fungi and some single-celled beasts, too).

The University of Washington scientists began by filtering through some 90 litres of surface seawater from Puget Sound near Seattle to obtain its microbial inhabitants. They then extracted the DNA from all of the cells and began sequencing. Nearly 60 billion chemical letters of genetic code (called bases) were read, in strands of just 50 bases in length. A mammoth computational task ensued, trying to link overlapping strands into larger sequencing chunks. This was no mean feat, considering that most genomes are sequenced from a pure sample of DNA from just one organism. For Vaughn Iverson and his colleagues, their starting material was a complex jumble of sequences from an unknown number of microbes.

Eventually sequences long enough to represent entire genomes emerged from the data, one of which was Euryarchaeota. And from Euryarchaeota’s genome, the researchers were able to infer quite a lot about its habits. For example, the presence of archaeal flagellar genes suggest that Euryarchaeota is probably motile, and propels itself through the water using a flagellum. The scientists also surmise that Euryarchaeota is a photo-heterotroph, using light for energy, and absorbing proteins, fatty acids and other organic compounds to meet their dietary carbon needs.

The importance of understanding our environmental microbiota cannot be understated. While only a few marine bacteria cause human disease – some Vibrio species can cause food poisoning and diarrhoea, for example – from an ecosystem perspective, they’re huge contributors to marine health and stasis. The ocean’s microbial populations are crucial for the biogeochemical cycling of elements such as carbon between the oceans and the atmosphere. How much these microbes are resilient to the effects of climate change, and whether they will enhance or alleviate human influences on atmospheric and oceanic composition is not known. Nor is the role they play in the vast ecosystems that they are members of.

As Iverson and colleagues have now shown, metagenomics may be a clever way of unveiling the mysteries of microbial ecosystems – from the seas and elsewhere – without ever having to accommodate the finicky needs of their diverse masses in the lab.

Citation:

Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales R, Armbrust EV. 2012. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science, 335: 587–590.  [DOI: 10.1126/science.1212665]

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