Oceanic microorganisms

2007-03-22

in Daily updates, Science

St. Cross College chapel

One of the most interesting points repeatedly discussed in Bill Bryson’s A Short History of Nearly Everything is the astonishing variety of microbial life that exists on earth. Regardless of how you arrange your taxonomy, there is far more variety in single-celled life than in the more familiar multicellular variety. What’s more, it seems that single-celled creatures may be more diverse in the ways they carry out essential biological tasks like energy collection, movement, and communication.

One of the more interesting bits of research being done right now is the work of Craig Venter through the Global Ocean Sampling Expedition. Using samples taken from seawater from around the world and ‘scattershot’ techniques of genetic sequencing, some new information about that variety has been uncovered. This one program has tripled the number of genes that have been sequenced by humanity (from three to nine million). For instance, the project discovered a great deal about a class of messenger molecules called kinases. Previously, they were believed to consist of a single family of proteins, used by plants and animals. Now, nineteen new families have been discovered, all in bacteria.

In every age, there is a certain temptation to think we have most of the basic knowledge about how the world works mapped out. Projects like this help to reveal just how much there is left to come to grips with.

PS. Those curious about some of the ongoing debates in biology should have a look at two Wikipedia entries: Kingdom and Taxonomy. Some of that Kingdom-Phylum-Class-Order-Family-Genus-Species stuff we all learned in high school is coming under challenge, at the same time as there is a big schism between those seeking to categorize organisms by similarity in structure and those intent to do so on the basis of tracking genetic progressions.

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{ 8 comments… read them below or add one }

Hilary March 22, 2007 at 6:53 pm

King Phillip Came Over For Great Sex.

Oh Mrs Martin.

Milan March 22, 2007 at 6:55 pm

Hilary,

I remember that mnemonic, though I had my own version.

Anonymous March 23, 2007 at 5:23 pm

Unrelated to the above, but this new classification of drugs may interest you. It is related to biochem, at least.

R.K. March 23, 2007 at 4:16 pm

It seems to make sense that there should be more variety among smaller creatures. With fewer interconnected systems and shorter lifetimes, it seems they should be able to develop into new species more quickly.

AR71 March 23, 2007 at 11:58 pm

Since when was anything we learned in high school accurate?

Remember stoichiometry?

Milan September 4, 2007 at 7:25 pm

I did end up getting Planet Earth.

. December 19, 2007 at 4:04 pm

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

Shibu Yooseph of the J. Craig Venter Institute in Rockville, Maryland, and his colleagues have revealed more of the oceans’ genetic diversity than has ever previously been seen.

Sea-water samples collected by Venter’s yacht, Sorcerer II, on a trip around the world (route pictured above) contained gene fragments predicted to represent more than six million proteins. In March, when the work was published, that was enough to almost double the number of proteins listed in online databases. The data set included new members of nearly all known protein families from bacteria and archaea, and a large number of viral genes, suggesting viral diversity has to date been undersampled.

. December 19, 2007 at 4:05 pm

Author Summary

The rapidly emerging field of metagenomics seeks to examine the genomic content of communities of organisms to understand their roles and interactions in an ecosystem. Given the wide-ranging roles microbes play in many ecosystems, metagenomics studies of microbial communities will reveal insights into protein families and their evolution. Because most microbes will not grow in the laboratory using current cultivation techniques, scientists have turned to cultivation-independent techniques to study microbial diversity. One such technique—shotgun sequencing—allows random sampling of DNA sequences to examine the genomic material present in a microbial community. We used shotgun sequencing to examine microbial communities in water samples collected by the Sorcerer II Global Ocean Sampling (GOS) expedition. Our analysis predicted more than six million proteins in the GOS data—nearly twice the number of proteins present in current databases. These predictions add tremendous diversity to known protein families and cover nearly all known prokaryotic protein families. Some of the predicted proteins had no similarity to any currently known proteins and therefore represent new families. A higher than expected fraction of these novel families is predicted to be of viral origin. We also found that several protein domains that were previously thought to be kingdom specific have GOS examples in other kingdoms. Our analysis opens the door for a multitude of follow-up protein family analyses and indicates that we are a long way from sampling all the protein families that exist in nature.

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