A new domain?

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The tree of life, the ingenious device used to visualize the evolution of the various taxa, is constantly undergoing changes and revisions. With new improvements in gene sequencing, coupled with the discovery of new life forms, we are gaining an ever-expanding view into the history of life.

Now, researchers from the University of California are proposing that a new domain be established in light of recent findings. It’s not unheard of that new domains be established — the Archaea were only deemed a domain in the 1970s, bringing the current system to three domains, the remaining two being Bacteria and Eukarya.

The findings consist of new marine life forms that were discovered during the Global Ocean Sampling Expedition, which began in 2003 off the coast of Halifax. Using a sailing yacht dubbed “The Sorcerer II,” a team of scientists employed a method called “whole environment shotgun genomics” to gain a comprehensive understanding of the genetic base of entire marine ecosystems.

The yacht circumnavigated the globe and took “shotgun sequence[s] of microbial samples from approximately 150 open-ocean and coastal sites, and deep sequencing of 16S and 18S rRNA genes were performed to investigate the distribution of organisms and genomic variation across ecosystems.” In layman’s terms, the team collected countless microorganisms and sequenced their ribosomal genes to look for differences.

The project was launched after 148 new phylotypes possessing more than 1.2 million genes were found in the Sargasso Sea, also in 2003. Both projects were organized by the J. Craig Venter Institute. The projects were the debut of the previously mentioned whole-environment genomics, or metagenomics, which is an extension of shotgun genome sequencing.

The so-called “shotgun” approach to gene mapping was perfected during the human genome project. It developed from “hierarchical shotgun sequencing” in which genomic DNA is cut into small pieces and replicated inside of bacteria. The pieces are then isolated from the bacteria and sequenced. Once the fragments have been sequenced, a computer looks for overlapping regions and reassembles the genome based on the results.

According to department of biology at Davidson College, the shotgun method employed by the whole ecosystem genomics method skips placing the DNA into bacteria, and therefore is much quicker.

Whole environment genomics is now building on this method and applying it to a larger scope. This field of gene analysis is called “metagenomics” and it “involves studying the genetic makeup of many microbes in an environment simultaneously, and makes accessible the many types of microbes that cannot be grown in the laboratory and therefore cannot be studied using the central tool of classical microbiology.”

The key to the findings lie in the fact that these organisms could not have been grown successfully in a laboratory setting. NewScientist.com explains that the cells brought back from the expedition are essentially “biological dark matter” as “the vast majority of these cells species — 99 per cent of them is a reasonable bet — refuse to be cultured.” In traditional gene sequencing methods, the scientists must culture the cells for analysis before being able to place them on the tree of life.

Researchers Jonathan Eisen and Venter from the J. Craig Venture Institute in Maryland “found that some sequences belonging to two superfamilies of genes — recA and rpoB — were unlike any seen before.” They hypothesizes that these life forms are only distantly related to the domains we know now and branched off early on in life’s evolutionary history.

Though their work is regarded as thorough and well done, other researchers are more cautious and suggest alternate explanations for the strange genes. Radhey Gupta at McMaster University in Hamilton, Ontario believes that the organisms are not ancient, distant relatives but rather that they evolved rapidly when isolated in their habitat, writes NewScientist.com. Gupta also cautions that “there is still debate [over] how to clearly distinguish the three proposed domains of life, and how they are interrelated,” and that “the suggestion [of] a fourth domain will only add to the confusion.”

Whatever the case, as gene research methods improve, we are getting an ever more accurate view of the tree of life. With the ability to sequence whole ecosystems, we may be able to more accurately place how life arose. First though, we need to realize that scientific groupings — taxa — must be able to change as quickly as new information arises, or they risk being relics.