DNA Analysis Hints At a Fourth Domain of Life

ecesar writes "The Economist is reporting on a recent paper published in the Public Library of Science, which suggests there might be at least one other, previously hidden, domain of life (besides eukaryotes, bacteria and archaea). Using DNA sequence data generated directly from environmental samples, the authors found sequences not yet seen in any cultured organism."

Obviously...

[NecroPuppy]

It's the seeds of life left by the Great Old Ones.

More details from an author

[2br02b]

One of the paper's authors has posted more details on his blog here http://phylogenomics.blogspot.com/2011/03/story-behind-story-of-my-new-plosone.html

We do not have a conclusive explanation for the origin of these sequences. They may be from novel viruses. They may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses. But we just don't know.

Carl Zimmer has also written on this

[Ranger]

for a lay audience. And did a great write up. Glimpses of the Fourth Domain? http://blogs.discovermagazine.com/loom/2011/03/18/glimpses-of-the-fourth-domain/ [discovermagazine.com]

Re:"Environmental samples"?

[reverseengineer]

Yes, for an environmental sample like this, the totality of the sample's DNA is isolated and sequenced together, producing a library of mostly partial genomes. The original Venter paper http://www.sciencemag.org/content/suppl/2004/04/01/1093857.DC1/Venter.SOM.pdf [sciencemag.org] (might require registration) about the expedition/ yacht cruise details the methods used to collect and extract the sample:

Sampling on the RV Weatherbird II was done as follows: Seawater (170 liters) from stations 11 and 13 was directly filtered through a 0.8m Supor membrane disc filter (Pall Life Sciences) followed in series by a 0.22m Supor membrane disc filter (Pall Life Sciences). The sample from station 3 was pumped into a 250 L carboy prior to being filtered through the impact filters. The length of time from collection of the sample until the end of the filtration step was approximately one hour. Filters were placed in 5ml of sucrose lysis buffer (20mM EDTA, 400mM NaCl, 0.75 M Sucrose, 50mM Tris-HCl, pH 9.0) and stored in liquid nitrogen on the Weatherbird then placed at -80C until DNA extractions were done.

Sample preparation. The impact filters were cut into quarters and placed in individual 50 ml conical tubes. TE buffer (5 ml, pH 8) containing 150 ug/ml lysozyme was added to each tube. The tubes were incubated at 37oC for 2 hours. SDS was added to 0.1% and the samples were then put through three freeze/thaw cycles. The lysate was then treated with Proteinase K (100 ug/mL) for one hour at 55oC followed by three aqueous phenol extractions and one extraction with phenol/chloroform. The supernatant was then precipitated with two volumes of 100% ethanol and the DNA pellet washed with 70% ethanol.

Which is all to say that a large amount of seawater was filtered through filters of appropriate pore size to catch microbes, the cells were broken open and the proteins were broken down, and the DNA was extracted with alcohol. The DNA extraction procedure is pretty standard for anything whose genes you'd like to sequence; more commonly, the sample would be made of cells from a single species or organism, like a human blood sample or a bacteria cell culture, but in this case, the sample is a mixture of all of the microbes in 175 liters of seawater.