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."

Comments

Obviously...

[NecroPuppy]

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

I looked at two phyl. trees presented there

[mapkinase]

.. and I am underwhelmed.

First figure does not identify (at cursory look) domains and the second figure shows "unknown" samples mixed up between bacteria and killer plasmids or between different branches of eukaryota.

Frankly, I spent only a minute looking at this paper, so anybody who went deeper please share

Re:I looked at two phyl. trees presented there

[Anonymous Coward]

I too am underwhelmed, and irritated to have read the article. At first it sounded good, but this is clearly just some washed up douche looking for grant money claiming a new form of life without comparing sequences to any known virii (except the ones that actually matched it, which he dismisses), has made past mistakes in this exact line of research both business-wise and in the more recent time (which he cited, i don't know why) thinking this mystery new life he's searching for was something he later found to be bacteria, and trying really hard to not lie, thus avoiding later legal recourse for misappropriated grant money.

Re:I looked at two phyl. trees presented there

[De_Boswachter]

Not underwhelmed here. It really is just a hint, as the title says. I spent a few minutes looking at it. At first sight, they could have been new sequences representing life forms from either of the three existing domains, or viruses. And, indeed, in the discussion section, they are careful with their explanations. The last two of four are deemed the most plausible.

"[...] A third possibility is that the genes from novel subfamilies come from novel heretofore uncharacterized viruses. Given that the known viral world represents but a small fraction of the total extant diversity, and given some of the unexpected discoveries coming from viral genomics recently, this is entirely possible. For example, viruses have been characterized with markedly larger genomes that contain not only more genes, but genes previously found only in cellular organisms. In some cases, the viral forms of these genes appear to be phylogenetically novel compared to those in cellular organisms.

[Explanation 4:] It has not escaped our notice that the characteristics of these novel sequences are consistent with the possibility that they come from a new (i.e., fourth) major branch of cellular organisms on the tree of life. That is, their phylogenetic novelty could indicate phylogenetic novelty of the organisms from which they come. Clearly, confirmation or refutation of this possibility requires follow-up studies such as determining what is the source of these novel, deeply branching sequences (e.g., cellular organisms or viruses). Then, depending on the answers obtained, more targeted metagenomics or single-cell studies may help determine whether the novelty extends to all genes in the genome or is just seen for a few gene families."

Most likely, these new sequences are from viruses, but I can't suppress hoping that there really are more domains out there.

DNA is limiting

[mbone]

The Venter approach is something akin to taking a library, putting the whole thing through a paper shredder, and trying to figure out how many languages there were in the library from a statistical analysis of the groupings of the letters on each piece of paper. It is marvelous, but it has its limits.

If there were true aliens among us (microscopic organisms that did not use DNA for genetics), the Venter approach would not see them. I do not know of a good way to luck for such creatures, but I wish someone would figure one out, and apply it to something like Venter's samples.

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.

More than one domain?

[MrEricSir]

I mean there's life.com, life.net, life.org, life.co.uk...

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/

Re:Fake?

[Lazareth]

I've learned to, very effectively, bring my eyes out of focus before clicking a link from an untrusted source. The result is a heavily lessened impact should the link be, ah, "visually malicious" while I can still recognize patterns without getting the details burned onto my retina.

It is amazing how one can learn to defend themselves mentally while browsing the internet.

Re:"Environmental samples"?

[mapkinase]

Basically it's sequencing ocean instead of organism (the latter is more complicated and thus does not have a future). Or human gut. Or soil.

When identifying organism sequence analysis relies on many markers in many genes. Here it's not possible, because you have just separated genes from many organisms.

Re:you meen the Ancients?

[bmo]

No, I think he means the Old Ones.

And they will return some day.

Web version:
http://www.fredvanlente.com/cthulhutract/pages/index.html

PDF version:
http://www.fredvanlente.com/downloads/WhyWeHere.pdf

Your only hope is suicide or to be eaten first.

ph'nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn!

--
BMO - The button says submit and I have the choice now, but when the Old Ones appear, I may lose that choice.

Re:Bigfoot

[flyingsquid]

The four domains of life are as follows: eukaryotes, bacteria, archaea, William Shatner.

Viral DNA?

[Guppy]

http://phylogenomics.blogspot.com/2011/03/story-behind-story-of-my-new-plosone.html

They may be from novel viruses. The 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.

I'm going to go with this last opinion as well, it's probably from some virus, which would account for the sequence wackiness. I'm wondering if they can construct some speculative primers and (without isolating the organism) start sequencing outwards from these novel sequences, maybe get enough to tell if it's a virus or a novel organism.

Re:Viral DNA?

[Sulphur]

http://phylogenomics.blogspot.com/2011/03/story-behind-story-of-my-new-plosone.html

They may be from novel viruses. The 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.

I'm going to go with this last opinion as well, it's probably from some virus, which would account for the sequence wackiness. I'm wondering if they can construct some speculative primers and (without isolating the organism) start sequencing outwards from these novel sequences, maybe get enough to tell if it's a virus or a novel organism.

They nearly destroyed Skynet last time, but some of the Novell viruses survived.

Re:you meen the Ancients?

[buchner.johannes]

No, I think he means the Old Ones.

And they will return some day.

[...]

Your only hope is suicide or to be eaten first.

Well hopefully not tomorrow, I have a dentist's appointment.

Who'd a thunk it?

[Jane Q. Public]

"... the authors found sequences not yet seen in any cultured organism."

Hillbilly DNA. Will wonders never cease?

fourth domain of life

[slick7]

The fourth domain of life must be the politicians, they appear to be intelligent but are mostly flat-liners.

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 (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.

Re:Dnamaged ?

[Altrag]

Absolutely. However, there's a few caveats:

- Each "damage" will only affect one specimen for any given damage pattern. The chance that two individuals of species get genetically damaged in exactly the same way is pretty slim.

- If the "damage" is detrimental to the species, the genetic change isn't likely to last long on evolutionary time scales.

- Each "damage" will only affect a small number of genes -- likely only one or two. Geneticists create families of species by comparing the various genetic similarities. So if you have two very simple viruses that have 9 of their 10 genes in common, there's a good chance that they're fairly closely related.

- And even that one gene is probably only slightly modified (a C replaced with a T in the DNA or something along those lines), so there's an even deeper comparative level for genetic matching.

The probability of a catastrophic genetic change to the extent that we couldn't recognize its origin still producing a viable creature is so unbelievably small as to be ignored -- at best, it would get lost in the midst of basic human error.

Of course its theoretically possible. In the same sense that its theoretically possible for all of the atoms in your body to simultaneously quantum tunnel in exactly the right way such that you pass through the nearest wall in-tact.

I love Plos One...

[wherrera]

Plos One, the New Internet Age's online quicker-to-publish-than-verify journal.

Its record: 10% genuine breakthroughs, 50% hype, and 40% bad data. (Caveat: the previous sentence may be bad data.)

Your call on this one.

We can't culture most organisms

[mlush]

Take a soil or a skin sample we don't know the correct conditions to grow >%90 of the organisms in that sample you can lob them in jar of nutrient broth but some simply won't grow while others will out-compete everything. Saying found sequences not yet seen in any cultured organism is a bit like saying found paving slabs not seen under any streetlight.

Re:So...

[camperdave]

...they discovered The Jersey Shore?

No... They said cultured organism.