Study tracing ancestor microorganisms suggests life started in a hydrothermal environment

July 26, 2016 by Jeff Errington, The Conversation
Grand Prismatic Spring and Midway Geyser Basin from above. Credit: Brocken Inaglory/wikimedia, CC BY-SA

It's one of the greatest mysteries of modern science: how did life begin exactly? While most scientists believe that all lifeforms evolved from a common, primitive ancestor microorganism, the details are blurry. What kinds of genes did this lifeform carry and where did it live? A new study, published in Nature Microbiology, now sheds some light on this early organism and the environment it evolved in.

Experimental scientists interested in the origins of generally tackle the problem in two distinct ways. One is a bottom-up approach in which they try to imagine how early life might have emerged and then try to recreate the key steps in the laboratory. The alternative, a top-down approach, is to analyse or strip down modern cells to simplify them and deduce how the key stages in the evolution of complexity might have taken place.

Informaticians interested in this problem exploit the huge amounts of data emerging from the revolution in DNA sequencing. This has resulted in a sea of information about the genomes of organisms – from bacteria to humans. Hidden in this should be the echoes of DNA sequences from primitive cells – the first cells on the planet to use the modern genetic code – passed on through billions of generations.

The "last universal " is a hypothetical very early single cell from which all life on Earth descended. The relationship between this ancestor and modern organisms is often visualised in the form of evolutionary trees, of which the most famous early examples were those by Charles Darwin.

A speculatively rooted tree for rRNA genes, showing the three life domains Bacteria, Archaea, and Eucaryota, and linking the three branches of living organisms to the last universal common ancestor (the black trunk at the bottom of the tree). Note that the most modern models now place the origin of the eukaryotes within the archaeal lineage. Credit: wikimedia, CC BY-SA

The advent of DNA sequencing provided a wonderful, highly quantitative measure of genetic relatedness that transcended the whole of biology. The same four-base code of A, C, G and T is used by virtually all organisms on the planet. So in principle, it can be used to construct evolutionary trees for the whole of life. We know that certain , such as the one encoding a small RNA subunit of the ribosome (the protein synthesisers of a cell), existed at the dawn of cellular life on Earth and seem to have been inherited by all subsequent forms of life. Over four billion years, copies of this particular gene – 16S rRNA – have gradually changed by random mutation in the separate lineages that have led to different forms of life. This means each has a characteristic sequence that is similar in recently diverged organisms but increasingly different in lineages that diverged earlier in evolution.

The first analyses of these "universal" DNA sequences about 30 years ago led to dramatic changes in our appreciation of the diversity of life on Earth, and especially the staggering degree of diversity in with no nucleus (the prokaryotes). It also highlighted the existence of a huge new "domain" of prokarytic life – now called the archaea.

Attempts to develop truly universal trees that would define how all modern cells descended from this last universal ancestor have been thwarted by a number of technical issues. One problem lies in the sheer number of groups that have separated from each other since life first began. What's more, bacteria can also exchange genes with each other, which makes it harder to identify how they've been passed down.

Scanning electron micrograph of Clostridium difficile bacteria from a stool sample. Credit: CDC/ Lois S. Wiggs/wikimedia

Hydrogen-powered organism?

The researchers behind the new study applied a sophisticated state-of-the-art method to organise some 6m sequenced prokaryotic genes into families. They then looked for patterns of similarity across all bacterial groups and found a small set of genes that were present in both archaea and bacteria. They could show that these genes were really likely to have been inherited directly from a common ancestor rather than by lateral exchange along the way.

The result is important because it identifies specific groups of bacteria (clostridia) and archaea (methanogens) that carry early versions of these genes, meaning they are very ancient and may be similar to the very earliest organisms that gave rise to the separate bacterial and archaeal lineages.

More importantly, the nature of the genes that are conserved tells an amazing story about the kind of environment in which this last common ancestor lived – including how it extracted energy to survive and thrive. The study suggests that the world inhabited by these organisms nearly four billion years ago was very different to the one we live in now. There was no available oxygen, but according to the genes, this common ancestor probably obtained energy from hydrogen gas, presumably made by geochemical activity in the Earth's crust. "Inert" gases including carbon dioxide and nitrogen would have provided the key building blocks for making all cellular structures. Iron was freely available, with no oxygen to turn it into insoluble rust, and so this element was used by many enzymes in the early cell. Some of the genes are believed to be involved in adaptation to high temperatures, which suggests these organisms evolved in a hydrothermal environment – perhaps equivalent to modern hydrothermal vents or hot springs, where some bacteria still thrive.

Sadly, without a time machine, there is no way to directly verify these results. Nevertheless, this information will now be of great interest, not least to those scientists wishing to use the information to inform their bottom-up experiments in recreating modern forms of primitive life. But it will not be easy, given the requirement for high temperature, nitrogen, carbon dioxide and explosive hydrogen gas.

Explore further: Genetic comparisons provide insight into the evolution of a crucial filament protein in animals, plants and bacteria

More information: Madeline C. Weiss et al. The physiology and habitat of the last universal common ancestor, Nature Microbiology (2016). DOI: 10.1038/nmicrobiol.2016.116

Related Stories

Recommended for you

A world of parasites

May 25, 2018

Alex Betts, Craig MacLean and Kayla King from the Department of Zoology, shed light on their recent research published in Science, which addressed the impact that parasite communities have on evolutionary change and diversity.

A better B1 building block

May 25, 2018

Humans aren't the only earth-bound organisms that need to take their vitamins. Thiamine – commonly known as vitamin B1 – is vital to the survival of most every living thing on earth. But the average bacterium or plant ...

Bumblebees confused by iridescent colors

May 25, 2018

Iridescence is a form of structural colour which uses regular repeating nanostructures to reflect light at slightly different angles, causing a colour-change effect.

Plant symbioses—fragile partnerships

May 25, 2018

All plants require an adequate supply of inorganic nutrients, such as fixed nitrogen (usually in the form of ammonia or nitrate), for growth. A special group of flowering plants thus depends on close symbiotic relationships ...

22 comments

Adjust slider to filter visible comments by rank

Display comments: newest first

Jeffhans1
4.8 / 5 (4) Jul 26, 2016
We have multiple moons in the solar system that have both water and active volcanism. They should have vents of their own that we can check for life to confirm if this is how most life forms and survives when oxygen is not a major component of the atmosphere.
Gigel
2.5 / 5 (2) Jul 26, 2016
Jupiter's moons are cold, at least at the surface. Below they may be warm enough to melt ice, but there may be no hydrothermal vent there.
gkam
2.2 / 5 (10) Jul 26, 2016
Enceladus has water, geysers, and hydrothermal activity as assessed by our own spacecraft, which sampled it while flying by.

Saturnian moons may yet hold the proof.
Gigel
1.3 / 5 (3) Jul 26, 2016
Enceladus's geysers may be just cryovolcanoes erupting at low temperatures. There is no proof of hydrothermal activity at temperatures comparable to the boiling point of water.
gkam
2.3 / 5 (9) Jul 26, 2016
Nope. They found the minerals from the activity in the plumes, if I remember right.

I'll look it up..
gkam
2.7 / 5 (11) Jul 26, 2016
Gigel
5 / 5 (5) Jul 26, 2016
If true, that would be interesting indeed. There may be life on Enceladus if conditions are favourable, even if it went there from Earth as a result of asteroid impact.
BongThePuffin
Jul 26, 2016
This comment has been removed by a moderator.
gkam
1.8 / 5 (8) Jul 26, 2016
Damn interesting, I have to admit.

All we need now is for an orbiter to video the huge tube worms blown into space.
torbjorn_b_g_larsson
4 / 5 (4) Jul 26, 2016
An intriguing result (which I need to study now) and an interesting debate.

Martin seems to have given up the old Bacteria/Archaea dichotomy, which he and Lane theorized as happening before a semipermeable cell membrane evolved. Having chemiosmosis means the membrane must have been semipermeable already (see below), not permeable lipids.

Martin remains oddly weak on the testing of his theories, compared to vent theory founder Russell et al, who utilizes all the geological and phylogenetic tests they can do.

We already knew that chemiosmosis of the LUCA could only evolve at the surface of an alkaline hydrothermal vent. [ http://nick-lane....logy.pdf ]

Now Martin et al has showed that, as predicted by vent theory, nucleotide and amino acid synthesis (in that order) was captured by evolution from the vent/ocean environment earlier.
gkam
1.3 / 5 (8) Jul 26, 2016
There must be a process which fits our definition of life but is too far removed from us to be recognizable at first.
Captain Stumpy
3.9 / 5 (7) Jul 26, 2016
Now Martin et al has showed that, as predicted by vent theory, nucleotide and amino acid synthesis (in that order) was captured by evolution from the vent/ocean environment earlier
@TorbjornBGL
i wonder how this would apply to a non-carbon based life form as speculated by Asimov (re: Not as We Know it - The Chemistry of Life; http://www.bigear...9p05.htm )

also see: http://www.dailyt...7218.htm

Jayarava
5 / 5 (1) Jul 27, 2016
Martin seems to have given up the old Bacteria/Archaea dichotomy, which he and Lane theorized as happening before a semipermeable cell membrane evolved.
- @torbjorn_b_g_larsson

I'm not sure that this is implied by the article. But I also wondered where this important aspect of Lane's theory had gone. I'll have to look at the Nature paper in detail, but it seems to me that the differences in the ways that bacteria and archaea form their cell-walls make it fairly certain that they evolved the mechanism separately. A mineral-membrane LUCA could have developed a sophisticated metabolism + RNA-world-style genetics before developing phospholipid membranes.

Most theorists are weak on testing their own theories. They rely on experimentalists to do that. Lane has been working on testing the model, but has not published much recently.

torbjorn_b_g_larsson
4 / 5 (4) Jul 27, 2016
@Jayarava: My impression is that Martin and Lane thought they found a useful handle on the earliest split. The outcome seems to be correct, archaea and bacteria split early, but the membrane pathway is arguable.

Here is a review and hypothesis that would be consistent with a lipid membrane UCA lineage that would form the basis for Sojo's and Lane's work on chemiosmosis. [See my previous comment.]

"The two key dehydrogenase enzymes that produce G1P and G3P, G1PDH and G3PDH, respectively, are not homologous. ... G1PDH and G3PDH belong to two separate superfamilies that are universally distributed, suggesting that members of both superfamilies existed in the cenancestor. Furthermore, archaea possess homologues to known bacterial genes involved in fatty acid metabolism and synthesize fatty acid phospholipids. The cenancestor seems likely to have been endowed with membrane lipids whose synthesis was enzymatic but probably non-stereospecific."

[tbctd]
torbjorn_b_g_larsson
4 / 5 (4) Jul 27, 2016
[ctd]

[ http://max2.ese.u...df40.pdf ]

It is an old work, but I don't know of any better. If their phylogeny is correct, Martin and Lane were incorrect. The author's propose a more complex LUCA than Martin et al's.

@CS: I don't think it applies, vent theory is carbon based as Earth life is.

There is no known alternative to carbon chemistry. For reasons of chemistry neither boron (too fragile) nor silicon (too non-fragile) works, and I don't know of any other elements that gives a reasonable rich biochemistry.

@gkam: I don't think there "must" be something or other in biology. Except possibly a water/carbon base and evolution, because we don't know any alternatives to those.
gkam
1.9 / 5 (8) Jul 27, 2016
tbglarson, I was not referring to non-carbon-based life, but carbon-based stuff we would not recognize. There may be other ways to arrange hydrocarbons to fit what we could define as "life", the analog of a virus, or other set of processes.

We continue to be surprised by those moons.
Captain Stumpy
4.3 / 5 (6) Jul 27, 2016
@CS: I don't think it applies, vent theory is carbon based as Earth life is.
@TBGL
yeah, i know that one...
I was speculating about the application of heat into the chemistry and how it would affect things overall, like say: silicon

we know that heat affects silicon in certain ways, and we are well aware of it's role in plant life:
http://www.tandfo...10408447

http://ieeexplore...D4338431

that was one thing i wondered about regarding the heat, vents and applicability to other potential materials for life to form...

like Asimov, it's just mulling about in me noggin'

or call it "speculating"
gkam
1.4 / 5 (7) Jul 27, 2016
Si has not the ability to bond like Carbon does, and the resultants are in other forms, such as the differences between CO2, a gas, and SiO2, a glass. If you get hotter, enough for the glass to be liquid, the biology we understand cannot work.
taka
not rated yet Jul 28, 2016
All life with DNA is most likely result of infection with viruses. They should be included in tree of life. Also, first life most likely multiply not by cell splitting but by cell bursting emitting virus like particles.That can be still present and that can be the reason they are not cultivable.
torbjorn_b_g_larsson
2 / 5 (2) Jul 28, 2016
@taka: Separating the gene archive into DNA and functions (proteins, RNA) has been seen to be a fitness increasing response to parasitism in models. But the first parasites were cells, obviously.

A specialist in the field, Koonin, has proposed how +ssRNA, +ssRNA-RT and dsDNA (several clades) viruses would split from cells, the +ssRNA viruses likely simplified descendants of the first parasites. However there is no consensus on that or the ancestry of any other of the 7 types of viruses in the Baltimore classification.

Vent theory, as here, has the first cells as rock (vent wall) pores, with constrictions and inorganic FeS or organic membranes.

I haven't seen much of a formal model of cell proliferation there, it is early days. FWIW, my preliminary take is that they were multiplying by growing from pore to pore, with first their constrictions as chemical separation and later by the organic membranes that started to take over as cell walls.
humy
4 / 5 (1) Jul 30, 2016
although I am impressed by this research, I am annoyed how this link implies a seriously logically flawed inference from its chosen title of;

"...Study tracing ancestor microorganisms suggests life started in a hydrothermal environment..."

This is because what this study actually suggests is merely the LAST common ancestor common to all living things that still survive today had evolved in an hydrothermal environment and that "LAST common ancestor" is not be equated or confused with the "FIRST life".
Thus that doesn't logically imply in the slightest that the FIRST life started there; -why cannot the FIRST life came to exist in the very different environment from the LAST common ancestor common to all living things that still survive today BUT THEN have multiplied and spread and evolved to fill many niches in other environments and one of those other environments was the hydrothermal environment and there evolved the LAST common ancestor to modern life?
epoxy
Jul 30, 2016
This comment has been removed by a moderator.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.