A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Source: http://www.nature.com/nature/journal/v462/n7276/fig_tab/nature08656_F1.html

Bacteria

Sauce: Bill Bryson - A Short History Of Nearly Everything

IT’S PROBABLY NOT a good idea to take too personal an interest in your microbes. Louis Pasteur, the great French chemist and bacteriologist, became so preoccupied with them that he took to peering critically at every dish placed before him with a magnifying glass, a habit that presumably did not win him many repeat invitations to dinner.

In fact, there is no point in trying to hide from your bacteria, for they are on and around you always, in numbers you can’t conceive. If you are in good health and averagely diligent about hygiene, you will have a herd of about one trillion bacteria grazing on your fleshy plains—about a hundred thousand of them on every square centimeter of skin. They are there to dine off the ten billion or so flakes of skin you shed every day, plus all the tasty oils and fortifying minerals that seep out from every pore and fissure. You are for them the ultimate food court, with the convenience of warmth and constant mobility thrown in. By way of thanks, they give you B.O.

And those are just the bacteria that inhabit your skin. There are trillions more tucked away in your gut and nasal passages, clinging to your hair and eyelashes, swimming over the surface of your eyes, drilling through the enamel of your teeth. Your digestive system alone is host to more than a hundred trillion microbes, of at least four hundred types. Some deal with sugars, some with starches, some attack other bacteria. A surprising number, like the ubiquitous intestinal spirochetes, have no detectable function at all. They just seem to like to be with you. Every human body consists of about 10 quadrillion cells, but about 100 quadrillion bacterial cells. They are, in short, a big part of us. From the bacteria’s point of view, of course, we are a rather small part of them.

Because we humans are big and clever enough to produce and utilize antibiotics and disinfectants, it is easy to convince ourselves that we have banished bacteria to the fringes of existence. Don’t you believe it. Bacteria may not build cities or have interesting social lives, but they will be here when the Sun explodes. This is their planet, and we are on it only because they allow us to be.

Bacteria, never forget, got along for billions of years without us. We couldn’t survive a day without them. They process our wastes and make them usable again; without their diligent munching nothing would rot. They purify our water and keep our soils productive. Bacteria synthesize vitamins in our gut, convert the things we eat into useful sugars and polysaccharides, and go to war on alien microbes that slip down our gullet.

We depend totally on bacteria to pluck nitrogen from the air and convert it into useful nucleotides and amino acids for us. It is a prodigious and gratifying feat. As Margulis and Sagan note, to do the same thing industrially (as when making fertilizers) manufacturers must heat the source materials to 500 degrees centigrade and squeeze them to three hundred times normal pressures. Bacteria do it all the time without fuss, and thank goodness, for no larger organism could survive without the nitrogen they pass on. Above all, microbes continue to provide us with the air we breathe and to keep the atmosphere stable. Microbes, including the modern versions of cyanobacteria, supply the greater part of the planet’s breathable oxygen. Algae and other tiny organisms bubbling away in the sea blow out about 150 billion kilos of the stuff every year.

And they are amazingly prolific. The more frantic among them can yield a new generation in less than ten minutes; Clostridium perfringens, the disagreeable little organism that causes gangrene, can reproduce in nine minutes. At such a rate, a single bacterium could theoretically produce more offspring in two days than there are protons in the universe. “Given an adequate supply of nutrients, a single bacterial cell can generate 280,000 billion individuals in a single day,” according to the Belgian biochemist and Nobel laureate Christian de Duve. In the same period, a human cell can just about manage a single division.

About once every million divisions, they produce a mutant. Usually this is bad luck for the mutant—change is always risky for an organism—but just occasionally the new bacterium is endowed with some accidental advantage, such as the ability to elude or shrug off an attack of antibiotics. With this ability to evolve rapidly goes another, even scarier advantage. Bacteria share information. Any bacterium can take pieces of genetic coding from any other. Essentially, as Margulis and Sagan put it, all bacteria swim in a single gene pool. Any adaptive change that occurs in one area of the bacterial universe can spread to any other. It’s rather as if a human could go to an insect to get the necessary genetic coding to sprout wings or walk on ceilings. It means that from a genetic point of view bacteria have become a single superorganism—tiny, dispersed, but invincible.

They will live and thrive on almost anything you spill, dribble, or shake loose. Just give them a little moisture—as when you run a damp cloth over a counter—and they will bloom as if created from nothing. They will eat wood, the glue in wallpaper, the metals in hardened paint. Scientists in Australia found microbes known as Thiobacillus concretivorans that lived in—indeed, could not live without—concentrations of sulfuric acid strong enough to dissolve metal. A species called Micrococcus radiophilus was found living happily in the waste tanks of nuclear reactors, gorging itself on plutonium and whatever else was there. Some bacteria break down chemical materials from which, as far as we can tell, they gain no benefit at all.

They have been found living in boiling mud pots and lakes of caustic soda, deep inside rocks, at the bottom of the sea, in hidden pools of icy water in the McMurdo Dry Valleys of Antarctica, and seven miles down in the Pacific Ocean where pressures are more than a thousand times greater than at the surface, or equivalent to being squashed beneath fifty jumbo jets. Some of them seem to be practically indestructible. Deinococcus radiodurans is, according to theEconomist , “almost immune to radioactivity.” Blast its DNA with radiation, and the pieces immediately reform “like the scuttling limbs of an undead creature from a horror movie.”

Perhaps the most extraordinary survival yet found was that of a Streptococcus bacterium that was recovered from the sealed lens of a camera that had stood on the Moon for two years. In short, there are few environments in which bacteria aren’t prepared to live. “They are finding now that when they push probes into ocean vents so hot that the probes actually start to melt, there are bacteria even there,” Victoria Bennett told me.

We now know that there are a lot of microbes living deep within the Earth, many of which have nothing at all to do with the organic world. They eat rocks or, rather, the stuff that’s in rocks—iron, sulfur, manganese, and so on. And they breathe odd things too—iron, chromium, cobalt, even uranium. Such processes may be instrumental in concentrating gold, copper, and other precious metals, and possibly deposits of oil and natural gas. It has even been suggested that their tireless nibblings created the Earth’s crust.

Some scientists now think that there could be as much as 100 trillion tons of bacteria living beneath our feet in what are known as subsurface lithoautotrophic microbial ecosystems—SLiME for short. Thomas Gold of Cornell has estimated that if you took all the bacteria out of the Earth’s interior and dumped it on the surface, it would cover the planet to a depth of five feet. If the estimates are correct, there could be more life under the Earth than on top of it.

At depth microbes shrink in size and become extremely sluggish. The liveliest of them may divide no more than once a century, some no more than perhaps once in five hundred years. As the Economist has put it: “The key to long life, it seems, is not to do too much.” When things are really tough, bacteria are prepared to shut down all systems and wait for better times. In 1997 scientists successfully activated some anthrax spores that had lain dormant for eighty years in a museum display in Trondheim, Norway. Other microorganisms have leapt back to life after being released from a 118-year-old can of meat and a 166-year-old bottle of beer. In 1996, scientists at the Russian Academy of Science claimed to have revived bacteria frozen in Siberian permafrost for three million years. But the record claim for durability so far is one made by Russell Vreeland and colleagues at West Chester University in Pennsylvania in 2000, when they announced that they had resuscitated 250-million-year-old bacteria called Bacillus permians that had been trapped in salt deposits two thousand feet underground in Carlsbad, New Mexico. If so, this microbe is older than the continents.

It is a natural human impulse to think of evolution as a long chain of improvements, of a never-ending advance toward largeness and complexity—in a word, toward us. We flatter ourselves. Most of the real diversity in evolution has been small-scale. We large things are just flukes—an interesting side branch. Of the twenty-three main divisions of life, only three—plants, animals, and fungi—are large enough to be seen by the human eye, and even they contain species that are microscopic. Indeed, according to Woese, if you totaled up all the biomass of the planet—every living thing, plants included—microbes would account for at least 80 percent of all there is, perhaps more. The world belongs to the very small—and it has for a very long time.

Study catches 2 bird populations as they split into separate species

A new study finds that a change in a single gene has sent two closely related bird populations on their way to becoming two distinct species. The study, published in the August issue of the American Naturalist, is one of only a few to investigate the specific genetic changes that drive two populations toward speciation.

Speciation, the process by which different populations of the same species split into separate species, is central to evolution. But it's notoriously hard to observe in action. This study, led by biologist J. Albert Uy of Syracuse University, captures two populations of monarch flycatcher birds just as they arrive at that evolutionary crossroads.

Monarch flycatchers are small, insect-eating birds common in the Solomon Islands, east of Papua New Guinea. Uy and his team looked at two flycatcher populations: one found mostly on the large island of Makira, the other on smaller surrounding islands. Besides where they live, the only discernable difference between the two populations is the color of their feathers. The birds on Makira have all black feathers. Birds on the smaller islands have the same black feathers, but with a chestnut-colored belly.

The question of whether these two populations are on the road to speciation comes down to sex. When two populations stop exchanging genes-that is, stop mating with each other-then they can be considered distinct species. Uy and his team wanted to see if these flycatchers were heading in that direction.

It would be all but impossible to try to catalog every occasion on which an all-black flycatcher mated with a chestnut-bellied. So Uy and his team used another test.

Flycatcher males defend their mating territories. If a potential rival male enters another's territory, fights often ensue. If all-black males react less violently to chestnut-bellied males and vice versa, that's an indication that the two don't recognize each other as reproductive rivals. If they don't see each other as rivals, then one can assume that mating between members of the two populations is rare.


So Uy and his team made all-black and chestnut-bellied taxidermy models. They used the models to invade mating territories in each population. As expected, when all-black birds were presented with all-black models, they attacked. But when all-black birds encountered chestnut-bellied models, they were much less likely to go on the offensive. The same scenario held for the chestnut-bellied birds.

That males from the two populations no longer view the other as a reproductive threat is a good indication that not much mating is taking place between the two groups. Their evolutionary paths are diverging, Uy and his team found-all because of a change in plumage.

The researchers then went a step further. They looked into the birds' genomes to see what genes may have played a role in the different plumage pattern. They found only one: the melanocortin-1 receptor gene (MC1R). The MC1R gene regulates the production of melanin, which gives skin and feathers their color. The all-black and chestnut-bellied birds had different versions of the MC1R gene, which gave rise to the plumage change.

That change appears to have been enough to create a reproductive barrier for flycatchers. Not every species is so picky, so a color change doesn't always drive speciation. Nonetheless, these results suggest that it can take as little as one gene, in the right spot in the genome, to cause a fork in the evolutionary road.
Reference:

J. Albert C. Uy, Robert G. Moyle, Christopher E. Filardi, Zachary A. Cheviron, "Difference in Plumage Color Used in Species Recognition between Incipient Species Is Linked to a Single Amino Acid Substitution in the Melanocortin-1 Receptor." The American Naturalist August 2009.

Note: This story has been adapted from a news release issued by the University of Chicago Press Journals

http://www.geneticarchaeology.com/research/Study_catches_2_bird_populations_as_they_split_into_separate_species.asp

DNA-like Molecule Replicates Without Help

DNA-like Molecule Replicates Without Help

By Robert F. Service
ScienceNOW Daily News
11 June 2009
Researchers pondering the origin of life have long struggled to crack the ultimate chicken-and-egg paradox. How did nucleic acids like DNA and RNA--which encode proteins--first form, when proteins are needed for their synthesis? Now, scientists report that they've cooked up molecular hybrids of proteins and nucleic acids that skirt the dreaded paradox. Although it's unknown whether such molecules existed prior to the emergence of life, they offer insight into a chemical pathway that might have helped life arise.

DNA and RNA sport a backbone of sugar and phosphate groups linked to the nucleotide bases that spell out the genetic code. Certain proteins help copy nucleic acids by fashioning complementary strands that carry matching nucleotides. But how could nucleic acids originate without proteins, and vice versa? Proponents of the "RNA World" hypothesis argue that RNA itself was the key because of its dual abilities: It not only carries genetic information but also can catalyze chemical reactions. That view received a big boost earlier this year, when researchers at The Scripps Research Institute in San Diego, California, showed that small RNA fragments can catalyze their own reproduction. "The question remains, how those first RNA molecules appeared," says Luke Leman, a chemist at Scripps who was not part of the study. Other researchers have synthesized DNA and RNA analogs with simpler sugar backbones that may have done the job. Yet those are still complex, lessening the chance that they were the primordial replicating molecules, Leman says.

In hopes of finding something simpler, Leman and colleagues did away with the sugar-phosphate backbones altogether. Instead, they turned to amino acids, protein building blocks that have been shown to assemble under prebiotic conditions. The researchers report online today in Science Express that when they combined just two amino acids, a backbone readily assembled without the need for additional enzymes. They then found that DNA bases could bind to a sulfur group in one of the amino acids, cysteine, creating a protein-DNA hybrid strand. But because the nucleic acid bases attach weakly to the cysteines--think Velcro instead of glue--the bases can jump on and off in solution. As a result, when the researchers placed their hybrids in solution with single strands of DNA and RNA, the hybrids were able to rearrange their nucleic acid makeup to form complementary strands that would bind to the DNAs and RNAs. The researchers discovered that the hybrids could also form strands that would bind to other complementary hybrids, which shows that such molecules have the potential to copy themselves.

"This is very interesting and creative," says Eric Kool, a chemist at Stanford University in Palo Alto, California, who studies nucleic acid analogs. These particular hybrids change so rapidly in solution, it's unclear if they would remain stable long enough to propagate genetic information over several generations. However, Kool says, "It's an idea worth considering."

http://sciencenow.sciencemag.org/cgi/content/full/2009/611/1

Wired Science News for Your Neurons Life’s First Spark Re-Created in the Laboratory

A fundamental but elusive step in the early evolution of life on Earth has been replicated in a laboratory.

Researchers synthesized the basic ingredients of RNA, a molecule from which the simplest self-replicating structures are made. Until now, they couldn’t explain how these ingredients might have formed.

“It’s like molecular choreography, where the molecules choreograph their own behavior,” said organic chemist John Sutherland of the University of Manchester, co-author of a study in Nature Wednesday.

RNA is now found in living cells, where it carries information between genes and protein-manufacturing cellular components. Scientists think RNA existed early in Earth’s history, providing a necessary intermediate platform between pre-biotic chemicals and DNA, its double-stranded, more-stable descendant.

However, though researchers have been able to show how RNA’s component molecules, called ribonucleotides, could assemble into RNA, their many attempts to synthesize these ribonucleotides have failed. No matter how they combined the ingredients — a sugar, a phosphate, and one of four different nitrogenous molecules, or nucleobases — ribonucleotides just wouldn’t form.

Sutherland’s team took a different approach in what Harvard molecular biologist Jack Szostak called a “synthetic tour de force” in an accompanying commentary in Nature.

“By changing the way we mix the ingredients together, we managed to make ribonucleotides,” said Sutherland. “The chemistry works very effectively from simple precursors, and the conditions required are not distinct from what one might imagine took place on the early Earth.”

Like other would-be nucleotide synthesizers, Sutherland’s team included phosphate in their mix, but rather than adding it to sugars and nucleobases, they started with an array of even simpler molecules that were probably also in Earth’s primordial ooze.

They mixed the molecules in water, heated the solution, then allowed it to evaporate, leaving behind a residue of hybrid, half-sugar, half-nucleobase molecules. To this residue they again added water, heated it, allowed it evaporate, and then irradiated it.

At each stage of the cycle, the resulting molecules were more complex. At the final stage, Sutherland’s team added phosphate. “Remarkably, it transformed into the ribonucleotide!” said Sutherland.

According to Sutherland, these laboratory conditions resembled those of the life-originating “warm little pond” hypothesized by Charles Darwin if the pond “evaporated, got heated, and then it rained and the sun shone.”

Such conditions are plausible, and Szostak imagined the ongoing cycle of evaporation, heating and condensation providing “a kind of organic snow which could accumulate as a reservoir of material ready for the next step in RNA synthesis.”

Intriguingly, the precursor molecules used by Sutherland’s team have been identified in interstellar dust clouds and on meteorites.

“Ribonucleotides are simply an expression of the fundamental principles of organic chemistry,” said Sutherland. “They’re doing it unwittingly. The instructions for them to do it are inherent in the structure of the precursor materials. And if they can self-assemble so easily, perhaps they shouldn’t be viewed as complicated.”

http://www.wired.com/wiredscience/2009/05/ribonucleotides/

http://www.newscientist.com/article/mg20227084.200-molecule-of-life-emerges-from-laboratory-slime.html

12 Elegant Examples of Evolution

In preparation for Charles Darwin's upcoming 200th birthday, the editors of Nature compiled a selection of especially elegant and enlightening examples of evolution.  

They describe it as a resource "for those wishing to spread awareness of evidence for evolution by natural selection." Given the continuing battles over evolution in America's public schools — and, for that matter, the Islamic world — such a resource is most welcome. 

However, I'd like to suggest another way of looking at the findings below, which range from the moray eel's remarkable second jaw to the unexpected plumage of dinosaurs. They are, quite simply, wondrous — glimpses through an evolutionary frame of life's incredible narrative, expanding to fill every possible nook and cranny of Earth's biosphere. 

After all, it's hard to stir passion about the scientific validity of evolution without first captivating minds and imaginations. And this is a fine place to start.

http://blog.wired.com/wiredscience/2008/12/evolutionexampl.html

A simple fusion to jump-start evolution

With the aid of a straightforward experiment, researchers have provided some clues to one of biology's most complex questions: how ancient organic molecules came together to form the basis of life.

Specifically, this study, appearing online this week in JBC, demonstrated how ancient RNA joined together to reach a biologically relevant length.

RNA, the single-stranded precursor to DNA, normally expands one nucleic base at a time, growing sequentially like a linked chain. The problem is that in the primordial world RNA molecules didn't have enzymes to catalyze this reaction, and while RNA growth can proceed naturally, the rate would be so slow the RNA could never get more than a few pieces long (for as nucleic bases attach to one end, they can also drop off the other). 

Ernesto Di Mauro and colleagues examined if there was some mechanism to overcome this thermodynamic barrier, by incubating short RNA fragments in water of different temperatures and pH. 

They found that under favorable conditions (acidic environment and temperature lower than 70 C), pieces ranging from 10-24 in length could naturally fuse into larger fragments, generally within 14 hours.

The RNA fragments came together as double-stranded structures then joined at the ends. The fragments did not have to be the same size, but the efficiency of the reactions was dependent on fragment size (larger is better, though efficiency drops again after reaching around 100) and the similarity of the fragment sequences. 

The researchers note that this spontaneous fusing, or ligation, would a simple way for RNA to overcome initial barriers to growth and reach a biologically important size; at around 100 bases long, RNA molecules can begin to fold into functional, 3D shapes.

http://www.geneticarchaeology.com/Research/A_simple_fusion_to_jump-start_evolution.asp