Carl Woese, Discoverer of the Archaea, RIP

One of the first things that students learn today about the diversity of life is the concept of the Three Domains of Bacteria, Archaea, and Eukarya. In the past, they would have learned about the Five Kingdoms — Prokaryotes, Animals, Plants, Fungi, and Protists —a concept popularized by the late Lynn Margulis, but we now know that the animals, plants, and fungi are relative newcomers on the evolutionary scene, and that the "prokaryotes" actually contain two ancient lineages, the Bacteria and Archaea, which split long before the eukaryotic kingdoms.

Carl Woese in 2006, via U Illinois

For this insight, we can thank Carl Woese, who passed away just before the New Year at the age of 84 (U Illinois press release, NY Times obituary). Woese made his discovery in the 1970s, when sequencing DNA and RNA was anything but routine. At that time, the prokaryotes were classified primarily by physiological characteristics and morphological appearance. There was little attention paid to microbial evolution, except in a speculative way, simply because there was no easy way to go about studying it.

Living fossil stromatolites found in Northern Ireland

Stromatolites don't look like very much when you actually see them, but they are among the oldest evidence for life on Earth. They are interpreted as layers of sediment aggregated by mats of microbial organisms, which lived in shallow waters receiving lots of sunlight. Although traces of the microorganisms themselves are very rarely preserved, the characteristic cushion-shaped mats remain. Such structures are called "microbialites".

They appear in the fossil record in the late Archaean, about 3.5 billion years ago, and in the Proterozoic, from 2.5 billion years ago, they are believed to have been mostly made by cyanobacteria. The University of California Museum of Paleontology has a great introduction to cyanobacterial fossils and Proterozoic life on its history of life website.

Stromatolites are rare today, and one of the main hypotheses for this is that herbivore grazers would readily attack such a concentrated source of food. The best known examples of modern stromatolites are those in Shark Bay, Western Australia, where they live in highly saline water, which is not conducive to such herbivore grazers.

So it's a surprise to hear that a small stromatolite colony has been found among the rocks of the famous Giant's Causeway in Northern Ireland. The colony is in brackish water that is exposed to waves and potential grazers. It was found by environmental scientists from the University of Ulster who were out looking for other some geological features.

The basaltic columns of the Giant's Causeway, where the stromatolite was found.

The Causeway itself is an extraordinary geological structure, composed of interlocking "pillars" of basalt formed by volcanic activity. These pillars are more or less hexagonal in cross-section, making it look like a set of giant stepping stones.

A little more browsing on Wikipedia throws up a list of other modern stromatolites around the world, some of which are in fresh water. It's amazing how quickly the news report on the new stromatolite find was picked up and incorporated into Wikipedia.

I'm quite a fan of stromatolites. I had the opportunity to see some fossilized stromatolites in the field when my palaeontology class in college went out to upstate New York, to the fossil-rich area around Utica. Unfortunately most fossils look much better in the full glare of the sun (and the excitement of the moment!) than when they are photographed:

Stromatolite fossils in the ground. There's really something there, I swear!

The scientist who found them suggested that they could be much more common than we think they are. It would be really intriguing to see them live in the field, and even more informative to compare the cyanobacteria from different stromatolite colonies around the world: are they always the same kind of bacteria? What else is in these mats? How fast do they grow? What triggers the formation of these microbial mats? How curious, that slimy mats of microbes are the ones to tell us about the early origins of life on our planet!

Afterword on "arsenic-life" affair

Popular Science magazine has recently published a profile by Tom Clynes on the scientist in the middle of the "arsenic life" controversy, Felisa Wolfe-Simon (see previous Biology Refugia post). This comes after the Science finally published her paper in its 3 June 2011 print issue, along with a selection of responses from her critics (see the editor's note for links).

The magazine feature is sympathetic to her, and notes how much of the initial criticism started by criticizing the science then moved into questioning the scientists' motivations. Many accusations were made at the time, including that they were motivated by fame as a result doing "bad science". But Science didn't publish her paper without peer-review. In fact, additional evidence was gathered as a result of peer review. Were the results inadequate for the claims which were made in the media ("new form of life", "proof that extraterrestrial life is possible", etc.)? Yes, certainly.

My opinion is that this was a "perfect storm" caused by the confluence of mass media and science. Without making any assumptions about anyone's motivations, Wolfe-Simon's team or their critics, we can say that (i) the hyped-up press conference organized by NASA was a mistake, and the oversimplified media kit only led to a proliferation of misinformed headlines, (ii) the quick criticisms by scientists posted to their blogs and websites appeared much faster than any research team could possibly respond to carefully, (iii) the media attention on Wolfe-Simon made it difficult to respond to technical criticisms and also increased their defensive posture (reading the Pop Sci article, I'm struck by how overwhelming it must have been for her) – simply finding the time to do it would have been difficult. I quote Clynes's article:

I find it hard not to feel sympathy for her. In a matter of weeks she was catapulted to fame, then singled out and assaulted with professional and personal criticism, some of which resulted from missteps beyond her control. Wolfe-Simon is an early-career researcher in a field dominated by older men. Few scientists, no matter how established, would have the skills to navigate the situation that she found herself in. What made the level of criticism so extraordinary is that the paper, in itself, is not so flawed that it should not have been published. The argument was compelling, the conclusions were measured, the data was thorough, and the paper made it through the same peer-review process as other articles in Science. 

Some who initially blasted Wolfe-Simon have since changed their mind. Blogger Alan Townsend, who directs the environmental studies program at the University of Colorado, says he was guilty of rash judgment, and that his preliminary opinions—expressed in writing and conversations with his colleagues—contributed to a response from the scientific community that was “often unprofessional, and at times became downright shameful.” He says, “Absent major ethical violations, no junior scientist full of passion for an idea deserves crucifixion for a professional failure or two. If a paper is flawed, it should be dismissed. The scientist should not.”

Learning to deal with the media is not typically part of a scientist's education. After all, most could only wish they were so lucky. If the need should arise at all, it's probably handled by PR departments of their institutions or employers, or from the agencies that fund them, like NASA in this case. Perhaps it's time for scientists to come together and figure out what a code of conduct for publicizing their work should be like. For example, is it a conflict of interest to write a newspaper column that trumpets your own work while raising criticism of your competitors, especially if this is unpublished research? How far should we go in "jazzing up" the science in order to sell it to the public? Some degree of spin and oversimplification is unavoidable, but a technical audience would know where to look when reading a scientific paper to judge for themselves whether a specific claim is justifiable (typically buried somewhere in the Materials and Methods). Should we always be cautious and measured in our pronouncements? What if the issue is something politically-charged like climate change, where climate change "deniers" seize upon caution and use it as supposed evidence of falsehood? Difficult questions for difficult times, and scientists should take the lead in trying to figure them out.

Arsenic claim petering out

So it seems like the claim for bacteria using arsenic in their biomolecules was never strong to begin with. During the original press conference, the token skeptic was a chemist, and most of the criticism comes from those who are convinced that the chemistry of the matter is quite unlikely. The bacteria are not 'thriving' on arsenic, by any means, but merely tolerating it.

The original paper claimed that only a fraction of the phosphorus was being replaced by arsenic, but it seems likely that as other labs try to replicate their results, this value will be revised downwards.

Red faces all around - including this one! - for feeding the hype, and many people are pointing to NASA's infamous 'life on Mars' claim as prior precedent for the dangers of mixing science and the media.

Read more:
The authors released a technical statement responding to criticism on methods (pdf original, html version on USA Today)
A good newsy summary from the Philadelphia Inquirer.
Ed Yong at Discover Magazine summarizes the timeline and reflects on the practice of science journalism.

Bacterium using Arsenic instead of Phosphorus discovered

Mono Lake in California is one of the so-called 'soda lakes', not filled with fizzy pop but with caustic alkali and high salt concentrations. What could possibly live in these harsh conditions? Well, microbes, of course. What's more, arsenic concentrations in this like are at levels which would be toxic to most organisms. If we're going to look for weird life forms, Mono Lake would be the place to go!


Mono Lake in California (Google Maps). View Larger Map

One such weird life form has just been discovered. It's a bacterium that uses arsenic in place of phosphorus in its biomolecules, including DNA. In intro biology we learn that all living things have DNA, and that DNA has a sugar-phosphate backbone along which the four bases (A, T, C, and G) are arranged. The phosphate groups in the backbone of DNA are supposedly universal, and it's hard to imagine how any organism could have a different chemistry for something so fundamental, but apparently such a creature does exist. In place of the phosphorus atoms in the phosphate groups, it has instead arsenic. Arsenic is an element that is in the same group as phosphorus, and so has the same chemical valence, and in theory can substitute for phosphorus because it can form similar chemical bonds. Until now such a scenario has seemed to be entirely in the realm of science fiction, but that appears now to be reality.

Using a combination of radioisotope labeling and spectroscopy, a team from NASA's Astrobiology Institute led by Felisa Wolfe-Simon (disclaimer: she was the TF for a class that I took two years ago) has shown that a strain of bacteria isolated from Mono Lake is capable of taking up arsenic, and further that the arsenic is localized in the biomolecules of the organism. This is an exciting discovery because it suggests that alternative chemistries of life are possible, and that organisms need not be limited to the canonical 'six fundamental elements of life': carbon, nitrogen, oxygen, phosphorus, sulfur, and hydrogen.

While this is a very important discovery, it is also crucial to emphasize what it is not, especially given the hype and publicity that this new piece of research has received. The fact that the work was done through the NASA Astrobiology Institute has led some to think that perhaps it has something to do with extraterrestrial life or new life forms. It is emphatically not the case: The bacterium is a member of the Halomonadaceae, a known family of the gamma-Proteobacteria. It is not part of the so-called 'shadow biosphere' (Wikipedia), which is the idea that alongside the canonical DNA/RNA/protein based life that we know of, there are 'organisms' based on fundamentally different chemistry (e.g. with some other form of information-coding molecules instead of DNA, or some other means of catalyzing biochemical reactions...). This discovery 'only' shows that one particular component of the highly-conserved basic biochemistry, namely the use of phosphorus in biomolecules like the nucleic acids, can be swapped out for an element with similar chemical properties. This is not a form of primitive life; if anything it represents an extreme form of specialization to an extreme habitat. Phosphorus is typically a highly limiting nutrient for life - this is why algae tend to form 'blooms' when phosphorus-containing fertilizers or detergents seep into water bodies - because the sudden influx of phosphorus allows a great burst of growth. In the case of this bacterium, called strain GFAJ-1, it is able to capitalize on the high arsenic concentration to replace some of its need for phosphorus.

Hence, not to detract from the excitement about this really cool piece of natural history, but these clarifications really needed to be made in the face of what was inevitably a lot of misunderstanding and misrepresentation in the popular press (with sensational headlines like "Alien life forms discovered?" and so on). What is exciting is certainly the fact that life like this has been discussed as a theoretical possibility for a long time, and is now finally known to be real.

Sources:

• The original paper as published in Science Express
• NASA press release
• Felisa's website
• Astrobiology Magazine 

Update (3 Dec 2010, 0043 EST):
Even the geek-cool comic strip xkcd has gotten into the act:

Source: xkcd by Randall Munroe

On Rice, Mosquito Ferns, and Cyanobacteria...

This blog has been veering towards the theme of food in recent posts. Perhaps the most important staple food in Asia is rice, traditionally grown in irrigated paddy fields. A piece of natural history trivia that has stuck with me from my childhood fascination with ferns is how paddy farmers encourage the growth of the mosquito fern Azolla, because it has nitrogen-fixing cyanobacteria that live in symbiosis with it, thereby contributing to the nitrogen content of the soil.

Don't Fear the Microbe

"Most of life's diversity springs from microbial organisms, which carry out the lion's share of the chemical transformations that drive the biosphere. It is therefore remarkable that the microbial world is so little recognized by the general public except in the context of disease and rot...."

-- Norm Pace reviews March of the Microbes: Sighting the Unseen by John Ingraham.

---

Conservation biologists often talk about the "Bambi Effect", where cute, big-eyed animals get the most attention and therefore conservation funding. The very opposite could be said of microbes, which get very little positive publicity in the popular press, except as germs and diseases.

Lately there's been more awareness of the beneficial effects that microbes living in close association with us can bring. The old concept of 'probiotic' (remember Yakult and Vitagen?) has been deepened and updated. It's no longer believed that beneficial effects come from having only one or two 'good species' living in one's gut - instead it's whole communities of microbes that matter, just like how the concept of a 'keystone species' in ecology is now thought to be an oversimplification.

Appreciation of the so-called human microbiome is also reaching the medical community. In a recent report, a vigorous antibiotic-resistant infection of Clostridium in a woman's gut was only stopped by transplanting a quantity of her husband's fecal material - containing 'normal' bacterial biota - into her gut. Her husband's gut bacterial community displaced the abnormal community that had colonized her system, and cured her of the infection.

We also hear frequently about how methane gas passed by cows (by burping from their mouths and not from the other end, it turns out) because of the fermentation which goes on in their guts is a major contributor to greenhouse gas emissions. It's no surprise, then, that some researchers are trying to modify the gut microbes of cows to make them less gassy, like kangaroos.

Certainly something to chew on, if you get my whiff... I mean, drift.

Bacteria aiding breakdown of Gulf oil spill

Naturally-occurring bacteria are able to break down the oil from the Gulf of Mexico oil spill, and their abundance is already increasing in samples of oil-laden water. Researchers suggest how this knowledge might help us: adding fertilizer to the water can encourage their growth, for example. Yet among the bacterial species that are feasting on the oil is the genus Vibrio, many of which (like the cholera agent) are human and animal pathogens, so we have to be aware and wary. The bacterial communities, like other organisms, will be 'reshuffled' by the spill, and their metabolism will also lower oxygen levels in the water as they break down the chemicals in the oil.

Bacterial Biofilms

This recent article in PLoS Biology gives a very readable review of bacterial biofilms and the kinds of problems they pose in medical settings. A familiar example of a bacterial biofilm is plaque on our teeth. Bacteria, when they reach a certain critical density on a surface, begin to aggregate and secrete a slimy polymeric matrix which aids further establishment and eventually builds up to a complex structure with channels and pores through which fluid can flow, carrying in nutrients and carrying away waste materials.

A few interesting points to think about:

• The means by which the bacteria detect the critical population density needed to form biofilms is called quorum sensing. How does it work?
  
• Previously it was thought that the slimy matrix protected bacteria by preventing them from being engulfed or attacked by other cells or substances, but the matrix has to be permeable to most substances because waste and nutrients must reach the bacteria. So how do they defend themselves?
  
• Biofilms usually form on surfaces over which there is regular fluid flow. Why would the biofilm growth form be advantageous?
  
• Bacteria living in biofilms reproduce at a slower rate than free living ones. How might this be understood by analogy to life-history trait selection in r- and K-selective environments?
  

Space bacteria

Bacteria (Salmonella typhimurium) flown in space on the shuttle were shown to be more virulent than the control strains held on Earth.

What I found pretty neat was something that one of the researchers said: "Wherever humans go, microbes go; you can't sterilise humans. Wherever we go, under the oceans or orbiting the Earth, the microbes go with us, and it's important that we understand... how they're going to change."

This is a good reminder that microbes, the prokaryotes but also the protists, play extremely important ecological roles in the environment and within other organisms, that we frequently overlook because of their small size. Concepts which seem 'exotic', such as parasitism, 'alternative' metabolisms, and even perhaps the ecology of soil bacteria, are actually more commonplace than we think.

In terms of sheer number and biomass, the microbes are the rule, not the exception, and they're everywhere. Even in space flight, the pinnacle of human technological achievement, we've still not figured out how to deal with the 'problem' of microbial hitch-hikers.

Perhaps we shouldn't think of them as problems to be eliminated. After all, they've been with us since the beginning and have had a hand in our own evolution (for example vitamins produced by gut bacteria which our own metabolisms cannot produce). They've pretty much become part of us, and attempting to eliminate them would be a sign of hubris and only put our own selves in the way of illness.

PNAS article link.