archaea

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Salt Pond Ecosystem

The color of salt ponds range from pale green to deep coral pink, and indicate the salinity of the ponds. Microorganisms create these spectacular colors, changing their own hues in response to increasing salinity.

In low-to mid-salinity ponds, green algae proliferate and lend the water a green cast. As the salinity increases, an algae called Dunaliella out-competes other microorganisms in the pond, and the color shifts to an even lighter shade of green. In mid-salinity ponds, millions of tiny brine shrimp clarify the brine and contribute an orange cast to the water. And in mid-to high-salinity ponds, high salt concentrations actually trigger the Dunaliella to produce a red carotenoid pigment. Halophiles, such as Halobacteria and Stichococcus, also contribute red tints to the hypersaline brine.

Kite aerial photographs by Charles “Cris” Benton.

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How genetic plunder transformed a microbe into a pink, salt-loving scavenger

Most cells would shrivel to death in a salt lake. But not the Halobacteria. These microbes thrive in brine, painting waters a gentle pink or crimson red wherever they bloom. The Halobacteria live in every salt lake on this planet, from the Dead Sea of Israel to the vast salt flats at the feet of the Sierra Nevada. But these hardy microbes haven’t always called salty depths their home. Their genomes reveal a tale of a dramatic transformation through genetic plunder.

Organisms that can survive in waters of extreme salinity are called ‘halophiles’ – or salt lovers. There exist salt-tolerant algae, fungi and even shrimp. But of all the salt lovers in the world, the pink Halobacteria are the most passionate. They don’t just cope with brine. They embrace it.

Most halophiles do their best to keep their cells clear of salt. But the Halobacteria just don’t care. The insides of their cells are as salty as the lakes they live in. This strategy, the Halobacteria have come to utterly dependent on salt, up to the point were fresh water is as deadly for them as salt water is for others. Placed in a freshwater lake, their cells would swell and pop like bloated water balloons.

Confusing enough, Halobacteria are not bacteria, but archaea, which have a completely different biochemistry. As a general rule, archaea are more hardy and robust than their bacterial counterparts, living in a wider range of extreme environments.

Microbiologists have long noted something odd about the Halobacteria. In all their evolutionary analyses, they found that Halobacteria are part of a branch of archaea called the ‘methanogens’. What bothers microbiologists is that as microbes, methanogens and Halobacteria couldn’t be more different. In every scheme ever devised to differentiate among micro-organisms, methanogens and Halobacteria end up on opposing sides of the divide. If microbes were spices, methanogens would be the pepper to the halobacterial salt.

Methanogens are the self-reliant survivalists, able to liberate energy from the most basic of molecules. A pinch of hydrogen (H2), a dash of carbon dioxide (CO2) and a spoonful of minerals is all a methanogen needs to carve out a living. This sober lifestyle has earned them the moniker of ‘rock eaters’ (lithotrophs).

Halobacteria, on the other hand, fancy their molecules ready-to-eat. They are scavengers, scrounging the salty waters for carbon compounds that they burn using oxygen (methanogens loathe oxygen). As an alternative energy supply, halobacteria are also able to harvest energy from sunlight.

Two types of microbes with radically different life strategies, yet one evolved from the other. So how did the Halobacteria cross the line?

Shijulal Nelson-Sathi thinks he has found the answer. In their latest paper, he and his colleagues show that the ancestor of all Halobacteria acquired as much as a thousand genes from another microbe, a bacterium. And through this act of plunder, the microbiologists write, the Halobacteria left their methanogenic ways behind, becoming salt-loving scavengers in the process.

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Explore The Human Microbiome

The human microbiome refers to all of the microbial organisms that reside in the body including bacteria, fungi, and archaea.  Notably, the human body contains over 10 times more microbial cells than human cells.

To illustrate the diversity of these ‘body bugs’, Scientific American have profiled this impressive, interactive map of the key microorganisms commonly identified in the human body and their predominant location.

Interest in the human microbiome has increased in recent years, following reports that the type and number of microorganisms seem to play a role in the onset of several medical conditions including obesity, cancer, and diabetes

(via freshphotons)

A research team has discovered a complex and diverse microbial ecosystem of bacteria and archaea in the waters and sediments of sub-glacial Lake Whillans, lying 800 meters beneath the surface of the West Antarctic ice sheet.

Researcher Dr. Brent Christner says of this discovery: “It is the first definitive evidence that there is not only life, but active ecosystems underneath the Antarctic ice sheet, something that we have been guessing about for decades. Given the prevalence of subglacial water in Antarctica, our data lead us to contend that aquatic microbial systems are common features of the subsurface environment that exists beneath the Antarctic ice sheet.”

This microbial community is dominated by Betaprotoebacteria, Thaumarchaeota, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, Chloroflexi, and Bacteriodetes, among many others.

Learn more about this fascinating community here

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Boldly Illuminating Biology’s “Dark Matter”

Is space really the final frontier, or are the greatest mysteries closer to home?  In cosmology, dark matter is said to account for the majority of mass in the universe, however its presence is inferred by indirect effects rather than detected through telescopes.

The biological equivalent is “microbial dark matter,” that pervasive yet practically invisible infrastructure of life on the planet, which can have profound influences on the most significant environmental processes from plant growth and health, to nutrient cycles in terrestrial and marine environments, the global carbon cycle, and possibly even climate processes.

By employing next generation DNA sequencing of genomes isolated from single cells, great strides are being made in the monumental task of systematically bringing to light and filling in uncharted branches in the bacterial and archaeal tree of life.  In an international collaboration led by the U.S. Department of Energy Joint Genome Institute (DOE JGI), the most recent findings from exploring microbial dark matter were published online July 14, 2013 in the journal Nature.

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Our ancestor’s ‘leaky’ membrane answers big questions in biology

All life on Earth came from one common ancestor – a single-celled organism – but what it looked like, how it lived and how it evolved into today’s modern cells is a four billion year old mystery being solved by researchers at UCL using mathematical modelling.

Findings published today in PLOS Biology suggest for the first time that life’s Last Universal Common Ancestor (LUCA) had a 'leaky’ membrane, which helps scientists answer two of biology’s biggest questions:

1. Why all cells use the same complex mechanism to harvest energy

2. Why two types of single-celled organism that form the deepest branch on the tree of life – bacteria and archaea – have completely different cell membranes

The leakiness of the membrane allowed LUCA to be powered by energy in its surroundings, most likely vents deep on the ocean floor, whilst holding in all the other components necessary for life.

The team modeled how the membrane changed, enabling LUCA’s descendants to move to new, more challenging environments and evolve into two distinct types of single-celled organism, bacteria and archaea, creating the deepest branch of the tree of life.

Caption: Pumping and phospholipid membranes arose independently in archaea and bacteria. Credit: Victor Sojo et al.

Rita Levi-Montalcini is not the only science great who passed away last week. Carl R. Woese, who discovered archaebacteria, died December 30.

Up until about 30 years ago, it was thought that all life could be classified as either prokaryotes (simple single-celled organisms without a nucleus - essentially, bacteria) or eukaryotes (organisms ranging from single-celled to the very complex - like us - whose cells contain a nucleus). In 1980, Woese’s research uncovered a previously unknown third domain of life: archaebacteria, or archaea (as it’s now, less confusingly, known). Archaebacteria are also prokaryotes, but differ from bacteria in fundamental ways related to their biochemistry and the structure of their cell wall. Despite their superficial similarity with bacteria, they are, surprisingly, as closely related to eukaryotes as they are to prokaryotes.

They are thought to be more ancient than either of the other domains of life, and indeed their unique biochemistry is suited to the conditions of life on early Earth. Archaea are the missing link needed to better understand the evolution of life on Earth: comparing different aspects of the three domains of life helps us pin down when they diverged and what their common ancestor (the ancestor of all life) must have looked like.

Scientific American is making a long (and, admittedly, rather dense) article that Woese penned in 1981 describing his discovery available for a limited time. So what are you still doing here? Go slog through it.

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Professor Discovers How Microbes Survive at Bare Minimum

Beneath the ocean floor is a desolate place with no oxygen and sunlight. Yet microbes have thrived in this environment for millions of years. Scientists have puzzled over how these microbes survive, but today there are more answers.

A study led by Karen Lloyd, an assistant professor of microbiology, reveals that these microscopic life-forms called archaea slowly eat tiny bits of protein. The study was released today in Nature.

The finding has implications for understanding the bare minimum conditions needed to support life.

“Subseafloor microbes are some of the most common organisms on earth,” said Lloyd. “There are more of them than there are stars or sand grains. If you go to a mud flat and stick your toes into the squishy mud, you’re touching these archaea. Even though they’ve literally been right under our noses for all of human history, we’ve never known what they’re doing down there.”


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Scientists classify life into three groups, called domains. They are: Eukarya (which includes the plants and animals we usually think of), Bacteria, and Archaea. Eukarya is made up entirely of eukaryotes. It includes unicellular organisms like diatoms, as well as multicellular organisms like sponges, crabs, and turtles. Bacteria and Archaea are prokaryotes. You can learn about the difference between prokaryotic and eukaryotic cells here.

So what types of life does the domain Archaea encompass?

Archaea are tiny prokaryotic organisms that can live in extreme environments. They can be found in deep sea vents and hot springs. They thrive in extremely salty, acidic and hot environments, and anaerobic (without oxygen) environments. They can even be found inside of humans!

Archaea for the most part cannot be classified into species because they are very hard to identify with a microscope. Most scientists sort them into groups based on function and/or structure. The classification of archaea is a relatively new field with a lot of contention, but the two main groups are:

Euryarchaeota- This includes halophiles (archaea that can only survive in very high salt concentrations), thermophiles (archaea that thrive at high temperatures), acidophiles that survive in extreme acid environments, and methanogens that produce methane and aid in human digestion.

Crenarchaeota- A smaller group than Euryarchaeota, made up of organisms that thrive in very hot environments (volcanoes, deep sea vents) and very cold environments (the Antarctic).

How do they get energy?

There are three types of archaea with different metabolism types.

  1. Phototrophs get energy from sunlight and organic compounds.
  2. Lithotrophs get energy from inorganic compounds and organic compounds or carbon fixation.
  3. Organotrophs get energy from organic compounds and sometimes carbon fixation.

Some archaea are autotrophs, which means they produce their own energy. Photoautotrophs produce energy from sunlight, and chemoautotrophs produce energy from organic or inorganic molecules. The counterparts to autotrophs are heterotrophs; they consume energy produced by autotrophs.

Pushing the limits of life

Here are some of the incredibly extreme environments archaea are known to survive in:

  • Geysers, hydrothermal vents, hot springs above 212 F/100 C. Some can reproduce in temperatures as high as 252 F/122 C.
  • Habitats with salinities (salt concentrations) as high as 20 to 25% (for comparison: the ocean has a salinity of 3.5%!)
  • Acidic habitats with a pH as low as 0 (pH of some battery acid or hydrochloric acid).

The artist Dan Piraro writes, on Bizarro Blog!:

[It’s] amazing how so many people in the modern world–in 21st century America–still deny that evolution is the process by which the creatures of the earth got to where they are and will get to where they are going. …

The irony of all of this is that the stranglehold that mythology has on the human mind is a direct result of evolution. Predictably–and perhaps worst of all–those who would seek power in human government routinely use this knowledge to sway the masses with fear and superstition.

This has nothing to do with cartoon soup, of course, but it was on my mind.

By the way, “archaea” is a word referring to the first kinds of micro-critters that developed in the sea billions of years ago. As it turns out, I used the wrong tense in this cartoon. “Archaea” is plural and I’m using it as singular. Wikipedia says I should have used “archaeon.” Damn.

(Bizarro Blog!)

Not that it detracts at all from the cartoon, but archaea were first classified as such by Carl Woese in 1977.

Discovering life’s last universal common ancestor, or LUCA for short, is one of the great unresolved quests of science. Researchers scouring for traces of the elusive LUCA look for shared traits that exist between all three of the major branches of life: archaea, bacteria and eukaryotes (the cells that make up plants, animals,fungi, algae and everything else). Now scientists based at the University of Illinois think they may have uncovered a breakthrough: a primitive organelle that can be found within all types of organisms, reports Physorg.com.
“This is the only organelle to our knowledge now that is common to eukaryotes, that is common to bacteria and that is most likely common to archaea,” said professor Manfredo Seufferheld, who led the study. “It is the only one that is universal." The newly identified organelle is so primitive that it consists of little more than a cluster of polyphosphate, which is a type of energy currency in cells. It therefore likely functions as a polyphosphate storage site within the cell.

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What’s a thermophile? It’s basically exactly as the name implies: a heat-loving microorganism (thermo- heat, phile- love). Most thermophiles are archaea, which I talked about here. Some thermophiles are also bacteria, and are considered to be the oldest type of bacteria. The colors in the hot spring above are produced by all of the thermophiles living in the incredibly hot water!

Thermophiles can be found in really hot environments like deep sea hydrothermal vents. (pic credit)

Thermophiles like environments from 50 to 70 degrees Celsius. Hyperthermophiles (basically extreme thermophiles) like environments 75 degrees and even higher. Some can grow in temperatures as high as 110 degrees Celsius/ 230 degrees Fahrenheit!

The secret to surviving in these temperatures are their enzymes. Known as extremozymes, they can withstand temperatures without falling apart where any other enzymes would unfold and become useless. They have a variety of technical applications for us humans that require enzymes to work at very high temperatures.

A collaboration of Dutch chemists and microbiologists at Radboud University Nijmegen has confirmed the existence of a uniquely shaped enzyme. CS₂ hydrolase, in a form known as a catenane, consists of two (one single- and one double-ringed) interlocked macrocycles, maintained via weak non-covalent interactions in a manner never before seen in biology.

Verification by size exclusion chromatography, multi-angle laser light scattering and native mass spectrometric analyes has established that the enzyme structure, from thermophilic archaeon Acidianus A1-3 is indeed entwined.

In an earlier paper, the regulatory role this odd conformation plays in catalysis is described by microbiologist Mike Jetten, who first found the primal archaeon in the mudpots of Italian volcanic solfataras, where they had been obtaining their energy by converting CS₂ into H₂S and CO₂ using CS₂ hydrolase.

The enzyme monomer displays a typical β-carbonic anhydrase fold and active site, yet CO₂ is not one of its substrates. Owing to large carboxy- and amino-terminal arms, an unusual hexadecameric catenane oligomer has evolved. This structure results in the blocking of the entrance to the active site that is found in canonical β-carbonic anhydrases and the formation of a single 15-Å-long, highly hydrophobic tunnel that functions as a specificity filter.

The tunnel determines the enzyme's substrate specificity for CS₂, which is hydrophobic.

Van Eldijk et al., “Evidence that the catenane form of CS₂ hydrolase is not an artefact”. Chemical Communications, advance article, doi: 10.1039/c3cc43219j (2013).