Posts Tagged ‘Archaea’

Life on Mars

Friday, January 16th, 2009

MORE: There has been speculation that evolution on earth took a different path from that on other planets when mitochondria, which were originally free-living organisms like Rickettsia, developed a symbiotic relationship with eukaryotes (cells with a nucleus) and made possible multi-celled organisms. This crucial step may have occurred only once. Or, it may occur in any oxygen rich atmosphere. We should not be surprised to find single cell life on Mars but multicellular life might very, very rare.

I have already posted on the new developments in bacteriology and life forms like Archea. Now, we are starting to see evidence that Mars may host similar organisms. Here is evidence of methane on Mars.

At a NASA news conference this afternoon, a team of scientists led by Michael Mumma of the Goddard Space Flight Center announced the discovery of plumes of methane emanating from the surface of Mars during the planet’s late spring and early summer. Methane is a key component of natural gas, and much of the Earth’s supply of the chemical comes from organisms that release it as they digest nutrients. But the five scientists were cautious to avoid claiming the methane spouts as evidence of life, saying that geologic activity could also put pressure on the methane and blast it through cracks in the surface. Either way, Mumma said, the plumes show that Mars is not merely a dead planet that once may have hosted life or liquid water. “We are entering a new era,” he said. “Now we’re looking at an active Mars.”

I have previously commented on extremophiles and other organisms that might survive in the Martian environment. Here and here.

There is more on this topic here.

To learn whether life could exist in a barren landscape such as that seen on the surface of Mars, where any water present is mostly present in the frozen state, some microbiologists have journeyed to a part of Earth that resembles Mars in some respects: the polar deserts of Antarctica.

Antarctica proves that microbes survive in barren landscapes.

This region of Antarctica has very little water, and most of the year what little water there is exists in the form of ice.

The hole in the ozone layer that has developed over Antarctica allows high levels of ultraviolet radiation to reach Earth’s surface, a condition that would be experienced by any creatures located on the Martian surface.

The level of radiation encountered in Antarctica is not nearly as high as that encountered on the surface of Mars, but it is higher than that encountered on most other parts of Earth’s surface.
Is there life in the polar desert of Antarctica? The answer is an unequivocal Yes. Bacteria and fungi have been found in the Antarctic deserts, not only in the soil of the region but also inside rocks. Scientists speculate that bacteria enter the porous matrix of rocks as a means of protecting themselves from radiation.

The atmosphere on Mars is much thinner than Earth’s.
A major difference between the environment found in the high deserts of Antarctica and that encountered on the surface of Mars is the atmosphere. The Martian atmosphere is much thinner than that of Earth. It consists mostly of carbon dioxide, or CO2 (about 95%), and contains virtually no oxygen (O2). Because many bacteria, archaea, and algae can use inorganic carbon dioxide as their source of carbon (used to build proteins and other cell components), the predominance of carbon dioxide would be a plus. Also, as noted earlier, many of Earth’s microbes do not require O2, so the lack of O2 does not preclude life.

So all these points are permissive. Life could exist on Mars. There is a problem, though.

A more troubling feature of the Martian atmosphere is the very low level of nitrogen (N2). On Earth, N2 makes up 78% of atmospheric gases. On Mars it only composes 3%. Many bacteria can use N2 as a sole source of the nitrogen they need for proteins, nucleic acids, and other cell components, but the low level of N2 would certainly limit the amount of microbial growth. Thus, if there is microbial life on Mars, it is unlikely to be as abundant and as widespread as on Earth and may thus be harder to find.

Different compositions and concentrations of gases may exist in some areas under the Martian surface. Such a possibility would be difficult to prove—unless it is proved indirectly the presence of life in the subsurface regions and in greater abundance than expected.

We may have to consider a life form that does not use Nitrogen. Phosphorus and Arsenic are members of the family of Nitrogen in the periodic table. on Earth, Nitrogen is a gas and a large part of the atmosphere. On Mars, it is a small part. One problem is thinking about Exobiology, the biology of other systems. Phosphorus is abundant on Mars. What does this mean ? I don’t know.

Tags:, , , , ,
Posted in science, Uncategorized | 8 Comments »

The Third Kingdom

Tuesday, April 1st, 2008

I’m reading a book about Archaea and the discovery of these organisms. One of the first great characters to appear is Karl Stetter, professor of biology at Regensburg and expert on extremeophiles. He is also an entrepreneur who developed a new “organic” form of sauerkraut using the L-form of lactobacillus which makes better tasting sauerkraut. I don’t know how organic the stuff is if the fermenting organism was modified but we won’t go into that here.

Stetter has been studying thermophiles or organisms that live at high temperatures for many years. He provided important help to Karl Woese when the American microbiology community rejected the Archaea concept in the 1970s. Germany became the great center of this research and he was one of the first to be able to culture organisms that live only at high temperatures and in extreme environments. Botany is a hobby and he also raises rare orchids. A book about thermphiles gives a taste of the enthusiasm that these exotic life forms stimulate.

Karl Stetter a Kamchatka

Here, Stetter stands with some of his collecting apparatus in the Kamchatka Penninsula on a field trip. He enjoys poking around in boiling hot springs that would boil him alive if he were to fall in. A couple of times, he has come close. His newest work is on the tiniest member of the Kingdom he has discovered so far, Nanoarcheota, a tiny parasitic or symbiotic organism that is an excellent candidate for interplanetary travel at some point in evolution. These organsms are strict anerobes, will tolerate one hour of autoclaving, live at temperatures about 100 degree centigrade and require extreme acidity in some cases with a pH as low as 2. They will also tolerate temperatures as low as 140 degree below zero.

Morris Kates

Another pioneer in this research is Morris Kates, of the University of Ottawa, whose study of the lipids in these organisms showed that they were not bacteria.

The highlight of my scientific career, from a professional point of view, was the discovery that membrane lipids of
halophiles (bacteria living in environments of high salt concentration), methanogens (anaerobic autotrophs that obtain energy
from the synthesis of methane gas), and thermoacidophiles (bacteria growing at high temperature and low pH) have struc-
tures different from all other organisms and are synthesized through a very unusual and unexpected pathway. Our findings
provided an important clue that was used by Carl Woese in proposing the existence of a third class of organisms called
Archaea, to which the extreme halophiles and methanogens belong. A survey of lipids from many species of extreme
halophiles showed there was a good correlation between the lipid structures and the genus of the species and made it possible to classify these species taxonomically on a generic level.

Yellowstone National Park is one prime collecting site for exotic organisms that live in extreme environments.

Another is the wreck of the Titanic 1200 feet below the surface of the ocean. The “rusticles” described by Ballard, and named because he thought they were made up of rust and looked like icicles or stalactites, are actually huge colonies of organisms metabolizing the iron in the hull of the ship and making oxygen. The water around Titanic should be an anerobic zone but oxygen is increasing and drawing more species to the site. The rusticles even have a sort of multicelled structure. The organisms and structure have been studied and classified by scientists who are interested in these iron metabolizng creatures that also inhabit water wells and plug them up with rusticles.

In the water well industry, it is now acknowledged that the bulk of the plugging and clogging events that occur down a well are actually biologically derived. Comparable studies have revealed that it is the same groups of bacteria that are involved in these events both down in water wells and deep down at the site of the RMS Titanic. Similar rusticle structures are observed at both sites. The question therefore becomes whether steel fabricated ships floating on the surface, or the RMS Titanic, a splintered steel structure lying on the ocean’s floor, are subject to the same bacterial challenges as water wells, which involve steel structures set into the ground water.

More to come.

Tags:, , , , , ,
Posted in science | 2 Comments »

Craig Venter

Thursday, March 20th, 2008

Bradley Fikes and I spent the afternoon at UCSD to hear Craig Venter speak. I was not disappointed. I wrote the first review on Amazon of his autobiography and he knew this today, commenting that it was the most credited as “helpful.” His accomplishments go well beyond medicine although that seems to be the part that fascinates reporters.

He discussed the sequencing of the genome but the most important part is the environmental potential of his work. For example, the methanobacteria are now properly known as Methanococci as they are now known to be a member of Archaea, a new kingdom of life. If you really want to know about Archaea,
this is the source, although a PDF version can be downloaded and printed. These organisms can exist at the extremes of nature, such as steam vents on the ocean floor.

Some of them are capable of regenerating oil or natural gas from CO2. Some can metabolize coal in underground deposits and release methane gas. Some can metabolize sulfuric acid and release metallic sulfur and water. Some bacteria can generate nanowires and potentially function as a battery with electricity generation from animal waste.

Some of them will take up uranium and some may even be able to metabolize radioactive elements. Some may function as a bacterial fuel cell. Some of these fuel cells involve bacteria with nanowires. These systems are getting close to practical use.

The great advantage of all of these systems is that energy inputs are far less than the inorganic equivalent, such as burning or conversion to ethanol of plant substrate. The bacterial systems can convert the substrate directly to methane or a higher carbon molecule by enzyme action that takes place at ambient temperature.

Methane has one carbon. Ethane has two and octane, the ideal form of gasoline, has eight. These systems may be the way to refine tar sands or high sulfur crude oil that is not yet economical to use as fuel. Some of them will make fuel from waste. Some may even reduce nuclear waste to safe deposits that do not require isolation.

Right now, Venter is working on ways to analyze the genome of organisms with exotic properties and transfer the gene to more common or faster growing organisms. His company is called Synthetic Genomics. and is in southern California. He has other companies in the east but this application is more important, I think, than the medical applications right now. He calls it “digitizing life” and says that creating a synthetic chromosome is not difficult. The problem is “rebooting it.” He is about to announce an artificial bacterium and I thought the announcement might come today. It will be soon.

We’ll see what the next steps are.

Tags:, , , , ,
Posted in medicine, science | 6 Comments »

Cell biology and Evolution

Saturday, December 15th, 2007

This video is a nice illustration of the incredible advances of molecular biology in the past 25 years. When I was a medical student, a long time ago, we learned all the anatomic structures of the cell but had no idea what many of them did. We knew that mitochondria made energy from oxygen but, aside from basic genetics (very basic) we didn’t understand most of what went on in the cell. Over the past six or seven years, I have spent some time reading about molecular biology so I could appreciate what has been learned and in an attempt to appear better informed to my students. Along the way, I got very interested in mitochondria.

 

First, a nonbiologist must learn the difference between a Eukaryote and a Prokaryote. A eukaryote is a cell, or an organism made up of cells, that has a nucleus (containing the chromosomes) enclosed by a membrane and a structure of cell organelles that carry out cell functions. Plants, for example, are eukaryotes and have a larger number of genes than humans do. They also have mitochondria. The prokaryote has its genetic material, often a single chromosome, lying free in the cytoplasm. Bacteria are prokaryotes. Yeasts are eukaryotes with nuclei.

If you don’t believe in evolution, it would be best if you stopped reading here.

It is generally accepted that the first living cells were some form of prokaryote and may have developed out of protobionts. Fossilized prokaryotes approximately 3.5 billion years old have been discovered (less than 1 billion years after the formation of the earth’s crust), and prokaryotes are perhaps the most successful and abundant organism even today. Eukaryotes only formed later, from symbiosis of multiple prokaryote ancestors; their first evidence in the fossil record appears approximately 1.7 billion years ago, although genetic evidence suggests they could have formed as early as 3 billion years ago.

 

Protobionts are thought to be the precursors of living cells. Maybe the prion, which causes mad cow disease is actually the ancestor of all life. Because of the extreme conditions existing early in the Earth’s history, proteins may have been the original genetic material. Christian de Duve, a Nobel Prize winning biologist, has written a book on the subject. Until the discovery of DNA, proteins were thought to be the genetic material by most biologists. Frederick Griffith began the modern field of genetics when he discovered Transforming Material, which was DNA. DNA “melts” at 87 degrees centigrade, however, and RNA, which will tolerate higher temperature, does not seem to be able to replicate itself without DNA. The origins of life may involve self replicating proteins, like prions.

There has been considerable interest in Archea, a class of organisms found in extreme conditions, because they may have been able to survive in those conditions. Perhaps, they were the first life forms. Originally thought to be bacteria, and first called “Archaeabacteria”, they are quite different and have a different cell membrane composition. First discovered in extreme conditions, like steam vents in the ocean floor or geysers, they are now recognized as widely distributed in all conditions, including ocean plankton. Craig Venter, whom I have previously discussed is collecting ocean water samples looking for useful Archaea samples to study their genome. They may hold the solution to the energy problem, for example.

Mitochondria were probably early prokaryotes in the evolution of life. They carried a unique characteristic. They can create energy from oxygen. As the earth cooled and plants began to develop, the atmosphere, at first made up of methane (which Archaea love) and carbon dioxide (which plants use as fuel), began to contain measurable oxygen. The ability to use that oxygen became desirable. The origin of mitochondria has stimulated intense research. Mitochondria may have been ingested by early eukaryotes and, because they carried the ability to use oxygen and produce more energy than anerobic metabolism, the relationship may have changed from predator to cooperation. Genome sequencing has allowed proof of theories that were only speculation 25 years ago. The mitochondrion has its own DNA. It was almost certainly once freeliving but, as it adapted to symbiosis, it lost unused genes until some types have only three. The study of mitochondrial DNA has contributed to the study of human origins. The “African Eve” theory is derived from the fact that all mitochondria are inherited from the mother. There are no mitochondria in the sperm.

UPDATE: An astute reader pointed out that my statement above is incorrect. Actually, it is a sign of how old I am as this was the previous understanding. However, sperm do have mitochondria but they are tagged for destruction and do not survive in the egg. Why this is, is not explained although the paternal mitochondria may be harmful in some fashion.

Other evidence that mitochondria were once free living come from the study of Rickettsia, cause of diseases such as typhus (which defeated Napoleon’s Grand Army in Russia) and Rocky Mountain Spotted Fever. The organism is named for Ricketts who discovered the organism and lost his life in the process.

That’s enough cell biology for a Saturday morning. The basics of evolution are contained in this story, however.

Tags:, , , , , ,
Posted in general, science | 18 Comments »