A Bug's Life November 26, 1999

Bacteria have been found in some of the harshest environments on Earth. But remember that our immune system makes us an extremely harsh environment also. And bacteria continue to cause us problems. While we may be working to bend bacteria to our will, they are trying to find new and better ways to replicate. Three new papers give just a hint of what is going on in the natural world that we are altering, as we are being altered by the natural world.

Some of the most toxic byproducts of our world today are highly concentrated heavy metal waste. Life does not generally like high concentrations of iron, cobalt, mercury, lead, uranium or cadmium. At least multicellular life. Some bacteria, on the other hand, have learned to live in this sort of an environment. The ability of bacteria to survive the most extreme conditions is both fascinating and frightening. A recent paper in PNAS examines a strain of Pseudomonas which can not only grow on silver, it can "fabricate" it for us also.

As much as 25% of the dry weight of these bacteria can be accumulated as silver. The particular strain examined, Pseudomonas stutzeri AG259, was originally isolated in a silver mine. It is cultured in 50 mM silver nitrate which is very toxic. Three mls of this is enough to kill a mouse. An electron microscope revealed that bacteria grown on silver nitrate were secreting the silver into the periplasmic space. The silver was deposited in vacuole-like granules and was often found in a crystalline form, up to 200 nm in diameter. It is very difficult to manufacture materials on a nanometer scale. Purely physical means are often inadequate. Biological approaches, on the other hand, offer much greater potential for constructing small things. The ability to create and possible deposit nanometer sized crystals of silver has tremendous potential in overcoming many of the problems now being seen in the semiconductor industry. Whether a bacteria like P. stutzeri will have a place can only be seen by future experimentation.

The second report discusses the complete genomic sequence of a nonpathogenic organism I have talked about before, Deinococcus radiodurans. Why is this organism so interesting? Anyone having a passing knowledge of Latin will get a clue from its name. Well, it was first isolated in the '50s -- as a contaminant of irradiated meat. Treating foodstuffs with radiation has some fascinating potential to prevent spoilage. Radiation destroys the DNA of any bacteria and thus, as long as the food is subsequently segregated from a contaminating source, the irradiated food will be edible without refrigeration and will not rot. Get rid of that nasty Salmonella on the chicken, or E. coli on the hamburger. Critics have been worried about alterations the radiation might create in the makeup of the food, so-called daughter products, whose effect in unknown. A problem that I see is that some bacteria have already evolved that can withstand huge amounts of radiation and we might select for others.

Deinococcus has been found in normal environments, such as soil, but it has also been found in Antarctica, in some of the remotest and harshest areas on Earth. Exponentially growing cells are able to withstand 200 times the amount of radiation that E. coli can. Deinococcus is also very resistant to UV irradiation and is extremely resistant to desiccation. This is one tough bug.

How does this bacteria survive these extreme conditions? It most likely evolved survival mechanisms to deal with dehydration. The lack of water has similar effects on bacteria as those caused by radiation -- the cell's DNA is fragmented. This fragmentation was dramatically demonstrated in an earlier paper dealing with the optical mapping of Deinocccus. Cells were treated with 17.5 Grays of radiation. This is almost 10,000 times the amount a human receives in 1 year. Following treatment, the average size of the DNA fragments was 15 kb with over 200 double-stranded breaks per genome. Deinococcus has a tremendous ability to "heal" itself. Analysis of the lengths of DNA show linear elongation with respect to time, with the genome being completely repaired in 24 hours. How this bacteria is able to properly restore its genome to working order is largely unknown, but is an area of active research. Having the complete sequence of the genome should help. There are some exciting hints. Creating forms of Deinococcus that are more efficient at degrading radioactive waste is a possibility. However, the fact that several of the important genes involved in repairing DNA are found on smaller episomes raises the possibility of horizontal transfer of these genes to other bacteria. So, irradiating food may reduce biocontaminants in the short term, it is also possible that we could select for forms that are resistant to radiation, much in the same way antibiotic-resistant forms of bacteria have evolved. If bacteria can do it once, they could do it again. And the next one might not be as harmless as Deinococcus radiodurans.

A bacterium that is anything but harmless is Yersinia pestis, the cause of bubonic plague, the Black Death. This disease has probably wrought more changes in Western civilization than any other single organism. Although endemic in Asia, human trade and warfare are most likely responsible for transporting it to Europe, a population with little natural immunity. The plague has a very distinctive progression. The disease often kills in less than 1 week. The major diagnostic symptom is the appearance of buboes, large, blood-filled nodules on the skin. Lymph glands under the arms and in the neck can be grossly enlarged, weighing up to 1 pound. The disease at this stage is not directly contagious, requiring blood-to-blood contact (i.e. a flea bite) but is fatal in about 50% of the cases. However, about 5-10% of the people develop the pneumonic form, where the bacteria enter the lung. This form is highly contagious and almost always fatal.

The first known outbreak of the plague in Europe occurred around 540 AD and is known as the Justinian plague. Chroniclers of the time state that 70,000 people in Constantinople died in a single year. Justinian was attempting to reunify the Roman empire and might have succeeded but for the plague. It took Europe several hundred years to regain its population. The Moslem populations in the Middle East were spared this outbreak and were able to take advantage of the situation in the succeeding years. A huge effect was seen in the tax receipts of the time (a civilization may fall but accounting records survive forever). There were fewer people to farm the land but the landowners were still responsible for paying taxes. The effects of the labor shortage were profound then, but were even more important in the next outbreak.

This pandemic, starting about 1346, killed almost 33% of all the people in Europe. Think about that. In some areas, the death toll was over 70%. No one was farming and an unknown number of people simply starved. The spread of the disease can almost be traced by the ports of call of specific ships, with the disease rapidly decimating the population (Although decimating literally means killing 1 in 10 and the plague killed 1 in 3). This pandemic had profound effects on the governments and religions that echoed down the centuries. The feudal system was weakened and the resulting labor shortage required changes in the economic systems, helped engender the rise of democracy and increase the power of the middle class.

We are now in the midst of a third pandemic that started in China in the mid-19th century and was responsible for a recent outbreak in India. While not as deadly so far, it still is a potentially fatal disease that antibiotics can only partially control. Proper sanitary conditions and effective rodent control are the best long term defenses.

Now to the final paper. There are 2 other pathogenic species of Yersinia, Yersinia pseudotuberculosis and Yersinia enterocolitica, both waterborne, neither fatal. Y. pestis appears to be extremely similar to Y. pseudotuberculosis. Their 16S rRNAs are identical. Sequencing 6 housekeeping genes only served to further demonstrate the similarities. There are fewer allelic differences between Y. pseudotuberculosis and Y. pestis than there are between strains of Y. pseudotuberculosis. Many of these differences had no effect on the encoded protein. Except for the difference in pathogenicity, these 2 bacteria are more like subspecies.

There are 3 known forms of Y. pestis, called Antiqua, Medievalis and Orientalis. Each form may be responsible for one of the three recent pandemics. A phylogenetic tree comparing the three strains has Orientalis as the youngest form, with the other 2 forms being older. Dating of the last common ancestor between Y. pestis and Y. pseudotuberculosis produces an age between 1500 and 20,000 years ago, depending on the confidence level.

This appears similar to what I discussed in an earlier column. A strain of Y. pseudotuberculosis picked up some genes which allowed it to live in the gut of fleas. Humans, having large stores of grain that attracted rats harboring the fleas, were a ripe niche for the bacteria to invade. The disease killed the most susceptible people, selecting for those that could survive. After almost 1000 years, the bacteria shifted in some fashion, again evading our immune system, and killing millions. Luckily, the third shift does not appear to be as devastating as before. But remember that even as we work to select useful bacteria, they are also working to select us. After all, that is a bug's life.