Tag Archives: microbiology

The Bacteria Files: Pseudomonas — What it is and why you should know about it

It may not be a household name on the level of E. coli or Salmonella, but this troublesome bacterium is very well known. In medicine and manufacturing, Pseudomonas is high on the list of things you don’t want to have nearby. It all comes down to one particular tendency it has: like a freeloader, a rash, or that one gray hair, once Pseudomonas shows up, it simply will not go away.

Pseudomonas is a genus of gram-negative, rod-shaped bacteria which use flagella for movement. They are typically found in soil and water as obligate aerobes (needing oxygen for survival), but also colonize plant and animal tissues. A colorful group, many of them produce blue-green pigments called pyocyanins. P. fluorescens, as the name suggests, produces a pigment that even glows in the dark. In a lab setting, seeing growth media turn green is a suspicious sign that the organism may be present.

Pseudomonas fluorescens under UV light. Image credits: Biotech Michael / Wikipedia.

A Hospital Hazard

When it comes to Pseudomonads as pathogens, P. aeruginosa is the star of the show. It likes to spend its time in hospitals, thriving on medical equipment, such as catheters and ventilators. It will settle on a surface, get comfortable, and form a large extended family — but it won’t be content to remain there. This microbial opportunist is simply waiting for the right moment to strike.

Supervillain that it is, it has quite a few accomplishments under its belt. Pseudomonas aeruginosa alone is associated with sepsis, pneumonia, dermatitis, urinary tract infections, and infections in cystic fibrosis patients and the otherwise immunocompromised. It’s also special within its genus because it is one of the only Pseudomonads that can maintain metabolism in the absence of oxygen. This is what enables it to stay functional in damaged lung tissue.

In cystic fibrosis, a genetic disorder causes cells to produce a much thicker, more viscous mucus than is typical. In the lungs, this blocks ducts and passageways, and generally makes it difficult for the natural defenses (such as cilia) to function. This is when your opportunist sees its chance. It enters with moist air from a contaminated ventilator, or simply from unwitting, unclean hands touching your face, and settles in the altered mucus of the lung. Now it can do the thing it’s most hated for: it forms a structure called a biofilm.

Scanning electron micrograph of P. aeruginosa. Image credits: Janice Haney Carr, USCDCP.

Once settled, the cells rapidly reproduce and then literally stick together, releasing cellular products to form a slimy matrix. In the end, you have layers and layers of bacteria forming on top of one another until all medication can truly do is cut away at the upper surface. And if the fact that it’s so anchored wasn’t enough, along with Staphylococcus aureus and Klebsiella species, P. aeruginosa is among the best known bacteria in the world for laughing in the face of antibiotics.

As it turns out, P. aeruginosa isn’t limited to only affecting humans from within. It can be the bane of any water bottling plant. Since they tend to live in springs, wells, and other natural sources, with one small error in the process, Pseudomonas could become attached to a factory line. And once the biofilm fully establishes on the equipment, no amount of scrubbing will make it go away. Heavy-duty chemical treatment is required. Their presence can be so pervasive, that manufacturers have been known to just toss out expensive equipment, rather than waste further resources trying to rid themselves of this plague.

Silver Linings

Still, it isn’t all bad news. Many Pseudomonads have made significant positive contributions to human activity as well — from antibiotics and research opportunities to even cleaning up our messes:

P. fluorescens, can be cultured to produce an antibiotic called Mupirocin, used in the treatment of highly resistant bacterial species. It is also found around plant roots and acts to protect them from fungal growths.

P. deceptionensis lives in the Antarctic and has provided multiple avenues of interest. Strain M1T has presented with a previously unknown internal structure called a stack, meanwhile strain DC5 produces silver particles during metabolic processes.

P. aeruginosa, P. putida and a few other species can decompose hydrocarbons and are used in bioremediation. In fact, a strain of P. putida is the first organism to be patented (with much difficulty) because of its potential for use in degrading toluene and naphthalene in soil, as well as converting styrene to a biodegradable plastic, without being a threat to human health.

Deception Island, Antarctica where P. deceptionensis was discovered. Image credits: W. Bulach / Wikipedia.

So, you see, even the worst of them can be used for positive things – it can break down hydrocarbons and is an excellent model for biofilm formation. As with most bacteria, the majority are harmless to humans. But it is always good to be informed and Pseudomonas is just one more thing you should know about.

First biological function of mercury discovered

The element mercury (Hg) is extremely toxic to most organisms, including humans.  It’s deadly effects are thought to be due to it’s ability to block the function of certain key metabolic enzymes.  Being so toxic, it has long been thought that mercury had no biological functions in the living world at all.  At least that was presumption until a research team published the first evidence that a unique group of organisms can not only stand being around the stuff, but actually benefit by the presence of Mercury.   In a paper published this month in Nature Geoscience, D. S. Gregoire and A. J. Poulain show that photosynthetic microorganisms called purple non-sulfur bacteria can use mercury as an electron acceptor during photosynthesis.  These bacteria rely on a primitive form of photosynthesis that differs from the type common to plants.  In the case of photosynthesis in plants, water is used as an electron donor, with carbon dioxide the electron acceptor.  The result of this process is the production of sugars, the release of oxygen, and the removal of carbon dioxide from the air.  Purple non-sulfur bacteria, on the other hand, usually prefer to live in watery environments where light is available to them, but the oxygen levels are low.

Image via Wikipedia.

They use hydrogen as the electron donor, and an organic molecule such as glycerol or fatty acids, as the electron acceptor.  This also results in the production of sugars, but does not release oxygen or remove carbon dioxide from the atmosphere.  This process also generates too many electrons for for their organic electron donor to handle, leading to the potential for damage to other molecules in the cell.

The researcher showed that purple non-sulfur bacteria grow better when mercury is in their environment.  The reason seems to be that the bacteria use the mercury to accept those extra electrons, reducing mercury from a high oxidation state to a low one.  The oxidation state refers to the number of electrons that an atom can gain or lose.  In the case of mercury, when it goes to its low oxidation state after gaining the extra electrons, it becomes a vapor and evaporates away into the atmosphere.  In mercury’s high oxidation state it can form the soluble compound methyl-mercury, which can be toxic to other organisms.

It’s quite possible that the impact of mercury reduction by photosynthesis may extend far beyond the health of these unusual little microbes.  Jeffry K. Schaefer, in the Department of Environmental Sciences at Rutgers University speculates that, “By limiting methyl-mercury formation and accumulation in aquatic food webs from microorganisms to fish, this process may even contribute to less toxic mercury ultimately ending up on our dinner plates.”

Journal Reference:

A physiological role for HgII during phototrophic growth.  Nature Geoscience.  February 2016, Volume 9 No 2  pp121 – 125  D. S. Grégoire & A. J. Poulain  doi:10.1038/ngeo2629

Biogeochemistry: Better living through mercury.  Jeffry K. Schaefer.  Nature Geoscience: News and Views.  18, January 2016.

Louis Pasteur

5 Ways Louis Pasteur Changed the World

Louis Pasteur

Louis Pasteur. Image via Wikipedia.

Widely considered one of the most brilliant scientists in history, Louis Pasteur revolutionized the world as we know it. His breakthroughs have saved countless lives and improved the quality of life for people around the world, and his work paved the way for the field of microbiology. We owe him a lot, at the very least knowing the things he did to change the world:

Germ Theory of Diseases

To most, Pasteur is remembered for his studies on pasteurization, a process named after him, but before he could demonstrate pasteurization, he needed an extra tool — the germ theory of diseases. For most of the medieval times, the prevalent theory regarding illnesses was the miasma theory. The miasma theory claims that diseases such as cholera, chlamydia and the plague were caused by a miasma — a noxious bad air.

In the 1800s, people started questioning the theory, and some scientists (like John Snow) started writing essays about their observations regarding the invalidity of miasma theory. However, it was Pasteur that first proved that germs make us sick. He found not only that microorganisms can make us sick, but he also wrote recommendations on how to kill the germs and protect ourselves.

In order to support his theory, he exposed freshly boiled broth to air in vessels that contained a filter to stop all particles from entering. Nothing grew inside the broths, so it was clear that the things that usually grow in such broths come from outside.


Pasteurization is what Pasteur is chiefly known for today — hey, if they named a word after him, it’s pretty obvious he accomplished something huge. Having previously demonstrated that microorganisms not only cause diseases but also cause foods to ferment and go stale, he realized that by heating beer or wine, he could prevent them from turning sour. This process eliminated pathogenic microbes and lowered microbial numbers to prolong the quality of the beverage.

This is not complete sterilization (which wipes out all the microorganisms) but rather reduces the number of pathogens to the point where it’s very unlikely that the food or drink turns sour. This process is still widely used today, especially for dairy products and beers. So if you like milk or beer, you have Pasteur to thank.

Image via Biographic.com.

Saving the European Silk Industry

While he was working on germ theory, Pasteur also had another major accomplishment: he found that a serious disease of silkworms, pebrine, was caused by a small microscopic organism now known as Nosema bombycis. The French silk industry was already seriously affected, and the disease was starting to spread to other areas.

Pasteur saved the silk industry in France by developing a method to screen silkworms eggs for those that are not infected — this method is still used today.

Immunology and Vaccination

As the man that finally proved how dangerous germs can be, Pasteur felt responsible to work tirelessly on fighting diseases. After a rather strange series of events which included his assistant going on vacation and not doing the work he was supposed to do, Pasteur realized that he accidentally found a way to develop a vaccine.

The notion of a weak form of a disease causing immunity to the virulent version was not entirely new, but Pasteur wanted to develop this method for things like anthrax and cholera. Unfortunately, historical records now show that he took credit for something that wasn’t his idea — he used the method of rival Jean-Joseph-Henri Toussaint, a Toulouse veterinary surgeon, to create the anthrax vaccine. Toussaint never received credit for his work.

So if you read somewhere that Pasteur developed an anthrax vaccine, there’s another side to the story — it’s one of science’s great injustices. However, he still made other great contributions to immunology and vaccination.

The Pasteur Institute

Pasteur founded an institute to carry on his legacy and continue his research. Today, the Institut Pasteur is one of the world’s leading research centers. It houses 100 research units and close to 2,700 people, including 500 permanent scientists and even more visiting scientists.

Among the achievements of scientists working at the institute is a better understanding of diphtheria, a disease that used to kill thousands of children each year, a tuberculosis vaccine, a typhoid vaccine, and many other important achievements.

These are just some of the events which Louis Pasteur, the brilliant scientist, is revered for today. His life wasn’t always glamorous, and he had his fair share of controversy, but he remains one of the most brilliant scientists ever to have lived.