Petri and his dishes (and then some)

I was inspired by today's Google doodle, honoring Julius Richard Petri's birthday, to discuss the Petri dish.

A Petri dish culture of a Legionella sp. The genus includes Legionella pneumophila which causes Legionnaires' disease. This is a streak plate, a method used to dilute down a sample to the point where individual colonies can be seen and then counted. 

In modern science, Petri dishes have become a vital tool. Of course, much has changed since the days of Julius Richard Petri. Though the concept of the Petri dish is rather simple--a small isolated environment used for growing whatever small organism the scientist desires--these dishes are used quite widely. Most important, perhaps, are the uses in microbiology, especially in relation to the study of disease.

Bacteria, fungi, and other life cannot simply be grown in a plastic dish. They need a source of food and water. This is provided through some sort of growth medium that is added prior to the addition of the bacteria or other lifeforms. This medium is usually agar-based, agar being an extract from red algae that gels in a similar manner to gelatin. Nutrients are added to the mix, the types of nutrients depending on what is being grown on the plate. Trypticase soy agar, for example, is a very basic medium that a lot of bacteria will readily grow on. After the addition of the growth medium, Petri dishes can referred to as Petri plates.

There are a variety of specialized nutrient media that are used when more information is needed beyond a basic "yep, it's a bacterium." There are selective media, which will prevent the growth of certain lifeforms. This can be helpful when, for example, a scientists wants to know what bacteria are present in a soil sample. Fungi in the soil can overwhelm a plate unless the sample is grown on a medium that inhibits fungal growth.

A plate showing Alpha, Beta, and Gamma hemolysis

Differential media are especially helpful when trying to identify a specific species. Bacteria can show widely different characteristics when grown in contact with various nutrients. A blood plate, one type of differential media, is often used to identify whether bacteria can digest blood cells. This is especially useful when diagnosing infection diseases. Streptococcus pneumoniae, a species that causes one type of pneumonia, can be identified partly thanks to its hemolytic activity, hemolysis being the breakdown of red blood cells. There are three different characteristic types of hemolysis that can be seen by growing bacteria on blood agar: alpha, beta, and gamma. Alpha hemolytic bacteria will only affect the medium that the colony is touching, turning the agar from red to green. Beta hemolytic bacteria cause a rather more dramatic change, removing the color from the media for some distance around each colony. Alpha hemolysis is only a partial digestion of the blood cells, while beta is a complete breakdown of the blood; thus the difference in the results. Gamma hemolytic bacteria, in contrast, cannot digest blood at all. They will feed on the other nutrients in the medium, but the blood will be completely unaffected. The results of growing a pathogen on blood agar can help provide a diagnosis for a sick patient.

One of the most important parts of the process of growing something in a Petri plate is cleanliness. Aseptic technique is vital to prevent contamination of samples, which would skew results. This includes everything from flame sterilization to autoclaving materials; anything that can possibly be done to keep unwanted contaminants away from the sample. I'll never forget the hours I spent in the laboratory during my days learning Microbiology, going through the procedures for aseptic technique over and over again.

Interestingly enough, after an inoculum is added dishes are actually incubated upside down, which may surprise many of you. One of the main reasons for this is to prevent contamination, as spores from various living things then cannot fall down onto the growth medium. Also, condensation cannot drip down from the lid, which would interfere with the otherwise rather stable conditions the Petri dishes provide.

Source is Microbiology with Diseases by Taxonomy, 2nd edition. Images are from Wikimedia Commons and are under Creative Commons licensing or are copyright free: one, two.

The Role of Fire

Generally when people hear the word "fire" all they think of is devastation. However, in nature fire is a complex thing that brings many changes to the environment, not all of which are negative.

Fire can be a great source of good in environments. It cuts back on plant growth, clearing out underbrush. This provides open space for young plants to receive enough sun to grow. Some young plants are even fire resistant and will thrive after others burn. In addition, fire is actually a requirement for certain plants to reproduce. The cone of the jack pine (Pinus banksiana), for example, will only open after they have been exposed to the heat only a fire can provide. There is a natural fire cycle, with the fire clearing out space that plants will then quickly colonize. This is why some plants reproduce only after a fire sweeps through an area: it gives their offspring a better chance of survival.

New life sprouting after a controlled burn

For a very long time the prevailing view concerning fire was that all fire was bad and must immediately be extinguished. This led to some very costly lessons being learned nearly twenty-five years ago.

The fairly recent history of Yellowstone National Park tells how blanket fire suppression can be a very dangerous policy. Many years of suppression combined with a drought in the summer of 1988 turned the park into a tinderbox. The forest ignited and by the time an early September snowfall finally brought the fires down enough to be controlled over one million acres had been touched by flames. Hundreds of large animals died, including over three hundred elk. Dozens of buildings had been destroyed and all told there was approximately $3 million in property damage. $120 million had been spent fighting the fires. Up to nine thousand firefighters at a time had battled the flames.

Perhaps the most tragic aspect to the devastation that hit such a large part of the National Park is the fact that it was largely preventable. Fire management policies have changed significantly since the Yellowstone "Summer of Fire" and for very good reason. The natural fire cycle cuts back on underbrush, preventing it from building up too much. A great many tree species have fire-resistant trunks, so if underbrush is fairly sparse and low to the ground flames can never reach high enough to kill the life that makes a forest a forest: the trees.  If there is a large amount of underbrush, on the other hand, the flames can burn hotter and higher, potentially reaching all the way up to the crown of a tree. Crown fires are far more devastating than fires that stay low to the ground as they can jump from one crown of a tree to the next. This is especially true in areas where the trees grow very close together.  Crown fires can lead to the complete devastation of a forest.

Many small fires will keep a huge, terrible fire from happening in the future.

I have concentrated on forests here, but any environment can be affected by flames. In the future I plan to discuss the link between fire and mudslides in California.

Sources are the Florida Forest Service, National Park Service, and PBS NOVA Online. Image was taken by me.

Running Free in North Carolina

Finally posting these. I went to North Carolina with my family over the weekend. My father found us a series of trails through a forested area that was surrounded by fencing where we let the dogs go. This is the first time I've seen the greys have a chance to do this.

Happy dogs

It was a warm day after a lot of heavy rain and Ebon took a dip in every patch of water we came across. Willow was having an absolute blast. We don't trust her off lead very much yet, for good reason, so this was a treat for her. She saw the long stretch of sand that was the trail and decided it was a good day to run, probably recalling her track days. All three of them ran while we were there. Willow was by far the most entertaining. She was the first to run, and the other two would take off after her. Then, when they got too far away I was very happy to see how quickly she responded to a whistle. Her recall is surprisingly good, but I have no idea how that would change if there was something interesting to chase. Ebon was keeping up with the greyhounds rather well, but they weren't really even trying to run as fast as they can.

Willow also found a huge mud puddle that she decided was a fun thing to run through. The thing was pretty shallow for the most part and she was having a blast running through it until the water deepened and then she froze, not knowing what to do. I don't think she knows how to swim very well. The boys seemed like they rushed to her aid, though Siggy wasn't so sure about the deeper water either. Ebon happily joined her in the puddle and they both then made their way to dry ground.

Poor Willow doesn't know her limits, unfortunately. Her poorly healed back leg is a frequent issues since she just wants to go and go, but the more she runs the more likely it will hurt. She ran until she limped and my father carried her much of the way back to the car.