Microbial Ecology: Methods & Techniques

Instructor: Yuanxin (Amy) Yang Alcocer

Amy has a master's degree in secondary education and has taught math at a public charter high school.

In this lesson, you will learn why tiny organisms are garnering ever more attention from scientists. Also learn about the methods and techniques these scientists use to figure out how crucial these tiny organisms are to life.

Microbial Ecology

Before people knew about viruses and bacteria, scientists and doctors didn't just how much impact these little tiny organisms have on us. But now, thanks to all the scientists that have studies viruses and bacteria and how they affect the human body, you can take antibiotics to control the growth of unwanted bacteria. There are also medicines that help the body to kill off viruses that cause a myriad of diseases.

In addition to microorganisms that affect the body, there are many more that affect the world around us. For example, microorganisms play a big role in the health of the oceans. Many marine animals rely on the ocean's microorganisms for food. The ocean's microorganisms, particularly phytoplankton, are responsible for producing 80% of the oxygen on this planet.

Microbial ecology refers to the study of microorganisms and how they relate to their surrounding environments. This involves not only identifying them, but figuring out what kind of role they play in the world.

A tiny microorganism


Microbial ecologists use a number of methods to accomplish their studies. They'll use the traditional Petri dishes to culture microorganisms, or go out in the field and use various technologies to help them acquire data. This can involve sampling from various environments and using equipment like drones and sensors to gather more data.

For example, when researchers studied the Ligurian Sea in 2013, they used a drone with oxygen and fluorescence sensors to fly over the waters and collect readings. In addition to taking water samples, they also lowered an instrument into the sea from a boat that collected data about temperature, depth, and conductivity.

Testing for phospholipid fatty acids (PLFA) is used to find the presence of microoraganisms in soil samples. Microorganisms impact the nutrients present in soils and so are an important factor to the success of farmers. Some known microorganisms have specific PLFA biomarkers so can be identified with this method.

How can we estimate just how much of a soil sample is made up of microorganisms? Well, one way is the soil fumigate method which uses chloroform to kill off the microorganisms in a sample. Researchers measure the carbon content before and after the fumigation to determine just how many microorganisms died.

Another technique is the staining and counting method, where scientists count the number present in the soil sample, which become easy to spot with the use of stain.

One challenge is that of measuring microorganisms accurately. They are so small, mere nanometers long at time, that new measuring instruments may need to be designed. Just one millimeter is equal to 1,000,000 nanometers.


Because many microorganisms have never been studied before, DNA and RNA sequencing is used to identify them. Using a DNA sequencing machine, scientists are able to discover many new genes as well.

But, DNA sequencing isn't always fast. So, another technique that microbial ecologists use is that of 16S ribosomal RNA sequencing, which gained popularity in the 1970s. This technique looks at just one gene (16S rRNA gene) in the microorganism. It sequences just that one gene and if the difference between two neighbors is less than 97%, then the neighbors are different microorganisms.

To study how these microorganisms relate to their environment, many different sensors are used to gather data. Some studies take samples all on one day. Others sample data over time. Sensors include temperature and oxygen sensors such as those used to study the Ligurian Sea.

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