Peering into the Mysterious Microbial World

About the Author: Jacob Metch is a PhD student in Civil and Environmental Engineering at Virginia Tech. Check out his profile on the VTSuN student page.

Bacteria definitely have their dark side occasionally, but as I learn more and more about bacteria it becomes clear that they are actually mostly good, hardworking, intelligent survivors that we can use to protect us from other bad bacteria, clean our water, and nurture our bodies by driving chemical reactions.

Bacteria March Madness
The importance of bacteria in the human body and engineered systems have been underestimated like a Cinderella team in March Madness.


Bacteria are like a Cinderella team in the March Madness NCAA basketball tournament, written off for most of the regular season as not a big player in making a run for the championship, but now researchers can see they may not just make the final four, but win the whole thing! For years we’ve researched important systems like the human body, aquatic environments, and even plumbing in our homes and we failed to recognize bacteria as a key player in all of these systems. Now, to be fair, the tools to really understand them weren’t available until recent years. BUT NOW THEY ARE! And how important bacteria are turning out to be in all of these systems!

The tool that has probably been the most important in this new research is called high throughput sequencing. This is where we take a sample, extract DNA, then sequence a large amount of that DNA to better understand what bacteria are present in that sample.

There is a really interesting Ted Talk given by Dr. Rob Knight about the human microbiome (microbiome just being a fancy word for all the microbes that live in your body). In this talk, he details the importance of the microbiome saying that it weighs about the same as our brains and is likely just as important to our bodies. Microbes are involved in serious conditions, such as obesity and autism, and in other things we would have never imagined, such as whether or not a mosquito wants to bite you.

In engineered systems there are similar revelations happening where we are finally seeing that we have underestimated the importance and capabilities of bacteria. Now researchers are using some of the same tools to look at the microbes growing in the water pipes of your home, and even trying to use good bacteria to beat out the bad bacteria growing in those pipes (Wang et al. 2013).

How beneficial microbes could be used to compete with opportunistic pathogens to make drinking water safer.
How beneficial microbes could be used to compete with opportunistic pathogens to make drinking water safer.

We’re also using these tools to look out for our cleaning bacteria in wastewater treatment plants. Here we basically use a big tank of bacteria to eat and even breathe our contaminates to get them out of the water. This is a large diverse community of bacteria that all have different jobs to do get our water clean. You can think of this kind of like a town, some bacteria are house builders, some are black smiths, some are farmers, and so on. So when we get a new pollutant in our sewer (an emerging contaminant), we need to be able to understand how this will affect our community of bacteria. We don’t want this new contaminant to take out the farmers in our community now do we?

Mini batch reactor
At Virginia Tech, we operate mini wastewater treatment plants and does nanoparticles to them. Then DNA is extracted and the microbial community profiled by high throughput sequencing.

This is what some of us are doing to help out our wastewater cleaning bacteria, we’re seeing how new pollutants affect their community. One of these new possible pollutants is nanoparticles which you can read about in previous blog posts (Dr. Pruden’s, Gargi’s, Ron’s, and mine).   We’ve now seen that when we dose nanoparticles to mini wastewater treatment plants in the lab, indeed some nanoparticles do change our bacteria community (Ma et al. 2015). Fortunately it doesn’t seem to be enough of a change to deter them from cleaning our wastewater for us. This is good news, but also concerning because if we change their community too much it may not work for us in the future. Luckily, with the tools that we have now we can keep looking out for our bacteria friends.


Kight, R. (February, 2014). Rob Knight: How Our Microbes Make Us Who We Are.

Wang, Hong, et al. “Probiotic approach to pathogen control in premise plumbing systems? A review.” Environmental science & technology 47.18 (2013): 10117-10128.

Ma, Yanjun, et al. “Microbial community response of nitrifying sequencing batch reactors to silver, zero-valent iron, titanium dioxide and cerium dioxide nanomaterials.” Water research 68 (2015): 87-97.

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