Can DNA Sequencing Technology Help Treat Bacteria?

DNA sequencing can give water and wastewater operators a much clearer picture of the microbial side of their plant processes.
Can DNA Sequencing Technology Help Treat Bacteria?
Trevor Gyhlin, Ph.D., P.E.

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Wastewater treatment plants depend on multiple microbes for their performance, and yet operators typically lack deep information about the different bacteria at work.
Drinking water plants, meanwhile, need to battle microbes that could cause problems in their distribution systems or at customers’ taps.

Now, DNA sequencing technology holds promise to give water and wastewater operators more complete information about the bacteria in their systems. One company offering the technology is Microbe Detectives, formed in 2012. From a sample of mixed liquor (from a wastewater plant) or a sample of well water, tap water or raw water (from a water utility), the company promises a complete microbial profile.

Trevor Ghylin, Ph.D., P.E., founder and chief technology officer, says more complete knowledge of the microbes in their processes can help operators more effectively diagnose problems and make better process control decisions. Ghylin, a former wastewater process engineer and a licensed wastewater operator in Wisconsin, talked about the technology and its promise in an interview with Treatment Plant Operator.

TPO: Please describe in simple terms what your technology does for water and wastewater operations and why it’s better than existing methods.

Ghylin: With DNA sequencing technology we use, we can essentially identify and quantify almost every single microbe that’s in a water sample. Other tools like culturing and microscopy typically are limited to identifying a handful or maybe even just one type of bacteria, depending on the method being used. So those are pretty crude instruments.

TPO: What is an example of where this technology can be useful on the wastewater side?

Ghylin: In wastewater, it allows us to detect things like nitrifying bacteria, phosphorus-removing bacteria, and all the filaments — the foaming bacteria. We can even identify methanogens in digesters. It’s a very powerful tool.

TPO: And where might the technology come into play for a drinking water utility?

Ghylin: In drinking water, coliform is a good example. The total coliform test is the most common test in drinking water, but it is also a very crude tool. It’s supposed to indicate potential fecal contamination, but in reality it picks up various environmental bacteria that are not harmful at all, and doesn’t end up revealing a whole lot about anything. With DNA sequencing, we identify by name everything that is in the sample and how much is there, so there is no ambiguity on whether there is fecal contamination or not.

TPO: Why is it important to know everything that is in a sample? Isn’t it enough to know the main constituents?

Ghylin: It’s true that there are really a dozen or less bacteria that are important in wastewater. But take for example phosphorus-removing bacteria. There are at least three types of bacteria that can remove phosphorus in wastewater plants. If you design a test to target just one of those, that specific microbe might be present, and yet the process still might be removing phosphorus because one of the others is present.

Because we can see everything, you don’t need to start out knowing what is in there or knowing what you’re looking for. The same goes for ammonia-removing bacteria. There are probably a dozen different genera of such bacteria. We don’t have to know which one we’re looking for. We see them all.

TPO: In simple terms, what is DNA sequencing and how does it work?

Ghylin: If you remember from high school biology, DNA is made up of four chemical bases: adenine, thymine, guanine and cytosine, abbreviated by the letters A, T, G and C. An organism’s genetic code consists of arrangements of those letters that make up different genes.

We now have technology that can read the DNA.

So we receive a sample of activated sludge from a wastewater plant and extract the DNA from it. Once we have the pure DNA, we put that into the DNA sequencing machine, which reads the letters from the sample. In a given sample we usually read about 10,000 strings, representing 10,000 bacterial cells. Once we have the strings of letters, we compare them to our database of bacteria to figure out what bacteria and how many are in the sample.

TPO: Can you give an example of how this technology has helped solve an actual problem for a wastewater treatment plant?

Ghylin: One of the clearest examples is biological P removal. Bio-P can be frustrating because you have no information about what is going on in your system other than measuring effluent phosphorus and crossing your fingers. You don’t know if you have got phosphorus-removing bacteria or not.

I had firsthand experience trying to do bio-P with absolutely no information. We finally did DNA sequencing and we found we didn’t have any bio-P bacteria in the system. So obviously we weren’t creating the proper conditions for those bacteria. Once you know that, you can look at adding volatile fatty acids (VFAs) to the system and creating conditions so those bacteria have what they need to grow.

TPO: What is a specific case where this technology is helpful in the drinking water side?

Ghylin: A good example is with nitrification in distribution systems. Many utilities use chloramine as a residual disinfectant. Sometimes they get nitrifying bacteria growing in their pipes and consuming the disinfectant. Again, this is a case where existing tools can’t tell you if you have nitrifying bacteria or not, but DNA sequencing can. We worked with a utility in California on this type of problem. It was very helpful to them to identify that they had nitrifying bacteria, so they could look at remedies.

TPO: In its essence, what makes this method a better way to help monitor and control a treatment operation?

Ghylin: Right now, treatment plants are operated with almost no information about the biology in the system. Typically they have a dissolved oxygen concentration, an MLSS concentration, an effluent BOD level and some other effluent parameters, but that’s about it. It’s pretty limited information, especially if you’re trying to do more sophisticated treatment like nitrification/denitrification or bio-P, or if you have a problem with filaments or foaming. Our method brings information that can be much more powerful.

TPO: Is that true even for plants that make extensive use of microscopy?

Ghylin: Microscopy is great. If you’re trained and you’re willing to do it, it can give you some really fast information. Some bacteria, like Microthrix and a couple of others, are fairly easy to recognize. But it’s pretty limited. A lot of filaments are hard to classify with a microscope. You can’t identify ammonia-removing bacteria or bio-P bacteria.

The other limitation is that it’s difficult to quantify bacteria. Outside of sitting there counting, it’s a pretty subjective measure of how many Microthrix and how many other filaments you have. On the other hand, the DNA data is extremely quantitative.

TPO: How would a water or wastewater operator start working with you on an analysis?

Ghylin: We have online ordering through our website. We ship out a sampling kit with detailed instructions. It’s a simple process, similar to what they would do for any other lab analysis. We provide prepaid return shipping.


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