DNA Sequencing: The Future Of Water And Wastewater Analysis?

By Peter Chawaga

A new tool, one that makes use of cutting-edge technology, has emerged as a potential solution to bacteria contamination in water and wastewater.

Wisconsin-based Microbe Detectives has developed a method of DNA sequencing that can be put to use for analysis of water and wastewater — an improvement, the company claims, to traditional analytical methods.

“DNA sequencing is a new tool for microbiology that provides much more information than conventional culturing tools such as coliform testing,” said John Tillotson, Microbe Detectives’ CEO. “DNA sequencing can identify and quantify nearly all of the microbes in a sample, whereas culturing or even PCR-based methods are limited to detecting one or a small number of target organisms. Additionally, scientists estimate that only about 1 percent of bacteria in a sample will grow in typical culture conditions.”

Stemming from the PhD work of its founder, Dr. Trevor Ghylin, Microbe Detectives is the only company to offer commercial DNA sequencing focused on the water and wastewater treatment industries. To receive an analysis, first its clients use a sampling kit to collect the substance in question. They then ship it to the Microbe Detectives laboratory where DNA sequencing is performed through extraction, PCR amplification, library preparation, bioinformatics, and data analysis.

“Microbe Detectives takes the customer sample, extracts all of the DNA from it, and puts it through a machine called a sequencer,” said Pat Whalen, president and CEO of LuminUltra, who struck a partnership with Microbe Detectives after seeing Dr. Ghylin present at a conference. “The sequencer then reads each individual DNA strand and gives a combination of letters that can be millions of characters long. Those sequences are then referenced against a database to determine from what organism the sequence came and in what general proportion that sequence is present. Once all that data has been compiled, a report is generated indicating what microorganisms are there and at what percentage levels of the total population.”

For drinking water operations, DNA sequencing can provide information on source water quality, on the biofilms used in the distribution system, the biologically-activated filters, and nitrification. It can also clarify positive coliform tests or concerns about taste, odor, and color. While it can’t replace regulation-driven testing, it is a new and more accurate solution for culture testing, contamination diagnosis, and troubleshooting.

On the wastewater side, where operators often rely on bacteria for treatment, DNA sequencing can be used to identify and quantify critical elements like nitrifiers for ammonia removal and bacteria for phosphorus removal. It can provide more information than microscopy or culturing on microbes in an anaerobic digester.

While it is confident about the advantages of DNA sequencing, Microbe Detectives is still working to get such a novel technology adopted as widely as possible.

“Most operators are accustomed to operating their plants in ways that they have for decades, or in some cases, a century or more,” said Whalen. “The solution to that is education and publication. We have to spread the word. Once people are aware of the capabilities and the cost benefit of leveraging these new technologies, there are really no barriers to benefits being realized.”

In one such publicity move, Microbe Detectives tested a puddle on Bourbon Street in New Orleans during the Water Environment Federation’s annual technical exhibition and conference in September. The sequencing found an abundance of fecal-associated bacteria and was able to identify one strain, Prevotella, that is not abundant in the gut of humans in the Western Hemisphere and therefore likely came from a large animal. With the prevalence of parades on Bourbon Street, the company concluded that the contamination was likely from horse manure.

“Compare these results to results we would have gotten from the standard tools used for water quality analysis, such as HPC [heterotrophic plate count] culturing, coliform culturingii, or microscopy,” said Tillotson. “HPC culturing would have provided an inaccurate bacterial count that would be about 1 percent of the actual bacteria in the sample. Coliform culturing may have, or may not have, indicated there are coliforms present, indicating potential fecal contamination, but would provide no identity and no accurate quantification. Finally, a standard microscope would have provided almost no information other than seeing that there are indeed microbes in the sample.”

For those operations that see potential in DNA sequencing to improving their analyses, Tillotson recommends focusing on the most pressing issue and starting there.

“If a drinking water utility is having aesthetic issues, nitrification issues, or unexplainable coliform issues, those would be good problems to start working on,” he said. “On the wastewater side, clients may want to better understand issues with settling, foaming, or ammonia or phosphorus removal.”

Whatever problem they identify, choosing this solution to solve it would put them on the cutting edge.

i PCR, or polymerase chain reaction, is an analytical technique that copies a sample of DNA thousands or millions of times to better understand it.

ii Heterotrophs are microorganisms that require organic carbon for growth, and HPC culturing is a testing method used to recover them from water.