CSU environmental engineers developing tool to sustainably clean water using microbes

Researcher Neh Sachdeva collects sediment samples from a ditch where effluent water is discharged after treatment.
Neha Sachdeva collects sediment samples from a ditch where effluent water is discharged after treatment.

Treated wastewater can contain very small amounts of pollutants that are not entirely removed through standard treatment methods and could end up in our drinking water. Colorado State University scientists are creating a new molecular tool to identify bacteria that could be key to cleaning our water and protecting human and ecosystem health.

Chronic exposure to trace contaminants – which come from medicines, personal care products, sunscreen, antimicrobial chemicals, flame retardants, pesticides and herbicides – may be bad for human health. Fortunately, many of these contaminants can be broken down by bacteria, although we don’t yet know which bacteria are most useful for this purpose.

Susan De Long, an associate professor in the Department of Civil and Environmental Engineering, and postdoctoral fellow Neha Sachdeva are developing a Functional gene Amplicon Sequencing test, or FASt, to find and measure these important bacteria. FASt will use next-generation gene-sequencing technology to identify specific, “functional” genes that control the chemical reactions bacteria use to break down trace organic contaminants, or TOrCs.

“We’re dealing with this really complex system of a bunch of different contaminants at once,” De Long said. “Our goal is to use high throughput, newer techniques to study a bunch of contaminants at once, a bunch of microbes at once, and use next-generation gene sequencing-enabled technologies to figure out which microbes are able to degrade these compounds.”

More than a catchy acronym

Erlenmeyer flasks containing sediment samples rest on a shelf.
Sediment samples are cultivated with pharmaceuticals to activate microbes capable of degrading them.

An amplicon is the result of amplification, or replication, of genetic material. Amplification is helpful in detecting genes of interest. This technique is used in PCR tests to find SARS-CoV-2, the virus that causes COVID-19. If the test is positive, an amplicon is present.

Sequencing reveals the exact content of an amplicon. De Long and Sachdeva will use amplicon sequencing to figure out which genes are active when the contaminants are broken down.

The new test is intended to quickly find the useful bacteria that can degrade the contaminants, and the genes that are key to that process – hence its name, “FASt.”

Once De Long and Sachdeva narrow the microbe selection to those that are useful, they can design engineered systems that grow and support those types of microbes.

A greener approach

Many of the current treatment technologies are energy intensive; they require resources and leave behind waste products. This project aims for a more sustainable approach by using bacteria that can naturally biodegrade contaminants.

“Water resources are getting scarce,” Sachdeva said. “We need to recycle water to meet the needs. It’s important that we use cost-effective and energy-efficient technologies for that. This project will bring us a step closer to achieving that goal.”

Microbes of interest

The researchers are targeting enzymes responsible for the metabolism of pharmaceuticals in human bodies. These enzymes are found in our bodies’ microbiota and throughout nature.

De Long and Sachdeva have found promising bacteria near wastewater treatment facilities, in the sediment over which treated effluent water flows on its way to rejoin surface water. De Long believes the microbes in this sediment may have adapted to low levels of pharmaceuticals and other common contaminants that are not completely filtered out during the treatment process.

The researchers sampled this sediment and subjected its microbes to high concentrations of 12 pharmaceutical compounds for eight weeks. They then genetically analyzed the samples and found an abundance of the targeted enzymes. Now they are working to sort out which enzymes were activated in response to the pharmaceuticals.

These early results are encouraging, as De Long and Sachdeva set their sights on a scalable, sustainable water purification method.

About the team

Neha Sachdeva examines a flask containing sediment samples.
Neha Sachdeva checks cultures for growth and takes samples for DNA extraction.

The National Science Foundation funded this research. Jessica Prenni, an analytical chemist and associate professor in the Department of Horticulture and Landscape Architecture, and Julia Sharp, an associate professor and director of the Graybill Statistics and Data Science Laboratory, are co-investigators.

De Long recruited Sachdeva to CSU to make this project possible. Sachdeva brought expertise in fundamental biology, molecular tools, bioprocess engineering, and bioreactor design and operation. She received her Ph.D. from the University of Mons in Belgium, where she studied wastewater remediation for space applications in collaboration with the European Space Agency. A former scientist at the Roche pharmaceutical company, Sachdeva has experience developing tools to detect biological markers, a critical skill for this project’s objectives.