Clarkson Applying Novel Techniques to Study the Microbiome of the St Lawrence River

Clarkson University biologists are participating in a scientific research cruise on the St Lawrence River onboard the research vessel Lampsilis, the chief research vessel of the Université du Québec à Trois-Rivières. This 12-day research expedition will traverse the entire length of the St. Lawrence River, from its headwaters at Lake Ontario downstream past the City of Montreal to Quebec City where the river enters the Atlantic Ocean as it phases through an estuary. According to Biology Professors Shantanu Sur and Michael Twiss, the principal investigators of the Clarkson-led research project that is an integral component of the overall research plan, the objective is to determine how the microbiome – the composition of microbes such as bacteria, cyanobacteria, microalgae and fungi – changes with changes in water quality as the river flows downstream.

Twiss explains "The Saint Lawrence River is a globally significant river that is the largest riverine source of freshwater to the North Atlantic Ocean. It is the natural outflow of freshwater from the Great Lakes system, which contains 20% of the world's freshwater. It is impacted by human activity in its headwaters and as it passes both point sources, like sewage outfalls, and non-point sources of pollution, such as tributaries that drain agriculturally intense regions in the St. Lawrence River valley. Similar research we did in 2018 showed changes in nutrient levels and phytoplankton community. This time we are opening the doors wide open to investigate more closely the microbiome in this major river."

"We are going to use nanopore DNA sequencing technology to study the microbes in river water samples," Sur mentions. "This emerging technology offers several advantages over conventional sequencing techniques, including the ability to sequence very long lengths of DNA even for samples from complex microbial environment. Therefore, we will not only identify the microbes in a sample but also be able to extract any additional information, such as the profile of antimicrobial resistance genes in the microbiome. More importantly, the sequencing will be performed in the lab by our students, and therefore, they will have the opportunity to experience the entire process from sample collection to bioinformatics analysis."

Onboard the Lampsilis are Clarkson graduate students Kelsey Cullen (Alexandria Bay, NY) and Maria Pelusi (Ogdensburg, NY). Cullen is in the Interdisciplinary Bioscience & Biotechnology program and Pelusi is a graduate student in the Environmental Science & Engineering program. Together with Austin Marshall (Clayton, NY) these graduate students will be collecting the required samples, processing the samples on the ship and back in the campus laboratory, and initiating the data analysis that will explain the ecological changes that occur in the river. "Interestingly, each of the students grew up along the St Lawrence River, graduated with bachelor degrees from Clarkson, and now are committing themselves to higher degrees and expanding our understanding of this great river. They jumped at the chance to participate in the project, which is akin to getting time onboard the International Space Station – not everyone gets to go", states Twiss.

This research is funded by a grant from the Reseau Quebec Maritime to Dr. Francois Guillemette of UQTR, and the chief scientist of the cruise is Elizabeth Grater, UQTR. Clarkson University support for research is provided by a grant to Drs. Sur and Twiss from the St Lawrence River Research and Education Fund.