The core of my lab’s research program is based on interactions between aquatic ecosystem features and microbial communities. Within this general framework, I am particularly interested in how human activity influences the genetic content, community distribution, and ecosystem-level output of microorganisms in both natural and built aquatic systems. My scientific training has included microbial-based research in: 1) inland freshwaters examining the spatial and temporal distribution of bacteria in lakes around the world, 2) coastal oceans interrogating the gene expression of a model ocean bacterium and identifying the response of bacterial communities to ecosystem disturbance, and 3) built aquatic systems describing how human environmental inputs combine to create a unique ecosystem in urban pipes.
My students and I are currently pursuing research that integrates microbial ecology at the interface between built and natural water systems. We have active projects on the microbial gene patterns in the Laurentian Great Lakes, the genes and microbial composition in wastewater and drinking water conveyance systems and activated sludge, and the influence of diet and fish gut microbial communities. We also are working to develop tools to tease apart the environmental sources of microbial mixtures found in many surface water systems.
FRSHWTR 514 - Analytical Techniques in Freshwater Sciences (Spring semester every year)
This course is co-taught with Dr. Laodong Guo. This course focuses on two groups of techniques that are used to study aquatic systems: a) modern analytical/geochemical techniques (2 credit hours) and b) nucleic acids/genomics principles and methods (1 credit hour). The course is designed to provide students with the theoretical basis for and hands on experience in using analytical instruments/techniques and genomic methods as applied to aquatic systems. Students will gain an understanding of the principles, procedures, instrumentation, and applications of these methods. The knowledge and skills gained from this course should provide a broad range of approaches that can be applied to student research projects or in the workplace.
FRSHWTR 564 – Water Quality in Aquaculture (Spring 2016, 2017, 2019, 2020)
This is a blended course (1/2 online and 1/2 in laboratory) and is part of the School’s Undergraduate Certificate in Applied Urban Aquaculture. Students learn fundamental knowledge about how water properties and the microbiome of aquaculture systems impact operations and contribute to fish health and how operator controls can alter these dynamics.
FRSHWTR 640 - Sequence Analysis (Spring semester in odd years)
This course is designed to give students an understanding of biological sequence information (i.e. nucleic and amino acid sequences). Students will explore the relationship between the biology of nucleic and amino acids and the assignment of computational information to represent that biology for sequence-based analyses. Emphasis will be placed on how sequence information is generated and formatted, how sequences are compared and assembled computationally, and what modern online tools are available to interrogate individuals, populations, and communities. Examples in class will draw heavily from studies of microorganisms.
FRSHWTR 660 & 661 - Professional Capstone Planning & Undergraduate Capstone (Spring & Fall every year)
This is a two part course that serves as the culmination of the BS degree in Freshwater Sciences. Students participate in a 1-credit planning course (660) to learn about communicating with environmental professionals and form a team to develop a capstone project proposal. This proposal will be implemented by the team in the following semester (661).
FRSHWTR 512 – Practicum: Developing Technologies for Aquatic Sciences (Spring 2016)
This course typically runs in the spring. The primary instructor is Dr. Matthew Smith. Students work in groups to research, propose, and then develop a technology for use in the aquatic sciences. Technology development can include a range of projects from instrumentation to molecular biotechnology.
FRSHWTR 650 – Intro to Aquatic Genomic Methods (summer 2016)
This is a blended course designed as both a credit-based course and as a workshop for non-students. Participants/students in the course will learn about proper lab techniques for collecting a processing water samples for DNA extractions, PCR, qPCR, microbial community composition analysis, and genomics. The class is offered with a 1-week intensive lab component and 4 weeks of online content.
FRSHWTR 690/901 - The Zen of Water & Beer (Fall 2015, Fall 2016, Spring 2018)
This course typically runs in the fall. It is a seminar based course that allows students to interact with local professionals in the brewing industry. Students will visit local brewing facilities ranging from one-room 0.5 barrel production operations to global businesses to discuss the procedures, environmental constraints, and business of brewing.