Aquarium microbial ecology: a living room approach to citizen science

By March 13th, 2012 at 6:39 pm | Comment 1

 Neufeld office Cyphotilapia frontosa. Photo credit: Eric Wheeler

Neufeld office Cyphotilapia frontosa. Photo credit: Eric Wheeler

Sergei Winogradsky discovered nitrifying bacteria in 1890, recognizing that these microbes convert ammonia to nitrate (via nitrite). In aquatic environments, ammonia toxicity to fish is avoided almost exclusively due to the activity of these bacteria…or so it was thought. The ability to remove (or oxidize) ammonia was discovered recently in Archaea, which are an entirely different group of microbes from the bacteria. This discovery overturned a century of dogma regarding nitrogen cycling in the environment.

In 2009, I was beginning a study of wastewater treatment plants and the roles of ammonia-oxidizing bacteria (AOB) and archaea (AOA). To test our protocols, I asked an asked an undergraduate assistant to test our DNA-based detection assay on a sample of sponge filter. Having worked in a large Montreal pet store selling fish for 10 years, I was well aware that AOB were assumed to metabolize ammonia that fish produce. The initial test results from my office were shocking: we could not detect AOB in the filter. Instead, our assay demonstrated lots (and lots!) of AOA DNA.

To confirm this initial observation, we  wanted access to aquariums – dozens of them. For this, we needed help from citizen scientists! We didn’t need to go far. The Kitchener Waterloo Aquarium Society (KWAS) is a large group of hobbyists that meet monthly in a local community centre. We contacted them ahead of their upcoming meeting and requested as many filter samples as we could get, providing careful instructions for sampling both filter and water samples. We also visited aquarium stores in Kitchener, Waterloo and Cambridge; these unsuspecting store managers became voluntary citizen scientists as well.

The results from the aquarium filter in my office were reflected in the aquarium filters we sampled. AOA were dominant ammonia oxidizers in most of the filters – AOB were not detected at all in nearly half of the freshwater aquarium filters. Interestingly, aquaria with higher concentrations of ammonia (overfed, overstocked) had higher proportions of AOB.

So, what started as a test of our protocol on an office filter turned into an exciting citizen science pilot project. Along with my graduate student, Laura Sauder, we returned to KWAS with our results, acknowledged them in our publication in PLoS ONE, and will publish a summary of our study in the next issue of their newsletter. We are also working to expand the citizen science study (stay tuned) to see if we can identify factors that influence the diversity and composition of AOA communities, using aquariums as controlled and distinct microenvironments.

Citizen science is the only way this research would be possible.

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This is a guest blog post by Dr. Josh Neufeld, an assistant professor of microbiology at the University of Waterloo. His research focuses on understanding microbial diversity through next-generation sequencing, characterizing the function of uncultured microbes, and better understanding nitrogen cycling in terrestrial and aquatic environments.

One Response to 'Aquarium microbial ecology: a living room approach to citizen science'

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  1. Any plans to do this in salt-water aquarium?  Do you think this will change the results?


    14 Mar 12 at 1:30 am

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