Aquaculture is a growing industry in Ohio and the Great Lakes region, providing farm-raised seafood ranging from crawfish to walleye. And just like land-based farms, fish farmers spend a lot of time making sure their animals are healthy. Ohio Sea Grant researchers at Bowling Green State University (BGSU) are helping with that.
Dr. Zhaohui Xu, Associate Professor in the Department of Biological Sciences at BGSU, recently provided a baseline of bacterial populations in fish farm ponds that can be used as a reference for future studies. Ohio fish farmers often use commercial probiotics in their aquaculture ponds, but little independent research has been done to determine whether these probiotics actually affect water quality and microbe communities in a meaningful way.
To help future research projects make that determination, the research team monitored water quality at an Ohio sunfish farm over several weeks, and also performed DNA testing on microbial communities drawn from water samples. They found that communities differed quite a lot between ponds on the same farm, between samples taken from the edges of a pond and the center, and with water temperature, regardless of whether they had been treated with probiotics or not.
“Somehow even in those ponds on the same farm, you see that their water and their microbes are very different from each other,” Xu said. “We also interviewed the owner about the history of the ponds, and we suspect the management of the ponds is the biggest contributor of those differences.”
About half of the bacteria found in the samples were not yet identified. “The scientific community estimates that we only know less than one percent [of bacteria in the world],” Xu explained. “Even though microbiology has been established as a discipline for several centuries, we still just know a very tiny fraction about the microbes out there. We know they exist, based on DNA and what we see under a microscope, but we don’t always know who they are or what they do.”
While most of those unknown microbes will likely turn out to be harmless, some of the ones researchers already know about can cause diseases, including in fish that are raised in aquaculture operations.
Dr. Vipa Phuntumart, Associate Professor in BGSU’s Department of Biological Sciences, along with collaborators at The Conservation Fund’s Freshwater Institute in West Virginia and at the USDA Agricultural Research Service’s National Aquaculture Research Center in Arkansas, have developed a method to detect a fish disease caused by Saprolegnia species, a fungal-like pathogen that result in an estimated loss of $40 million to U.S. aquaculture operations.
“Saprolegnia is usually not very serious in aquaculture operations,” Phuntumart said. “However, if the fish are stressed by a rapid change in water temperature, they become immunocompromised and susceptible to these pathogens.” Another potential cause for a decreased immune response is vaccination to protect the fish from viral infections.
By detecting the pathogen in the water before fish show symptoms, aquaculture operations can begin treatment earlier. So the research team developed an assay that combines various molecular testing methods to quantify Saprolegnia in water samples from recirculating aquaculture systems (RAS) that were provided by the Freshwater Institute.
Two molecular assays, loop-mediated isothermal amplification (LAMP) and quantitative polymerase chain reaction (qPCR), were developed to detect the presence of the pathogen in the aquaculture operation, letting fish managers know when to treat the water.
“When people are being treated with HIV drugs, they take a blood sample and they monitor how good the drug is by looking at how much virus is present in the patient sample. So we use the same strategy when they send us a water sample,” Phuntumart explained. “From that sample, we can calculate how much pathogen is present in the larger volume of water, and if it is above the threshold, we would recommend water treatment.”
Treatments include eco-friendly options like hydrogen peroxide or peracetic acid, which break down into non-toxic molecules like water and oxygen.
The researchers expect the same detection method to also work for other pathogens, from fish to plants to humans. In fact, the detection system Phuntumart and her team developed for Saprolegnia includes a dye component that is now being used in a COVID-19 testing kit.
“One of my PhD graduates is now working at a company, using the techniques he learned here, to develop a test for COVID-19,” Phuntumart said, rightfully beaming with pride. That’s the kind of interdisciplinary application of research that any scientist would be proud of.