Research Highlight: Study Suggests Which Feeds Could Work Best for Small-scale Freshwater Aquaculture


A PhD student at Scripps Institution of Oceanography at the University of California San Diego conducted research that could improve freshwater fish farming in developing nations. The study was published recently in the journal MicrobiologyOpen.

Aquaculture–fish, shellfish, or algae farming–accounts for more than 50 percent of total seafood production worldwide and is the fastest growing food sector. Sixty percent of finfish farming is done in freshwater, with most occurring in China and Southeast Asia. With a global population estimated to reach 9 billion by 2050, rapidly-growing developing nations could benefit from investment in aquaculture. In the landlocked southeast African country of Malawi, aquaculture currently amounts to 5 percent of fish production, leaving room for huge opportunities for growth. However, barriers such as feed production and low investment have kept aquaculture at small-scale levels.

Jeremiah Minich, a Scripps Oceanography PhD student in the labs of microbiologists Rob Knight and Eric Allen, studies microbiomes–microbial communities or organisms–that live in and on fish. He wanted to know what small steps could be taken to put fish farming on the path to increased production. He was awarded a Fulbright Scholarship to do just this, and spent seven months in Malawi working directly with local communities that farm tilapia and catfish.

“This experience changed my life, and I am extremely grateful for the Fulbright fellowship,” said Minich. “While living and working amongst the world’s most materially poor, I encountered the deepest joys of community. I became part of a family of 40-plus kids from a local nonprofit children’s home and understood the hardships of village life. From this, I was motivated to continue on with a PhD upon returning to the U.S. and strive to make a difference in these kids’ lives in the future through promoting food security and education.”

In many small-scale aquaculture farms, manure is an efficient fertilizer used to promote natural algal growth that in turn becomes a low-cost feedstock for fish. Common practice teaches that bird manure outperforms cattle or pig manure, but Minich wanted to know if that was the case, and if so, then why.

He and his team, which included recent high school graduates from the village at which he worked, along with researchers from the Malawi National Aquaculture Center, tested different manures–broiler chicken, layer chicken, quail, guinea fowl, cow and pig–in polyculture aquafarms. Each manure was tested for four weeks. Before and after the testing period, the catfish and tilapia were weighed and basic measurements were taken. Microbiome samples of the pond water before and after treatments along with the fish feces were collected and DNA extracted in Malawi and then sequenced and analyzed at the Center for Microbiome Innovation in Rob Knight’s lab.

Minich’s team found that each fish species responded differently to manure treatment; the catfish had great variability between the fertilizers and did best with quail and broiler chicken, and tilapia showed the most growth when they were fed broiler chicken manure. Specifically, tilapia had an 82 percent in weight gain when fed broiler chicken manure for four weeks. When fed quail and broiler chicken manure, the catfish experienced a 125 percent weight gain and a 95 percent weight gain, respectively. A 100 percent weight gain is indicative of a doubling of biomass in the system.

Aware of the health concerns of using manure as feed, and from his initial interest in fish microbiomes, Minich examined the microbiomes of the pond water and fish feces under each manure scenario to test for beneficial (prebiotic or probiotic) effects along with potentially harmful effects including presence of antibiotic-resistance genes (ARGs).

He found that although manure treatments influenced the microbiomes of the water column and the fish, the majority of manure microbes were not detectable in the water column or fish. This suggests that the manure serves as a prebiotic on the system. The microbes that were present comprised less than 13 percent of the total microbial diversity. In addition, ARGs were indeed present in the manure and pond water at similar abundance levels, but much lower in the fish. This would suggest that exposure rates to ARGs may be higher in drinking water than eating fish.

Intercultural exchange undergrad Malawian Moses Simwaka, who is now considering a PhD degree himself, also worked on this project from the Malawi National Aquaculture Center. He helped teach the high school students from the village about aquaculture and research.

“The research gave me a lot of ideas. For instance, it helped me understand the efficiency of different livestock manure apart from the usual chicken manure that we have been using,” said Simwaka. “The research data obtained will help inform new investors and the existing fish farmers.”

"When I arrived at the research lab for microbiome processing, I had an idea to study aquaculture as a course at the university,” said student Cassim Tembo. “This experience gave me additional knowledge and even skills which helped prepare me for college. After this project, I successfully received a government scholarship to study nutrition.”

This research was supported by the Fulbright Scholarship.

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