Aquaculture is the fastest growing food production system in the world and shrimp is currently the most popular seafood in the USA. Like all food production systems, shrimp production needs to intensify to provide for an ever growing demand. However, intensive shrimp farming can have negative environmental and social impacts. There is potential for shrimp farming to expand in the USA, but to culture a warm-water marine shrimp such as Litopenaeus vannamei in the USA, indoor operations need to be explored. In general, shrimp farmers face two major challenges: increase production capacity and achieve this while dealing with nitrogenous (mainly ammonia) waste excreted by shrimp. There are two production systems that can be best adopted for indoor farming: recirculating aquaculture systems (RAS) and bio-floc systems (BFS). The most important microbial groups playing dominant roles in each system are the chemolithoautotrophic nitrifiers and the heterotrophic bacteria in the RAS and BFS, respectively. In aquaculture, microbial communities play roles related to maintaining water quality, providing supplemental nutrition and health benefits for shrimp, and waste management. Managing the microbial resources of shrimp farms will play an essential role in developing a viable indoor shrimp aquaculture industry in the USA that is both competitive and sustainable.
The research will evaluate these two competing technologies in lab-scale systems through a series of experiments using advanced molecular biology and stable isotope methods and will answer the following questions: Will the promotion of a more diverse microbial community of nitrifiers create a more stable RAS? Can the waste produced on RAS biofilters be recycled back into the production tanks to improve feed utilization efficiency? Will the performance of BFS be improved by manipulating solids retention times? How susceptible are shrimp raised in the two systems to an opportunistic shrimp bacterial pathogen such as Vibrio harveyi? The final question of which system we will recommend to shrimp farmers will be answered based on results of these experiments as well as on a rational and comprehensive cost-benefit analysis, which will be provided using life cycle analysis (LCA). To our knowledge, microbial resource management and LCA have not been combined to study and evaluate indoor shrimp aquaculture systems, and have rarely been performed separately on any aquaculture system.