Carp polyculture is the most widely practiced fish production system in the world that makes use of the diverse trophic and spatial niches of a pond to maximize fish output per unit space. In Bangladesh, with over 1.1 million tons of annual carp production (2019-20), WorldFish has supported hundreds of thousands of farmers in improving their production over several decades. While microbiome management has been hailed as the next generation of advice to farmers to improve productivity and minimize disease incidence, there exists a large knowledge gap to connect the sparse scientific data with practical farm implementation. WorldFish commissioned a review of the current status of carp polyculture microbiomes from contemporary scientific, grey literature and current best management practices.
Here we present the current state-of-the-art knowledge of carp microbiomes and highlight the knowledge gaps and opportunities for future microbiome management. Research on microbial communities in carp polyculture is still in its early stages, with most studies performing exploratory analyses of the microbial assemblages of fish organs (skin, gill, gut) and their rearing environments. As a result, disentangling interactions and identifying keystone species for specific functions in microbial communities has proven difficult because of the complex structure of these communities (viruses, bacteria, microalgae, fungi, etc.), especially when environmental impacts on population dynamics and metabolic pathways are taken into consideration. The functions of these microorganisms, as well as correlations and causation in relation to enhancing carp production, remain largely unknown. Despite industry awareness, little work has been undertaken to determine the effect of input factors such as substrate, feeds, fertilizers, sanitizers, and microbial products on carp polyculture microbiomes and how their manipulation, together with environmental parameters, can be better managed and used productively.
Technological issues, in addition to the sparse scientific data, have also hindered the research and development of microbiome management strategies. To date, most studies of carp microbiomes have relied on semi-quantitative molecular approaches, such as 16S rRNA gene amplicon sequencing. However, we argue that combining this technology with alternative and quantitative methods will be crucial to understanding and steering the compositional community dynamics in aquaculture ecosystems. Such integrated approaches, utilizing new tools such as flow cytometry (e.g. Kytos) will facilitate a far greater understanding of the microbial ecology of carp polyculture systems. Future research should be organized in a holistic way to document the composition, diversity, functional roles, and potential manipulation of carp polyculture microbiomes. This holistically curated database will lay the foundations on which novel microbiome management advice will be based and through which resilient and productive carp polyculture systems can be achieved.