Biofloc technology (BFT) is considered the new "blue revolution" in aquaculture. Such technique is based on in situ microorganism production which plays three major roles: (i) maintenance of water quality, by the uptake of nitrogen compounds generating in situ microbial protein; (ii) nutrition, increasing culture feasibility by reducing feed conversion ratio (FCR) and a decrease of feed costs; and (iii) competition with pathogens. The aggregates (bioflocs) are a rich protein-lipid natural source of food available in situ 24 hours per day due to a complex interaction between organic matter, physical substrate, and large range of microorganisms. This natural productivity plays an important role recycling nutrients and maintaining the water quality. The present chapter will discuss some insights of the role of microorganisms in BFT, main water quality parameters, the importance of the correct carbon-to-nitrogen ratio in the culture media, its calculations, and different types, as well as metagenomics of microorganisms and future perspectives.

The continuous development of world aquaculture demands new strategies and alternatives aimed to achieve sustainability. The use or microorganisms in aquaculture has greatly evolved during the last two decades. From being considered as a potential threat, during the last years, they have been used as probiotics and inclusively as food source for fish and crustacean. The microbial‐based systems represent one of the most viable strategies to achieve a sustainable aquaculture. In short, these systems are based on the promotion of microbial proliferation, either autotrophic or heterotrophic microorganisms; these microbes are expected to use, recycle and transform the excess of nutrients from faeces, dead organisms, unconsumed food and diverse metabolites into biomass, which would be further consumed by the cultured organisms. Successful results on using microbial‐based systems have been documented around the world; however, there are key aspects to consider and yet to experiment before a system could be implemented. Some of those aspects are analysed in this manuscript, while new advances in the use of microbial‐based systems and recommendations are also presented.

Aquaculture has been considered as an option to cope with the world food demand. However, criticisms have arisen around aquaculture, most of them related to the destruction of ecosystems such as mangrove forest to construct aquaculture farms, as well as the environmental impacts of the effluents on the receiving ecosystems. The inherent benefits of aquaculture such as massive food production and economical profits have led the scientific community to seek for diverse strategies to minimize the negative impacts, rather than just prohibiting the activity. Aquaculture is a possible panacea, but at present is also responsible for diverse problems related with the environmental health; however the new strategies proposed during the last decade have proven that it is possible to achieve a sustainable aquaculture, but such strategies should be supported and proclaimed by the different federal environmental agencies from all countries. Additionally there is an urgent need to improve legislation and regulation for aquaculture. Only under such scenario, aquaculture will be a sustainable practice.

The use and study of microbes in aquaculture has become a common practice in the last decade. Metagenomics is a relative recent genomics subdiscipline that has emerged as a promising scientific tool to analyse the complex genomes contained within microbial communities. However, despite the potential of metagenomics, its use is not yet common in some agro-industrial disciplines such as aquaculture. In this review, we analyse some of the potential uses of metagenomics in aquaculture to highlight the microbial diversity and dynamics of the culture systems. This review addresses some potential uses of metagenomics in the study of microbial diversity, microbial roles in microcosms, antibiotic resistance genes, novel and potential pathogens, microbial communities forming bioflocs, probiotics and other applications.

Shrimp polyculture is not yet a common practice among farmers; however, this activity represents an important alternative to solving and ⁄ or minimizing some of the problems that shrimp aquaculture has faced in the past two decades (environmental pollution, diseases and decreasing prices). In this context, many benefits have been achieved with some polyculture practices. Several species from diverse trophic levels have the potential to be co-cultured with shrimps. A good knowledge of the species that are candidates for polyculture and an adequately designed culture system are the most important points to consider when co-culturing shrimp with other species. The present paper is a review of the past, present and future of shrimp polyculture with other organisms.