Metagenomic Analyses of Biofilms on Whiteleg Shrimp (Litopenaeus vannamei) Effluents: Implications for Worldwide Aquaculture Bioremediation and Environmental Sustainability in the Current Trend of Climate Change and Global Warming–State of the Art and Experimental Proof of Concept

Aquaculture is considered the fastest-growing food supply, invertebrates being a key element; in particular, whiteleg shrimp (Litopenaeus vannamei). They contribute to human welfare, albeit potential negative environmental effects should be properly addressed. Indeed, the environmental impact of aquaculture is lower than using wild captures. Therefore, shrimp aquaculture is reviewed in relation to bioremediation and sustainability, from an ecological perspective. Since metagenomics has great potential for aquaculture, an experimental research using biofilms on whiteleg shrimp effluents is also included, as a proof of concept, given the lack of published results. That revealed a great diversity of microbes: Bacteria, Archaea, Viridiplantae, Fungi and Protozoa. They included 972 species, grouped in 638 genera and 221 families. Interestingly, the Basic Local-Alignment Search Tool (BLAST) algorithm, against the National Center for Biotechnology Information (NCBI) databases, identified 12 species (or genera as spp.) involved in nitrification processes, which are relevant from an ecological point of view, using a restrictive threshold of ≥97%. They included Candidatus nitrosopumilus, Nitratireductor aquibiodomus, Nitratireductor spp., Nitratiruptor spp., Nitriliruptor spp., Nitrosococcus spp., Nitrosomonas aestuarii, Nitrosomonas marina, Nitrosomonas spp., Nitrosopumilus maritimus, Nitrospina spp. and Nitrospira spp. To the best of our knowledge, this is the first report of comprehensive metagenomics on microbiotas of Litopenaeus vannamei effluents. These results have clear implications for such cultures, mainly related to nitrification enhancement, as well as worldwide aquaculture bioremediation and environmental sustainability, in general. That is especially relevant to ameliorate pollution, which is particularly, in the current scenario of climate change and global warming.