Intensive aquaculture food production has been continually increasing over the past decades. Recirculating aquaculture is an innovative technology which relies on water reuse and removal of toxic metabolites by utilizing specific prokaryotic groups such as nitrifiers, settled in special biofilters. Focused on recent next generation sequencing-based studies on the microbiome of recirculating aquaculture systems, this review highlights dominant genera and families, and investigates their possible metabolic function in key niches within recirculating aquaculture systems (rearing water, biofilters and fish mucosal microbiome), while aiming to identify core prokaryotic groups across studies. A total of 136 genera belonging to 77 families and 13 phyla have been characterized as dominant or functionally important in relevant studies, mainly isolated from nitrification biofilters, system water and intestinal samples of the farmed species. Proteobacteria is undoubtedly the most abundant phylum, followed by Bacteroidetes, Firmicutes and Actinobacteria, while Rhodobacteriaceae and Flavobacteriaceae are the common dominant families. Nitrosomonadaceae and Nitrospira members are enriched in biofilter samples and serve as the most common ammonium and nitrite oxidizers, respectively. Composition of dominant genera appears system specific due to unique characteristics of individual RAS designs, although faint community patterns emerge when examining RAS by their salinity level. Considering the number of ribosomal RNA operon copies, 75% of genera are likely slow growers, dominating biofilter and water communities, whereas the few fast-growing opportunists are mainly associated with the intestine of farmed species. Finally, this review stresses the lack of information regarding archaeal and microeukaryotic communities in recirculating aquaculture systems and prokaryotic–protist interactions.

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海洋和淡水循环水产养殖系统中的原核生物多样性

在过去的几十年中，集约化水产养殖食品产量不断增加。循环水产养殖是一项创新技术，它依赖于水的再利用和通过利用特定的原核生物群（如硝化菌）去除有毒代谢物，并放置在特殊的生物过滤器中。本综述重点关注最近基于下一代测序的循环水产养殖系统微生物组研究，重点介绍了优势属和科，并研究了它们在循环水产养殖系统（养殖水、生物过滤器和鱼类粘膜微生物组）关键生态位中可能的代谢功能，同时旨在确定跨研究的核心原核生物群。在相关研究中，共有 136 个属属于 77 个科和 13 个门，已被定性为显性或功能重要，主要从养殖物种的硝化生物过滤器、系统水和肠道样本中分离。变形菌门无疑是最丰富的门，其次是拟杆菌门、厚壁菌门和放线菌门，而红杆菌科和黄杆菌科是常见的优势科。亚硝化单胞菌科和Nitrospira成员富含生物过滤器样品，分别作为最常见的铵和亚硝酸盐氧化剂。由于个别 RAS 设计的独特特征，优势属的组成出现系统特异性，尽管在通过盐度水平检查 RAS 时会出现微弱的群落模式。考虑到核糖体 RNA 操纵子拷贝的数量，75% 的属可能是缓慢生长的，主宰生物过滤器和水群落，而少数快速生长的机会主义者主要与养殖物种的肠道有关。最后，本综述强调缺乏关于循环水产养殖系统和原核-原生生物相互作用中古细菌和微真核生物群落的信息。