Abstract：
Recirculating aquaculture systems (RAS) are increasingly being used to grow fish, as intensive water reuse reduces water consumption and environmental impact. RAS use biofilters containing nitrogen-cycling microorganisms that remove ammonia from the aquaculture water. Knowledge of how RAS microbial communities relate to the fish-associated microbiome is limited, as is knowledge of fish-associated microbiota in general. Recently, nitrogen-cycling bacteria have been discovered in zebrafish and carp gills and shown to detoxify ammonia in a manner similar to the RAS biofilter. Here, we compared RAS water and biofilter microbiomes with fish-associated gut and gill microbial communities in laboratory RAS housing either zebrafish (Danio rerio) or common carp (Cyprinus carpio) using 16S rRNA gene amplicon sequencing. The phylogeny of ammonia-oxidizing bacteria in the gills and the RAS environment was investigated in more detail by phylogenetic analysis of the ammonia monooxygenase subunit A (amoA). The location from which the microbiome was sampled (RAS compartments and gills or gut) had a stronger effect on community composition than the fish species, but species-specific differences were also observed. We found that carp- and zebrafish-associated microbiomes were highly distinct from their respective RAS microbiomes, characterized by lower overall diversity and a small core microbiome consisting of taxa specifically adapted to the respective organ. The gill microbiome was also defined by a high proportion of unique taxa. Finally, we found that amoA sequences from the gills were distinct from those from the RAS biofilter and water. Our results showed that the gut and gill microbiomes of carp and zebrafish share a common and species-specific core microbiome that is distinct from the microbially-rich RAS environment.
摘要：
循环水产养殖系统（RAS）越来越多地用于养鱼，集水回用减少了水的消耗和对环境的影响。RAS使用含有氮循环微生物的生物过滤器，可从水产养殖水中去除氨。关于RAS微生物群落如何与鱼类相关微生物组相关的知识是有限的，一般与鱼类相关的微生物群的知识也是如此。最近,在斑马鱼和鲤鱼g中发现了氮循环细菌，并显示出以类似于RAS生物滤池的方式对氨进行解毒。这里,我们使用16SrRNA基因扩增子测序比较了RAS水和生物滤池微生物与实验室RAS中斑马鱼（Daniorerio）或鲤鱼（Cyprinuscarpio）的鱼类相关肠道和g微生物群落。通过对氨单加氧酶亚基A（amoA）的系统发育分析，更详细地研究了g和RAS环境中氨氧化细菌的系统发育。微生物组采样的位置（RAS隔室和g或肠道）对群落组成的影响比鱼类更强，但也观察到物种特异性差异。我们发现与鲤鱼和斑马鱼相关的微生物组与其各自的RAS微生物组高度不同，其特征在于较低的总体多样性和由专门适应各自器官的分类单元组成的小核心微生物组。g微生物组也由高比例的独特分类单元定义。最后,我们发现，来自the的amoA序列与来自RAS生物滤池和水的amoA序列不同。我们的结果表明，鲤鱼和斑马鱼的肠道和g微生物具有共同的和物种特异性的核心微生物组，与富含微生物的RAS环境不同。
