A Temporally Dynamic Gut Microbiome in Atlantic Salmon During Freshwater Recirculating Aquaculture System (RAS) Production and Post-seawater Transfer
A Temporally Dynamic Gut Microbiome in Atlantic Salmon During Freshwater Recirculating Aquaculture System (RAS) Production and Post-seawater Transfer
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DOI：
10.3389/fmars.2021.711797
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发表时间：
2021-07-06
影响因子：
3.7
通讯作者：
Martin, Samuel A. M.
中科院分区：
文献类型：
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作者：
Lorgen-Ritchie, Marlene;Clarkson, Michael;Martin, Samuel A. M.
大西洋鲑鱼养殖正在扩大陆基循环水养殖系统，特别是淡水生产阶段。幼鱼经历幼鱼转化，也称为幼鱼化，并成为预适应海水（SW）。需要研究的一个方面是微生物群落在这一时期的发展，特别是在RAS系统中。在这里，我们分析了大西洋鲑鱼在商业RAS生产设施的小鲑鱼生产期间与肠道相关的微生物组的时间变化，并使用16S rRNA基因测序跟踪了海水转移（SWT）后的同一队列鱼。微生物多样性和丰富度随着时间的推移呈增加趋势，但在swt后1周急剧下降，4周后重新建立起完全不同的群落结构。核心微生物类群可划分为三个不同的类别；(1)无所不在，(2)盐度特异性，或(3)瞬态。通过将饮食和水样品纳入分析，我们将与宿主相关的真正核心分类群，与饮食相关的分类群以及与水箱水中微生物群落相关的短暂核心分类群进行了分类。水中微生物丰富度的上升趋势可能是有机负荷增加的结果，而弧菌科的优势可能归因于RAS生产过程中保持的较高温度和swt后高于平均水平的自然水温。功能分析表明swt后代谢途径的调节，但在商业环境中对鱼类生长和健康的下游影响仍有待阐明。更深入地了解微生物组成和功能之间的相互作用，可以在严格调控RAS生产的情况下优化鱼类生产性能。
Atlantic salmon aquaculture is undergoing an expansion of land-based recirculating aquaculture systems (RAS), especially for freshwater (FW) stages of production. Juvenile salmon undergo parr-smolt transformation, also known as smoltification and become pre-adapted to tolerate seawater (SW). One aspect requiring study is the development of microbial communities during this time, especially in RAS systems. Here we analyzed temporal changes in microbiome associated with the intestine in Atlantic salmon during smolt production in a commercial RAS production facility and followed the same cohort of fish post-seawater transfer (SWT), using 16S rRNA gene sequencing. Microbial diversity and richness showed an increase over time across FW production, but declined sharply and significantly 1-week post-SWT before re-establishing itself with a completely different community structure after 4 weeks. Core microbial taxa could be assigned to three distinct categories; (1) omnipresent, (2) salinity specific, or (3) transient. By including diet and water samples in the analyses, we classified true core taxa associated with the host, those associated with the diet, and transient cores associated with microbial communities in tank water. The rising trend observed in microbial richness in the water may be a consequence of a temporal increase in organic load while dominance of Vibrionaceae may be attributed to the higher temperatures maintained during RAS production and above average natural water temperatures post-SWT. Functional analysis suggests modulation of metabolic pathways post-SWT, but downstream impacts on fish growth and health in a commercial setting remain to be elucidated. A deeper understanding of the interplay between microbial composition and functionality can play a role in optimizing fish performance in tightly regulated RAS production.