Time is a stronger predictor of microbiome community composition than tissue in external mucosal surfaces of Atlantic salmon (Salmo salar) reared in a semi-natural freshwater environment
Time is a stronger predictor of microbiome community composition than tissue in external mucosal surfaces of Atlantic salmon (Salmo salar) reared in a semi-natural freshwater environment
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DOI：
10.1016/j.aquaculture.2022.739211
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发表时间：
2022-12
期刊：
影响因子：
4.5
通讯作者：
Marlene Lorgen-Ritchie;Lynn Chalmers;M. Clarkson;J. Taylor;H. Migaud;S. Martin
中科院分区：
文献类型：
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作者：
Marlene Lorgen-Ritchie;Lynn Chalmers;M. Clarkson;J. Taylor;H. Migaud;S. Martin
粘膜表面为外部环境中的机会性病原体提供第一道防线以及其他生理功能，包括肠道中的呼吸调节、气体交换或营养吸收。大西洋鲑鱼是全球养殖的最有价值的鲑鱼物种，其溯河产卵的生命周期决定了在淡水和海水中的生长时期。鱼类在这两种生境之间的过渡往往伴随着高死亡率。栖息在粘膜表面的浮游微生物群落对鱼类健康至关重要，并且在大西洋鲑鱼的海水转移过程中也会受到盐度和温度的突然变化的影响。在这项研究中，我们遵循了一个队列的大西洋鲑鱼通过parr-smolt转换在一个开放的淡水洛赫暴露于自然下降的水温，并在第一个月后转移到大海。从鳃和皮肤采集粘液拭子，并在转移到海洋后的第一周和第四周从淡水（FW）中的四个采样点的一式三份围栏中的n = 6条鱼收集后肠（每次采样共n= 18条）。不同的时间动态和社区被确定在三个粘膜表面。后肠微生物组多样性是稳定的，其特征是在群落组成方面具有较高的个体间变异性。在整个FW饲养过程中和转移到海上后立即，皮肤中的微生物组多样性下降，但在海上一个月后恢复到转移前的水平。鳃微生物组多样性也下降后转移，但继续下降，进一步由于一个单一的优势类群确定为clavichlamydiasalmonicola，一个成员的门衣。所有表面的粘液菌微生物群落在很大程度上与周围的水不同。这项研究强调了在确定鱼类微生物组组成时，考虑时间以及水温和盐度影响的重要性，并敦促在从单个时间点推断微生物组的一般功能时要谨慎。
The mucosal surfaces provide the first line of defence to opportunistic pathogens in the external environment as well as other physiological functions including osmoregulation, gas exchange or nutrient absorption in the gut. Atlantic salmon is the most valuable salmonid species cultured worldwide and its anadromous life cycle dictates periods of growth in both fresh and seawater. The transition of fish between these two habitats is often accompanied by high levels of mortality. Communities of commensal microbes inhabiting mucosal surfaces are vital in fish health and are also subjected to an abrupt change in salinity and often temperature during seawater transfer of Atlantic salmon. In this study we followed a cohort of Atlantic salmon through parr-smolt transformation in an open freshwater loch exposed to a natural decline in water temperature and during the first month post-transfer to sea. Mucus swabs were taken from gill and skin, and hindgut were collected fromn= 6 fish from triplicate pens at four sampling points in freshwater (FW) and in the first- and fourth-weeks post transfer to sea (n= 18 total per sampling). Distinct temporal dynamics and communities were identified in the three mucosal surfaces. The hindgut microbiome diversity was stable and characterized by high inter-individual variability in terms of community composition. Microbiome diversity decreased in the skin throughout FW rearing and immediately post-transfer to sea but recovered to pre-transfer levels after one month at sea. Gill microbiome diversity also declined post-transfer but continued to decline further due to a single dominant taxon identified asCandidatus Clavichlamydiasalmonicola, a member of the phylumChlamydiae. Mucosal microbiome communities in all surfaces were largely distinct from the surrounding water. This study highlights the importance of considering the impact of time, in conjunction with water temperature and salinity, when determining microbiome composition in fish and urges caution when inferring general functionality of the microbiome from a single time point.