Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus
Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus
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DOI：
10.1128/msphere.00401-20
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发表时间：
2019-08
期刊：
影响因子：
4.8
通讯作者：
J. Minich;Semar Petrus;J. Michael;T. Michael;R. Knight;E. Allen
中科院分区：
文献类型：
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作者：
J. Minich;Semar Petrus;J. Michael;T. Michael;R. Knight;E. Allen
太平洋鲭鱼（Scomber japonicus）是世界上最大且最具经济重要性的渔业之一。收获这些鱼既可以供人类食用，也可以用作鱼粉。由气候变化等人为压力因素驱动的海洋条件的变化可能会对渔业产生负面影响。一种机制是通过疾病。随着水域变暖和化学变化，与鱼类相关的微生物群落可能会发生变化。在这项研究中，我们对一年时间序列中鱼类的所有粘膜位点进行了整体分析，以探索季节性变化并了解微生物组的环境驱动因素。了解鱼类微生物组的季节性也适用于水产养殖生产，使生产者能够根据海洋环境条件的变化更好地了解和预测何时可能发生疾病爆发。摘要 人类活动导致的海洋条件变化可能会增加压力和疾病，从而对渔业产生负面影响。为了了解环境和宿主生物学如何驱动海洋鱼类的粘膜微生物群，我们调查了 229 条太平洋鲭鱼 (Scuber japonicus) 的 5 个身体部位（鳃、皮肤、食糜、胃肠道 [GI] 和幽门盲肠），这些部位是从斯克里普斯海洋学研究所码头（加利福尼亚州拉霍亚）跨度 1 年的 38 个时间点收集的。粘膜场所具有与周围海水和沉积物群落显着不同的独特微生物群落，其总多样性是海水的 10 倍以上。皮肤和鳃的外表面更类似于海水，而消化物更类似于沉积物。皮肤和鳃的α和β多样性是由环境和生物因素解释的，特别是海面温度、叶绿素a和鱼龄，与暴露梯度关系一致。我们通过对所有时间鱼类样本的 16,568 bp 线粒体的 14,769 bp 区域进行纳米孔测序，验证了季节性微生物变化不会受到鲭鱼亚群的区域迁移的干扰。一种世界性病原体——少女发光杆菌（Photobacter damselae），全年在身体多个部位普遍存在，但在六月到九月海洋最温暖的时候，在皮肤、胃肠道和食糜中含量最高。纵向鱼类微生物组研究评估了环境和宿主生物学驱动粘膜微生物生态的程度，并为将环境压力源与野生海洋鱼类粘膜健康联系起来的长期调查建立了基线。重要性 太平洋鲭鱼（Scommber japonicus）是世界上最大且最具经济重要性的渔业之一。收获这些鱼既可以供人类食用，也可以用作鱼粉。由气候变化等人为压力因素驱动的海洋条件的变化可能会对渔业产生负面影响。一种机制是通过疾病。随着水域变暖和化学变化，与鱼类相关的微生物群落可能会发生变化。在这项研究中，我们对一年时间序列中鱼类的所有粘膜位点进行了整体分析，以探索季节性变化并了解微生物组的环境驱动因素。了解鱼类微生物组的季节性也适用于水产养殖生产，使生产者能够根据海洋环境条件的变化更好地了解和预测何时可能发生疾病爆发。
Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean. ABSTRACT Changing ocean conditions driven by anthropogenic activities may have a negative impact on fisheries by increasing stress and disease. To understand how environment and host biology drives mucosal microbiomes in a marine fish, we surveyed five body sites (gill, skin, digesta, gastrointestinal tract [GI], and pyloric ceca) from 229 Pacific chub mackerel, Scomber japonicus, collected across 38 time points spanning 1 year from the Scripps Institution of Oceanography Pier (La Jolla, CA). Mucosal sites had unique microbial communities significantly different from the surrounding seawater and sediment communities with over 10 times more total diversity than seawater. The external surfaces of skin and gill were more similar to seawater, while digesta was more similar to sediment. Alpha and beta diversity of the skin and gill was explained by environmental and biological factors, specifically, sea surface temperature, chlorophyll a, and fish age, consistent with an exposure gradient relationship. We verified that seasonal microbial changes were not confounded by regional migration of chub mackerel subpopulations by nanopore sequencing a 14,769-bp region of the 16,568-bp mitochondria across all temporal fish specimens. A cosmopolitan pathogen, Photobacterium damselae, was prevalent across multiple body sites all year but highest in the skin, GI, and digesta between June and September, when the ocean is warmest. The longitudinal fish microbiome study evaluates the extent to which the environment and host biology drives mucosal microbial ecology and establishes a baseline for long-term surveys linking environment stressors to mucosal health of wild marine fish. IMPORTANCE Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may change. In this study, we performed a holistic analysis of all mucosal sites on the fish over a 1-year time series to explore seasonal variation and to understand the environmental drivers of the microbiome. Understanding seasonality in the fish microbiome is also applicable to aquaculture production for producers to better understand and predict when disease outbreaks may occur based on changing environmental conditions in the ocean.