Minich Jeremiah J, Nowak Barbara, Elizur Abigail, Knight Rob, Fielder Stewart, Allen Eric E
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.
Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia.
Front Mar Sci. 2021 May;8. doi: 10.3389/fmars.2021.676731. Epub 2021 May 13.
The fish gut microbiome is impacted by a number of biological and environmental factors including fish feed formulations. Unlike mammals, vertical microbiome transmission is largely absent in fish and thus little is known about how the gut microbiome is initially colonized during hatchery rearing nor the stability throughout growout stages. Here we investigate how various microbial-rich surfaces from the built environment "BE" and feed influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, , over time. For the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish mucous (gill, skin, and digesta), the BE (tank side, water, inlet pipe, airstones, and air diffusers) and feed were sampled from indoor reared fish at three ages (43, 137, and 430 dph; = 12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. The gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut "allochthonous" microbiome becomes increasingly differentiated from the environment over time. Feed had a relatively low impact on driving microbial communities. Our findings suggest that mucosal microbiomes are differentially influenced by the BE with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to biofouling in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.
鱼类肠道微生物群受到包括鱼饲料配方在内的多种生物和环境因素的影响。与哺乳动物不同，鱼类中基本不存在微生物群的垂直传播，因此对于在孵化场养殖期间肠道微生物群最初是如何定殖的，以及在整个生长阶段的稳定性知之甚少。在这里，我们研究了养殖环境“BE”中的各种富含微生物的表面和饲料如何随时间影响一种经济上重要的海洋鱼类——黄尾鰤的粘膜微生物群（鳃、皮肤和消化物）的发育。在第一个实验中，我们从饲养在三种水箱条件下的36条鱼中采集了鳃和皮肤微生物群，并证明鳃比皮肤更容易受到周围环境的影响。在第二个实验中，从三个年龄（43、137和430日龄；每个年龄n = 12）的室内养殖鱼中采集鱼粘液（鳃、皮肤和消化物）、BE（水箱壁、水、进水管、气石和空气扩散器）和饲料。在430日龄时，从室外海洋网箱中额外采集了20条鱼。总共处理了304个样本用于16S rRNA基因测序。鳃和皮肤的α多样性随年龄增加，而肠道多样性随年龄降低。与室内养殖的鱼相比，海洋网箱中的鱼的多样性要低得多。鳃和皮肤在发育早期最受BE影响，曝气设备在后期影响更大，而肠道“外来”微生物群随着时间的推移与环境的差异越来越大。饲料对驱动微生物群落的影响相对较小。我们的研究结果表明，粘膜微生物群受到BE的不同影响，鳃和皮肤中微生物群周转快、演替迅速，而肠道微生物群更稳定。我们展示了孵化场系统的各个组成部分，特别是曝气设备，如何直接促进海洋鱼类微生物群的发育。此外，结果表明养殖环境中早期（幼体）接触生物污垢可能会影响鱼类微生物群的发育，这对动物健康和水产养殖生产很重要。
