Abstract

The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.

中文翻译：

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通过微生物组分析揭示了海洋水产养殖中的营养不良：逆向生态以实现环境可持续性

摘要

对人类消费产品的需求不断增长，导致许多食品部门的快速增长，例如海洋水产养殖（海水养殖）。但是，过多的养分和污染物投入会改变海洋生态系统。在这里，我们采用了宏基因组学的方法来研究来自金头鲷养殖海洋农场样本中的这些扰动。结果显示，网箱内的菌丝异常和功能失衡具有独特的结构，对鱼类微生物群或远离海岸的样本几乎没有干扰。值得注意的是，在笼子下面，原核生物群落与光化学离岸样品的海洋微生物组高度相似。我们回收了48个新的元基因组组装基因组。元基因组募集揭示了微生物群落的显着变化，该变化主要由几种变形杆菌命令（鞘氨醇，假单胞菌，拟杆菌和根瘤菌）主导。这些微生物丰富了生物修复过程的基因组潜力，包括通过好氧反硝化去除硝酸盐，降解芳香族化合物和其他有毒产物。有害的副作用是增加了抗菌素耐药基因的数量，并出现了潜在的病原体。关于这种代谢多样性和参与生态平衡恢复的微生物的知识可用于减少这些做法对环境的影响。这些微生物丰富了生物修复过程的基因组潜力，包括通过好氧反硝化去除硝酸盐，降解芳香族化合物和其他有毒产物。有害的副作用是增加了抗菌素耐药基因的数量，并出现了潜在的病原体。关于这种代谢多样性和参与生态平衡恢复的微生物的知识可用于减少这些做法对环境的影响。这些微生物丰富了生物修复过程的基因组潜力，包括通过好氧反硝化去除硝酸盐，降解芳香族化合物和其他有毒产物。有害的副作用是增加了抗菌素耐药基因的数量，并出现了潜在的病原体。关于这种代谢多样性和参与生态平衡恢复的微生物的知识可用于减少这些做法对环境的影响。