Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan 03550, Alicante, Spain.
Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Burjassot, E-46100 Valencia, Spain.
FEMS Microbiol Ecol. 2020 Dec 9;96(12). doi: 10.1093/femsec/fiaa218.
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.
人类对消费产品的需求不断增加，导致众多食品行业（如海水养殖）迅速扩张。然而，过多的营养物质和污染物输入会改变海洋生态系统。在这里，我们应用宏基因组学方法来研究来自金头鲷养殖网箱的样本中的这些干扰。结果显示，具有独特结构的网箱内存在着生物失调和功能失衡，而对来自鱼类微生物群或远离海岸采集的样本的干扰很小。值得注意的是，网箱下方的原核生物群落与近海透光区的海洋微生物组高度相似。我们回收了 48 个新的宏基因组组装基因组。宏基因组分析揭示了微生物群落的显著变化，其中几个变形菌门（鞘氨醇单胞菌目、假单胞菌目、考克氏菌目和根瘤菌目）占主导地位。这些微生物中富含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，以及降解芳香族化合物和其他有毒产物。不利的副作用是抗生素耐药基因数量的增加和潜在出现的病原体的存在。了解这种代谢多样性以及参与生态平衡恢复的微生物，可以用来减少这些实践的环境影响。
