Bony fish 12S rRNA sequencing data from coastal water samples in gulf of Maine

Ecosystems in coastal waters of Gulf of Maine (GOM) are undergoing environmental challenges in response to climate change and anthropogenic stressors. eDNA metabarcoding, a powerful tool for assessing fish community structure, was used to identify fish communities in three types of GOM aquatic environments (sand, macroalgae, and eelgrass) in Maine and New Hampshire, USA. The available 12S rRNA fish universal primer analysis system was modified using nested PCR (MiFish and 12S-V5) to improve targeting of fish products and reduce to non-target products. The nested PCR strategy allowed successful amplification of 12S rRNA genes in fishes without production of non-target products and identified 28 fish groups at the genus level. Presence/Absence data and Relative Abundance showed significant differences among locales but not among habitats. Myoxocephalus sp. were found at all sampling sites. Relative Abundance data revealed that Menidia menidia and Brevoortia sp. were statistical indicator species in Goosefare, Maine and New castle, New Hampshire, respectively. Although beta diversity indicated that fish communities were not different across habitats, statistical analysis found that Pholis sp. and Ammodytes sp. were dominant species in macroalgae and sand respectively. To our knowledge, this is the first metabarcoding study to assess fish communities in the Western Atlantic region using the MiFish primer set and the study suggests that metabarcoding is useful for mapping geographic and temporal marine fish diversity.缅因湾（Gulf of Maine, 以下简称GOM）近岸水域生态系统正面临气候变化与人为胁迫带来的多重环境挑战。环境DNA代谢条形码技术（eDNA metabarcoding）作为评估鱼类群落结构的有力工具，被用于鉴定美国缅因州与新罕布什尔州境内三类GOM水生环境（沙质生境、大型藻类生境与鳗草生境）中的鱼类群落。研究人员对现有鱼类12S核糖体RNA（12S rRNA）通用引物分析体系进行优化，采用嵌套式聚合酶链式反应（nested PCR）结合MiFish与12S-V5引物，以提升鱼类靶序列的扩增特异性，减少非靶扩增产物的生成。该嵌套PCR策略可成功扩增鱼类的12S rRNA基因，且未产生非靶扩增产物，最终在属水平上鉴定出28个鱼类类群。物种存在/缺失数据与相对丰度数据均显示，不同采样区域间的鱼类群落存在显著差异，但不同生境间无显著差异。杜父鱼属（Myoxocephalus sp.）物种在所有采样点均有检出。相对丰度数据显示，大西洋银汉鱼（Menidia menidia）与布雷沃鲱属（Brevoortia sp.）物种分别为缅因州古斯菲尔（Goosefare）与新罕布什尔州纽卡斯尔（New Castle）的统计指示物种。尽管β多样性分析表明不同生境间的鱼类群落并无显著差异，但统计分析结果显示，绵鳚属（Pholis sp.）与玉筋鱼属（Ammodytes sp.）物种分别为大型藻类生境与沙质生境中的优势物种。据我们所知，本研究是首个利用MiFish引物体系在西大西洋海域开展鱼类群落评估的代谢条形码研究，结果表明代谢条形码技术可有效用于绘制海洋鱼类多样性的地理与时间分布图谱。