Marine sediment infauna-based environmental assessment using metabarcoding identifies potential impact indicator species

Developing large-scale monitoring strategies for marine habitats with appropriate temporal and spatial resolution is challenging logistically and economically. We compare potential DNA metabarcoding infaunal identification methods with traditional morphological assessment of marine intertidal biodiversity across two protected sites of contrasting anthropogenic impact on the south coast of England. We show that all the methodologies are effective at distinguishing the distinct communities present at each site. While morphological methods provide community abundance and biomass information, data derived from 18S metabarcoding of sediment scrapes showed the strongest discriminations between sites with contrasting anthropogenic pressures. This difference is due to the inclusion of more taxa from a wider spectrum of biodiversity in this dataset. However, OTU abundance was a poor predictor of morphological taxa abundance and biomass. Examination of the presence or absence of taxa at the more or less impacted site allow us to identify potential indicator taxa for future surveys, such as families in the phyla the Ascidiacea, Cnidaria, Nematoda, and Platyhelminthes; taxa which are not traditionally incorporated into morphology-based assessments due to the difficulty and expense of identification. DNA metabarcoding tools provide a more comprehensive snapshot of marine biodiversity compared to morphological surveys, and therefore an opportunity assess the responses of more organisms to environmental stressors and develop novel metrics for habitat assessment, which could greatly benefit future monitoring programmes and the assessment of management impacts in marine habitats. This dataset provides the FASTQ sequences with primers removed of the metabarcoding datasets (COI and 18S) generated by Nature Metrics.

构建具备适配时空分辨率的海洋生境大规模监测策略，在后勤保障与经济成本层面均面临显著挑战。本研究针对英格兰南海岸两处人为影响程度迥异的保护地，对比了潜在的DNA元条形码（DNA metabarcoding）底内动物鉴定方法与传统形态学潮间带生物多样性评估方案。研究结果显示，所有方法均能有效区分两处采样点各自独特的生物群落。尽管形态学方法可提供群落丰度与生物量信息，但基于沉积物刮样所得的18S核糖体RNA（18S rRNA）元条形码数据，在区分人为压力迥异的采样点时表现出最优的分辨能力。这一差异源于该数据集涵盖了更广生物多样性谱系下的更多分类单元。但操作分类单元（Operational Taxonomic Unit, OTU）丰度并不能很好地预测形态学分类单元的丰度与生物量。通过对受影响程度不同的采样点中分类单元的有无进行分析，我们得以识别出可用于未来调查的潜在指示分类单元，例如海鞘纲（Ascidiacea）、刺胞动物门（Cnidaria）、线虫动物门（Nematoda）与扁形动物门（Platyhelminthes）下的各科类群——这类类群因鉴定难度高、成本高昂，传统上未被纳入形态学评估范畴。相较于形态学调查，DNA元条形码技术可提供更为全面的海洋生物多样性快照，因此为探究更多生物对环境胁迫因子的响应、开发全新的生境评估指标提供了可能，这将极大助力未来的海洋生境监测计划与管理措施影响评估工作。本数据集包含由Nature Metrics生成的元条形码数据集（COI与18S，即细胞色素c氧化酶亚基I与18S核糖体RNA）中已去除引物的FASTQ格式序列。