Data from: Wangensteen, O.S., Palacín, C., Guardiola, M. & Turon, X. Metabarcoding shallow marine hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers

We developed a metabarcoding method for biodiversity characterization of structurally complex natural marine hard-bottom communities. Novel primer sets for two different molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase, COI, and the V7 region of ribosomal RNA 18S were used to analyse eight different marine shallow benthic communities from two National Parks in Spain (one in the Atlantic and another in the Mediterranean). Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. We found unexpectedly high values for MOTU richness, suggesting that these communities host an astonishing amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignation of the detected sequences. Nevertheless, over 90% (in abundance) of the sequenced reads could be successfully assigned to phylum or lower taxonomical level. This identification rate might be significantly improved in the future, as reference databases are updated. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples, and emerges as a robust, fast, objective and affordable method for comprehensively characterizing the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans, allowing for standardized biomonitoring of these ecologically important communities.本研究开发了一种用于结构复杂的自然海洋硬质底栖群落生物多样性表征的元条形码测序（metabarcoding）方法。针对两种不同分子标记设计的新型引物组——线粒体细胞色素c氧化酶的"Leray片段"（COI）以及核糖体RNA 18S的V7区——被用于分析西班牙两处国家公园（一处位于大西洋，另一处位于地中海）的8种不同海洋浅海底栖群落。将样品筛分至三个粒径分级，并分别从各分级中提取脱氧核糖核酸（DNA）。采用贝叶斯聚类法划分分子操作分类单元（Molecular Operational Taxonomic Units，缩写MOTUs），并构建定制化参考数据库以完成分类学赋值。本研究发现MOTU丰富度数值远超预期，表明此类群落蕴含着数量惊人的、尚未被记录的真核生物多样性。当前序列参考数据库仍存在显著缺口，这导致目前无法对检测到的序列完成完整的分类学赋值。尽管如此，超过90%（按丰度计）的测序读段可被成功赋值至门级及更低的分类阶元。随着参考数据库的更新，该鉴定准确率有望在未来得到显著提升。本研究结果表明，当前多应用于浮游生物或沉积物的海洋元条形码测序技术，可适配结构复杂的硬质底质样品；该技术可作为一种稳健、快速、客观且经济的方法，全面表征以大型海藻、群居或模块化固着后生动物为主的海洋底栖群落的多样性，从而为这些具有重要生态意义的群落提供标准化生物监测手段。