Eukaryotic 18S rRNA Sequences as part of eDNA analyses of Diel Vertical Migration of Mixed Consortia in the Gulf of Mexico from 2016-05-03 to 2017-05-11

Oceanic diel vertical migration (DVM) constitutes the movement of various mesopelagic organisms migrating vertically daily from depth to feed shallow and return to deeper water during the day. Accurate classification of taxa that participate in DVM remains non-trivial, and there can be discrepancies between methods. DEEPEND consortium (www.deependconsortium.org) scientists have been characterizing the diversity and trophic structure of pelagic communities in the northern Gulf of Mexico (GOM). Profiling has included acoustic echo sounders to provide accurate and quantitative estimates of organismal density and timing. In addition, microbial communities (also known as “microbiomes”) can be characterized via environmental DNA (eDNA) remnants they leave from the surface down to 1600 m depth. We demonstrate that high throughput (HT) sequence analyses would complement ongoing characterizations of DVM via acoustic and net sampling. During two DEEPEND cruises in the GOM, we examined the fine-scale acoustic responses of a vertically migrating layer using an autonomous multifrequency echosounder at about 320 m. We then placed CTDs to collect water samples before and during the upward DVM of organisms. Multiple amplicon libraries (n=40) of 16S rRNA (for prokaryotes) and 18S rRNA (for eukaryotes) were derived and sequenced from 19 pre-, 18 during and 3 post DVM samples. Comparisons of acoustic and microbiome data types have tested the limits of microbial forensics, inferring organismal identities and co-occurrences that could elucidate ecological patterns. This dataset contains genetic sequences collected from seawater samples taken at various depths.

海洋昼夜垂直迁移（Diel Vertical Migration，DVM）指各类中层浮游生物每日开展的垂直迁移活动：日间从深水层移动至浅水区觅食，随后返回深水层栖息。精准鉴定参与该迁移活动的生物类群仍颇具挑战，且不同检测方法间可能存在结果偏差。DEEPEND联盟（www.deependconsortium.org）的科研人员一直致力于解析墨西哥湾北部（Gulf of Mexico，简称GOM）浮游生物群落的多样性与营养结构。本次调查采用声学回声测深仪，以精准定量估算生物的密度与迁移时间。此外，微生物群落（亦称微生物组，microbiome）可通过其在表层至1600米水深范围内遗留的环境DNA（environmental DNA，简称eDNA）进行解析。我们证实，高通量（High Throughput，HT）测序分析可作为声学与网采采样方法的有效补充，助力当前针对DVM的相关研究。在墨西哥湾北部的两次DEEPEND科考航次中，我们借助部署在约320米水深的自主多频回声测深仪，对垂直迁移层的精细声学响应展开了观测。随后我们布设了温盐深仪（Conductivity-Temperature-Depth，CTD），在生物向上进行DVM迁移的前后时段采集水样。研究人员从19份迁移前、18份迁移期间以及3份迁移后的水样中，构建了共计40个扩增子文库（n=40）：其中16S rRNA文库用于原核生物检测，18S rRNA文库用于真核生物检测，并完成了测序。通过对比声学与微生物组数据，本研究验证了微生物溯源技术的应用边界，同时通过推断生物类群的身份与共现关系，阐明了相关生态模式。本数据集包含从不同水深的海水样本中获取的遗传序列。