18S metabarcoding of Arctic meiobenthic nematodes

The nema_novaseq_raw dataset contains DNA reads from a total of 156 samples including extraction negatives, and nematodes. The purpose of the study was to investigate the trophic interactions of Arctic meiobenthic nematodes using a "brute force" prey metabarcoding approach (Flo et al., 2024). Sediment was collected on four locations (process stations P1, P4, P6 and P7) along a transect from the Barents Sea to the Arctic Nansen Basin in August 2019 (Q3), December 2019 (Q4), March 2021 (Q1) and April/May 2021 (Q2) with a box-corer, and fixed on ice-cold ethanol (96%, -20 deg C). Up to 11 biological replicates of nematodes were picked from each station from each cruise, and the samples are named accordingly (i.e. nm_1_7_11 contains a nematode from cruise Q1, station P7, and biological replicate number 11). Replicate number 12 in each set if samples (i.e. nm_1_7_12) are always extraction negatives. DNA from picked specimen were extracted using the E.Z.N.A Tissue DNA kit (Omega Bio-Tek), and tested for contamination by amplification of V7 18S SSU rDNA and subsequent 1% gel-electrophoresis. We amplified the 18S SSU rRNA V7 region (~100 – 110 bp) with 18S_allshorts primers (Forward 5’-TTTGTCTGSTTAATTSCG-3’, and Reverse 5’-GCAATAACAGGTCTGTG-3’, Guardiola et al., 2015) and sequenced cleaned product on two lanes of the Illumina Novaseq platform using 150 PE chemistry. The raw data was explored and processed on an HPC into a zOTU-table with sample-wise numerical abundances and taxonomy from the Protist Ribosomal database (PR2/v.4.14.0), using a combination of FastQC/0.11.9, BLAST+/2.8.1, OBITools/1.2.12 and VSEARCH/2.9.1 utilities. More information about processing, including scripts used - is openly available on github (https://github.com/snflo/bruteforce).

nema_novaseq_raw 数据集包含156份样本的DNA测序读段，样本涵盖提取空白对照与线虫样本。本研究旨在采用‘强力’猎物元条形码（metabarcoding）方法（Flo等，2024），探究北极小型底栖线虫的营养相互作用。2019年8月（Q3）、2019年12月（Q4）、2021年3月（Q1）及2021年4/5月（Q2），研究团队使用箱式采泥器，从巴伦支海至南森北极盆地的样带上的4个采样站位（P1、P4、P6、P7）采集沉积物样品，并将样品置于96%冰浴乙醇（-20℃）中固定。每次航次的每个站位可采集至多11个生物学重复线虫样本，样本命名规则如下：例如nm_1_7_11代表来自Q1航次、P7站位的第11号生物学重复线虫样本。各样本组中的第12号重复（如nm_1_7_12）始终为提取空白对照。研究团队使用E.Z.N.A组织DNA提取试剂盒（Omega Bio-Tek公司）对挑取的线虫样本进行DNA提取，并通过扩增V7区18S SSU rDNA并进行1%凝胶电泳以检测样本污染。采用18S_allshorts引物（上游引物：5’-TTTGTCTGSTTAATTSCG-3’，下游引物：5’-GCAATAACAGGTCTGTG-3’；Guardiola等，2015）扩增18S SSU rRNA的V7区（片段长度约100~110 bp），将纯化后的扩增产物在Illumina Novaseq平台的两个测序泳道上采用150 PE双端测序化学方法完成测序。原始数据在高性能计算集群（HPC）上进行分析与处理，结合使用FastQC/0.11.9、BLAST+/2.8.1、OBITools/1.2.12及VSEARCH/2.9.1工具，最终生成包含样本丰度数值及原生动物核糖体数据库（PR2/v.4.14.0）分类注释的zOTU（零半径操作分类单元）表。更多关于数据分析流程（包括所用脚本）的公开信息可在GitHub仓库https://github.com/snflo/bruteforce获取。