Malaspina Expedition 2010 bathypelagic metagenomes co-assembly. Malaspina bathypelagic co-assembly

A total of 58 120 l seawater samples were taken during the Malaspina 2010 expedition (http://www.expedicionmalaspina.es; Duarte 2015) corresponding to 32 different sampling stations globally distributed across the world’s oceans. We focused on the samples collected at the depth of 4000 m, although a few samples were taken at shallower depths, all within the bathypelagic realm (average depth: 3731 m +/- 495; standard deviation) in the tropical and subtropical oceans. After filtering water through a 200 and a 20 μm mesh to remove large plankton, two different size fractions were recovered in each station by pumping water serially through 142-mm polycarbonate membrane filters of 0.8 μm and 0.2 μm pore sizes with a peristaltic pump, representing the free-living (FL, 0.2– 0.8 μm) and particle-attached (PA, 0.8– 20 μm) prokaryotic communities. DNA was extracted using a standard phenol-chloroform protocol and was sequenced at the U.S. Department of Energy Joint Genome Institute, supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02 05CH11231 (CSP 612 “Microbial metagenomics and transcriptomics from a global deep-ocean expedition”, PI: Silvia G. Acinas) on the Illumina HiSeq2000 sequencing platform utilizing a TruSeq paired-end cluster kit, v3, following a 2x150 indexed run recipe. All 58 metagenomes from bathypelagic samples were pooled together and co-assembled (megahit v1.2.8; options: --presets meta-large --min-contig-len 2000). Duarte CM. 2015. Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition. Limnology and Oceanography Bulletin 24:11-14

本数据集包含马拉斯皮纳2010科考航次（Malaspina 2010 expedition，http://www.expedicionmalaspina.es; Duarte 2015）采集的总计58120升海水样本，覆盖全球各大洋的32个不同采样站位。本研究聚焦于4000米水深采集的样本，尽管少量样本采自更浅水深，但所有样本均采自半深海带（bathypelagic realm），采样海域位于热带与亚热带大洋，平均采样深度为3731±495米（标准差）。实验处理阶段，首先通过200μm与20μm孔径的网筛去除大型浮游生物；随后使用蠕动泵（peristaltic pump）将水样依次通过孔径分别为0.8μm和0.2μm的142mm聚碳酸酯膜滤器，从而在每个采样站位获得两类粒径组分的样品，分别对应自由生活型（free-living, FL, 0.2–0.8μm）与颗粒附着型（particle-attached, PA, 0.8–20μm）原核生物群落。DNA提取采用标准苯酚-氯仿法，样本交由美国能源部联合基因组研究所（U.S. Department of Energy Joint Genome Institute）完成测序。该测序工作由美国能源部科学办公室根据合同号DE-AC02-05CH11231资助，项目编号为CSP 612 "全球深海科考微生物宏基因组与宏转录组学研究"，项目负责人为Silvia G. Acinas；测序平台采用Illumina HiSeq2000，使用TruSeq双端簇制备试剂盒v3，遵循2×150索引双端测序流程。本研究将所有58份半深海带样本的宏基因组数据进行合并，使用megahit v1.2.8进行共组装，组装参数设置为：--presets meta-large --min-contig-len 2000。参考文献：Duarte CM. 2015. 21世纪远洋科考：马拉斯皮纳2010环球航行航次. 《湖沼学与海洋学通报》24:11-14