ena-STUDY-Institut de Ciencies del Mar ICM-CSIC-22-09-2020-17:06:06:649-171
Malaspina Expedition 2010 bathypelagic metagenomes 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
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