ena-STUDY-INSTITUT DE CIENCIES DEL MAR-27-02-2018-15:20:42:729-292
Picoplankton 16S rRNA genes from the tropical and sub-tropical global-ocean sampled during the Malaspina-2010 expedition
Surface waters (3m depth) from a total of 122 globally-distributed stations located in the tropical and sub-tropical global ocean were sampled from December 2010 to July 2011 as part of the Malaspina-2010 expedition (Duarte 2015). Water samples were obtained with Niskin bottles attached to a CTD profiler that included sensors for conductivity, temperature, oxygen, fluorescence and turbidity. About 12L of seawater were sequentially filtered through a 20µm nylon mesh, followed by a 3µm and 0.2µm polycarbonate filters of 47mm diameter. Only the picoplankton size-fraction (0.2-3 µm) was used for sequencing. DNA was extracted using a standard phenol-chloroform protocol (Massana, et al. 1997). The V4-V5 region of the 16S rRNA gene was amplified with the primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT)  (Parada et al. 2016) and sequenced in an Illumina MiSeq platform (2x250bp) at the Research and Testing Laboratory  (Lubbock, Texas, USA; http://www.researchandtesting.com).  Duarte CM. 2015. Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition. Limnology and Oceanography Bulletin 24:11-14.  Massana R, Murray AE, Preston CM, DeLong EF. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Applied and environmental microbiology 63:50-56.  Parada AE, Needham DM, Fuhrman JA. 2016 Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 18: 1403-14.
Surface waters (3m depth) from a total of 122 globally-distributed stations located in the tropical and sub-tropical global ocean were sampled from December 2010 to July 2011 as part of the Malaspina-2010 expedition (Duarte 2015). Water samples were obtained with Niskin bottles attached to a CTD profiler that included sensors for conductivity, temperature, oxygen, fluorescence and turbidity. About 12L of seawater were sequentially filtered through a 20µm nylon mesh, followed by a 3µm and 0.2µm polycarbonate filters of 47mm diameter. Only the picoplankton size-fraction (0.2-3 µm) was used for sequencing. DNA was extracted using a standard phenol-chloroform protocol (Massana, et al. 1997). The V4-V5 region of the 16S rRNA gene was amplified with the primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT)  (Parada et al. 2016) and sequenced in an Illumina MiSeq platform (2x250bp) at the Research and Testing Laboratory  (Lubbock, Texas, USA; http://www.researchandtesting.com).  Duarte CM. 2015. Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition. Limnology and Oceanography Bulletin 24:11-14.  Massana R, Murray AE, Preston CM, DeLong EF. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Applied and environmental microbiology 63:50-56.  Parada AE, Needham DM, Fuhrman JA. 2016 Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 18: 1403-14.