Amplicon sequencing dataset (Illumina HiSeq) of Eukaryotes (18S) in lakes along a latitudinal gradient from Southern Argentina to maritime Antarctica
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Schiaffino R, Lara E, Fernandez L, Balagué V, Singer D, Seppey C, Massana R, Izaguirre I (2019): microbial Eukaryotes in lakes along an Argentinian-Antarctic geographical gradient. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbial_eukaryotes_in_antarctic_and_argentinian_lakes&v=1.0
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Latitudinal gradient from Patagonia and Terra del Fuego (Argentina) to the Antarctic Peninsula
|Bounding Coordinates||South West [-63.4, -71.51], North East [-45.55, -57]|
microbial eukaryotes were profiled by targeting the 18S ssu rRNA gene (v9 region)
|Start Date / End Date||2004-01-15 / 2008-10-20|
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|Title||microbial Eukaryotes in lakes along an Argentinian-Antarctic geographical gradient|
|Funding||This work was supported by a grant from the Argentinean Funds for Technical and Scientific Investigation (FONCYT, PICT 32732 and PICT 2013‐0794), the Spanish Project MIXANTAR (REN 2002‐11396‐E/ANT), the Swiss NSF project 310003A_143960 and the Program ‘Luis Santaló’ of the National Research Council of Spain and the National Council of Scientific and Technical Research of Argentina (CSIC‐CONICET, PROBA 2007AR0018).|
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Integrated samples were collected within the euphotic zone from the surface down to 5 m in deep lakes and from about 30 cm below the surface in shallow lakes.
|Study Extent||Samples were collected once in 14 freshwater bodies (ranging from oligotrophic to eutrophic) from Chubut Province, Argentinean Patagonia, to Hope Bay, Antarctic Peninsula (45º22′ to 63º24′ S of latitude) (Fig. 1). In Antarctic lakes, samples were taken during the austral summer 2004, whereas in Patagonian lakes, samples were collected in late spring 2007 and 2008.|
Method step description:
- Water samples were pre‐filtered in situ through a 50 µm net to remove zooplankton, then filtered with a vacuum pump first through a 20 µm pore‐size polycarbonate filter and then through a 3 µm and 0.2 µm pore‐size polycarbonate filters (diameter 47 mm; Millipore, Cork, Ireland). The filters were placed in cryovials with 1.8 ml of lysis buffer (40 mM EDTA, 50 mM Tris‐HCl, 0.75 M sucrose) and stored at −80°C until DNA extraction. The 0.2–3 µm size fraction was used for this study. The procedures followed for DNA extraction (phenol/chloroform extraction) and touchdown polymerase chain reaction (PCR) amplifications were previously described in detail (Unrein et al., 2005).
- We amplified extracted DNA using primers specific to the V9 variable region of the 18S rRNA gene using the protocol as in Amaral‐Zettler et al. (2009), and adapted after Lara et al. (2015). Sequencing was performed by the company Fasteris (Geneva, Switzerland) using Illumina HiSeq 2500 technology; paired end reads were around 200 bp in length.
- Schiaffino, M. R., Lara, E., Fernández, L. D., Balagué, V., Singer, D., Seppey, C. C., ... & Izaguirre, I. (2016). Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes. Environmental microbiology, 18(12), 5249-5264. https://doi.org/10.1111/1462-2920.13566