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Filtration<\/b>\nWater samples were pre-screened through 200 \u00b5m Nitex mesh followed by 80 \u00b5m Nitex mesh\n(to reduce microbial metazoa e.g., larval stages, copepods, etc.) directly from Niskin\nsampling bottles. Microbial biomass in the < 80 \u00b5m size-fraction was collected onto GF\/F\nfilters at low vacuum pressure (< 10 mm Hg) and stored with 2 ml of lysis buffer (as in\nCountway et al., 2005) at -80\u00b0C until extraction. \u00a0Sediments were retrieved from the seafloor\ncores, sectioned on board ship at one centimeter intervals, and stored at -80\u00b0C until processing\nin our home laboratories. Samples from microbial mats were not pre-screened prior to freezing\nat -80\u00b0C.\n\nMolecular processing<\/b>\nHigh molecular weight DNA was extracted from sediment samples using the MoBio power soil\nkit (MoBio, Carlsbad, CA. USA). DNA from water samples collected on GF\/Fs was extracted\nusing a standard Phenol:Chloroform:Isoamyl alcohol method and precipitated with 95% ethanol. \nAll extracted samples were quantified on a Nanodrop 1000 (University of Delaware) or by\nfluorometry (University of Southern California) using PicoGreen (Invitrogen). DNA samples\nfor eukaryote \u2018pyrotag sequencing\u2019 were sent to the MBL in Woods Hole, MA for amplification\nby PCR and subsequent library preparation as described in Amaral-Zettler et al. (2009).\nPreliminary taxonomic assignments were made for all pyrotag sequences using the \u2018GAST\u2019\napproach described in the previous reference.\n\nAmaral-Zettler, L.A., McCliment, E.A., Ducklow, H.W., and Huse, S.M. (2009) A Method for Studying\nProtistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit\nRibosomal RNA Genes. PLoS ONE 4: e6372. doi:6310.1371\/journal.pone.0006372.\n\nCountway, P.D., Gast, R.J., Savai, P., and Caron, D.A. (2005) Protistan diversity estimates based\non 18S rDNA from seawater incubations in the western North Atlantic. 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