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Integrated Ocean Drilling Program (IODP) Expedition 329 to the South Pacific Gyre was conducted to document the extent and character of life in sedimentary habitats with very low biomass and rates of activity (D’Hondt et al., 2013). To meet these objectives, Expedition 329 scientists cored the entire sediment column at seven sites along two transects in the South Pacific Gyre (see the “Expedition 329 summary” chapter [Expedition 329 Scientists, 2011]). Characterization of microbial communities in the recovered sediment requires precise constraints on the maximum potential for microbiological contamination associated with the coring process. Surface seawater used as the drilling fluid is a ubiquitous potential contaminating medium (Smith et al., 2000). With about three orders of magnitude difference between in situ (sediment) cell abundances and cell abundances in South Pacific Gyre surface seawater, the potential for microbial contamination is of major concern (see D’Hondt et al., 2011; D’Hondt et al., 2015). We monitored the intrusion potential of drilling fluid during the coring operations by adding a water-soluble perfluorocarbon tracer (PFT) to the drilling fluid and subsequently measuring the PFT concentration in sediment samples immediately adjacent to dedicated microbiology samples. The addition of PFT to drilling fluid is an effective way to quantify drilling-induced contamination, as it is inert and can be detected with high sensitivity (Colwell et al., 1992). The measured PFT concentration in the sediment can then be used as an indirect measure of drilling fluid intrusion and potential associated entrainment of nonindigenous cells. PFT analyses have been successfully applied to detect contaminants prior to microbiological studies on numerous other deep-biosphere projects, such as Ocean Drilling Program (ODP) Leg 201 (House et al., 2003) and IODP Expedition 301 (Lever et al., 2006).

The R/V JOIDES Resolution piston cored sediment at all seven sites (IODP Sites U1365–U1371) during Expedition 329 (Fig. F1; see the “Expedition 329 summary” chapter [Expedition 329 Scientists, 2011]). A total of 556 sediment samples were recovered from these sites to analyze their PFT content for (1) quantification of potential drilling fluid intrusion and (2) introduction of nonindigenous cells during coring. The primary objective of these analyses was to identify core intervals with the least potential coring contamination for microbiological studies.