Summary of samples extracted, variables tested, and controls used

Filter testVariable(s)aIDbSample typecVol processed, ml (type of processing)dControl(s)e
Flow rateTemp (7–35°C), pressure (25–214 kPa)Seawater, AW96–97 (F)
Seawater, ALOHA1,000–1,100 (F)
Pure waterVariable
Extraction efficiencyFlush directionSeawater (<0.22 μm), KB200 (F)
Seawater, KB200 (F)
APhage2 (F)Liquid
BBacterial culture3 (F)Liquid
CProtist culture1 (F)Pelleted*
% recoveryD, ESeawater, KB11.7 (F)Liquid, pelleted**
Vol loadedF, GSeawater, KB10, 50, 250, 500, 1,000 (F)Liquid, pelleted**
HProtist culture1, 2, 4 (F)Liquid
Buffer chemistry (SDS vs GuHCl), filter material (AAO, PES)I, JBacterial culture3 (F)Liquid
Proteinase K, lysozymeSeawater, AW2 (C), 50 (F)Pelleted*
Buffer chemistry (SDS vs LB3)Seawater, KB500 (F)
Buffer chemistry (SDS vs LB1)KSeawater, AW50 (F)Pelleted*
DNA trappingDNA sizeDNA, 5-kb ladder0.5 (F)Unfiltered ladder
  • a For buffer chemistry, SDS refers to extractions using the MasterPure kit, GuHCl refers to extractions using the DNeasy kit, and LB1 and LB3 refer to nonproprietary lysis buffers. The SDS-versus-LB1 extraction was conducted with and without lysozyme.

  • b Experiments for which extraction efficiency was calculated are assigned an identification (ID) letter (A to K) for cross-referencing to Table 3.

  • c For environmental samples, locations were Ala Wai Canal (AW), Station ALOHA (ALOHA), and Kāne‘ohe Bay (KB).

  • d Processing consisted of filtration (F) or centrifugation (C).

  • e Controls for extraction efficiency tests consisted of direct extractions of cells or viruses, including the liquid in which they were suspended (liquid) or after centrifuging to sediment primarily cells (*) or cells and viruses (**) as indicated (pelleted).