TABLE 1.
Summary of samples extracted, variables tested, and controls used
| Filter test | Variable(s)a | IDb | Sample typec | Vol processed, ml (type of processing)d | Control(s)e |
|---|---|---|---|---|---|
| Flow rate | Temp (7–35°C), pressure (25–214 kPa) | Seawater, AW | 96–97 (F) | ||
| Seawater, ALOHA | 1,000–1,100 (F) | ||||
| Pure water | Variable | ||||
| Extraction efficiency | Flush direction | Seawater (<0.22 μm), KB | 200 (F) | ||
| Seawater, KB | 200 (F) | ||||
| A | Phage | 2 (F) | Liquid | ||
| B | Bacterial culture | 3 (F) | Liquid | ||
| C | Protist culture | 1 (F) | Pelleted* | ||
| % recovery | D, E | Seawater, KB | 11.7 (F) | Liquid, pelleted** | |
| Vol loaded | F, G | Seawater, KB | 10, 50, 250, 500, 1,000 (F) | Liquid, pelleted** | |
| H | Protist culture | 1, 2, 4 (F) | Liquid | ||
| Buffer chemistry (SDS vs GuHCl), filter material (AAO, PES) | I, J | Bacterial culture | 3 (F) | Liquid | |
| Proteinase K, lysozyme | Seawater, AW | 2 (C), 50 (F) | Pelleted* | ||
| Buffer chemistry (SDS vs LB3) | Seawater, KB | 500 (F) | |||
| Buffer chemistry (SDS vs LB1) | K | Seawater, AW | 50 (F) | Pelleted* | |
| DNA trapping | DNA size | DNA, 5-kb ladder | 0.5 (F) | Unfiltered ladder |
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.
Experiments for which extraction efficiency was calculated are assigned an identification (ID) letter (A to K) for cross-referencing to Table 3.
For environmental samples, locations were Ala Wai Canal (AW), Station ALOHA (ALOHA), and Kāne‘ohe Bay (KB).
Processing consisted of filtration (F) or centrifugation (C).
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).