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Smith-Root eDNA Autosampler User Manual

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User Manual
v1.0
Smith-Root
www.smith-root.com/support
info@smith-root.com
1-360-573-0202
16603 NE 50th Ave • Vancouver, WA 98686 USA

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Summary of Contents for Smith-Root eDNA Autosampler

  • Page 1 User Manual v1.0 Smith-Root www.smith-root.com/support info@smith-root.com 1-360-573-0202 16603 NE 50th Ave • Vancouver, WA 98686 USA...

  • Page 2: Table Of Contents

    Contents 1 Safety & Warnings Safety ....... . Warnings ......1.2.1 Battery Warnings .
  • Page 3 6.7.2 Power LED ......20 6.7.3 Beeper ......20 7 Maintenance Battery .
  • Page 4 Symbol Description Action may result in injury or damage. Action may result in suboptimal results. Information on how long an action takes. Description of an automated process. Tips & tricks.

  • Page 5: Safety & Warnings

    1 SAFETY & WARNINGS 1 Safety & Warnings 1.1 Safety Keep fingers and tubing clear when articulating the manifold. Two-person lift required. Equipment exceeds 100 lbs. Do not move with tubing attached. Obtain permission from property owners before installing. Secure tubing so that it does not pose a trip hazard. Be aware of trip/slip hazards and uneven terrain.

  • Page 6: Overview

    2 OVERVIEW 2 Overview Figure 2.1: Components provided by Smith-Root 1. eDNA Autosampler (1) 2. Battery (1) 3. External battery charger (1) 4. AC power cable (1) 5. Intake strainer (1) 6. Tubing (100') 7. Filterless nylon housings (8) Additions items in the combo package: 8.

  • Page 7: Components

    2 OVERVIEW 2.1 Components Figure 2.2: Rear Figure 2.3: Front A. Out port D. Lock B. In port E. Power LED C. AC power inlet F. GPS antenna Figure 2.4: Control Panel Figure 2.5: Open manifold G. Control panel L. Upper manifold USB data port M.

  • Page 8: Setup

    3 SETUP 3 Setup 3.1 Select a Location • Locate the unit in a stable area with minimal direct sun exposure. • Locate the intake strainer in an area with moderate flow not subject to high current velocities. • Keep lift height under 2 meters. Large lift heights reduce filtration pressure.

  • Page 9: Install

    3 SETUP 3.2 Install Supplies: • Scissors or tubing cutter • Zip ties • Diagonal cutters • Rebar or stake • U stakes • Mallet Procedure: 1. Cut inlet and outlet tubing to length. Allow a bit of excess. 2. Attach one end of the inlet tube to the intake strainer, and the other end to the in port.

  • Page 10: Secondary Enclosure

    3 SETUP Figure 3.3: Tubing looped and secured Figure 3.2: Strainer install 3.3 Secondary Enclosure Use a secondary enclosure when installing in direct sunlight. The eDNA Autosampler enclosure is weather resistant, however, direct sun expo- sure may result in high temperatures that damage the preserved DNA. If possible, install in a shaded location.

  • Page 11: Basic Operation

    4 BASIC OPERATION 3. Lock shed with padlock. 4 Basic Operation 4.1 Display Figure 4.1: Main display view 1. GPS signal strength. 2. Clock. 3. Schedule active indicator – when a schedule is running, when no schedule is running. 4. Battery life. 5.

  • Page 12: Open Manifold

    4 BASIC OPERATION sampling. For more details see 9.3 The Autosampling Process (page 32). 10. Flow profile – Profile of the last 3.5 minutes of flow readings. 11. Flow readout. 12. Pressure profile – Profile of the last 3.5 minutes of pressure readings.

  • Page 13: Connect Tubing

    5 THE SAMPLING PROCESS Figure 4.4: Bolt tightening/loosening star pattern 1. Close the top manifold by articulating it into position and pressing gently downward until it makes contact with the lower manifold. 2. Install manifold bolts. If it is difficult to thread the bolts, apply gentle downward pressure with your free hand.
  • Page 14 1. Open the manifold. See section 4.2 Open Manifold (page 8). 2. Put on a fresh pair of single-use gloves. 3. Remove a Smith-Root self-preserving filter from its packet by grab- bing the barbed end (figure 5.1). Do not place hands directly over the open nozzle of the filter housing to minimize risk of contamination.

  • Page 15: Schedule A Sample Run

    5 THE SAMPLING PROCESS 5.2 Schedule a Sample Run Figure 5.3: New Sample Run Figure 5.4: Page 1 Figure 5.5: Page 2 Figure 5.6: Page 3 Figure 5.7: Page 4 To start a new run of samples: 1. Load filters following directions in section 5.1 Load Manifold (page 2.

  • Page 16: Recover Samples

    5 THE SAMPLING PROCESS (a) Total Samples – Enter total number of samples to take (1–8). (b) Start At – Enter manifold ID of the first sample (A1–B4). Sam- ples are taken sequentially starting at this position. 5. On the Schedule page (figure 5.5): (a) Samples per Interval –...
  • Page 17 5 THE SAMPLING PROCESS • Sample: 00345 - A1 • Notes: 7/8/23, 14:30, 1.9 L At minimum, label the 5-digit sample ID so that samples can be matched with log data. 4. Open the manifold. See section 4.2 Open Manifold (page 8). 5.

  • Page 18: Download Logs

    5 THE SAMPLING PROCESS Figure 5.10: Remove filter 7.7 Sample Storage & Transport (page 24). 5.4 Download Logs Retrieve logs with a FAT32-formatted USB thumb drive. To retrieve logs: 1. Insert drive into the USB data port. You are presented with a time frame selection menu. 2.

  • Page 19: Advanced Operation

    6 ADVANCED OPERATION Figure 6.1: Cancel Sample Run 6 Advanced Operation 6.1 Cancel a Sample Run To cancel a sample run: 1. Select Cancel Sample Run. Only available when a sample run is in-progress. 2. Press twice to confirm. Cancelling a run may leave unused filters in the manifold. These filters may be utilized without unsealing the manifold by starting a new sample run with the Start At setting set to the position of the first unused filter.

  • Page 20: Filter Clog Point

    6 ADVANCED OPERATION Figure 6.2: In-between samples 6.3 Filter Clog Point To prevent clogging, a sample aborts when flow falls below a set point. Small values ensure target volume is achieved, large values promote better filter drying. Ideal value is as large as possible, but not so large that target volume is not achieved.

  • Page 21: Prime Time

    6 ADVANCED OPERATION 6.4 Prime Time To prevent the automatic sampling process from getting “stuck,” a sample aborts when no water is drawn for a timeout period. Small timeouts allow closer back-to-back sampling, large timeouts accommodate longer tubing. Figure 6.4: Prime Time To adjust prime time: 1.

  • Page 22: Load Schedule File

    It is good practice to occasionally collect a field negative control to assess the potential for cross-sample contamination or other sources of field contamination. Supplies: • Smith-Root self-preserving 5µm filter (1) • Reservoirs with openings large enough to insert the intake strainer (2)

  • Page 23: Other Features

    6 ADVANCED OPERATION • DNA-free water (12 L) Required volume depends on Rinse Volume and Target Volume settings. Typically around 12 liters. There are two methods for collecting a field blank: in a run of samples or in a separate run. Method #1—Collect blank in a run of samples: 1.

  • Page 24: Power Led

    1. Connect to AC outlet using the provided AC cord. To charge out of unit: Only charge with the provided Smith-Root charger. 1. Remove battery. See section 7.1.2 Remove Battery (page 21). 2. Connect battery to the provided charger and plug into AC outlet.

  • Page 25: Remove Battery

    All batteries are subject to disposal and recycling regulations that vary by country and region. Always check and follow your applicable regulations before disposing of any battery. Contact your local battery recycling organization or return to Smith-Root for recycling. 7.2 Cleaning Do not use solvent-based cleaners.
  • Page 26 7 MAINTENANCE Figure 7.1: Pre-drain Figure 7.2: Sterilize Figure 7.3: Rinse Figure 7.4: Final drain • Low-lint cloths (2) Procedure: 1. Open the manifold. See section 4.2 Open Manifold (page 8). 2. Wipe manifold with a cloth dampened in sterilization fluid. 3.

  • Page 27: Update Software

    Cycles may be ran individually or out of sequence. 7.4 Update Software Contact Smith-Root to obtain a .psc update file. Software update procedure: 1. On a PC, save the .psc update file to an empty, FAT32-formatted USB thumb drive.

  • Page 28: Battery Storage

    8 TROUBLESHOOTING 7.6 Battery Storage Batteries slowly discharge during storage. Fully charge the batteries before storing. Recharge once every 6 months of storage at 20°C. Storing batteries at temperatures above 40°C may reduce their cycle life and increase their self-discharge rate. Batteries store better at low tempera- tures.
  • Page 29 8 TROUBLESHOOTING Figure 8.1: Diagnostics screen 6. Flow – Instantaneous flow reading. 7. Volume – Instantaneous volume reading. • Autosampler 1. Version – Autosampler board firmware version. 2. Board revision – Autosampler control board hardware version. 3. Battery – Battery voltage. 4.

  • Page 30: Manual Control

    8 TROUBLESHOOTING 0000 0000 | 0 0 0 0000 0000 | 0 0 0 Air 1 Unused Water Unused Purge Air 2 ··· ··· Figure 8.2: Inlet/upper valves Figure 8.3: Outlet/lower valves 8.2 Manual Control Manual control helps identify malfunctioning components. It is not nec- essary for normal operation.

  • Page 31: Flow Diagram

    8 TROUBLESHOOTING (b) Pump speed – Set pump speed, where 0% is (effectively) off and 100% is full speed. (c) Junctions – Open/close the purge, water, air1, and air2 valves. (d) Filter – Open/close the inlet and outlet valves for each mani- fold position.

  • Page 32: Can't Download Logs

    9 SPECIFICATIONS • A few drops on the manifold after a run is normal. • Wipe pools with an absorbent towelette. Leave open to dry. Do not cover unit with tarp or plastic sheeting. 8.3.3 Can’t download logs • Is the drive full? •...

  • Page 33: Log File Format

    9 SPECIFICATIONS Flow Range 0.3–1.4 L/min Flow Accuracy ±0.1 L/min Volume Sensor Type Derived from flow Volume Range 0.2–999.9 L Volume Accuracy ±80 mL per liter of target volume Compatibility GNSS GPS, Galileo, GLONASS, BeiDou Acccuracy 2.5 m Pump Ports 3/8'' OD push-to-connect Tubing 3/8'' OD 1/4'' ID polyurethane...

  • Page 34: Header Section

    9.2.1 Header Section The header section (figure 9.2) contains general information and statistics that pertain to all samples in the run. 1. Serial Number – The eDNA Autosampler unit serial number. 2. Sample ID – The auto-incrementing sample identifier (00000– 99999).

  • Page 35: Data Section

    9 SPECIFICATIONS Autosampling Process (page 32). 6. Target Volume – The Target Volume setting for this sample. 7. Target Flow – The Target Flow setting for this sample. 8. Flush Volume – The Flush Volume setting for this sample. 9. Filter Clog Point – The Filter Clog Point setting for this sample. 10.

  • Page 36: The Autosampling Process

    9 SPECIFICATIONS 9.3 The Autosampling Process The sampling process consists of five stages, each represented by a segment in the main screen progress bar. Should any stage fail, that stage is aborted and the process continues at the next stage. 1.

  • Page 37: Index

    Index Battery, 1, 7, 20 GPS, 7, 28 Sample ID, 7 Beeper, 3, 20 Schedule, 11, 15 Logs, 14, 29 Software update, Clock, 7 Manifold ID, 7 CSV, 17, 18, 29 Sterilize, 21 Manual control, 26 Diagnostics, 24 USB, 3, 14, 17, 18, 23 Power LED, 20 UTC, 24 Pressure, 8...
  • Page 40 Smith-Root...

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