text:
Animated Gif of yesterday's Webcam
Summer 2002
Prepared By
M. Bahr
N. Bettez
A. Hershey
J. Hobbie
G. Kipphut
G. Kling
J. Laundre
M. McDonald
M. Miller
J. O'Brien
P. Rublee
A. Hydrolab multiprobe.............................................................................................................................................. 4
B. Licor light sensor.................................................................................................................................................... 2
II. Calibration of Laboratory Equipment................................................................................................
A. Prior Preparation..................................................................................................................................................... 3
B. Sampling Strategies................................................................................................................................................ 3
C. Field Checklist for sampling of inner lakes......................................................................................................... 4
D. Checklist of gear required for biological sampling of outer lakes and surveys............................................ 5
E. Field Checklist for full sampling of outer lakes and surveys............................................................................ 6
F. Checklist of gear to remain in packs at all times................................................................................................. 6
G. Personal gear required for sampling.................................................................................................................... 6
A. Oxygen, conductivity, temperature..................................................................................................................... 7
B. Secchi depth............................................................................................................................................................ 7
C. Integrated Phytoplankton sampling.................................................................................................................... 7
D. Light......................................................................................................................................................................... 7
E. Water sample Collection for Primary production, chlorophyll, and nutrients............................................... 7
F. Field Filtering for nutrients.................................................................................................................................... 7
G. Collection of survey Water Sample..................................................................................................................... 8
H. Collection of a Grab sample.................................................................................................................................. 8
I. Zooplankton Sampling........................................................................................................................................... .8
J. Microplankton Sampling........................................................................................................................................ 9
K. Benthos Sampling................................................................................................................................................ 10
L. Fish Sampling........................................................................................................................................................ 11
A. Water Collection.................................................................................................................................................. 12
B. Bacteria Counts..................................................................................................................................................... 13
C. Bacteria Production.............................................................................................................................................. 13
A. Primary Production.............................................................................................................................................. 15
B. Alkalinity (Gran Titration)................................................................................................................................... 16
C. Winkler Oxygen Titration.................................................................................................................................... 16
A. Surveyor download............................................................................................................................................. 15
B. Licor download..................................................................................................................................................... 16
C. Winkler Oxygen Titration.................................................................................................................................... 16
XI. Arctic LTER Procedures for on-line Data Management....................................................... 22
XV. USE LTER MOTOR BOATS (Toolik Lake Map)............................................................................................... 30
A. The Hydrolab unit consists of the H2O multi-parameter water quality data transmitter and the Surveyor 3 Multi-parameter water quality logging system. The H20 is capable of measuring Temperature, specific conductance, pH, and Dissolved Oxygen.
Before the field season all routine maintenance on sensors should be performed. This includes cleaning specific conductance and pH sensors, service to the reference electrode and changing the DO sensor membrane.
The specific conductance calibration is stable for six months and should be calibrated at the start of the field season. The dissolved oxygen and pH are stable for 1 month but are calibrated weekly while at Toolik. All sensors are inspected weekly for wear and cleanliness. This is usually done on Friday since most require over night equilibration after maintenance.
The maintenance scheduled for the H20 is:
Specific conductance sensor clean and calibrate monthly
pH glass electrode inspect and calibrate weekly
Reference electrode replace electrolyte weekly and inspect to make sure it passes electrolyte freely.
Dissolved Oxygen membrane: inspect and calibrate weekly and replace membrane and electrolyte monthly.
Depth sensor inspect monthly clean if needed.
The surveyor has internal lithium batteries that require replacement every two years. If the surveyor fails to keep track of Dates the batteries need to be replaced.
The manuals for these pieces of equipment are thorough in explaining use and calibration. Calibration should be done each Saturday before the following week's sampling run. The surveyor unit must be charged to between 14.4 and 16 volts. An over night charge before sampling is usually adequate. Following is a brief synopsis of the oxygen calibration..
1. Get the barometric pressure either from the hand held barometer or data logger. To read the barometric pressure off the hand held unit look at the window in the 12 o'clock position to see what color the white arrow above the km is pointing to. This is your height above sea level and indicates the scale you should read of off (my guess is it will be red or maybe yellow). After this tap the glass lightly then read the BP off the correct scale.
2. Plug appropriate end of cable into right side (back) of surveyor 3 (Transmitter). Plug other end into H20 datasond unit making sure the plugs are aligned correctly. This involves aligning the dots on the plug end of the cable with the largest prong on the male plug end of the H2O datasond unit (Hydrolab multiprobe). Some force is involved but not too much, so be patient and make sure it is correct before applying too much force.
3. Turn the surveyor 3 on [On / Off] The response time varies for each parameter but all are usually less than one minute.
4. Remove cup containing DI water covering sensors.
5. Hit blue [calibrate] key followed by the [% / S / DO] key. The screen will show the following % O. Highlight the % using the arrow keys followed by the enter key.
6. You will then be prompted for the barometric pressure, enter it followed by the [enter] key. You will see the message Sending….. (this is the surveyor 3 sending the calibration to the H20 datasond unit). The other possible message is Out of tolerance no calibration saved. If this appears make sure the Barometric pressure is correct, other possible reasons are, a damaged membrane, or low battery. If the membrane is intact and battery charged (checked by hitting the screen key, charge should appear in the lower right and should be above 15.00 V&
B. Licor light meter: The batteries should be checked weekly on the Licor. There are no means for calibrating this meter at Toolik so all calibration should be done prior to the field season. LI-COR recommends that the probes be calibrated every 2 years. Sensor must be connected to correct connection ports since each quantum sensor has its own multiplier.
The LI 1400 has two light sensors the deck (Q25190 ) and the submersible (UWQ 4879). Each sensor has a unique calibration multiplier assigned to it by Licor. Both calibration multipliers are stored in a set up file on computers used to download files as well as on the disk containing the software. Log routines for either logging (logroutinesetup.L14) and no logging set up (licorsetup.L14) are both stored on the diskette containing the Licor manual. The calibration constants for each of the sensors are:
Underwater (UWQ 4879): -242.13
Deck (Q 25190): -214.59
To Use the Licor for instantaneous measurements
1. plug each sensor into its correct current channel (I1 for the Deck and I2 for the sub.
2. Turn Logger on [on/off]
3. hit [view] scroll between {log data} and new data using the arrow key [à]
4. Select New data by hitting enter [enter] This menu is an array of 4 lines each with 7 choices (see diagram). Each of the four lines can display any of the seven choices.
You will be on the first line of the 4. Move among the 7 choices using the left or right arrow keys. Your choices are:
Data and time (YYYYMMDD) (HHMMSS)
Memory (total avail) (amount used)
Channel 1 (light data) DEC
Channel 1 log status [on or off]
Channel 2 (light data) DEC
Channel 2 log status [on or off]
Battery voltage
5. When I1 I DEC (or Q25190) appears. Hit down arrow to move to next line in menu.
6. Scroll left or right until I2 I Sub (or UWQ 4879) appears
7. If Q 25190 and UWQ appear hit the [view] key to toggle to Dec and sub ID's. The data is the same but it is easier to keep sensors straight using Dec and sub.
8. When ready to store data simply press enter key. Remember that no ID are stored with data so you must remember for what and where you are storing data. This is why it is often easier to also write the numbers down as you collect the data in this mode.
To set the LI1400 up for logging
1. plug each sensor into its correct current channel (I1 for the Deck and I2 for the sub.
2. Turn Logger on [on/off]
3. Hit [set up] One of 7 choices will appear in the menu. Scroll though using the left of right arrow keys [à] until logging appears
4. hit enter[enter]
5. Toggle between choices on and off using arrow keys
6. LI1400 is now logging and will continue to do so until logging is turned off. If you fail to turn it off the batteries will die in about three days.
7. When logging is done repeat steps 2-6 and toggle logging to off.
8. Note. As with most limnological equipment the Licor is not waterproof and when left out to log it should be kept in a zip lock.
Downloading Licor LI1400 data logger
1. Using Beige null modem cable, plug 9 pin (female) to male 9 pin on bottom of LI1400. Plug other 9 pin female to com 1 on laptop (other 9 pin male).
2. Open Licor download software. If not installed install using enclosed disks.
3. On top drop down menu click on Remote then click on connect. You can also hit [alt] R [Return]. You are now connected to LI 1400.
4. To down load data: Click on remote menu again followed by receive data.
5. You will be prompted for a range. I usually select all [return]
6. You will then be asked to pick a directory and name the file.
7. Hit save and file will be saved to directory.
8. The file is a delimited text file, which is readable by, excel.
9. Before clearing the database open the file and make sure the download was a success. Once it is and the data is backed up clear the database for the next log.
10. Click on remote and select clear database or [Alt] R [Shift] C.
11. You then have the choice to clear all or portions of the database. You will then be warned again that you are about to clear the database. If this is ok go for it.
II. Calibration of the Turner Designs 10-AU for Chlorophyll measurements.
If you are not sure that the correct filter set and lamp are installed for measurement of chlorophyll you must open the machine and check. However, once this is done you will be required to recalibrate the fluorometer. The Arctic LTER has used Turner Designs optical kit (10-037R), which is for the measurement of invivo and extractive measurement of chlorophyll. This kit is used for the traditional in vivo measurement of chlorophyll (Lorenzen) and invivo /extractive acidification methods, including Strickland and parsons, standard methods for water and wastewater and EPA 445.
The Turner Designs chlorophyll optical kit (10-037R) contains:
1. 10-AU-600 Red sensitive photomultiplier tube
2. 10-AU 45 daylight white lamp (F4T5D),
3. 10-050R Round Excitation filter (340-500 nm)
4. 10-051R Round emission filter >665 nm
5. 10-032 Square reference filter 400-700 (1ND)
In order to access any of the screens you must first get to the home screen. This is accomplished by hitting enter [ENT]
Calibration is begun from screen 2 <2> on the main menu. The basic operating parameters and level of the 10-AU must be set prior to your calibrating the machine.
1. Operational parameters
1.2. Home display
Readout conc
Units None
1.4. Output
Full scale V:2V
Zero 0
2. Calibration
2.1. Blanking
Subtract blank NO
2.2. Standard SOL
Standard conc. Concentration of solid standard (54.988)
1. Display range Yes
2. Set range High
3. Set range control Man
Also prior to calibration the range for the instrument must be set. There is a trade off between range and sensitivity. The larger the range that an instrument is set to measure the less sensitive it becomes. Sensitivity can be thought of as the degree of precision. Because chlorophyll is only linear up to 250 ug/l we have chosen that as our upper limit, so our range is 0-250. There are three ranges on the 10-AU each 1 order of magnitude apart. Low 0-2.5, Med 2.5-25, and High 25-250.
To set the range of the 10-AU place a standard in the cuvette that is approximately 20% of the maximum concentration that you wish to read (~ 50 ug). Go to screen 2.3 and set the span to between 30 and 50 using the up and down arrow, remember that the higher the span the higher the sensitivity. Next adjust the FS% so that the high is 250, med is 25 and low is 2.5 using the sensitivity adjustment knob, which is located to the right of the keypad. After each adjustment of the sensitivity knob you will need to wait 1-8 seconds for the machine to stabilize again. Turning the knob clockwise will make the machine more sensitive and reduce the range while turning it counter clockwise will do the opposite. Once the high reading has stabilized around 250 hit enter. Note that you can also adjust the span up or down for fine scale adjustment of the sensitivity (increasing the span will decrease the range).
When this is done go to screen 3 (Diagnostics) and with the high standard still in the cuvette holder record the following, when finished repeat for the low standard.
PWR level
Chopper RPM
High volt
Fluor readout
PM (photo multiplier) signal output
Cal STD value
FS: % of
The fluorometer gives readings in total ug chlorophyll ml-1 Acetone. This must be converted to ug /L water (seston) or ug/cm2 of rock surface (rock scrubs). To calculate concentration from your fluorometer readings you will need to know volume filtered and volume of acetone used to extract your sample.
If you are reading sestonic samples the equation would be ug total chlorophyll liter -1 = (reading) x (liters acetone / liters filtered)
If you are reading scrub samples the equation would be ug total chlorophyll liter -1 = (reading) x (liters acetone / liters of scrub sample filtered) x (L of water in scrub sample/cm2 of rock area scrubbed)
A. Water samples are stored in 1 liter amber bottles and brought back to the lab for processing.
Chlorophyll (47 mm GF/C)
Particulate N and C, Particulate P, (25mm GF/C
Alkalinity, (60 ml HDPE round)
Cations, (60 ml HDPE round)
Anions, (30 ml HDPE round)
C. Samples to be analyzed for Phosphate and ammonium by hand using wet chemistry are collected in 60 ml HDPE amber bottles. These bottles are labeled and dedicated for each lake.
D. Integrated Phytoplankton samples are collected in 125 ml bottles. Preserved in the lab concentrated and shipped to Hedy Kling in Aug.
Zooplankton samples are collected in
250 ml
wide mouth bottles preserved with
Buffered Formalin and shipped to
John O'Brien in
F. Microplankton are collected in 60 ml square polypropylene bottles.
G. Total dissolved Nitrogen are collected in clear round 60ml trace metal clean LDPE bottles, preserved with 100 ul/ 60ml 6N Ultrex HCL, and frozen at Toolik for shipment to MBL.
F. Total dissolved Phosphorus are collected in clear round 60 ml HDPE, preserved with 100 ul/ 60ml 6N Ultrex HCL, and stored at 4 C at Toolik and shipped to MBL.
A. The 1 liter field sampling bottles should be rinsed with DDW after sample water is processed.
B. Bottles for inorganic nutrient sampling should be soaked in the acid bath (10% HCl) for at least a few hours and then rinsed 3 times with DI water and filled DI until samples are taken.
C. Water for Primary productivity is collected in a 500 ml amber bottle and brought back to the lab for processing.
There will be a calendar in the lab indicating the sampling schedule for this summer.
A. Prior to sampling (the night before) make sure all bottles and Petri dishes are clean and labeled. Indicate on label the lake, depth, date sampled. USE TAPE!! Writing on the bottle only results in a lot of blank bottles when it comes time for the samples to be analyzed. Each lake is color-coded to facilitate later analyses. Fill 15 ml centrifuge tubes with 10 ml acetone (for chlorophyll a analyses). Fill out Filter and Chlorophyll books and label Nutrient and chlorophyll tubes with corresponding numbers.
B. We are using 2 sampling strategies. Biological samples and measurements will be taken every time while full sampling (biological and nutrient samples and measurements) will occur only when indicated.
The sampling depths for lakes are as follows:
Toolik: 0,1,3,5,8,12,16
The remainder are sampled at epilimnion, metalimnion and hypolimnion
Biological sampling includes:
1. Zooplankton and phytoplankton samples are collected on each sampling trip.
2. Microplankton samples are taken at every lake and depth sampled (except I series inlets and outlets)
3. Primary Production samples are taken at every lake and depth sampled.
4. Chlorophyll a samples are taken are taken at every lake and depth sampled.
5. pH, temperature, conductivity, oxygen, measured at every meter on every lake and light (0, .1, .2, .5, 1 and every meter to the bottom).
6. Secchi depth is measured on every lake
7. Alkalinity samples are taken at every lake and depth sampled. In Toolik samples are taken from each sampled depth for the first sample date only. For the remainder of the summer only epilimnion, metalimnion and hypolimnion samples are taken.
Full sampling includes the following in addition to Biological sampling:
1. Cation and anion samples are taken at every lake and depth sampled. In Toolik samples are taken from each sampled depth for the first sample date only. For the remainder of the summer only epilimnion, metalimnion and hypolimnion samples are taken.
2. Inorganic nutrient samples (NH-4, NO-3, PO-4) are collected from each depth sampled in each lake (or inlet) .
3. TDN and TDP samples are collected from each depth sampled in each lake (or inlet) .
4. Particulate (N, C, P) samples are collected from each depth sampled in each lake (or inlet) .
5. DOC samples are collected from each depth sampled in Toolik, N1, N2, S6, S7, and the I series.
6. Bacteria samples are collected from each depth sampled in Toolik.
1. Zooplankton net
2. Squeeze bottle for rinsing microplankton and zooplankton nets
3. Integrated Phytoplankton Sampler (meter-marked Tygon tubing)
4. 3 l pitcher and 20 um nitex for microplankton concentration
5. Bottles for collection of primary productivity samples (500 ml amber)
7. Van Dorn or water pump/pump tubing.
8. Hydrolab (H2O) and Surveyor 3, including cable and stirrer
9. Secchi disk
10. Licor light meter, including cable
11. Field notebook (Rite-in-Rain), pencil, Sharpie
12. Nalgene filter rig, hand-held vacuum pump, and .45 micron Millipore filters, forceps
13. 1 liter amber bottle for collection of water to return to lab from which Cations, anions, alkalinity, PN,PC, PP DOC, and chlorophyll a will be taken.
14. Bag containing sample bottles for each sample depth:.
17. Sample bottles for zooplankton and integrated phytoplankton
1. Zooplankton net
2. Squeeze bottle for rinsing microplankton and zooplankton nets
3. Integrated Phytoplankton Sampler (meter-marked Tygon tubing)
4. 3 liter pitcher and 20 um nitex for microplankton concentration
5. Bottles for collection of primary productivity samples (500 ml amber)
7. Van Dorn or water pump/pump tubing (only if profiles are to be taken).
8. Hydrolab (H2O) and Surveyor 3, including cable and stirrer
9. Secchi disk
10. Licor light meter, including cable
11. Field notebook (Rite-in-Rain), pencil, Sharpie
13. Raft
14. Paddles
15. Anchor bag and marked anchor line
16. Two 60 ml syringes for field filtering.
17. For each depth sampled one 500 ml amber bottle for Primary production samples.
18. Filter kit for field filtering and preservation
1. 60 ml bottle of Lugols solution for phytoplankton preservation
2. 30 ml bottle of 6N Ultrex HCL for preservation of cations, NO3, TDN, and TDP.
3. 60 ml bottle of 50% glutaraldehyde for microplankton preservation
4. Syringe for dispensing Glutaraldehyde
5. Pipette set to 60 ul and tips.
6. Forceps for filter handling
7. Extra filters (GF/F and GF/C) for reloading cassettes.
19. Filter cassettes and bottles for biological Sampling required for each depth sampled:
20. Sample bottles for zooplankton and integrated phytoplankton
1. Full sampling requires the additional filters and bottles for each depth sampled: Gelman 25 mm filter holders loaded with 25 mm GF/F (ashed) filters for PN/PP/PC samples and field filtering of cations, anions, TDN,TDP, NH4, NO3, and DOC (I series)
F. Gear to remain in packs at all times
1. Extra length of Rope (may be needed for any variety of reasons)
3. Radio (if remote sampling)
4. USGS Philip Smith Mountains (C-5) quadrangle (Toolik LTER area map) or map of survey area.
5. Zip lock bag containing: spare science supplies
whirl pack bags, label tape, sharpie, pencil, syringe, disposable filters, spare field notebook, extra .45 millipore filters. Spare forceps, extra GF/F, GF/C filters. Hydrolab maintenance kit (Oxygen membrane and electrolyte)
6. Zip lock bag containing emergency supplies:
Small first aid kit, space blanket, Compass, whistle, spare head net, candy bars, Duct tape, spare pack parts (rings and pins), zip ties.
G. Personal Gear required for field sampling
1. Rain gear (pants and jacket)
2. Hats, ball cap and cold weather
3. Swiss Army Knife or any similar field tool
4. Mosquito headnet
5. Camera and film
6. Food if walking to remote lakes
7. Sunglasses
8. Gloves, either cotton (bugs) or wool and rubber (warmth) depending on weather.
9. Extra layer of clothing (polypro top and bottom, and sweater or fleece top).
Physical measurements chemical sampling is done in the deepest portion of the lake. To find the deepest part of the lake use the Speed tech Depth mate portable sounder. To operate: hold front cap in water, against solid hull, or black ice at 90 % angle to bottom. It will not operate through air. Push switch, remove and read depth. Unit will turn off after 10 seconds. Once the deep hole is located drop the anchor and begin sampling from the surface in order to allow the sediments to settle.
Oxygen, temperature, pH and
conductivity readings.
Attach stirrer to Hydrolab.
Attach cables to Surveyor and Hydrolab.
Annotate pertinent data on Surveyor (lake, etc.). This is done by hitting the [[annotate key on the right side of the Surveyor 3 followed by the data you words you with to enter. Enter letters by hitting shift key (i.e [shift abc] for the letter a on the [7 abc] key).followed by [Enter]. No shift key is required to enter a number.
Measurements should be taken at the surface and continuing at 1 meter intervals to the bottom. Once readings stabilize (Oxygen readings can take up to a minute to stabilize) hit the [Store] button. Failure to do this will result in no data being stored.
B. Secchi Reading: The secchi reading is a measurement of water clarity.
Step-by-step instructions for taking a secchi reading:
1. Take the secchi reading from the shady side of the boat. If there is no shade you will need to use your hand to cut down the sun glare.
2. Lower the secchi disk slowly until the white quadrants disappear, and determine the depth to the nearest quarter foot (or tenth of a meter, depending on how the line is marked).
3. Lower the secchi disk so it is about 2 feet below the first reading.
Slowly pull the disk up until it reappears, and determine this depth to the nearest quarter foot (or tenth of a meter).
4. Average the two depths to get the secchi depth that you will record on the data sheet.
C. Integrated Phytoplankton sampling. Lower Tygon tubing for phytoplankton sample slowly into lake to desired depth (meter off the bottom, but no more than nine meters).
1. Phytoplankton samples are collected in clean, labeled 125 mL amber plastic bottles.
2. In shallow waters, the bottle is rinsed once with sample water, then filled to the "shoulder".
3. In deep waters, twice rinse a tygon tube of length sufficient to reach the bottom of the upper mixing layer by lowering the tube slowly, pinching off the surface end of the tube, retrieving the tube from depth, then releasing the surface end of the tube allowing it to drain. The sample is collected in the same way except that the sample is drained into the collection bottle.
D. Light reading. Place deck sensor on level surface in boat. Hold underwater sensor frame at 90O angle to water surface and take reading as at 0,.1,,5,1,2,3,4,5,6,7,8,9, meters. Allow reading to stabilize for 5 seconds after lowering of sensor. To store reading hit [Ent]. .
E. Water sample collection. Lower the Van Dorn into water (or pump line) and begin sampling at one meter depth (can get surface sample without using Van Dorn or pumping). If using pump, there is a need to clear line before taking sample. Fill amber bottle, rinsing three times first with sample water. Water in the amber bottle is brought back to the lab and filtered for chlorophyll, PN/PC/PP. The filtrate is used for alkalinity samples, DOC, cations and anions
F. Prior to filling bottles make sure the label has the correct site and date on the label. Set up filter rig by placing, with forceps, a .45 Millipore filter on frit and then making sure upper reservoir is securely screwed on (no leaks). Pour about 100 ml of sample water into upper reservoir and filter using hand-held vacuum pump. Discard this rinse water. Fill the reservoir to the top (250 ml) and filter. Pour filtrate from lower reservoir into NH3 sample bottle, but do not fill completely. Rinse out the 30 ml nutrient bottle at least three times with filtrate and fill. If sampling for TDN and TDP, rinse the vials three times with filtrate and fill nearly to the shoulder. Be careful not to overfill because they have to be shipped and reagents have to be added before they are analyzed. Discard filter (into plastic bag used for carrying filters and forceps into the field) after each depth is filtered.
If using a syringe to filter water for chemistry be sure to rinse the syringe three times prior to use and to expel 10 mL of sample water through the filter in order to rinse the filter. (Note: if there is little water, fill the alkalinity bottle first. This will help rinse the filter and should not affect alkalinity). Rinse each bottle with a few mL of filtered water, then collect the sample. The order that bottles are filled for different samples is as follows.
1. Inorganic nutrients
4. Anions
5. Cations
6. Alkalinity
G. On surveys samples are taken from the surface above the deep hole on the lake. This sampling is similar to sampling of the outer lake except only one depth (0 meters) is taken for each lake. Measurements are still taken at every meter with the hydrolab. All filtering and preservation is done in the field.
H. For some lakes on surveys a grab sample is collected and brought back to the Lake crew instead. This requires that a 2-liter plastic bottle be used to collect a water sample from near the center of the lake. The water samples will be tested for chlorophyll 250 ml), total nitrogen, and phosphorus, particulate N&C (200 ml), Particulate P (200 ml), Microplankton (1 liter), Primary productivity 300 ml
Step-by-step instructions for how to take a GRAB SAMPLE of lake water:
1. Position your boat at your appropriate lake site location.
2. Rinse the 2-L bottles two times with lake water. This step is important to condition the bottle, removing any DI water that might still be in the bottle from its previous cleaning.
3. Take your water sample from the windward (the upwind) side of the boat to lessen any contamination from the boat.
4. With side of the 2-L bottle, quickly swish and sweep the surface of the water to move away any possible scum or other floating material.
5. Then, holding the 2-L sample bottle upside down (opening downward), plunge the sample bottle into the water straight down to elbow depth.
6. Under water, turn the bottle upward to allow it to fill with water.
7. Cap the sample bottle and store in the packs. Keeping the water sample in the dark and cool is important, because direct sun and dramatic temperature changes in your lake water sample can affect our measurements.
I. Zooplankton Sampling: There are 13 lakes and ponds that are sampled for crustacean zooplankton at least twice a summer during the standard lake sampling trips.
*This lake or pond must be sampled for zooplankton more frequently than standard lake monitoring.
1. The protocol for taking a sample from these lakes is to bring the correct net for a lake. Toolik, N-2 and N-1 all have dedicated nets for each lake with a fourth net used for the other lakes. Sample bottles are to be prepared by someone from the O'Brien lab. This is done by wrapping tape around a 250-ml Nalgene bottle and labeling it using a black Sharpie for lake, date, and depth of the vertical tow. Once on the lake the net is slowly lowered being sure that it goes down open side up, stopping briefly at the depth of the tow and then at about a meter per second pulling the net to the surface. The contents of the net are washed down until it will fill about half the sample bottle. It is then emptied into the labeled sample bottle. The bottles are returned to the O'Brien lab where they will be inspected and then preserved. The preservative is 100% ethanol with about 5% formalin added. It is added to the sample bottles in roughly 1:1 sample volume to preservative volume. The identification and enumeration, as well as sizing in certain cases, is done during the autumn and winter back at the O'Brien lab at the University of Kansas.
2. Two other lakes are routinely sampled for zooplankton, S-1 and S-2.
However, these are done by a member of the O'Brien lab if at all possible. These are very shallow ponds, less than 1 m deep and must be sampled using a specially designed sweep net. The sweep net is affixed to a PVC pipe, and 2 180° sweeps of radius 2 m are taken per sample bottle with this replicated. The resulting samples are handled as above.
3. On occasion zooplankton samples are taken during limnological surveys. If the lake is deep enough and the raft not moving, a vertical tow should be taken during limnological surveys. If the lake is less than 4 m or the raft is moving, a qualitative tow should be taken by pulling the net behind the raft being careful that the net does not scoop up sediment. If that should happen the net must be washed out and another sample taken. It is imperative that survey samples not be preserved until they are inspected because once preserved, several zooplankton species cannot be accurately identified.
J. Microplankton Sampling: Samples for microplankton are collected synoptically with routine collection of physical/chemical, phytoplankton, and zooplankton samples at the LTER site. Additionally, microplankton samples should be collected on any surveys of the lakes.
1. Materials/Supplies:
a. 60 ml plastic bottles--1 for each sample to be collected (note ahead of time a mark where 60 ml comes to on the bottles— usually the bottom of the neck)
b. Waterproof marking pen
c. Labeling tape
d. Filter (plexiglass cylinder with 20 µm nitex net glued to one end
e. 2 liter beaker or small bucket with 2 liter mark on it
f. Tygon tubing (approximately 3/8-1/2" internal diameter)
g. Glutaraldehyde stock solution (usually comes in 25-50% concentration) in plastic bottle
h. Pipette and bulb or autopipette to transfer up to 3 ml of glutaraldehyde
i. Squeeze bottle filled with lake water (filtered through a glass fiber filter is preferred, but unfiltered lake water from other than fertilized lake is OK)
2. Prior to departure to field stations (perhaps the night before):
a. Wrap a piece of label tape entirely around each sample bottle.
b. Sample bottles may be labeled ahead of time; make sure to note lake, station (if applicable), date (include year), depth.
c. Dispense sufficient glutaraldehyde into small plastic bottle to preserve samples in field (about 60 ml).
3. Samples should be collected from the following depths: 0, 1, 3, 5, 8, 12, 16, and 20 meters.
4. For each sample:
a. Fill a beaker (or bucket) to the 2 liter mark with water from a Van Dorn sampler or Niskin bottle collected at appropriate depth.
b. Concentrate the sample by "reverse flow filtration":
i. Place the filter (mesh side down) on the water sample.
ii. Let the water gently flow into the plexiglass filter tube.
iii. Remove water from inside the filter tube by either starting a siphon with the tygon tubing, or by carefully lifting the tube from the beaker and pouring the filtered water overboard.
iv. Continue concentrating the sample until it is less than 50 ml total volume.
c. Carefully pour the sample from the beaker into a labeled 60 ml sample bottle.
d. Rinse the beaker with 5-10 ml filtered water or lake water from a squeeze bottle, and add this to the sample.
e. Use rinse water to bring total sample volume in the bottle to 60 ml.
f. Repeat for each depth.
g. After all samples are collected, add the appropriate volume of glutaraldehyde preservative to each sample bottle to bring it to a final concentration of approximately 1% (vol/vol): If glutaraldehyde stock solution is 50% - add 1.25 ml. If glutaraldehyde stock solution is 25% - add 2.5 ml.
h. Make sure cap is on tight.
i. Store the filters at room temperature or refrigerate. DO NOT FREEZE!!!
5. Shipping:
a. Prior to shipping, check to make sure all caps are tight.
b. Pack plastic bags within a cardboard box.
c. Ship samples to:
Dr. Parke Rublee
Biology Department
312 Eberhart Bldg.
University of North Carolina at Greensboro
Greensboro, NC 27412-5001
1. Diver cores: Diver and buddy go down to sampling depth and location together, bringing with them a large bucket holding 5 core tubes and 10 corks. One SCUBA diver carefully rests on the bottom and hands an empty core tube and pair of corks to the other diver, who gently swims a few feet away (to reach undisturbed sediment). After the second diver reaches an undisturbed area, that diver carefully pushes the tube halfway into the muck and corks both ends. They do this 5 times, then surface bringing the bucket and the full core tubes with them. Helpers (usually 2) on shore then take each core tube and individually rinse its sediment through a 250 µm net. After the tube's contents are rinsed down well, the sample is put into a 250 ml bottle and topped off with 95% EtOH.
2. Snail counts: Snail density is measured for inshore and offshore locations for each lake sampled. (The inshore locale is specifically as far inshore as possible while still being on the muddy bottom. Off shore is at least 10 m further out from the inshore counts.) All counts are performed using a 10 m weighted line. The line is dropped from above the selected area and a SCUBA diver counts all adult Lymnaea snails (approximately _ 15 mm long) adjacent and within 1 m of one side of the dropped line. The idea is to get a 10 m2 transect. This is done three times each for inshore and offshore locations. Densities are shouted to helpers on shore as needed; they note whether they are inshore or offshore counts.
3. Eckman samples: Eckman's may be substituted for diver cores where diving is inaccessible or difficult (i.e. cold, dark, and lonely N1 depths > 20 feet). The Eckman dredge is used to retrieve five samples which are then rinsed one at a time through a 250 µm net just like the diver cores. When finished rinsing, transfer net contents to 250 ml poly bottles and top with 95% EtOH. When operating the dredge keep in mind the bottom density (hard or flocculus); it's probably not a bad idea to try a couple of practice dredges. Make sure, though, that when the Eckman is brought to the surface, there is undisturbed sediment and water in the top (the flaps in the top of the Eckman allow you to look).
1. Mark and recapture: Catching and releasing fish with data collection is basically what happens here. The analysis is all performed back home at UMD from the data collected during the summer. We usually try to use slightly crimped barbed hooks (to minimize damage to fish when removing the hook; a completely barbless hook, however, seems to be more trouble than it's worth because of too many lost fish). If treble hooks are used, one of the hooks is cut off. The data collection portion is very important here. We have several complete "tagging kits" available for people to use so fisher-folks can spread out. When a fish is caught, it is landed quickly to minimize shock, then measured on the board. After a reliable measurement for total length is determined (and written down) the fish is weighed with one of three appropriately sized scales. This too is written down. Finally, the fish gets a tag placed in its back and it is tossed back in the lake. When placing the tag, choose a spot approximately midway between the lateral line and the base of the dorsal fin. Flick a scale off and plunge the tagging gun into the flesh of the fish, while trying to go deep enough to make sure the tag's T-bar design catches on the deep dorsal fin rays. We have found a helper helps a lot on the first several tries.
2. Gill netting: When gill nets are used we try to fold them neatly into the boat we're going to deploy them from first. Those few extra moments of time really pay off later when setting it. When pre-folding the net in the boat, tie a bag of rocks or a rock at each end of the bottom of the net (on each end of the weighted line). Tie a float and a long rope as deep as the net will be on each end of the float line. We usually set the nets perpendicular to shore with the small mesh inshore. (Of course that means you need to fold it in the correct orientation if you're going to start from shore and paddle out with it.) Toss out one end of the net and paddle away from shore, letting the net spool out behind you. After the net is out, let it work for about one to three days (depending on how many fish you wish to catch). Sometimes, even 12 hours will do the trick in some lakes if you're not sure about how many fish you will get and you don't want to clean fish for the next two days. When retrieving the net, start from the shore end and pull it into the boat, laying it fairly neatly while you do. As it comes in, take the fish out. If there are many fish and you have helpers on shore, go ahead and pull it in quickly and the helpers can help take fish out of it. The cleaning of the fish can be done on site or back at camp. Cleaning the fish can be a tiresome job. Generate a number for each fish and make a tag for that number. Include on each tag: number, lake, date, species, total length, weight, and sex. Mark the same information in the data book. Gut the fish to determine sex and save the stomach. Put a tag in the sample bottle with the stomach. Now, remove the otoliths and note in the data book whether you retrieved both of them or not, and put them in a Whirl-Pak with their own tag. For help on getting the otoliths out (sometimes tricky) ask Mike McDonald or Jason McCrea. Now just clean up and you're done. The fish carcasses can be deposited in the middle of the lake; make sure you pop the air bladders so they sink.
A. Water collection for bacteria samples: The microbiology lab will provide acid-washed 60 ml bottles labeled for Toolik 0, 1, 3, 5, 8, 12, and 16 m and Toolik Inlet. This will be sufficient volume for both cell counts and productivity measurements. Rinse the bottle with water from each depth, then fill. Hold in a small cooler and return to the microbiology lab for preservation/processing as soon as possible (< 1 h).
1. Supplies:
a. 60 ml polypropylene bottles
b. 20 ml plastic scintillation vials
c. 1 ml syringe or pipet
d. 2 ml (or larger) syringe or pipet
e. Millipore 15 ml filtration unit—tower, clamp and frit in rubber stopper
f. 500 or 1000 ml filtration flask
g. Hand pump with tubing to attach to filtration flask
h. 0.22 µm Acrodisc filters (or equivalent)
i. 0.22 µm pore size, 25 mm black Nuclepore filters
j. GF/C filters
k. Microscope slides
l. Cover slips
m. Forceps
n. Cargille B immersion oil
o. Zeiss microscope equipped for epifluorescence at 390 nm
2. Solutions
a. 0.2 µm filtered 50% glutaraldehyde
b. 4', 6 diamidino-2-phenylindole (DAPI), Sigma # D 9542. Stock solution: 1000 µg/ml 0.2 µm filtered DI water. Working solution: 100 µg/ml; filter through 0.2 µm acrodisc
c. 0.2 µm filtered 0.9% NaCl
3. Protocol
a. Preservation of bacteria: Rinse one 20 ml plastic scintillation vial with lake water for each depth sampled. Fill with 20 ml lake water (just below the vial shoulder). Add 1 ml 50% glutaraldehyde. Store at 4°C.
b. Staining bacteria for counting: Place a GF/C filter on the Millipore frit and dampen with water. Place a 0.22 µm pore size black Nuclepore filter on the backing filter. Clamp on the 15 ml filter tower. Add a minimum of 2 ml preserved lake water and 200 µl DAPI working solution (final concentration 10 µg/ml). After 5 minutes, filter the sample using the hand pump (or low pressure vacuum filtration). Rinse the sides of the filter tower with 2 ml 0.9% NaCl. Add 1 drop of immersion oil to a microscope slide and transfer the filter with forceps. Place a cover slip on the filter and add another drop of oil. Count at least 10 fields using the Zeiss epifluorescence microscope with the 100x objective.
1. Supplies
15 ml conical polypropylene centrifuge tubes with caps
test tube rack
10 ml pipet & bulb
Eppendorf pipettes- 1 ml & blue tips, 200 ul & yellow tips
Hamilton syringe- 25 ul
sterile syringe needles, any thin size
filters- Millipore 0.22 um, 25 mm
Millipore filtration manifold, 12 place with vacuum pump
0.2 um sterile disposable filter unit (or equivalent)
ice/ice bucket
squirt bottle
20 ml plastic scintillation vials
incubator set at lake temperature
5% Trichloracetic acid, ~200 ml/12 samples, cold
0.2 um filtered DI water, 1 ml for isotope dilution
0.2 um filtered lake water, 100 ml/12 samples, cold
cellusolve (ethylene glycol monoethyl ether)
scintillation cocktail, e.g, ScintiSafe 30%
14C leucine stock solution: activity = 314.8 mCi/mmol
concentration = 0.1 mCi/ml= 0.32 umol/ml
working solution: 15 ul stock soln
810 ul 0.2 um filtered DI
825 ul working solution
insert thin sterile needle into stock solution rubber cap for pressure release- this needle can be re-used
use another sterile needle with 25 ul Hamilton syringe for withdrawal
add 50 ul (30 nM)/10 ml sample, 600 ml/12 samples
Pipet duplicate 10 ml water samples into 15 ml tubes
Add 1 ml 50% TCA to control tube and mix
Add 50 ul 14C working solution to each of the tubes. Note the time of the addition.
Place the rack of samples in the incubator at lake temp (or 5o C) for 1.5 h
After the incubation has ended, add 1 ml 50% TCA to each sample tube
Place 0.2 Millipore filters in filtration unit; pour one sample through each opening
Rinse each sample with 5 ml cold 0.2 um filtered lake water
Turn off vacuum
Add 5 ml ice-cold 5% TCA and extract for 5'
Apply vacuum
Rinse filter with 5 ml 5% cold TCA
Remove filter unit top
Rinse filter with 5 ml 5% cold TCA, paying particular attention to rinsing edges
Transfer filter to 20 ml plastic scintillation vial
Add 1 ml Cellusolve, let filter dissolve a couple of hours to overnight
Add 10 ml scintillation cocktail
A. Filter water from amber bottles through Gelman filtration set-up. Chlorophyll, Cations, Anions, Particulate Phosphorus, Particulate Nitrogen and Carbon.
1. Place pre-combusted (450 F for 5 hours)Whatman GF/C (47 cm) glass fiber filter onto frit; attach upper reservoir to filter holder.
2. Rinse graduated cylinder a few times with a small amount of sample water.
3. Measure 250 ml of sample (200 ml from 500 ml bottles) in graduated cylinder. Pour into filter reservoir. Be sure not to allow pressure differential to exceed .3 ATMs, to minimize damage to delicate organisms.
4. Place filter into 90 buffered (1mg/l) 90% acetone(1mg MgCO3/l)-filled centrifuge tubes (10 ml) Keep tubes out of direct sunlight while processing samples. Chlorophyll is analyzed after a 24-hr extraction period. Room temp.
5. Pour out filtrate into a waste bucket.
6. Change filter tower (25 mm polysulfone screw top)Place 25 mm GF/F pre-combusted (re-combusted prior to field season at MBL) glass fiber filter onto frit.
7. Into same graduated cylinder, pour 250 ml of sample.
8. Pour a small amount into filter reservoir to rinse. Pour remaining water into filter reservoir and filter. Reserve filtrate.
9. Place filter in petri dish reserved for particulate nitrogen and carbon.
10. A blank must be included for each set of PP and PN/PC samples filtered each day for blank correction.
11. Into same graduated cylinder, pour 250 ml of sample.
12. Pour into filter reservoir and filter. Reserve filtrate.
13. Place filter in petri dish reserved for particulate phosphorus.
14. A blank must be included for each set of PP and PN/PC samples filtered each day for blank correction. [Note: the volumes filtered are not absolute, just guidelines. Just be certain to record volume filtered in filter log book.]
15. When filtering for Toolik, N1, N2R and N2F take DOC samples for George Kling. Who will provide Scint vials. When finished return to Kling for preservation.
16. When finished processing Chl a samples, place centrifuge tubes in dark cool place. Then place petri dishes (lids ajar)into oven set no higher than 60 C for 12 hours. Particulate N/C and P samples should be placed in separate bags 1 for each lake.
17. Pour off cation (60 HDPE) and anion (30 ml HDPE) samples from filtrate. Rinse bottles a few times first. Acidify cation samples with 50 µl of Ultrex HCl. Put bottles in a box for later shipment to MBL.
18. A 50 ml volumetric pipet is used to measure filtrate for alkalinity titration. Dedicated 60 ml HDPE bottles are used to store samples (4 C) if being analyzed later.
19. Discard remaining filtrate.
20. Record all necessary information in filter log book.
B. Preserve the phytoplankton samples with Lugols. Add enough (usually two squirts from the pipet) to turn sample the color of tea (1:100).
Lugols Iodine
10 g Iodine
20 g Potassium iodine
200 mls H2O
20 ml glacial acetic acid
Place in box for further processing and shipment to Hedy Kling. After waiting a minimum of three days for organisms to settle use a 60 ml syringe with a piece of tubing on end and suck out all but 20 mls. Be careful lowering the tube and stop about .8cm above bottom of bottle. Put remainder in scint vial for shipping making sure to record the total volume and what it is concentrated to (i.e. 125 to 20).
1. Principle: Introduction of H14CO3 into a small bottle of natural waters will label the cellular carbon in an incubation of 4-24 hours in proportion to the rate of photosynthesis and proportional to the available diluting carbon 12 as CO2 and HCO3-. The assay measures net production in mesotrophic and eutrophic waters but is the subject of systematic errors of overestimation in oligotrophic water (Peterson Ann. Rev. Ecol. Sys.). Thus the results are reported as 14C-production in mg or mM Carbon assimilation per m3 per hour or day. The measurement requires the uCi of 14 C injected, the dpm uptake of 14C in algae, the temperature, pH, and alkalinity at the time of incubation. Underwater light transmission is necessary to interpret and model the results.
2. Equipment required:
a. Laboratory
i. 25 mm diameter filtration units (6 is optimal) and a vacuum pump (-1/2 atmosphere 10 lbs psi)
ii. 25 mm Millipore HA cellulose acetate filters or Gelman GN-6 membrane filters and flat forceps
iii. Scintillation vials, 5 or 7 ml, with sequentially labeled tops entered into the MASTER FILTER BOOK.
b. Field
i. Set of 73 ml Falcon tissue culture bottles, 2 light and 1 opaque per depth, for 0, 1, 3, 5, 8, 12, and 16 meters depending upon depth of the lake. Thus a set of bottles numbers from 15-21 per lake. Bottles should be labeled and stored in a light-proof field case.
ii. For each lake a suspension line that holds 6 bottles per depth is required. Bottle suspension lines are suspended on hooks outside 1 Duct Tape Lane.
iii. Van Dorn
bottle, 2 or 4 liter, metered line
and heavy messenger or submersible
electric pump with 12-16 meters of
tygon tubing marked at each meter
and a 500 or 800 watt portable
Honda-type generator (stored under
door-side counter, inside
3. Protocol:
a. Once on station, collect water from each depth, 0, 1, 3, 5, 8, 12, and 16 meters depending upon lake depth. Fill three bottles from Van Dorn bottle at each depth. Keep the bottles in the shade out of direct sunshine while filling or injecting, until submersed in lake water for re-suspension.
b. Using latex gloves, take a sterile ampoule of 14C, 5 ml, and crack off the top. Using a 100 ul pipette, inject exactly 0.1 ml (25-40 uCi/ml) of 14C-NaHCO3 into each bottle ( ~2.5 uCi/bottle). Place neck of bottle in suspension line holder for each depth, screw on top securely, and mix well. Keeping the injected bottles covered, in a box and out of the sunshine, continue until the entire bottle line has been injected, attached and mixed. Suspend the bottle line from a float by sliding the deepest sample over the side to the boat first. Attach the clip of the bottle line to an incubation float, designed not to shade the bottles. Tie the loose end to the float as a security line. Note the time of injection of the median bottle. Record this time in the field book.
c. For the computation, temperature, pH, and alkalinity are needed at each depth. Collaborative chlorophyll concentration and underwater light measurements are beneficial. Thus, doing the 14 C-production measurement at the time of the regular Hydrolab run is optimal. Temperature, pH, and conductivity will be taken at every meter. Minimally alkalinity must be done at three depths--1 m, 5 m, 8 m or 12 m. Underwater light transmission should be measured at 0, .1, .2, .5, 1 and every meter to the bottom.
d. Leave the bottles to incubate at natural light levels for 24 hours normally +/- a half an hour. Record the time out as the time the bottles or the entire bottle line are placed in complete darkness inside the boat (a box, pack or dark bag).
e. On return to the laboratory, titrate the alkalinity at a minimum of three depths, 1, 5, 8-12 meters using the Gran Titration. Filter and set up chlorophyll extractions.
f. 24 hours later, return the bottles to the laboratory. Filter each bottle through a single 25 mm membrane filter (GN-6 or HAWP 0.45 µM). Release the vacuum the minute that the filter goes dry. Release the filter and place each filter in a labeled mini-scintillation vial. Place the top on each vial loosely, in order to allow it to dry quickly.
g. Care of 14 C waste should be carefully watched. Keep the filter rig in a large tray to contain spillage. Use latex gloves. Place the filtrate that has passed through the filters into 5 gallon storage containers, supplied and marked for shipment. Record the mls of 14 C used and date on the sheet attached to the storage cabinet door. Solid waste (ampoules, towels, etc.) should go into a marked Ziploc bag and boxed as padding with the liquid. Record the number of bottles filtered on the sheet on each disposal carton. Scan the area with the Beta meter to find and eliminate contamination. No food and drink in the filter room. The bookkeeping is strictly required by University of Cincinnati and University of Alaska (Dr. Susan Hendricks) Radiation Safety Officers. All persons handling the isotope should be qualified by their own radiation safety officer and by Michael Miller in the field.
Dried scintillation boxes are marked
as waste and sent to the University
of Cincinnati Radiation Safety
Officer from the
B. Alkalinity: (Gran Titration)
1. Principle: Alkalinity is the measurement of the Acid Neutralizing Capacity (ANC) of a water sample. Alkalinity is usually reported in units of milliequivalents per liter of sample (meq/L). In Toolik area waters, ANC is due primarily to HCO3, CO3-2, OH-, and certain organic bases. Of these, HCO3 is usually by far the most important species. We are interested in measuring alkalinity for a couple of reasons. When coupled with a measurement of pH, alkalinity can be used to compute total dissolved inorganic carbon (needed for primary production measurements), and the partial pressure CO2 gas in the water (useful for atmosphere-water interaction studies). In waters which have a near-neutral pH (most of the Toolik area), alkalinity correlates well with the total concentration of dissolved ions, and hence can be useful in categorizing the overall ionic state of a water sample. Also, when used as a long-term monitoring tool, it can detect acidic impacts on lakes and rivers. Alkalinity is usually measured by titrating a water sample with a strong acid. The alkalinity is a measurement of the amount (equivalents) of acid needed to exactly neutralize the original ANC of the water sample. There are two common methods of performing this titration; both are based on monitoring pH as acid is added to a water sample. The procedure outlined below is based on the "Gran" methodology. In the Gran method, a series of pH measurements are made. The alkalinity is determined by an analysis of the rate at which pH changes in response to acid additions. In practice, the alkalinity is computed with a computer program written for this purpose.
2. Water samples: Water may be drawn from either a Van Dorn sampler or a pump. Either plastic or glass sample bottles are acceptable. If sample bottles were previously acid-cleaned, then bottle should be rinsed thoroughly with sample water if possible to insure that sample is not exposed to acid. Samples CANNOT be treated with either acidic or basic preservatives. This includes all acids and bases, and many preservatives such as formaldehyde. Samples should not be frozen. Analyses should be conducted within 24 hours. EITHER filtered or unfiltered water may be used for analyses.
a. If there is going to be a delay of more than one day between collection and analysis, then filtering is recommended. Alkalinity can change if biological activity results in either the production or dissolution of organic particles. If samples are going to be kept for more extended periods, then they should be stored in completely full, tightly stopper bottles.
b. If water samples are suspected of containing particles of calcium carbonate, sample MUST be filtered before analysis. If the sample is turbid, but composition of particles is not known, then filtering is an advisable precaution.
c. Anoxic water samples present special problems. Anoxic water samples from the Toolik area usually contain high concentrations of dissolved iron. When the anoxic water comes in contact with oxygen from the atmosphere, the dissolved iron will begin to precipitate. Iron precipitation strongly decreases alkalinity, and must be avoided. The best solution is to collect anoxic water samples by completely filling to overflowing GLASS dissolved oxygen bottles. Bottles must remain tightly stoppered until analysis. Bottles should be opened individually JUST BEFORE analysis is to begin.
4. All samples should be at room temperature when analyzed because pH is strongly influenced by changes in temperature.
5. The laboratory room where the measurements are made must be free of acid and base fumes. These vapors will dissolve in water and change the alkalinity. Likewise, if samples are filtered or otherwise processed in the laboratory, care must be taken to avoid contamination.
6. The methodology described below presumes that the alkalinity analyses will be made using the Mettler "Auto-Titrator." The pH electordes should be calibrated at least once per day. pH calibration procedures are described in the Mettler manual. The normality of the acid used for titration MUST be known very accurately. The acid routinely used at Toolik is 0.1 N H2SO4, and is usually purchased commercially. However, other normalities may be used if necessary.
7. Before beginning analyses, make sure acid dispensing and delivery tubes on the titrator are free of air bubbles. This can be a common problem at the start of each day and after the burette is refilled. Bubbles can usually be removed by gentle tapping to free the bubble from the tubing walls, followed by the dispensing of several mL of acid to flush the bubble from the tube.
8. Special Mettler titration cups are used for the samples. Titration cups MUST be clean and completely dry before use. Fill the titration cups with a KNOWN volume of sample. 50 mL samples are routinely used for Toolik measurements; however, other volumes may be used. The accuracy of the alkalinity measurement depends DIRECTLY on the accuracy of the sample volume. The preferred method for measuring and dispensing sample volumes is a volumetric pipette. The second choice for measuring and dispensing samples is a graduated cylinder.
9. Rinse the electrode 10 x with pump followed by wiping the electrode free of liquid. Screw the titration cup into the electrode/stirrer/dispenser holder.
10. Begin alkalinity titration:
a. Press "Stir" and "pH meas" watch the pH rise to 7-8.
b. Press "Reset"
c. Press "ENDPOINT" to set pH endpoint for initial titration. Enter a value of 4.1. and press "ENDPOINT" again.
d. Press "START" four times to begin titration. MAKE SURE stirrer is on and is at a moderate speed (about 3).
e. Titrator will beep when the endpoint has been reached.
*Write down amount of acid added*
f. Allow sample to stir for at least one minute after the endpoint has been reached. This allows CO2 to degas from the sample and permits stable pH measurement.
1. Hit [ml pH] write down acid added
2. Hit [Reset]
3. Hit [Stir]
4. Hit [pH meas]
5. Let stir 1 minute
g. Turn off the stirrer and press the "ml/pH" button. Continued pushing of this button causes readout to switch between "mL" and "pH." At this step in the analysis, pH should be between 3.95 and 4.05. If pH is >4.05, reset ENDPOINT for 4.0 and proceed again as above. When proper pH range has been achieved, record BOTH mL and pH.
h. Press "RESET," enter 0.02, and press "DOSE ml." This will cause 0.02 mL of acid to be dispensed into the titration cup.
I. Turn on stirrer for a few seconds. With stirrer OFF, press "pH MEAS" to measure pH. When pH reading has stabilized, record BOTH pH AND the TOTAL volume of acid which has been added to that point.
j. Press "DOSE mL" to dispense more acid and repeat as above. A pH change of about 0.1 pH unit is desirable. It will probably be necessary to increase the amount of acid dispensed as the titration proceeds. This can be done as described above.
k. Continue until at least eight readings have been determined which cover the pH range of approximately 3.0 - 4.0. Again, it is necessary to record BOTH the pH and TOTAL volume of acid dispensed for each set of measurements.
L. Compute alkalinity by entering data into Quattro Pro spreadsheet Alkalinity program. Data entered for each sample are 1) sample volume; 2) acidic normality; 3) sets of volume and pH measurements. Alkalinity is computed by running the macro program which is part of the spreadsheet. Check the output file for Correlation Coefficient and Predicted Acid Normality. If Correlation Coefficient is not greater than 0.98, or if Predicted Acid Normality differs greatly from actual acid normality, then there has probably been an error in the titration or data entry.
Measurements of dissolved oxygen concentrations are very useful in defining the general chemical and biological conditions within lake waters. The method described here is the "Winkler" method for dissolved oxygen measurement. The Winkler technique has the advantage of making very accurate measurement of dissolved oxygen concentration in small volumes of water. The disadvantage of the Winkler method, compared to measurement via oxygen electrode, is that water samples must be carefully collected and treated. Dissolved oxygen concentration is then determined by a field or laboratory chemical titration. At Toolik Lake, the Winkler method has been used primarily to make dissolved oxygen measurements in benthic chambers, in bottle respiration experiments, in soil waters, and to aid in calibration of the Hydrolab oxygen electrode. Theory of Winkler Method: Dissolved oxygen, O2, reacts with reduced manganese ion (Mn+2) under basic conditions to form a brownish precipitate of oxidized manganese hydroxide. When the precipitate is dissolved with sulfuric acid, oxidized manganese ion (Mn+4) reacts rapidly with iodide ion (I-) to produce molecular iodine (I2). The iodine produced is then titrated with sodium thiosulfate. The end point is detected using a starch indicator (Thyodene). In effect, the dissolved oxygen in the sample quantitatively oxidizes iodide to iodine.
General Note:
The method described below presumes that 60 mL sample bottles will be used, and that titrations will be done with a Hach Titrator. Weights for all reagents described below, with the exception of the thiosulfate titrant, are approximate. The success of the Winkler method does not depend on the exact concentrations of the manganese, alkaline/iodide, sulfuric acid, or Thyodene reagents described below. However, the concentration of the sodium thiosulfate reagent must be known accurately. The hydroxide and sulfuric acid reagents described below are quite concentrated. They will burn or discolor skin and can cause severe eye damage. Wear protective gloves and eyewear when making reagents. For safety, it recommended that reagents be stored in plastic rather than glass bottles.
1) Set of calibrated, numbered, dissolved oxygen bottles. The bottles routinely used at Toolik have a nominal volume of 60 mL, but the exact volumes of the bottles must be determined for accurate oxygen concentration measurements. This is usually done by weighing bottles before and after filling with deionized water.
2) Four pipettes, one each for reagents #3-6 described below. Less than four pipettes are needed if disposable pipette tips are used. The PREFERRED volume for reagents 3-6 is 0.2 mL. However, the actual volumes can differ from this slightly as the Winkler method is based on adding the reagents in excess amounts. For example, 0.25 mL pipettes can be used if these are the only size available. Reagent bottles and pipettes used for manganese and alkaline/iodide reagents must be kept separated. If they come in contact, precipitates will form in reagent bottles and pipettes.
3) Manganese Reagent (REAGENT A) - Dissolve approximately 42 grams of manganous chloride tetrahydrate (MnCl2.4H2O) in 100 mL deionized water. Other manganese salts can be used; weights required will be different depending on the molecular weight of the salt used. Bring only small volumes of this reagent into the field.
4) Alkaline/Iodide Reagent (REAGENT B) - Dissolve approximately 50 grams of sodium hydroxide (NaOH) and 13.5 grams of sodium iodide (NaI) in 100 mL of deionized water. CAUTION: This reaction will generate a great amount of heat. It may take some time for reagents to dissolve. Bring only small volumes of this reagent into the field.
5) Sulfuric Acid - Slowly and carefully add 50 mL concentrated sulfuric acid to 50 mL deionized water. After mixing and cooling, carefully add more water if necessary to bring total volume to 100 mL. CAUTION: This reaction generates a great deal of heat. Add concentrated acid to water, not vice versa. Do this in a glass container; enough heat can generated to melt some types of plastic bottles. After solution has cooled, transfer it to a plastic bottle.
6) Thyodene Indicator Solution - To 50 mL of deionized water, add a few grams of Thyodene powder. Shake or stir bottle to dissolve. Add a few more grams of Thyodene and shake again. Repeat until a nearly saturated solution is obtained. This should require several grams of Thyodene.
7) Sodium Thiosulfate Titrating Solution - concentration must be accurately known. At Toolik, we have been routinely been using titration cartridges provided by the Hach Company. The concentration of the cartridges is 0.200 N. If necessary, titrating solution can be made by dissolving a known amount of sodium thiosulfate salt in deionized water. The concentration need not be 0.2 N, but it must be known accurately. Note: for thiosulfate, normality (N) equals molarity (M).
8) Hach titrator apparatus
9) Magnetic Stirrer
10) Magnetic Stir Bar
11) Stir Bar retriever
A) Filling bottles Sampling technique is critical for this method. Oxygen in the air, or bubbles introduced while collecting samples or filling oxygen bottles can easily have an effect on the results. Water can be collected with a Van Dorn Bottle, a pump, or syringes. All three methods have been successfully used in Toolik sampling. For all methods, the outlet of the sampling device must be fitted with a length of Tygon tubing which will reach the bottom of the oxygen bottles. Water samples should be processed soon after collection. It is NOT a good idea to bring water back to the laboratory before adding reagents. Dissolved oxygen bottles are filled from the BOTTOM. Let water flow from the sampling device or syringe until the tubing is free of bubbles. Then, place the tubing at the bottom of the oxygen bottle and let the water fill up the bottle to overflowing. If enough water is available, the bottle should be flushed with at least 60 mL of excess water. The tygon tubing should be withdrawn from the oxygen bottle while water is STILL FLOWING. This will result in the bottle being completely full.
B) Adding Reagents: This method described below presumes that 60 mL bottles will be used. If bottles used are significantly smaller or larger than 60 mL, volumes of added reagents should be adjusted accordingly. Pipetting technique for adding reagents is important. The proper method is to insert the pipette tip a few mm below the water surface before adding reagent. The high density of the added reagents will carry them to the bottom of the bottle. The pipette must be withdrawn from sample bottle WITHOUT drawing sample water into the pipette tip. The order of addition of reagents is important. If reagent order is not followed, errors in concentration measurement are likely.
1) As soon as is practical after filling oxygen bottle, add 0.2 mL of Reagent A, followed by 0.2 mL of Reagent B.
2) Slide the tapered stopper into the bottle displacing the water from the neck of the bottle. Invert bottle several times to mix re- agents. A white to brown precipitate should form immediately.
3) Let the precipitate settle for a few minutes, then invert to mix again. If the bottles must be transported long distances to the laboratory, care must be taken to keep bottles upright with the stoppers in place. If stoppers come loose, samples can not be analyzed. Samples are best analyzed as soon as is practical, but analysis can be delayed several days if necessary. If that is the case, oxygen bottles should be kept out of direct sunlight in a relatively constant temperature environment. DO NOT FREEZE.
Once the analysis of a sample begins, it should not be delayed or interrupted. As mentioned earlier, this methodology presumes that a Hach Titrator will be used. One digit on the Hach titrator equals (1/800) mL. However, any dispensing device that is accurate to 0.01 mL may be used. The detection of the end point of the titration is not difficult, but it does take practice to achieve consistent results. The best viewing conditions have been found to be when the titration unit is well illuminated by a light source close to the unit, and the bottle is viewed against a white background. Practice is highly desirable BEFORE analyzing real samples.
1) Make sure that the Titrator is loaded with a 0.2 N Sodium Thiosu- fate cartridge, the cartridge is free of bubbles, and that the delivery tube is flowing freely. Wipe outside of delivery tube free of thiosulfate.
2) Zero the titrator readout.
3) Precipitate should be at the bottom of the bottle; DO NOT shake sample before analysis. Remove the stopper from an oxygen bottle and drop in a stir bar. Immediately add 0.2 mL of sulfuric acid reagent and place bottle on the magnetic stirrer. The stir bar should be provide rapid mixing and should remain on for the remainder of the analysis.
4) Most of the precipitate should dissolve very quickly. If particles of precipitate remain after about 15 seconds, add a second 0.2 mL volume of sulfuric acid. The color of the solution at this point can vary from very pale yellow to quite brownish. The brown color is due to the presence of molecular iodine. Sometimes it is difficult to distinguish between precipitate particles and small amounts of sediment or biological particles from the water sample. Small amounts of sediment particles will not interfere with analysis.
5) Lower delivery tube into bottle. Outlet of delivery tube should be below the neck of the oxygen bottle for best results. Titrate the solution with thiosulfate. The brown color will decrease as iodine is consumed.
6) When color has changed to pale yellow, add 0.2 mL of Thyodene indicator. Color should change to BLACK or BLUE. If color change does not occur, the end point of the titration has already been exceeded.
7) Slowly add more titrant while closely observing the bottle. The End Point of the titration is when the last bit of blue color disappears, and the solution is clear.
8) Record digits on Titrator readout.
9) Empty bottle into waste bucket, retrieve stir bar. 10) Let bottle drain in inverted position on paper towel for a few minutes. Make sure stopper stays with bottle. No further cleaning of bottles is necessary unless particles remain in bottles, or if bottles have become stained with manganese reagent.
The following formulas may be used for calculating dissolved oxygen concentrations from Hach titrations (1 & 2). Formulas are derived assuming that the titrant was 0.200 N sodium thiosulfate. General formulas for use when using other titrators or other normalities are also provided (3 & 4). Bottle volumes (BV) are in mL.
1) O2 (mg/L) = (Hach Digits)*(2)/(Bottle Volume)
2) O2 (umoles/L) = (Hach Digits)*(62.5)/(Bottle Volume) General formulas (all volumes in mL):
3) O2 (mg/L) = (Titrant Volume)*(Titrant Normality)*(8000)/(BV)
4) O2 (umoles/L) = (Titrant Volume)*(Titrant Normality)*(250,000)/(BV)
A. The Surveyor is down loaded at the end of every sample day.
1. Boot communications program on PC (HyperTerminal) if you have windows 95 of Pro comm plus for Dos). Hyperteminal is located in the program files \ accessories directories. Procomm is Pcplus\pcplus
The following parameters must be set for downloading using either software
Baud = 9600
Data bits = 8
Parity = none
Stop bits = 1
Flow control = Xon / Xoff
2. Use interface cable to connect Surveyor to PC
3. Turn Surveyor 3 on. Message "<computer connected> front panel disabled" should appear.
4. Open either Hyperterminal or Procomm Plus
5. Hit space bar to produce Basic menu
6. Type L for logging menu
7. DESTRAO will appear on screen. Type D for dump
8. Answer Yes to power down probes for dump
9. Select file to be dumped (file 5)
10. [Return]
10. Select S to dump file formatted for spreadsheet.
11. The SFC: selections allow you to choose calibrations you wish your variables to be calculated with. Select S for calibrations at time of set up.
12. Depending on the type of software the directions are as follows:
Hyper Terminal downloading instructions
1. Receive the file by hitting [Alt] [t] then [r]
2. Choose a directory to download the file to
3. Use X modem as the protocol
4. [Return]
5. Name the file to be downloaded. (no extension, spaces or more than 8 characters)
6. [return]
7. Transfer completed message should appear
Pro Comm Plus downloading instructions
1. Hit return. Starting X modem transfer should appear
2. Hit Page down and option 1
3. Name the file using the month and day i.e. jun12
4. Transfer completed will appear when finished.
5. Close Procomm and open file using spreadsheet program.
6. Modify file and save as spreadsheet while also keeping original dump file.
B. For the data base all data are recorded in coma delimited ascii text files separated according to lake. Hydrolab data is recorded in files named yr(lake name abbreviation)dat.dat. Nutrient data is recorded in files called yr(lakename)nut.dat. Chlorophyll data is recorded in files called yr(lakename)chl.dat. For example, Toolik files are called yrtlkdat.dat, yrtlknut.dat and yrtlkchl.dat. And so on. This convention will greatly facilitate data analyses later on. Unlike in the past, separate sampling dates will not have separate spreadsheets.
C. Nutrient data is recorded when available from the nutrientRA.
D. Chl a data is recorded in a spreadsheet.
E. Back up data files after each entry onto floppy disks.
F. Data floppy disks and log books must be carried back to MBL, not mailed.
G. Print outs of all data should be made before leaving Toolik and mailed to MBL.
H. Computer hard drive should be backed up on Omega drive prior to leaving Toolik.
XI. Arctic LTER Procedures for On-Line Data Management.
Introduction. All on-line data ( MACROBUTTON Arctic LTER On-Line Data) are stored as ASCII delimited files and can be accessed through the world wide web. The web pages have a tree-like structure that branch out from five main data areas: lakes, streams, terrestrial, land-water, and weather. Within each data area the structure and information are maintained by a research assistant who is responsible for that particular data area and in most cases also oversees data collection in the field. This insures that the person managing the data is also familiar with how the data are collected and with valid data values. One research assistant is designated the Arctic (ARC) LTER data manager. This person is responsible for the overall integrity of the on-line system and for the LTER wide data management issues.
Data Collection and Quality Control: Data analysis, documentation and quality control are the responsibility of the investigators collecting the data. Once the investigators are satisfied with the quality of the data, an ASCII documentation file and an ASCII comma delimited file are sent to the appropriate research assistant at the Marine Biological Lab (see PRIVATE HREF="datab_ra.html"MACROBUTTON HtmlResAnchor research assistant list). The document file is checked to see if it adheres to the documentation format standard of the arctic LTER and that the comma delimited file agrees with the documentation. See PRIVATE HREF="docprotocol.html"MACROBUTTON HtmlResAnchor data documentation protocol. If there are any discrepancies the investigator is contacted.
On-Line Data Web Pages. The document file and the comma delimited file are then placed in the appropriate data directories on the web server. A PRIVATE HREF="build"MACROBUTTON HtmlResAnchor perl script is then run to add the document filenames to an index file and to create a html version of each document file with a link to the data file. If a file is to be restricted to ARC LTER investigators the word "Restricted" is added to the first line of the document file and the data file is moved to a password access only directory. Generally restricted files are those for which the grant or project have not ended and data write up is still in progress.
This is a concise explanation of how data files are entered and validated into the Arctic LTER database. This process is continually being revised and updated to respond to the growing needs and demands on the database. The final format of the data files is comma delimited ASCII and the documentation is ASCII text. See PRIVATE HREF="instruct.html"MACROBUTTON HtmlResAnchor instructions for information on documenting data files and PRIVATE HREF="94tlknut.html"MACROBUTTON HtmlResAnchor 94tlknut.doc for an example documentation file.
(1) Data and documentation files are received at the main office (The Marine Biological Laboratory in Woods Hole, MA) via floppy disk or over the Internet. The principal investigators and /or their research assistants are responsible for entering, analyzing, documenting and error checking the data.. Before entering the data files into the database the appropriate research assistant at MBL compares the documentation and the data to make sure they correspond. Minor changes are made only to the copy on the hard drive (leaving the original unaltered).
(2) If there are any major changes or discrepancies between the data and the documentation, the data manager will either call, e-mail or write to the principal investigator (PI) to reevaluate the data. The process will begin again on the new version of the file. (Go back to 1)
(3) After all corrections are made, the data files are copied to the LTER database directory on the network server. They are separated according to their availability status. Data files available to the public are copied to the MBL gopher server while data files that are not yet ready for public release are copied to a password protected directory. All document files are processed into html pages and copied to the MBL web server. The document html pages include links to the data files. When the password protected data files are made publicly available they are moved to the MBL gopher sever. The document file is changed, removing the word "restricted" and reprocessed into a html page that reflects the new location of the data.
Availability Status is defined as
Data storage information:
The data are stored on a Unix network server which is backed up on tape twice each week. In addition, the data is backed up to MO read/write disks which are stored in a separate building.
NOTE: The data manager does not validate the accuracy or precision of the data (However, large discrepancies are noted). The PIs are responsible for making sure the data that is submitted to the database is scientifically accurate.
In each section of the .DOC file additional spacing may be added or deleted as needed.
Note: If the data file is to restricted to Arctic LTER investigators, add the word Restricted on the first line.
(1) FILE NAME: This name will be assigned by the PI. (Please be consistent within the File Naming System for the LTER database See Filename.doc file for details).
(2) YEAR: The year or years that the data were collected.
(3) PI: Fill in the name of the PI responsible for the data collection.
(4) OTHERS: PIs, RAs or Techs who were also involved in the data collection or compilation.
(5) BRIEF DESCRIPTION OF DATA FILE: Short, accurate explanation of the data set.
(6) KEYWORDS: Words that may be helpful in cross-referencing or cataloging the data. These should be in lower case format, unless the word is a proper name.
(7) SITE TYPE: This should be one of four types: TERRESTRIAL, AQUATIC-LAKES, AQUATIC-STREAMS, or LAND-WATER.
(8) RESEARCH LOCATION: The name of the
sampling location. Remember to
include not only the name, but, when
necessary , details and descriptions
of the sampling location. Examples
would be specific reaches of rivers,
sections of lakes, treatment areas
(treatment or control side of Lake
N-2, mouth of the
(9) EXPERIMENTAL DESIGNS AND METHODS: The description of methods should be fairly detailed and include any literature references (including author, title, journal and page numbers) pertaining to the methods.
(10) NOTES AND COMMENTS: Notes and comments about the data can go in two different places. Those with reference to the whole data set, including explanations of any problems with data collection or the data set, or reasons for missing data should be placed in this section. Comments about individual data points will not normally be included here, but will be placed in the actual data file (see first paragraph under VARIABLE DESCRIPTION below).
Variable name -----Variable
description.------ Precis./Units
This section describes the variables in the data set. The Variable Description should be a brief explanation of what the variable name represents.
The variables Date and Comments must be included in every data file.. Comments must be the last column in the file, and includes any additional information about individual data points. All Comments for a data point must be entered on a single line which can be no longer than 250 characters.
The variable Site, a numerical 3 digit code, should be taken from the Site Name Code List (code for PRIVATE HREF="../data_doc/streams/streams8.html"MACROBUTTON HtmlResAnchor streams, code for PRIVATE HREF="../data_doc/lakes/sitecode.html"MACROBUTTON HtmlResAnchor lakes). If you have a new site that is not on the list, do not code it yourself; ask the data manager to add it to the master list. The variable D/D (for depth/distance) must be included in every aquatic file, as it corresponds to the depth in a lake or the distance along a river from which a sample was taken. For those working on the Kuparuk River, D/D needs to be relative to the 1984 phosphorous dripper, and Oksrukuyik Creek should be relative to the 0.0 K dripper site set in 1989.
Variables for time in Hours are to be in 24 hour format (not AM or PM) and based on Alaska Standard Time, not Alaska Daylight Savings Time. Entries should be 4 places, hours and minutes, without any punctuation (examples 0458 or 2133). Individual PIs need to responsible for making these time corrections. Precision/Units should describe the units for the data and how precise the data are. Date should be in the format DD-MMM-YY (i.e. 01-Jun-88). This format avoids confusion between Canadian and USA forms of dates.
Missing data shall be designated by a Missing Data Value. The value used should be noted , i.e. BLANK, period, N/A. The value -9999 should be used with caution since it can be a real value in rare cases.
(12) CALCULATIONS: Any variables that have been calculated, along with their corresponding formula(s).
(13) FOR MORE INFORMATION, CONTACT: List here the name and address of the PI, or person, most knowledgeable about the data set.
(14) OTHER DATA FILES TO REFERENCE: This is a list of other files, or work by other PIs, that you feel may be of interest to a person looking at this file.
(15) REFERENCE CITATIONS: List in proper form both the published literature, and unpublished references, relating to this data set.
File Name:
File Type:
Variable Name-----Type Decimals
This section describes the structure of the data file. FILE NAME: This is the name of the data file. It must be the same name as this documentation file but with the .DAT extension. FILE TYPE: The data file must be in one of the following formats, in order of preference: 1) ASCII comma delimited (.DAT),. 2) spreadsheet (i.e. Lotus .WK1) or 3 Dbase (.DBF). Remember to specify the format
VARIABLE NAME: List here the names of all the data columns. They must be listed in order of occurrence in the data file from left to right. TYPE: Note if the variable is text, numeric, alphanumeric or date. DECIMALS: Designate how many decimal places there are in the numeric entries. Please include only significant digits + 1.
(17) NUMBER OF RECORDS: This states how many records are in the data file that is being referenced. This ensures that no data is lost during the transition of data.
(18) STATUS: Type of Availability Status
Type 1: Published data and 'meta-data' (data about data) are available on-line
Type 2: Collective data of LTER site (usually routine measurements). Available on-line 1 year after data are generated.
Type 3: Data from individual investigators (experimental data). Available 2 years after the termination of the grant or with permission of the investigator.
(19) FOR ARCHIVAL USE: The data manager will fill this in, noting when the file was received and who entered it into the data base. A quality control check of the data will then be made, by using summary statistics and generating a few plots. The PI will be asked to check these and validate the accuracy of the data in the database file. The name of the data confirmation person and the date of confirmation will be recorded, and any changes made to the file will be logged.
The Arctic LTER owns 2 GPS receivers.
1. A Basic Plus rover unit which is taken into the field.
2. A Pathfinder community base station placed at Toolik and connected to the LTER database computer.
The GPS Pathfinder Basic Plus is a high performance 6 channel receiver capable of tracking up to eight satellites simultaneously. The receiver can hold up to 10,000 positions which can be calculated approximately once per second and can be stored for later transfer to a PC for processing. It will provide accuracy of 2-5 meters after differential correction. Differential correction is a technique using GPS satellites and software that increases the accuracy of positions. Differential correction requires that at least two receivers be used. The first receiver or base station, is placed on a known location. (Ours is placed at a surveyed location at Toolik). The computed locations of the base receiver are then compared to the known base station location and the off set differences are used to increase the accuracy of the rover units to better than 5 meters. (50% of the collected points are within a five meter radius circle on a horizontal plane).
All data collected will be in NON-Differential GPS mode or what is known as post-processed differential correction. Important information for this is:
1. For the rover file to be differentially corrected the base station must be collecting data at the same time.
2. The base station must be tracking every satellite that the rover might use for positions. Use the default elevation angle mask values of 10o for the base station and 15o for the rover.
3. The rover must be within 300 miles (500K) of the base station if it is farther away, accuracy may degrade.
4. The computer currently used to collect base station data must be in turbo mode in order to work.
To adjust settings on the receiver the <L R> knob will move you from category to category and the <+ -> knob changes values within a category.
1. Check the differential correction and critical settings. These settings directly affect the way that positions are computed or that data is stored in the receiver. These should be checked every time the receiver is used.
SET UP position. There are two screens at this setting. The settings in these screens control how the receiver initially acquires satellites and the type of position to be computed.
On the set up screen the critical settings are in BOLD:
LAND if you are working on land
3D This ensures that the receiver calculates positions in 3 dimensions (latitude, longitude, and altitude) This gives the most accurate data however there may be some gaps in a file when enough satellites are not available.
The non-critical settings on this screen are:
North reference either
MG (magnetic)
True (TR)
Altitude reference
MSL (mean sea level)
HAE (height above ellipsoid)
Clock time zone
UTC (universal time coordinate)
Local time with offset is the local time - UTC= local offsett. examples:
London = 0
New York = -5
San Francisco = -8
Unit of Measure English, metric,
Coordinate system
DMS (degrees, minute, seconds)
DMD (degrees, minutes, fractional minutes)
UTM (Universal trans mercator)
OSB (ordinance survey of Great Britain)
TGL (trimble grid locator)
Datum can choose from over 70 or define your own. These are reference earth models used for mapping
99 or 999 is the number of waypoints available, do not change this setting or all waypoints currently in the receiver will be lost.
More - will take you to the next screen which is the communications screen. These need to be checked when transferring data. They should be on XMODEM, 9600, N,8,1. The differential mode needs to be set on nondifferential GPS for post processed differential correction using the PFINDER software.
STS position (status). There are 8 screens at this position
1. Mask Screen all settings are critical they are:
Max PDOD (default is 12)is the highest predicted dilution of position the receiver will accept if now constellation of satellites has a low enough PDOP no positions will be calculated. 4 or below is likely to yield highly accurate positions 5-8 is acceptable 9 or more is considered poor.
PDOD switch only used when rover is in auto 2D/3D
Elevation Mask controls the min elevation above the horizon at which satellites are used to compute positions. 15 is recommended for the rover. 10 is recommended for the base.
Signal Level Mask when satellite signal drops below a certain level it will not be used to compute positions. 6 is recommended
2. Summary Status Screen (no critical settings) Summarizes satellite tracking status
Tracking # satellites or SV space vehicles
Calc-sat-avail calculates satellite availability will calculate the length of time that 2D or 3D coverage is available for a given area or time until next window.
Quality of satellite geometry (OK,BAD,na)
Estimate of position accuracy (+or- a #) If over 300 selective availability is active. This is used by department of defense to downgrade quality in times of crisis to deny GPS to hostile forces.
3. Diagnostic status screen (no critical settings) Used primarily by service personnel
4. DOP screen (no critical settings) Displays which satellites are being used and their DOPs (dilution of precision) less is more a 4 is excellent.
5. Satellite status screen (no critical settings) displays individual satellite status
6. Datalogging screen The critical settings under this screen only need to be checked when waypoints are stored and differentially corrected later on the PC. They are:
Logging Mode rover or Base set it to rover
Position Logging interval Determines how often positions are saved in a file. They are:
1-999 -increment between positions can be in either time or distance (sec,meters, feet) You should stay at a position long enough to collect 180 positions
All- every position is recorded as calculated.
Off- no position information is recorded to a file. When logging a file you can switch this to off to move to another site or to temporarily stop logging with out closing the file and then enable when ready to begin.
Velocity will report velocity
Memory for recording data files
File name beginning with file name prefix A-Z followed by MMDDHH. These can also be user generated using the <+ -> switch.
Start / stop begins and ends logging of data
7. Recording screen displays information about a file while it is being logged.
8. Review screen displays information about closed files.
WPT (way point)position of the knob enters edits and deletes waypoints. A way point is a position coordinate (latitude longitude and altitude that is stored in the receiver and given a name. It is possible to navigate back to waypoints. The receiver can store up to 999 but usually only space for 99 is allocated.
To store a waypoint as a point feature while logging data to a file select <edit> name the waypoint if not time of position will be the name select <save>
DIST or distance displays the distance and bearing between two way points. If 0 is entered for to or from it will use last waypoint.
TIME Displays he current date time and ETA to a selected waypoint
NAV Navigation provides navigation information using selected waypoints. Within the navigation screen the headings are
Range- the distance to or from a position
Heading- your current direction of travel
Bearing- the direction you should go to get to a destination
XTE- Cross track error. which is the distance and direction (left or right) of your current location in regard to an imaginary line connecting the starting point and the destination. The statement XTE 2 miles right means your 2 miles right of the line and you should turn left 2 miles to get back to the line.
POS position displays he current date, time and position, whether positions are being computed and type of positions being computed. If the receiver has just been turned on it may take up to 5 minutes to calculate a position. If it has moved a great distance it may take up to 15 minutes. If the receiver stops computing positions it will say OLD in the lower right corner.
2 To increase the accuracy of the readings:
1. Record data at a point for 3 minutes for accuracy to 5 meters to increase to 2 meters average the positions after differential correction. You must differentially correct a positions before averaging them, you can not differentially correct positions that have been averaged. (Averaging by time,file,feature will create a new file that contains the averaged positions).
2. Collect data when PDOP (position dilution of precision)this indicates quality of satellite geometry. PDOP of less than 4 is excellent greater than 12 is poor.
3. Increase the elevation mask slightly. by using an elevation mask of 15 in stead of the default of 10.
4. Collect 3D positions these are more accurate than 2D.
3. Almanac Files are created by data transmitted by GPS satellites. They contain orbit, clock and health information of all satellites. They are collected each time you use the GPS device (for 12.5 minutes) and are usually good for 3 months from time of collection and can be used to check for satellite availability.
The short form for using the GPS
1. Check the differential correction and critical settings.
STS knob
PDOD mask - 9-12
PDOP switch - 8
Elevation mask - 15
Signal level mask - 6
Data logging screen
logging mode - rover
Position logging interval - sec
measurement logging interval
File name
Set up knob
set up screen
position fix mode - 3D
comm screen
differential mode - non differential GPS
STS knob
PDOD mask - 9-12
PDOP switch - 8
Elevation mask - 10 (should be lower than rover)
Signal level mask - 6
Data logging screen
logging mode - Base
Position logging interval - sec same or higher than rover
measurement logging interval 3-5 sec if SA is on 10-15 if SA is off
File name
Set up knob
set up screen
position fix mode - 3D
comm screen
differential mode - non differential GPS
2. Start logging data to a rover file
STS knob
Data logging toggle <start> when finished go to recording screen and toggle <stop>
3. Store way points as point features for post processed differential correction.
WPT knob position will be displayed toggle <save> to store as point feature.
4. If moving to another site to store point features and route is unimportant set position logging interval to OFF
5. End data logging and transfer file to PC using PFINDER
1. connect Rover to PC using 7 pin round connector.
2. Start PFINDER on PC by typing PFINDER at the DOS prompt.
3. Turn to the STS knob and select XMODEM
4. Transfer Data to the PC
COMM select data file to PC and enter
The directory of file in the Data logger will appear
Select the desired files and click OK
6. Differentially correct file using PFINDER
1. If the rover was collecting data for more than one hour several base files will have been created each being 1 hour long.
To combine these so different correction only needs to be run once. Under UTILS select combine SSF files. This will concatenate files end to end in the order you select by clicking <INPUT> followed by output. Click on the box labeled chronologically.
2. Enter the correct reference position of the SSF base file. Under UTILs select reference position and enter base file name and position.
3. select Differential correction under UTILS. Enter base file name. The difference file name will be entered automatically (same 8 character name followed by .&SF). Click on rover box and enter the name of the rover file. the name of the corrected file will be supplied and will be the same with the extension .COR.
4. Select the appropriate Out put uncorrected Records option. Check if you want the output file to also contain only points that are corrected. Leave blank if you want the file to contain points that were not differentially corrected for some reason.
5. Click <OKAY> differential correction will be performed.
XV. USE OF LTER Motorized BOATS
There are three motorized boats on Toolik lake purchased by the LTER. The three boats are:
1. 18 foot Lowe big John (sn OMCL 1948 A 494 ) (MBL ID 22213023) purchased new in 1994. Powered by a 4 stroke Honda 15 hp purchased in 1994.
2. 16 foot Lowe tunnel boat (sn OMCL 2732A 494) (MBL 22216074) purchased new in 1994, Powered by a 4 stroke Honda 8 hp purchased in 1994.
3. 20 foot river boat (The Schell boat) donated by Don Schell in 1993. Powered by a 4 stroke Honda 15 hp long shaft purchased in 1993.
There is one boat and motor owned and maintained by IAB for non LTER projects.
Priority for use of these boats is given to LTER projects. During periods of heavy use a coordination meeting will be held following breakfast at John O'Brien's lab.
Due to the many underwater obstacles which can damage motors and boats, everyone using boats a must be given a check out ride by the lakes RA. This consist of basic boating safety as well as a tour of the lake in order to see areas of potential problems.
Please refer to the map and follow known safe travel paths as well.
Routes of safe travel are shown with heavy line ( ).
A. Bring in rafts from remote lakes and canoes from N1.
B. Release float from Toolik Main.
C. Pull other floats out of lakes and leave on shore.
D. Pull boats at S6 and S7 on shore. Leave right side up so they aren't crushed by snow.
E Carefully label and document all waste with contents. radioactive waste and fill out logs for shipment to IAB.
F. Pack up PN/PC, PP, cation, anion, TDN, and TDP samples and ship to MBL. Boxes should be numbered sequentially and given an internal tracking number. This will help track down boxes that are lost in transit.
G. Pack up phytoplankton samples and ship to Hedy Kling.
H. Frozen inorganic nutrient samples have to be taken back on plane in a cooler.
I. Send chemicals that need warm storage to IAB. Label clearly. Indicate when they should be shipped back to Toolik next June. Be sure to inventory these items carefully and note where they are headed.
J. Send depth sounder, Hydrolab and Surveyor to MBL. Insure for $5,000. Don't forget the maintenance kit, Hydrolab cable or Surveyor cable hooked up to the computer.
K. Pack up the Autotitrator and store at Toolik. Empty the electrode (pasteur pipette works) so it doesn't freeze or ship back to MBL.
L. Put pipettes and re-pipettes back in boxes and mail to MBL.
M. Take a thorough inventory. Record on paper & as ASCII or in excel file.
Send Zooplankton samples to O'Brien
Send Microplankton to Parke Rublee
Q. Crate Honda boat motors and ship to IAB along with directions for annual maintenance
R. Pull docks and boats out of lake put drain plugs in box above lakes RA desk.
S. Put all sampling gear in hallway ready for early season use.
T. Empty weatherport of all sampling gear (put in hallway).
U. Bring vacuum pump inside from beneath trailer.
V. Pack GPS insure $10,000 and ship to MBL.
W. Pack Spectrophotometer and warm store at IAB.
X. Pack fluorometer and warm store at IAB.
XVII. List of Important Addresses.
Michael A. Abels
Toolik Field Station Manager
University of Alaska-Fairbanks
LTERnet address: email@example.com
E-Mail: email@example.com
Phone: (907) 474-5063
Neil Bettez
Marine Biological Laboratory
Woods Hole, Ma 02543
E-Mail: firstname.lastname@example.com
Phone: (508) 289-7486
Anne E. Hershey
University of Minnesota-Duluth
Department of Biological Sciences
LTERnet address: email@example.com
E-Mail: email@example.com
Phone: (218) 726-8200
George W. Kipphut
Department of Geosciences
LTERnet address: firstname.lastname@example.com
E-Mail: firstname.lastname@example.com
Phone: (502) 762-2847
George W. Kling
Department of Biology
LTERnet address: email@example.com
E-Mail: email@example.com
Phone: (313) 747-0894
(313) 747-0898
Hedy Kling
Freshwater Institute
501 University Cresc.
Logistic Services
Logistics Office (907) 474-7641
IAB Fax (907) 474-6967
Toolik Fax (907)
Michael E. McDonald
University of Minnesota-Duluth
Department of Chemical Engineering
LTERnet address: email@example.com
E-Mail: email@example.com
Phone: (218) 726-6306
Michael C. Miller
Department of Biological Sciences ML06
LTERnet address: email@example.com
E-Mail: mMiller@ucbeh (Bitnet)
Phone: (513) 556-9758
Dr. Parke Rublee
312 Eberhart Bldg
E-Mail: email@example.com
Phone: (336) 256-0067
Dr. John O'Brien
Email: email@example.com
Chris Crockett
Marine Biological Laboratory
Woods Hole, Ma 02543
E-Mail: email@example.com
Phone: (508) 289-7584
Stainton, M. P. & Capel, M. J.,
1974. Particulate Phosphorus.
In: The chemical Analysis of fresh
water. (Eds. : Stainton, M, P.
Capel, M, J) Fisheries Research
Board of
Straskraba, M. & P.
Javornicky, 1973.
Limnology of two re-regulation
reservoirs in
Strickland, J. D. & Parsons, T. R., (Eds.)
1972. A practical handbook of seawater
analysis. second edition. Fisheries
Research Board of
Stumm, W. &J. J. Morgan 1981.
Aquatic Chemistry , 2nd
edition. John Wiley & Sons,
Methods for Chemical analysis of
water and wastes.
Wetzel, R. & G. Likens, Gene, E (Eds.) 1979. Limnological Analysis. W.B. Saunders,
|Please contact email@example.com questions, comments, or for technical assistance regarding this web site.