US Long-Term Ecological Research Network
Sample Collection:
  • Samples are surface water, filtered in the field through 0.45u nuclepore membrane filters into 125-ml poly bottles. The minimum amount needed is about 60 ml; if filtering is easy, fill the bottles to allow for the possibility of running duplicate scans. Biocomplexity color samples are collected once each summer, during the water chemistry sampling for each lake. Store samples cold and dark, then allow them to warm to room temperature just before running the scans.
  • Turn on spec and allow to warm up for at least 1 hour with no cells in the spec chamber. The room light should always be off when running the spectrophotometer.
  • Log on to the Trout network.
  • Select the UVIKON for Windows icon.
  • In EXECUTE menu, select BASELINE; ok the default wavelength parameters. The baseline will take several minutes to run. There should be no cells in the spec chamber during the baseline run.
  • In METHODS menu, select LOAD USER METHOD. Select the pkm-lter method from the Wavelength Scan files. (Parameters are already set, but should be: scan range=200-800nm, interval=1, no. samples=8, scan speed=200nm/min)
  • Rinse and fill the 10cm cells with milliQ water. Dry and polish the cell windows with lens paper.
  • Both the 10cm and 1cm cells we use have quartz windows. They are expensive and extremely vulnerable to scratching, which renders them useless. Do not use anything other than lens paper to wipe the windows of the spec cells.
  • Place the cells in the spec chamber, close cover and press MEASURE. When the scan is complete, remove the sample cell (the one toward the front of the spec), rinse 2X with the next sample, fill, replace, MEASURE. Leave the reference cell in the rear of the spec chamber filled with milliQ throughout the scans. 
  • We run the samples from clear to stained lakes to reduce the possibility of contamination between samples. Run scans of all lakes in the 10 cm quartz cells. 
  • In FILE menu SAVE to groups\Biocomplexity\Cross Lake Comparison\Data\Year\Biocom year\Chem year\Color. Our convention is to name the 10cm cell file BCMYr-run# (as BCM04-1, BCM04-2, etc). You will need to keep track of the order of the scans within each file on the color/chloro datasheets as there is no way to label the individual scans. Get a printout of the plot of absorbance values. 
  • Run a second set of scans in 1cm quartz cuvettes for any lakes that had absorbance values >2. You may need to change the “number of samples” parameter, but do not save the change to the pkm-lter method.

Clean up
  • Rinse spec cells well with milliQ water. Store the 10cm cells full of milliQ. Allow the 1cm cells to air dry before storing them. Return all spec cells to their homes in Pam’s office.
  • Rinse sample bottles 3x with milliQ and let dry before capping and storing.
Data Handling
  • In FILE menu, EXPORT each file in ascii format to groups\ Biocomplexity\Cross Lake Comparison\Data\Year\Biocom year\Chem year\Color. Open the files in Excel, sort (descending) to remove blank rows, add column headers and save as Excel Workbook. Notify Dave Balsiger that the color data are ready for inclusion in the Biocomplexity database, and note this on the lab form.


LTER Keywords
Protocol Format
Protocol ID
Protocol Type