Sampling & laboratory methods
Field & Laboratory Methods
Good data begin with consistent methods. This page sets out how SCC students will document sites, measure water and habitat, and collect and examine biofilms and plankton — with units, methods and quality control recorded for every value. These are working drafts: faculty will review and adapt them to the equipment available before the first field season. The scientific background is in Chapter 8.
Safety first
- Go only with a faculty member or an approved team; tell someone where you are going and when you will return.
- Check weather and current Kentucky HAB advisories (opens in a new tab) before leaving.
- Never enter fast, deep, rising or turbid water, or work in a stream during or right after a storm. Sample from the bank when possible.
- Wear closed-toe shoes with grip and nitrile gloves; cover cuts; wash hands before eating or drinking.
- Do not touch, wade through or collect surface scums or detached mats. Photograph from a distance and report them.
- Respect property boundaries and permissions. Stay clear of road culverts and traffic.
- No dogs at field sites.
- Treat all environmental water and biofilm as potentially hazardous: gloves, eye protection, no mouth contact, disinfect surfaces afterward.
- Do not culture, concentrate, centrifuge, aerosolize or freeze–thaw material from a suspected toxic bloom without an approved laboratory protocol and risk assessment.
- Toxin analysis is performed by qualified laboratories, arranged by faculty (see Chapter 5).
- Dispose of samples as directed by the laboratory supervisor.
Site documentation and GPS
Every observation is tied to a place and a time. Record the station code (once stations exist), the date and time with time zone, and the GPS position with its stated accuracy in meters and the device used. Take a photograph looking upstream and one looking downstream from the same marked point on each visit. Do not publish a position more precise than the accuracy you recorded.
Canopy cover
Shading is a key variable for stream biofilms. Measure canopy cover at each station with one consistent method — a spherical densiometer reading in four directions, or a vertical photograph of the canopy from a fixed height analyzed for percent sky — and record which method you used. Repeat across seasons, because leaf-out changes cover dramatically.
Flow and depth
Record flow as a category (dry, pooled, trickle, low, moderate, high, flood). Where safe, measure depth at a marked point with a meter stick (cm) and estimate surface velocity with a timed float over a measured distance (m/s). Because Allen Branch is mapped as intermittent, documenting when it flows, pools and dries is itself an important dataset. Record rainfall for the previous 24 and 72 hours from the nearest Kentucky Mesonet station rather than estimating it.
Water chemistry: units, methods and quality control
No measurement is stored without its unit and method. The table is the portal's measurement dictionary; values outside a method's range or below its detection limit are recorded as such, never rounded to zero.
| Parameter | Unit | Typical method | Record and check |
|---|---|---|---|
| water_temperature | °C | Calibrated thermometer or meter probe | Time of reading; probe in flowing water, out of direct sun |
| ph | pH units | Meter calibrated the same day with at least two buffers; or test strips | Buffers used; strips are low-precision and must be labeled as such |
| specific_conductance | µS/cm at 25 °C | Temperature-compensated conductivity meter | Calibration standard and date |
| dissolved_oxygen | mg/L and % saturation | Optical or membrane DO meter | Calibration; time of day (oxygen varies daily) |
| turbidity | NTU or FNU; or cm (transparency tube) | Turbidimeter, or transparency tube for screening | Instrument or tube length; report units as measured |
| nitrate_n | mg/L as N | Colorimetric kit or photometer | Kit name, detection limit; state "as N" (nitrate as NO₃⁻ is 4.43 × nitrate-N) |
| orthophosphate_p | mg/L as P | Colorimetric (molybdate/ascorbic acid) kit or photometer | Kit name, detection limit; filtered or unfiltered |
| water_depth | cm | Meter stick at a marked point | Location of the measurement |
| canopy_cover | % | Densiometer or canopy photograph | Method and height |
| rain_last_24h, rain_last_72h | mm | Kentucky Mesonet nearest station | Station name |
Quality control. Keep a calibration log for each instrument. At least once per visit, take a duplicate reading or sample. For kits, run a blank with distilled water. Flag values that are estimated, out of range, below detection, or affected by instrument drift (qc_flag in the data model).
Biofilm sampling
To compare biofilms between stations, sample the same way every time: choose rocks of similar size from the same habitat type (for example, riffle cobbles), scrub a measured area defined by a template into a known volume of stream water, and keep the sample cool and dark until examination the same day. Record the number of rocks, area scrubbed, volume, and a description of what was visible (thin film, thick film, mat; color). Never sample detached floating mats.
Microscopy, calibration and photomicrography
- Calibrate the ocular micrometer against a stage micrometer for each objective and record the micrometers per ocular division in the calibration log.
- Prepare a wet mount from a well-mixed subsample; add India ink to a second mount to reveal mucilage.
- Scan at 100×, then examine at 400× and, where needed, 1000× oil immersion.
- Measure cell width and length (and heterocyte and akinete dimensions) for at least 10 cells per morphotype.
- Photograph each distinct morphotype with a scale bar created from the calibration, and record magnification, camera and file name.
- Identify provisionally with the teaching key and the Atlas, and record your confidence.
Photographs become portal media only with photographer credit, a license, and faculty review.
Zooplankton
In ponds and lake embayments, collect zooplankton with a fine-mesh plankton net, towed from shore or a dock at a recorded depth and distance. Observe and count live specimens under a dissecting microscope, identify major groups (rotifers, copepods, cladocerans such as Daphnia), and return or dispose of samples as directed. Record net mesh size, tow length and volume filtered so that densities can be compared.
GIS: delineation and land cover
Delineate the drainage area above a defined station with USGS StreamStats, saving the basin file, the pour-point coordinates, the date and the application version. Land-cover summaries (for example, NLCD 2021 classes) are calculated in QGIS only inside a delineated basin, and are reported with the dataset year, resolution and method. In karst, note that a surface delineation may not represent the true contributing area.
Recording and review
Field data are entered with the observation form, which follows the format described on the Observations page. Attach your upstream, downstream and close-up photos: the form reads each photo's time and GPS position, and you should still check both against your field notebook. Records are drafts until a faculty reviewer approves them; only approved records are published. Student names appear publicly only with consent.
