Oceanography | Vol. 38, No. 2
76
(or lake, or any phytoplankton-rich water) sample, or even bet
ter, with a phytoplankton culture in a test tube. With all human
eyes protected from exposure, point the blue laser at the tube in
the dark, and the Chl-a molecules present in the phytoplank
ton will be seen to emit red light through fluorescence. Laser
light emission can be harmful to the eyes. Ensure you take pre
cautions to avoid directing the laser beam toward anyone’s eyes.
Fluorometers used by oceanographers use exactly the same prin
ciple, with a blue light exciting Chl-a present in natural assem
blages of phytoplankton and recording the intensity of the red
light thus emitted.
LAB ACTIVITY
MATERIALS AND SKILLS NEEDED
The instructions for the lab activities are provided in the online
supplementary materials. The data required for the lab activi
ties are also provided in the supplementary materials and are
accessible online through open-access databases and portals. To
facilitate the activities, open-access templates (OpenDocument
Spreadsheet, .ods) are included in the supplementary materials.
Additionally, .ods files containing the expected results for each
activity are provided to ensure students can complete all tasks,
even if they face challenges with specific steps. Instructors will
also find png-format figures illustrating each activity in the sup
plementary materials.
Students need individual computers with internet access
and a spreadsheet application, such as OpenOffice Calc (open
access) or Microsoft Excel, to complete the activities. They
should be comfortable using spreadsheet software and familiar
with basic functions like copying and pasting, calculating aver
ages and standard deviations, creating plots, and performing
linear regressions.
Instructors should be familiar with concepts in oceanogra
phy (e.g., phytoplankton and fluorescence). While experience
with deploying oceanographic instruments, such as fluorom
eters, and analyzing the resulting data can be helpful, it is not
required. However, proficiency in data handling and analysis
using spreadsheet software is highly recommended, as students
may encounter difficulties during the activities that require
additional support.
SECTION 1. ACCESSING AND EXPLORING
SENSOR-BASED FLUORESCENCE AND DISCRETE
CHL-A DATA (1.5 hours)
Accessing and working with observational data can be challeng
ing due to material or geographical constraints that limit data
availability. Here, we aim to familiarize students with openly
accessible oceanographic data and to help them develop skills in
analyzing sensor-based fluorescence and discrete Chl-a data col
lected as part of the Northeast US Shelf Long-Term Ecological
Research (NES-LTER) project. Students will work with authen
tic data and learn quality control procedures, with the goals
of acquiring valuable skills and addressing critical questions
about data quality assurance and the management of obser
vational datasets.
PART 1. SENSOR-BASED FLUORESCENCE CHL-a DATA
Goal. Access and work with authentic raw underway fluores
cence data, followed by preliminary interpretation of these data.
Expected Outcomes. Develop familiarity with underway fluo
rescence data, including the challenges of handling raw datasets
and navigating complex formats, such as date/time. Produce fig
ures to interpret general patterns in the data and engage students
in critical discussions about the observed trends.
Narrative. Fluorometers that record Chl-a fluorescence are
widely used by the scientific community to estimate phyto
plankton biomass in water bodies and to investigate the dynam
ics of phytoplankton communities. Chl-a fluorescence data
can be found on many open access databases. Some examples
from US-based research programs are the University-National
Oceanographic Laboratory System (UNOLS) Rolling Deck to
Repository (R2R), the Environmental Data Initiative (EDI),
the Ocean Observatories Initiative (OOI), and the Biological &
Chemical Oceanography Data Management Office (BCO-DMO).
Here, we use data from six NES-LTER cruises (EN644, EN649,
EN655, EN657, EN661, and EN668) on R/V Endeavor. During
each cruise, a pump located near the ship’s bow collects water
from 5 m below the ocean’s surface through a system of tubing
throughout the ship—called an underway system. Such under
way systems are present on most oceanographic research ves
sels. The underway data are recorded along the cruise tracks and
include a suite of navigation (e.g., latitude, longitude, speed),
meteorological (e.g., wind speed and direction, light intensity),
and oceanographic (e.g., temperature, salinity, Chl-a fluores
cence) data. On R/V Endeavor, some of the oceanographic data
collected are obtained from an underway water flow-through
system that includes temperature and salinity sensors, and two
fluorometers, a WETLabs ECO-FLRTD and a WETStar fluo
rometer. Fluorescence is measured and recorded every second
along the ship track. The WETLabs ECO-FLRTD reads Chl-a
fluorescence by exciting at a wavelength of 460 nm, the WETStar
fluorometer excites at 470 nm, and both fluorometers read emis
sions at 695 nm (Figure 1). The raw fluorescence is recorded in
volts (V) and then converted to Chl-a concentration expressed
in units of mg m–3 based on a manufacturer calibration using a
scale factor and blanks including pure water and dark counts.
Ship-provided raw underway data are publicly available through
the R2R data portal. Raw underway fluorescence data are
stored within the TSG Sea-Bird SBE-21 datasets, along with
other underway data such as temperature, conductivity, salin
ity (Sosik, 2019, 2020a, 2020b, 2020c, 2021a, 2021b). These
raw data can be challenging to access because of their formats