June 2025

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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

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