June 2025

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Oceanography | Vol. 38, No. 2

80

diatom cells was observed along the transect. This bloom was

comprised of nitrogen-fixing bacteria living in symbiosis with

a diatom species (Hemiaulus), providing the necessary nitrogen

that was not available as nitrate (Castillo Cieza et al., 2024).

We demonstrated that post-calibrating Chl-a fluorescence

values are essential for accurate comparison, as the calibration

substantially altered the estimated Chl-a concentrations. In this

study, we used fluorescence values from different cruises, where

fluorometers either underwent manufacturer calibrations or

were replaced by spare instruments of the same model. A similar

approach can be applied when comparing fluorescence values

from the same study area but obtained from different research

vessels or other platforms such as moorings, CTDs, or gliders.

Without proper post-calibration, raw Chl-a fluorescence values

cannot be reliably compared.

FEEDBACK FROM STUDENTS AND

RECOMMENDATION TO INSTRUCTORS

The exercise described here was repeatedly tested with stu­

dents in class and in self-paced assignments. The major feed­

back from students was that they struggled with obtaining the

data from online repositories in reproducible ways. Different

versions of the same spreadsheet tool interpreted dates and

number formatting differently. To accommodate these chal­

lenges—which could not easily be alleviated as students may

have many different software types and settings—we have

developed a more explicit step-by-step guide and provided

standardized files for each intermediary step, so students can

access properly formatted files for each step and can avoid lack

of data accessibility or formatting issues. These elements raise

awareness for students as they will certainly encounter similar

challenges related to data management in their own research

or classes. This requirement for troubleshooting often fosters

learning and confidence in the gained competency, as students

overcome obstacles and find solutions independently. As large-

scale open-access databases become increasingly prevalent, the

skills developed through this activity are essential and founda­

tional for many researchers.

STUDENT BENEFITS

Our proposed activity offers students a valuable opportu­

nity to better understand the limitations of relying on raw,

manufacturer-​calibrated Chl-a values, and more broadly, on

any biogeochemical data obtained from sensors. This serves

as a general example of working with calibrated instruments.

Data users may assume that fluorescence-derived Chl-a con­

centrations provided by manufacturers represent accurate and

true measurements of Chl-a and possibly by extension, biomass.

However, as demonstrated in this study, this is not the case.

This exercise shows students critical concepts in data valida­

tion and underscores the need for quality control by research­

ers. This is exemplified by differences between fluorometers with

varying specifications that can lead to discrepancies between

nighttime and daytime measurements (Figure 2c). These vari­

ations suggest that non-photochemical quenching (NPQ) of

Chl-a molecules occurs during daylight hours when light inten­

sity is high (Marra, 1998; Xing et al., 2012), with some instru­

ments being more sensitive to this process than others. Ideally,

FIGURE 5. (a) Map and bathymetry of summer (in Northern Hemisphere) NES-LTER transect cruises from August 2019 (EN644, green), July 2020 (EN655,

light green), and July 2021 (EN668, yellow) from Narragansett Bay, Rhode Island, to the shelf break. (b) Raw underway fluorescence (mg Chl-a m–3) from

each cruise vs. latitude (°N; note the reverse x-axis from higher latitudes in the north [left] to lower latitude in the south [right]). (c) Post-calibrated under­

way fluorescence (mg Chl-a m–3) vs latitude. For clarity, only data from the outbound leg of the transect (north to south) are shown.

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