June 2025

Welcome to interactive presentation, created with Publuu. Enjoy the reading!

June 2025 | Oceanography

81

only nighttime fluorescence data should be used for post-​

calibration, while daytime values should be corrected for NPQ

(Carberry et al., 2019). In our case, we show that the NPQ effect

is negligible for our post-calibration. Using discrete data, we

show that the relatively high variance in our calibration is likely

due to the inclusion of both daytime and nighttime data.

Students also engaged with the importance of clarifying what

an instrument measures and what the measurement represents.

The concept of C:Chl ratios is fundamental in biomass assess­

ments in oceanographic studies and plays a key role in student

learning outcomes by highlighting how data or model estimates

are influenced by the conversion factors used. We encourage

educators to engage students in discussions on the deep Chl-a

maximum (DCM) in oligotrophic waters and the effects of

photo­acclimation on cellular Chl-a content. The DCM has often

been interpreted in scientific literature and textbooks as a bio­

mass maximum. However, it primarily reflects photoacclima­

tion processes and variations in the C:Chl-a ratio (Mignot et al.,

2014; Cullen, 2015; Maranon et al., 2021). This serves as a crucial

example of why Chl-a should be used with caution as a proxy for

phytoplankton biomass.

Lastly, and this is our central topic, our goal was to empower

students with the formal tools of data science, data manage­

ment, and FAIR practices. A career in data science and man­

agement can represent a career pathway in itself or a bridge to

other professional opportunities for students. Expertise in data

science is highly transferable and can be applied across a wide

range of professional fields, within sciences and beyond. A nota­

ble example is Amanda Herbst, a coauthor of this study, who

after completing a summer internship using the skills covered

here, pursued a Master of Environmental Data Science degree

at the Bren School of Environmental Science and Management

at the University of California, Santa Barbara, and who recently

accepted a position as Environmental Analyst for the New

England Interstate Water Pollution Control Commission

(NEIWPCC) and will be working at the New York State

Department of Environmental Conservation.

Students are exposed to the vast universe of freely available

data and how to handle them. When sourced from data portals

with rigorous quality control procedures and well-documented

metadata, these datasets can be valuable resources for research

and analyses at minimal cost. Many students, researchers, and

institutions face financial constraints when conducting field

studies, which often require expensive platforms (e.g., research

vessels) and instrumentation (e.g.,  biogeochemical sensors).

By increasing awareness of existing high-quality, open-access

datasets, the oceanographic community could make signifi­

cant advancements. In fact, some long-term observational data­

sets remain underutilized despite being collected, processed,

and stored following state-of-the-art standards (e.g., NSF Dear

Colleague Letters 2024). Leveraging these resources could

greatly enhance our understanding of oceanographic processes.

CONCLUDING REMARKS

The main goal of this contribution to Oceanography’s Ocean

Education article category is to emphasize to students the

importance of proper handling and sharing of post-calibrated

data by publishing it in open-access data portals. All the data

used in this hands-on activity are openly available, allowing

researchers worldwide to access and utilize them. However,

as demonstrated, interpreting raw Chl-a fluorescence has lim­

itations. Therefore, providing the scientific community with

high-quality post-calibrated Chl-a fluorescence data is essential

for advancing research.

An important aspect of sharing high-quality data in open-​

access repositories is to include all information necessary for

understanding how the data were acquired and analyzed. This

additional information, known as metadata, includes intel­

ligible and descriptive data product names, precise tempo­

ral and spatial coverage, accurate and complete lists of science

keywords, and concise yet readable descriptions of the data

products. Instrument calibration documentation (e.g.,  man­

ufacturer calibration) and data analysis workflows are also

crucial metadata components. Publishing open-access data

packages following FAIR principles ensures that the science

is open, transparent, accessible, inclusive, and reproducible

(Wilkinson et al., 2016).

In our case, we created an EDI data package that compiles

post-calibrated underway fluorescence data for six NES-LTER

cruises, spanning from summer 2019 to summer 2021, as part of

coauthor Amanda Herbst’s summer 2021 REU project. The REU

research project included all aspects of the research this exer­

cise drew on, including cruise participation to acquire calibra­

tion data. The NES-LTER Information Management team sup­

ported us in the creation of this data package (Menden-Deuer

et al., 2022). Essential steps in creating a data package include a

clear description of the methods used to process the data, data

quality checks, and additional metadata to improve findability.

These steps benefited greatly from the experience of data man­

agers, who play an essential role in modern research projects.

Please note that publishing the data package is not included in

this activity, as all sample data are already published, and multi­

ple publications of the same data package are not desirable.

SUPPLEMENTARY MATERIALS

The supplementary materials are available online at https://doi.org/10.5670/

oceanog.2025.314.

REFERENCES

Carberry, L., C. Roesler, and S. Drapeau. 2019. Correcting in situ chlorophyll fluores­

cence time-series observations for nonphotochemical quenching and tidal vari­

ability reveals nonconservative phytoplankton variability in coastal waters.

Limnology & Oceanography: Methods 17:462–473, https://doi.org/10.1002/

lom3.10325.

Cullen, J.J. 1982. The deep chlorophyll maximum: Comparing verti­

cal profiles of chlorophyll a. Canadian Journal of Fisheries and Aquatic

Sciences 39(5):791–803, https://doi.org/10.1139/f82-108.

Cullen, J.J. 2015. Subsurface chlorophyll maximum layers: Enduring enigma or

mystery solved? Annual Review of Marine Science 7:207–239, https://doi.org/​

10.1146/annurev-marine-010213-135111.

Made with Publuu - flipbook maker