Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Curation Notes
  • Problem Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

 fDOM samples were stored in amber glass vials at 4 °C until further processing. Heterotrophic bacterial counts were taken from 1.5 mL unfiltered seawater and stored in 0.5% paraformaldehyde (amended with 100 μL 8% ampulated paraformaldehyde, Electron MicroscopySciences, Hatfield, PA, USA) in a 2 mL polypropylene cryovial, mixed briefly and then frozen to -20 °C. All storage vials were triple rinsed with sample water prior to sample storage. fDOM samples were processed on a Horiba Aqualog scanning fluorometer with 1 cm quartz cuvettes at the University of Hawai’i at Mānoa following Nelson et al. (2015).

All samples were brought to room temperature prior to analysis. Prior to running samples, cuvettes were washed thoroughly with DI water and wiped clear with Kim wipes. Cuvettes were triple rinsed with DI between each sample. A DI blank was run after every 7 samples. Excitation-Emission Matrices (EEMS) were generated with excitation values ranging from 240 nm to 500 nm and emission values were measured ranging from 250 nm to 825 nm.

Excitation wavelengths were increased at 5 nm increments and measurements were integrated over 4 s at each increment. Inner filter correction was applied to account for fluorescence quenching by absorbance (Kothawala et al. 2013). Fluorescence values were scaled to Raman Units by dividing by the integrated emission range of 381 nm to 426 nm at an excitation of 350 nm in averaged DI blanks. The average blank EEMs, from DI blanks run immediately before and after each set of samples, were subtracted from the sample EEMs.

Two biogeochemical informative indices were calculated for this study which included M:C (the relative amount of marine to terrestrial humics) (Burdige et al. 2004) and BIX (biological index) (Huguet et al. 2009). Heterotrophic bacterial counts were analyzed using flow cytometry on an Attune Acoustic Focusing Cytometer with Autosampler Attachment (Life Technologies, Eugene, OR, USA) with methods following Nelson et al. (2015).

Flow cytometry samples were analyzed on fixed 1ml samples run on a Cytoflex Flow Cytometer stained with 7 μL of 40 μL mL−1 Hoechst 34580 (1 μg mL−1 , final concentration) following standard protocols (Nelson et al. 2015; Selph 2021).

Stained cells were distinguished from instrument noise using stained and unstained blank water, and autofluorescent cells containing phytopigments were subtracted from the total to derive the subset of heterotrophic bacterioplankton.

R code and data files used for statistical analysis and figure generation for the results publication Silbiger et al. (2025). The fDOM and heterotrophic bacteria in this BCO-DMO dataset were incorporated into the joined data file used for analysis and plotting.  All data and code are available at https://github.com/njsilbiger/Intertidal-Benthic-Pelagic and at https://doi.org/10.5281/zenodo.17717287 on Zenodo (Silbiger 2025).

Curation Actions Performed on Data File

- Loaded fDOM_bacteria_Silbiger2026.csv using the first row as headers and treating empty strings and NA as missing values. The table was named 1009817_v1_tidal_fdom_and_heterotrophic_bacteria_counts.
- Converted sampling_day to a date formatted as %Y-%m-%d and sampling_time to a time formatted as %H:%M:%S. Renamed these fields to sampling_date and sampling_time_local, respectively.
- Combined the local sampling date and time, interpreted in the Canada/Pacific timezone, into a new ISO_DateTime_UTC field formatted as %Y-%m-%dT%H:%M:%SZ.
- Standardized column order and assigned appropriate data types, including strings for categorical and identifier fields, numbers for bacterial counts and fluorescence-related measurements, and date, time, and datetime types for temporal fields.
- Added taxonomic metadata based on foundation_spp: LSIDs and AphiaIDs for Mytilus and Phyllospadix, with "none" for Ocean samples. Taxonomic level and status values were also evaluated during processing.
- Removed the intermediate taxon_level, status, and rand columns and finalized the column order and data types.
- Updated parameter metadata, including descriptions, standard names, and units, and designated ISO_DateTime_UTC as a primary parameter.
- Saved the processed data as 1009817_v1_tidal_fdom_and_heterotrophic_bacteria_counts.csv.

NSF Award Abstract:
This award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2).

The devastating impacts of global warming and ocean acidification (OA) on rocky intertidal ecosystems are expected to increase as the oceans continue to warm and acidify. Further, loss of critical foundation species as a result of anthropogenic stressors lead to changes in local conditions that alter ecosystem functioning. While data exist on the physiological response of individual organisms to OA and warming in rocky systems, far less research has been conducted on community and ecosystem-scale metabolic responses. The proposed work provides a critical step in understanding how altered environmental conditions affect ecosystem functioning in rocky intertidal systems through the combination of controlled laboratory studies, field experiments, and a synthetic modeling approach integrating experimental results with pre-existing time-series data. The proposed work is focused on the overarching question: How does shifting environmental variability and loss of foundation species interact to affect ecosystem functioning in rocky intertidal communities? The PI is integrating research with ecological and quantitative educational opportunities including classroom and hands-on training in lab/field methods in marine ecology, and data science and coding bootcamps for undergraduate students. Importantly, these opportunities financially and educationally support traditionally underrepresented students at one of the largest minority-serving institutions in the country. This project provides support for intensive mentoring and training for 35 undergraduate students (25 in data science and 10 in field/lab science, all paid), 2-3 masters students, and hands-on marine ecology opportunities in the classroom (~125 students). In addition to formal education, the PI is collaborating with an artist-in-residence to communicate science to the broader public through interactive and immersive art installations in Los Angeles.

Because rocky intertidal systems provide important ecosystem services including food production, coastal protection, and tourism, it is critical to understand how warming (both air and ocean), acidification, and altered community states affect reef-scale ecosystem metabolism. While information exists on responses of a variety of individual intertidal taxa to temperature stress, ocean acidification, and habitat loss, there is notably less on the response of ecosystem metabolism (e.g. NEP and NEC) to these stressors. This proposed work is focused on a series of conceptual knowledge gaps and tests mechanisms through which different warming regimes, lowered pH, and community disturbance lead to altered community metabolism and ultimately affect ecosystem function. Specifically, this study: 1) Describes community thermal performance curves of multiple ecosystem functions under differing pH conditions in experimental mesocosms, 2) characterizes drivers of ecosystem functioning (e.g. Net Ecosystem Production [NEP] and Net Ecosystem Calcification [NEC]) in situ using natural changes in environmental variability before and after a disturbance, and 3) integrates 16 years of publicly available community composition and environmental time-series data with lab and field data to hindcast ecosystem metabolic rates and predict how ecosystem metabolism may change in the future.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.