Table of Contents

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

Water profiles were conducted during each dive with a multi-parameter sonde (YSI EXO-1 or EXO-2; YSI Inc.) measuring depth (m), temperature (°C), salinity, dissolved oxygen (% saturation), pH, and turbidity (FNU) at 0.5 or 1 second intervals. EXO-2 deployments also included ORP, and Fluorescent Dissolved Organic Matter. The sonde was calibrated prior to deployment following the manufacturer’s recommendations. To ensure an undisturbed water-column profile, the sonde was carried by the lead diver with the sensor array oriented forward.

Water profiles were cleaned on R 4.6.0 with the R package dplyr 1.2.1. Data cleanup was restricted to removal of data outside of the water and removal of outliers.

Curation actions performed on the data files

- Loaded `Cave_Benthos_Profiles_DM.csv` as table `1009304_v1_cave_ctd_water_profiles`, using row 1 as the header and treating blank values and `NA` as missing.
- Loaded `Profile Summary_DM.csv` as table `1009304_v1_cave_ctd_water_profiles_summary`, using row 2 as the header and treating blank values and `nd` as missing.
- Renamed columns in `1009304_v1_cave_ctd_water_profiles` to standardized names, including `Date`, `Time`, `Time_Fract_Sec`, `Site_Name`, `Cond`, `nLF_Cond`, `ODO_sat`, `ODO_local`, `ODO_mgL`, `Pressure`, `Sal`, `SpCond`, `TDS`, `Turbidity`, `TSS`, `Temp`, `fDOM_QSU`, `fDOM_RFU`, and `ORP`.
- Renamed columns in `1009304_v1_cave_ctd_water_profiles_summary` to standardized names, including `Profile_number`, `Sampling_rate`, `Cond`, `Depth`, `fDOM_QSU`, `fDOM_RFU`, `nLF_Cond`, `ODO_sat`, `ODO_local`, `ODO_mgL`, `ORP`, `Pressure`, `Sal`, `SpCond`, `TDS`, `Turbidity`, `TSS`, `pH_mV`, and `Temp`.
- Combined the `Date` and `Time` columns in `1009304_v1_cave_ctd_water_profiles` into a new `ISO_DateTime_UTC` column, converting timestamps from `Etc/GMT-5` to UTC and formatting them as `%Y-%m-%dT%H:%M:%SZ`.
- Reordered the columns in `1009304_v1_cave_ctd_water_profiles` as follows: `ISO_DateTime_UTC`, `Date`, `Time`, `Time_Fract_Sec`, `Site_Name`, `Cond`, `Depth`, `nLF_Cond`, `ODO_sat`, `ODO_local`, `ODO_mgL`, `Pressure`, `Sal`, `SpCond`, `TDS`, `Turbidity`, `TSS`, `pH`, `Temp`, `fDOM_QSU`, `fDOM_RFU`, and `ORP`.
- Converted the `Date` column in `1009304_v1_cave_ctd_water_profiles_summary` from `%m/%d/%y` to a date type formatted as `%Y-%m-%d`.
- Set column types in `1009304_v1_cave_ctd_water_profiles`: measurement fields were set as numeric, `TDS` as integer, `Date` and `Site_Name` as strings, `ISO_DateTime_UTC` as UTC datetime, `Time` as time, and `Time_Fract_Sec` as numeric.
- Set column types in `1009304_v1_cave_ctd_water_profiles_summary`: `Date` as date, `Profile_number` as integer, `Sampling_rate` as numeric, and all remaining columns as strings.
- Updated column metadata for `1009304_v1_cave_ctd_water_profiles`, including BCO-DMO standard name IDs, descriptions, and supplied units. `Depth` was designated as the primary parameter.
- Saved the final tables as `1009304_v1_cave_ctd_water_profiles.csv` and `1009304_v1_cave_ctd_water_profiles_summary.csv`.

NSF Award Abstract:
Karst subterranean estuaries (KSEs) occur worldwide where fresh and marine-derived waters mix within coastal aquifers, creating a chemical reaction zone that alters the composition of materials transported to the sea and sustains characteristic aquatic communities. Approximately one quarter of Earth’s population depends on karst (eroded limestone) water supplies that – within coastal regions – are directly threatened by rising sea level, uncontrolled groundwater extraction, and rapid coastal development. Yet, the role of these ecosystems in coastal biogeochemical cycling and groundwater health remains unknown. While pelagic constituents of flooded caves in KSEs have been studied for decades, the living benthic (cave floor / seafloor-hosted) fauna of these caves and caverns remains understudied. The overarching goal of this project is to better understand how benthic biodiversity affects ecosystem functioning across subsurface environmental gradients between freshwater aquifers and the marine environment. Flooded coastal caves allow the team to access the KSEs and make direct observations. Results of this work benefit marine benthic ecology and biology, biogeochemistry, paleoecology and biodiversity assessments. This interdisciplinary project establishes a multinational, multi-institutional collaboration, enhance research and scholarship opportunities at a predominantly undergraduate Hispanic-serving institution in Texas and support young investigators from under-represented groups in the sciences. For outreach, the project-associated PhD student, who is an African American female, is co-authoring a semi-autobiographical children’s book about cave diving and the wonders of cave-associated organisms.

KSEs influence coastal carbon and nitrogen cycling because they buffer terrestrial material inputs with groundwater discharge into the oceans. While pelagic communities of flooded cave environments in KSEs have been studied for decades due to their adaptations, biogeography, and evolutionary origin, the living benthic fauna and their role in KSE elemental cycling remains understudied. The overall aim of this project is to establish the diversity and ecology of benthic eukaryotes across environmental gradients in extensive coastal caves flooded by the KSE in the Yucatan Peninsula and Cozumel Island (Mexico) and determine how they interact with benthic elemental cycles. This study provides a holistic characterization of KSE benthos using interdisciplinary field- and lab-based approaches including barcoding/meta-barcoding, meta-transcriptomics, ultrastructural analysis, and lab culturing that are being integrated with biogeochemical and hydrological measurements. Specifically, the investigators are characterizing (1) the drivers of spatial biodiversity patterns in coastal cave eukaryotic benthic communities across salinity/oxygen gradients, relative to organic inputs; (2) the role of benthic meiofauna (to nanobiota) communities, with emphasis on foraminifera, in ecosystem function relative to dominant biogeochemical processes that mediate organic matter transformations and nitrogen cycling; and (3) the temporal constraints of benthic meiofauna (to nanobiota) biodiversity and ecosystem resilience in response to seasonal hydrological variation associated with meteorological events.

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.