Overview

This dataset contains environmental and coral physiological data used to investigate how long-term exposure to contrasting reef environments influences the holobiont phenotype of the coral Pocillopora damicornis at Heron Island, southern Great Barrier Reef, Australia.

The study examined six geomorphologically distinct reef sites:

• HB — Harry's Bommie
• FP — Fourth Point
• DL — Deep Lagoon
• SL — Shallow Lagoon
• RC — Reef Crest
• RF — Reef Flat

The dataset integrates approximately one year of high-frequency environmental observations with measurements of coral physiology and thermal tolerance. Associated bacterial microbiome and Symbiodiniaceae ITS2 sequence data are archived separately in the NCBI Sequence Read Archive under BioProject PRJNA1456108.

Environmental variables include temperature, dissolved oxygen, photosynthetically active radiation, salinity, turbidity, chlorophyll fluorescence, depth, and pCO₂ where available.

Coral physiological measurements include tissue biomass, chlorophyll-a, Symbiodiniaceae density, protein, skeletal density, fluorescent pigmentation, mycosporine-like amino acids, photophysiology, and thermal tolerance.

These data can be reused to investigate relationships among reef-scale environmental variability, coral physiology, thermal tolerance, algal symbiont communities, and bacterial microbiome structure.

Associated resources

Analysis code

Analysis code associated with this dataset is available at:

https://github.com/mmartynek/Heron-Pdam-Physiology-Microbiome

The repository contains R Markdown scripts used for environmental, physiological, Symbiodiniaceae, and bacterial microbiome analyses.

Principal analysis scripts include:

• Environmental_Parameters.Rmd — environmental data processing, summarization, statistical analysis, and visualization
  • Rendered HTML (Environmental-Parameters.html) output generated from Environmental_Parameters.Rmd
• Physiology.Rmd — analysis and visualization of coral physiological measurements and thermal tolerance
  • Rendered HTML (Physiology.html) output generated from Physiology.Rmd
• Microbiome.Rmd — processing and analysis of bacterial 16S rRNA gene community data
• its2.Rmd — processing and analysis of Symbiodiniaceae ITS2 data

Users wishing to reproduce analyses should consult these scripts together with the methods described in the associated manuscript.

Raw sequence data

Raw bacterial 16S rRNA gene and Symbiodiniaceae ITS2 amplicon sequence reads are archived in the NCBI Sequence Read Archive under:

NCBI BioProject: PRJNA1456108

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1456108

Data files

allsites_filtered.csv

High-frequency environmental observations combined across the six reef sites after quality-control filtering.

Observations are identified by site, date, and date/time where applicable.

Major environmental variables include:

Environmental measurements were screened for erroneous or biologically implausible values before analysis. Negative turbidity and fluorescence values were treated as missing values. Periods affected by identified sensor fouling or instrument problems were also excluded or converted to missing values before analysis.

Missing values are represented as NA or blank cells.

salinity_filtered.csv

Daily summarized salinity data generated from the environmental time series after quality control.

Two anomalous daily salinity observations identified during quality control were excluded from this summarized dataset:

• Harry's Bommie on 17 August 2016
• Deep Lagoon on 26 January 2016

Pdam_comparative_physiology_CURRENT.csv

Coral-level physiological dataset containing measurements from Pocillopora damicornis colonies collected across the six reef sites.

Each row represents an individual coral colony or associated physiological observation.

Coral ID provides the colony identifier and Origin identifies the collection site.

Identification variables

Mycosporine-like amino acids and pigments

Coral physiology

Environmental descriptors associated with coral collection sites

Missing physiological observations are represented as NA or blank cells.

Missing values may reflect measurements that were not obtained, failed quality-control criteria, or were excluded as documented in the associated analysis scripts.

Environmental data

Environmental conditions were monitored across six reef habitats representing different geomorphological settings around Heron Island.

Environmental data from individual sites were standardized and combined into a common dataset.

Variables used to characterize environmental regimes included:

• temperature
• photosynthetically active radiation
• dissolved oxygen
• salinity
• turbidity
• chlorophyll fluorescence
• depth
• pCO₂ where available

For core environmental variables, daily means and diel amplitudes were calculated by site and date. Diel amplitude was calculated as the daily maximum minus the daily minimum.

Quality-control procedures included removal of identified periods of sensor fouling or instrument malfunction and conversion of invalid measurements to missing values.

Because sensors differed among variables and deployment periods, not every environmental variable contains observations for every site and date.

Coral physiological data

Coral physiological measurements were collected from Pocillopora damicornis colonies originating from the six reef environments.

Measurements characterize several aspects of coral holobiont physiology, including:

• tissue biomass
• skeletal density
• protein content
• Symbiodiniaceae density
• chlorophyll content
• mycosporine-like amino acids
• fluorescent pigmentation (Pocilloporin)
• photochemical efficiency
• thermal tolerance

Physiological measurements were normalized to coral surface area or other appropriate biological quantities where described in the associated manuscript and analysis scripts.

Thermal tolerance is represented by ED50, an estimated temperature associated with a 50% response threshold during the thermal stress assay.

Symbiodiniaceae data

Symbiodiniaceae communities associated with sampled Pocillopora damicornis colonies were characterized using ITS2 amplicon sequencing.

Raw ITS2 sequence data are deposited in the NCBI Sequence Read Archive under BioProject:

PRJNA1456108

Processed Symbiodiniaceae data were used to characterize community composition across the six reef habitats.

The associated its2.Rmd script documents filtering, community analysis, and visualization procedures.

Symbiodiniaceae communities in the study were dominated by Cladocopium latusorum.

Bacterial microbiome data

Coral-associated bacterial communities were characterized using 16S rRNA gene amplicon sequencing.

Raw 16S rRNA gene sequence data are deposited in the NCBI Sequence Read Archive under BioProject:

PRJNA1456108

Processed bacterial community data were used to characterize microbiome composition among reef sites and investigate associations with coral physiology and environmental conditions.

Sample metadata link bacterial community profiles to coral samples and reef collection sites.

The associated Microbiome.Rmd script documents filtering, community analysis, taxonomic analysis, statistical testing, and visualization.

Relationships among datasets

The datasets can primarily be linked using reef site and coral sample identifiers.

Environmental observations characterize the long-term environmental regime experienced at each of the six reef sites.

The physiology dataset contains individual coral-level measurements together with environmental summary variables associated with each colony's site of origin.

Symbiodiniaceae and bacterial microbiome datasets are linked to coral samples through sequencing metadata and collection-site information.

The general data structure is:

Reef site
    |
    +-- Environmental time series
    |
    +-- Coral colony / sample
            |
            +-- Physiology
            +-- Thermal tolerance
            +-- Symbiodiniaceae ITS2 community
            +-- Bacterial 16S microbiome

Users joining datasets should retain the original coral and sequencing sample identifiers and verify identifier formatting before merging tables.

Site abbreviations

Missing data and exclusions

Missing values are represented as NA or blank cells.

Missing observations may result from:

• sensor failure or fouling
• unavailable measurements
• measurements failing quality-control procedures
• excluded biological samples
• failed sequencing or insufficient sequencing quality
• individual observations excluded during quality-control review

Users should not interpret missing values as zero.

Known environmental quality-control procedures are documented in Environmental Parameters.Rmd.

Known physiological exclusions are documented in Physiology.Rmd.

Software and reproducibility

Analyses were performed primarily in R.

The associated .Rmd files document data preparation, statistical analyses, and figure-generation workflows.

Because some scripts were originally developed using local file paths, users reproducing the workflow may need to modify file paths to match their local directory structure.

Users should install the R packages loaded within each script. Package versions may differ from those used during the original analyses.

Reuse potential

These data can be reused to:

• evaluate coral physiological variation across naturally contrasting reef habitats
• test relationships between environmental variability and coral thermal tolerance
• investigate relationships between environmental regimes and coral energetic allocation
• compare Symbiodiniaceae communities among reef habitats
• compare bacterial microbiome composition among coral populations and habitats
• examine relationships among environmental conditions, host physiology, algal symbionts, and bacterial communities
• develop or validate metrics of environmental variability
• incorporate Heron Island observations into comparative studies or meta-analyses of coral reef environments and coral resilience

The high-frequency environmental observations may also be reused independently of the coral biological measurements.

Legal and ethical considerations

The dataset does not contain human participant data or personally identifiable information.

Coral samples were collected and handled under the permits and approvals described in the associated publication.

Users should consult the associated manuscript for complete sampling, permitting, and methodological information.

Users should also consider any applicable requirements governing the reuse of biological samples, sequence data, or sensitive species-location information.

Related resources

GitHub repository

https://github.com/mmartynek/Heron-Pdam-Physiology-Microbiome

NCBI sequence archive

BioProject: PRJNA1456108

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1456108

This BioProject contains the raw bacterial 16S rRNA gene and Symbiodiniaceae ITS2 amplicon sequencing data associated with the study.

Associated publication

Martynek et al. 2026

Reef-scale environmental mosaics shape coral physiological and microbial signatures of resilience.

Notes for reuse

The R scripts provide additional information regarding data filtering, transformations, statistical models, and observations excluded from specific analyses.

Some variable names in the CSV files reflect names used during the original analysis and have been retained to maintain compatibility with the supplied code.

For interpretation of measurement protocols and analytical methods, users should consult the Methods section of the associated publication together with this README.