This dataset includes accession numbers and related information for 16S rRNA genes characterizing microbiome changes in Agaricia tenuifolia and Siderastrea siderea coral species after being exposed to hypoxia and after a short period of recovery. Corals for the experiment were collected by SCUBA divers in summer 2022. Sequence data are available in The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject accession PRJNA1197146.

Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • BCO-DMO Processing Description
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

We conducted in situ experiments in which oxygen was manipulated with benthic tent-like enclosures.  Experimental plots were 60 x 60 cm, spaced > 2 m apart, and were randomly assigned to one of three treatments: a) Fully closed tents made of 60 x 60 cm greenhouse-grade clear vinyl with a 60 cm flange extending outward from the edges. Water was circulated within tents with a submersible aquarium pump; b) Partially closed tents used as procedural controls consisting of tents with parts of two sides cut away and no flange; and c) Open plots with no tent. The treatment was imposed for two days followed by a recovery period. During the recovery, colonies were taken from the plots and placed nearby for an additional three days under ambient conditions.

 

Coral microbiome samples were collected a) 'before': just before the experiment, following one day of acclimatization, b) ‘during': after two days of exposure to the treatment of either fully closed tent, partially closed tent, or open plot, and c) ‘after’: three days after the end of the treatment period. 

For each sampled coral colony, 5 millimeter (mm) circular cores (consisting of tissue and skeleton) were collected by SCUBA divers using sterile disposable stainless-steel biopsy punches (Integra Miltex). On shore, coral fragments were preserved with RNAlater and frozen until processing at the University of Florida. DNA was extracted with a DNeasy PowerBiofilm kit (Qiagen). The V4 region of the 16S rRNA gene was amplified with the 515F and 806RB Earth Microbiome primers and thermocycler protocol.

* Data table within submitted file Tent.txt was imported into the BCO-DMO system. It will appear in this dataset as "986518_v1_hypoxia-tent-experiment.csv"

* column "accession number" changed to BioSample for clarity and additional accession columns were added for SRA accessions using information from the NCBI SRA Run selector for the BioProject PRJNA1197146. This indeed has all 96 SRA info corresponding to the 96 BioSamples in Tent.txt.
Extracted from run selector https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA1197146&o=acc_s%3Aa

Missing Data Identifiers:
* In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.

* Organism names in this dataset were matched to Life Science Identifiers (LSIDs) using the World Register of Marine Species (WoRMS) on 2025-10-17. LSIDs for "host" were added to the column descriptions in the Parameters section.

Coverage: Caribbean Coast of Panama 9 N 82 W

NSF Award Abstract:
The world's oceans are facing the threat of deoxygenation - events of low dissolved oxygen insufficient for marine life and healthy ecosystems - which is accelerating along with other global crises including climate change and ocean acidification. The pace of these changes can lead to rapid shifts in the structure of marine communities due to changes in the distribution, abundance, and diversity of species. This collaborative project is among the first to examine the consequences of deoxygenation on coral reefs, which are sentinel ecosystems for studying ecological responses to global change because of their importance to human society, sensitivity to stress, and intricate relationships among their inhabitants. Specifically, the research team investigates why and how some coral species are more tolerant than others and the role that bacteria associated with the corals have in such tolerance. This predictive understanding is important to support conservation and management efforts by identifying stress-tolerant coral species and establishing indicators for assessment of hypoxia stress. The project provides training for multiple undergraduate and graduate students and postdoctoral researchers. Findings from this project are disseminated through undergraduate and graduate courses taught at the University of Florida, a teacher training program at the Bocas del Toro Research Station at STRI in Panama, a workshop in Panama to build a community of scientists and informed practitioners, and webinars, toolkits, and other resources communicated through established networks of coral conservation and management practitioners.

Understanding the responses of coral reefs to ocean deoxygenation is limited to a few post hoc assessments of how unanticipated hypoxic events have impacted macrofauna. This project employs a predictive approach to examine the resilience of coral reef communities to ocean deoxygenation by examining both corals and their associated microbiomes. Complimentary manipulative laboratory and field experiments and surveys along natural gradients of hypoxic stress are being used to answer the following three fundamental questions about how variation in the tolerance of corals and their microbiomes predicts the resilience of reefs to deoxygenation: (1) How does the physiological response of the coral to hypoxia predict community shifts in the microbiome with deoxygenation? (2) To what degree do corals and their microbiomes show evidence of acclimatization to reduced oxygen, and how do these functional shifts confer increased resistance to subsequent hypoxic stress? (3) How are the feedbacks between coral hosts and their microbiomes apparent in the recovery of coral communities from hypoxia and patterns of community structure at the seascape scale? This project aims at developing a mechanistic and predictive understanding of coral reef community responses to ocean deoxygenation by examining stability and resilience at two levels of ecological organization: the assemblage of coral species at the reef scale, and the assemblage of microbes at the holobiont scale. Moreover, this study examines how those responses are coupled by feedbacks at the colony scale through coral physiological responses and microbial functional shifts.

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.