Table of Contents

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

Coral colonies were collected in the field from two sites (Cayo Roldan and Hospital Point), fragmented into smaller samples, and acclimated in aquaria for seven days. Ten 40-L aquaria were set up for ex situ manipulation of dissolved oxygen. Five tanks were bubbled with nitrogen gas to induce hypoxic conditions. Five tanks were maintained as normoxic conditions. During the two-week treatment period, corals in hypoxia tanks were exposed to low oxygen conditions (0.3 mg/L dissolved oxygen) for 6 hours each night. Samples were collected after the two-week treatment period and after a two-week recovery period with no induced low oxygen conditions. Whole fragments were preserved in RNAlater and frozen until processing at the University of Florida. RNA extractions were performed with the Qiagen RNeasy Mini Kit with the addition of bashing beads. RNAseq libraries were constructed with the NuGEN Universal Prokaryotic RNA-Seq, Prokaryotic AnyDeplete kit. Libraries were submitted to the University of Florida Interdisciplinary Center for Biotechnology Research (RRID:SCR_019152) for sequencing on an Illumina NovaSeq6000 with paired 150-bp reads.

* Data table within submitted file rnaseq.txt was imported into the BCO-DMO system. It will appear in this dataset as "986522_v1_coral-microbiome-metatranscr-seq.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 BioProjects PRJNA1041355 (40 SRAs) and PRJNA1098207 (38 SRAs). This indeed has all SRA info corresponding to the 78 BioSamples listed in rnaseq.txt.
Extracted from run selector https://www.ncbi.nlm.nih.gov/Traces/study/?acc=%09PRJNA1098207&o=acc_s%3Aa and https://www.ncbi.nlm.nih.gov/Traces/study/?acc=%09PRJNA1041355&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.

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.