Coral Microbiome Research in the world’s hottest sea: the Arabian Gulf
Coral reefs in the Arabian Gulf persist in the warmest and most thermally variable seawater on Earth, making this region a natural laboratory for understanding and potentially enhancing coral resilience to climate change. In the Marine Microbiomics Lab, we study the complex and dynamic microbial communities that live on and within corals, and how individual microbes influence coral health, stress tolerance, and disease resistance.
Our approach spans field sampling, controlled aquarium experiments, and computational biology to uncover how coral-associated microbes function across space, time, and environmental extremes. We use multi-omics, including 16S rRNA profiling, (meta)genomics, (meta)transcriptomics, and metabolomics to generate testable hypotheses about key microbial interactions and metabolic pathways. These analyses are supported by major in-house resources at NYU Abu Dhabi, including high-performance computing (HPC) capacity and mass spectrometry capabilities, alongside an expanding library of chemical standards.
From correlation to functional mechanistic insights
Integrating multi-omics, microbial cultivation, and comparative genomics enables the identification of key microbial functions and the development of testable hypotheses. Targeted experiments and coral heat-stress assays help uncover causal mechanisms underlying coral–microbe interactions.
From correlations to functional mechanistic insights
Current microbiome studies are often limited to identifying patterns within 16S rRNA amplicon data and correlations with coral health under environmental changes. A defining feature of our lab’s approach is incorporating multi-omics data as a starting point to generate testable hypotheses, which we then interrogate through targeted validation experiments to establish causal mechanisms. This integrative strategy includes isolating and culturing key microbial partners, sequencing and comparative analysis of their genomes to inform unrecognized metabolic capacities. We then perform focused culture-based functional assays and conduct host heat-stress experiments to directly test microbial or metabolite effects on coral performance. By coupling these experiments with mechanistic analyses, we move beyond association to identify the biological processes that drive observed outcomes.
Defining the functional role of the microbiome in coral health and disease
One major focus of the lab is to define how the coral microbiome contributes to health, disease resistance, and heat tolerance in Arabian Gulf corals. We assess changes in bacterial diversity and functional potential across space and time, linking shifts in microbial communities to environmental conditions and coral phenotypes. By identifying key microbial taxa, their interactions, and functions predicted from their genomes, we can pinpoint candidate organisms that may play central roles in nutrient cycling, stress mitigation, or host defense. These candidates are then isolated and cultured in the laboratory. Whole-genome sequencing of these bacterial isolates enables us to connect genomic features with functional traits observed in both field and experimental contexts. Co-culture experiments allow us to directly test their metabolic capacity and validate our prior hypotheses.
Coral host gene expression and epigenetic regulation
In parallel with our microbiome-focused work, we additionally investigate how coral hosts respond to extreme environments at the molecular level. This project examines transcriptional changes in corals originating from distinct thermal regimes and explores how these responses are regulated through epigenetic mechanisms. By integrating gene expression data from the holobiont with environmental history, we aim to identify genes and their regulatory networks that may stabilize stress-response pathways or contribute to long-term acclimatization within this extreme thermal environment. This work provides critical context for interpreting microbial effects, as coral resilience emerges from the interaction between host regulation and associated symbionts.
Heat-tolerant coral photosymbionts from the Arabian Gulf
The Gulf provides a unique natural laboratory for studying symbiont heat tolerance, as corals here survive the warmest and most thermally variable marine environments on Earth. This region hosts thermotolerant coral photosymbionts that are likely critical to coral performance under extreme heat stress, yet these taxa remain poorly characterized due to persistent challenges in their isolation and long-term maintenance in laboratory culture. We isolate and culture these photosymbionts from Gulf corals and characterize their physiological and molecular responses to thermal stress. We intend to uncover mechanisms that enable photosymbionts to function at temperatures that exceed typical coral bleaching thresholds elsewhere. Understanding these mechanisms may help clarify whether traits associated with Gulf photosymbionts could inform predictions or interventions for corals facing future climate change in other regions.
Microscopic view of Symbiodiniaceae, photosynthetic dinoflagellates associated with corals.
Endozoicomonas as producers of steroid hormones: Unexpected metabolic capacity that helps corals during stress
A flagship project in the lab centers on the coral-associated bacterium Endozoicomonas, a genus that is the most common bacterial symbiont and frequently linked to coral health, yet its functional roles remain poorly understood. We attempt to isolate Endozoicomonas strains from Arabian Gulf corals and use genome sequencing and pangenomic analyses to identify conserved and strain-specific functional traits. Guided by multi-omics data from field and laboratory studies, we perform targeted culture-based experiments to validate predicted metabolic functions, for example, iron utilization. A major discovery from this work is the unique ability of Endozoicomonas to metabolize steroid compounds, including the first experimental evidence of progesterone and testosterone production from the hormone precursors. We further investigate how these microbial transformations interact with coral physiology by demonstrating coral uptake of labeled hormones. We examine how steroid accumulation during heat stress affects the coral host's immune regulation and stress responses. Together, these experiments link unrecognised microbial metabolism to host-level outcomes, providing a clear mechanistic framework for understanding coral–microbe interactions under extreme conditions.
Publications
Amin R. Mohamed, Michael A. Ochsenkühn, Trent D. Haydon, Salah Abdelrazig, Lisa S.Y. Coe, Gabriel Mochales-Riaño, Woonkee S. Jo, Alan R. Healy, David Abrego, Jean-Baptiste Raina, John A. Burt, Shady A. Amin.
Christian R. Voolstra, Jean-Baptiste Raina, Melanie Dörr, Anny Cárdenas, Claudia Pogoreutz, Cynthia B. Silveira, Amin R. Mohamed, David G. Bourne, Haiwei Luo, Shady A. Amin & Raquel S. Peixoto
Amin R Mohamed, Michael A Ochsenkühn, Ahmed M Kazlak, Ahmed Moustafa, Shady A Amin
Amin R. Mohamed, Shady A. Amin, Christian R. Voolstra & Anny Cárdenas
https://link.springer.com/chapter/10.1007/978-3-031-76692-3_8
