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Coral Microbiome and Microbial Ecology

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 July 2026 | Viewed by 3766

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Special Issue Editor

Dr. Esti Kramarsky-Winter

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Guest Editor

Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
Interests: coral ecology; coral culture; marine microbilogy
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Special Issue Information

Dear Colleagues,

Corals are cosmopolitan marine organisms found in all environments ranging from shallow to deep seas and from warm to very cold environments. They are an evolutionarily ancient group of organisms, originating 415 million years ago. Of these, scleractinian, or stony corals, are the basis of coral reefs that make up vast oceanographic structures such as barrier and fringing reefs, as well as island atolls. These reefs provide shelter to shorelines, a source of food and pleasure for many countries and important sources of novel biomaterials. The evolutionary success of corals is due in part to their complex associations with a variety of microorganisms ranging from protists to bacteria and viruses. The close association between coral animal hosts and their accompanying microorganisms has resulted in their definition as holobionts. These associations range from parasitic to mutualistic in nature, playing important roles in coral health, nutrition, physical protection, and disease mitigation. Understanding the nature of these associations provides an important impetus to the ongoing study of microbial ecology of corals. This Special Issue provides a glimpse into the varied associations between corals and their accompanying microorganisms in an attempt to elucidate the diverse roles of these microorganisms in these holobionts’ ecological and evolutionary success.

Dr. Esti Kramarsky-Winter
Guest Editor

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Keywords

coral
holobiont
microbiota
polyp
protist
skeleton
microbiome

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Published Papers (4 papers)

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22 pages, 2755 KB

Open AccessArticle

Differential Responses to Heat Stress Between Freshly Isolated and Long-Term Cultured Symbiodinium

by Silvia Arossa, Shannon Grace Klein, Jacqueline Victoria Alva Garcia, Alexandra Steckbauer, Naira Pluma, Luca Genchi, Sergey P. Laptenok, Shiou-Han Hung, Octavio R. Salazar, Manuel Aranda, Carlo Liberale and Carlos Manuel Duarte

Microorganisms 2026, 14(2), 455; https://doi.org/10.3390/microorganisms14020455 - 13 Feb 2026

Cited by 1 | Viewed by 808 | Correction

Abstract

Symbiotic dinoflagellates from the family Symbiodiniaceae play a central role in coral reef ecosystems by forming mutualistic relationships with reef invertebrates, particularly stony corals. These relationships underpin reef productivity in nutrient-poor waters but are vulnerable to disruption from marine heatwaves and climate change. While laboratory culturing of symbionts has enabled controlled studies of thermal stress, prolonged culturing may lead to physiological changes that do not reflect in hospite conditions. Here, we examined the thermal stress responses of two axenic cultures of Symbiodinium A1, freshly isolated and long-term cultured (2.5 years), originally from the jellyfish Cassiopea andromeda in the Red Sea. Both cultures were exposed to a daily temperature increase of 1 °C, up to 37 °C. Freshly isolated symbionts consistently showed higher photochemical efficiency (0.515 ± 0.007) and growth rates (1.68 ± 0.60 µ day⁻¹) compared to long-term cultured cells (0.401 ± 0.007; −2.25 ± 0.38 µ day⁻¹), which collapsed at 37 °C. Heat stress also led to decreases in O₂ and increases in pCO₂ across treatments. Long-term cultured symbionts exhibited greater lipid body accumulation, suggesting a shift to anaerobic metabolism. These findings demonstrate that extended batch culturing alters symbiont physiology and stress responses, highlighting the need to consider culture history in experimental designs to avoid bias in interpreting holobiont resilience. Full article

(This article belongs to the Special Issue Coral Microbiome and Microbial Ecology)

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18 pages, 5260 KB

Open AccessArticle

Host Evolutionary Lineage Shapes Assembly, Network Topology, and Metabolic Potential of Coral Skeletal Endolithic Microbiomes

by Chuanzhu Bai, Huimin Ju, Jian Zhang and Jie Li

Microorganisms 2026, 14(1), 195; https://doi.org/10.3390/microorganisms14010195 - 15 Jan 2026

Viewed by 698

Abstract

Evolutionary history of the host may influence the skeletal morphology of scleractinian corals. However, its effects on the assembly and function of endolithic microbiomes remain unknown. We analyzed bacterial and archaeal microbiomes from the coral skeleton by using 16S rRNA gene sequencing. We collected the samples of seven coral genera distributed among the diverse “Complex” and “Robust” clades. In this study, bacterial α-diversity was significantly higher in the Complex clade relative to the Robust clade. Archaea, on the other hand, remained stable and showed no significant differences between the two host clades, and were most abundantly Nanoarchaeota and Thermoproteota. Analysis of the network topologies showed that network structures were different between the Complex group and the Robust clade. The Robust clade formed a dense and closely knit network among bacteria and archaea. The Com-plex group formed a more modular network structure. Functional predictions further highlighted lineage-specific metabolic strategies. Enrichment was apparent in both nitrification genes (amoB, amoC) and denitrification genes (nirK, nirS) in the Complex clade. This suggests that the coupling of these nitrogen cycles is possible. The opposite was observed for the Robust clade, which had low potential for both types of nitrogen cycling. This reflects the degree of diffusion limitation in the more massive skeleton of this host lineage. Overall, species evolutionary lineage is a pre-eminent driver for the selective filtering of endolithic assembly. It generates discrete skeletal micro-niches on which microbial strategies diverge. In particular, Complex corals favor fast metabolic flux, and Robust corals favor strong network connectivity. Full article

(This article belongs to the Special Issue Coral Microbiome and Microbial Ecology)

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17 pages, 4160 KB

Open AccessArticle

Photoendosymbiosis of the Blue Subtropical Montipora Corals of Norfolk Island, South Pacific

by Sophie Vuleta, William P. Leggat and Tracy D. Ainsworth

Microorganisms 2025, 13(9), 2155; https://doi.org/10.3390/microorganisms13092155 - 16 Sep 2025

Viewed by 1036

Abstract

Corals exhibit complex and diverse relationships with dinoflagellates of the family Symbiodiniaceae. Montiporid corals within Norfolk Island’s shallow water lagoonal reef systems have been observed to turn a deep fluorescent blue during winter, suggesting potential environmentally driven changes to their photoendosymbiosis. Here, we investigate the photoendosymbiosis of blue Montipora sp. corals over a year-long study, demonstrating that photosynthetic yield and Symbiodiniaceae densities vary seasonally, with the lowest photosynthetic yield occurring within winter periods. We also provide the first characterisation of Symbiodiniaceae species associated with corals from Norfolk Island, identifying blue Montipora sp. as predominantly associating with Cladocopium (formerly Clade C) genotypes (C3aap, C3ig, and C3aao). Finally, we also report on the impact of recent bleaching conditions (March 2024) on blue Montipora sp. photoendosymbiosis and find the genera is susceptible to increasing sea surface temperatures. Our findings provide insight into the unique biology of subtropical corals within this remote reef and the susceptibility of corals in the region to increasing sea surface temperatures. Full article

(This article belongs to the Special Issue Coral Microbiome and Microbial Ecology)

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