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1. Selective Uptake of Pelagic Microbial Community Members by Caribbean Reef Corals

   https://doi.org/10.1128/AEM.03175-20  

   Hoadley, Kenneth D.; Hamilton, Maria; Poirier, Camille L.; Choi, Chang Jae; Yung, Cheuk-Man; Worden, Alexandra Z. (April 2021, Applied and Environmental Microbiology)

   Johnson, Karyn N. (Ed.)

   ABSTRACT Coral reefs are possible sinks for microbes; however, the removal mechanisms at play are not well understood. Here, we characterize pelagic microbial groups at the CARMABI reef (Curaçao) and examine microbial consumption by three coral species: Madracis mirabilis , Porites astreoides , and Stephanocoenia intersepta . Flow cytometry analyses of water samples collected from a depth of 10 m identified 6 microbial groups: Prochlorococcus , three groups of Synechococcus , photosynthetic eukaryotes, and heterotrophic bacteria. Minimum growth rates (μ) for Prochlorococcus , all Synechococcus groups, and photosynthetic eukaryotes were 0.55, 0.29, and 0.45 μ day −1 , respectively, and suggest relatively high rates of productivity despite low nutrient conditions on the reef. During a series of 5-h incubations with reef corals performed just after sunset or prior to sunrise, reductions in the abundance of photosynthetic picoeukaryotes, Prochlorococcus and Synechococcus cells, were observed. Of the three Synechococcus groups, one decreased significantly during incubations with each coral and the other two only with M. mirabilis. Removal of carbon from the water column is based on coral consumption rates of phytoplankton and averaged between 138 ng h −1 and 387 ng h −1 , depending on the coral species. A lack of coral-dependent reduction in heterotrophic bacteria, differences in Synechococcus reductions, and diurnal variation in reductions of Synechococcus and Prochlorococcus , coinciding with peak cell division, point to selective feeding by corals. Our study indicates that bentho-pelagic coupling via selective grazing of microbial groups influences carbon flow and supports heterogeneity of microbial communities overlying coral reefs. IMPORTANCE We identify interactions between coral grazing behavior and the growth rates and cell abundances of pelagic microbial groups found surrounding a Caribbean reef. During incubation experiments with three reef corals, reductions in microbial cell abundance differed according to coral species and suggest specific coral or microbial mechanisms are at play. Peaks in removal rates of Prochlorococcus and Synechococcus cyanobacteria appear highest during postsunset incubations and coincide with microbial cell division. Grazing rates and effort vary across coral species and picoplankton groups, possibly influencing overall microbial composition and abundance over coral reefs. For reef corals, use of such a numerically abundant source of nutrition may be advantageous, especially under environmentally stressful conditions when symbioses with dinoflagellate algae break down. 

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2. Depth-dependent trophic strategies of Caribbean sponges on mesophotic coral reefs

   https://doi.org/10.3354/meps14059  

   Macartney, KJ; Pankey, MS; Clayshulte Abraham, A; Slattery, M; Lesser, MP (July 2022, Marine Ecology Progress Series)

   Mesophotic coral reef ecosystems (MCEs) are characterized by gradients in irradiance, temperature and trophic resources. As depth increases on Caribbean mesophotic reefs, particulate organic matter increases while dissolved organic matter decreases, and the increase in particulate organic matter is directly related to the increase in sponge abundances and growth rates on MCEs. To further understand the trophic ecology of sponges, changes in microbiome composition and function, stable isotopic composition and proximate biochemical composition of 4 Caribbean reef sponges ( Amphimedon compressa , Agelas tubulata , Plakortis angulospiculatus and Xestospongia muta) were quantified along a shallow to mesophotic depth gradient on Grand Cayman Island. Increases in δ 15 N for all sponges were observed as depth increased, indicating an increasing reliance on heterotrophic food resources. Species-specific changes in symbiotic microbial community composition were also observed as depth increased, and the predicted functional genes associated with nitrogen and carbon cycling showed species-specific changes between depths. Regardless of species-specific changes in microbiome community structure or function, or whether sponges were classified as high microbial or low microbial abundance, sponges increased their consumption of particulate organic matter with increasing depth into the lower mesophotic zone. 

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3. Wave‐driven transport controls bacterioplankton community differentiation among coral reef habitats

   https://doi.org/10.1002/lol2.70076  

   Comstock, Jacqueline; Nelson, Craig E; James, Anna; Washburn, Libe; Remple, Kristina; Carlson, Craig A (December 2025, Limnology and Oceanography Letters)

   Abstract The existence of highly productive coral reefs within oligotrophic gyres is in part due to intensive recycling of macronutrients and organic matter by microbes. Therefore, characterizing reef bacterioplankton communities is key for understanding reef metabolism and biogeochemical transformations. We performed a high‐resolution survey of waters surrounding Mo'orea (French Polynesia), coupling 16S metabarcoding with biogeochemical and physical measurements. Bacterioplankton communities differed markedly among reef ecosystems on three sides of the island, and within each system distinct communities emerged in forereef, backreef and reef pass habitats. The degree of habitat differentiation varied among the island sides according to current speeds inferred from wave power. Oceanic‐associated taxa were enriched in forereefs and throughout western reefs with highest wave power and lowest productivity. Reef‐associated taxa were enriched in backreef and pass habitats most strongly on northern reefs with lowest wave power and highest productivity. Our results offer insight into dynamics regulating reef microbial communities. 

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4. Coral high molecular weight carbohydrates support opportunistic microbes in bacterioplankton from an algae-dominated reef

   https://doi.org/10.1128/msystems.00832-24  

   Thobor, Bianca M; Haas, Andreas F; Wild, Christian; Nelson, Craig E; Wegley_Kelly, Linda; Hehemann, Jan-Hendrik; Arts, Milou; Boer, Meine; Buck-Wiese, Hagen; Nguyen, Nguyen P; et al (November 2024, mSystems)

   Meyer, Julie L (Ed.)

   High molecular weight (HMW; >1 kDa) carbohydrates are a major component of dissolved organic matter (DOM) released by benthic primary producers. Despite shifts from coral to algae dominance on many reefs, little is known about the effects of exuded carbohydrates on bacterioplankton communities in reef waters. We compared the monosaccharide composition of HMW carbohydrates exuded by hard corals and brown macroalgae and investigated the response of the bacterioplankton community of an algae-dominated Caribbean reef to the respective HMW fractions. HMW coral exudates were compositionally distinct from the ambient, algae-dominated reef waters and similar to coral mucus (high in arabinose). They further selected for opportunistic bacterioplankton taxa commonly associated with coral stress (i.e.,Rhodobacteraceae,Phycisphaeraceae,Vibrionaceae, andFlavobacteriales) and significantly increased the predicted energy-, amino acid-, and carbohydrate-metabolism by 28%, 44%, and 111%, respectively. In contrast, HMW carbohydrates exuded by algae were similar to those in algae tissue extracts and reef water (high in fucose) and did not significantly alter the composition and predicted metabolism of the bacterioplankton community. These results confirm earlier findings of coral exudates supporting efficient trophic transfer, while algae exudates may have stimulated microbial respiration instead of biomass production, thereby supporting the microbialization of reefs. In contrast to previous studies, HMW coral and not algal exudates selected for opportunistic microbes, suggesting that a shift in the prevalent DOM composition and not the exudate type (i.e., coral vs algae)per se, may induce the rise of opportunistic microbial taxa. IMPORTANCEDissolved organic matter (DOM) released by benthic primary producers fuels coral reef food webs. Anthropogenic stressors cause shifts from coral to algae dominance on many reefs, and resulting alterations in the DOM pool can promote opportunistic microbes and potential coral pathogens in reef water. To better understand these DOM-induced effects on bacterioplankton communities, we compared the carbohydrate composition of coral- and macroalgae-DOM and analyzed the response of bacterioplankton from an algae-dominated reef to these DOM types. In line with the proposed microbialization of reefs, coral-DOM was efficiently utilized, promoting energy transfer to higher trophic levels, whereas macroalgae-DOM likely stimulated microbial respiration over biomass production. Contrary to earlier findings, coral- and not algal-DOM selected for opportunistic microbial taxa, indicating that a change in the prevalent DOM composition, and not DOM type, may promote the rise of opportunistic microbes. Presented results may also apply to other coastal marine ecosystems undergoing benthic community shifts. 

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5. Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida’s Coral Reef

   https://doi.org/10.7717/peerj.13574  

   Williams, Sara D.; Klinges, J. Grace; Zinman, Samara; Clark, Abigail S.; Bartels, Erich; Villoch Diaz Maurino, Marina; Muller, Erinn M. (January 2022, PeerJ)

   Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont—the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals’ health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida’s Coral Reef and sampled after residing within Mote Marine Laboratory’s in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys ( n  = 40 genotypes), the Middle Florida Keys ( n  = 15 genotypes), and the Upper Florida Keys ( n  = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia . Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia , resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low- Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta . The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low- Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management. 

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