Search Results (11)

Functional genomics is a powerful approach for uncovering molecular mechanisms underlying complex biological processes by linking genetic changes to observable phenotypes. In the context of algal symbiosis, this framework offers significant potential for advancing our understanding of the molecular interactions between marine dinoflagellates and their cnidarian hosts, such as corals—organisms that are foundational to marine ecosystems and biodiversity. As coral bleaching and reef degradation intensify due to environmental stressors, novel strategies are urgently needed to enhance the resilience of these symbiotic partnerships. This opinion piece explores emerging directions in functional genomics as applied to coral–algal symbiosis, with a focus on uncovering the molecular pathways that govern photosynthesis and stress tolerance. We discuss the challenges and opportunities in applying functional genomics to support coral health, improve ecosystem resilience, and inform biotechnological applications in agriculture and medicine. Together, these insights posit the potential for engineered symbioses as a needed focus in mitigating biodiversity loss and supporting sustainable ecosystem management in the face of accelerating environmental change. Full article

Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies in reefs of contrasted salinities. Here, we analyzed their bacterial community’s composition and plasticity in response to salinity. Multiple cultures of Pocillopora coral-isolated Ostreobium strains from two distinct rbcL lineages representative of IndoPacific environmental phylotypes were pre-acclimatized (>9 months) to three ecologically relevant reef salinities: 32.9, 35.1, and 40.2 psu. Bacterial phylotypes were visualized for the first time at filament scale by CARD-FISH in algal tissue sections, within siphons, at their surface or in their mucilage. Ostreobium-associated microbiota, characterized by bacterial 16S rDNA metabarcoding of cultured thalli and their corresponding supernatants, were structured by host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae or Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on Ostreobium lineage, and shifted Rhizobiales’ abundances in response to the salinity increase. A small core microbiota composed of seven ASVs (~1.5% of thalli ASVs, 19–36% cumulated proportions) was persistent across three salinities in both genotypes, with putative intracellular Amoebophilaceae and Rickettsiales_AB1, as well as Hyphomonadaceae and Rhodospirillaceae also detected within environmental (Ostreobium-colonized) Pocillopora coral skeletons. This novel knowledge on the taxonomic diversity of Ostreobium bacteria paves the way to functional interaction studies within the coral holobiont. Full article

Coastal marine ecosystems worldwide are increasingly affected by tide alterations and anthropogenic disturbances affecting the water quality and leading to frequent algal blooms. Increased bloom persistence is a serious threat due to the long-lasting impacts on ecological processes and services, such as carbon cycling and sequestration. The exploration of eco-environmental feedback and algal bloom patterns remains challenging and poorly investigated, mostly due to the paucity of data and lack of model-free approaches to infer universal bloom dynamics. Florida Bay, taken as an epitome for biodiversity and blooms, has long experienced algal blooms in its central and western regions, and, in 2006, an unprecedented bloom occurred in the eastern habitats rich in corals and vulnerable habitats. With global aims, we analyze the occurrence of blooms in Florida Bay from three perspectives: (1) the spatial spreading networks of chlorophyll-a (CHLa) that pinpoint the source and unbalanced habitats; (2) the fluctuations of water quality factors pre- and post-bloom outbreaks to assess the environmental impacts of ecological imbalances and target the prevention and control of algal blooms; and (3) the topological co-evolution of biogeochemical and spreading networks to quantify ecosystem stability and the likelihood of ecological shifts toward endemic blooms in the long term. Here, we propose the transfer entropy (TE) difference to infer salient dynamical inter actions between the spatial areas and biogeochemical factors (ecosystem connectome) underpinning bloom emergence and spread as well as environmental effects. A Pareto principle, defining the top 20% of areal interactions, is found to identify bloom spreading and the salient eco-environmental interactions of CHLa associated with endemic and epidemic regimes. We quantify the spatial dynamics of algal blooms and, thus, obtain areas in critical need for ecological monitoring and potential bloom control. The results show that algal blooms are increasingly persistent over space with long-term negative effects on water quality factors, in particular, about how blooms affect temperature locally. A dichotomy is reported between spatial ecological corridors of spreading and biogeochemical networks as well as divergence from the optimal eco-organization: randomization of the former due to nutrient overload and temperature increase leads to scale-free CHLa spreading and extreme outbreaks a posteriori. Subsequently, the occurrence of blooms increases bloom persistence, turbidity and salinity with potentially strong ecological effects on highly biodiverse and vulnerable habitats, such as tidal flats, salt-marshes and mangroves. The probabilistic distribution of CHLa is found to be indicative of endemic and epidemic regimes, where the former sets the system to higher energy dissipation, larger instability and lower predictability. Algal blooms are important ecosystem regulators of nutrient cycles; however, chlorophyll-a outbreaks cause vast ecosystem impacts, such as aquatic species mortality and carbon flux alteration due to their effects on water turbidity, nutrient cycling (nitrogen and phosphorus in particular), salinity and temperature. Beyond compromising the local water quality, other socio-ecological services are also compromised at large scales, including carbon sequestration, which affects climate regulation from local to global environments. Yet, ecological assessment models, such as the one presented, inferring bloom regions and their stability to pinpoint risks, are in need of application in aquatic ecosystems, such as subtropical and tropical bays, to assess optimal preventive controls. Full article

Photographic evidence of some important coral diseases (black band disease, black disease/Terpios hoshinota, white syndrome, pink line syndrome, pink spots, invertebrate galls, skeletal growth anomalies, tissue loss), coral competing sponges, and coral–algal phase shifts (competitive overgrowth of the seaweed Caulerpa spp. over corals and competitive scleractinian interactions such as with Halimeda spp.) have been collected during field observations in a few atolls within the Lakshadweep archipelago, Arabian Sea. Further, earlier reports of similar diseases and other stressors within the Indian Exclusive Economic Zone (EEZ) and its contiguous international waters, including the reefs of the Maldives and Sri Lanka, are highlighted and their distributional ranges are shown. Full article

Dinoflagellates are a major aquatic protist group with amphiesma, multiple cortical membranous “cell wall” layers that contain large circum-cortical alveolar sacs (AVs). AVs undergo extensive remodeling during cell- and life-cycle transitions, including ecdysal cysts (ECs) and resting cysts that are important in some harmful algal bloom initiation–termination. AVs are large cortical vesicular compartments, within which are elaborate cellulosic thecal plates (CTPs), in thecate species, and the pellicular layer (PL). AV-CTPs provide cellular mechanical protection and are targets of vesicular transport that are replaced during EC-swarmer cell transition, or with increased deposition during the cellular growth cycle. AV-PL exhibits dynamical-replacement with vesicular trafficking that are orchestrated with amphiesmal chlortetracycline-labeled Ca²⁺ stores signaling, integrating cellular growth with different modes of cell division cycle/progression. We reviewed the dynamics of amphiesma during different cell division cycle modes and life cycle stages, and its multifaceted regulations, focusing on the regulatory and functional readouts, including the coral–zooxanthellae interactions. Full article

Microbes play a key role in reef dynamics, mediating the competition between scleractinian corals and benthic algae; however, major shifts in bacterial communities among coral species in response to increases in the abundance of algae are not well understood. We investigated the taxonomic composition of coral-associated microbial communities under algae-overgrowth conditions using 16S rRNA gene sequencing. The results showed that non-algal (i.e., healthy) tissue (HH) had lower bacterial abundance and diversity than tissue collected from the coral–algae interface boundary (HA) and areas of algae growth (AA). Specifically, the HA and AA samples had higher relative abundances of Saprospiraceae, Rhodobacteraceae, and Alteromonadaceae. Compared with Platygyra sp. and Montipora sp., the physiological response of Pocillopora sp. was more intense under algae-induced stress based on microbial gene function prediction. Our results indicate that algal pressure can significantly alter the microbial community structure and function of coral ecosystems. Our data thus provide new insight into the relationship between corals and their microbiome under environmental stress. Full article

Reef-building corals show a marked decrease in total species richness from the tropics to high latitude regions. Several hypotheses have been proposed to account for this pattern in the context of abiotic and biotic factors, including temperature thresholds, light limitation, aragonite saturation, nutrient or sediment loads, larval dispersal constraints, competition with macro-algae or other invertebrates, and availability of suitable settlement cues or micro-algal symbionts. Surprisingly, there is a paucity of data supporting several of these hypotheses. Given the immense pressures faced by corals in the Anthropocene, it is critical to understand the factors limiting their distribution in order to predict potential range expansions and the role that high latitude reefs can play as refuges from climate change. This review examines these factors and outlines critical research areas to address knowledge gaps in our understanding of light/temperature interactions, coral-Symbiodiniaceae associations, settlement cues, and competition in high latitude reefs. Full article

While studies show that nutrient pollution shifts reef trophic interactions between fish, macroalgae, and corals, we know less about how the microbiomes associated with these organisms react to such disturbances. To investigate how microbiome dynamics are affected during nutrient pollution, we exposed replicate Porites lobata corals colonized by the fish Stegastes nigricans, which farm an algal matrix on the coral, to a pulse of nutrient enrichment over a two-month period and examined the microbiome of each partner using 16S amplicon analysis. We found 51 amplicon sequence variants (ASVs) shared among the three hosts. Coral microbiomes had the lowest diversity with over 98% of the microbiome dominated by a single genus, Endozoicomonas. Fish and algal matrix microbiomes were ~20 to 70× more diverse and had higher evenness compared to the corals. The addition of nutrients significantly increased species richness and community variability between samples of coral microbiomes but not the fish or algal matrix microbiomes, demonstrating that coral microbiomes are less resistant to nutrient pollution than their trophic partners. Furthermore, the 51 common ASVs within the 3 hosts indicate microbes that may be shared or transmitted between these closely associated organisms, including Vibrionaceae bacteria, many of which can be pathogenic to corals. Full article

Coral reef community composition, function, and resilience have been altered by natural and anthropogenic stressors. Future anthropogenic ocean and coastal acidification (together termed “acidification”) may exacerbate this reef degradation. Accurately predicting reef resilience requires an understanding of not only direct impacts of acidification on marine organisms but also indirect effects on species interactions that influence community composition and reef ecosystem functions. In this 28-day experiment, we assessed the effect of acidification on coral–algal, coral–sponge, and algal–sponge interactions. We quantified growth of corals (Siderastrea radians), fleshy macroalgae (Dictyota spp.), and sponges (Pione lampa) that were exposed to local summer ambient (603 μatm) or elevated (1105 μatm) pCO₂ seawater. These species are common to hard-bottom communities, including shallow reefs, in the Florida Keys. Each individual was maintained in isolation or paired with another organism. Coral growth (net calcification) was similar across seawater pCO₂ and interaction treatments. Fleshy macroalgae had increased biomass when paired with a sponge but lost biomass when growing in isolation or paired with coral. Sponges grew more volumetrically in the elevated seawater pCO₂ treatment (i.e., under acidification conditions). Although these results are limited in temporal and spatial scales due to the experimental design, they do lend support to the hypothesis that acidification may facilitate a shift towards increased sponge and macroalgae abundance by directly benefiting sponge growth which in turn may provide more dissolved inorganic nitrogen to macroalgae in the Florida Keys. Full article

The integrity of coral reef ecosystems worldwide rests on a fine-tuned symbiotic interaction between an invertebrate and a dinoflagellate microalga from the family Symbiodiniaceae. Recent advances in bottom-up shotgun proteomic approaches and the availability of vast amounts of genetic information about Symbiodiniaceae have provided a unique opportunity to better understand the molecular mechanisms underpinning the interactions of coral-Symbiodiniaceae. However, the resilience of this dinoflagellate cell wall, as well as the presence of polyanionic and phenolics cell wall components, requires the optimization of sample preparation techniques for successful implementation of bottom-up proteomics. Therefore, in this study we compare three different workflows—filter-aided sample preparation (FASP), single-pot solid-phase-enhanced sample preparation (SP3), and stop-and-go-extraction tips (STAGETips, ST)—to develop a high-throughput proteotyping protocol for Symbiodiniaceae algal research. We used the model isolate Symbiodinium tridacnidorum. We show that SP3 outperformed ST and FASP with regard to robustness, digestion efficiency, and contaminant removal, which led to the highest number of total (3799) and unique proteins detected from 23,593 peptides. Most of these proteins were detected with ≥2 unique peptides (73%), zero missed tryptic peptide cleavages (91%), and hydrophilic peptides (>70%). To demonstrate the functionality of this optimized SP3 sample preparation workflow, we examined the proteome of S. tridacnidorum to better understand the molecular mechanism of peridinin-chlorophyll-protein complex (PCP, light harvesting protein) accumulation under low light (LL, 30 μmol photon m⁻² s⁻¹). Cells exposed to LL for 7 days upregulated various light harvesting complex (LHCs) proteins through the mevalonate-independent pathway; proteins of this pathway were at 2- to 6-fold higher levels than the control of 120 μmol photon m⁻² s⁻¹. Potentially, LHCs which were maintained in an active phosphorylated state by serine/threonine-protein kinase were also upregulated to 10-fold over control. Collectively, our results show that the SP3 method is an efficient high-throughput proteotyping tool for Symbiodiniaceae algal research. Full article

Understanding the evolution of scientific literature is a critical and necessary step for the development and strengthening of a research field. However, an overview of global dinoflagellate research remains unavailable. Herein, global dinoflagellate research output was analyzed based on a scientometric approach using the Scopus data archive. The basic characteristics and worldwide interactions of dinoflagellate research output were analyzed to determine the temporal evolution and new emerging trends. The results confirm that dinoflagellate research output, reflected in the number of publications, is a fast-growing area since the mid-1990s. In total, five research subareas emerged using a bibliometric keywords analysis: (1) “symbiosis with coral reefs”, (2) “phylogeny”, (3) “palynology”, (4) “harmful algal blooms” and (5) “nutrition strategies”. Dinoflagellate publications were modeled by fish production (both aquaculture and fisheries) and economic and social indexes. Finally, directions for future research are proposed and discussed. The presented scientometric analysis confirms that dinoflagellate research is an active and important area with focus on mitigating economic impacts, especially in regard to fish production. Full article