Integrative transcriptomic and epigenomic analysis reveals the molecular mechanism of light-enhanced calcification in giant clams

Bivalves possess a diverse array of photoreceptive organs that are significant for their evolutionary success and systematic classification. Giant clams are the largest bivalve mollusks, with mantle tissue permanently extended in nature to maintain symbiosis with zooxanthellae and perceive environmental cues. Eyes serve as critical sensory organs for these organisms, yet the structural and functional characteristics of tridacnine eyes remain inadequately understood. This study systematically investigated the ocular traits and visual resolution of three ecologically distinct giant clam species (Tridacna crocea, T. squamosa, T. maxima) using morphometric analysis, hematoxylin-eosin (HE) staining, transmission electron microscopy (TEM), and grating stimulation assays. Significant interspecific differences were observed in eye count, diameter, and pupil-to-eye ratio (PER): T. maxima exhibited the highest mean eye count (221 ± 8), T. squamosa the largest mean eye diameter (0.490 ± 0.082 mm), and T. crocea the highest mean PER (0.363 ± 0.041). Eyes were numerically symmetric on the left and right mantles but positionally asymmetric, showing random distribution patterns along the mantle margin without fixed corresponding locations across species. All three species possessed typical pinhole eyes lacking lenses and retinas, primarily composed of filler cells, receptor cells, and sparse neurons, with symbiotic zooxanthellae distributed in the surrounding mantle tissue. Grating stimulation assays revealed resolvable stripe periods of 5.82-11.64° (T. crocea), 8.62-13.16° (T. squamosa), and 10.15-12.26° (T. maxima), confirming T. crocea as the species with the highest visual resolution. These ocular variations are inferred to reflect adaptive evolution driven by ecological niches and habitat-specific factors (water depth or light intensity), while the simplified pinhole morphology is consistent with their sedentary lifestyle and metabolic dependence on symbiotic zooxanthellae. These ocular variations provide potential morphological markers for the systematic classification of Tridacninae and offer valuable insights for researchers studying the evolutionary plasticity of bivalve visual systems.

Abstract. Ramah S, Kaullysing D, Soondur M, Taleb-Hossenkhan N, Bhagooli R. 2025. Decadal variation in the Tridacna population at two marine protected areas in Rodrigues Island, Republic of Mauritius. Indo Pac J Ocean Life 9: 172-178. Giant clams (Tridacninae) are largely threatened worldwide, but information regarding their distribution and abundance is limited in the Western Indian Ocean, especially in the waters of the Republic of Mauritius, including the island of Rodrigues. This study provides the first decadal assessment (2015-2024) of the population density of Tridacna maxima and T. squamosa within two marine protected areas: Southeast Marine Protected Area (SEMPA) and English Bay Marine Reserve (EBMR) found in Rodrigues Island. Annual surveys were carried out by placing five permanent belt transects of 50 m × 5 m (250 m²) at both sites. The data were extrapolated to individuals per hectare (ind./ha), and Mixed-effect models were used to assess temporal and spatial differences. Across the 10 years, SEMPA consistently supported higher Tridacna densities than EBMR, particularly for T. maxima (peak 640 ind./ha vs. 360 ind./ha). Species identity and interactions were significant, with T. squamosa occurring only in SEMPA, ranging from 13 to 120 ind./ha, and was absent from EBMR throughout the study. Statistical analyses revealed significant effects of site and species identity, as well as strong site × species and year × species interactions, indicating that temporal dynamics differed remarkedly between species and between MPAs. Surveys revealed significant site- and species-specific variations in giant clam densities in Rodrigues. Mean densities of T. maxima and T. squamosa were significantly higher in SEMPA compared to EBMR (p<0.001). Both species persisted across survey years in SEMPA, whereas densities in EBMR remained consistently low with no significant increase over time (p=0.01). These results indicate spatial heterogeneity in population trajectories and identify SEMPA as a key area of persistence. The findings of this study provide baseline evidence of site- and species-specific variation in giant clam populations in Rodrigues, contributing to broader understanding of spatial heterogeneity and long-term dynamics for future comparative research in the Western Indian Ocean.

Abstract. Giant clams such as Tridacna are exceptionally well suited for studying past environmental changes on daily to multidecadal timescales. The visible growth bands in their shells, which can be yearly, seasonal or even daily, are accompanied by changes in the elemental composition of the shell and provide insights into their growth and environmental history. The daily elemental cycles, particularly in Mg/Ca and Sr/Ca, can be used to determine age and growth rates. However, the mechanisms creating the visible day and night banding and the associated elemental cycles, remain unclear. To better understand the mechanisms of El/Ca incorporation into the shells of Tridacna during day and night growth, we performed controlled growth experiments using 135Ba-labelled seawater. The isotope spike was alternatingly applied in 12 h intervals in order to individually and unequivocally mark day and night growth segments in Tridacna. These experiments show that Tridacna calcification rates are nearly five times higher during the day than at night. In addition, based on the observed changes in shell composition we deduce that the bivalve's extrapallial fluid (EPF) reacts to changes in seawater chemistry within tens of minutes, both during day and night. A full compositional replenishment is achieved after approximately 1 d, assuming a similar residence time for all elements. During daytime, El/Ca (for El = B, Mg, Sr, Ba) decrease, while Na/Ca increases. The opposite behaviour occurs at night. The night peak in El/Ca occurs in the earliest morning, shortly before the change between spiked and non-spiked water at 07:30 UTC+2. Daily El/Ca cycles are likely dominantly driven by variations in active Ca2+ and HCO3- transport into the EPF, influenced by light availability, circadian rhythms and/or energy availability (from both photosymbionts and filter feeding), rather than a closed-system Rayleigh fractionation process driven by contrasting El-distribution coefficients alone. We propose that active Ca2+ and HCO3- pumping into the EPF might also drive diurnal changes of growth rate, shell structure and possibly organic content.

Optimising light intensity and ammonium enrichment enhances ex-situ growth and survival of the cultured boring Giant clam, Tridacna crocea

Reef fish assemblages show limited response to giant clam density and restocking

KEY POINTS •Populations of all giant clam species in the Philippines have declined significantly over the past four decades, with a collective decline of 98%. • Despite massive culture and restocking efforts for the true giant clam (Tridacna gigas) since the 1980s, recruitment rates for the species are still very low, mainly because of persistent threats from anthropogenic activities, habitat degradation, and extreme weather events. • The harvest and trade of giant clams and their derivatives have been completely banned in the Philippines since the 1990s; however, live giant clams, meat, and shells are still sold illegally around the country up to the present. • Based on the best available information gathered, the assessment showed that the harvest and trade of giant clam shells pose a high risk to all species and are detrimental to the survival of wild giant clam populations in the Philippines. • The Scientific Authority is, therefore, unable to issue a positive non-detriment finding (NDF) for giant clam shells at this time, and trade must be confined to certified captive-bred specimens and their derivatives.

Ecosystems are influenced by competition for limited resources, a driver of niche partitioning. Over time, the emergence of novel traits facilitating new resource exploitation can reduce competition. However, additional layers of complexity, like symbiosis, complicate our understanding of the patterns shaping reef communities. Therefore, empirical evidence of niche partitioning reducing competition in symbiotic benthic communities is limited. Using a unique common garden experiment, we examined the nutritional strategies of six giant clam holobionts and characterized their symbiont assemblages. Variation in trophic strategies confirmed trophic niche partitioning, as species fell along a continuum from highly heterotrophic to highly autotrophic. Tridacna gigas and T. derasa, listed as critically endangered and endangered, respectively, were the most autotrophic and fast-growing species. We found significant phylogenetic signals in trophic niche scores, growth rate, and shell length, indicating the role of natural selection in shaping giant clam nutritional ecology. We conclude that niche partitioning is a driver of giant clam evolution with benefits and costs; high autotrophy reliance results in greater growth rates yet may increase vulnerability to disturbances. Given the impact of human activities on giant clams, conservation efforts should focus on these ecosystem engineers, especially highly autotrophic and geographically constrained species.

This study aimed to provide an updated distribution range of Tridacna noae (Röding, 1798) in Palawan with notes on its habitat characteristics and conservation status. Data on the distribution and habitat characteristics were obtained from reef assessments from 2010-2023 and 10 Key Informants (KIs) and plotted using QGIS v3.28 software to illustrate its distribution in a map. A total of 12 reef sites within 8 municipalities in Palawan showed the presence of T. noae. Majority of these reefs were found in open-access coastal areas facing the West Philippine Sea. The clams were partially buried or settled on the top of dead or live coral in a depth of 1-5 meters from reef flat to reef slope surrounded by macroalgae. Tridacna noae remained unlisted in international, national, and local lists of protected species although it was confirmed in 2014 as a distinct species of giant clam, hence; the inclusion of T. noae in the lists of protected species in the Philippines is needed. Knowing the distribution, habitat characteristics, and conservation status of a certain threatened species such as the giant clam is an important step in managing and conserving wild population.

Oxidative stress responses of the giant clam (Tridacna maxima (Röding, 1798)) to seasonal variations and contaminations on the Red Sea Coast of Egypt

A typology of giant clam shell deposits in eastern Tuamotu-Gambier atolls (French Polynesia) to guide conservation and exploitation measures

Introduction Coral reef ecosystems are increasingly threatened by climate change-induced thermal stress, leading to widespread bleaching events. Giant clams ( Tridacna spp.) are key photosymbiotic reef inhabitants that harbor extracellular dinoflagellate symbionts (Symbiodiniaceae) and contribute to reef structure and nutrient cycling. However, the molecular mechanisms underlying their response to heat stress remain poorly understood. Methods A non-lethal plasma sampling technique was employeed to characterize the proteomic profile of Tridacna crocea under controlled thermal stress. iTRAQ-based quantitative proteomics profiled host plasma proteins, and integrated transcriptomic analyses across five tissues assessed tissue-specific expression and the contribution of secretory factors to host–symbiont interactions. Results We quantified 554 host plasma proteins that differentially expressed, with significant enrichment in immune response pathways, lectin-mediated recognition, and complement system components. Integrated transcriptomic analysis of five tissues revealed tissue-specific expression patterns and underscored the role of secretory proteins in host-symbiont interactions. Key biomarkers, including C1q domain-containing proteins and lectin family members, exhibited consistent dysregulation under stress, reflecting a shift from symbiosis maintenance to immune defense. Discussion These data delineate a plasma proteomic signature of bleaching in T. crocea and implicate innate immune pathways in restructuring host–symbiont dynamics under heat stress. The non-lethal plasma assay, coupled with proteogenomic readouts, offers a scalable framework for monitoring giant clam health and, by extension, reef condition under ongoing climate change.

Giant clams (subfamily Tridacninae) serve diverse ecological functions in coral reef ecosystems but have experienced severe populatiaon declines across much of their native ranges. Continued overharvesting, habitat degradation, and climate change impacts reinforce the need for updated population assessments and have prompted consideration for endangered species status. Here, we report a territory-wide evaluation of giant clam populations in American Sāmoa, integrating historical data (1994/95, 2002, and 2018) with new surveys conducted from 2022 to 2024 to assess the population status of these ecologically important bivalves. Using belt transects (50 m × 2 m at 10 m depth), we examined clam densities, size-class distributions, species composition, and population trends across six islands—Tutuila, Aunuʻu, Ofu, Olosega, Taʻū, and Muliāva. This study added 264 transects to the historical dataset and showed population densities of giant clams varied among islands but have remained relatively consistent over time. Using univariate and factorial ANOVAs of giant clam abundance and size data, we assessed spatial and temporal variation across American Sāmoa, and our analyses tested for effects of island, year, protection status, and their interactions. The lowest recent clam densities (83.5 individuals per hectare in 2022) were observed on the main island of Tutuila, where 98% of residents live. Mean clam density on Tutuila has increased from 14.1/ha in 1994/95, but the island has considerable variation amongst locations. Remote islands, such as Taʻū and Muliāva, showed higher densities, up to 812 and 1,166/ha, respectively. Most (96.7%) of giant clams found on transects were identified as Tridacna maxima, with infrequent occurrences of the cryptic species T. squamosa and T. noae, primarily within specific, village-managed protected areas. On Tutuila, surveys sites included a variety of jurisdictions and levels of management, with village protected areas and remote sites supporting both higher clam densities and larger individuals. Overall, inaccessible remote sites and those under traditional village enforcement significantly outperformed all other management strategies, including federally designated no-take zones. These findings suggest that empowering traditional Indigenous community stewardship may offer a viable alternative to blanket federal restrictions, and support the importance of localized, community-based management practices in American Sāmoa. We emphasize the need for more frequent monitoring across varying depths, anthropogenic influences, and management regimes to better understand the population dynamics of these valuable coral reef species.

Adapting to hypo-salinity: Molecular mechanisms in giant clams and symbionts with implications for coral reef resilience under climate change.

Partial bleaching and survival responses in the outer mantle of the giant clam Tridacna squamosa exposed to temperature stress

A novel C1q domain-containing protein from Tridacna crocea exhibits dual functionality in symbiont recognition and immune defense.

Boat noise alters behaviour of two coral reef macroinvertebrates, Lambis lambis and Tridacna maxima.

Exploring the symbiotic resilience of boring giant clams and zooxanthellae during heatwave conditions: An investigation into strategic countermeasures

ABSTRACTVarious hypotheses have been proposed to explain the origin of the high biodiversity in the Indo‐Malay Archipelago (IMA), such as the center of origin, overlap zone, and accumulation center; yet these theories remain subjects of ongoing debate. The small giant clams, Tridacna maxima, are iconic inhabitants of coral reefs and are widely distributed in the Indo‐West Pacific. However, due to overexploitation and climate change, wild populations of most giant clam species worldwide have been severely impacted and are now endangered. In this study, cytochrome c oxidase I (COI) gene sequences of 35 T. maxima individuals from two populations in the South China Sea (SCS) were amplified and sequenced. These data were integrated with published COI sequences of T. maxima from other studies. A total of 610 individuals in 34 locations across the Indian Ocean to the Central Pacific were included in the population genetic analysis based on a 417 bp fragment of COI. The genetic differentiation index Φst = 0.856 (p = 0.000) shows a significantly differentiated genetic structure, which can be categorized into six distinct groups from west to east, as previously suggested. The populations in the SCS exhibited strong connectivity with the IMA populations, forming a single group. Gene‐flow analysis revealed a pattern of migration from the Seas of Southeastern Asia (SEA) towards both the eastern and western directions, supporting the center of origin hypothesis for the high biodiversity of IMA. Historical population dynamics analysis indicated that most groups experienced expansion, primarily associated with the late Pleistocene glaciations. Moreover, the Species Distribution Model (SDM) predicted that climate change might lead to a significant reduction in suitable habitats for T. maxima and a slight shift towards higher latitudes. These results are expected to provide insights into the origin of the biodiversity in the IMA and baseline data for the conservation of giant clams.

ABSTRACTGiant clams are key denizens of coral reef ecosystems, forming holobionts through symbiotic relationships with algae of the family Symbiodiniaceae, as in reef‐building corals. In this study, we performed a tissue‐specific microbiome analysis of the boring giant clam, Tridacna crocea and evaluated the impact of dark‐induced bleaching on its outer mantle bacterial community. Using 16S rRNA metabarcoding, Endozoicomonas was identified as the dominant bacterial genus in most tissues, particularly in gills, implying an important contribution to the giant clam holobiont. In contrast, in the outer mantle, where algal symbionts reside, the microbiome exhibited greater diversity, with a significant presence of carotenoid‐producing bacteria such as Rubritalea (Rubritaleaceae) and Muricauda (Flavobacteriaceae). These bacteria may protect symbiotic algae from light and thermal stresses, potentially enhancing holobiont resilience in coral reef environments. Although dark‐induced bleaching significantly reduced algal cell density, bacterial diversity remained largely unaffected, suggesting a robust bacterial association, independent of algal dynamics. This study highlights the potential ecological significance of Endozoicomonas and carotenoid‐producing bacteria in sustaining giant clam holobiont health and provides insights into microbial mechanisms that support stress tolerance in coral reef organisms.