Giant Clam Research Articles

Of Clams and Clades: Genetic Diversity and Connectivity of Small Giant Clams (Tridacna maxima) in the Southern Pacific Ocean.

Giant clams (Tridacna and Hippopus) are large marine bivalves occupying tropical and subtropical reefs in the Indo-Pacific. Giant clam populations have declined in many areas of the Indo-Pacific and continue to be threatened by harvesting and environmental change. The small giant clam (Tridacna maxima) occurs throughout the Indo-Pacific and has been subject to several phylogeographic studies across its range. However, given its broad range, there are several areas where the genetic diversity and connectivity of T. maxima populations has not been characterised. Here, we analyse the mitochondrial marker cytochrome oxidase 1 (CO1) to examine the genetic diversity and connectivity of T. maxima in two regions: Australia's Coral Sea Marine Park and the Cook Islands. Samples were collected from 13 reefs within the Coral Sea Marine Park and ten islands within the Cook Islands archipelago. Tridacna maxima across the sampled region of the Coral Sea did not display any population structure, whereas significant population structure was detected for T. maxima within the Cook Islands. For the Cook Islands, most pairwise comparisons involving an island in the northern group (Manihiki) were significant, as were comparisons for Palmerston (a more centrally located island) and the southern islands, Rarotonga and Mangaia. Both regions displayed high haplotype diversities (> 0.90), indicating that they are important repositories of genetic diversity. Additional CO1 data from throughout T. maxima's distribution showed that the Coral Sea clams belonged to the clade occurring in the South-Western Pacific Ocean, whilst those from the Cook Islands belonged to a unique clade found in the Central Pacific Ocean. This clade extended from Fiji in the west to French Polynesia in the east and the atolls of Palmyra and Tarawa (Kiribati) in the north. Our assessment of genetic diversity and population structure in these regions will assist with management decisions for the species.

The growth and nitrogen utilization strategies in two dominant Symbiodiniaceae species facing nitrogen deficiency and enrichment

Symbiodiniaceae, a diverse group of unicellular dinoflagellates, are well known as endosymbionts of marine invertebrates (e.g., corals, giant clams and foraminiferans). Currently, how in vitro cultured Symbiodiniaceae cope with nitrogen (N) deficiency and enhancement remain largely unexplored. To address this knowledge gap, this study investigated the dynamics of growth, photosynthesis and crystalline guanine formation in response to differential N supplies in two dominant Symbiodiniaceae species: Durusdinium trenchii and Cladocopium goreaui. The results indicated growth rate and photosynthesis were closely related to N sources and concentrations. Under N deficiency, cell growth was inhibited. As N concentration increased, both D. trenchii and C. goreaui exhibited flexible strategies for utilizing different N sources. When provided with nitrate (NO3−), C. goreaui and D. trenchii showed an enhancement in the algal growth and photosynthetic efficiency (Fv/Fm). When ammonium (NH4+) was supplied, a moderate increase of NH4+ can benefit cell growth and photosynthesis, but excessive enrichment adversely affected algal growth. Additionally, Raman microscopy demonstrated that cellular crystalline guanine was formed by C. goreaui when exposed to N supply, but gradually decreased as N was consumed in medium. A similar phenomenon was observed in D. trenchii. We proposed that crystalline guanine may serve as an important N storage and utilization strategy. This study delved into the growth strategies and adaptability of Symbiodiniaceae to varying N nutritional environments, which contributes to understanding the symbiotic relationship between Symbiodiniaceae and corals.

Symbiodiniaceae‐Derived Fatty Acids Are Stored Differentially Across Giant Clam Species and Organs

ABSTRACTGiant clams are invertebrates that form mutualistic associations with Symbiodiniaceae dinoflagellates. Despite their ecological significance, gaps persist regarding our understanding of their trophic ecology. Specifically, it is unknown whether Symbiodiniaceae‐derived photosynthates are metabolized differently according to species and organ. Therefore, we maintained Tridacna derasa and T. noae for 3 months in a well‐lit recirculated system without food supply. Samples were taken from eight organs and underwent lipid extraction and fatty acid esterification before analysis of three symbiont‐derived fatty acids (stearidonic acid, docosapentaenoic acid, and docosahexaenoic acid—SDA, DPA, and DHA, respectively) using gas chromatography. Results show considerable variation in fatty acids concentration among species and organs. SDA was found in higher concentrations in T. noae, especially in the adductor muscle. DPA was detected in low concentrations across T. noae organs and absent for T. derasa. DHA did not vary significantly among species and organs. Our findings indicate that Symbiodiniaceae supply clams with fatty acids, which are stored differentially according to species and organs. This demonstrates that these compounds are translocated to multiple organs throughout the complex giant clam anatomical system, in contrast to simpler hosts like corals. These results advance our understanding of the physiological dynamics of the mollusk‐algae association.

The genome of a giant clam zooxanthella (Cladocopium infistulum) offers few clues to adaptation as an extracellular symbiont with high thermotolerance

BackgroundCladocopium infistulum (Symbiodiniaceae) is a dinoflagellate specialized to live in symbiosis with western Pacific giant clams (Tridacnidae). Unlike coral-associated symbionts, which reside within the host cells, C. infistulum inhabits the extracellular spaces of the clam’s digestive diverticula. It is phylogenetically basal to a large species complex of stress-tolerant Cladocopium, many of which are associated with important reef-building corals in the genus Porites. This close phylogenetic relationship may explain why C. infistulum exhibits high thermotolerance relative to other tridacnid symbionts. Moreover, past analyses of microsatellite loci indicated that Cladocopium underwent whole-genome duplication prior to the adaptive radiations that led to its present diversity.ResultsA draft genome assembly of C. infistulum was produced using long- and short-read sequences to explore the genomic basis for adaptations underlying thermotolerance and extracellular symbiosis among dinoflagellates and to look for evidence of genome duplication. Comparison to three other Cladocopium genomes revealed no obvious over-representation of gene groups or families whose functions would be important for maintaining C. infistulum’s unique physiological and ecological properties. Preliminary analyses support the existence of partial or whole-genome duplication among Cladocopium, but additional high-quality genomes are required to substantiate these findings.ConclusionAlthough this investigation of Cladocopium infistulum revealed no patterns diagnostic of heat tolerance or extracellular symbiosis in terms of overrepresentation of gene functions or genes under selection, it provided a valuable genomic resource for comparative analyses. It also indicates that ecological divergence among Cladocopium species, and potentially among other dinoflagellates, is partially governed by mechanisms other than gene content. Thus, additional high-quality, multiomic data are needed to explore the molecular basis of key phenotypes among symbiotic microalgae.

EDGARDO D. GOMEZ: Vignettes of an Eminent Marine Scientist and Institution Builder

Dr. Edgardo D. Gomez is recognized for his significant pioneering contributions to invertebrate biology and ecology, giant clam culture and restoration, coral reef assessment and conservation, and in the strengthening of marine science education and research. He established the Marine Science Institute and developed it from a small university center to a world-recognized institution in marine sciences. Dr. Gomez is also known for his advocacy of indigenous trees.

Guardians of the clams: a decadal monitoring effort of endangered giant clams by citizen scientists

ABSTRACT Giant clams are highly conspicuous marine bivalves in the tropical oceans because of their large shells and colourful outer mantle tissues. This makes them an appropriate iconic species for both trained and untrained citizen science surveys. In Singapore, because of good public awareness of giant clams, they are often reported by citizen scientists, who document marine species using photography. Furthermore, these opportunistic records are captured in a comprehensive public blog (Wild Shores of Singapore; https://wildshores.blogspot.com) with specific details of the field surveys. This study presents the first feasible effort in establishing a long-term dataset based on citizen science observations to report giant clam species-level population status and trends over time. Between 2011 and 2020, citizen scientists covered 8.53 km2 of intertidal reef areas and consistently recorded only two giant clam species (Tridacna squamosa and T. crocea) annually. Despite the more comprehensive coverage and sampling of reef areas, the citizen scientists did not encounter the other native species: Hippopus hippopus, T. gigas and T. maxima. Also, the respective densities of T. squamosa and T. crocea were 0.00120 and 0.00034 individuals per 100 m2, which makes them the smallest known giant clam populations in the Indo-Pacific region. Regardless, the sampling efforts of citizen scientists were generally similar across the years, but future surveys could adapt different survey protocols for the respective giant clam species. Findings from this study also support the marine conservation efforts in Singapore, such as using active intervention measures to protect their giant clams. Additionally, lessons learnt from these citizen science observations can be harnessed to encourage monitoring of giant clams throughout the Indo-Pacific region.

Using YOLOv5, SAHI, and GIS with Drone Mapping to Detect Giant Clams on the Great Barrier Reef

Despite the ecological importance of giant clams (Tridacninae), their effective management and conservation is challenging due to their widespread distribution and labour-intensive monitoring methods. In this study, we present an alternative approach to detecting and mapping clam density at Pioneer Bay on Goolboddi (Orpheus) Island on the Great Barrier Reef using drone data with a combination of deep learning tools and a geographic information system (GIS). We trained and evaluated 11 models using YOLOv5 (You Only Look Once, version 5) with varying numbers of input image tiles and augmentations (mean average precision—mAP: 63–83%). We incorporated the Slicing Aided Hyper Inference (SAHI) library to detect clams across orthomosaics, eliminating duplicate counts of clams straddling multiple tiles, and further, applied our models in three other geographic locations on the Great Barrier Reef, demonstrating transferability. Finally, by linking detections with their original geographic coordinates, we illustrate the workflow required to quantify animal densities, mapping up to seven clams per square meter in Pioneer Bay. Our workflow brings together several otherwise disparate steps to create an end-to-end approach for detecting and mapping animals with aerial drones. This provides ecologists and conservationists with actionable and clear quantitative and visual insights from drone mapping data.

Potential environment effect on ultrahigh resolution Sr/Ca of giant clam shells from South China Sea

Potential environment effect on ultrahigh resolution Sr/Ca of giant clam shells from South China Sea

The genome sequence of the smooth giant clam, Tridacna derasa Röding, 1798.

We present a genome assembly from an individual Tridacna derasa (the smooth giant clam; Mollusca; Bivalvia;Cardiida; Cardiidae). The genome sequence is 1,060.2 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.95 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,638 protein coding genes.

Correction: Effects of the daily light-dark cycle on rhythms of behavior and physiology in boring giant clam Tridacna crocea

Correction: Effects of the daily light-dark cycle on rhythms of behavior and physiology in boring giant clam Tridacna crocea

Analysis of molecular identity and function of putative serotonin receptors in the Giant clam (Tridacna crocea) and the potential role of 5-HT1D-like receptor in reproduction

5-hydroxytryptamine (5-HT) is a secondary metabolite that interacts with a corresponding receptor, mediating various processes in organisms. However, the molecular function and characteristics of 5-HT receptor (5-HTR) in giant clam gonads remain unknown. In this study, we cloned full-length complementary DNA (cDNA) of four putative 5-HTRs from Tridacna crocea, designated Tc5-HTR1A-like, Tc5-HTR1D-like, Tc5-HTR2-like and Tc5-HTR4-like genes. SMART analysis revealed that all four Tc5-HTR-like proteins contained a seven-transmembrane structural domain, spanning from GN and ending at Y. Phylogenetic analysis showed that the four Tc5-HTR-like proteins were clustered into four distinct groups. The results of RT-qPCR showed that Tc5-HTR-like genes were widely expressed in all tested tissues, including gonads, suggesting that the function of Tc5-HTR-like genes involves the regulation of reproduction, including gametogenesis and embryonic development. Notably, the Tc5-HTR1D-like gene is highly expressed in oocytes of hermaphrodite and female stages. Estradiol-17β (E2) induced the upregulation of Tc5-HTR1A-like, Tc5-HTR1D-like and Tc5-HTR2-like genes, as well as downregulation of Tc5-HTR4-like gene in the gonad within 72 h. In situ hybridization showed that the Tc5-HTR1D-like gene had a positive signal in oocytes, indicating its role in oogenesis. The knockdown of the Tc5-HTR1D-like gene resulted in a significant reduction in oocyte growth and the number of oocytes. Whole-mount in situ hybridization and RT-qPCR analyses suggested that the spatiotemporal expression pattern of the Tc5-HTR1D-like gene is related to the physiological activities of embryonic development. Our data demonstrate that Tc5-HTR-like genes, especially Tc5-HTR1D-like gene, are essential for regulating gamete growth in T. crocea.

Simple Mechanism for Optimal Light-Use Efficiency of Photosynthesis Inspired by Giant Clams

Simple Mechanism for Optimal Light-Use Efficiency of Photosynthesis Inspired by Giant Clams

Giant Clams Are Models of Solar-Energy Efficiency

Giant Clams Are Models of Solar-Energy Efficiency

Revealing macrozoobenthos diversity of Java coral reefs, Indonesia: a review on research trends and species assemblages

Macrozoobenthos communities play significant ecological roles in coral reef ecosystems. However, they are frequently overlooked due to their cryptic appearance, and their diversity remains undiscovered, particularly in Indonesia. This comprehensive review of publications on the macrozoobenthos in the coral reef ecosystems of Java - the most populated island in Indonesia, was conducted to compile a species list and gain an overview of its community composition. We also assessed the existence of species that are frequently reported, endemic, protected, and threatened. Data analysis was performed with data from 53 publications appearing from the 1980s to 2022. In total, 482 species belonging to 4 phyla and 9 classes have been recorded. Mollusca is the most speciose phylum (n = 321), followed by Echinodermata (n = 106), Arthropoda (n = 49), and Platyhelminthes (n = 6). Generally, the northern part of Java is well studied and has larger numbers of recorded phyla and species. The highest species number (n = 266) has been recorded off the northern coast of West Java, while there are around 25–99 species in other regions. Echinoderms species such as Culcita novaeguineae, Diadema setosum, Echinothrix calamaris, and Holothuria atra had relatively higher occurrences than other taxa. We also noted the occurrence of giant clam Hippopus hippopus, which is protected by Indonesian law. This review provides fundamental knowledge of macrozoobenthic diversity in the coral reefs of Java, making it available to global audiences. However, it revealed a lack of research on benthic fauna in several areas with moderate to good coral cover conditions. Further research is needed to explore macrozoobenthic species richness in this region thoroughly, and periodic monitoring is essential to provide early warnings of possible changes and biodiversity loss.

First report of Noah’s clam Tridacna noae (Röding, 1798) in the reef of Culion: An addition to the distribution range in Palawan, Philippines

This study provides additional information regarding the distribution range and habitat characteristics of two specimens Tridacna noae (Röding, 1798), a previously misidentified giant clam species, encountered in Barangay Malaking Patag, Culion, Palawan, Philippines. The giant clams were identified as T. noae due to the presence of ocellate spots or teardrops and sparse hyaline organs on the mantle. The specimens measured 7.8 and 7.9 cm in shell length and were found partially buried in dead coral substrates at a depth of 2 meters. The current findings provide additional information on the distribution range of T. noae in the province of Palawan and the Philippines. Identification of the distribution of certain threatened species, such as the giant clams, is crucial step in protecting and conserving their population in the wild.

Effects of the daily light-dark cycle on rhythms of behavior and physiology in boring giant clam Tridacna crocea

Effects of the daily light-dark cycle on rhythms of behavior and physiology in boring giant clam Tridacna crocea

A Testis-Specific DMRT1 (Double Sex and Mab-3-Related Transcription Factor 1) Plays a Role in Spermatogenesis and Gonadal Development in the Hermaphrodite Boring Giant Clam Tridacna crocea.

The testis-specific double sex and mab-3-related transcription factor 1 (DMRT1) has long been recognized as a crucial player in sex determination across vertebrates, and its essential role in gonadal development and the regulation of spermatogenesis is well established. Here, we report the cloning of the key spermatogenesis-related DMRT1 cDNA, named Tc-DMRT1, from the gonads of Tridacna crocea (T. crocea), with a molecular weight of 41.93 kDa and an isoelectric point of 7.83 (pI). Our hypothesis is that DMRT1 machinery governs spermatogenesis and regulates gonadogenesis. RNAi-mediated Tc-DMRT1 knockdown revealed its critical role in hindering spermatogenesis and reducing expression levels in boring giant clams. A histological analysis showed structural changes, with normal sperm cell counts in the control group (ds-EGFP) but significantly lower concentrations of sperm cells in the experimental group (ds-DMRT1). DMRT1 transcripts during embryogenesis exhibited a significantly high expression pattern (p < 0.05) during the early zygote stage, and whole-embryo in-situ hybridization confirmed its expression pattern throughout embryogenesis. A qRT-PCR analysis of various reproductive stages revealed an abundant expression of Tc-DMRT1 in the gonads during the male reproductive stage. In-situ hybridization showed tissue-specific expression of DMRT1, with a positive signal detected in male-stage gonadal tissues comprising sperm cells, while no signal was detected in other stages. Our study findings provide an initial understanding of the DMRT1 molecular machinery controlling spermatogenesis and its specificity in male-stage gonads of the key bivalve species, Tridacna crocea, and suggest that DMRT1 predominantly functions as a key regulator of spermatogenesis in giant clams.

Bleaching and recovery in the giant clam Tridacna crocea from the sub-tropical waters of Okinawa

Bleaching and recovery in the giant clam Tridacna crocea from the sub-tropical waters of Okinawa

Vanishing giants: An assessment on the population status of giant clams across Malaysia

The iconic giant clams are known for its multifaceted importance throughout the Indo-Pacific –for functional, ecological, or cultural purposes. In Malaysia, habitat destruction and illegal poaching were main reasons behind the declining populations of giant clams. As previous surveys date back to 1990 s, an update on the status of giant clam populations in Malaysia is overdue. Using the extensive monitoring data from Reef Check Malaysia, we analysed and provided an assessment of population trends of giant clams between 2007 and 2021 in Malaysia. This study showed a decline in giant clam population in the east coast Peninsula and Sabah, while their abundances have always been low in the west coast Peninsula and Sarawak. In the east coast Peninsula, Tridacna maxima and T. crocea were most common (2.7 ± 7.3 and 1.4 ± 7.6 clams per 100 m2, respectively), followed by T. squamosa (0.7 ± 1.4 clams per 100 m2), and Hippopus hippopus (0.3 ± 2.5 clams per 100 m2). The boring species, T. maxima and T. crocea, typically displayed highly aggregated populations, reaching densities of 41.5 and 70 clams per 100 m2, where a reciprocal abundance shift between both species was observed between northern and southern sites of east coast Peninsula. The demography of T. maxima and T. crocea is either positively skewed or normally distributed, indicating abundant recruits that correspond to their higher densities. In contrast, T. squamosa showed a negative skew, suggesting poor recruitment rates. Findings here underscore the need to tailor conservation strategies for respective giant clam species in Malaysia. Proposed initiatives include establishing conservation zones in key areas like Perhentian, Lang Tengah, Redang, and Tioman Islands, which have significant T. maxima and T. crocea recruit populations. Also, targeted restocking efforts are necessary for T. squamosa and H. hippopus to ensure long-term viability of populations.

Ecological potential of giant clams in Ambon Island waters, Eastern Indonesia

Giant clams are protected marine organisms universally, thus information on giant clams is important for management purposes. This research was conducted in July to August 2021 in Morella and Suli, Ambon Island Maluku Province to get information on ecological potential which consist of species composition, density, occurrence frequency and diversity of giant clams. Sample was collected by using linear quadrat transect line. As many as 25 quadrants (10x10m) were used in both locations. Every individual of giant clams found in the quadrant was identified, photographed and counted. There were three species of giant clams found in Morella namely Tridacna crocea, T. maxima, and T. squamosa while four species were found in Suli i.e. those three species mentions earlier and Hippopus Hippopus. Totally, T. crocea had more individuals followed by T. squamosa and then T. maxima while the lesser belonged to H. Hippopus with one individual. Density of giant clams in Morella (428 ind./ha) was much higher than density of giant clams in Suli (48 ind./ha). Giant clams in Morella can be found in 16 - 19 quadrants of 25 quadrants used while in Suli only found in 1 - 6 quadrants. Ecological indexes for diversity, evenness and dominance showed that giant clams in Morella and Suli had moderate diversity, high evenness and low dominance.