Ontogenetic and temperature-dependent changes in tolerance to hypoxia and hydrogen sulfide during the early life stages of the Manila clam Ruditapes philippinarum

Effective capping of dissolved sulfide generated in Ulva prolifera-rich marine sediments by iron-rich red soil

Bloom-induced macroalgal enrichment on the seafloor can substantially facilitate dissolved sulfide (DS) production through sulfate reduction. The reaction of DS with sedimentary reactive iron (Fe) is the main mechanism of DS consumption, which however usually could not effectively prevent DS accumulation caused by pulsed macroalgal enrichment. Here we used incubations to investigate the performance of Fe-rich red soil for buffering of DS produced from macroalgae (Ulva prolifera)-enriched sediment. Based on our results, a combination of red soil additions (6.8 kg/m2) before and immediately after pulsed macroalgal deposition (455 g/m2) can effectively cap DS within the red soil layer. The effective DS buffering is mainly due to ample Fe-oxide surface sites available for reaction with DS. Only a small loss (4 %) of buffering capacity after 18-d incubation suggests that the red soil is capable of prolonged DS buffering in macroalgae-enriched sediments.

Environmental influence on summer survival of Manila Clam Ruditapes philippinarum: A case study in an aquaculture bay

The aquaculture of Manila clam (Ruditapes philippinarum) is under threat due to its high mortality in summer. To investigate the environmental influence on mortality of the species, we have conducted field surveys in the aquaculture area in Laizhou Bay, during the summers of 2019 and 2020. Environmental and biological data were collected. The results of data analysis have shown that in 2020, large-scale mortality events were not recorded and spatial variations of environmental variables were no significant within the survey area. However, in August 2019, significant variations of environmental variables were detected in the middle tidal area. This area was charactered with relatively high-water temperature (with maximum temperature of 31.49 °C and mean value of 26.17 ± 1.62 °C), elevated hydrogen sulfide concentrations (with a maximum concentration of 24.72 μmol/L and a mean concentration of 7.89 ± 4.14 μmol/L), and low dissolved oxygen concentrations (with a minimum concentration of 3.35 mg/L and a mean concentration of 6.27 ± 0.42 mg/L). Correspondingly, high mortality of the clam was recorded in the area, the abundance of live Manila clams has decreased by 80%. No significant abnormalities of environmental variables and clam growth were observed in other regions in 2019. Glycogen content and condition index of the clam were analyzed to investigate the relationship between environmental stress and the health of the clam. Compared to the condition index, glycogen content is a more sensitive indicator of the health status of the clam because changes in glycogen content appeared earlier than changes in condition index and mortality. A principal component analysis further indicated that the high mortality of the clam corresponds with a few environmental variables, including elevated temperature, hypoxia and the concentration of hydrogen sulfide. The simultaneous presence of these multiple environmental stressors could have triggered alterations in the physiological responses of the clam.

Defense System of the Manila Clam Ruditapes philippinarum under High-Temperature and Hydrogen Sulfide Conditions

Hydrogen sulfide (H₂S) acts as an environmental toxin. Despite its toxicity, little is known about the defense strategies of marine bivalves against it. Thus, the tolerance, behavioral characteristics, and physiological response strategies against H₂S treatment in the sentinel organism Manila clam Ruditapes philippinarum were examined. We monitored the survival and behavioral status of Manila clams exposed to different combinations of temperature and H₂S. The physiological response strategies were examined by measuring the enzymatic activity of cytochrome C oxidase (CCO), fumarate reductase (FRD), superoxide dismutase (SOD), and catalase enzymes (CAT). Moreover, adverse effects of H₂S on the tissue and cell structure of Manila clams were also examined under a transmission electron microscope. Manila clams responded to H₂S stress through behavioral and chemical defenses. With exposure to H₂S alone, Manila clams primarily enhanced aerobic respiratory metabolic pathways in the beginning stages by opening the shell and increasing the CCO activity to obtain more oxygen; with increasing exposure time, when aerobic respiration was inhibited, the shell was closed, and FRD, CAT, and SOD were activated. At this point, Manila clams responded to H₂S stress through the anaerobic metabolism and antioxidant defense systems. However, high temperatures (≥28 °C) altered the defense strategy of Manila clams. With co-exposure to high temperatures and high H₂S concentrations (≥20 μmol/L), the Manila clams immediately closed their shells and changed from aerobic respiration to anaerobic metabolism while immediately activating antioxidant defense systems. Nevertheless, this defense strategy was short lived. In addition to this, apparent damage to tissue and cell structures, including mitochondrial ridge dissolution and many vacuoles, was observed in Manila clams exposed to high temperatures and high H₂S concentrations. Thus, prolonged exposure to high temperature and H₂S damages the tissue structure of Manila clams, affecting their behavioral capacity and future survival. In summary, profiling Manila clams' physiological response strategies to H₂S exposure provided ecological behavioral support for our current understanding of H₂S detrimental toxicity on marine bivalves.

A high-quality chromosome-level genome assembly of the bivalve mollusk Mactra veneriformis

Mactra veneriformis (Bivalvia: Mactridae) is a bivalve mollusk of major economic importance in China. Decreased natural yields of M. veneriformis have led to an urgent need for genomic resources. To address this problem and the currently limited knowledge of molecular evolution in this genus, we here report a high-quality chromosome-level genome assembly of M. veneriformis. Our approach yielded a 939.32 Mb assembled genome with an N50 contig length of 7,977.84 kb. Hi-C scaffolding of the genome resulted in assembly of 19 pseudochromosomes. Repetitive elements made up ∼51.79% of the genome assembly. A total of 29,315 protein-coding genes (PCGs) were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and Ruditapes philippinarum diverged around 231 million years ago (MYA). Inter-species comparisons revealed that 493 gene families have undergone expansion and 449 have undergone contraction in the M. veneriformis genome. Chromosome-based macrosynteny analysis revealed a high degree of synteny between the 19 chromosomes of M. veneriformis and those of Patinopecten yessoensis. These results suggested that M. veneriformis has a similar karyotype to that of P. yessoensis, and that a highly conserved 19-chromosome karyotype was formed in the early differentiation stages of bivalves. In summary, the genomic resources generated in this work serve as a valuable reference for investigating the molecular mechanisms underlying biological functions in M. veneriformis and will facilitate future genetic improvement and disease treatment in this economically important species. Furthermore, the assembled genome greatly improves our understanding of early genomic evolution of the Bivalvia.

Thermal stress affects bioturbators' burrowing behavior: A mesocosm experiment on common cockles (Cerastoderma edule)

The intensity of marine heatwaves is increasing due to climate change. Heatwaves may affect macroinvertebrates' bioturbating behavior in intertidal areas, thereby altering the deposition-erosion balance at tidal flats. Moreover, small-scale topographic features on tidal flats can create tidal pools during the low tide, thus changing the heat capacity of tidal flats. These pools could then potentially operate as refuge environments during marine heatwaves. We studied behavior responses to heat waves using the well-known bioturbating cockle Cerastoderma edule as a model species. Different temperature regimes (i.e., fluctuating between 20 and 40 °C) and micro-topographies (i.e., presence vs. absence of tidal water pools) were mimicked in a mesocosm experiment with regular tidal regimes. Our results demonstrate that behavioral responses to heat stress strongly depend on the site-specific morphological features. Cockles covered by shallow water pools moved up when exposed to thermal stress, while burrowing deeper into the sediment in the absence of water pools. But in both cases, their migratory behavior increased under heat stress compared to regular ambient treatments. Moreover, long-term cumulative heat stress increased cockles' respiration rates and decreased their health conditions, causing mass mortality after four weeks of gradually increasing heat exposure. Overall, the present findings provide the first insights into how bioturbating behavior on tidal flats may change in response to global warming.

Assessing the impacts of differential depositional settings and/or anthropogenic perturbations on sulfur and iron diagenesis in sediments of the Bohai Sea and North Yellow Sea

Natural processes and human activities exert important impacts on elemental cycling in coastal sediments, which has not been well documented. Sediments in the Bohai Sea and North Yellow Sea were investigated to assess the impacts of the Yellow River inputs and/or anthropogenic perturbations on diagenesis of iron and sulfur. Labile iron (0.5 M HCl-extractable iron) in the sediments is low due to iron-poor nature of source materials. Dynamic regimes and low availability of labile organic carbon (OC) result in relatively low sulfide contents in deltaic sediments. However, low but continuous supply of labile OC exported from an anthropogenically impacted bay could substantially elevate sulfide burial in sediments near the bay. Neither offshore oil exploitations nor frequent algal blooms in the seas have detectable influences on iron and sulfur diagenesis in the sediments. The sediments are capable of quickly consuming porewater sulfide by reaction with reactive iron under the current conditions.

Genome-wide investigation and expression analysis of MACPF gene family reveals its immune role in response to bacterial challenge of Manila clam

In this study, 18 MACPF genes (RpMACPF) were identified and classed into three types (Macrophage-expressed gene 1, Apextrin, and MACPF domain contain protein) based on gene structure and phylogenetic relationship in R. philippinarum. The length of RpMACPF proteins varied from 287 to 785 amino acids. The molecular weights and Theoretical PI values ranged from 3.2 kDa to 8.7 kDa and 4.7 to 8.6, respectively. RNA-seq data analysis revealed that 14 of 18 RpMACPF genes were highly expressed at the pediveliger larvae stage indicate RpMACPF might contribute to the early development and metamorphosis processes of the R. philippinarum. Besides, we found RpMACPF genes were significantly regulated by pathogen-associated molecular patterns (PAMPs) and Vibrio parahemolyticus, which indicates RpMACPF genes may play significant roles in response to invading pathogens. The results obtained in this work will provide valuable insight into the immune function of MACPF gene in R. philippinarum.

Genome-wide identification and transcriptome-based expression profiling of Wnt gene family in Ruditapes philippinarum

The Wnt genes encode a set of conserved glycoproteins regulating early development, cell proliferation and differentiation, and tissue regeneration in metazoans. In some mollusks, the knowledge of Wnt gene family has been limited because of the short of the genomic and transcriptomic resources. Ruditapes philippinarum is an economically important bivalve with a variety of shell coloration patterns and ability to regenerate its siphon. To gain a greater understanding of the evolutionary dynamics of Wnt gene family, we carried out a genome-wide identification and phylogenetic analysis of Wnt gene family in R. philippinarum and other four mollusks. A total of 12 Wnt genes were identified in the genome of R. philippinarum, and the dynamic patterns of gene conservation, loss and duplication of Wnt genes were analyzed in mollusks and model organisms. Furthermore, the transcriptome analyses demonstrated the expression profiles of the Wnt genes at different developmental stage, in adult tissues, during siphon regeneration, in four different shell color strains, and at uncolored and colored developmental stages in two different shell color strains. These findings suggest that the expansion of Wnt genes may play vital roles in the larval development, the formation of shell color pattern and siphon regeneration in R. philippinarum. This study provides a valuable insight into Wnt function and evolution in mollusks.

Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity

Ruditapes philippinarum is an economically important bivalve with remarkable diversity in its shell coloration patterns. In this study, we sequenced the whole genome of the Manila clam and investigated the molecular basis of its adaptation to hypoxia, acidification, and parasite stress with transcriptome sequencing and an RNA sequence analysis of different tissues and developmental stages to clarify these major issues. A number of immune-related gene families are expanded in the R. philippinarum genome, such as TEP, C3, C1qDC, Hsp70, SABL, and lysozyme, which are potentially important for its stress resistance and adaptation to a coastal benthic life. The transcriptome analyses demonstrated the dynamic and orchestrated specific expression of numerous innate immune-related genes in response to experimental challenge with pathogens. These findings suggest that the expansion of immune- and stress-related genes may play vital roles in resistance to adverse environments and has a profound effect on the clam's adaptation to benthic life.

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We present a new genome assembly of the Manila clam Ruditapes philippinarum

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Analysis of gene family expansions and transcriptome characterization were conducted

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Tyr and mitf genes were potentially involved in shell color patterns of Manila clam

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Expansion of GPCRs and immune-related genes were found in R. philippinarum

Sulfur, iron, and phosphorus geochemistry in an intertidal mudflat impacted by shellfish aquaculture

Dissolved sulfide, iron (Fe), and phosphorus (P) in a mudflat (Jiaozhou Bay, China) impacted by shellfish aquaculture were measured in situ by the diffusive gradients in thin films (DGT) technique. A combination of porewater and solid-phase chemistry was used to characterize the interplays of Fe and S, and their control on P mobilization. Below the subsurface layer, two times higher fluxes (F_DGT) of dissolved Fe²⁺ from porewater to the DGT device than those of dissolved sulfide indicate that dissimilatory iron reduction (DIR) dominates over sulfate reduction (SR). Spatial coupling of dissolved Fe²⁺ and P points to P release driven mainly by reductive dissolution of Fe. Much higher F_DGT values of dissolved Fe²⁺ relative to dissolved P imply that oxidative regeneration of Fe oxides at the sediment-water interfaces (SWIs) of the transitional mudflat serves as an effective "iron curtain" of upward diffusing P. In the mudflat sediments of DIR prevalence, the accumulation of total reduced inorganic sulfur (TRIS) is dampened, which can largely ascribed to enhanced oxidative loss of sulfide and/or limited availability of degradable organic carbon in the dynamic regimes. Low dissolved sulfide concentrations in the sediments leave the majority of reactive Fe unsulfidized and thus abundantly available to buffer newly produced sulfide.