ResearchPad - bivalves https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Transcriptome analysis of Catarina scallop (<i>Argopecten ventricosus</i>) juveniles treated with highly-diluted immunomodulatory compounds reveals activation of non-self-recognition system]]> https://www.researchpad.co/article/elastic_article_14633 Marine bivalve hatchery productivity is continuously challenged by apparition and propagation of new diseases, mainly those related to vibriosis. Disinfectants and antibiotics are frequently overused to prevent pathogen presence, generating a potential negative impact on the environment. Recently, the use of highly diluted compounds with immunostimulant properties in marine organisms has been trailed successfully to activate the self-protection mechanisms of marine bivalves. Despite their potential as immunostimulants, little is known about their way of action. To understand their effect, a comparative transcriptomic analysis was performed with Argopecten ventricosus juveniles. The experimental design consisted of four treatments formulated from pathogenic Vibrio lysates at two dilutions: [(T1) Vibrio parahaemolyticus and Vibrio alginolyticus 1D; (T2) V. parahaemolyticus and V. alginolyticus 7C]; minerals [(T3) PhA+SiT 7C], scorpion venom [(T4) ViT 31C]; and one control (C1) hydro-alcoholic solution (ethanol 1%). The RNA sequencing (RNAseq) analysis showed a higher modulation of differentially expressed genes (DEG) in mantle tissue compared to gill tissue. The scallops that showed a higher number of DEG related to immune response in mantle tissue corresponded to T1 (V. parahaemolyticus and V. alginolyticus lysate) and T3 (Silicea terra® - Phosphoric acid®). The transcriptome analysis allowed understanding some interactions between A. ventricosus juveniles and highly-diluted treatments.

]]>
<![CDATA[SNP Identification by Transcriptome Sequencing and Candidate Gene-Based Association Analysis for Heat Tolerance in the Bay Scallop Argopecten irradians]]> https://www.researchpad.co/article/5989da90ab0ee8fa60b9fe9f

The northern bay scallop Argopecten irradians irradians (Lamarck) and the southern bay scallop Argopecten irradians concentricus (Say) were introduced into China in the 1980s and 1990s, and are now major aquaculture molluscs in China. Here, we report the transcriptome sequencing of the two subspecies and the subsequent association analysis on candidate gene on the trait of heat tolerance. In total, RNA from six tissues of 67 and 42 individuals of northern and southern bay scallops, respectively, were used and 55.5 and 34.9 million raw reads were generated, respectively. There were 82,267 unigenes produced in total, of which 32,595 were annotated. Altogether, 32,206 and 23,312 high-quality SNPs were identified for northern and southern bay scallops, respectively. For case-control analysis, two intercrossed populations were heat stress treated, and both heat-susceptible and heat-resistant individuals were collected. According to annotation and SNP allele frequency analysis, 476 unigenes were selected, and 399 pairs of primers were designed. Genotyping was conducted using the high-resolution melting method, and Fisher’s exact test was performed for allele frequency comparison between the heat-susceptible and heat-resistant groups. SNP all-53308-760 T/C showed a significant difference in allele frequency between the heat-susceptible and heat-resistant groups. Notably, considerable difference in allele frequency at this locus was also observed between the sequenced natural populations. These results suggest that SNP all-53308-760 T/C may be related to the heat tolerance of the bay scallop. Moreover, quantitative expression analysis revealed that the expression level of all-53308 was negatively correlated with heat tolerance of the bay scallop.

]]>
<![CDATA[Towards a sampling design for characterizing habitat-specific benthic biodiversity related to oxygen flux dynamics using Aquatic Eddy Covariance]]> https://www.researchpad.co/article/5c61e8b6d5eed0c48496f005

The Aquatic Eddy Covariance (AEC) technique has emerged as an important method to quantify in situ seafloor metabolism over large areas of heterogeneous benthic communities, enabling cross-habitat comparisons of seafloor productivity. However, the lack of a corresponding sampling protocol to perform biodiversity comparisons across habitats is impeding a full assessment of marine ecosystem metabolism. Here, we study a range of coastal benthic habitats, from rocky-bed communities defined by either perennial macroalgae or blue mussel beds to soft-sediment communities comprised of either seagrass, patches of different macrophyte species or bare sand. We estimated that the maximum contribution to the AEC metabolic flux can be found for a seafloor area of approximately 80 m2 with a 5 meter upstream distance of the instrument across all the habitats. We conducted a sampling approach to characterize and quantify the dominant features of biodiversity (i.e., community biomass) within the main seafloor area of maximum metabolic contribution (i.e., gross primary production and community respiration) measured by the AEC. We documented a high biomass contribution of the macroalgal Fucus vesiculosus, the seagrass Zostera marina and the macroinvertebrate Mytilus edulis to the net ecosystem metabolism of the habitats. We also documented a significant role of the bare sediments for primary productivity compared to vegetated canopies of the soft sediments. The AEC also provided insight into dynamic short-term drivers of productivity such as PAR availability and water flow velocity for the productivity estimate. We regard this study as an important step forward, setting a framework for upcoming research focusing on linking biodiversity metrics and AEC flux measurements across habitats.

]]>
<![CDATA[High rates of apoptosis visualized in the symbiont-bearing gills of deep-sea Bathymodiolus mussels]]> https://www.researchpad.co/article/5c61e8c2d5eed0c48496f0dc

Symbiosis between Bathymodiolus and Gammaproteobacteria allows these deep-sea mussels to live in toxic environments such as hydrothermal vents and cold seeps. The quantity of endosymbionts within the gill-bacteriocytes appears to vary according to the hosts environment; however, the mechanisms of endosymbiont population size regulation remain obscure. We investigated the possibility of a control of endosymbiont density by apoptosis, a programmed cell death, in three mussel species. Fluorometric TUNEL and active Caspase-3-targeting antibodies were used to visualize and quantify apoptotic cells in mussel gills. To control for potential artefacts due to depressurization upon specimen recovery from the deep-sea, the apoptotic rates between mussels recovered unpressurised, versus mussels recovered in a pressure-maintaining device, were compared in two species from hydrothermal vents on the Mid-Atlantic Ridge: Bathymodiolus azoricus and B. puteoserpentis. Results show that pressurized recovery had no significant effect on the apoptotic rate in the gill filaments. Apoptotic levels were highest in the ciliated zone and in the circulating hemocytes, compared to the bacteriocyte zone. Apoptotic gill-cells in B. aff. boomerang from cold seeps off the Gulf of Guinea show similar distribution patterns. Deep-sea symbiotic mussels have much higher rates of apoptosis in their gills than the coastal mussel Mytilus edulis, which lacks chemolithoautotrophic symbionts. We discuss how apoptosis might be one of the mechanisms that contribute to the adaptation of deep-sea mussels to toxic environments and/or to symbiosis.

]]>
<![CDATA[Integrating ecosystem services considerations within a GIS-based habitat suitability index for oyster restoration]]> https://www.researchpad.co/article/5c57e667d5eed0c484ef3039

Geospatial habitat suitability index (HSI) models have emerged as powerful tools that integrate pertinent spatial information to guide habitat restoration efforts, but have rarely accounted for spatial variation in ecosystem service provision. In this study, we utilized satellite-derived chlorophyll a concentrations for Pamlico Sound, North Carolina, USA in conjunction with data on water flow velocities and dissolved oxygen concentrations to identify potential restoration locations that would maximize the oyster reef-associated ecosystem service of water filtration. We integrated these novel factors associated with oyster water filtration ecosystem services within an existing, ‘Metapopulation Persistence’ focused GIS-based, HSI model containing biophysical (e.g., salinity, oyster larval connectivity) and logistical (e.g., distance to nearest restoration material stockpile site) factors to identify suitable locations for oyster restoration that maximize long-term persistence of restored oyster populations and water filtration ecosystem service provision. Furthermore, we compared the ‘Water Filtration’ optimized HSI with the HSI optimized for ‘Metapopulation Persistence,’ as well as a hybrid model that optimized for both water filtration and metapopulation persistence. Optimal restoration locations (i.e., locations corresponding to the top 1% of suitability scores) were identified that were consistent among the three HSI scenarios (i.e., “win-win” locations), as well as optimal locations unique to a given HSI scenario (i.e., “tradeoff” locations). The modeling framework utilized in this study can provide guidance to restoration practitioners to maximize the cost-efficiency and ecosystem services value of habitat restoration efforts. Furthermore, the functional relationships between oyster water filtration and chlorophyll a concentrations, water flow velocities, and dissolved oxygen applied in this study can guide field- and lab-testing of hypotheses related to optimal conditions for oyster reef restoration to maximize water quality enhancement benefits.

]]>
<![CDATA[Age structure of the Australian lungfish (Neoceratodus forsteri)]]> https://www.researchpad.co/article/5c52180fd5eed0c484796f65

The Australian lungfish has been studied for more than a century without any knowledge of the longevity of the species. Traditional methods for ageing fish, such as analysis of otolith (ear stone) rings is complicated in that lungfish otoliths differ from teleost fish in composition. As otolith sampling is also lethal, this is not appropriate for a protected species listed under Australian legislation. Lungfish scales were removed from 500 fish from the Brisbane, Burnett and Mary rivers. A sub–sample of scales (85) were aged using bomb radiocarbon techniques and validated using scales marked previously with oxytetracycline. Lungfish ages ranged from 2.5–77 years of age. Estimated population age structures derived using an Age Length Key revealed different recruitment patterns between river systems. There were statistically significant von Bertalanffy growth model parameters estimated for each of the three rivers based on limited sample sizes. In addition, length frequency distributions between river systems were also significantly different. Further studies will be conducted to review drivers that may explain these inter-river differences.

]]>
<![CDATA[Optimization of extraction of antioxidant polysaccharide from Pleurotus ostreatus (Jacq.) P. Kumm and its cytotoxic activity against murine lymphoid cancer cell line]]> https://www.researchpad.co/article/5c37b784d5eed0c48449027e

The purpose of this study was to optimize the extraction method for polysaccharide from the fruiting bodies of Pleurotus ostreatus (Jacq.) P. Kumm and to assess the antioxidant and cytotoxic potentials of polysaccharide. In this investigation, polysaccharides from Pleurotus ostreatus (Jacq.) P. Kumm were extricated by utilizing the hot water. One-single factor and response surface methodology was established to optimize the extraction conditions for polysaccharide from Pleurotus ostreatus (Jacq.) P. Kumm. Examination of antioxidant activity of Pleurotus ostreatus polysaccharide (POP) was directed by utilizing 2, 2-diphenyl-1-picrylhydrazyl (DPPH) and 2, 2-azino-bis-3-ethyl-benzothiazoline-6-sulfonic acid (ABTS) techniques. Cytotoxicity of POP was evaluated using an MTT assay. The experimental data were fitted to a quadratic equation utilizing multiple regression investigations, and the ideal conditions were as per the following: water/crude material proportion, 26.04 mL/g; an extraction time of 62.08 minutes; and an extraction temperature 70.5°C. Under such conditions, the polysaccharide yield was 5.32 ± 0.12% with the anticipated yield. POP showed good scavenging activity against DPPH radical (p<0.001, EC50 = 1036.38 μg/mL, R2 = 0.8313) and ABTS radicals (p<0.001, EC50 = 824.37 μg/mL, R2 = 0.8223), with a dose (p<0.001)-and-time (p<0.001) dependent cytotoxic potential on Ehrlich ascites carcinoma cell line in vitro. This demonstrated that polysaccharides (POP) had certain cancer prevention agent exercises. In this manner, these examinations give reference to additionally research and reasonable improvement of Pleurotus ostreatus (Jacq.) P. Kumm polysaccharide and POP may prove a useful therapeutic agent, due to its robust antioxidant and cytotoxic activity.

]]>
<![CDATA[Transcriptome analysis of sex-related genes in the blood clam Tegillarca granosa]]> https://www.researchpad.co/article/5b43f9bb463d7e320c6eb9a1

Background

Blood clams (Tegillarca granosa) are one of the most commercial shellfish in China and South Asia with wide distribution in Indo-Pacific tropical to temperate estuaries. However, recent data indicate a decline in the germplasm of this species. Furthermore, the molecular mechanisms underpinning reproductive regulation remain unclear and information regarding genetic diversity is limited. Understanding the reproductive biology of shellfish is important in interpreting their embryology development, reproduction and population structure. Transcriptome sequencing (RNA-seq) rapidly obtains genetic sequence information from almost all transcripts of a particular tissue and currently represents the most prevalent and effective method for constructing genetic expression profiles.

Results

Non-reference RNA-seq, an Illumina HiSeq2500 Solexa system, and de novo assembly were used to construct a gonadal expression profile of the blood clam. A total of 63.75 Gb of clean data, with at least 89.46% of Quality30 (Q30), were generated which was then combined into 214,440 transcripts and 125,673 unigenes with a mean length of 1,122.63 and 781.30 base pairs (bp). In total, 27,325 genes were annotated by comparison with public databases. Of these, 2,140 and 2,070 differentially expressed genes (DEGs) were obtained (T05 T08 vs T01 T02 T04, T06 T07 vs T01 T02 T04; in which T01-T04 and T05-T08 represent biological replicates of individual female and male clams, respectively) and classified into two groups according to the evaluation of biological replicates. Then 35 DEGs and 5 sex-related unigenes, in other similar species, were investigated using qRT-PCR, the results of which were confirmed to data arising from RNA-seq. Among the DEGs, sex-related genes were identified, including forkhead box L2 (Foxl2), sex determining region Y-box (Sox), beta-catenin (β-catenin), chromobox homolog (CBX) and Sex-lethal (Sxl). In addition, 6,283 simple sequence repeats (SSRs) and 614,710 single nucleotide polymorphisms (SNPs) were identified from the RNA-seq results.

Conclusions

This study provided the first complete gonadal transcriptome data for the blood clam and allowed us to search many aspects of gene sequence information, not limited to gender. This data will improve our understanding of the transcriptomics and reproductive biology of the blood clam. Furthermore, molecular markers such as SSRs and SNPs will be useful in the analysis of genetic evolution, bulked segregant analysis (BSA) and genome-wide association studies (GWAS). Our transcriptome data will therefore provide important genetic information for the breeding and conservation of germplasm.

]]>
<![CDATA[Transcriptome Analysis of the Sydney Rock Oyster, Saccostrea glomerata: Insights into Molluscan Immunity]]> https://www.researchpad.co/article/5989daefab0ee8fa60bc0801

Background

Oysters have important ecological functions in their natural environment, acting as global carbon sinks and improving water quality by removing excess nutrients from the water column. During their life-time oysters are exposed to a variety of pathogens that can cause severe mortality in a range of oyster species. Environmental stressors encountered in their habitat can increase the susceptibility of oysters to these pathogens and in general have been shown to impact on oyster immunity, making immune parameters expressed in these marine animals an important research topic.

Results

Paired-end Illumina high throughput sequencing of six S. glomerata tissues exposed to different environmental stressors resulted in a total of 484,121,702 paired-end reads. When reads and assembled transcripts were compared to the C. gigas genome, an overall low level of similarity at the nucleotide level, but a relatively high similarity at the protein level was observed. Examination of the tissue expression pattern showed that some transcripts coding for cathepsins, heat shock proteins and antioxidant proteins were exclusively expressed in the haemolymph of S. glomerata, suggesting a role in innate immunity. Furthermore, analysis of the S. glomerata ORFs showed a wide range of genes potentially involved in innate immunity, from pattern recognition receptors, components of the Toll-like signalling and apoptosis pathways to a complex antioxidant defence mechanism.

Conclusions

This is the first large scale RNA-Seq study carried out in S. glomerata, showing the complex network of innate immune components that exist in this species. The results confirmed that many of the innate immune system components observed in mammals are also conserved in oysters; however, some, such as the TLR adaptors MAL, TRIF and TRAM are either missing or have been modified significantly. The components identified in this study could help explain the oysters’ natural resilience against pathogenic microorganisms encountered in their natural environment.

]]>
<![CDATA[Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes]]> https://www.researchpad.co/article/5989db5cab0ee8fa60bdfeec

Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA) demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring. We employed careful primer design and in vitro testing with mock communities to assess ability of the markers to amplify and sequence targeted species DNA, while retaining rank abundance information. In our mock communities, read abundances reflected the initial input abundance, with regressions having significant slopes (p<0.05) and high coefficients of determination (R2) for all comparisons. Tests on field environmental samples revealed similar ability of our markers to measure relative abundance. Due to the limited reference sequence data available for these invertebrate species, care must be taken when analyzing results and identifying sequence reads to species level. These markers extend eDNA metabarcoding research for molluscs and appear relevant to other invertebrate taxa, such as rotifers and bryozoans. Furthermore, the sphaeriid mussel assay is group-specific, exclusively amplifying bivalves in the Sphaeridae family and providing species-level identification. Our assays provide useful tools for managers and conservation scientists, facilitating early detection of invasive species as well as improving resolution of mollusc diversity.

]]>
<![CDATA[Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdc175

Single nucleotide polymorphisms (SNPs) are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas) is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an oyster 190K SNP array using Affymetrix Axiom genotyping technology. We designed 190,420 SNPs on the chip; these SNPs were selected from 54 million SNPs identified through re-sequencing of 472 Pacific oysters collected in China, Japan, Korea, and Canada. Our genotyping results indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. The SNPs were distributed evenly throughout the oyster genome, located in 3,595 scaffolds with a length of ~509.4 million; the average interval spacing was 4,210 bp. In addition, 111,158 SNPs were distributed in 21,050 coding genes, with an average of 5.3 SNPs per gene. In comparison with genotypes obtained through re-sequencing, ~69% of the converted SNPs had a concordance rate of >0.971; the mean concordance rate was 0.966. Evaluation based on genotypes of full-sib family individuals revealed that the average genotyping accuracy rate was 0.975. Carrying 133 K polymorphic SNPs, our oyster 190K SNP array is the first commercially available high-density SNP chip for mollusks, with the highest throughput. It represents a valuable tool for oyster genome-wide association studies, fine linkage mapping, and population genetics.

]]>
<![CDATA[Spatial and Temporal Examination of Bivalve Communities in Several Estuaries of Southern California and Northern Baja California, MX]]> https://www.researchpad.co/article/5989daf8ab0ee8fa60bc3a9b

A combination of historical bivalve surveys spanning 30–50 years and contemporary sampling were used to document the changes in bivalve community structure over time at four southern California and one northern Baja California estuaries. While there are limitations to the interpretation of historic data, we observed generally similar trends of reduced total bivalve species richness, losses of relatively large and/or deeper-dwelling natives, and gains of relatively small, surface dwelling introduced species across the southern California estuaries, despite fairly distinct bivalve communities. A nearly 50-year absence of bivalves from two wetlands surveyed in a Baja California estuary continued. A combination of site history and current characteristics (e.g., location, depth) likely contributes to maintenance of distinct communities, and both episodic and gradual environmental changes likely contribute to within-estuary temporal shifts (or absences). We highlight future research needed to determine mechanisms underlying patterns so that we can better predict responses of bivalve communities to future scenarios, including climate change and restoration.

]]>
<![CDATA[Monogamy in a Hyper-Symbiotic Shrimp]]> https://www.researchpad.co/article/5989db3aab0ee8fa60bd459a

Theory predicts that monogamy is adaptive in resource-specialist symbiotic crustaceans inhabiting relatively small and morphologically simple hosts in tropical environments where predation risk away from hosts is high. We tested this prediction in Pontonia manningi, a hyper-symbiotic shrimp that dwells in the mantle cavity of the Atlantic winged oyster Pteria colymbus that, in turn, infects gorgonians from the genus Pseudopterogorgia in the Caribbean Sea. In agreement with theory, P. manningi were found dwelling as heterosexual pairs in oysters more frequently than expected by chance alone. Males and females also inhabited the same host individual independent of the female gravid condition or of the developmental stage of brooded embryos. While the observations above argue in favor of monogamy in P. manningi, there is evidence to suggest that males of the studied species are moderately promiscuous. That females found living solitary in oysters most often brooded embryos, and that males allocated more to weaponry (major claw size) than females at any given size suggest that males might be roaming among host individuals in search of and, fighting for, receptive females. All available information depicts a rather complex mating system in P. manningi: primarily monogamous but with moderately promiscuous males.

]]>
<![CDATA[Freshwater Detention by Oyster Reefs: Quantifying a Keystone Ecosystem Service]]> https://www.researchpad.co/article/5989da21ab0ee8fa60b7f163

Oyster reefs provide myriad ecosystem services, including water quality improvement, fisheries and other faunal support, shoreline protection from erosion and storm surge, and economic productivity. However, their role in directing flow during non-storm conditions has been largely neglected. In regions where oyster reefs form near the mouth of estuarine rivers, they likely alter ocean-estuary exchange by acting as fresh water “dams”. We hypothesize that these reefs have the potential to detain fresh water and influence salinity over extensive areas, thus providing a “keystone” ecosystem service by supporting estuarine functions that rely on the maintenance of estuarine (i.e., brackish) conditions in the near-shore environment. In this work, we investigated the effects of shore-parallel reefs on estuarine salinity using field data and hydrodynamic modeling in a degraded reef complex in the northeastern Gulf of Mexico. Results suggested that freshwater detention by long linear chains of oyster reefs plays an important role in modulating salinities, not only in the oysters’ local environment, but over extensive estuarine areas (tens of square kilometers). Field data confirmed the presence of salinity differences between landward and seaward sides of the reef, with long-term mean salinity differences of >30% between sides. Modeled results expanded experimental findings by illustrating how oyster reefs affect the lateral and offshore extent of freshwater influence. In general, the effects of simulated reefs were most pronounced when they were highest in elevation, without gaps, and when riverine discharge was low. Taken together, these results describe a poorly documented ecosystem service provided by oyster reefs; provide an estimate of the magnitude and spatial extent of this service; and offer quantitative information to help guide future oyster reef restoration.

]]>
<![CDATA[Genetic Variation and Breeding Signature in Mass Selection Lines of the Pacific Oyster (Crassostrea gigas) Assessed by SNP Markers]]> https://www.researchpad.co/article/5989daaaab0ee8fa60ba8ecf

In breeding industries, a challenging problem is how to keep genetic diversity over generations. To investigate genetic variation and identify breeding signatures in mass selected lines of Pacific oyster (Crassostrea gigas), three sixth-generation selected lines and four wild populations were assessed using 103 single nucleotide polymorphism (SNP) markers. The genetic diversity data indicated that the selected lines exhibited a significant reduction in the observed heterozygosity and observed number of alleles per locus compared with the wild populations (P≤0.05), indicating the selected lines tended to lose genetic diversity contrasted with the wild populations. The unweighted pair-group method with arithmetic mean (UPGMA) analysis showed that the wild populations and selected lines were not separated into two groups. Using four outlier tests, a total of 17 loci were found under selection at two levels. The global outlier detection suggested that 4 common outlier loci were subject to selection using both the hierarchical island model and Bayesian likelihood approaches. At regional level, 3 SNPs were detected as outlier using at least two outlier tests and one outlier SNP (CgSNP309) was overlapped in the two wild-selected population comparisons. The candidate outlier SNPs provide valuable resources for future association studies in C. gigas.

]]>
<![CDATA[The Influence of Organic Material and Temperature on the Burial Tolerance of the Blue Mussel, Mytilus edulis: Considerations for the Management of Marine Aggregate Dredging]]> https://www.researchpad.co/article/5989da08ab0ee8fa60b7674e

Rationale and Experimental Approach

Aggregate dredging is a growing source of anthropogenic disturbance in coastal UK waters and has the potential to impact marine systems through the smothering of benthic fauna with organically loaded screening discards. This study investigates the tolerance of the blue mussel, Mytilus edulis to such episodic smothering events using a multi-factorial design, including organic matter concentration, temperature, sediment fraction size and duration of burial as important predictor variables.

Results and Discussion

Mussel mortality was significantly higher in organically loaded burials when compared to control sediments after just 2 days. Particularly, M. edulis specimens under burial in fine sediment with high (1%) concentrations of organic matter experienced a significantly higher mortality rate (p<0.01) than those under coarse control aggregates. Additionally, mussels exposed to the summer maximum temperature treatment (20°C) exhibited significantly increased mortality (p<0.01) compared to those in the ambient treatment group (15°C). Total Oxygen Uptake rates of experimental aggregates were greatest (112.7 mmol m-2 day-1) with 1% organic loadings in coarse sediment at 20°C. Elevated oxygen flux rates in porous coarse sediments are likely to be a function of increased vertical migration of anaerobically liberated sulphides to the sediment-water interface. However, survival of M. edulis under bacterial mats of Beggiatoa spp. indicates the species’ resilience to sulphides and so we propose that the presence of reactive organic matter within the burial medium may facilitate bacterial growth and increase mortality through pathogenic infection. This may be exacerbated under the stable interstitial conditions in fine sediment and increased bacterial metabolism under high temperatures. Furthermore, increased temperature may impose metabolic demands upon the mussel that cannot be met during burial-induced anaerobiosis.

Summary

Lack of consideration for the role of organic matter and temperature during sedimentation events may lead to an overestimation of the tolerance of benthic species to smothering from dredged material.

]]>
<![CDATA[Spatio-Temporal Variation in Effects of Upwelling on the Fatty Acid Composition of Benthic Filter Feeders in the Southern Benguela Ecosystem: Not All Upwelling Is Equal]]> https://www.researchpad.co/article/5989d9efab0ee8fa60b6dbcc

Variability in mesoscale nearshore oceanographic conditions plays an important role in the distribution of primary production and food availability for intertidal consumers. Advection of nutrient rich waters by upwelling usually allows the proliferation of diatoms, later replaced by dinoflagellates. We examined upwelling effects on the fatty acid (FA) signature of a benthic intertidal filter feeder to identify its response to pulsed variability in food availability. The study took place in two contrasting seasons and at two upwelling and two non-upwelling sites interspersed within the southern Benguela upwelling system of South Africa. We investigated the FA composition of the adductor muscles and gonads of the mussel Mytilus galloprovincialis to assess how FA are apportioned to the different tissues and whether this changes between upwelling and non-upwelling conditions. In situ temperature loggers used to identify upwelling conditions at the four sites indicated that such events occurred only at the upwelling centres and only in summer. Tissues differed strongly, with gonads presenting a higher proportion of essential FAs. This could reflect the faster turnover rate of gonad tissue or preferential retention of specific FA for reproductive purposes. FA composition did not vary as a direct function of upwelling, but there were strong dissimilarities among sites. Upwelling influenced mussel diets at one upwelling site while at the other, the expected signature of upwelling was displaced downstream of the core of upwelling. Condition Index (CI) and Gonad Index (GI) differed among sites and were not influenced by upwelling, with GI being comparable among sites. In addition, FA proportions were consistent among sites, indicating similar food quality and quantity over time and under upwelling and non-upwelling conditions. This suggests that the influence of upwelling on the west coast of South Africa is pervasive and diffuse, rather than discrete; while nearshore retention or advection of upwelled water is critical and site-specific so that the effects of upwelling differ even among sites categorised as upwelling centres.

]]>
<![CDATA[Phylogeography of bivalve Meretrix petechialis in the Northwestern Pacific indicated by mitochondrial and nuclear DNA data]]> https://www.researchpad.co/article/5aafcc7a463d7e7f05234525

The marine clam Meretrix petechialis is an important economic shellfish species in Northwestern Pacific, but little is known about its phylogeographical pattern. Here, we analyzed 311 samples from 22 locations along the northwestern Pacific using combined profiling of one mitochondrial gene (the first subunit of cytochrome coxidase, COI) and one nuclear DNA marker (the internal transcribed spacer region 1, ITS-1) to investigate contemporary genetic structure and reconstruct phylogenetic history of this species. The results revealed that two distinct phylogeographic lineages dominated marginal seas—the East China Sea (ECS) and the South China Sea (SCS) respectively. The estimation of divergence time between two lineages was 2.1–3.8 Ma, corresponding to a period of the early Pleistocene to late Pliocene. The vicariance of the two lineages was connected to the historical isolation of marginal seas and sea surface temperature (SST) gradient, pointing that SST might play an important role in maintaining phylogeographical patterns of M. petachialis. Significant overlaps between two lineages were observed in 23° to 29° N, located at the adjacent area of the ECS and SCS, which might be promoted by the connectivity of China Coast Current. However, the influence of ocean currents on mixings between two lineages was limited. In comparison, significant relationships were found between genetic distances and geographic distances if the North and South populations were analyzed separately, result of which might be due to some small reciprocal, rotating flows along coastal areas and special geographical conditions.

]]>
<![CDATA[Calibrating coseismic coastal land-level changes during the 2014 Iquique (Mw=8.2) earthquake (northern Chile) with leveling, GPS and intertidal biota]]> https://www.researchpad.co/article/5989db50ab0ee8fa60bdbfbd

The April 1st 2014 Iquique earthquake (MW 8.1) occurred along the northern Chile margin where the Nazca plate is subducted below the South American continent. The last great megathrust earthquake here, in 1877 of Mw ~8.8 opened a seismic gap, which was only partly closed by the 2014 earthquake. Prior to the earthquake in 2013, and shortly after it we compared data from leveled benchmarks, deployed campaign GPS instruments, continuous GPS stations and estimated sea levels using the upper vertical level of rocky shore benthic organisms including algae, barnacles, and mussels. Land-level changes estimated from mean elevations of benchmarks indicate subsidence along a ~100-km stretch of coast, ranging from 3 to 9 cm at Corazones (18°30’S) to between 30 and 50 cm at Pisagua (19°30’S). About 15 cm of uplift was measured along the southern part of the rupture at Chanabaya (20°50’S). Land-level changes obtained from benchmarks and campaign GPS were similar at most sites (mean difference 3.7±3.2 cm). Higher differences however, were found between benchmarks and continuous GPS (mean difference 8.5±3.6 cm), possibly because sites were not collocated and separated by several kilometers. Subsidence estimated from the upper limits of intertidal fauna at Pisagua ranged between 40 to 60 cm, in general agreement with benchmarks and GPS. At Chanavaya, the magnitude and sense of displacement of the upper marine limit was variable across species, possibly due to species—dependent differences in ecology. Among the studied species, measurements on lithothamnioid calcareous algae most closely matched those made with benchmarks and GPS. When properly calibrated, rocky shore benthic species may be used to accurately measure land-level changes along coasts affected by subduction earthquakes. Our calibration of those methods will improve their accuracy when applied to coasts lacking pre-earthquake data and in estimating deformation during pre–instrumental earthquakes.

]]>
<![CDATA[Characterization of CgHIFα-Like, a Novel bHLH-PAS Transcription Factor Family Member, and Its Role under Hypoxia Stress in the Pacific Oyster Crassostrea gigas]]> https://www.researchpad.co/article/5989da10ab0ee8fa60b79585

Hypoxia-inducible factor (HIF), a critical member of the basic-helix-loop-helix (bHLH)-containing Per-Arnt-Sim (PAS) protein family, is a master transcription factor involved in maintaining oxygen homeostasis. In the present study, we isolated and characterized a novel bHLH-PAS family member, CgHIFα-like gene, from the Pacific oyster Crassostrea gigas, and determined its importance during hypoxia stress. The 3020-bp CgHIFα-like cDNA encoded a protein of 888 amino acids. The predicted CgHIFα-like amino acid sequence was conserved in the N-terminal bHLH, PAS, and PAC domains (but not in the C-terminal domain) and was most closely related to the HIF family in the bHLH-PAS protein phylogenic tree. Similar to the mammalian HIF-1α, CgHIFα-like could be expressed as four mRNA isoforms containing alternative 5′-untranslated regions and different translation initiation codons. At the mRNA level, these isoforms were expressed in a tissue-specific manner and showed increased transcription to varying degrees under hypoxic conditions. Additionally, the western blot analysis demonstrated that CgHIFα-like was induced by hypoxia. Electrophoretic mobility shift assay indicated that CgHIFα-like could bind to the hypoxia responsive element (HRE), whereas dual-luciferase reporter analysis demonstrated that CgHIFα-like could transactivate the reporter gene containing the HREs. In addition to CgHIFα-like, we identified CgARNT from the C. gigas, analyzed its expression pattern, and confirmed its interaction with CgHIFα-like using a yeast two-hybrid assay. In conclusion, this is the first report on the cloning and characterization of a novel hypoxia transcription factor in mollusks, which could accumulate under hypoxia and regulate hypoxia related gene expression by binding to HRE and dimerizing with CgARNT. As only one member of HIF has been identified in invertebrates to date, our results provide new insights into the unique mechanisms of hypoxia tolerance in mollusks.

]]>