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  • 1
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    Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors (2016)
    PANGAEA
    In:  Supplement to: Dineshram, R; Chandramouli, K; Ko, W K Ginger; Zhang, Huoming; Qian, Pei Yuan; Ravasi, Timothy; Thiyagarajan, Vengatesen (2016): Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors. Global Change Biology, 22(6), 2054-2068, https://doi.org/10.1111/gcb.13249
    Details
    Publication Date: 2024-03-15
    Description: The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life-history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change-related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression profiling using iTRAQ-LC-MS/MS identified more than 1300 proteins. Decreased pH had a negative effect on metamorphosis by down-regulating several proteins involved in energy production, metabolism, and protein synthesis. However, warming switched on these down-regulated pathways at pH 7.4. Under multiple stressors, cell signaling, energy production, growth, and developmental pathways were up-regulated, although metamorphosis was still reduced. Despite the lack of lethal effects, significant physiological responses to both individual and interacting climate change related stressors were observed at proteome level. The metamorphosing larvae of the C. gigas population in the Yellow Sea appear to have adequate phenotypic plasticity at the proteome level to survive in future coastal oceans, but with developmental and physiological costs.
    Keywords: Accession number; Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Bicarbonate ion; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); Crassostrea gigas; EXP; Experiment; Fold change; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Gene expression (incl. proteomics); Identification; Individuals; Jiaozhou_Bay; Laboratory experiment; Mollusca; Mortality/Survival; North Pacific; Number of expressed proteins; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; pH, standard deviation; Proteins; Registration number of species; Salinity; Salinity, standard deviation; Single species; Species; Survival; Temperate; Temperature; Temperature, water; Temperature, water, standard deviation; Treatment; Type; Uniform resource locator/link to reference; Zooplankton
    Type: Dataset
    Format: text/tab-separated-values, 269779 data points
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    DATA PANGAEA
  • 2
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    Seawater carbonate chemistry and calcification of juvenile Pocillopora damicornis (2017)
    PANGAEA
    In:  Supplement to: Jiang, Lei; Zhang, Fang; Guo, Ming-Lan; Guo, Ya Juan; Zhang, Yuyang; Zhou, Guowei; Cai, Lin; Lian, Jian-Sheng; Qian, Pei Yuan; Huang, Hui (2018): Increased temperature mitigates the effects of ocean acidification on the calcification of juvenile Pocillopora damicornis, but at a cost. Coral Reefs, 37(1), 71-79, https://doi.org/10.1007/s00338-017-1634-1
    Details
    Publication Date: 2024-03-15
    Description: This study tested the interactive effects of increased seawater temperature and CO2 partial pressure (pCO2) on the photochemistry, bleaching, and early growth of the reef coral Pocillopora damicornis. New recruits were maintained at ambient or high temperature (29 or 30.8 °C) and pCO2 (500 and 1100 µatm) in a full-factorial experiment for 3 weeks. Neither a sharp decline in photochemical efficiency (Fv/Fm) nor evident bleaching was observed at high temperature and/or high pCO2. Furthermore, elevated temperature greatly promoted lateral growth and calcification, while polyp budding exhibited temperature-dependent responses to pCO2. High pCO2 depressed calcification by 28% at ambient temperature, but did not impact calcification at 30.8 °C. Interestingly, elevated temperature in concert with high pCO2 significantly retarded the budding process. These results suggest that increased temperature can mitigate the adverse effects of acidification on the calcification of juvenile P. damicornis, but at a substantial cost to asexual budding.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Aragonite saturation state, standard deviation; Benthic animals; Benthos; Bicarbonate ion; Bleaching; Budding rate; Calcification/Dissolution; Calcification rate; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Cnidaria; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); EXP; Experiment; Experiment duration; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Growth/Morphology; Growth rate; Laboratory experiment; Luhuitou_fringing_reef; Maximum photochemical quantum yield of photosystem II; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); pH; pH, standard deviation; Pocillopora damicornis; Potentiometric; Potentiometric titration; Primary production/Photosynthesis; Registration number of species; Salinity; Single species; Species; Temperature; Temperature, water; Temperature, water, standard deviation; Tropical; Type; Uniform resource locator/link to reference
    Type: Dataset
    Format: text/tab-separated-values, 9660 data points
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    DATA PANGAEA
  • 3
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    Analysis of Pacific oyster larval proteome and its response to high-CO2 (2012)
    PANGAEA
    In:  Supplement to: Dineshram, R; Wong, Kevin K W; Shu, Xiao; Yu, Ziniu; Qian, Pei Yuan; Thiyagarajan, Vengatesen (2012): Analysis of Pacific oyster larval proteome and its response to high-CO2. Marine Pollution Bulletin, 64(10), 2160-2167, https://doi.org/10.1016/j.marpolbul.2012.07.043
    Details
    Publication Date: 2024-03-15
    Description: Most calcifying organisms show depressed metabolic, growth and calcification rates as symptoms to high-CO(2) due to ocean acidification (OA) process. Analysis of the global expression pattern of proteins (proteome analysis) represents a powerful tool to examine these physiological symptoms at molecular level, but its applications are inadequate. To address this knowledge gap, 2-DE coupled with mass spectrophotometer was used to compare the global protein expression pattern of oyster larvae exposed to ambient and to high-CO(2). Exposure to OA resulted in marked reduction of global protein expression with a decrease or loss of 71 proteins (18% of the expressed proteins in control), indicating a wide-spread depression of metabolic genes expression in larvae reared under OA. This is, to our knowledge, the first proteome analysis that provides insights into the link between physiological suppression and protein down-regulation under OA in oyster larvae.
    Keywords: Alkalinity, total; Animalia; Aragonite saturation state; Bicarbonate ion; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); Crassostrea gigas; Duration, number of days; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Gene expression (incl. proteomics); Growth/Morphology; Identification; Laboratory experiment; Mollusca; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; Protein name; Replicate; Salinity; Shell length; Single species; Species; Spot intensity, relative; Temperature, water; Treatment; Tropical; Zooplankton
    Type: Dataset
    Format: text/tab-separated-values, 1861 data points
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    DATA PANGAEA
  • 4
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    Seawater carbonate chemistry and physiological responses of coral recruits (2019)
    PANGAEA
    Details
    Publication Date: 2024-03-20
    Description: Diurnal pCO2 fluctuations have the potential to modulate the biological impact of ocean acidification (OA) on reef calcifiers, yet little is known about the physiological and biochemical responses of scleractinian corals to fluctuating carbonate chemistry under OA. Here, we exposed newly settled Pocillopora damicornis for 7 days to ambient pCO2, steady and elevated pCO2 (stable OA) and diurnally fluctuating pCO2 under future OA scenario (fluctuating OA). We measured the photo-physiology, growth (lateral growth, budding and calcification), oxidative stress and activities of carbonic anhydrase (CA), Ca-ATPase and Mg-ATPase. Results showed that while OA enhanced the photochemical performance of in hospite symbionts, it also increased catalase activity and lipid peroxidation. Furthermore, both OA treatments altered the activities of host and symbiont CA, suggesting functional changes in the uptake of dissolved inorganic carbon (DIC) for photosynthesis and calcification. Most importantly, only the fluctuating OA treatment resulted in a slight drop in calcification with concurrent up-regulation of Ca-ATPase and Mg-ATPase, implying increased energy expenditure on calcification. Consequently, asexual budding rates decreased by 50% under fluctuating OA. These results suggest that diel pCO2 oscillations could modify the physiological responses and potentially alter the energy budget of coral recruits under future OA, and that fluctuating OA is more energetically expensive for the maintenance of coral recruits than stable OA.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Aragonite saturation state, standard deviation; Benthic animals; Benthos; Bicarbonate ion; Biomass per individual; Budding rate; Calcification/Dissolution; Calcification per individual; Calcite saturation state; Calcium adenosine triphosphatase activity; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Catalase, unit per protein mass; Catalase activity, unit per protein mass; Cnidaria; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); Effective quantum yield; Excitation pressure; EXP; Experiment; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Growth/Morphology; Growth rate; Identification; Laboratory experiment; Lipid peroxidation, per protein; Luhuitou_reef; Magnesium adenosine triphosphatase activity; Maximum quantum yield of photosystem II; Non photochemical quenching; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Other; Other metabolic rates; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); pH; pH, standard deviation; Pocillopora damicornis; Potentiometric; Potentiometric titration; Primary production/Photosynthesis; Registration number of species; Reproduction; Salinity; Salinity, standard deviation; Single species; Species; Temperature, water; Temperature, water, standard deviation; Time point, descriptive; Treatment; Tropical; Type; Uniform resource locator/link to reference
    Type: Dataset
    Format: text/tab-separated-values, 10497 data points
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    DATA PANGAEA
  • 5
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    Toward an understanding of the molecular mechanisms of barnacle larval settlement : a comparative transcriptomic approach (2011)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e22913, doi:10.1371/journal.pone.0022913.
    Description: The barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement. Using 454 pyrosequencing, we collected totally 630,845 reads including 215,308 from the larval stages and 415,537 from the adults; 23,451 contigs were generated while 77,785 remained as singletons. We annotated 31,720 of the 92,322 predicted open reading frames, which matched hits in the NCBI NR database, and identified 7,954 putative genes that were differentially expressed between the larval and adult stages. Of these, several genes were further characterized with quantitative real-time PCR and in situ hybridization, revealing some key findings: 1) vitellogenin was uniquely expressed in late nauplius stage, suggesting it may be an energy source for the subsequent non-feeding cyprid stage; 2) the locations of mannose receptors suggested they may be involved in the sensory system of cyprids; 3) 20 kDa-cement protein homologues were expressed in the cyprid cement gland and probably function during attachment; and 4) receptor tyrosine kinases were expressed higher in cyprid stage and may be involved in signal perception during larval settlement. Our results provide not only the basis of several new hypotheses about gene functions during larval settlement, but also the availability of this large transcriptome dataset in B. amphitrite for further exploration of larval settlement and developmental pathways in this important marine species.
    Description: This work was supported by grants (N-HKUST602/09 and AoE/P-04/04-II) from the Research Grants Council of the Hong Kong Special Administrative Region and an award (SA-C0040/UK-C0016) made by KAUST to P-Y Qian.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: application/msword
    Format: application/vnd.ms-excel
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  • 6
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    Population genetic structure of the deep‐sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific (2018)
    John Wiley & Sons
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Evolutionary Applications 11 (2018): 1915-1930, doi:10.1111/eva.12696.
    Description: Studying population genetics of deep‐sea animals helps us understand their history of habitat colonization and population divergence. Here, we report a population genetic study of the deep‐sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) widely distributed in chemosynthesis‐based ecosystems in the Northwest Pacific. Three mitochondrial genes (i.e., atp6, cox1, and nad4) and 6,398 genomewide single nucleotide polymorphisms (SNPs) were obtained from 110 individuals from four hydrothermal vents and two methane seeps. When using the three mitochondrial genes, nearly no genetic differentiation was detected for B. platifrons in the Northwest Pacific. Nevertheless, when using SNP datasets, all individuals in the South China Sea (SCS) and three individuals in Sagami Bay (SB) together formed one genetic cluster that was distinct from the remaining individuals. Such genetic divergence indicated a genetic barrier to gene flow between the SCS and the open Northwest Pacific, resulting in the co‐occurrence of two cryptic semi‐isolated lineages. When using 125 outlier SNPs identified focusing on individuals in the Okinawa Trough (OT) and SB, a minor genetic subdivision was detected between individuals in the southern OT (S‐OT) and those in the middle OT (M‐OT) and SB. This result indicated that, although under the influence of the Kuroshio Current and the North Pacific Intermediate Water, subtle geographic barriers may exist between the S‐OT and the M‐OT. Introgression analyses based on these outlier SNPs revealed that Hatoma Knoll in the S‐OT represents a possible contact zone for individuals in the OT‐SB region. Furthermore, migration dynamic analyses uncovered stronger gene flow from Dai‐yon Yonaguni Knoll in the S‐OT to the other local populations, compared to the reverse directions. Taken together, the present study offered novel perspectives on the genetic connectivity of B. platifrons mussels, revealing the potential interaction of ocean currents and geographic barriers with adaption and reproductive isolation in shaping their migration patterns and genetic differentiation in the Northwest Pacific.
    Description: General Research Fund Grant Number: HKBU12302917; Hong Kong Baptist University Grant Number: 15‐1012‐P04
    Keywords: Bathymodiolus ; Deep‐sea ; Genetic structure ; Introgression ; Migration patterns ; Mitochondrial genes ; Population connectivity ; RAD‐seq
    Repository Name: Woods Hole Open Access Server
    Type: Article
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    PAPER (OA)
  • 7
    Electronic Resource
    Electronic Resource
    A distinctive epibiotic bacterial community on the soft coral Dendronephthya sp. and antibacterial activity of coral tissue extracts suggest a chemical mechanism against bacterial epibiosis (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 43 (2003), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Different bacterial community profiles were observed on the soft coral Dendronephthya sp. and an inanimate reference site using terminal restriction fragment length polymorphism analysis of bacterial community DNA. To correlate the observation with a chemical defense mechanism against bacterial epibiosis, antibacterial effects of coral tissue extracts and waterborne products of coral-associated bacterial isolates (11 morphotypes) were tested against indigenous benthic bacterial isolates (33 morphotypes) obtained in the vicinity of the coral colonies. The coral tissue extracts and waterborne products of coral-associated bacteria inhibited growth and attachment of indigenous bacterial isolates, suggesting an endogenous chemical and an exogenous biological mechanism against bacterial epibiosis in this soft coral.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6941.2003.tb01074.x
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  • 8
    Electronic Resource
    Electronic Resource
    A bacterial culture-independent method to investigate chemically mediated control of bacterial epibiosis in marine invertebrates by using TRFLP analysis and natural bacterial populations (2004)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 47 (2004), S. 0 
    Details
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: It has been postulated that a variety of physically undefended marine invertebrates have evolved strategies to control microbial epibiosis chemically. Ecologically meaningful experiments that demonstrate chemically mediated antibacterial effects are difficult due to the small number of cultivable bacteria. Based on the example of three sponges, this study introduces a culture-independent methodology to investigate chemically mediated control of bacterial epibiosis by analyzing the natural bacterial consortia. Organic extracts of sponges were immobilized in hydrogels at tissue level concentrations and exposed to the same source of natural seawater for bacterial colonization. Terminal restriction fragment length polymorphism analysis of polymerase chain reaction-amplified bacterial community DNA obtained from these gels was shown to be a useful tool to study bacterial community shifts in response to sponge metabolites by comparing bacterial ribotypes obtained from the gel surfaces. Several terminal restriction fragments were absent relative to the control suggesting that settlement of specific bacteria was prevented. On the other hand, additional fragments occurred in some treatments, coinciding with higher bacterial abundance evidenced by DAPI counts of bacterial cells, indicating the bacterial utilization of sponge extract components. The advantages of this method are (1) a culture-independent approach, i.e. the assessment of antimicrobial activities against natural bacterial communities, (2) no restriction to particular modes of microbial colonization, i.e. antibiotic and repellant, and (3) the in situ assessment of antimicrobial compounds under flow conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0168-6496(03)00246-0
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  • 9
    Electronic Resource
    Electronic Resource
    Analysing energy content: a new micro-assay and an assessment of the applicability of acid dichromate assays (1998)
    Springer
    Hydrobiologia 390 (1998), S. 141-151 
    Details
    ISSN: 1573-5117
    Keywords: carbohydrate ; early juvenile ; egg ; embryos ; larvae ; lipid ; organic carbon ; protein
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This study describes a micro-assay, based on acid dichromate oxidation, with a resolution of at least 0.5 μg organic carbon and an upper limit of ≤20 μg C. We also document several important properties of acid dichromate assays and establish their effectiveness for quantifying organic carbon and energy content of marine and freshwater organisms. Both the micro-assay and the previously described standard assay are highly sensitive to chloride: absorbance readings were significantly depressed by the presence of only 0.5–1.0 μl of seawater, and the effect of seawater was shown to be due to its chloride content. The amount of chloride contained within the bodies of very small marine organisms may therefore be sufficient to interfere with the assay. Contrary to previous claims, we found that incubating samples with phosphoric acid did not prevent chloride from interfering with the assays. The micro- and standard assays were not sensitive to inorganic carbon and were therefore specific to organic carbon. The assays were effective in estimating total energy content of carbohydrate and lipid material, but underestimated the energy content of protein material by 47–69%. This limitation can be overcome by using a protein micro-assay to correct for underestimation by the acid dichromate assays. Based on our findings, the reliability of acid dichromate oxidation assays for analysing samples of marine organisms is questionable. The assays are effective, however, for analysing chloride-free tissues or extracts. In addition, the assays have considerable potential for determining energy content of small freshwater organisms. In particular, the micro-assay is at least an order of magnitude more sensitive than the standard assay, and constitutes a relatively simple way of measuring energy content of very small samples, such as individual embryos or early juveniles of aquatic animals and plants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003598828105
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  • 10
    Electronic Resource
    Electronic Resource
    Larval settlement of polychaetes (1999)
    Springer
    Hydrobiologia 402 (1999), S. 239-253 
    Details
    ISSN: 1573-5117
    Keywords: larval settlement ; chemical settlement cues ; larval settlement inducers ; juveniles ; metamorphosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Many benthic marine invertebrate species have a dispersive larval stage in their life histories. Larvae typically spend hours, weeks, or months developing in plankton before they become competent to settle and metamorphose. Recruitment to benthic populations depends on the numbers of competent larvae transported to sites and/or the interaction between larvae and the surface of substratum. While there is considerable evidence that on large spatial scales, the number of competent larvae transported to sites is determined primarily by hydrodynamics, success of larval settlement on small spatial scales is mediated by biotic and abiotic characteristics of substratum. Larvae of many marine polychaetes require specific cues to settle and metamorphose. Cues can originate from conspecific or congeneric individuals, microbial films, sympatric species, food items, or habitat. Larval settlement in an individual species can be controlled by a single cue or a mixture of cues. Larval settlement of multiple species can be mediated by a common cue or a mixture of cues. Although a variety of chemicals, including proteins, free fatty acids, polysaccharides, inorganic ions, and neurotransmitters, have been suggested as inducing larval settlement of marine polychaetes, few natural cues have been isolated and structurally identified.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003704928668
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