Archive for May, 2020

The pH dependency of the boron isotopic composition of diatom opal (Thalassiosira weissflogii) (update)

The high-latitude oceans are key areas of carbon and heat exchange between the atmosphere and the ocean. As such, they are a focus of both modern oceanographic and palaeoclimate research. However, most palaeoclimate proxies that could provide a long-term perspective are based on calcareous organisms, such as foraminifera, that are scarce or entirely absent in deep-sea sediments south of 50 S in the Southern Ocean and north of 40 N in the North Pacific. As a result, proxies need to be developed for the opal-based organisms (e.g. diatoms) found at these high latitudes, which dominate the biogenic sediments recovered from these regions. Here we present a method for the analysis of the boron (B) content and isotopic composition (δ11B) of diatom opal. We apply it for the first time to evaluate the relationship between seawater pH, δ11B and B concentration ([B]) in the frustules of the diatom Thalassiosira weissflogii, cultured across a range of carbon dioxide partial pressure (pCO2) and pH values. In agreement with existing data, we find that the [B] of the cultured diatom frustules increases with increasing pH (Mejía et al., 2013). δ11B shows a relatively well defined negative trend with increasing pH, completely distinct from any other biomineral previously measured. This relationship not only has implications for the magnitude of the isotopic fractionation that occurs during boron incorporation into opal, but also allows us to explore the potential of the boron-based proxies for palaeo-pH and palaeo-CO2 reconstruction in high-latitude marine sediments that have, up until now, eluded study due to the lack of suitable carbonate material.

Continue reading ‘The pH dependency of the boron isotopic composition of diatom opal (Thalassiosira weissflogii) (update)’

Transgenerational regulation of cbln11 gene expression in the olfactory rosette of the European sea bass (Dicentrarchus labrax) exposed to ocean acidification


Cbln11 mRNA is mainly expressed in the olfactory rosettes and in the gills of European sea bass.

Cbln11 mRNA expression is localized in the non-sensory epithelium of the olfactory rosettes.

•Long term exposure to ocean acidification induces a stimulation of cbln11 mRNA expression in the olfactory rosette of European sea bass.

•Ocean acidification-induced stimulation of cbln11 mRNA expression suggests a regulation of innate immune function.


Elevated amounts of atmospheric CO2 are causing ocean acidification (OA) that may affect marine organisms including fish species. While several studies carried out in fish revealed that OA induces short term dysfunction in sensory systems including regulation of neurons activity in olfactory epithelium, information on the effects of OA on other physiological processes and actors is scarcer. In the present study we focused our attention on a European sea bass (Dicentrarchus labrax) sghC1q gene, a member of the C1q-domain-containing (C1qDC) protein family. In vertebrates, C1qDC family includes actors involved in different physiological processes including immune response and synaptic organization. Our microsynteny analysis revealed that this sghC1q gene is the orthologous gene in European sea bass to zebrafish (Danio rerio) cbln11 gene. We cloned the full length cbln11 mRNA and identified the different domains (the signal peptide, the coiled coil region and the globular C1q domain) of the deduced protein sequence. Investigation of mRNA expression by qPCR and in situ hybridization revealed that cbln11gene is especially expressed in the non-sensory epithelium of the olfactory rosette at larval and adult stages. The expression of cbln11 mRNA was analysed by qPCR in the first generation (F0) of European sea bass broodstock exposed since larval stages to water pH of 8.0 (control) or 7.6 (predicted for year 2100) and in their offspring (F1) maintained in the environmental conditions of their parents. Our results showed that cbln11 mRNA expression level was lower in larvae exposed to OA then up-regulated at adult stage in the olfactory rosette of F0 and that this up-regulation is maintained under OA at larval and juvenile stages in F1. Overall, this work provides evidence of a transgenerational inheritance of OA-induced up-regulation of cbln11 gene expression in European sea bass. Further studies will investigate the potential immune function of cbln11 gene and the consequences of these regulations, as well as the possible implications in terms of fitness and adaptation to OA in European sea bass.

Continue reading ‘Transgenerational regulation of cbln11 gene expression in the olfactory rosette of the European sea bass (Dicentrarchus labrax) exposed to ocean acidification’

Response of the red algae Pyropia yezoensis grown at different light intensities to CO2-induced seawater acidification at different life cycle stages


•Elevated CO2 enhanced conchocelis growth regardless of light intensity.

•Elevated CO2 enhanced thallus growth at high light but reduced it at low light.

•Elevated CO2 did not affect conchocelis respiration rate at either light intensity.

•Elevated CO2 increased thallus respiration rate at each light intensity.


Increasing CO2 levels in the surface water of oceans are expected to decrease oceanic pH and lead to seawater acidification. The responses of macroalgaea to this acidification of coastal waters have been studied in detail; however, most reports have focused on the adult stage only, while ignoring other life cycle stages. In this study, the economically important seaweed species Pyropia yezoensis was cultured under two CO2 concentrations (ambient CO2: 400 μatm; elevated CO2: 1000 μatm) and two light intensities (low light intensity: 80 μmol photons m−2 s−1; and high light intensity: 240 μmol photons m−2 s−1). The effects on the growth and photosynthetic performance of P. yezoensis were explored at different life cycle stages. Relative growth rates were significantly elevated at the conchocelis stage under high light intensity and elevated CO2 concentration. Moreover, the Pmax of P. yezoensis was also increased under high light intensity. However, this positive effect inversed at the thallus stage. The relative growth rate, relative electron transport rate (rETR), and net photosynthetic rate decreased at the thallus stage in response to high CO2 concentration. Under low light intensity, elevated CO2 concentration significantly increased the relative growth rates of conchocelis and thallus stages. These were 269% and 45% higher at elevated CO2 concentration compared with ambient CO2 concentrations, respectively. The Chl a and phycoerythrin levels were also higher under elevated CO2 level at the conchocelis stage. However, the rETR for the thallus stage was elevated under low light. This suggests that seawater acidification could positively affect algae at low light conditions (especially at the conchocelis stage). Different growth stages of P. yezoensis may respond differently to seawater acidification and changes of light intensity. Thalli growth stage, stocking density, and seawater depth should be considered in different areas to optimize the primary production of macroalgae.

Continue reading ‘Response of the red algae Pyropia yezoensis grown at different light intensities to CO2-induced seawater acidification at different life cycle stages’

Changes in biofilm bacterial communities in response to combined effects of hypoxia, ocean acidification and nutrients from aquaculture activity in Three Fathoms Cove


•Combined occurrence of hypoxia, acidification and nutrients increased biofilm bacterial diversity and richness

•Elevated nutrients, and depleted oxygen and pH levels resulted in different bacterial community composition

•Higher abundance of Flavobacteriales, Epsilonproteobacteria and Vibrionales, but less Oceanospirillales and Alteromonadales

•Suggests the identities of bacterial groups affected under the ocean trend of pollution, deoxygenation and acidification


Anthropogenic nutrient enrichment results in hypoxia, ocean acidification and elevated nutrients (HOAN) in coastal environments throughout the world. Here, we examined the composition of biofilm bacterial communities from a nutrient-excessive fish farm with low dissolved oxygen (DO) and pH levels using 16S rRNA gene sequencing. HOAN was accompanied by higher bacterial diversity and richness, and resulted in an altered community composition than the control site. HOAN resulted in more Flavobacteriales, Rhizobiales, Epsilonproteobacteria and Vibrionales, but less Oceanospirillales and Alteromonadales. Photobacterium sp. and Vibrio sp. were mostly found to be exclusive to HOAN conditions, suggesting that HOAN could possibly proliferate the presence of these potential pathogens. Our study suggests the complexity of bacterial communities to hypoxia and acidification in response to increased nutrient loads, along with identities of nutrient, oxygen and pH-susceptible bacterial groups that are most likely affected under this ocean trend.

Continue reading ‘Changes in biofilm bacterial communities in response to combined effects of hypoxia, ocean acidification and nutrients from aquaculture activity in Three Fathoms Cove’

Differential gene expression patterns related to lipid metabolism in response to ocean acidification in larvae and juveniles of Atlantic cod


•Larvae upregulate genes associated with fatty acid and glycogen synthesis under moderate ocean acidification (OA)

•Larvae under high levels of OA fail to regulate

•Dysfunctional metabolism and stress associated with pathologies in internal organs

•Juveniles do not differentially regulate genes under OA, associated with higher resilience and lack of physiological response to OA as a stressor at this stage


Elevated environmental carbon dioxide (pCO2) levels have been found to cause organ damage in the early life stages of different commercial fish species, including Atlantic cod (Gadus morhua). To illuminate the underlying mechanisms causing pathologies in the intestines, the kidney, the pancreas and the liver in response to elevated pCO2, we examined related gene expression patterns in Atlantic cod reared for two months under three different pCO2 regimes: 380 μatm (control), 1800 μatm (medium) and 4200 μatm (high). We extracted RNA from whole fish sampled during the larval (32 dph) and early juvenile stage (46 dph) for relative expression analysis of 18 different genes related to essential metabolic pathways. At 32 dph, larvae subjected to the medium treatment displayed an up-regulation of genes mainly associated with fatty acid and glycogen synthesis (GYS2, 6PGL, ACoA, CPTA1, FAS and PPAR1b). Larvae exposed to the high pCO2 treatment upregulated fewer but similar genes (6PGL, ACoA and PPAR1b,). These data suggest stress-induced alterations in the lipid and fatty acid metabolism and a disrupted lipid homeostasis in larvae, providing a mechanistic link to the findings of lipid droplet overload in the liver and organ pathologies. At 46 dph, no significant differences in gene expression were detected, confirming a higher resilience of juveniles in comparison to larvae when exposed to elevated pCO2 up to 4200 μatm.

Continue reading ‘Differential gene expression patterns related to lipid metabolism in response to ocean acidification in larvae and juveniles of Atlantic cod’

Device and method for continuous analysis of the concentration of dissolved inorganic carbon (DIC) and of the isotopic carbon and oxygen compositions thereof (United States Patent)


Sans-jofre, Pierre (CHARENTON-LE-PONT, FR)
Lalonde, Stefan (BREST, FR)
Liorzou, Céline (BREST, FR)

The present invention relates to a novel analysis device and method for obtaining the concentration of dissolved inorganic carbon (DIC) and isotopic carbon and oxygen concentration thereof, continuously from a liquid sample.

Continue reading ‘Device and method for continuous analysis of the concentration of dissolved inorganic carbon (DIC) and of the isotopic carbon and oxygen compositions thereof (United States Patent)’

The Olympia oyster (Ostrea lurida) at risk for local extinction: addressing climate change impacts

The Olympia oyster is native to San Francisco Bay (Ostrea lurida Carpenter 1864) (Barrett 1963). Their habitat ranges from Sitka, Alaska to Baja, California (Dall 1914). Historically, the Olympia oyster was abundant throughout the Pacific Northwest. However, their population has declined over the last few centuries due to anthropogenic influences, urbanization, and erosion (Groth and Rumrill 2009; McGraw 2009) Native Americans, pioneers, and gold miners consumed Olympia oysters which reduced the population. Remnants of native oyster shell middens around the Bay are evidence of the abundance prior to Spanish settlement. (Groth and Rumrill 2009; Coastal Conservancy and NOAA 2010). Over-harvesting reduced the oyster population and provided an opportunity to bring in non-native oysters due to the demand for oyster meat. Approximately 150 tons of oyster meat was processed (15% of the total oyster harvest represented the native oyster) during the height of the oyster industry which was from the late 1880s until 1904. (Barrett 1963). The resulting demand provided an opportunity to introduce the non-native Atlantic oyster in the San Francisco Bay, which further reduced the population of the native Olympia oyster as the nonnative Atlantic oyster was more significant in size and competed for space (Barrett 1963). Nonnative species of oysters such as the Eastern oyster from 1869-1940 and Pacific oysters from 1928-1950 were introduced into the San Francisco Bay. Ship ballasts brought in non-native species and fouling species (Ruiz et al. 2011), which preyed on the native oyster. However, the native oyster continues to live in the San Francisco Bay.

Continue reading ‘The Olympia oyster (Ostrea lurida) at risk for local extinction: addressing climate change impacts’

Maine to collect ocean acidification data with new sensors

BOOTHBAY HARBOR (AP) — Maine marine officials said three new sensors installed in a coastal community will help scientists get a better understanding of ocean acidifcation.

The growing acid levels in the ocean are a hazard for some kinds of sea life, including some of those sought by Maine fishermen. Scientists have linked acidification to factors that also drive climate change.

The Maine Department of Marine Resources said it has installed the three sensors in Boothbay Harbor. The department said the sensors will help researchers get a better understanding of how ocean acidification and dissolved oxygen levels can change the health of the state’s marine life and ecosystems.

Marine department scientist Jesica Waller said data from the sensors will also be incorporated into undergraduate programs at the University of Maine and Bigelow Laboratory for Ocean Sciences.

Continue reading ‘Maine to collect ocean acidification data with new sensors’

Coastal Rivers to host online talk on coastal acidification in Midcoast May 27

Coastal Rivers volunteers collect water quality data in the Damariscotta River estuary.

Levels of acidification can be different in coastal marine waters than in the open ocean. Inputs from freshwater rivers and nutrient runoff from land can change water chemistry in coastal areas.

Sarah Gladu and Kathleen Thornton will offer an online presentation from 4 to 6 p.m. Wednesday, May 27, about the coastal acidification and what data gathered by the Maine Coastal Observing Alliance are documenting in Midcoast Maine. They will also cover what is being done locally to better understand this problem and related water quality issues.

The presentation is free. Registration is required online at

MCOA is a coalition of nonprofits focusing on gathering water quality data along the coast from Harraseeket to Belfast Harbor. Kathleen Thornton is a research specialist at the University of Maine’s Darling Marine Center. Sarah Gladu chairs MCOA and is director of education and citizen science at Coastal Rivers.

Coastal Rivers Conservation Trust is a nonprofit, nationally accredited land trust with active programs in land conservation, water quality, trails and public access, and nature education in the Damariscotta-Pemaquid region. For more information, email or visit

Continue reading ‘Coastal Rivers to host online talk on coastal acidification in Midcoast May 27’

Porewater carbonate chemistry dynamics in a temperate and a subtropical seagrass system

Seagrass systems are integral components of both local and global carbon cycles and can substantially modify seawater biogeochemistry, which has ecological ramifications. However, the influence of seagrass on porewater biogeochemistry has not been fully described, and the exact role of this marine macrophyte and associated microbial communities in the modification of porewater chemistry remains equivocal. In the present study, carbonate chemistry in the water column and porewater was investigated over diel timescales in contrasting, tidally influenced seagrass systems in Southern California and Bermuda, including vegetated (Zostera marina) and unvegetated biomes (0–16 cm) in Mission Bay, San Diego, USA and a vegetated system (Thallasia testudinium) in Mangrove Bay, Ferry Reach, Bermuda. In Mission Bay, dissolved inorganic carbon (DIC) and total alkalinity (TA) exhibited strong increasing gradients with sediment depth. Vertical porewater profiles differed between the sites, with almost twice as high concentrations of DIC and TA observed in the vegetated compared to the unvegetated sediments. In Mangrove Bay, both the range and vertical profiles of porewater carbonate parameters such as DIC and TA were much lower and, in contrast to Mission Bay where no distinct temporal signal was observed, biogeochemical parameters followed the semi-diurnal tidal signal in the water column. The observed differences between the study sites most likely reflect a differential influence of biological (biomass, detritus and infauna) and physical processes (e.g., sediment permeability, residence time and mixing) on porewater carbonate chemistry in the different settings.

Continue reading ‘Porewater carbonate chemistry dynamics in a temperate and a subtropical seagrass system’

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Ocean acidification in the IPCC AR5 WG II

OUP book