Posts Tagged 'methods'

Investigating controls on boron isotope ratios in shallow marine carbonates

The boron isotope-pH proxy has been widely used to reconstruct past ocean pH values. In both planktic foraminifera and corals, species-specific calibrations are required in order to reconstruct absolute values of pH, due to the prevalence of so-called vital effects — physiological modification of the primary environmental signals by the calcifying organisms. Shallow marine abiotic carbonate (e.g. ooids and cements) could conceivably avoid any such calibration requirement, and therefore provide a potentially useful archive for reconstructions in deep (pre-Cenozoic) time. However, shallow marine abiotic carbonates could also be affected by local shifts in pH caused by microbial photosynthesis and respiration, something that has up to now not been fully tested. In this study, we present boron isotope measurements from shallow modern marine carbonates, from the Bahama Bank and Belize to investigate the potential of using shallow water carbonates as pH archives, and to explore the role of microbial processes in driving nominally ‘abiogenic’ carbonate deposition. For Bahama bank samples, our boron-based pH estimates derived from a range of carbonate types (i.e. ooids, peloids, hardground cements, carbonate mud, stromatolitic micrite and calcified filament micrite) are higher than the estimated modern mean-annual seawater pH values for this region. Furthermore, the majority (73%) of our marine carbonate-based pH estimates fall out of the range of the estimated pre-industrial seawater pH values for this region. In shallow sediment cores, we did not observe a correlation between measured pore water pH and boron-derived pH estimates, suggesting boron isotope variability is a depositional rather than early diagenetic signal. For Belize reef cements, conversely, the pH estimates are lower than likely in situ seawater pH at the time of cement formation. This study indicates the potential for complications when using shallow marine non-skeletal carbonates as marine pH archives. In addition, variability in δ11B based pH estimates provides additional support for the idea that photosynthetic CO2 uptake plays a significant role in driving carbonate precipitation in a wide range of shallow water carbonates.

Continue reading ‘Investigating controls on boron isotope ratios in shallow marine carbonates’

Development and application of foraminiferal carbonate system proxies to quantify ocean acidification in the California Current

The oceanic uptake of anthropogenic carbon has mitigated climate change, but has also resulted in a global average 0.1 decline in surface ocean pH over 20th century known as ocean acidification. The parallel reduction in carbonate ion concentration ([CO32-]) and the saturation state of seawater (Ω) has caused many major calcium carbonate-secreting organisms such as planktonic foraminifera to exhibit impaired calcification. We develop proxy calibrations and down core records that use calcification and geochemical characteristics of planktonic foraminifera as proxies for the marine carbonate system. This study focuses specifically on the surface ocean chemistry of the California Current Ecosystem (CCE), which has been identified as a region of rapidly progressing ocean acidification due to natural upwelling processes and the low buffering capacity of these waters. The calibration portion of this study uses marine sediments collected by the Santa Barbara Basin (SBB), California sediment-trapping program located in the central region of the CCE. We calibrate the relationships of Globigerina bulloides calcification intensity to [CO3 2-] and the B/Ca ratios of G. bulloides, Neogloboquadrina dutertrei and Neogloboquadrina incompta shells to Ω calcite using in situ measurements and model simulations of these independent variables. By applying these proxy methods to down core, our records from the SBB indicate a 20% reduction in foraminiferal calcification since ~1900, translating to a 35% decline in [CO 32-] in the CCE over this period. Our high-resolution calcification record also reveals a substantial interannual to decadal modulation of ocean acidification in the CCE related to the sign of Pacific Decadal Oscillation and El Niño Southern Oscillation. In the future we can expect these climatic modes to both enhance and moderate anthropogenic ocean acidification. Based on our historic record, we predict that if atmospheric CO2 reaches 540 ppm by the year 2100 as predicted by a conservative CO3 pathway, [CO32-] will experience a net reduction of 55%, resulting in at least a 30% reduction in calcification of planktonic foraminifera that will likely be mirrored by other adversely affected marine calcifiers.

Continue reading ‘Development and application of foraminiferal carbonate system proxies to quantify ocean acidification in the California Current’

The uronic acid content of coccolith-associated polysaccharides provides insight into coccolithogenesis and past climate

Unicellular phytoplanktonic algae (coccolithophores) are among the most prolific producers of calcium carbonate on the planet, with a production of ∼1026 coccoliths per year. During their lith formation, coccolithophores mainly employ coccolith-associated polysaccharides (CAPs) for the regulation of crystal nucleation and growth. These macromolecules interact with the intracellular calcifying compartment (coccolith vesicle) through the charged carboxyl groups of their uronic acid residues. Here we report the isolation of CAPs from modern day coccolithophores and their prehistoric predecessors and we demonstrate that their uronic acid content (UAC) offers a species-specific signature. We also show that there is a correlation between the UAC of CAPs and the internal saturation state of the coccolith vesicle that, for most geologically abundant species, is inextricably linked to carbon availability. These findings suggest that the UAC of CAPs reports on the adaptation of coccolithogenesis to environmental changes and can be used for the estimation of past CO2 concentrations.

Continue reading ‘The uronic acid content of coccolith-associated polysaccharides provides insight into coccolithogenesis and past climate’

Using prokaryotes for carbon capture storage

Geological storage of CO2 is a fast-developing technology that can mitigate rising carbon emissions. However, there are environmental concerns with the long-term storage and implications of a leak from a carbon capture storage (CCS) site. Traditional monitoring lacks clear protocols and relies heavily on physical methods. Here, we discuss the potential of biotechnology, focusing on microbes with a natural ability to utilize and assimilate CO2 through different metabolic pathways. We propose the use of natural microbial communities for CCS monitoring and CO2 utilization, and, with examples, demonstrate how synthetic biology may maximize CO2 uptake within and above storage sites. An integrated physical and biological approach, combined with metagenomics data and biotechnological advances, will enhance CO2 sequestration and prevent large-scale leakages.


Microorganisms have the ability to respond quickly to environmental changes and to bind CO2, potentially removing it from the surrounding environment.

High-throughput sequencing can be used to identify the microbial metagenomic fingerprint, which can be used to develop simplified, efficient genetic methods to monitor CCS sites.

CCS monitoring would be most effective with a multidisciplinary monitoring program, combining geology, biogeochemistry, physics, microbiology, molecular biology, and genomics.

The advances in our knowledge in prokaryotic genomics, metabolic pathways, microbial communities, and the potential to engineer CO2 binding properties in microbes provide opportunities for transforming CCS sites into bioreactors for value-added chemicals.

Continue reading ‘Using prokaryotes for carbon capture storage’

KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)

Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans). The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2 levels. The database gives access to: 1) the full list of assembled genes and transcripts; 2) their level of similarity to transcripts and proteins from other species; 3) the predicted protein domains contained within each transcript; 4) their predicted GO terms; 5) the level of expression of each transcript in the different larval stages and CO2 treatments. All references to external entities (sequences, domains, GO terms) are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web.

Continue reading ‘KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)’

Quantitative analysis of anthropogenic influences on coastal water – A new perspective

Coastal environment has been disturbed by human activities for a long time, especially in the rapidly urbanizing and industrializing areas. Although the surrounding area has achieved great economic success in the past 30 years, Western Xiamen Bay (China) is seriously affected by pollutants and is facing increasing ecological pressure. Because of this, Xiamen was selected in 1994 as a demonstration site for implementing an integrated coastal management program, which included a series of measures for protecting the coastal environment. However, coastal environment is dynamic, complex and site-specific, and thus a scientific quantitative evaluation framework is necessary for environment quality analysis and effective coastal management. In this study, we used oceanographic knowledge together with quantitative methods (Bai-Perron’s structural break test) to analyze the long-term variations of water quality indices (pH, DO, COD, DIN, PO4-P and Oil) in Western Xiamen Bay. In addition, we compared with other coastal areas to identify the effectiveness of phosphorus-based nutrient management measures and predicted the probable variation trend in the future. The results show that in Western Xiamen Bay: (1) the concentrations of DO and Oil in seawater are effectively controlled by local coastal management measures; (2) seawater acidification will continue to worsen based on the present situation; and (3) the P-limitation treatment strategies are effective and PO4-P concentration starts to fall according to the multiple statistical analysis and Environmental Kuznets Curve. This paper hopes to provide an epitome of the conflicts and consolations between socioeconomic development and environmental quality in the past, and hints for coastal management in the future.

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Conus Shell δ13C values as proxies for δ13CDIC in tropical waters

We use time-series δ18O and δ13C data from seawater and live-collected Conus shells from Panama’s Pacific coast to test the fidelity of the gastropod’s δ13C values as a proxy for the δ13C of marine dissolved inorganic carbon (DIC), and the potential of δ18O-δ13C correlations in shell profiles for resolving relative magnitudes of seasonal upwelling and freshening. Water samples were collected from March 2011 to August 2012 from Naos Island Marine Laboratory, and Conus specimens were collected from nearby Veracruz Beach in July 2013. In general, patterns corresponded with seasonal changes in rainfall and upwelling on the Pacific coast of Panama. During the long rainy season, the upwelling signal is absent and seawater salinity, δ18O, and δ13CDIC all decline. During the dry season, the upwelling signal increases and runoff declines increasing salinity, δ18O, and δ13CDIC values. Shell δ13C values strongly correlate with measured δ13CDIC values, but are lower than expected equilibrium for aragonite by approximately + 2‰ reflecting the incorporation of light metabolic C. The co-dependences of δ18O and δ13C provide reliable indicators of upwelling (negative correlation) and freshening (positive correlation) for nearshore environments, allowing for the study of historical climate change and upwelling based on beach-collected museum specimens.

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Ocean acidification in the IPCC AR5 WG II

OUP book