Characterization of the molecular mechanisms of silicon uptake in coccolithophores.

Coccolithophores are an important group of calcifying marine phytoplankton. Although coccolithophores are not silicified, some species exhibit a requirement for Si in the calcification process. These species also possess a novel protein (SITL) that resembles the SIT family of Si transporters found in diatoms. However, the nature of Si transport in coccolithophores is not yet known, making it difficult to determine the wider role of Si in coccolithophore biology. Here, we show that coccolithophore SITLs act as Na+ -coupled Si transporters when expressed in heterologous systems and exhibit similar characteristics to diatom SITs. We find that CbSITL from Coccolithus braarudii is transcriptionally regulated by Si availability and is expressed in environmental coccolithophore populations. However, the Si requirement of C. braarudii and other coccolithophores is very low, with transport rates of exogenous Si below the level of detection in sensitive assays of Si transport. As coccoliths contain only low levels of Si, we propose that Si acts to support the calcification process, rather than forming a structural component of the coccolith itself. Si is therefore acting as a micronutrient in coccolithophores and natural populations are only likely to experience Si limitation in circumstances where dissolved silicon (DSi) is depleted to extreme levels.

Wildfires enhance phytoplankton production in tropical oceans.

Wildfire magnitude and frequency have greatly escalated on a global scale. Wildfire products rich in biogenic elements can enter the ocean through atmospheric and river inputs, but their contribution to marine phytoplankton production is poorly understood. Here, using geochemical paleo-reconstructions, a century-long relationship between wildfire magnitude and marine phytoplankton production is established in a fire-prone region of Kimberley coast, Australia. A positive correlation is identified between wildfire and phytoplankton production on a decadal scale. The importance of wildfire on marine phytoplankton production is statistically higher than that of tropical cyclones and rainfall, when strong El Niño Southern Oscillation coincides with the positive phase of Indian Ocean Dipole. Interdecadal chlorophyll-a variation along the Kimberley coast validates the spatial connection of this phenomenon. Findings from this study suggest that the role of additional nutrients from wildfires has to be considered when projecting impacts of global warming on marine phytoplankton production.

Heavy metal incorporation in foraminiferal calcite under variable environmental and acute level seawater pollution: multi-element culture experiments for Amphisorus hemprichii.

The accelerated release of heavy metals into the coastal environments due to increasing anthropogenic activities poses a severe threat to local marine ecosystems and food chains. Although some heavy metals are essential nutrients for plants and animals, higher concentrations can be toxic and hazardous. To mitigate this threat, developing quantifiable proxies for monitoring heavy metal concentrations in near-shore marine environments is essential. Here, we describe culture experiments to quantify uptake of some heavy metals using live juvenile specimens of the large benthic foraminifera (LBF) Amphisorus hemprichii collected from the subtropical waters of Rottnest Island located ~20 km offshore Perth, South West Australia. The uptake of Mn, Ni, Cd, and Pb in the newly precipitated chambers of Amphisorus hemprichii in the laboratory was characterized using the micro-analytical technique, laser ablation inductively coupled plasma mass spectrometry. We found no significant increase in Mn, Ni, Cd, and Pb incorporation in the tests of Amphisorus hemprichii with increasing temperature and light intensities. Importantly, we found that changes in the concentrations of Mn, Ni, and Cd in the A. hemprichii tests are directly proportional to those in the culture solution over a wide range of concentrations. The calculated partition coefficients for Mn, Ni, and Cd from our culture experiments are 1.3±0.2, 0.3±0.04, 2.6±0.3, respectively. These multi-element calibration studies now enable A. hemprichii to be utilized as a naturally occurring bio-archive to quantitatively monitor the anthropogenic pollution of Mn, Ni, and Cd in coastal waters.

First report of mitochondrial COI in foraminifera and implications for DNA barcoding.

Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences ("barcodes") of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.

Benthic foraminifera geochemistry as a monitoring tool for heavy metal and phosphorus pollution - A post fish-farm removal case study.

Measuring environmental contaminants in coastal areas is critical for monitoring and managing their impacts. Commonly used techniques involve repetitive field sampling, which provides a single moment in time during each effort. In this study, we examine the potential for using foraminifera in monitoring and risk assessment as recorders of bioavailable pollutants. Geochemical analysis of benthic foraminifera (Operculina ammonoides) shells sampled annually at a previous fish farm location showed extremely high levels of copper (Cu), zinc (Zn), and phosphorus (P) during the three years following the fish cages removal, with a general reduction afterwards. Levels of Cu/Ca were still more than 4-fold higher than background levels 10 years after the removal of the fish cages. Based on our finds, it is concluded that the geochemical analysis of recent benthic foraminifera shells can serve as a powerful monitoring tool of bioavailable contaminants in seawater. Additionally, the results highlight the need for heavy metal monitoring near marine aquaculture facilities and suggest that long-term effects extend spatially and temporally far beyond the original point source. Finally, we observed variations in micro-distribution of elements within the top 1-2 µm of the shells, where Cu/Ca, Zn/Ca and P/Ca are consistently higher in the chamber wall than in the septa. This observation is relevant for studies conducting single chamber analyses.

Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia.

Foraminifera are a group of mostly marine protists with high taxonomic diversity. Species identification is often complex, as both morphological and molecular approaches can be challenging due to a lack of unique characters and reference sequences. An integrative approach combining state of the art morphological and molecular tools is therefore promising. In this study, we analysed large benthic Foraminifera of the genus Amphisorus from Western Australia and Indonesia. Based on previous findings on high morphological variability observed in the Soritidae and the discontinuous distribution of Amphisorus along the coast of western Australia, we expected to find multiple morphologically and genetically unique Amphisorus types. In order to gain detailed insights into the diversity of Amphisorus, we applied micro CT scanning and shotgun metagenomic sequencing. We identified four distinct morphotypes of Amphisorus, two each in Australia and Indonesia, and showed that each morphotype is a distinct genotype. Furthermore, metagenomics revealed the presence of three dinoflagellate symbiont clades. The most common symbiont was Fugacium Fr5, and we could show that its genotypes were mostly specific to Amphisorus morphotypes. Finally, we assembled the microbial taxa associated with the two Western Australian morphotypes, and analysed their microbial community composition. Even though each Amphisorus morphotype harboured distinct bacterial communities, sampling location had a stronger influence on bacterial community composition, and we infer that the prokaryotic community is primarily shaped by the microhabitat rather than host identity. The integrated approach combining analyses of host morphology and genetics, dinoflagellate symbionts, and associated microbes leads to the conclusion that we identified distinct, yet undescribed taxa of Amphisorus. We argue that the combination of morphological and molecular methods provides unprecedented insights into the diversity of foraminifera, which paves the way for a deeper understanding of their biodiversity, and facilitates future taxonomic and ecological work.

Geochemistry of large benthic foraminifera Amphisorus hemprichii as a high-resolution proxy for lead pollution in coastal environments.

Anthropogenic lead (Pb) contamination resulting from the rapid growth of industrialization in coastal environments poses significant challenges. In this study, we report a novel approach utilising the large benthic foraminifera Amphisorus hemprichii as a biogeochemical archive for monitoring Pb pollution in tropical to warm-temperate coastal waters. Live juvenile specimens of A. hemprichii were cultured in the laboratory for 16 weeks with a range of seawater Pb concentrations. Lead uptake in both newly grown and pre-existing chambers of individual specimens was characterised using the microanalytical technique, Laser ablation-ICP mass spectrometry. We found that Pb concentration in the tests of cultured foraminifera in the laboratory is proportional to seawater [Pb] with the lead partition coefficient (KDPb) of 8.37 ± 0.3. This calibration together with a new biomineralisation model now enables A. hemprichii to be utilised as a naturally occurring bio-archive to quantitatively monitor anthropogenic Pb pollution in coastal waters.

In situ Mg isotope measurements of biogenic carbonates using laser ablation multi-collector inductively coupled plasma mass spectrometry: A new tool to understand biomineralisation.

RATIONALE: Magnesium is one of the most abundant elements in the earth's crust and in seawater. Fractionation of its stable isotopes has been shown to be a useful indicator of many geological, chemical, and biological processes. For example, biogenic carbonates display an ~5‰ range of δ26 Mg values, which is attributed to variable degrees of biological control on Mg ions during biomineralisation. Understanding this biological control is essential for developing proxies based on biogenic carbonates. METHODS: In this work, we present a new approach of measuring Mg isotopes in biogenic carbonates using Laser Ablation Multi-Collector Inductively Coupled Plasma Mass Spectrometry (LA-MC-ICPMS). RESULTS: Our results show that this microanalytical approach provides relatively fast, high spatial resolution (<0.2 µm) measurements with high precision and accuracy down to 0.2‰ (2SE). To achieve high levels of precision and accuracy, baseline interferences need to be monitored and a carbonate standard with a relatively low trace metal composition similar to biogenic carbonates should be used. We also demonstrate that the matrix effect on Mg isotopes in carbonates with low Fe and Mn is limited to less than 0.2‰ fractionation under different laser parameters and low oxide condition (<0.3% ThO/Th). CONCLUSIONS: Our newly developed LA-MC-ICPMS method and its applications to biogenic carbonates show significant advantages provided by the microanalytical approach in understanding complex processes of biomineralisation in marine calcifiers.

Investigating marine bio-calcification mechanisms in a changing ocean with in vivo and high-resolution ex vivo Raman spectroscopy.

Ocean acidification poses a serious threat to marine calcifying organisms, yet experimental and field studies have found highly diverse responses among species and environments. Our understanding of the underlying drivers of differential responses to ocean acidification is currently limited by difficulties in directly observing and quantifying the mechanisms of bio-calcification. Here, we present Raman spectroscopy techniques for characterizing the skeletal mineralogy and calcifying fluid chemistry of marine calcifying organisms such as corals, coralline algae, foraminifera, and fish (carbonate otoliths). First, our in vivo Raman technique is the ideal tool for investigating non-classical mineralization pathways. This includes calcification by amorphous particle attachment, which has recently been controversially suggested as a mechanism by which corals resist the negative effects of ocean acidification. Second, high-resolution ex vivo Raman mapping reveals complex banding structures in the mineralogy of marine calcifiers, and provides a tool to quantify calcification responses to environmental variability on various timescales from days to years. We describe the new insights into marine bio-calcification that our techniques have already uncovered, and we consider the wide range of questions regarding calcifier responses to global change that can now be proposed and addressed with these new Raman spectroscopy tools.

Foraminiferal single chamber analyses of heavy metals as a tool for monitoring permanent and short term anthropogenic footprints.

In order to establish environmentally sustainable industries there is a need for high-resolution temporal and spatial monitoring of heavy metal pollutants even at low concentrations before they become hazardous for local ecosystems. Here we present single chamber records of Cu, Zn and Pb in shells of two benthic foraminifera species with different shell types from two shallow coastal stations in Israel: An area adjacent to an electrical power plant and desalination factory (Hadera) and an industrially free nature reserve (Nachsholim). Records of both foraminifera species show elevated metal concentrations in Hadera clearly identifying the footprint of the local industrial facilities. Moreover, short-term events of elevated Cu and Pb concentrations were detected by single chamber analyses. This study demonstrates the potential of using heavy metals anomalies in foraminiferal single chambers as a tool for detecting the industrial footprint of coastal facilities as well as short term events of elevated heavy metals.

Application of 1013 ohm Faraday cup current amplifiers for boron isotopic analyses by solution mode and laser ablation multicollector inductively coupled plasma mass spectrometry.

RATIONALE: Boron isotope ratios (δ11 B values) are used as a proxy for seawater paleo-pH, amongst several other applications. The analytical precision can be limited by the detection of low intensity ion beams from limited sample amounts. High-gain amplifiers offer improvements in signal/noise ratio and can be used to increase measurement precision and reduce sample amounts. METHODS: 1013 ohm amplifier technology has previously been applied to several radiogenic systems, but has thus far not been applied to non-traditional stable isotopes. Here we apply 1013 ohm amplifier technology for the measurement of boron isotope ratios using solution mode MC-ICP-MS and laser ablation mode (LA-)MC-ICP-MS techniques. Precision is shown for reference materials as well as for low-volume foraminifera samples. RESULTS: The baseline uncertainty for a 0.1 pA 10 B+ ion beam is reduced to <0.1 ‰ for a typical measurement period. The external precision is better than 0.2 ‰ (2SD) for δ11 B measurements for solution samples containing as little as 0.8 ng total boron. For in situ microanalyses with LA-MC-ICP-MS, the external precision of 11 B/10 B from an in-house calcite standard was 1 ‰ (2SD) for individual spot analyses, and 0.3 ‰ for the mean of ≥10 replicate spot analyses. CONCLUSIONS: 1013 ohm amplifier technology is demonstrated to offer advantages for the determination of δ11 B values by both MC-ICP-MS and LA-MC-ICP-MS for small samples of biogenic carbonates, such as foraminifera shells. 1013 ohm amplifier technology will also be of benefit to other non-traditional stable isotope measurements.

Geochemical signatures of benthic foraminiferal shells from a heat-polluted shallow marine environment provide field evidence for growth and calcification under extreme warmth.

Shallow marine calcifiers play an important role as marine ecosystem engineers and in the global carbon cycle. Understanding their response to warming is essential to evaluate the fate of marine ecosystems under global change scenarios. A rare opportunity to test the effect of warming acting on natural ecosystems is by investigation of heat-polluted areas. Here, we study growth and calcification in benthic foraminifera that inhabit a thermally polluted coastal area in Israel, where they are exposed to elevated temperatures reaching up to ~42°C in summer. Live specimens of two known heat-tolerant species Lachlanella sp. 1 and Pararotalia calcariformata were collected over a period of 1 year from two stations, representing thermally polluted and undisturbed (control) shallow hard bottom habitats. Single-chamber element ratios of these specimens were obtained using laser ablation, and the Mg/Ca of the most recently grown final chambers were used to calculate their calcification temperatures. Our results provide the first direct field evidence that these foraminifera species not only persist at extreme warm temperatures but continue to calcify and grow. Species-specific Mg/Ca thermometry indicates that P. calcariformata precipitate their shells at temperatures as high as 40°C and Lachlanella sp. 1 at least up to 36°C, but both species show a threshold for calcification at cold temperatures: calcification in P. calcariformata only occurred above 22°C and in Lachlanella sp. 1 above 15°C. Our observations from the heat-polluted area indicate that under future warming scenarios, calcification in heat-tolerant foraminifera species will not be inhibited during summer, but instead the temperature window for their calcification will be expanded throughout much of the year. The observed inhibition of calcification at low temperatures indicates that the role of heat-tolerant foraminifera in carbonate production will most likely increase in future decades.

Palaeoclimate reconstructions reveal a strong link between El Niño-Southern Oscillation and Tropical Pacific mean state.

The El Niño-Southern Oscillation (ENSO) is one of the most important components of the global climate system, but its potential response to an anthropogenic increase in atmospheric CO2 remains largely unknown. One of the major limitations in ENSO prediction is our poor understanding of the relationship between ENSO variability and long-term changes in Tropical Pacific oceanography. Here we investigate this relationship using palaeorecords derived from the geochemistry of planktonic foraminifera. Our results indicate a strong negative correlation between ENSO variability and zonal gradient of sea-surface temperatures across the Tropical Pacific during the last 22 ky. This strong correlation implies a mechanistic link that tightly couples zonal sea-surface temperature gradient and ENSO variability during large climate changes and provides a unique insight into potential ENSO evolution in the future by suggesting enhanced ENSO variability under a global warming scenario.