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15. Quantitative assessment of reef foraminifera community from metabarcoding data.

Author

Girard, Elsa B., Didaskalou, Emilie A., Pratama, Andi M. A., Rattner, Carolina, Morard, Raphaël, and Renema, Willem

Subjects
CORAL reefs & islands, CORALS, CORRECTION factors, GENETIC barcoding, SEDIMENT sampling
Abstract

Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species‐specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon‐specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine‐scale processes, such as seasonal and pollution‐driven dynamics, that require high‐throughput sampling treatment. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna.

Author

Macher, Jan‐Niklas, Martínez, Alejandro, Çakir, Sude, Cholley, Pierre‐Etienne, Christoforou, Eleni, Curini Galletti, Marco, van Galen, Lotte, García‐Cobo, Marta, Jondelius, Ulf, de Jong, Daphne, Leasi, Francesca, Lemke, Michael, Rubio Lopez, Iñigo, Sánchez, Nuria, Sørensen, Martin Vinther, Todaro, M. Antonio, Renema, Willem, and Fontaneto, Diego

Subjects
BIOLOGICAL classification, BIOTIC communities, INVERTEBRATE communities, COASTAL biodiversity, GENETIC barcoding, BEACHES
Abstract

Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5‐fold increase in sequence annotation and a doubling of species‐level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell‐shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems. [ABSTRACT FROM AUTHOR]

Published
2024
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25. A global database for metacommunity ecology, integrating species, traits, environment and space

Author

Jeliazkov, Alienor, Mijatovic, Darko, Chantepie, Stéphane, Andrew, Nigel, Arlettaz, Raphaël, Barbaro, Luc, Barsoum, Nadia, Bartonova, Alena, Belskaya, Elena, Bonada, Núria, Brind’Amour, Anik, Carvalho, Rodrigo, Castro, Helena, Chmura, Damian, Choler, Philippe, Chong-Seng, Karen, Cleary, Daniel, Cormont, Anouk, Cornwell, William, de Campos, Ramiro, de Voogd, Nicole, Doledec, Sylvain, Drew, Joshua, Dziock, Frank, Eallonardo, Anthony, Edgar, Melanie J., Farneda, Fábio, Hernandez, Domingo Flores, Frenette-Dussault, Cédric, Fried, Guillaume, Gallardo, Belinda, Gibb, Heloise, Gonçalves-Souza, Thiago, Higuti, Janet, Humbert, Jean-Yves, Krasnov, Boris R., Saux, Eric Le, Lindo, Zoe, Lopez-Baucells, Adria, Lowe, Elizabeth, Marteinsdottir, Bryndis, Martens, Koen, Meffert, Peter, Mellado-Díaz, Andres, Menz, Myles H. M., Meyer, Christoph F. J., Miranda, Julia Ramos, Mouillot, David, Ossola, Alessandro, Pakeman, Robin, Pavoine, Sandrine, Pekin, Burak, Pino, Joan, Pocheville, Arnaud, Pomati, Francesco, Poschlod, Peter, Prentice, Honor C., Purschke, Oliver, Raevel, Valerie, Reitalu, Triin, Renema, Willem, Ribera, Ignacio, Robinson, Natalie, Robroek, Bjorn, Rocha, Ricardo, Shieh, Sen-Her, Spake, Rebecca, Staniaszek-Kik, Monika, Stanko, Michal, Tejerina-Garro, Francisco Leonardo, Braak, Cajo ter, Urban, Mark C., Klink, Roel van, Villéger, Sébastien, Wegman, Ruut, Westgate, Martin J., Wolff, Jonas, Żarnowiec, Jan, Zolotarev, Maxim, and Chase, Jonathan M.

Published
2020
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26. Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space

Author

Jeliazkov, Alienor, Mijatovic, Darko, Chantepie, Stéphane, Andrew, Nigel, Arlettaz, Raphaël, Barbaro, Luc, Barsoum, Nadia, Bartonova, Alena, Belskaya, Elena, Bonada, Núria, Brind’Amour, Anik, Carvalho, Rodrigo, Castro, Helena, Chmura, Damian, Choler, Philippe, Chong-Seng, Karen, Cleary, Daniel, Cormont, Anouk, Cornwell, William, de Campos, Ramiro, de Voogd, Nicole, Doledec, Sylvain, Drew, Joshua, Dziock, Frank, Eallonardo, Anthony, Edgar, Melanie J., Farneda, Fábio, Hernandez, Domingo Flores, Frenette-Dussault, Cédric, Fried, Guillaume, Gallardo, Belinda, Gibb, Heloise, Gonçalves-Souza, Thiago, Higuti, Janet, Humbert, Jean-Yves, Krasnov, Boris R., Saux, Eric Le, Lindo, Zoe, Lopez-Baucells, Adria, Lowe, Elizabeth, Marteinsdottir, Bryndis, Martens, Koen, Meffert, Peter, Mellado-Díaz, Andres, Menz, Myles H. M., Meyer, Christoph F. J., Miranda, Julia Ramos, Mouillot, David, Ossola, Alessandro, Pakeman, Robin, Pavoine, Sandrine, Pekin, Burak, Pino, Joan, Pocheville, Arnaud, Pomati, Francesco, Poschlod, Peter, Prentice, Honor C., Purschke, Oliver, Raevel, Valerie, Reitalu, Triin, Renema, Willem, Ribera, Ignacio, Robinson, Natalie, Robroek, Bjorn, Rocha, Ricardo, Shieh, Sen-Her, Spake, Rebecca, Staniaszek-Kik, Monika, Stanko, Michal, Tejerina-Garro, Francisco Leonardo, Braak, Cajo ter, Urban, Mark C., Klink, Roel van, Villéger, Sébastien, Wegman, Ruut, Westgate, Martin J., Wolff, Jonas, Żarnowiec, Jan, Zolotarev, Maxim, and Chase, Jonathan M.

Published
2020
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46. Quantifying Sub‐Seasonal Growth Rate Changes in Fossil Giant Clams Using Wavelet Transformation of Daily Mg/Ca Cycles.

Author

Arndt, Iris, Coenen, Douglas, Evans, David, Renema, Willem, and Müller, Wolfgang

Subjects
LASER ablation inductively coupled plasma mass spectrometry, INDUCTIVELY coupled plasma mass spectrometry, GEOCHEMICAL cycles, CLAMS
Abstract

Shells of the giant clam Tridacna can provide decade‐long records of past environmental conditions via their geochemical composition and structurally through growth banding. Counting the daily bands can give an accurate internal age model with high temporal resolution, but daily banding is not always visually retrievable, especially in fossil specimens. We show that daily geochemical cycles (e.g., Mg/Ca) are resolvable via highly spatially resolved laser‐ablation inductively coupled plasma mass spectrometry (LA‐ICPMS; 3 × 33 μm laser slit) in our Miocene (∼10 Ma) specimen, even in areas where daily banding is not visually discernible. By applying wavelet transformation on the measured daily geochemical cycles, we quantify varying daily growth rates throughout the shell. These growth rates are thus used to build an internal age model independent of optical daily band countability. Such an age model can be used to convert the measured elemental ratios from a function of distance to a function of time, which helps evaluate paleoenvironmental proxy data, for example, regarding the timing of sub‐seasonal events. Furthermore, the quantification of daily growth rates across the shell facilitates the evaluation of (co)dependencies between growth rates and corresponding elemental compositions. Plain Language Summary: Shells of giant clams exhibit growth bands, similar to tree rings, which form in both seasonal (visible by eye) and daily (resolvable by microscope) increments. However, the optical visibility of daily bands in fossil giant clam shells can be poor. Fortunately, growth bands are often accompanied by changes in the chemical composition of the shell. The incorporation of trace elements into the shell depends on environmental factors (like temperature and light) and biological controls, which are both characterized by cyclic daily variation. With our Python script Daydacna, we present a tool that enables daily resolution scale changes in growth rate to be evaluated using daily geochemical cycle lengths, that is, how much the shell has grown each day. Daydacna then creates an internal age model and converts the respective element compositions from being expressed over distance to being expressed over time. This information enables an unambiguous estimate of growth rate to be compared to elemental compositions, enabling (e.g.) potential (co)dependencies of these parameters to be identified. Time‐resolved data also allow to determine the timing of seasonal environmental changes, affecting the shell composition, with higher confidence and thus form an important basis for research on the seasonal aspects of the (paleo)climate. Key Points: We present an approach to quantify daily growth rates in mollusks with an internal age model based on wavelet transformation of Mg/Ca dataThe resulting highly resolved elemental data versus time can be used to evaluate the timing of (sub)seasonal environmental changesThe comparison of growth rate and elemental composition in a late‐Miocene specimen indicates a (co)dependence of Mg/Ca and growth rate [ABSTRACT FROM AUTHOR]

Published
2023
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48. Impact of dissolved CO2 on calcification in two large, benthic foraminiferal species.

Author

Dämmer, Linda Karoline, Ivkić, Angelina, de Nooijer, Lennart, Renema, Willem, Webb, Alice E., and Reichart, Gert-Jan

Subjects
CALCITE, CALCIUM carbonate, CALCIFICATION, OCEAN acidification, X-ray computed microtomography, SPECIES, ENERGY consumption
Abstract

Rising atmospheric CO2 shifts the marine inorganic carbonate system and decreases seawater pH, a process often abbreviated to 'ocean acidification'. Since acidification decreases the saturation state for crystalline calcium carbonate (e.g., calcite and aragonite), rising dissolved CO2 levels will either increase the energy demand for calcification or reduce the total amount of CaCO3 precipitated. Here we report growth of two large benthic photosymbiont-bearing foraminifera, Heterostegina depressa and Amphistegina lessonii, cultured at four different ocean acidification scenarios (400, 700, 1000 and 2200 ppm atmospheric pCO2). Using the alkalinity anomaly technique, we calculated the amount of calcium carbonate precipitated during the incubation and found that both species produced the most carbonate at intermediate CO2 levels. The chamber addition rates for each of the conditions were also determined and matched the changes in alkalinity. These results were complemented by micro-CT scanning of selected specimens to visualize the effect of CO2 on growth. The increased chamber addition rates at elevated CO2 concentrations suggest that both foraminifera species can take advantage of the increased availability of the inorganic carbon, despite a lower saturation state. This adds to the growing number of reports showing the variable response of foraminifera to elevated CO2 concentrations, which is likely a consequence of differences in calcification mechanisms. [ABSTRACT FROM AUTHOR]

Published
2023
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