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2. Marine phycotoxin levels in shellfish—14 years of data gathered along the Italian coast

Author

Accoroni, Stefano, Cangini, Monica, Angeletti, Roberto, Losasso, Carmen, Bacchiocchi, Simone, Costa, Antonella, Taranto, Aurelia Di, Escalera, Laura, Fedrizzi, Giorgio, Garzia, Angela, Longo, Francesca, Macaluso, Andrea, Melchiorre, Nunzia, Milandri, Anna, Milandri, Stefania, Montresor, Marina, Neri, Francesca, Piersanti, Arianna, Rubini, Silva, Suraci, Chiara, Susini, Francesca, Vadrucci, Maria Rosaria, Mudadu, Alessandro Graziano, Vivaldi, Barbara, Soro, Barbara, Totti, Cecilia, and Zingone, Adriana

Published
2024
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5. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J, Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R, Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B, Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, and Jaillon, Olivier

Subjects
Genetics, Life Below Water, Atmospheric Sciences, Geochemistry, Oceanography, Meteorology & Atmospheric Sciences
Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.

Published
2019

6. Automated next-generation profiling of genomic alterations in human cancers

Author

Keefer, Laurel A., White, James R., Wood, Derrick E., Gerding, Kelly M. R., Valkenburg, Kenneth C., Riley, David, Gault, Christopher, Papp, Eniko, Vollmer, Christine M., Greer, Amy, Hernandez, James, McGregor, III, Paul M., Zingone, Adriana, Ryan, Bríd M., Deak, Kristen, McCall, Shannon J., Datto, Michael B., Prescott, James L., Thompson, John F., Cerqueira, Gustavo C., Jones, Siân, Simmons, John K., McElhinny, Abigail, Dickey, Jennifer, Angiuoli, Samuel V., Diaz, Jr., Luis A., Velculescu, Victor E., and Sausen, Mark

Published
2022
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10. DRD1 suppresses cell proliferation and reduces EGFR activation and PD‐L1 expression in NSCLC.

Author

Grant, Christopher E., Flis, Amy L., Toulabi, Leila, Zingone, Adriana, Rossi, Emily, Aploks, Krist, Sheppard, Heather, and Ryan, Bríd M.

Abstract

Dopamine (DA) acts in various key neurological and physiological processes as both a neurotransmitter and circulating hormone. Over the past several decades, the DA signaling network has been shown to regulate the progression of several types of solid tumors, and considerable evidence has shown it is a druggable pathway in the cancer cell context. However, the specific activity and effect of these pathway components appears to be tissue‐type and cell‐context‐dependent. In the present study, expression and methylation of dopamine receptor D1 (DRD1) were measured using RNA sequencing (RNAseq) and reverse transcription polymerase chain reaction (RT‐PCR) in non‐small cell lung cancer (NSCLC) samples, and validated using publicly available datasets, including The Cancer Genome Atlas (TCGA). In vitro and in vivo functional experiments were performed for cell proliferation and tumor growth, respectively. Mechanistic analyses of the transcriptome and kinome in DRD1‐modulated cells informed further experiments, which characterized the effects on the epidermal growth factor receptor (EGFR) pathway and programmed cell death 1 ligand 1 (PD‐L1) proteins. Through these experiments, we identified the DRD1 gene as a negative regulator of disease progression in NSCLC. We show that DRD1, as well as other DA pathway components, are expressed in normal human lung tissue, and that loss of DRD1 expression through promoter hypermethylation is a common feature in NSCLC patients and is associated with worse survival. At the cellular level, DRD1 affects proliferation by inhibiting the activation of EGFR and mitogen‐activated protein kinase 1/2 (ERK1/2). Interestingly, we also found that DRD1 regulates the expression of PD‐L1 in lung cancer cells. Taken together, these results suggest that DRD1 methylation may constitute a biomarker of poor prognosis in NSCLC patients while other components of this pathway could be targeted to improve response to EGFR‐ and PD‐L1‐targeted therapies. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Perceived global increase in algal blooms is attributable to intensified monitoring and emerging bloom impacts

Author

Hallegraeff, Gustaaf M., Anderson, Donald M., Belin, Catherine, Bottein, Marie-Yasmine Dechraoui, Bresnan, Eileen, Chinain, Mireille, Enevoldsen, Henrik, Iwataki, Mitsunori, Karlson, Bengt, McKenzie, Cynthia H., Sunesen, Inés, Pitcher, Grant C., Provoost, Pieter, Richardson, Anthony, Schweibold, Laura, Tester, Patricia A., Trainer, Vera L., Yñiguez, Aletta T., and Zingone, Adriana

Published
2021
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16. The founding charter of the Genomic Observatories Network

Author

Davies, Neil, Field, Dawn, Amaral-Zettler, Linda, Clark, Melody S, Deck, John, Drummond, Alexei, Faith, Daniel P, Geller, Jonathan, Gilbert, Jack, Glöckner, Frank Oliver, Hirsch, Penny R, Leong, Jo-Ann, Meyer, Chris, Obst, Matthias, Planes, Serge, Scholin, Chris, Vogler, Alfried P, Gates, Ruth D, Toonen, Rob, Berteaux-Lecellier, Véronique, Barbier, Michèle, Barker, Katherine, Bertilsson, Stefan, Bicak, Mesude, Bietz, Matthew J, Bobe, Jason, Bodrossy, Levente, Borja, Angel, Coddington, Jonathan, Fuhrman, Jed, Gerdts, Gunnar, Gillespie, Rosemary, Goodwin, Kelly, Hanson, Paul C, Hero, Jean-Marc, Hoekman, David, Jansson, Janet, Jeanthon, Christian, Kao, Rebecca, Klindworth, Anna, Knight, Rob, Kottmann, Renzo, Koo, Michelle S, Kotoulas, Georgios, Lowe, Andrew J, Marteinsson, Viggó Thór, Meyer, Folker, Morrison, Norman, Myrold, David D, Pafilis, Evangelos, Parker, Stephanie, Parnell, John Jacob, Polymenakou, Paraskevi N, Ratnasingham, Sujeevan, Roderick, George K, Rodriguez-Ezpeleta, Naiara, Schonrogge, Karsten, Simon, Nathalie, Valette-Silver, Nathalie J, Springer, Yuri P, Stone, Graham N, Stones-Havas, Steve, Sansone, Susanna-Assunta, Thibault, Kate M, Wecker, Patricia, Wichels, Antje, Wooley, John C, Yahara, Tetsukazu, Zingone, Adriana, and GOs-COS

Subjects
Biodiversity, Genomics, Biocode, Earth observations, GOs-COS
Abstract

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

Published
2014

18. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

Author

Keeling, Patrick J, Burki, Fabien, Wilcox, Heather M, Allam, Bassem, Allen, Eric E, Amaral-Zettler, Linda A, Armbrust, E Virginia, Archibald, John M, Bharti, Arvind K, Bell, Callum J, Beszteri, Bank, Bidle, Kay D, Cameron, Connor T, Campbell, Lisa, Caron, David A, Cattolico, Rose Ann, Collier, Jackie L, Coyne, Kathryn, Davy, Simon K, Deschamps, Phillipe, Dyhrman, Sonya T, Edvardsen, Bente, Gates, Ruth D, Gobler, Christopher J, Greenwood, Spencer J, Guida, Stephanie M, Jacobi, Jennifer L, Jakobsen, Kjetill S, James, Erick R, Jenkins, Bethany, John, Uwe, Johnson, Matthew D, Juhl, Andrew R, Kamp, Anja, Katz, Laura A, Kiene, Ronald, Kudryavtsev, Alexander, Leander, Brian S, Lin, Senjie, Lovejoy, Connie, Lynn, Denis, Marchetti, Adrian, McManus, George, Nedelcu, Aurora M, Menden-Deuer, Susanne, Miceli, Cristina, Mock, Thomas, Montresor, Marina, Moran, Mary Ann, Murray, Shauna, Nadathur, Govind, Nagai, Satoshi, Ngam, Peter B, Palenik, Brian, Pawlowski, Jan, Petroni, Giulio, Piganeau, Gwenael, Posewitz, Matthew C, Rengefors, Karin, Romano, Giovanna, Rumpho, Mary E, Rynearson, Tatiana, Schilling, Kelly B, Schroeder, Declan C, Simpson, Alastair GB, Slamovits, Claudio H, Smith, David R, Smith, G Jason, Smith, Sarah R, Sosik, Heidi M, Stief, Peter, Theriot, Edward, Twary, Scott N, Umale, Pooja E, Vaulot, Daniel, Wawrik, Boris, Wheeler, Glen L, Wilson, William H, Xu, Yan, Zingone, Adriana, and Worden, Alexandra Z

Subjects
Sequence Analysis, Environmental Microbiology, Biodiversity, Molecular Sequence Data, Databases, Factual, Oceans and Seas, Eukaryota, Transcriptome, Databases, Factual, Developmental Biology, Biological Sciences, Medical and Health Sciences, Agricultural and Veterinary Sciences
Published
2014

23. Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

Author

Sato, Shinya, Nanjappa, Deepak, Dorrell, Richard G., Vieira, Fabio Rocha Jimenez, Kazamia, Elena, Tirichine, Leila, Veluchamy, Alaguraj, Heilig, Roland, Aury, Jean-Marc, Jaillon, Olivier, Wincker, Patrick, Fussy, Zoltan, Obornik, Miroslav, Muñoz-Gómez, Sergio A., Mann, David G., Bowler, Chris, and Zingone, Adriana

Published
2020
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24. Author Correction: Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans

Author

Mitchell, Khadijah A., Nichols, Noah, Tang, Wei, Walling, Jennifer, Stevenson, Holly, Pineda, Marbin, Stefanescu, Roxana, Edelman, Daniel C., Girvin, Andrew T., Zingone, Adriana, Sinha, Sanju, Bowman, Elise, Rossi, Emily L., Arauz, Rony F., Zhu, Yuelin Jack, Lack, Justin, Weingartner, Elizabeth, Waterfall, Joshua J., Pine, Sharon R., Simmons, John, Meltzer, Paul, and Ryan, Bríd M.

Published
2020
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25. Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans

Author

Mitchell, Khadijah A., Nichols, Noah, Tang, Wei, Walling, Jennifer, Stevenson, Holly, Pineda, Marbin, Stefanescu, Roxana, Edelman, Daniel C., Girvin, Andrew T., Zingone, Adriana, Sinha, Sanju, Bowman, Elise, Rossi, Emily L., Arauz, Rony F., Jack Zhu, Yuelin, Lack, Justin, Weingartner, Elizabeth, Waterfall, Joshua J., Pine, Sharon R., Simmons, John, Meltzer, Paul, and Ryan, Bríd M.

Published
2019
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26. VERDI [Dataset]

Author

European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Stazione Zoologica Anton Dohrn, Reñé, Albert [0000-0002-0488-3539], Timoneda Solé, Natàlia [0000-0001-9955-0712], Sarno, Diana [0000-0001-9697-5301], Zingone, Adriana [0000-0001-5946-6532], Margiotta, Francesca [0000-0001-5946-6532], Montresor, Marina [0000-0002-2475-1787], Garcés, Esther [0000-0002-2712-501X], Timoneda Solé, Natàlia ; Sarno, Diana; Zingone, Adriana; Margiotta, Francesca; Passarelli, Augusto; Gallia, Roberto; Tramontano, Ferdinando, Reñé, Albert, Timoneda Solé, Natàlia, Sarno, Diana, Zingone, Adriana, Margiotta, Francesca, Passarelli, Augusto, Gallia, Roberto, Tramontano, Ferdinando, Montresor, Marina, Garcés, Esther, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Stazione Zoologica Anton Dohrn, Reñé, Albert [0000-0002-0488-3539], Timoneda Solé, Natàlia [0000-0001-9955-0712], Sarno, Diana [0000-0001-9697-5301], Zingone, Adriana [0000-0001-5946-6532], Margiotta, Francesca [0000-0001-5946-6532], Montresor, Marina [0000-0002-2475-1787], Garcés, Esther [0000-0002-2712-501X], Timoneda Solé, Natàlia ; Sarno, Diana; Zingone, Adriana; Margiotta, Francesca; Passarelli, Augusto; Gallia, Roberto; Tramontano, Ferdinando, Reñé, Albert, Timoneda Solé, Natàlia, Sarno, Diana, Zingone, Adriana, Margiotta, Francesca, Passarelli, Augusto, Gallia, Roberto, Tramontano, Ferdinando, Montresor, Marina, and Garcés, Esther

Abstract

The presence of phytoplankton parasites along the water column was explored at the Long Term Ecological Station MareChiara (LTER-MC) in the Gulf of Naples (Mediterranean Sea) in October 2019. Microscopy analyses showed diatoms dominating the phytoplankton community in the upper layers (0-20 m). Metabarcoding data from the water column showed the presence of Chytridiomycota predominantly in the upper layers coinciding with the vertical distribution of diatoms. Laboratory incubations of natural samples enriched with different diatom cultures confirmed parasitic interactions of some of those chytrids – including members of Kappamyces – with diatom taxa. The temporal dynamics of diatoms and chytrids was also explored in a three-year metabarcoding time-series (2011-2013) from surface waters of the study area and in sediment samples. Chytrids were recurrently present at low relative abundances, and some taxa found to infect diatoms in the incubation experiments were also identified in the ASV time-series. However, co-occurrence analyses did not show any clear or recurrent pairing patterns for chytrid and diatom taxa along the three years. The chytrid community in the sediments showed a clearly different species composition compared to the recorded in the water column samples, with higher diversity and relative abundance. The combination of observations, incubations and metabarcoding confirmed that parasites are a common component of marine protist communities at LTER-MC. Host-parasite interactions must be determined and quantified to understand their role and the impact they have on phytoplankton dynamics

Published
2022

29. Supplementary Table 1 from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation

Author

Simmons, John K., primary, Michalowski, Aleksandra M., primary, Gamache, Benjamin J., primary, DuBois, Wendy, primary, Patel, Jyoti, primary, Zhang, Ke, primary, Gary, Joy, primary, Zhang, Shuling, primary, Gaikwad, Snehal, primary, Connors, Daniel, primary, Watson, Nicholas, primary, Leon, Elena, primary, Chen, Jin-Qiu, primary, Kuehl, W. Michael, primary, Lee, Maxwell P., primary, Zingone, Adriana, primary, Landgren, Ola, primary, Ordentlich, Peter, primary, Huang, Jing, primary, and Mock, Beverly A., primary

Published
2023
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30. supplementary methods from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation

Author

Simmons, John K., primary, Michalowski, Aleksandra M., primary, Gamache, Benjamin J., primary, DuBois, Wendy, primary, Patel, Jyoti, primary, Zhang, Ke, primary, Gary, Joy, primary, Zhang, Shuling, primary, Gaikwad, Snehal, primary, Connors, Daniel, primary, Watson, Nicholas, primary, Leon, Elena, primary, Chen, Jin-Qiu, primary, Kuehl, W. Michael, primary, Lee, Maxwell P., primary, Zingone, Adriana, primary, Landgren, Ola, primary, Ordentlich, Peter, primary, Huang, Jing, primary, and Mock, Beverly A., primary

Published
2023
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31. Supplementary Figures from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation

Author

Simmons, John K., primary, Michalowski, Aleksandra M., primary, Gamache, Benjamin J., primary, DuBois, Wendy, primary, Patel, Jyoti, primary, Zhang, Ke, primary, Gary, Joy, primary, Zhang, Shuling, primary, Gaikwad, Snehal, primary, Connors, Daniel, primary, Watson, Nicholas, primary, Leon, Elena, primary, Chen, Jin-Qiu, primary, Kuehl, W. Michael, primary, Lee, Maxwell P., primary, Zingone, Adriana, primary, Landgren, Ola, primary, Ordentlich, Peter, primary, Huang, Jing, primary, and Mock, Beverly A., primary

Published
2023
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32. Data from Cooperative Targets of Combined mTOR/HDAC Inhibition Promote MYC Degradation

Author

Simmons, John K., primary, Michalowski, Aleksandra M., primary, Gamache, Benjamin J., primary, DuBois, Wendy, primary, Patel, Jyoti, primary, Zhang, Ke, primary, Gary, Joy, primary, Zhang, Shuling, primary, Gaikwad, Snehal, primary, Connors, Daniel, primary, Watson, Nicholas, primary, Leon, Elena, primary, Chen, Jin-Qiu, primary, Kuehl, W. Michael, primary, Lee, Maxwell P., primary, Zingone, Adriana, primary, Landgren, Ola, primary, Ordentlich, Peter, primary, Huang, Jing, primary, and Mock, Beverly A., primary

Published
2023
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35. Pan-Arctic plankton community structure and its global connectivity

Author

Ibarbalz, Federico M., Henry, Nicolas, Mahe, Frédéric, Ardyna, Mathieu, Zingone, Adriana, Scalco, Eleonora, Lovejoy, Thomas E., Lombard, Fabien, Jaillon, Olivier, Iudicone, Daniele, Malviya, Shruti, Sullivan, Matthew B., Chaffron, Samuel, Karsenti, Eric, Babin, Marcel, Boss, Emmanuel, Wincker, Patrick, Zinger, Lucie, de Vargas, Colomban, Bowler, Chris, Karp-Boss, Lee, Ibarbalz, Federico M., Henry, Nicolas, Mahe, Frédéric, Ardyna, Mathieu, Zingone, Adriana, Scalco, Eleonora, Lovejoy, Thomas E., Lombard, Fabien, Jaillon, Olivier, Iudicone, Daniele, Malviya, Shruti, Sullivan, Matthew B., Chaffron, Samuel, Karsenti, Eric, Babin, Marcel, Boss, Emmanuel, Wincker, Patrick, Zinger, Lucie, de Vargas, Colomban, Bowler, Chris, and Karp-Boss, Lee

Abstract

The Arctic Ocean (AO) is being rapidly transformed by global warming, but its biodiversity remains understudied for many planktonic organisms, in particular for unicellular eukaryotes that play pivotal roles in marine food webs and biogeochemical cycles. The aim of this study was to characterize the biogeographic ranges of species that comprise the contemporary pool of unicellular eukaryotes in the AO as a first step toward understanding mechanisms that structure these communities and identifying potential target species for monitoring. Leveraging the Tara Oceans DNA metabarcoding data, we mapped the global distributions of operational taxonomic units (OTUs) found on Arctic shelves into five biogeographic categories, identified biogeographic indicators, and inferred the degree to which AO communities of unicellular eukaryotes share members with assemblages from lower latitudes. Arctic/Polar indicator OTUs, as well as some globally ubiquitous OTUs, dominated the detection and abundance of DNA reads in the Arctic samples. OTUs detected only in Arctic samples (Arctic-exclusives) showed restricted distribution with relatively low abundances, accounting for 10–16% of the total Arctic OTU pool. OTUs with high abundances in tropical and/or temperate latitudes (non-Polar indicators) were also found in the AO but mainly at its periphery. We observed a large change in community taxonomic composition across the Atlantic-Arctic continuum, supporting the idea that advection and environmental filtering are important processes that shape plankton assemblages in the AO. Altogether, this study highlights the connectivity between the AO and other oceans, and provides a framework for monitoring and assessing future changes in this vulnerable ecosystem.

Published
2023

36. Vertical and temporal distribution of chytrids infecting diatoms in the Gulf of Naples (Italy, Mediterranean Sea)

Author

European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Stazione Zoologica Anton Dohrn, Reñé, Albert, Timoneda Solé, Natàlia, Sarno, Diana, Piredda, Roberta, Zampicinini, Gianpaolo, Zingone, Adriana, Montresor, Marina, Garcés, Esther, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Stazione Zoologica Anton Dohrn, Reñé, Albert, Timoneda Solé, Natàlia, Sarno, Diana, Piredda, Roberta, Zampicinini, Gianpaolo, Zingone, Adriana, Montresor, Marina, and Garcés, Esther

Abstract

The presence of phytoplankton parasites along the water column was explored at the Long-Term Ecological Station MareChiara (LTER-MC) in the Gulf of Naples (Mediterranean Sea) in October 2019. Microscopy analyses showed diatoms dominating the phytoplankton community in the upper layers (0–20 m). Metabarcoding data from the water column showed the presence of Chytridiomycota predominantly in the upper layers coinciding with the vertical distribution of diatoms. Laboratory incubations of natural samples enriched with different diatom cultures confirmed parasitic interactions of some of those chytrids—including members of Kappamyces—with diatom taxa. The temporal dynamics of diatoms and chytrids was also explored in a 3-year metabarcoding time-series (2011–2013) from surface waters of the study area and in sediment samples. Chytrids were recurrently present at low relative abundances, and some taxa found to infect diatoms in the incubation experiments were also identified in the ASV time-series. However, co-occurrence analyses did not show any clear or recurrent pairing patterns for chytrid and diatom taxa along the 3 years. The chytrid community in the sediments showed a clearly different species composition compared with that recorded in the water column samples, with higher diversity and relative abundance. The combination of observations, incubations, and metabarcoding confirmed that parasites are a common component of marine protist communities at LTER-MC. Host–parasite interactions must be determined and quantified to understand their role and the impact they have on phytoplankton dynamics

Published
2023

37. A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Author

European Commission, Fonds Français pour l'Environnement Mondial, Université Paris Sciences & Lettres, Agencia Estatal de Investigación (España), Pierella Karlusich, Juan J., Pelletier, Eric, Zinger, Lucie, Lombard, Fabien, Zingone, Adriana, Colin, Sebastien, Gasol, Josep M., Dorrell, Richard G., Henry, Nicolas, Scalco, Eleonora, Acinas, Silvia G., Wincker, Patrick, Vargas, Colomban de, Bowler, Chris, European Commission, Fonds Français pour l'Environnement Mondial, Université Paris Sciences & Lettres, Agencia Estatal de Investigación (España), Pierella Karlusich, Juan J., Pelletier, Eric, Zinger, Lucie, Lombard, Fabien, Zingone, Adriana, Colin, Sebastien, Gasol, Josep M., Dorrell, Richard G., Henry, Nicolas, Scalco, Eleonora, Acinas, Silvia G., Wincker, Patrick, Vargas, Colomban de, and Bowler, Chris

Abstract

Phytoplankton account for >45% of global primary production, and have an enor-mous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages con-taining chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appre-ciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosyn-thetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular- based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular- based evaluations of entire phytoplankton communities

Published
2023

40. Diatom diversity through HTS-metabarcoding in coastal European seas

Author

Piredda, Roberta, Claverie, Jean-Michel, Decelle, Johan, de Vargas, Colomban, Dunthorn, Micah, Edvardsen, Bente, Eikrem, Wenche, Forster, Dominik, Kooistra, Wiebe H. C. F., Logares, Ramiro, Massana, Ramon, Montresor, Marina, Not, Fabrice, Ogata, Hiroyuki, Pawlowski, Jan, Romac, Sarah, Sarno, Diana, Stoeck, Thorsten, and Zingone, Adriana

Published
2018
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47. Toxic marine microalgae and associated phycotoxins in shellfish: 14 years of data from the Italian coasts

Author

Accoroni, Stefano, Cangini, Monica, Angeletti, Roberto, Arcangeli, Giuseppe, Bacchiocchi, Simone, Barile, Nadia, Contiero, Lidia, Costa, Antonella, Di Taranto, Aurelia, Escalera, Laura, Fedrizzi, Giorgio, Garzia, Angela, Longo, Francesca, Macaluso, Andrea, Melchiorre, Nunzia, Milandri, Anna, Milandri, Stefania, Montresor, Marina, Neri, Bruno, Neri, Francesca, Gallo, Pasquale, Piersanti, Arianna, Rubini, Silva, Scortichini, Giampiero, Suraci, Chiara, Susini, Francesca, Vadrucci, Maria Rosaria, Verniani, Daniela, Virgilio, Sebastiano, Vivaldi, Barbara, Vodret, Bruna, Totti, Cecilia, and Zingone, Adriana

Subjects
toxic algae, domoic acid, emerging toxins, marine lipophilic toxins, paralytic shellfish toxins
Abstract

Along the Italian coasts, toxins of algal origin in wild and cultivated shellfish have been reported since the 1970s. In this study, we used data gathered by the Veterinary Public Health Institutes and the Italian Environmental Health Protection Agencies from 2006 to 2019 to investigate toxicity events and relate them to the distribution of toxic species. Among detected toxins (OA and analogs, YTXs, PTXs, STXs, DAs, AZAs), OA and YTX were those most frequently reported in cases of seafood contamination. Levels of those toxins exceeding regulatory limits for OA were associated with high abundances of Dinophysis spp. and for YTX with blooms of Gonyaulax spinifera, Lingulodinium polyedra, and Protoceratium reticulatum. Seasonal blooms of Pseudo-nitzschia spp. occurred all along the Italian coast, but DA was only occasionally found in shellfish, at concentrations consistently below the regulatory limit. Alexandrium was recorded in many more areas than STXs, which only rarely exceeded the regulatory limit. Azadinium was sporadically recorded, and AZAs were sometimes detected in low quantities. Among the emerging toxins, PLTX-like toxins often accumulated in wild mussels and sea urchins due to the occurrences of Ostreopsis cf. ovata. Overall, Italian coastal waters harbour numerous potentially toxic species, with a few HAB hotspots related to DSP toxins. Still, rare cases of intoxications have occurred so far, reflecting the whole Mediterranean Sea conditions., Corresponding author's email: s.accoroni@univpm.it

Published
2022
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50. Assembly rules vary seasonally in stable phytoplankton associations of the Gulf of Naples (Mediterranean Sea).

Author

Zingone, Adriana, Tortora, Cristina, D′Alelio, Domenico, Margiotta, Francesca, and Sarno, Diana

Subjects
*PHYTOPLANKTON, *SPRING, *CLUSTER analysis (Statistics), *TIME series analysis, *COCCOLITHOPHORES, *DIATOMS, *WINTER
Abstract

Coastal phytoplankton present remarkable variability because of complex patterns and relationships of hydrological parameters at the land–sea interface. We analysed a time series of 917 phytoplankton samples collected in the period 1984–2010 at the coastal station LTER‐MC (Gulf of Naples, Mediterranean Sea) with the aims of determining: (i) whether recurrent species associations are recognizable in this variable coastal environment; (ii) what are their composition and seasonal patterns; (iii) what are the environmental variables driving their distributions, and (iv) to what extent those associations are functionally homogeneous. Using a cluster analysis of a dataset of the 87 more frequent and abundant species in the samples, we identified seven main groups of species. Five of them were recurrent over the years in the same seasons, while two other groups showed a bimodal occurrence or no clear seasonality, respectively. Differences in the occurrence of those assemblages were primarily associated with the season (i.e., temperature), and the coastal nature of the site (mainly salinity). Except for the winter cluster, which included mostly coccolithophores and silicoflagellates, diatoms were present in all associations, along with species belonging to diverse phylogenetic groups. The diversity of morphological features defining ecological traits varied across the different associations, with a maximum divergence in the spring association and a minimum in winter. We conclude that the stability of the associations is related to the marked phenological recurrence of their individual species and their overlap in specific periods of the year, while convergent or divergent trait compositions in the different associations indicate a variable strength of the environmental filtering across the seasonal succession. [ABSTRACT FROM AUTHOR]

Published
2023
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