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2. Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms.

Author

Luu, Gordon, Little, Jessica, Pierce, Emily, Morin, Manon, Ertekin, Celine, Wolfe, Benjamin, Baars, Oliver, Dutton, Rachel, and Sanchez, Laura

Subjects
Chromatography, Liquid, Tandem Mass Spectrometry, Siderophores, Bacteria, Metabolomics
Abstract

Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis sp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.

Published
2023

10. The GEOTRACES Intermediate Data Product 2017

Author

Schlitzer, Reiner, Anderson, Robert F., Dodas, Elena Masferrer, Lohan, Maeve, Geibert, Walter, Tagliabue, Alessandro, Bowie, Andrew, Jeandel, Catherine, Maldonado, Maria T., Landing, William M., Cockwell, Donna, Abadie, Cyril, Abouchami, Wafa, Achterberg, Eric P., Agather, Alison, Aguliar-Islas, Ana, van Aken, Hendrik M., Andersen, Morten, Archer, Corey, Auro, Maureen, de Baar, Hein J., Baars, Oliver, Baker, Alex R., Bakker, Karel, Basak, Chandranath, Baskaran, Mark, Bates, Nicholas R., Bauch, Dorothea, van Beek, Pieter, Behrens, Melanie K., Black, Erin, Bluhm, Katrin, Bopp, Laurent, Bouman, Heather, Bowman, Katlin, Bown, Johann, Boyd, Philip, Boye, Marie, Boyle, Edward A., Branellec, Pierre, Bridgestock, Luke, Brissebrat, Guillaume, Browning, Thomas, Bruland, Kenneth W., Brumsack, Hans-Jürgen, Brzezinski, Mark, Buck, Clifton S., Buck, Kristen N., Buesseler, Ken, Bull, Abby, Butler, Edward, Cai, Pinghe, Mor, Patricia Cámara, Cardinal, Damien, Carlson, Craig, Carrasco, Gonzalo, Casacuberta, Núria, Casciotti, Karen L., Castrillejo, Maxi, Chamizo, Elena, Chance, Rosie, Charette, Matthew A., Chaves, Joaquin E., Cheng, Hai, Chever, Fanny, Christl, Marcus, Church, Thomas M., Closset, Ivia, Colman, Albert, Conway, Tim M., Cossa, Daniel, Croot, Peter, Cullen, Jay T., Cutter, Gregory A., Daniels, Chris, Dehairs, Frank, Deng, Feifei, Dieu, Huong Thi, Duggan, Brian, Dulaquais, Gabriel, Dumousseaud, Cynthia, Echegoyen-Sanz, Yolanda, Edwards, R. Lawrence, Ellwood, Michael, Fahrbach, Eberhard, Fitzsimmons, Jessica N., Russell Flegal, A., Fleisher, Martin Q., van de Flierdt, Tina, Frank, Martin, Friedrich, Jana, Fripiat, Francois, Fröllje, Henning, Galer, Stephen J.G., Gamo, Toshitaka, Ganeshram, Raja S., Garcia-Orellana, Jordi, Garcia-Solsona, Ester, Gault-Ringold, Melanie, George, Ejin, Gerringa, Loes J.A., Gilbert, Melissa, Godoy, Jose M., Goldstein, Steven L., Gonzalez, Santiago R., Grissom, Karen, Hammerschmidt, Chad, Hartman, Alison, Hassler, Christel S., Hathorne, Ed C., Hatta, Mariko, Hawco, Nicholas, Hayes, Christopher T., Heimbürger, Lars-Eric, Helgoe, Josh, Heller, Maija, Henderson, Gideon M., Henderson, Paul B., van Heuven, Steven, Ho, Peng, Horner, Tristan J., Hsieh, Yu-Te, Huang, Kuo-Fang, Humphreys, Matthew P., Isshiki, Kenji, Jacquot, Jeremy E., Janssen, David J., Jenkins, William J., John, Seth, Jones, Elizabeth M., Jones, Janice L., Kadko, David C., Kayser, Rick, Kenna, Timothy C., Khondoker, Roulin, Kim, Taejin, Kipp, Lauren, Klar, Jessica K., Klunder, Maarten, Kretschmer, Sven, Kumamoto, Yuichiro, Laan, Patrick, Labatut, Marie, Lacan, Francois, Lam, Phoebe J., Lambelet, Myriam, Lamborg, Carl H., Le Moigne, Frédéric A.C., Le Roy, Emilie, Lechtenfeld, Oliver J., Lee, Jong-Mi, Lherminier, Pascale, Little, Susan, López-Lora, Mercedes, Lu, Yanbin, Masque, Pere, Mawji, Edward, Mcclain, Charles R., Measures, Christopher, Mehic, Sanjin, Barraqueta, Jan-Lukas Menzel, van der Merwe, Pier, Middag, Rob, Mieruch, Sebastian, Milne, Angela, Minami, Tomoharu, Moffett, James W., Moncoiffe, Gwenaelle, Moore, Willard S., Morris, Paul J., Morton, Peter L., Nakaguchi, Yuzuru, Nakayama, Noriko, Niedermiller, John, Nishioka, Jun, Nishiuchi, Akira, Noble, Abigail, Obata, Hajime, Ober, Sven, Ohnemus, Daniel C., van Ooijen, Jan, O'Sullivan, Jeanette, Owens, Stephanie, Pahnke, Katharina, Paul, Maxence, Pavia, Frank, Pena, Leopoldo D., Peters, Brian, Planchon, Frederic, Planquette, Helene, Pradoux, Catherine, Puigcorbé, Viena, Quay, Paul, Queroue, Fabien, Radic, Amandine, Rauschenberg, S., Rehkämper, Mark, Rember, Robert, Remenyi, Tomas, Resing, Joseph A., Rickli, Joerg, Rigaud, Sylvain, Rijkenberg, Micha J.A., Rintoul, Stephen, Robinson, Laura F., Roca-Martí, Montserrat, Rodellas, Valenti, Roeske, Tobias, Rolison, John M., Rosenberg, Mark, Roshan, Saeed, Rutgers van der Loeff, Michiel M., Ryabenko, Evgenia, Saito, Mak A., Salt, Lesley A., Sanial, Virginie, Sarthou, Geraldine, Schallenberg, Christina, Schauer, Ursula, Scher, Howie, Schlosser, Christian, Schnetger, Bernhard, Scott, Peter, Sedwick, Peter N., Semiletov, Igor, Shelley, Rachel, Sherrell, Robert M., Shiller, Alan M., Sigman, Daniel M., Singh, Sunil Kumar, Slagter, Hans A., Slater, Emma, Smethie, William M., Snaith, Helen, Sohrin, Yoshiki, Sohst, Bettina, Sonke, Jeroen E., Speich, Sabrina, Steinfeldt, Reiner, Stewart, Gillian, Stichel, Torben, Stirling, Claudine H., Stutsman, Johnny, Swarr, Gretchen J., Swift, James H., Thomas, Alexander, Thorne, Kay, Till, Claire P., Till, Ralph, Townsend, Ashley T., Townsend, Emily, Tuerena, Robyn, Twining, Benjamin S., Vance, Derek, Velazquez, Sue, Venchiarutti, Celia, Villa-Alfageme, Maria, Vivancos, Sebastian M., Voelker, Antje H.L., Wake, Bronwyn, Warner, Mark J., Watson, Ros, van Weerlee, Evaline, Alexandra Weigand, M., Weinstein, Yishai, Weiss, Dominik, Wisotzki, Andreas, Woodward, E. Malcolm S., Wu, Jingfeng, Wu, Yingzhe, Wuttig, Kathrin, Wyatt, Neil, Xiang, Yang, Xie, Ruifang C., Xue, Zichen, Yoshikawa, Hisayuki, Zhang, Jing, Zhang, Pu, Zhao, Ye, Zheng, Linjie, Zheng, Xin-Yuan, Zieringer, Moritz, Zimmer, Louise A., Ziveri, Patrizia, Zunino, Patricia, and Zurbrick, Cheryl

Published
2018
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16. Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control

Author

Molo, Megan S., primary, White, James B., additional, Cornish, Vicki, additional, Gell, Richard M., additional, Baars, Oliver, additional, Singh, Rakhi, additional, Carbone, Mary Anna, additional, Isakeit, Thomas, additional, Wise, Kiersten A., additional, Woloshuk, Charles P., additional, Bluhm, Burton H., additional, Horn, Bruce W., additional, Heiniger, Ron W., additional, and Carbone, Ignazio, additional

Published
2022
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18. Development of transgenic corn planthopper Peregrinus maidis that express the tetracycline transactivator.

Author

Patil, Anandrao A., Klobasa, William, Espinoza‐Rivera, Dina, Baars, Oliver, Lorenzen, Marcé D., and Scott, Maxwell J.

Subjects
CORN development, TETRACYCLINE, INSECTICIDE resistance, FUNCTIONAL genomics, TETRACYCLINES
Abstract

The corn planthopper, Peregrinus maidis, is a vector of several maize viruses and is consequently a significant agricultural pest in many tropical and subtropical regions. As P. maidis has developed resistance to insecticides, the aim of this study was to develop transgenic P. maidis strains that could be used for future genetic biocontrol programs. To facilitate the identification of transgenic P. maidis, we isolated and characterized the promoters for the P. maidisubiquitin‐like and profilin genes. Transient expression assays with P. maidis embryos showed that both promoters were active. Transgenic lines were established using piggyBac vectors and fluorescent protein marker genes. The lines carried an auto‐regulated tetracyclinetransactivator (tTA) gene, which has been widely used to establish conditional lethal strains in other insect species. The transgenic lines showed low levels of tTA expression but were viable on diet with or without doxycycline, which inhibits the binding of tTA to DNA. We discuss possible modifications to the tTA overexpression system that could lead to the successful development of conditional lethal strains. To our knowledge, this is the first report of a transgenic Hemiptera. The approach we have taken could potentially be applied to other Hemiptera and, for P. maidis, the technology will facilitate future functional genomics studies. [ABSTRACT FROM AUTHOR]

Published
2023
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19. Meteorology and oceanography of the Atlantic sector of the Southern Ocean—a review of German achievements from the last decade

Author

Hellmer, Hartmut H., Rhein, Monika, Heinemann, Günther, Abalichin, Janna, Abouchami, Wafa, Baars, Oliver, Cubasch, Ulrich, Dethloff, Klaus, Ebner, Lars, Fahrbach, Eberhard, Frank, Martin, Gollan, Gereon, Greatbatch, Richard J., Grieger, Jens, Gryanik, Vladimir M., Gryschka, Micha, Hauck, Judith, Hoppema, Mario, Huhn, Oliver, Kanzow, Torsten, Koch, Boris P., König-Langlo, Gert, Langematz, Ulrike, Leckebusch, Gregor C., Lüpkes, Christof, Paul, Stephan, Rinke, Annette, Rost, Bjoern, van der Loeff, Michiel Rutgers, Schröder, Michael, Seckmeyer, Gunther, Stichel, Torben, Strass, Volker, Timmermann, Ralph, Trimborn, Scarlett, Ulbrich, Uwe, Venchiarutti, Celia, Wacker, Ulrike, Willmes, Sascha, and Wolf-Gladrow, Dieter

Published
2016
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23. Asymmetrical lineage introgression and recombination in populations ofAspergillus flavus: implications for biological control

Author

Molo, Megan S., primary, White, James B., additional, Cornish, Vicki, additional, Gell, Richard M, additional, Baars, Oliver, additional, Singh, Rakhi, additional, Carbone, Mary Anna, additional, Isakeit, Thomas, additional, Wise, Kiersten A., additional, Woloshuk, Charles P., additional, Bluhm, Burton H., additional, Horn, Bruce W., additional, Heiniger, Ron W., additional, and Carbone, Ignazio, additional

Published
2022
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28. Siderophore concentrations found in supernatants of Rhodopseudomonas palustris str. CGA009 grown under different aerobic and anaerobic conditions from laboratory experiments in 2016

Author

Morel, Francois, Baars, Oliver, Zhang, Xinning, Morel, Francois, Baars, Oliver, and Zhang, Xinning

Abstract

Dataset: Rpalustris_SiderophoreConcentrations, Siderophore concentrations found in supernatants of Rhodopseudomonas palustris str. CGA009 grown under different aerobic and anaerobic conditions from laboratory experiments in 2016. These data were published in Baars et al. (2018, Fig. 3). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/861145, NSF Division of Ocean Sciences (NSF OCE) OCE-1657639

Published
2021

34. Raw data of the ASV titration and Zn uptake experiments from The effect of acidification on the bioavailability and electrochemical lability of zinc in seawater

Author

Ja-Myung Kim, Baars, Oliver, and Morel, François M. M.

Subjects
fungi
Abstract

A poorly studied but potentially important consequence of the CO2-induced acidification of the surface ocean is a possible change in the bioavailability of trace metals, which play a critical role in the productivity and population dynamics of marine ecosystems. We report laboratory and field experiments designed to compare quantitatively the effects of acidification on the bioavailability of Zn, a metal essential to the growth of phytoplankton and on the extent of its complexation by model and natural ligands. We observed a good correspondence between the effects of pH on the rate of Zn uptake by a model diatom and the chemical lability of Zn measured by anodic stripping voltammetry (ASV). In model laboratory systems, the chemical lability and the bioavailability of Zn could either increase or decrease at low pH depending on the mix of complexing ligands. In a sample of coastal surface water, we observed similar increases in the ASV-labile and bioavailable Zn concentrations upon acidification, a result contrary to previous observations. These results, which can likely be generalized to other bioactive trace metals, mutatis mutandis, demonstrate the intricacy of the effects of ocean acidification on the chemistry and the ecology of surface seawater.

Published
2016
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35. Small Molecule LC-MS/MS Fragmentation Data Analysis and Application to Siderophore Identification

Author

Baars, Oliver

Subjects
Computers / Mathematical & Statistical Software
Abstract

Rapid developments in tandem liquid chromatography-mass spectrometry (LC-MS/MS) have created wide interest in applications for the analysis of small molecule mixtures. MS/MS spectra can contain rich structural information, but because of the structural diversity of small molecules and different data acquisition methods, analysis algorithms and workflows frequently need to be tailored to individual research questions. This chapter shows how MATLAB can be used for LC-MS/MS-based structural characterization of small molecules. Starting with the import of raw data, ways for visualization and the creation of graphical user interfaces (GUIs) for individual applications are demonstrated. A selection of frequently used algorithms for pre-processing and data analysis is reviewed in context of their MATLAB implementation. The approaches are then tailored and applied to the analysis of iron-binding peptides (peptidic siderophores) by high-resolution LC-MS/MS. The method uses a database with siderophore structures to exploit prior knowledge about siderophore structural diversity for the interpretation of MS/MS spectra from known and new siderophores.

Published
2016

38. The {GEOTRACES} Intermediate Data Product 2014

Author

Mawji, Edward, Schlitzer, Reiner, Dodas, Elena Masferrer, Abadie, Cyril, Abouchami, Wafa, Anderson, Robert F., Baars, Oliver, Bakker, Karel, Baskaran, Mark, Bates, Nicholas R., Bluhm, Katrin, Bowie, Andrew, Bown, Johann, Boye, Marie, Boyle, Edward A., Branellec, Pierre, Bruland, Kenneth W., Brzezinski, Mark A., Bucciarelli, Eva, Buesseler, Ken, Butler, Edward, Cai, Pinghe, Cardinal, Damien, Casciotti, Karen, Chaves, Joaquin, Cheng, Hai, Chever, Fanny, Church, Thomas M., Colman, Albert S., Conway, Tim M., Croot, Peter L., Cutter, Gregory A., de Baar, Hein J.W., de Souza, Gregory F., Dehairs, Frank, Deng, Feifei, Dieu, Huong Thi, Dulaquais, Gabriel, Echegoyen-Sanz, Yolanda, Edwards, R. Lawrence, Fahrbach, Eberhard, Fitzsimmons, Jessica, Fleisher, Martin, Frank, Martin, Friedrich, Jana, Fripiat, François, Galer, Stephen J.G., Gamo, Toshitaka, Solsona, Ester Garcia, Gerringa, Loes J.A., Godoy, José Marcus, Gonzalez, Santiago, Grossteffan, Emilie, Hatta, Mariko, Hayes, Christopher T., Heller, Maija Iris, Henderson, Gideon, Huang, Kuo-Fang, Jeandel, Catherine, Jenkins, William J., John, Seth, Kenna, Timothy C., Klunder, Maarten, Kretschmer, Sven, Kumamoto, Yuichiro, Laan, Patrick, Labatut, Marie, Lacan, Francois, Lam, Phoebe J., Lannuzel, Delphine, le Moigne, Frederique, Lechtenfeld, Oliver J., Lohan, Maeve C., Lu, Yanbin, Masqué, Pere, McClain, Charles R., Measures, Christopher, Middag, Rob, Moffett, James, Navidad, Alicia, Nishioka, Jun, Noble, Abigail, Obata, Hajime, Ohnemus, Daniel C., Owens, Stephanie, Planchon, Frédéric, Pradoux, Catherine, Puigcorbé, Viena, Quay, Paul, Radic, Amandine, Rehkämper, Mark, Remenyi, Tomas, Rijkenberg, Micha J.A., Rintoul, Stephen, Robinson, Laura F., Roeske, Tobias, Rosenberg, Mark, Rutgers van der Loeff, Michiel, Ryabenko, Evgenia, Saito, Mak A., Roshan, Saeed, Salt, Lesley, Sarthou, Géraldine, Schauer, Ursula, Scott, Peter, Sedwick, Peter N., Sha, Lijuan, Shiller, Alan M., Sigman, Daniel M., Smethie, William, Smith, Geoffrey J., Sohrin, Yoshiki, Speich, Sabrina, Stichel, Torben, Stutsman, Johnny, Swift, James H., Tagliabue, Alessandro, Thomas, Alexander, Tsunogai, Urumu, Twining, Benjamin S., van Aken, Hendrik M., van Heuven, Steven, van Ooijen, Jan, van Weerlee, Evaline, Venchiarutti, Celia, Voelker, Antje H.L., Wake, Bronwyn, Warner, Mark J., Woodward, E. Malcolm S., Wu, Jingfeng, Wyatt, Neil, Yoshikawa, Hisayuki, Zheng, Xin-Yuan, Xue, Zichen, Zieringer, Moritz, Zimmer, Louise A., Mawji, Edward, Schlitzer, Reiner, Dodas, Elena Masferrer, Abadie, Cyril, Abouchami, Wafa, Anderson, Robert F., Baars, Oliver, Bakker, Karel, Baskaran, Mark, Bates, Nicholas R., Bluhm, Katrin, Bowie, Andrew, Bown, Johann, Boye, Marie, Boyle, Edward A., Branellec, Pierre, Bruland, Kenneth W., Brzezinski, Mark A., Bucciarelli, Eva, Buesseler, Ken, Butler, Edward, Cai, Pinghe, Cardinal, Damien, Casciotti, Karen, Chaves, Joaquin, Cheng, Hai, Chever, Fanny, Church, Thomas M., Colman, Albert S., Conway, Tim M., Croot, Peter L., Cutter, Gregory A., de Baar, Hein J.W., de Souza, Gregory F., Dehairs, Frank, Deng, Feifei, Dieu, Huong Thi, Dulaquais, Gabriel, Echegoyen-Sanz, Yolanda, Edwards, R. Lawrence, Fahrbach, Eberhard, Fitzsimmons, Jessica, Fleisher, Martin, Frank, Martin, Friedrich, Jana, Fripiat, François, Galer, Stephen J.G., Gamo, Toshitaka, Solsona, Ester Garcia, Gerringa, Loes J.A., Godoy, José Marcus, Gonzalez, Santiago, Grossteffan, Emilie, Hatta, Mariko, Hayes, Christopher T., Heller, Maija Iris, Henderson, Gideon, Huang, Kuo-Fang, Jeandel, Catherine, Jenkins, William J., John, Seth, Kenna, Timothy C., Klunder, Maarten, Kretschmer, Sven, Kumamoto, Yuichiro, Laan, Patrick, Labatut, Marie, Lacan, Francois, Lam, Phoebe J., Lannuzel, Delphine, le Moigne, Frederique, Lechtenfeld, Oliver J., Lohan, Maeve C., Lu, Yanbin, Masqué, Pere, McClain, Charles R., Measures, Christopher, Middag, Rob, Moffett, James, Navidad, Alicia, Nishioka, Jun, Noble, Abigail, Obata, Hajime, Ohnemus, Daniel C., Owens, Stephanie, Planchon, Frédéric, Pradoux, Catherine, Puigcorbé, Viena, Quay, Paul, Radic, Amandine, Rehkämper, Mark, Remenyi, Tomas, Rijkenberg, Micha J.A., Rintoul, Stephen, Robinson, Laura F., Roeske, Tobias, Rosenberg, Mark, Rutgers van der Loeff, Michiel, Ryabenko, Evgenia, Saito, Mak A., Roshan, Saeed, Salt, Lesley, Sarthou, Géraldine, Schauer, Ursula, Scott, Peter, Sedwick, Peter N., Sha, Lijuan, Shiller, Alan M., Sigman, Daniel M., Smethie, William, Smith, Geoffrey J., Sohrin, Yoshiki, Speich, Sabrina, Stichel, Torben, Stutsman, Johnny, Swift, James H., Tagliabue, Alessandro, Thomas, Alexander, Tsunogai, Urumu, Twining, Benjamin S., van Aken, Hendrik M., van Heuven, Steven, van Ooijen, Jan, van Weerlee, Evaline, Venchiarutti, Celia, Voelker, Antje H.L., Wake, Bronwyn, Warner, Mark J., Woodward, E. Malcolm S., Wu, Jingfeng, Wyatt, Neil, Yoshikawa, Hisayuki, Zheng, Xin-Yuan, Xue, Zichen, Zieringer, Moritz, and Zimmer, Louise A.

Abstract

The {GEOTRACES} Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international {GEOTRACES} programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEIs) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The {IDP2014} covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The {TEI} data in the {IDP2014} are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at cross-over stations. The digital data are provided in several formats, including {ASCII} spreadsheet, Excel spreadsheet, netCDF, and Ocean Data View collection. In addition to the actual data values the {IDP2014} also contains data quality flags and 1-� data error values where available. Quality flags and error values are useful for data filtering. Metadata about data originators, analytical methods and original publications related to the data are linked to the data in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the {IDP2014} data providing section plots and a new kind of animated 3D scenes. The basin-wide 3D scenes allow for viewing of data from many cruises at the same time, thereby providing quick overviews of large-scale tracer distributions. In addition, the 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of observed tracer plumes, as well as for making inferences about controlling processes.

Published
2015

39. The GEOTRACES Intermediate Data Product 2014

Author

Mawji, Edward, primary, Schlitzer, Reiner, additional, Dodas, Elena Masferrer, additional, Abadie, Cyril, additional, Abouchami, Wafa, additional, Anderson, Robert F., additional, Baars, Oliver, additional, Bakker, Karel, additional, Baskaran, Mark, additional, Bates, Nicholas R., additional, Bluhm, Katrin, additional, Bowie, Andrew, additional, Bown, Johann, additional, Boye, Marie, additional, Boyle, Edward A., additional, Branellec, Pierre, additional, Bruland, Kenneth W., additional, Brzezinski, Mark A., additional, Bucciarelli, Eva, additional, Buesseler, Ken, additional, Butler, Edward, additional, Cai, Pinghe, additional, Cardinal, Damien, additional, Casciotti, Karen, additional, Chaves, Joaquin, additional, Cheng, Hai, additional, Chever, Fanny, additional, Church, Thomas M., additional, Colman, Albert S., additional, Conway, Tim M., additional, Croot, Peter L., additional, Cutter, Gregory A., additional, de Baar, Hein J.W., additional, de Souza, Gregory F., additional, Dehairs, Frank, additional, Deng, Feifei, additional, Dieu, Huong Thi, additional, Dulaquais, Gabriel, additional, Echegoyen-Sanz, Yolanda, additional, Lawrence Edwards, R., additional, Fahrbach, Eberhard, additional, Fitzsimmons, Jessica, additional, Fleisher, Martin, additional, Frank, Martin, additional, Friedrich, Jana, additional, Fripiat, François, additional, Galer, Stephen J.G., additional, Gamo, Toshitaka, additional, Solsona, Ester Garcia, additional, Gerringa, Loes J.A., additional, Godoy, José Marcus, additional, Gonzalez, Santiago, additional, Grossteffan, Emilie, additional, Hatta, Mariko, additional, Hayes, Christopher T., additional, Heller, Maija Iris, additional, Henderson, Gideon, additional, Huang, Kuo-Fang, additional, Jeandel, Catherine, additional, Jenkins, William J., additional, John, Seth, additional, Kenna, Timothy C., additional, Klunder, Maarten, additional, Kretschmer, Sven, additional, Kumamoto, Yuichiro, additional, Laan, Patrick, additional, Labatut, Marie, additional, Lacan, Francois, additional, Lam, Phoebe J., additional, Lannuzel, Delphine, additional, le Moigne, Frederique, additional, Lechtenfeld, Oliver J., additional, Lohan, Maeve C., additional, Lu, Yanbin, additional, Masqué, Pere, additional, McClain, Charles R., additional, Measures, Christopher, additional, Middag, Rob, additional, Moffett, James, additional, Navidad, Alicia, additional, Nishioka, Jun, additional, Noble, Abigail, additional, Obata, Hajime, additional, Ohnemus, Daniel C., additional, Owens, Stephanie, additional, Planchon, Frédéric, additional, Pradoux, Catherine, additional, Puigcorbé, Viena, additional, Quay, Paul, additional, Radic, Amandine, additional, Rehkämper, Mark, additional, Remenyi, Tomas, additional, Rijkenberg, Micha J.A., additional, Rintoul, Stephen, additional, Robinson, Laura F., additional, Roeske, Tobias, additional, Rosenberg, Mark, additional, van der Loeff, Michiel Rutgers, additional, Ryabenko, Evgenia, additional, Saito, Mak A., additional, Roshan, Saeed, additional, Salt, Lesley, additional, Sarthou, Géraldine, additional, Schauer, Ursula, additional, Scott, Peter, additional, Sedwick, Peter N., additional, Sha, Lijuan, additional, Shiller, Alan M., additional, Sigman, Daniel M., additional, Smethie, William, additional, Smith, Geoffrey J., additional, Sohrin, Yoshiki, additional, Speich, Sabrina, additional, Stichel, Torben, additional, Stutsman, Johnny, additional, Swift, James H., additional, Tagliabue, Alessandro, additional, Thomas, Alexander, additional, Tsunogai, Urumu, additional, Twining, Benjamin S., additional, van Aken, Hendrik M., additional, van Heuven, Steven, additional, van Ooijen, Jan, additional, van Weerlee, Evaline, additional, Venchiarutti, Celia, additional, Voelker, Antje H.L., additional, Wake, Bronwyn, additional, Warner, Mark J., additional, Woodward, E. Malcolm S., additional, Wu, Jingfeng, additional, Wyatt, Neil, additional, Yoshikawa, Hisayuki, additional, Zheng, Xin-Yuan, additional, Xue, Zichen, additional, Zieringer, Moritz, additional, and Zimmer, Louise A., additional

Published
2015
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40. Tracer Survey in the Cape Verde Region - Cruise No. MSM10/1 - October 31 ��� December 06, 2008 - Ponta Delgada (Portugal) ��� Mindelo (Cape Verde Islands)

Author

Visbeck, Martin, Baars, Oliver, Bancala, Severin, Banyte, Donata, Becker, Meike, Dengler, Marcus, Drees, Georg, Fehsenfeld, Sandra, Fischer, Tim, Karbe, Fritz, Link, Rudi, Manke, Anne, Rickels, Wilfried, Schlosser, Christian, Schneider, Anke, Schuett, Martina, Stange, Karen, Stramma, Lothar, Tanhua, Toste, Wilcken, Sara, and Zocher, Johanna

Subjects
Earth sciences and geology, Earth Science
Abstract

The research cruise MSM10/1 was extremely successful. All programs were able to collect high quality data and the anticipated goals of the expedition were fully met. We have been able to carry out the first comprehensive survey of a tracer release in the Guinea Upwelling region (GUTRE) roughly seven month after the tracer was released at 8��N 23��W in April 2008. We have estimated that a total of 40% of the tracer was found during this cruise. While the horizontal spreading and mixing was larger than anticipated, the vertical extent of the tracer found was small. The low vertical tracer spreading rate estimates are supported by the micro structure profile data. The extensive survey of the upper 1000m of the oxygen minimum zone (OMZ) allowed comparing our sections with several previous surveys. We found that the lowest oxygen values in the core of the OMZ have dropped at record low values below 40 ��mol/kg. The preliminary findings from the trace metal work focused on Fe ligand measurements shows a slight higher excess ligand concentration in the surface (50m) for three stations. The two other stations show a slight decrease at this depth. A large number of biochemical samples were taken and were analyzed in Kiel for DNA and RNA diversity. The tracer release experiment provided an ideal environment for repeated biochemical sampling in the same water mass., MARIA S. MERIAN-Berichte

Published
2013
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41. Guinea Upwelling Tracer Release Experiment - Cruise No. M80/2 - November 26 - December 22, 2009 - Mindelo (Cape Verde) - Dakar (Senegal)

Author

Wallace, Douglas, Tanhua, Toste, Banyte, Donata, Dippe, Tina, Karbe, Fritz, Link, Rudolf, Silva, Pericles, Franz, Jasmin, Hansen, Thomas, Hauss, Helena, Nachtigall, Kerstin, Franzke, Daniela, F��ssel, Jessica, Kalvelage, Tim, Fischer, Tim, Gill, Diana, Grosskopf, Tobias, Joshi, Falguni, L��scher, Carolin, Kock, Annette, Stange, Karen, Baars, Oliver, Dammsh��user, Anna, Manke, Anne, Noll, Lina, Syre, Stephanie, Zocher, Johanna, and Raeke, Andreas

Subjects
Earth sciences and geology, Earth Science
Abstract

METEOR cruise M80/2 conducted chemical, physical and biological oceanographic research in the northeastern tropical Atlantic in order to obtain a better understanding of the variability of tropical oxygen minimum zones within the framework of the SFB 754 (Climate - Biogeochemical interactions in the tropical Oceans). The main goal of the leg M80/2 was to resurvey the purposeful tracer release patch about 1.5 years after its injection in April 2008. Secondary objectives include 1) Water mass variability and oxygen/nutrient distributions in the survey region by transient tracer and oxygen data. 2) A trace metal program focused on understanding the controls on the solubility and cycling of aluminum, iron and titanium and the speciation of dissolved cobalt. 3) A molecular genetic approach was used to investigate the contribution of diazotrophs to the oceanic nitrogen cycle and in particular the fixation of molecular nitrogen. 4) The depth distribution of NH2OH was measured at selected stations, and ten incubation experiments on N2O/NH2OH production/consumption mechanisms were conducted. 5) One program focused on the nitrification and nutrient regeneration in the water column, i.e. the cycling of N-nutrients as mediated by microbes. Experiments were carried to quantify rates of remineralisation/respiration by heterotrophic archaea/bacteria by means of 13C/15N/18O-tracer incubations. 6) One project focused on the pelagic community response to changes in nutrient stoichiometry by conducting two mesocosm growth experiments and by conducting station work along transects., METEOR-Berichte

Published
2013
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42. The purple non‐sulfur bacterium <italic>Rhodopseudomonas palustris</italic> produces novel petrobactin‐related siderophores under aerobic and anaerobic conditions.

Author

Baars, Oliver, Morel, François M. M., and Zhang, Xinning

Subjects
*RHODOPSEUDOMONAS palustris, *SIDEROPHORES, *GENOMICS, *BIOAVAILABILITY, *IRON compounds
Abstract

Summary: Many bacteria produce siderophores to bind and take up Fe(III), an essential trace metal with extremely low solubility in oxygenated environments at circumneutral pH. The purple non‐sulfur bacterium Rhodopseudomonas palustris str. CGA009 is a metabolically versatile model organism with high iron requirements that is able to grow under aerobic and anaerobic conditions. Siderophore biosynthesis has been predicted by genomic analysis, however, siderophore structures were not identified. Here, we elucidate the structure of two novel siderophores from R. palustris: rhodopetrobactin A and B. Rhodopetrobactins are structural analogues of the known siderophore petrobactin in which the Fe chelating moieties are conserved, including two 3,4‐dihydroxybenzoate and a citrate substructure. In the place of two spermidine linker groups in petrobactin, rhodopetrobactins contain two 4,4′‐diaminodibutylamine groups of which one or both are acetylated at the central amine. We analyse siderophore production under different growth modes and show that rhodopetrobactins are produced in response to Fe limitation under aerobic as well as under anaerobic conditions. Evaluation of the chemical characteristics of rhodopetrobactins indicates that they are well suited to support Fe acquisition under variable oxygen and light conditions. [ABSTRACT FROM AUTHOR]

Published
2018
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43. Crochelins: Siderophores with an Unprecedented Iron-Chelating Moiety from the Nitrogen-Fixing Bacterium Azotobacter chroococcum.

Author

Baars, Oliver, Zhang, Xinning, Gibson, Marcus I., Stone, Alan T., Morel, François M. M., and Seyedsayamdost, Mohammad R.

Subjects
*SIDEROPHORES, *IRON, *CHELATING agents, *MOIETIES (Chemistry), *NITROGEN fixation, *AZOTOBACTER chroococcum
Abstract

Microbes use siderophores to access essential iron resources in the environment. Over 500 siderophores are known, but they utilize a small set of common moieties to bind iron. Azotobacter chroococcum expresses iron-rich nitrogenases, with which it reduces N2. Though an important agricultural inoculant, the structures of its iron-binding molecules remain unknown. Here, the 'chelome' of A. chroococcum is examined using small molecule discovery and bioinformatics. The bacterium produces vibrioferrin and amphibactins as well as a novel family of siderophores, the crochelins. Detailed characterization shows that the most abundant member, crochelin A, binds iron in a hexadentate fashion using a new iron-chelating γ-amino acid. Insights into the biosynthesis of crochelins and the mechanism by which iron may be removed upon import of the holo-siderophore are presented. This work expands the repertoire of iron-chelating moieties in microbial siderophores. [ABSTRACT FROM AUTHOR]

Published
2018
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45. Tracer Survey in the Cape Verde Region Traceraufnahme in der Kapverdenregion Cruise No. 10, Leg 1 October 31 – December 06, 2008 Ponta Delgada (Portugal) – Mindelo (Cape Verde Islands)

Author

Visbeck, Martin, Baars, Oliver, Bancala, Severin, Banyte, Donata, Becker, Meike, Dengler, Marcus, Drees, Georg, Fehsenfeld, Sandra, Fischer, Tim, Karbe, Fritz Richard, Link, Rudolf, Manke, Anne, Rickels, Wilfried, Schlosser, Christian, Schneider, Anke, Schütt, Martina, Stange, Karen, Stramma, Lothar, Tanhua, Toste, Wilcken, Sara, and Zocher, Johanna

Abstract

The research cruise MSM10/1 was extremely successful. All programs were able to collect high quality data and the anticipated goals of the expedition were fully met. We have been able to carry out the first comprehensive survey of a tracer release in the Guinea Upwelling region (GUTRE) roughly seven month after the tracer was released at 8°N 23°W in April 2008. We have estimated that a total of 40% of the tracer was found during this cruise. While the horizontal spreading and mixing was larger than anticipated, the vertical extent of the tracer found was small. The low vertical tracer spreading rate estimates are supported by the micro structure profile data. The extensive survey of the upper 1000m of the oxygen minimum zone (OMZ) allowed comparing our sections with several previous surveys. We found that the lowest oxygen values in the core of the OMZ have dropped at record low values below 40 μmol/kg. The preliminary findings from the trace metal work focused on Fe ligand measurements shows a slight higher excess ligand concentration in the surface (50m) for three stations. The two other stations show a slight decrease at this depth. A large number of biochemical samples were taken and were analyzed in Kiel for DNA and RNA diversity. The tracer release experiment provided an ideal environment for repeated biochemical sampling in the same water mass.

Published
2010

47. Guinea Upwelling Tracer Release Experiment – Cruise No. M80/2 – November 26 – December 22, 2009 – Mindelo (Cape Verde) – Dakar (Senegal)

Author

Wallace, Douglas W.R., Tanhua, Toste, Banyte, Donata, Dippe, Tina, Karbe, Fritz Richard, Link, Rudolf, Silva, P., Franz, Jasmin, Hansen, Thomas, Hauss, Helena, Nachtigall, Kerstin, Franzke, D., Fuessel, J., Kalvelage, T., Fischer, Tim, Gill, Diana, Kock, Annette, Stange, Karen, Baars, Oliver, Dammshäuser, Anna, Manke, A., Noll, L., Syre, S., Zocher, J., Raeke, A., Wallace, Douglas W.R., Tanhua, Toste, Banyte, Donata, Dippe, Tina, Karbe, Fritz Richard, Link, Rudolf, Silva, P., Franz, Jasmin, Hansen, Thomas, Hauss, Helena, Nachtigall, Kerstin, Franzke, D., Fuessel, J., Kalvelage, T., Fischer, Tim, Gill, Diana, Kock, Annette, Stange, Karen, Baars, Oliver, Dammshäuser, Anna, Manke, A., Noll, L., Syre, S., Zocher, J., and Raeke, A.

Published
2013
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49. The distribution of dissolved zinc in the Atlantic sector of the Southern Ocean

Author

Croot, Peter L., Baars, Oliver, Streu, Peter, Croot, Peter L., Baars, Oliver, and Streu, Peter

Abstract

The distribution of dissolved zinc (Zn) was investigated in the Atlantic sector of the Southern Ocean in the austral autumn of 2008 as part of the IPY GEOTRACES expedition ZERO & DRAKE. Research focused on transects across the major frontal systems along the Zero Meridian and across the Drake Passage. There was a strong gradient in surface zinc concentrations observed across the Antarctic Polar Front along both transects and high zinc levels were found in surface waters throughout the Southern Ocean. Vertical profiles for dissolved Zinc showed the presence of local minima and maxima in the upper 200 m consistent with significant uptake by phytoplankton and release by zooplankton grazing, respectively. Highest deep water zinc concentrations were found in the centre of the Weddell Gyre associated with Central Intermediate Water (CIW), a water mass which is depleted in O2, elevated in CO2 and is regionally a CFC minimum. Our data suggests that the remineralization of sinking particles is a key control on the distribution of Zn in the Southern Ocean. Disappearance ratios of zinc to phosphate (Zn:P) in the upper water column increased southwards along both transects and based on laboratory studies they suggest slower growth rates of phytoplankton due to iron or light limitation. Zinc and silicate were strongly correlated throughout the study region but the disappearance ratio (Zn:Si) was relatively uniform overall except for the region close to the ice edge on the Zero Meridian.

Published
2011

50. The distribution of dissolved zinc in the Atlantic sector of the Southern Ocean

Author

Croot, Peter, Baars, Oliver, Streu, Peter, Croot, Peter, Baars, Oliver, and Streu, Peter

Abstract

The distribution of dissolved zinc (Zn) was investigated in the Atlantic sector of the Southern Ocean in the austral autumn of 2008 as part of the IPY GEOTRACES expedition ZERO & DRAKE. Research focused on transects across the major frontal systems along the Zero Meridian and across the Drake Passage. There was a strong gradient in surface zinc concentrations observed across the Antarctic Polar Front along both transects and high zinc levels were found in surface waters throughout the Southern Ocean. Vertical profiles for dissolved Zinc showed the presence of local minima and maxima in the upper 200 m consistent with significant uptake by phytoplankton and release by zooplankton grazing, respectively. Highest deep water zinc concentrations were found in the centre of the Weddell Gyre associated with Central Intermediate Water (CIW), a water mass which is depleted in O2, elevated in CO2 and is regionally a CFC minimum. Our data suggests that the remineralization of sinking particles is a key control on the distribution of Zn in the Southern Ocean. Disappearance ratios of zinc to phosphate (Zn:P) in the upper water column increased southwards along both transects and based on laboratory studies they suggest slower growth rates of phytoplankton due to iron or light limitation. Zinc and silicate were strongly correlated throughout the study region but the disappearance ratio (Zn:Si) was relatively uniform overall except for the region close to the ice edge on the Zero Meridian.

Published
2011
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