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Distinct siderophores contribute to iron cycling in the mesopelagic at Station ALOHA (2018)

Bundy, Randelle M. ; Boiteau, Rene M. ; McLean, Craig ; [et al.]

Frontiers Media

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Publication Date: 2022-05-25

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 61, doi:10.3389/fmars.2018.00061.

Description: The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in the mesopelagic.

Description: This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747).

Keywords: Iron ; Siderophores ; Station ALOHA ; Organic ligands ; Iron limitation

Repository Name: Woods Hole Open Access Server

Type: Article

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Distinct siderophores contribute to iron cycling in the mesopelagic at station ALOHA (2019)

Bundy, Randelle M. ; Boiteau, Rene M. ; McLean, Craig ; [et al.]

Frontiers Media

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Publication Date: 2019-02-19

Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bundy, R. M., Boiteau, R. M., McLean, C., Turk-Kubo, K. A., Mcllvin, M. R., Saito, M. A., Van Mooy, B. A. S., & Repeta, D. J.. Distinct siderophores contribute to iron cycling in the mesopelagic at station ALOHA. Frontiers in Marine Science, 5, (2018): 61. doi:10.3389/fmars.2018.00061.

Description: The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in the mesopelagic.

Description: We thank Chief Scientists Tara Clemente and Sam Wilson for leading the SCOPE Diel cruises. We also thank the Captain and crew of the R/V Ka'imikai-O-Kanaloa, as well as Paul Henderson in the Woods Hole Oceanographic Nutrient Analytical Facility for nutrient analyses. This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747). We also thank two reviewers for helpful comments on the manuscript.

Keywords: iron ; siderophores ; Station ALOHA ; organic ligands ; iron limitation

Repository Name: Woods Hole Open Access Server

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A metabolic lens on phytoplankton physiology (2021)

McLean, Craig

Massachusetts Institute of Technology and Woods Hole Oceanographic Institution

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Publication Date: 2022-10-20

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.

Description: Phytoplankton are communities of diverse groups of prokaryotic and eukaryotic single-celled organisms responsible for nearly 50% of global primary production. The relative abundance of individual groups changes dynamically in response to environmental perturbations. Recent studies suggest that such changes are primarily driven by the distinct physiological responses employed by each group towards a particular perturbation. Although knowledge of some of these responses has come to light in recent years, many aspects of their metabolisms remain unknown. We attempt to address this gap by studying the metabolism of several phytoplankton groups using metabolomics. Firstly, we developed a method to enhance the analysis of untargeted metabolomics data. Secondly, we constructed two conceptual models describing how metabolism of the raphidophyte Heterosigma akashiwo responds to phosphorus and nitrogen stress. These conceptual models revealed several new stress response mechanisms not previously reported in other phytoplankton. Finally, we compared the metabolic changes of several distinct phytoplankton groups to uncover possible adaptation and acclimations that distinguish them. This analysis revealed several pathways and metabolites that represent the studied groups. The contributions of these pathways and metabolites towards physiology may support the ecological fitness of these organisms.

Description: None of this work would have been possible without a variety of funding sources. I was supported for three years by a National Science Foundation Graduate Research Fellowship and one year with a GEM fellowship. The research was carried out with grants from the MIT Microbiome Center (Award ID #6936800, EBK), the Simons Foundation (Award ID #509034, EBK), the Gordon and Betty Moore Foundation (Award ID #3304 EBK), the National Science Foundation (Award ID #OCE-0619608 to EBK and OCE-1057447 to EBK and MCKS) and the WHOI Ocean Ventures Fund.

Keywords: Phytoplankton ; Metabolism ; Metbolomics

Repository Name: Woods Hole Open Access Server

Type: Thesis

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Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer (2020)

Seyler, Lauren M. ; Brazelton, William J. ; McLean, Craig ; [et al.]

American Society for Microbiology

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Publication Date: 2022-10-26

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Brazelton, W. J., McLean, C., Putman, L. I., Hyer, A., Kubo, M. D. Y., Hoehler, T., Cardace, D., & Schrenk, M. O. . Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer. mSystems, 5(2), (2020): e00607-00619, doi: 10.1128/mSystems.00607-19.

Description: Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.

Description: We thank McLaughlin Reserve, in particular Paul Aigner and Cathy Koehler, for hosting sampling at CROMO and providing access to the wells, A. Daniel Jones and Anthony Schilmiller for their advice regarding metabolite extraction and mass spectrometry, Elizabeth Kujawinski for her guidance in metabolomics data analysis and interpretation, and Julia McGonigle, Christopher Thornton, and Katrina Twing for assistance with metagenomic and computational analyses.

Keywords: Carbon assimilation ; Carbon fixation ; Formaldehyde ; Formate ; Methane ; Serpentinization

Repository Name: Woods Hole Open Access Server

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AutoTuner: high fidelity and robust parameter selection for metabolomics data processing (2020)

McLean, Craig ; Kujawinski, Elizabeth B.

American Chemical Society

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Publication Date: 2022-05-26

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McLean, C., & Kujawinski, E. B. AutoTuner: high fidelity and robust parameter selection for metabolomics data processing. Analytical Chemistry, 92(8), (2020): 5724-5732, doi:10.1021/acs.analchem.9b04804.

Description: Untargeted metabolomics experiments provide a snapshot of cellular metabolism but remain challenging to interpret due to the computational complexity involved in data processing and analysis. Prior to any interpretation, raw data must be processed to remove noise and to align mass-spectral peaks across samples. This step requires selection of dataset-specific parameters, as erroneous parameters can result in noise inflation. While several algorithms exist to automate parameter selection, each depends on gradient descent optimization functions. In contrast, our new parameter optimization algorithm, AutoTuner, obtains parameter estimates from raw data in a single step as opposed to many iterations. Here, we tested the accuracy and the run-time of AutoTuner in comparison to isotopologue parameter optimization (IPO), the most commonly used parameter selection tool, and compared the resulting parameters’ influence on the properties of feature tables after processing. We performed a Monte Carlo experiment to test the robustness of AutoTuner parameter selection and found that AutoTuner generated similar parameter estimates from random subsets of samples. We conclude that AutoTuner is a desirable alternative to existing tools, because it is scalable, highly robust, and very fast (∼100–1000× speed improvement from other algorithms going from days to minutes). AutoTuner is freely available as an R package through BioConductor.

Description: We thank Titus Brown and Ben Temperton for advice on the algorithm validation, Arthur Eschenlauer for constructive feedback on the software design, Krista Longnecker for continuous support and discussions, Gabriel Leventhal for mathematics advice, the users of AutoTuner for debugging help through Github, and David Angeles-Albores and two anonymous reviewers for critical feedback on the manuscript. Funding support included the National GEM Consortium and NSF graduate research program fellowships (C.M.) and grants from the MIT Microbiome Center (Award 6936800, E.B.K.) and the Simons Foundation (Award ID #509034, E.B.K.).

Repository Name: Woods Hole Open Access Server

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Whole-genome landscape of pancreatic neuroendocrine tumours (2017)

Aldo Scarpa; David K. Chang; Katia Nones; Vincenzo Corbo; Ann-Marie Patch; Peter Bailey; Rita T. Lawlor; Amber L. Johns; David K. Miller; Andrea Mafficini; Borislav Rusev; Maria Scardoni; Davide Antonello; Stefano Barbi; Katarzyna O. Sikora; Sara Cingarlini; Caterina Vicentini; Skye McKay; Michael C. J. Quinn; Timothy J. C. Bruxner; Angelika N. Christ; Ivon Harliwong; Senel Idrisoglu; Suzanne McLean; Craig Nourse; Ehsan Nourbakhsh; Peter J. Wilson; Matthew J. Anderson; J. Lynn Fink; Felicity Newell; Nick Waddell; Oliver Holmes; Stephen H. Kazakoff; Conrad Leonard; Scott Wood; Qinying Xu; Shivashankar Hiriyur Nagaraj; Eliana Amato; Irene Dalai; Samantha Bersani; Ivana Cataldo; Angelo P. Dei Tos; Paola Capelli; Maria Vittoria DavìLuca Landoni; Anna Malpaga; Marco Miotto; Vicki L. J. Whitehall; Barbara A. Leggett; Janelle L. Harris; Jonathan Harris; Marc D. Jones; Jeremy Humphris; Lorraine A. Chantrill; Venessa Chin; Adnan M. Nagrial; Marina Pajic; Christopher J. Scarlett; Andreia Pinho; Ilse Rooman; Christopher Toon; Jianmin Wu; Mark Pinese; Mark Cowley; Andrew Barbour; Amanda Mawson; Emily S. Humphrey; Emily K. Colvin; Angela Chou; Jessica A. Lovell; Nigel B. Jamieson; Fraser Duthie; Marie-Claude Gingras; William E. Fisher; Rebecca A. Dagg; Loretta M. S. Lau; Michael Lee; Hilda A. Pickett; Roger R. Reddel; Jaswinder S. Samra; James G. Kench; Neil D. Merrett; Krishna Epari; Nam Q. Nguyen; Nikolajs Zeps; Massimo Falconi; Michele Simbolo; Giovanni Butturini; George Van Buren; Stefano Partelli; Matteo Fassan; Kum Kum Khanna; Anthony J. Gill; David A. Wheeler; Richard A. Gibbs; Elizabeth A. Musgrove; Claudio Bassi; Giampaolo Tortora; Paolo Pederzoli; John V. Pearson; Nicola Waddell; Andrew V. Biankin; Sean M. Grimmond

Springer Nature

In: Nature

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Publication Date: 2017-03-02

Description: Whole-genome landscape of pancreatic neuroendocrine tumours Nature 543, 7643 (2017). doi:10.1038/nature21063 Authors: Aldo Scarpa, David K. Chang, Katia Nones, Vincenzo Corbo, Ann-Marie Patch, Peter Bailey, Rita T. Lawlor, Amber L. Johns, David K. Miller, Andrea Mafficini, Borislav Rusev, Maria Scardoni, Davide Antonello, Stefano Barbi, Katarzyna O. Sikora, Sara Cingarlini, Caterina Vicentini, Skye McKay, Michael C. J. Quinn, Timothy J. C. Bruxner, Angelika N. Christ, Ivon Harliwong, Senel Idrisoglu, Suzanne McLean, Craig Nourse, Ehsan Nourbakhsh, Peter J. Wilson, Matthew J. Anderson, J. Lynn Fink, Felicity Newell, Nick Waddell, Oliver Holmes, Stephen H. Kazakoff, Conrad Leonard, Scott Wood, Qinying Xu, Shivashankar Hiriyur Nagaraj, Eliana Amato, Irene Dalai, Samantha Bersani, Ivana Cataldo, Angelo P. Dei Tos, Paola Capelli, Maria Vittoria Davì, Luca Landoni, Anna Malpaga, Marco Miotto, Vicki L. J. Whitehall, Barbara A. Leggett, Janelle L. Harris, Jonathan Harris, Marc D. Jones, Jeremy Humphris, Lorraine A. Chantrill, Venessa Chin, Adnan M. Nagrial, Marina Pajic, Christopher J. Scarlett, Andreia Pinho, Ilse Rooman, Christopher Toon, Jianmin Wu, Mark Pinese, Mark Cowley, Andrew Barbour, Amanda Mawson, Emily S. Humphrey, Emily K. Colvin, Angela Chou, Jessica A. Lovell, Nigel B. Jamieson, Fraser Duthie, Marie-Claude Gingras, William E. Fisher, Rebecca A. Dagg, Loretta M. S. Lau, Michael Lee, Hilda A. Pickett, Roger R. Reddel, Jaswinder S. Samra, James G. Kench, Neil D. Merrett, Krishna Epari, Nam Q. Nguyen, Nikolajs Zeps, Massimo Falconi, Michele Simbolo, Giovanni Butturini, George Van Buren, Stefano Partelli, Matteo Fassan, Kum Kum Khanna, Anthony J. Gill, David A. Wheeler, Richard A. Gibbs, Elizabeth A. Musgrove, Claudio Bassi, Giampaolo Tortora, Paolo Pederzoli, John V. Pearson, Nicola Waddell, Andrew V. Biankin & Sean M. Grimmond The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Springer Nature

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The National Earth System Prediction Capability: Coordinating the Giant (2017)

Carman, Jessie C. ; Eleuterio, Daniel P. ; Gallaudet, Timothy C. ; [et al.]

American Meteorological Society

In: Bulletin of the American Meteorological Society. 2017; 98(2): 239-252. Published 2017 Feb 01. doi: 10.1175/bams-d-16-0002.1.

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Publication Date: 2017-02-01

Description: The United States has had three operational numerical weather prediction centers since the Joint Numerical Weather Prediction Unit was closed in 1958. This led to separate paths for U.S. numerical weather prediction, research, technology, and operations, resulting in multiple community calls for better coordination. Since 2006, the three operational organizations—the U.S. Air Force, the U.S. Navy, and the National Weather Service—and, more recently, the Department of Energy, the National Aeronautics and Space Administration, the National Science Foundation, and the National Oceanic and Atmospheric Administration/Office of Oceanic and Atmospheric Research, have been working to increase coordination. This increasingly successful effort has resulted in the establishment of a National Earth System Prediction Capability (National ESPC) office with responsibility to further interagency coordination and collaboration. It has also resulted in sharing of data through an operational global ensemble, common software standards, and model components among the agencies. This article discusses the drivers, the progress, and the future of interagency collaboration.

Print ISSN: 0003-0007

Electronic ISSN: 1520-0477

Topics: Geography , Physics