IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-51583-4.html
   My bibliography  Save this article

Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling

Author

Listed:
  • Natalie R. Cohen

    (University of Georgia Skidaway Institute of Oceanography
    Woods Hole)

  • Arianna I. Krinos

    (Woods Hole
    Cambridge and Woods Hole)

  • Riss M. Kell

    (Woods Hole
    Gloucester Marine Genomics Institute)

  • Rebecca J. Chmiel

    (Woods Hole)

  • Dawn M. Moran

    (Woods Hole)

  • Matthew R. McIlvin

    (Woods Hole)

  • Paloma Z. Lopez

    (Woods Hole
    Bermuda Institute of Ocean Sciences)

  • Alexander J. Barth

    (University of South Carolina)

  • Joshua P. Stone

    (University of South Carolina)

  • Brianna A. Alanis

    (University of Texas Rio Grande Valley)

  • Eric W. Chan

    (University of Texas Rio Grande Valley)

  • John A. Breier

    (University of Texas Rio Grande Valley)

  • Michael V. Jakuba

    (Woods Hole)

  • Rod Johnson

    (Bermuda Institute of Ocean Sciences
    Arizona State University)

  • Harriet Alexander

    (Woods Hole)

  • Mak A. Saito

    (Woods Hole)

Abstract

Microeukaryotes are key contributors to marine carbon cycling. Their physiology, ecology, and interactions with the chemical environment are poorly understood in offshore ecosystems, and especially in the deep ocean. Using the Autonomous Underwater Vehicle Clio, microbial communities along a 1050 km transect in the western North Atlantic Ocean were surveyed at 10–200 m vertical depth increments to capture metabolic signatures spanning oligotrophic, continental margin, and productive coastal ecosystems. Microeukaryotes were examined using a paired metatranscriptomic and metaproteomic approach. Here we show a diverse surface assemblage consisting of stramenopiles, dinoflagellates and ciliates represented in both the transcript and protein fractions, with foraminifera, radiolaria, picozoa, and discoba proteins enriched at >200 m, and fungal proteins emerging in waters >3000 m. In the broad microeukaryote community, nitrogen stress biomarkers were found at coastal sites, with phosphorus stress biomarkers offshore. This multi-omics dataset broadens our understanding of how microeukaryotic taxa and their functional processes are structured along environmental gradients of temperature, light, and nutrients.

Suggested Citation

  • Natalie R. Cohen & Arianna I. Krinos & Riss M. Kell & Rebecca J. Chmiel & Dawn M. Moran & Matthew R. McIlvin & Paloma Z. Lopez & Alexander J. Barth & Joshua P. Stone & Brianna A. Alanis & Eric W. Chan, 2024. "Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51583-4
    DOI: 10.1038/s41467-024-51583-4
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-51583-4
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-51583-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. F. Delogu & B. J. Kunath & P. N. Evans & M. Ø. Arntzen & T. R. Hvidsten & P. B. Pope, 2020. "Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    2. T. J. Browning & E. P. Achterberg & J. C. Yong & I. Rapp & C. Utermann & A. Engel & C. M. Moore, 2017. "Iron limitation of microbial phosphorus acquisition in the tropical North Atlantic," Nature Communications, Nature, vol. 8(1), pages 1-7, August.
    3. Manuel Kleiner & Erin Thorson & Christine E. Sharp & Xiaoli Dong & Dan Liu & Carmen Li & Marc Strous, 2017. "Assessing species biomass contributions in microbial communities via metaproteomics," Nature Communications, Nature, vol. 8(1), pages 1-14, December.
    4. Adrian Marchetti & Micaela S. Parker & Lauren P. Moccia & Ellen O. Lin & Angele L. Arrieta & Francois Ribalet & Michael E. P. Murphy & Maria T. Maldonado & E. Virginia Armbrust, 2009. "Ferritin is used for iron storage in bloom-forming marine pennate diatoms," Nature, Nature, vol. 457(7228), pages 467-470, January.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Arianna I. Krinos & Margaret Mars Brisbin & Sarah K. Hu & Natalie R. Cohen & Tatiana A. Rynearson & Michael J. Follows & Frederik Schulz & Harriet Alexander, 2024. "Missing microbial eukaryotes and misleading meta-omic conclusions," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Clark, James R. & Daines, Stuart J. & Lenton, Timothy M. & Watson, Andrew J. & Williams, Hywel T.P., 2011. "Individual-based modelling of adaptation in marine microbial populations using genetically defined physiological parameters," Ecological Modelling, Elsevier, vol. 222(23), pages 3823-3837.
    2. Ray Sajulga & Caleb Easterly & Michael Riffle & Bart Mesuere & Thilo Muth & Subina Mehta & Praveen Kumar & James Johnson & Bjoern Andreas Gruening & Henning Schiebenhoefer & Carolin A Kolmeder & Steph, 2020. "Survey of metaproteomics software tools for functional microbiome analysis," PLOS ONE, Public Library of Science, vol. 15(11), pages 1-20, November.
    3. Zihao Zhao & Chie Amano & Thomas Reinthaler & Federico Baltar & Mónica V. Orellana & Gerhard J. Herndl, 2024. "Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. Thomas J. Browning & C. Mark Moore, 2023. "Global analysis of ocean phytoplankton nutrient limitation reveals high prevalence of co-limitation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Nils Giordano & Marinna Gaudin & Camille Trottier & Erwan Delage & Charlotte Nef & Chris Bowler & Samuel Chaffron, 2024. "Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    6. Leyuan Li & Tong Wang & Zhibin Ning & Xu Zhang & James Butcher & Joeselle M. Serrana & Caitlin M. A. Simopoulos & Janice Mayne & Alain Stintzi & David R. Mack & Yang-Yu Liu & Daniel Figeys, 2023. "Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    7. Haoyu Jin & Chao Zhang & Siyu Meng & Qin Wang & Xiaokun Ding & Ling Meng & Yunyun Zhuang & Xiaohong Yao & Yang Gao & Feng Shi & Thomas Mock & Huiwang Gao, 2024. "Atmospheric deposition and river runoff stimulate the utilization of dissolved organic phosphorus in coastal seas," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    8. Haider Ali & Dongda Zhang & Jonathan L. Wagner & Cheol Woo Park, 2018. "Two-Phase Flow Modeling of Solid Dissolution in Liquid for Nutrient Mixing Improvement in Algal Raceway Ponds," Energies, MDPI, vol. 11(4), pages 1-21, April.
    9. Guo-Wei Qiu & Wen-Can Zheng & Hao-Ming Yang & Yu-Ying Wang & Xing Qi & Da Huang & Guo-Zheng Dai & Huazhong Shi & Neil M. Price & Bao-Sheng Qiu, 2024. "Phosphorus deficiency alleviates iron limitation in Synechocystis cyanobacteria through direct PhoB-mediated gene regulation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    10. Lee, Eun Seo & Park, Seon Yeong & Kim, Chang Gyun, 2023. "Feasibility test anaerobically enhancing methane yield under the injection of hydrogen and carbon dioxide," Renewable Energy, Elsevier, vol. 212(C), pages 761-768.
    11. Leah A. Owens & Sagan Friant & Bruno Martorelli Di Genova & Laura J. Knoll & Monica Contreras & Oscar Noya-Alarcon & Maria G. Dominguez-Bello & Tony L. Goldberg, 2024. "VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    12. Zhang, Bing & Li, Wei & Guo, Yuan & Zhang, Zhiqiang & Shi, Wenxin & Cui, Fuyi & Lens, Piet N.L. & Tay, Joo Hwa, 2020. "Microalgal-bacterial consortia: From interspecies interactions to biotechnological applications," Renewable and Sustainable Energy Reviews, Elsevier, vol. 118(C).

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51583-4. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.