IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-36026-w.html
   My bibliography  Save this article

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

Author

Listed:
  • David Geller-McGrath

    (Woods Hole Oceanographic Institution)

  • Paraskevi Mara

    (Woods Hole Oceanographic Institution)

  • Gordon T. Taylor

    (Stony Brook University)

  • Elizabeth Suter

    (Stony Brook University
    Molloy College)

  • Virginia Edgcomb

    (Woods Hole Oceanographic Institution)

  • Maria Pachiadaki

    (Woods Hole Oceanographic Institution)

Abstract

Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.

Suggested Citation

  • David Geller-McGrath & Paraskevi Mara & Gordon T. Taylor & Elizabeth Suter & Virginia Edgcomb & Maria Pachiadaki, 2023. "Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36026-w
    DOI: 10.1038/s41467-023-36026-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-36026-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-36026-w?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. Kirstin Scherlach & Christian Hertweck, 2021. "Mining and unearthing hidden biosynthetic potential," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Sunke Schmidtko & Lothar Stramma & Martin Visbeck, 2017. "Decline in global oceanic oxygen content during the past five decades," Nature, Nature, vol. 542(7641), pages 335-339, February.
    3. Lucas Paoli & Hans-Joachim Ruscheweyh & Clarissa C. Forneris & Florian Hubrich & Satria Kautsar & Agneya Bhushan & Alessandro Lotti & Quentin Clayssen & Guillem Salazar & Alessio Milanese & Charlotte , 2022. "Biosynthetic potential of the global ocean microbiome," Nature, Nature, vol. 607(7917), pages 111-118, July.
    Full references (including those not matched with items on IDEAS)

    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. Chen, Haojie & Costanza, Robert & Kubiszewski, Ida, 2022. "Legitimacy and limitations of valuing the oxygen production of ecosystems," Ecosystem Services, Elsevier, vol. 58(C).
    2. Laetitia E. Pichevin & Massimo Bollasina & Alexandra J. Nederbragt & Raja S. Ganeshram, 2024. "North Atlantic temperature control on deoxygenation in the northern tropical Pacific," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Xianzhe Gong & Álvaro Rodríguez Río & Le Xu & Zhiyi Chen & Marguerite V. Langwig & Lei Su & Mingxue Sun & Jaime Huerta-Cepas & Valerie Anda & Brett J. Baker, 2022. "New globally distributed bacterial phyla within the FCB superphylum," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    4. 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.
    5. Georges P. Schmartz & Jacqueline Rehner & Miriam J. Schuff & Leidy-Alejandra G. Molano & Sören L. Becker & Marcin Krawczyk & Azat Tagirdzhanov & Alexey Gurevich & Richard Francke & Rolf Müller & Veren, 2024. "Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    6. Jinzhou Peng & Dengfeng Li & Simon W. Poulton & Gary J. O’Sullivan & David Chew & Yu Fu & Xiaoming Sun, 2024. "Episodic intensification of marine phosphorus burial over the last 80 million years," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    7. Hanna Chen & Lin Zhong & Haibo Zhou & Xianping Bai & Tao Sun & Xingyan Wang & Yiming Zhao & Xiaoqi Ji & Qiang Tu & Youming Zhang & Xiaoying Bian, 2023. "Biosynthesis and engineering of the nonribosomal peptides with a C-terminal putrescine," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    8. , European Marine Board & Boero, Ferdinando & Cummins, Valerie & Gault, Jeremy & Huse, Geir & Philippart, Catharina & Schneider, Ralph & Besiktepe, Sukru & Boeuf, Gilles & Coll, Marta, 2019. "Navigating the Future V: Marine Science for a Sustainable Future," MarXiv vps62, Center for Open Science.
    9. Angelina Beavogui & Auriane Lacroix & Nicolas Wiart & Julie Poulain & Tom O. Delmont & Lucas Paoli & Patrick Wincker & Pedro H. Oliveira, 2024. "The defensome of complex bacterial communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    10. Corentin Hochart & Lucas Paoli & Hans-Joachim Ruscheweyh & Guillem Salazar & Emilie Boissin & Sarah Romac & Julie Poulain & Guillaume Bourdin & Guillaume Iwankow & Clémentine Moulin & Maren Ziegler & , 2023. "Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    11. Kevin C. Rose & Britta Bierwagen & Scott D. Bridgham & Daren M. Carlisle & Charles P. Hawkins & N. LeRoy Poff & Jordan S. Read & Jason R. Rohr & Jasmine E. Saros & Craig E. Williamson, 2023. "Indicators of the effects of climate change on freshwater ecosystems," Climatic Change, Springer, vol. 176(3), pages 1-20, March.
    12. Jinfeng Li & Bao Chen & Zunyun Fu & Jingjing Mao & Lijun Liu & Xiaochen Chen & Mingyue Zheng & Chang-Yun Wang & Chengyuan Wang & Yue-Wei Guo & Baofu Xu, 2024. "Discovery of a terpene synthase synthesizing a nearly non-flexible eunicellane reveals the basis of flexibility," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    13. Kalyan Annamalai, 2024. "Breathing Planet Earth: Analysis of Keeling’s Data on CO 2 and O 2 with Respiratory Quotient (RQ), Part II: Energy-Based Global RQ and CO 2 Budget," Energies, MDPI, vol. 17(8), pages 1-46, April.
    14. Changyu Li & Jianping Huang & Xiaoyue Liu & Lei Ding & Yongli He & Yongkun Xie, 2024. "The ocean losing its breath under the heatwaves," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    15. Catherine V. Davis & Elizabeth C. Sibert & Peter H. Jacobs & Natalie Burls & Pincelli M. Hull, 2023. "Intermediate water circulation drives distribution of Pliocene Oxygen Minimum Zones," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    16. Bin Ma & Caiyu Lu & Yiling Wang & Jingwen Yu & Kankan Zhao & Ran Xue & Hao Ren & Xiaofei Lv & Ronghui Pan & Jiabao Zhang & Yongguan Zhu & Jianming Xu, 2023. "A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    17. Xiao Zhang & Shengchao Ye & Manhong Shen, 2023. "Driving Factors and Spatiotemporal Characteristics of CO 2 Emissions from Marine Fisheries in China: A Commonly Neglected Carbon-Intensive Sector," IJERPH, MDPI, vol. 20(1), pages 1-17, January.
    18. Alexander Bogdanov & Mariam N. Salib & Alexander B. Chase & Heinz Hammerlindl & Mitchell N. Muskat & Stephanie Luedtke & Elany Barbosa Silva & Anthony J. O’Donoghue & Lani F. Wu & Steven J. Altschuler, 2024. "Small molecule in situ resin capture provides a compound first approach to natural product discovery," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    19. Ziye Wang & Ronghui You & Haitao Han & Wei Liu & Fengzhu Sun & Shanfeng Zhu, 2024. "Effective binning of metagenomic contigs using contrastive multi-view representation learning," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    20. Lewis, Dakota M. & Vardi, Tali & Maher, Rebecca L. & Correa, Adrienne M.S. & Cook, Geoffrey S., 2022. "Predicting shifts in demography of Orbicella franksi following simulated disturbance and restoration," Ecological Modelling, Elsevier, vol. 472(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:14:y:2023:i:1:d:10.1038_s41467-023-36026-w. 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.