IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-47914-0.html
   My bibliography  Save this article

Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics

Author

Listed:
  • Joanne S. Boden

    (University of St. Andrews, Bute Building, Queen’s terrace)

  • Juntao Zhong

    (Washington University in St. Louis)

  • Rika E. Anderson

    (Carleton College)

  • Eva E. Stüeken

    (University of St. Andrews, Bute Building, Queen’s terrace)

Abstract

Phosphorus plays a crucial role in controlling biological productivity, but geological estimates of phosphate concentrations in the Precambrian ocean, during life’s origin and early evolution, vary over several orders of magnitude. While reduced phosphorus species may have served as alternative substrates to phosphate, their bioavailability on the early Earth remains unknown. Here, we reconstruct the phylogenomic record of life on Earth and find that phosphate transporting genes (pnas) evolved in the Paleoarchean (ca. 3.6-3.2 Ga) and are consistent with phosphate concentrations above modern levels ( > 3 µM). The first gene optimized for low phosphate levels (pstS;

Suggested Citation

  • Joanne S. Boden & Juntao Zhong & Rika E. Anderson & Eva E. Stüeken, 2024. "Timing the evolution of phosphorus-cycling enzymes through geological time using phylogenomics," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47914-0
    DOI: 10.1038/s41467-024-47914-0
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-47914-0
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-47914-0?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. Qiyun Zhu & Uyen Mai & Wayne Pfeiffer & Stefan Janssen & Francesco Asnicar & Jon G. Sanders & Pedro Belda-Ferre & Gabriel A. Al-Ghalith & Evguenia Kopylova & Daniel McDonald & Tomasz Kosciolek & John , 2019. "Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    2. Yuichiro Ueno & Keita Yamada & Naohiro Yoshida & Shigenori Maruyama & Yukio Isozaki, 2006. "Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era," Nature, Nature, vol. 440(7083), pages 516-519, March.
    3. Joanne S. Boden & Kurt O. Konhauser & Leslie J. Robbins & Patricia Sánchez-Baracaldo, 2021. "Timing the evolution of antioxidant enzymes in cyanobacteria," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Christopher T. Reinhard & Noah J. Planavsky & Benjamin C. Gill & Kazumi Ozaki & Leslie J. Robbins & Timothy W. Lyons & Woodward W. Fischer & Chunjiang Wang & Devon B. Cole & Kurt O. Konhauser, 2017. "Evolution of the global phosphorus cycle," Nature, Nature, vol. 541(7637), pages 386-389, January.
    5. Alexei J Drummond & Simon Y W Ho & Matthew J Phillips & Andrew Rambaut, 2006. "Relaxed Phylogenetics and Dating with Confidence," PLOS Biology, Public Library of Science, vol. 4(5), pages 1-1, March.
    6. Lawrence A. David & Eric J. Alm, 2011. "Rapid evolutionary innovation during an Archaean genetic expansion," Nature, Nature, vol. 469(7328), pages 93-96, January.
    7. Matthew P. Brady & Rosalie Tostevin & Nicholas J. Tosca, 2022. "Marine phosphate availability and the chemical origins of life on Earth," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    8. Stephen J. Mojzsis & T. Mark Harrison & Robert T. Pidgeon, 2001. "Oxygen-isotope evidence from ancient zircons for liquid water at the Earth's surface 4,300 Myr ago," Nature, Nature, vol. 409(6817), pages 178-181, January.
    9. Nicola Segata & Daniela Börnigen & Xochitl C. Morgan & Curtis Huttenhower, 2013. "PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes," Nature Communications, Nature, vol. 4(1), pages 1-11, October.
    10. Enqing Hou & Yiqi Luo & Yuanwen Kuang & Chengrong Chen & Xiankai Lu & Lifen Jiang & Xianzhen Luo & Dazhi Wen, 2020. "Global meta-analysis shows pervasive phosphorus limitation of aboveground plant production in natural terrestrial ecosystems," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    11. Robert C. Edgar, 2022. "Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    12. Simon A. Wilde & John W. Valley & William H. Peck & Colin M. Graham, 2001. "Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago," Nature, Nature, vol. 409(6817), pages 175-178, January.
    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. Hao Leng & Yinzhao Wang & Weishu Zhao & Stefan M. Sievert & Xiang Xiao, 2023. "Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Joachim Schmidt & Lars Opgenoorth & Steffen Höll & Ralf Bastrop, 2012. "Into the Himalayan Exile: The Phylogeography of the Ground Beetle Ethira clade Supports the Tibetan Origin of Forest-Dwelling Himalayan Species Groups," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-15, September.
    3. Iliana Bista & Jonathan M. D. Wood & Thomas Desvignes & Shane A. McCarthy & Michael Matschiner & Zemin Ning & Alan Tracey & James Torrance & Ying Sims & William Chow & Michelle Smith & Karen Oliver & , 2023. "Genomics of cold adaptations in the Antarctic notothenioid fish radiation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Haitao Shang & Daniel H. Rothman & Gregory P. Fournier, 2022. "Oxidative metabolisms catalyzed Earth’s oxygenation," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    5. Wang Zheng & Anwen Zhou & Swapan K. Sahoo & Morrison R. Nolan & Chadlin M. Ostrander & Ruoyu Sun & Ariel D. Anbar & Shuhai Xiao & Jiubin Chen, 2023. "Recurrent photic zone euxinia limited ocean oxygenation and animal evolution during the Ediacaran," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    6. Mekala Sundaram & Janna R Willoughby & Nathanael I Lichti & Michael A Steele & Robert K Swihart, 2015. "Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-16, June.
    7. Jonathon D. Gass & Nichola J. Hill & Lambodhar Damodaran & Elena N. Naumova & Felicia B. Nutter & Jonathan A. Runstadler, 2023. "Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016–Early 2022," IJERPH, MDPI, vol. 20(11), pages 1-17, June.
    8. Asada, K. & Kanda, T. & Yamashita, N. & Asano, M. & Eguchi, S., 2022. "Interpreting stoichiometric homeostasis and flexibility of soil microbial biomass carbon, nitrogen, and phosphorus," Ecological Modelling, Elsevier, vol. 470(C).
    9. Guoxiong Chen & Qiuming Cheng & Timothy W. Lyons & Jun Shen & Frits Agterberg & Ning Huang & Molei Zhao, 2022. "Reconstructing Earth’s atmospheric oxygenation history using machine learning," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    10. Nico Neureiter & Peter Ranacher & Nour Efrat-Kowalsky & Gereon A. Kaiping & Robert Weibel & Paul Widmer & Remco R. Bouckaert, 2022. "Detecting contact in language trees: a Bayesian phylogenetic model with horizontal transfer," Palgrave Communications, Palgrave Macmillan, vol. 9(1), pages 1-14, December.
    11. Matthew P. Brady & Rosalie Tostevin & Nicholas J. Tosca, 2022. "Marine phosphate availability and the chemical origins of life on Earth," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    12. Michael D Nowak & Andrew B Smith & Carl Simpson & Derrick J Zwickl, 2013. "A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-13, June.
    13. Liang, Zhongyao & Wu, Sifeng & Chen, Huili & Yu, Yanhong & Liu, Yong, 2018. "A probabilistic method to enhance understanding of nutrient limitation dynamics of phytoplankton," Ecological Modelling, Elsevier, vol. 368(C), pages 404-410.
    14. Bethany L Dearlove & Simon D W Frost, 2015. "Measuring Asymmetry in Time-Stamped Phylogenies," PLOS Computational Biology, Public Library of Science, vol. 11(7), pages 1-16, July.
    15. Hoan X. Dinh & Davinder Singh & Diana Gomez de la Cruz & Goetz Hensel & Jochen Kumlehn & Martin Mascher & Nils Stein & Dragan Perovic & Michael Ayliffe & Matthew J. Moscou & Robert F. Park & Mohammad , 2022. "The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    16. Wang, Linlin & Xie, Junhong & Luo, Zhuzhu & Niu, Yining & Coulter, Jeffrey A. & Zhang, Renzhi & Lingling, Li, 2021. "Forage yield, water use efficiency, and soil fertility response to alfalfa growing age in the semiarid Loess Plateau of China," Agricultural Water Management, Elsevier, vol. 243(C).
    17. Idrissa Nonmon Sanogo & Claire Guinat & Simon Dellicour & Mohamed Adama Diakité & Mamadou Niang & Ousmane A Koita & Christelle Camus & Mariette F. Ducatez & Mariette Ducatez, 2024. "Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa," Post-Print hal-04498485, HAL.
    18. Matheus Pontes-Nogueira & Marcio Martins & Laura R V Alencar & Ricardo J Sawaya, 2021. "The role of vicariance and dispersal on the temporal range dynamics of forest vipers in the Neotropical region," PLOS ONE, Public Library of Science, vol. 16(9), pages 1-18, September.
    19. Benjamin T. Uveges & Gareth Izon & Shuhei Ono & Nicolas J. Beukes & Roger E. Summons, 2023. "Reconciling discrepant minor sulfur isotope records of the Great Oxidation Event," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    20. Meng-Shu Hao & Scott Mazurkewich & He Li & Alma Kvammen & Srijani Saha & Salla Koskela & Annie R. Inman & Masahiro Nakajima & Nobukiyo Tanaka & Hiroyuki Nakai & Gisela Brändén & Vincent Bulone & Johan, 2024. "Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to β-glucans," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

    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_s41467-024-47914-0. 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.