IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-47348-8.html
   My bibliography  Save this article

Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally

Author

Listed:
  • Ziheng Peng

    (Northwest A&F University)

  • Xun Qian

    (Northwest A&F University)

  • Yu Liu

    (Northwest A&F University)

  • Xiaomeng Li

    (Northwest A&F University)

  • Hang Gao

    (Northwest A&F University)

  • Yining An

    (Northwest A&F University)

  • Jiejun Qi

    (Northwest A&F University)

  • Lan Jiang

    (Northwest A&F University)

  • Yiran Zhang

    (Northwest A&F University)

  • Shi Chen

    (Northwest A&F University)

  • Haibo Pan

    (Northwest A&F University)

  • Beibei Chen

    (Northwest A&F University)

  • Chunling Liang

    (Northwest A&F University)

  • Marcel G. A. Heijden

    (Agroscope
    University of Zurich)

  • Gehong Wei

    (Northwest A&F University)

  • Shuo Jiao

    (Northwest A&F University)

Abstract

Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.

Suggested Citation

  • Ziheng Peng & Xun Qian & Yu Liu & Xiaomeng Li & Hang Gao & Yining An & Jiejun Qi & Lan Jiang & Yiran Zhang & Shi Chen & Haibo Pan & Beibei Chen & Chunling Liang & Marcel G. A. Heijden & Gehong Wei & S, 2024. "Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47348-8
    DOI: 10.1038/s41467-024-47348-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-47348-8
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-47348-8?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. David U. Hooper & E. Carol Adair & Bradley J. Cardinale & Jarrett E. K. Byrnes & Bruce A. Hungate & Kristin L. Matulich & Andrew Gonzalez & J. Emmett Duffy & Lars Gamfeldt & Mary I. O’Connor, 2012. "A global synthesis reveals biodiversity loss as a major driver of ecosystem change," Nature, Nature, vol. 486(7401), pages 105-108, June.
    2. Maëva Labouyrie & Cristiano Ballabio & Ferran Romero & Panos Panagos & Arwyn Jones & Marc W. Schmid & Vladimir Mikryukov & Olesya Dulya & Leho Tedersoo & Mohammad Bahram & Emanuele Lugato & Marcel G. , 2023. "Patterns in soil microbial diversity across Europe," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    3. Xiaogang Li & Dele Chen & Víctor J. Carrión & Daniel Revillini & Shan Yin & Yuanhua Dong & Taolin Zhang & Xingxiang Wang & Manuel Delgado-Baquerizo, 2023. "Author Correction: Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections," Nature Communications, Nature, vol. 14(1), pages 1-1, December.
    4. Bates, Douglas & Mächler, Martin & Bolker, Ben & Walker, Steve, 2015. "Fitting Linear Mixed-Effects Models Using lme4," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 67(i01).
    5. Maëva Labouyrie & Cristiano Ballabio & Ferran Romero & Panos Panagos & Arwyn Jones & Marc W. Schmid & Vladimir Mikryukov & Olesya Dulya & Leho Tedersoo & Mohammad Bahram & Emanuele Lugato & Marcel G. , 2023. "Publisher Correction: Patterns in soil microbial diversity across Europe," Nature Communications, Nature, vol. 14(1), pages 1-1, December.
    6. Ning Ling & Tingting Wang & Yakov Kuzyakov, 2022. "Rhizosphere bacteriome structure and functions," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Sean L. Maxwell & Richard A. Fuller & Thomas M. Brooks & James E. M. Watson, 2016. "Biodiversity: The ravages of guns, nets and bulldozers," Nature, Nature, vol. 536(7615), pages 143-145, August.
    8. Wu-Bing Xu & Shane A. Blowes & Viviana Brambilla & Cher F. Y. Chow & Ada Fontrodona-Eslava & Inês S. Martins & Daniel McGlinn & Faye Moyes & Alban Sagouis & Hideyasu Shimadzu & Roel Klink & Anne E. Ma, 2023. "Regional occupancy increases for widespread species but decreases for narrowly distributed species in metacommunity time series," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    9. Diana H. Wall & Uffe N. Nielsen & Johan Six, 2015. "Soil biodiversity and human health," Nature, Nature, vol. 528(7580), pages 69-76, December.
    10. Barnabas H. Daru & T. Jonathan Davies & Charles G. Willis & Emily K. Meineke & Argo Ronk & Martin Zobel & Meelis Pärtel & Alexandre Antonelli & Charles C. Davis, 2021. "Widespread homogenization of plant communities in the Anthropocene," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    11. Liang Tian & Xu-Wen Wang & Ang-Kun Wu & Yuhang Fan & Jonathan Friedman & Amber Dahlin & Matthew K. Waldor & George M. Weinstock & Scott T. Weiss & Yang-Yu Liu, 2020. "Deciphering functional redundancy in the human microbiome," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    12. Xiaogang Li & Dele Chen & Víctor J. Carrión & Daniel Revillini & Shan Yin & Yuanhua Dong & Taolin Zhang & Xingxiang Wang & Manuel Delgado-Baquerizo, 2023. "Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    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. Andrea Visca & Luciana Di Gregorio & Manuela Costanzo & Elisa Clagnan & Lorenzo Nolfi & Roberta Bernini & Alberto Orgiazzi & Arwyn Jones & Francesco Vitali & Stefano Mocali & Annamaria Bevivino, 2025. "Microbial Bioindicators for Monitoring the Impact of Emerging Contaminants on Soil Health in the European Framework," Sustainability, MDPI, vol. 17(3), pages 1-16, January.
    2. Valeria Esther Álvarez & Verónica Andrea El Mujtar & Joana Falcão Salles & Xiu Jia & Elisa Castán & Andrea Gabriela Cardozo & Pablo Adrián Tittonell, 2024. "Micro-Environmental Variation in Soil Microbial Biodiversity in Forest Frontier Ecosystems—Implications for Sustainability Assessments," Sustainability, MDPI, vol. 16(3), pages 1-26, February.
    3. Daijun Liu & Philipp Semenchuk & Franz Essl & Bernd Lenzner & Dietmar Moser & Tim M. Blackburn & Phillip Cassey & Dino Biancolini & César Capinha & Wayne Dawson & Ellie E. Dyer & Benoit Guénard & Evan, 2023. "The impact of land use on non-native species incidence and number in local assemblages worldwide," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Zi-Teng Liu & Rui-Ao Ma & Dong Zhu & Konstantinos T. Konstantinidis & Yong-Guan Zhu & Si-Yu Zhang, 2024. "Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Samiran Banerjee & Cheng Zhao & Gina Garland & Anna Edlinger & Pablo García-Palacios & Sana Romdhane & Florine Degrune & David S. Pescador & Chantal Herzog & Lennel A. Camuy-Velez & Jordi Bascompte & , 2024. "Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    6. Yanyan Zhou & Zhen Yang & Jinguang Liu & Xudong Li & Xingxiang Wang & Chuanchao Dai & Taolin Zhang & Víctor J. Carrión & Zhong Wei & Fuliang Cao & Manuel Delgado-Baquerizo & Xiaogang Li, 2023. "Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    7. Shu-ya Fan & Qiang Yang & Shao-peng Li & Trevor S. Fristoe & Marc W. Cadotte & Franz Essl & Holger Kreft & Jan Pergl & Petr Pyšek & Patrick Weigelt & John Kartesz & Misako Nishino & Jan J. Wieringa & , 2023. "A latitudinal gradient in Darwin’s naturalization conundrum at the global scale for flowering plants," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    8. Wilken Boie & Markus Schemmel & Wanzhi Ye & Mario Hasler & Melanie Goll & Joseph-Alexander Verreet & Daguang Cai, 2024. "An assessment of the species diversity and disease potential of Pythium communities in Europe," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    9. JANSSENS, Jochen & DE CORTE, Annelies & SÖRENSEN, Kenneth, 2016. "Water distribution network design optimisation with respect to reliability," Working Papers 2016007, University of Antwerp, Faculty of Business and Economics.
    10. Teruaki Kido & Yuko Yotsumoto & Masamichi J. Hayashi, 2025. "Hierarchical representations of relative numerical magnitudes in the human frontoparietal cortex," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    11. Raymond Hernandez & Elizabeth A. Pyatak & Cheryl L. P. Vigen & Haomiao Jin & Stefan Schneider & Donna Spruijt-Metz & Shawn C. Roll, 2021. "Understanding Worker Well-Being Relative to High-Workload and Recovery Activities across a Whole Day: Pilot Testing an Ecological Momentary Assessment Technique," IJERPH, MDPI, vol. 18(19), pages 1-17, October.
    12. Elisabeth Beckmann & Lukas Olbrich & Joseph Sakshaug, 2024. "Multivariate assessment of interviewer-related errors in a cross-national economic survey (Lukas Olbrich, Elisabeth Beckmann, Joseph W. Sakshaug)," Working Papers 253, Oesterreichische Nationalbank (Austrian Central Bank).
    13. Kristian Steensen Nielsen & Theresa M. Marteau & Jan M. Bauer & Richard B. Bradbury & Steven Broad & Gayle Burgess & Mark Burgman & Hilary Byerly & Susan Clayton & Dulce Espelosin & Paul J. Ferraro & , 2021. "Biodiversity conservation as a promising frontier for behavioural science," Nature Human Behaviour, Nature, vol. 5(5), pages 550-556, May.
    14. Valentina Krenz & Arjen Alink & Tobias Sommer & Benno Roozendaal & Lars Schwabe, 2023. "Time-dependent memory transformation in hippocampus and neocortex is semantic in nature," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    15. Morán-Ordóñez, Alejandra & Ameztegui, Aitor & De Cáceres, Miquel & de-Miguel, Sergio & Lefèvre, François & Brotons, Lluís & Coll, Lluís, 2020. "Future trade-offs and synergies among ecosystem services in Mediterranean forests under global change scenarios," Ecosystem Services, Elsevier, vol. 45(C).
    16. Damian M. Herz & Manuel Bange & Gabriel Gonzalez-Escamilla & Miriam Auer & Keyoumars Ashkan & Petra Fischer & Huiling Tan & Rafal Bogacz & Muthuraman Muthuraman & Sergiu Groppa & Peter Brown, 2022. "Dynamic control of decision and movement speed in the human basal ganglia," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    17. Dongyan Liu & Chongran Zhou & John K. Keesing & Oscar Serrano & Axel Werner & Yin Fang & Yingjun Chen & Pere Masque & Janine Kinloch & Aleksey Sadekov & Yan Du, 2022. "Wildfires enhance phytoplankton production in tropical oceans," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    18. Zhaogeng Yang & Yanhui Li & Peijin Hu & Jun Ma & Yi Song, 2020. "Prevalence of Anemia and its Associated Factors among Chinese 9-, 12-, and 14-Year-Old Children: Results from 2014 Chinese National Survey on Students Constitution and Health," IJERPH, MDPI, vol. 17(5), pages 1-10, February.
    19. Marco Lopez-Cruz & Fernando M. Aguate & Jacob D. Washburn & Natalia Leon & Shawn M. Kaeppler & Dayane Cristina Lima & Ruijuan Tan & Addie Thompson & Laurence Willard Bretonne & Gustavo los Campos, 2023. "Leveraging data from the Genomes-to-Fields Initiative to investigate genotype-by-environment interactions in maize in North America," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    20. Baumann, Elias & Kern, Jana & Lessmann, Stefan, 2019. "Usage Continuance in Software-as-a-Service," IRTG 1792 Discussion Papers 2019-005, Humboldt University of Berlin, International Research Training Group 1792 "High Dimensional Nonstationary Time Series".

    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_s41467-024-47348-8. 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.