IDEAS home Printed from https://ideas.repec.org/a/eee/ecomod/v351y2017icp63-76.html
   My bibliography  Save this article

Influence of agricultural activities in the structure and metabolic functionality of paramo soil samples in Colombia studied using a metagenomics analysis in dynamic state

Author

Listed:
  • Alvarez-Yela, Astrid Catalina
  • Alvarez-Silva, María Camila
  • Restrepo, Silvia
  • Husserl, Johana
  • Zambrano, María Mercedes
  • Danies, Giovanna
  • Gómez, Jorge M.
  • González Barrios, Andrés Fernando

Abstract

Soil is one of the most variable and complex habitats on earth where microbial communities and their metabolic capabilities are greatly affected by agricultural activities. Nevertheless, the impact of these activities has been poorly studied and more detailed analyses are required in order to understand soil ecosystems at both a structural and metabolic level. Here, we conducted a detailed metagenomics analysis to establish the effect of anthropogenic interventions on microbial communities and on the biogeochemical cycle dynamics in soil. Our results suggest that the agricultural activities lead to shifts in the structure of microbial communities characterized by an increase in ammonia-oxidizing archaea, bacteria with copiotrophic features, and ascomycete fungi. The most important biogeochemical processes were related to the carbon and nitrogen cycles. These shifts in the composition of microbial communities led to a loss in the metabolic functional diversity, which was reflected by the lower metabolic activity found. On the other hand, in the non-intervened soil, an increased metabolic activity was observed. The biogeochemical cycles behaved in an interdependent and synergistic way. We were able to elucidate how soil ecosystems dynamics is influenced by agricultural activities in a paramo ecosystem in Colombia.

Suggested Citation

  • Alvarez-Yela, Astrid Catalina & Alvarez-Silva, María Camila & Restrepo, Silvia & Husserl, Johana & Zambrano, María Mercedes & Danies, Giovanna & Gómez, Jorge M. & González Barrios, Andrés Fernando, 2017. "Influence of agricultural activities in the structure and metabolic functionality of paramo soil samples in Colombia studied using a metagenomics analysis in dynamic state," Ecological Modelling, Elsevier, vol. 351(C), pages 63-76.
    • Handle: RePEc:eee:ecomod:v:351:y:2017:i:c:p:63-76
    DOI: 10.1016/j.ecolmodel.2017.02.010
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0304380016305002
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.ecolmodel.2017.02.010?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Zamora, Maria A. & Pinzón, Andres & Zambrano, Maria M. & Restrepo, Silvia & Broadbelt, Linda J. & Moura, Matthew & Husserl Orjuela, Johana & González Barrios, Andrés F., 2015. "A comparison between functional frequency and metabolic flows framed by biogeochemical cycles in metagenomes: The case of “El Coquito” hot spring located at Colombia's national Nevados park," Ecological Modelling, Elsevier, vol. 313(C), pages 259-265.
    2. S. Leininger & T. Urich & M. Schloter & L. Schwark & J. Qi & G. W. Nicol & J. I. Prosser & S. C. Schuster & C. Schleper, 2006. "Archaea predominate among ammonia-oxidizing prokaryotes in soils," Nature, Nature, vol. 442(7104), pages 806-809, August.
    3. H. Jeong & B. Tombor & R. Albert & Z. N. Oltvai & A.-L. Barabási, 2000. "The large-scale organization of metabolic networks," Nature, Nature, vol. 407(6804), pages 651-654, October.
    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. Ruiz-Moreno, Héctor Alejandro & López-Tamayo, Ana María & Caro-Quintero, Alejandro & Husserl, Johana & González Barrios, Andrés Fernando, 2019. "Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water," Ecological Modelling, Elsevier, vol. 399(C), pages 1-12.

    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. Jin Wang & Bo Huang & Xuefeng Xia & Zhirong Sun, 2006. "Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle," PLOS Computational Biology, Public Library of Science, vol. 2(11), pages 1-10, November.
    2. Zhou, Wei-Xing & Jiang, Zhi-Qiang & Sornette, Didier, 2007. "Exploring self-similarity of complex cellular networks: The edge-covering method with simulated annealing and log-periodic sampling," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 375(2), pages 741-752.
    3. Kehinde Abraham Odelade & Olubukola Oluranti Babalola, 2019. "Bacteria, Fungi and Archaea Domains in Rhizospheric Soil and Their Effects in Enhancing Agricultural Productivity," IJERPH, MDPI, vol. 16(20), pages 1-19, October.
    4. Jorge Peña & Yannick Rochat, 2012. "Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-13, September.
    5. Sgrignoli, P. & Agliari, E. & Burioni, R. & Schianchi, A., 2015. "Instability and network effects in innovative markets," Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 108(C), pages 260-271.
    6. Long Ma & Xiao Han & Zhesi Shen & Wen-Xu Wang & Zengru Di, 2015. "Efficient Reconstruction of Heterogeneous Networks from Time Series via Compressed Sensing," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-12, November.
    7. Christian F A Negre & Hayato Ushijima-Mwesigwa & Susan M Mniszewski, 2020. "Detecting multiple communities using quantum annealing on the D-Wave system," PLOS ONE, Public Library of Science, vol. 15(2), pages 1-14, February.
    8. Biggiero, Lucio & Angelini, Pier Paolo, 2015. "Hunting scale-free properties in R&D collaboration networks: Self-organization, power-law and policy issues in the European aerospace research area," Technological Forecasting and Social Change, Elsevier, vol. 94(C), pages 21-43.
    9. Tamás Nepusz & Tamás Vicsek, 2013. "Hierarchical Self-Organization of Non-Cooperating Individuals," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-9, December.
    10. Aslam, Faheem & Aziz, Saqib & Nguyen, Duc Khuong & Mughal, Khurrum S. & Khan, Maaz, 2020. "On the efficiency of foreign exchange markets in times of the COVID-19 pandemic," Technological Forecasting and Social Change, Elsevier, vol. 161(C).
    11. Semi Min & Juyong Park, 2019. "Modeling narrative structure and dynamics with networks, sentiment analysis, and topic modeling," PLOS ONE, Public Library of Science, vol. 14(12), pages 1-20, December.
    12. Jiang, Jingchi & Zheng, Jichuan & Zhao, Chao & Su, Jia & Guan, Yi & Yu, Qiubin, 2016. "Clinical-decision support based on medical literature: A complex network approach," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 459(C), pages 42-54.
    13. Gerhardt, Günther J.L. & Lemke, Ney & Corso, Gilberto, 2006. "Network clustering coefficient approach to DNA sequence analysis," Chaos, Solitons & Fractals, Elsevier, vol. 28(4), pages 1037-1045.
    14. Laurienti, Paul J. & Joyce, Karen E. & Telesford, Qawi K. & Burdette, Jonathan H. & Hayasaka, Satoru, 2011. "Universal fractal scaling of self-organized networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 390(20), pages 3608-3613.
    15. Chen, Qinghua & Shi, Dinghua, 2004. "The modeling of scale-free networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 335(1), pages 240-248.
    16. Liu, X. & Murata, T., 2010. "Advanced modularity-specialized label propagation algorithm for detecting communities in networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(7), pages 1493-1500.
    17. Wen, Xiangxi & Tu, Congliang & Wu, Minggong, 2018. "Node importance evaluation in aviation network based on “No Return” node deletion method," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 503(C), pages 546-559.
    18. Lawford, Steve & Mehmeti, Yll, 2020. "Cliques and a new measure of clustering: With application to U.S. domestic airlines," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 560(C).
    19. J. J. Esquivel-Gómez & J. G. Barajas-Ramírez, 2024. "Rapid disease spread on dense networks with power-law topology," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 97(5), pages 1-10, May.
    20. Wang, Huan & Xu, Chuan-Yun & Hu, Jing-Bo & Cao, Ke-Fei, 2014. "A complex network analysis of hypertension-related genes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 394(C), pages 166-176.

    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:eee:ecomod:v:351:y:2017:i:c:p:63-76. 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: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/ecological-modelling .

    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.