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Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water

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  • Ruiz-Moreno, Héctor Alejandro
  • López-Tamayo, Ana María
  • Caro-Quintero, Alejandro
  • Husserl, Johana
  • González Barrios, Andrés Fernando

Abstract

The microbiomes of contaminated water bodies have altered microbial communities and functional capacity. Metagenomic data provides information on the microbiome at taxonomic and functional level. However, metagenomes from different environmental samples have shown that differences in taxonomy don’t always reflect changes in metabolic functions. Here, curated metagenome level network reconstructions for the highly contaminated Bogotá River and five additional samples were constructed and compared through topological analysis and flux balance analysis, using a constraint-based optimization method. Active metabolic fluxes change depending on simulated conditions evidencing a distance between potential and active functions. Higher microbial diversity was found to have little effect on potential functions but a positive effect on metabolic network robustness. A high degree of contamination in the Bogotá River has altered the microbiome’s metabolic functions making the system distant from a natural state. The microbiome of the Bogotá River was found to be functionally similar to the microbiome of Produced Water. Metabolic network reconstructions increase the information obtainable from metagenomic data and allow modelling of complex ecosystems.

Suggested Citation

  • 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.
    • Handle: RePEc:eee:ecomod:v:399:y:2019:i:c:p:1-12
    DOI: 10.1016/j.ecolmodel.2019.02.001
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    References listed on IDEAS

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    1. 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.
    2. 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.
    3. Peter J. Turnbaugh & Ruth E. Ley & Micah Hamady & Claire M. Fraser-Liggett & Rob Knight & Jeffrey I. Gordon, 2007. "The Human Microbiome Project," Nature, Nature, vol. 449(7164), pages 804-810, October.
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