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Analysis of Ecological Networks in Multicomponent Communities of Microorganisms: Possibilities, Limitations, and Potential Errors

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Abstract—

Owing to the high resolving power and efficiency of DNA sequencing, researchers have discovered the extremely high diversity of bacterial, fungal, protist, and microinvertebrate communities in the soil, wood, phyllosphere, and other natural media. Studies on the properties of these communities require powerful tools for analyzing multicomponent systems. One of them is the analysis of ecological networks, which makes it possible to solve a broad range of problems. This review briefly describes the possibilities of network analysis, its concepts, and metrics of network topology.It also indicates limitations related to specific features of DNA sequencing (compositionality and data sparsity) and potential sources of errors in the interpretation of results (relic DNA, artifactual DNA sequences and spurious connections in a network). The focus is on the communities of microorganisms, but the discussed issues are relevant for most other groups of the biota.

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ACKNOWLEDGMENTS

The authors are grateful to M.V. Modorov, O.E. Likho-deevskaya, I.A. Shadrin, and E.A. Belsky for their valuable comments on the manuscript.

Funding

The collection of the material, network construction, bioinformatics analysis, and statistical data processing were supported by the Russian Foundation for Basic Research, project nos. 18-29-05042 and 19-04-00921; the manuscript was prepared for publication under state contract with the Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences. Bioinformatic analysis was performed using the Uran supercomputer at the Institute of Mathematics and Mechanics, Ural Branch, Russian Academy of Sciences.

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Correspondence to V. S. Mikryukov.

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Translated by N. Gorgolyuk

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Mikryukov, V.S., Dulya, O.V., Likhodeevskii, G.A. et al. Analysis of Ecological Networks in Multicomponent Communities of Microorganisms: Possibilities, Limitations, and Potential Errors. Russ J Ecol 52, 188–200 (2021). https://doi.org/10.1134/S1067413621030085

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