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Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: strengths and pitfalls: Microbial networks for biomonitoring

Barroso‐Bergada, Didac; Pauvert, Charlie; Vallance, Jessica; Deliere, Laurent; Bohan, David; Buee, Marc and Vacher, C. (2020) Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: strengths and pitfalls: Microbial networks for biomonitoring. Molecular Ecology Resources.

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Document available online at: https://hal.archives-ouvertes.fr/hal-03049733


Summary

Environmental DNA contains information on the species interaction networks that support ecosystem functions and services. Next‐Generation Biomonitoring proposes the use of this data to reconstruct ecological networks in real‐time and then compute network‐level properties to assess ecosystem change. We investigated the relevance of this proposal by assessing: (1) the replicability of DNA‐based networks in the absence of ecosystem change; and, (2) the benefits and shortcomings of community‐ and network‐level properties for monitoring change. We selected crop‐associated microbial networks as a case study since they support disease regulation services in agroecosystems and analyzed their response to change in agricultural practice between organic and conventional systems. Using two statistical methods of network inference, we showed that network‐level properties, especially β‐properties, could detect change. Moreover, consensus networks revealed robust signals of interactions between the most abundant species, that differed between agricultural systems. These findings complemented those obtained with community‐level data, that showed, in particular, a greater microbial diversity in the organic system. The limitations of network‐level data included (i) the very high variability of network replicates within each system; (ii) the low number of network replicates per system, due to the large number of samples needed to build each network; and, (iii) the difficulty in interpreting links of inferred networks. Tools and frameworks developed over the last decade to infer and compare microbial networks are therefore relevant to biomonitoring, provided that the DNA metabarcoding datasets are large enough to build many network replicates and progress is made to increase network replicability and interpretation.


EPrint Type:Journal paper
Keywords:Environmental DNA (en), Metabarcoding (en), Community ecology (en), Ecosystem services (en), Microbial networks (en), Network inference (en), Network comparison (en), Ecologie des communautés (fr)
Subjects:"Organics" in general
Research affiliation: France > INRAe - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement
ISSN:ISSN: 1755-098X
DOI:10.1111/1755-0998.13302
Related Links:https://hal.archives-ouvertes.fr/hal-03049733/document
Project ID:HAL-INRAe
Deposited By: PENVERN, Servane
ID Code:40440
Deposited On:12 Aug 2021 10:37
Last Modified:12 Aug 2021 10:37
Document Language:English

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