Advancing biomonitoring of eDNA studies with the Anaconda R package: Integrating soil and One Health perspectives in the face of evolving traditional agriculture practices

Stenger Pierre-Louis, Leopold Audrey, Dinh Kelly, Mournet Pierre, Robert Nadia, Drouin Julien, Wamejonengo Jacques, Russet Sylvie, Ibanez Thomas, Maggia Laurent, Carriconde Fabian. 2025. Advancing biomonitoring of eDNA studies with the Anaconda R package: Integrating soil and One Health perspectives in the face of evolving traditional agriculture practices. PloS One, 20 (1):e0311986, 32 p.

https://doi.org/10.1371/journal.pone.0311986

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Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Résumé : Soil health and One Health are global concerns, necessitating the development of refined indicators for effective monitoring. In response, we present the Anaconda R Package, a novel tool designed to enhance the analysis of eDNA data for biomonitoring purposes. Employing a combination of different approaches, this package allows for a comprehensive investigation of species abundance and community composition under diverse conditions. This study applied the Anaconda package to examine the impact of two types of duration fire-fallow cropping systems, using natural forests as a reference, on soil fungal and bacterial communities in Maré Island (New Caledonia). Condition-specific taxa were identified, particularly pathogenic fungi and bacteria, demonstrating the importance of long-term fallowing efforts. Notably, this package also revealed the potential contributions of beneficial soil microbes, including saprophytes and plant-endophyte fungi, in suppressing soil-borne pathogens. Over-represented microbial ASVs associated with both plant and animal pathogens, including those of potential concern for human health, were identified. This underscores the importance of maintaining intrinsic balance for effective disease suppression. Importantly, the advanced analytical and statistical methods offered by this package should be harnessed to comprehensively investigate the effects of agricultural practice changes on soil health within the One Health framework. Looking ahead, the application of this method extends beyond the realm of One Health, offering valuable insights into various ecological scenarios. Its versatility holds promise for elucidating complex interactions and dynamics within ecosystems. By leveraging this tool, researchers can explore the broader implications of agricultural practice modifications, facilitating informed decisions and sustainable environmental management.

Mots-clés Agrovoc : champignon pathogène, biomonitoring, pratique agricole, drone de surface naval, Champignon, technique analytique

Mots-clés géographiques Agrovoc : Nouvelle-Calédonie, France

Mots-clés libres : Fungi, Agricultural soil science, Plant fungal pathogens, Fungal pathogens, Taxonomy, Fungal structure, Community structure, Islands

Agences de financement hors UE : Institut Agronomique Néo-Calédonien

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