Stenger Pierre-Louis, Léopold Audrey, Dinh Kelly, Mournet Pierre, Robert Nadia, Drouin Julien, Wamejonengo Jacques, Russet Sylvie, Ibanez Thomas, Maggia Laurent, Carriconde Fabian
Équipe ' Sol & Végétation' (SolVeg), Institut Agronomique néo-Calédonien (IAC), Nouméa, New Caledonia.
UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
PLoS One. 2025 Jan 16;20(1):e0311986. doi: 10.1371/journal.pone.0311986. eCollection 2025.
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.
土壤健康和“同一健康”是全球关注的问题，需要开发精细的指标进行有效监测。为此，我们推出了Anaconda R软件包，这是一种新型工具，旨在加强对环境DNA数据的分析，用于生物监测目的。该软件包采用多种不同方法，能够在不同条件下对物种丰度和群落组成进行全面调查。本研究应用Anaconda软件包，以天然森林为参照，考察了两种不同休耕时长的轮作系统对马雷岛（新喀里多尼亚）土壤真菌和细菌群落的影响。确定了特定条件下的分类群，特别是致病真菌和细菌，这表明长期休耕措施的重要性。值得注意的是，该软件包还揭示了有益土壤微生物（包括腐生菌和植物内生真菌）在抑制土壤传播病原体方面的潜在作用。识别出了与植物和动物病原体相关的、过度富集的微生物扩增子序列变体（ASV），包括那些对人类健康可能构成威胁的变体。这凸显了维持内在平衡以有效抑制疾病的重要性。重要的是，应利用该软件包提供的先进分析和统计方法，在“同一健康”框架内全面研究农业实践变化对土壤健康的影响。展望未来，该方法的应用范围超出了“同一健康”领域，为各种生态情景提供了有价值的见解。其多功能性有望阐明生态系统内复杂的相互作用和动态变化。通过利用这一工具，研究人员可以探索农业实践改变的更广泛影响，促进明智决策和可持续环境管理。
