Monitoring sediment biota is an essential step for the quality assessment of aquatic ecosystems. Environmental DNA-based approaches for biomonitoring are increasing in popularity; yet, commercial kits and protocols for extracting total DNA from sediments remain expensive and time-consuming. Furthermore, they can accommodate only small amounts of sediments, potentially preventing an adequate representation of local biodiversity, especially for macro-organisms. Here, we assessed the reliability of a cost- and time-effective extracellular DNA extraction approach able to account for large volumes of starting material, for characterising bacterial, eukaryote and metazoan communities in three sedimentary environments. DNA concentrations extracted with the extracellular approach were at least similar to those obtained with the commercial kit. Local diversity estimates were not biased towards any particular extraction method, although specific responses were observed depending of the sediment type. Community composition and β-diversity patterns were moderately affected by the extraction approach and the initial amount of starting material; differences being more important for macro- than microorganisms. Thus, the extracellular DNA approach appears as robust and efficient as those based on the commercially available kit for biomonitoring sedimentary communities. Its low cost and fast processing time make it a promising alternative for large-scale ecological assessments of aquatic environments.

监测沉积物生物区系是水生生态系统质量评估的重要步骤。基于环境DNA的生物监测方法正在日益普及。然而，用于从沉积物中提取总DNA的商业试剂盒和方案仍然昂贵且耗时。此外，它们只能容纳少量的沉积物，从而有可能阻碍当地生物多样性的充分体现，特别是对于大型生物而言。在这里，我们评估了一种经济高效的省时细胞外DNA提取方法的可靠性，该方法能够解释大量起始材料，用于表征三种沉积环境中的细菌，真核生物和后生动物群落。用细胞外方法提取的DNA浓度至少与使用商业试剂盒获得的浓度相似。尽管根据沉积物类型观察到了特定的响应，但当地的多样性估计并未偏向于任何特定的提取方法。提取方法和起始原料的初始量对群落组成和β-多样性模式有中等程度的影响。对于微生物而言，差异比微生物更为重要。因此，细胞外DNA方法似乎与基于可商购的用于生物监测沉积群落的试剂盒一样稳健而有效。它的低成本和快速的处理时间使其成为水生环境大规模生态评估的有前途的替代方法。提取方法和起始原料的初始量对群落组成和β-多样性模式有中等程度的影响。对于微生物而言，差异比微生物更为重要。因此，细胞外DNA方法似乎与基于可商购的用于生物监测沉积群落的试剂盒一样稳健而有效。它的低成本和快速的处理时间使其成为水生环境大规模生态评估的有前途的替代方法。提取方法和起始原料的初始量对群落组成和β-多样性模式有中等程度的影响。对于微生物而言，差异比微生物更为重要。因此，细胞外DNA方法似乎与基于可商购的用于生物监测沉积群落的试剂盒一样稳健而有效。它的低成本和快速的处理时间使其成为水生环境大规模生态评估的有前途的替代方法。