Stauffer Salomé, Jucker Meret, Keggin Thomas, Marques Virginie, Andrello Marco, Bessudo Sandra, Cheutin Marie-Charlotte, Borrero-Pérez Giomar Helena, Richards Eilísh, Dejean Tony, Hocdé Régis, Juhel Jean-Baptiste, Ladino Felipe, Letessier Tom B, Loiseau Nicolas, Maire Eva, Mouillot David, Mutis Martinezguerra Maria, Manel Stéphanie, Polanco Fernández Andrea, Valentini Alice, Velez Laure, Albouy Camille, Pellissier Loïc, Waldock Conor
Landscape Ecology Institute of Terrestrial Ecosystems Department of Environmental Systems Science ETH Zürich Zürich Switzerland.
Unit of Land Change Science Swiss Federal Research Institute WSL Birmensdorf Switzerland.
Ecol Evol. 2021 Oct 6;11(21):14630-14643. doi: 10.1002/ece3.8150. eCollection 2021 Nov.
Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one another. As a result, non-saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false-negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.
在丰富的热带海洋环境中对鱼类物种多样性进行量化仍然具有挑战性。环境DNA（eDNA）宏条形码分析是一种很有前景的工具，可通过对水样中的DNA痕迹进行过滤、扩增和测序来应对这一挑战。然而，由于海洋环境中eDNA浓度较低，eDNA检测物种多样性的可靠性可能会受到限制。我们采用eDNA宏条形码分析方法，利用单个12S标记来识别鱼类分子分类单元（MOTUs），旨在评估采样重复次数和过滤水量如何影响生物多样性估计。我们在3个热带地区8个地点的68个珊瑚礁样带上采用了每个重复30升的配对采样设计。我们通过比较MOTU丰富度、组成周转率和组成嵌套性来量化局部和区域采样变异性。我们发现在相同地点、时间和条件下进行的重复配对样本之间，MOTUs有很强的周转率。配对样本包含不重叠的组合，而不是彼此的子集。因此，未饱和的局部多样性积累曲线表明，即使在同一地点进行6次重复（180升）采样，也可能低估局部多样性（对于面积<1平方公里的区域）。然而，在不同地点（通常覆盖数十公里）使用约25次重复采样区域多样性时，生物多样性积累曲线往往会饱和。我们的结果表明，除了eDNA处理过程中的变异性外，eDNA在海水中的异质分布以及每个MOTU的eDNA痕迹频率高度偏斜，都可能导致多样性估计的变异性。这种高组成变异性对利用eDNA监测局部组合中的时间和空间生物多样性变化具有影响。为了在未来的生物监测工作中避免假阴性检测，需要增加重复次数或采样水量，以便更好地利用eDNA为海洋生物多样性管理提供信息。
