与海洋有鳍鱼类水产养殖相关的有机富集是海洋沿海生态系统的局部压力源。为了维护生态系统服务,需要实施侧重于底栖多样性的生物监测计划。传统上,通过从样品中提取和鉴定底栖大型无脊椎动物来确定影响指数。然而,这是一种耗时且昂贵的方法,具有较低的升级潜力。更快速的,便宜,推断海洋环境环境质量的稳健方法是细菌群落的eDNA元编码。从元编码数据推断沿海栖息地的环境质量,两种无分类法方法已成功应用于不同的地理区域和监测目标,分位数回归样条(QRS)和监督机器学习(SML)。然而,它们的比较性能尚待监测水产养殖引入的有机富集对海洋沿海环境的影响。我们使用细菌metabarcoding数据比较了QRS和SML的性能,以推断从挪威的七个农场和苏格兰的七个农场收集的230个水产养殖样品沿有机富集梯度的环境质量。作为衡量环境质量的指标,我们使用了根据底栖大型动物数据(参考指数)计算的Infaunal质量指数(IQI)。QRS分析将扩增子序列变体(ASV)的丰度绘制为IQI的函数,从IQI将具有确定丰度峰的ASV分配给生态群,随后计算分子IQI。相比之下,SML方法建立了一个随机森林模型来直接预测基于大型动物的IQI。我们的结果表明,QRS和SML在推断环境质量方面表现良好,准确率为89%和90%。分别。对于这两个地理区域,参考IQI和两个推断的分子IQI之间存在高度对应(p<0.001),与QRS相比,SML模型显示出更高的确定系数。在SML方法确定的20个最重要的ASV中,15与通过QRS为挪威和苏格兰鲑鱼养殖场确定的优质样条ASV指标一致。有必要对ASV对有机富集的响应以及其他环境参数的共同影响进行更多研究,以最终选择最强大的压力源特异性指标。尽管这两种方法都有希望根据元编码数据推断环境质量,SML在处理自然变异性方面显示出更强大的功能。对于SML模型的改进,仍然需要添加新样品,由于高时空变异性引入的背景噪声可以减少。总的来说,我们建议开发一种强大的SML方法,该方法将应用于基于eDNA元编码数据监测水产养殖对海洋生态系统的影响.
Organic enrichment associated with marine finfish aquaculture is a local stressor of marine coastal ecosystems. To maintain ecosystem services, the implementation of biomonitoring programs focusing on benthic diversity is required. Traditionally, impact-indices are determined by extracting and identifying benthic macroinvertebrates from samples. However, this is a time-consuming and expensive method with low upscaling potential. A more rapid, inexpensive, and robust method to infer the environmental quality of marine environments is eDNA metabarcoding of bacterial communities. To infer the environmental quality of coastal habitats from metabarcoding data, two taxonomy-free approaches have been successfully applied for different geographical regions and monitoring goals, namely quantile regression splines (QRS) and supervised machine learning (SML). However, their comparative performance remains untested for monitoring the impact of organic enrichment introduced by aquaculture on marine coastal environments. We compared the performance of QRS and SML using bacterial metabarcoding data to infer the environmental quality of 230 aquaculture samples collected from seven farms in Norway and seven farms in Scotland along an organic enrichment gradient. As a measure of environmental quality, we used the Infaunal Quality Index (IQI) calculated from benthic macrofauna data (reference index). The QRS analysis plotted the abundance of amplicon sequence variants (ASVs) as a function to the IQI from which the ASVs with a defined abundance peak were assigned to eco-groups and a molecular IQI was subsequently calculated. In contrast, the SML approach built a random forest model to directly predict the macrofauna-based IQI. Our results show that both QRS and SML perform well in inferring the environmental quality with 89% and 90% accuracy, respectively. For both geographic regions, there was high correspondence between the reference IQI and both the inferred molecular IQIs (p < 0.001), with the SML model showing a higher coefficient of determination compared to QRS. Among the 20 most important ASVs identified by the SML approach, 15 were congruent with the good quality spline ASV indicators identified via QRS for both Norwegian and Scottish salmon farms. More research on the response of the ASVs to organic enrichment and the co-influence of other environmental parameters is necessary to eventually select the most powerful stressor-specific indicators. Even though both approaches are promising to infer environmental quality based on metabarcoding data, SML showed to be more powerful in handling the natural variability. For the improvement of the SML model, addition of new samples is still required, as background noise introduced by high spatio-temporal variability can be reduced. Overall, we recommend the development of a powerful SML approach that will be onwards applied for monitoring the impact of aquaculture on marine ecosystems based on eDNA metabarcoding data.