Abstract：
Urbanization of estuaries drastically changed existing shorelines and bathymetric contours, in turn modifying habitat for marine foundational species that host critical biodiversity. And yet we lack approaches to characterize a significant fraction of the biota that inhabit these ecosystems on time scales that align with rates of urbanization. Environmental DNA (or eDNA) metabarcoding that combines multiple assays targeting a broad range of taxonomic groups can provide a solution, but we need to determine whether the biological communities it detects ally with different habitats in these changing aquatic environments. In this study, we tested whether tree of life metabarcoding (ToL-metabarcoding) data extracted from filtered seawater samples correlated with four known geomorphic habitat zones across a heavily urbanized estuary (Sydney Harbour, Australia). Using this method, we substantially expanded our knowledge on the composition and spatial distribution of marine biodiversity across the tree of life in Sydney Harbour, particularly for organisms where existing records are sparse. Excluding terrestrial DNA inputs, we identified significant effects of both distance from the mouth of Sydney Harbour and geomorphic zone on biological community structure in the ToL-metabarcoding dataset (entire community), as well as in each of the taxonomic subgroups that we considered (fish, macroinvertebrates, algae and aquatic plants, bacteria). This effect appeared to be driven by taxa as a collective versus a few individual taxa, with each taxon explaining no more than 0.62% of the variation between geomorphic zones. Similarly, taxonomic richness was significantly higher within geomorphic zones with large sample sizes, but also decreased by 1% with each additional kilometer from the estuary mouth, a result consistent with a reduction in tidal inputs and available habitat in upper catchments. Based on these results, we suggest that ToL-metabarcoding can be used to benchmark biological monitoring in other urbanized estuaries globally, and in Sydney Harbour at future time points based on detection of bioindicators across the tree of life. We also suggest that robust biotic snapshots can be archived following extensive curation of taxonomic assignments that incorporates ecological affinities, supported by records from relevant and regional biodiversity repositories.
摘要：
河口的城市化彻底改变了现有的海岸线和测深轮廓，进而改变拥有关键生物多样性的海洋基础物种的栖息地。然而，我们缺乏方法来表征居住在这些生态系统中的大部分生物群，其时间尺度与城市化率一致。环境DNA（或eDNA）元编码结合了针对广泛分类组的多种检测方法，可以提供解决方案，但是我们需要确定在这些变化的水生环境中，它检测到的生物群落是否与不同的栖息地结盟。在这项研究中,我们测试了从过滤后的海水样本中提取的生命树元编码（ToL-元编码）数据是否与严重城市化的河口（悉尼港，澳大利亚)。使用此方法，我们大大扩展了我们对悉尼港生命树海洋生物多样性的组成和空间分布的认识，特别是对于现有记录稀疏的生物体。不包括陆地DNA输入，我们在ToL-metabarcoding数据集（整个群落）中确定了距悉尼港口和地貌带的距离对生物群落结构的显着影响，以及我们考虑的每个分类亚组(鱼，大型无脊椎动物,藻类和水生植物，细菌）。这种效应似乎是由作为一个集体的分类单元与几个单独的分类单元驱动的，每个分类单元解释不超过0.62％的地貌带之间的变化。同样，在大样本量的地貌带内，分类丰富度显着较高，而且从河口每增加一公里也减少了1%，结果与潮汐输入和上游流域可用栖息地的减少一致。基于这些结果,我们建议ToL-megabarcoding可用于全球其他城市化河口的生物监测基准，并在未来的时间点在悉尼港，基于其对整个生命树的生物指标的检测。我们还建议，在对包含其生态亲和力的分类学分配进行广泛的管理之后，可以存档强大的生物快照，由相关和区域生物多样性储存库的记录支持。
