Unveiling structure of tropical estuarine communities through eDNA and implications for biomonitoring

Tropical estuaries are hyper-diverse ecosystems, hosting essential
habitats for freshwater, euryhaline and marine life. Understanding how
biological communities are distributed in these systems has long been a
challenge because of their inherent dynamic nature, and the diversity of
interacting natural pressures and anthropogenic stressors they are
subjected to. In this study, we used environmental DNA (eDNA)
metabarcoding to examine the structure of multi-taxonomic communities in
estuarine ecosystems (diatoms, crustacean, fish and eukaryote as a whole)
and their relationships with environmental drivers in three differentially
impacted locations facing the Great Barrier Reef in Central Queensland
(Australia). We first demonstrated that eDNA signals from sediment and
water matrices provide complementary information, and that both should be
monitored for a more holistic understanding of community trajectories in
anthropogenically-impacted aquatic environments. We also observed that,
independently of the taxonomic group considered, communities were
primarily structured by the ecological conditions of the estuary. A
within-estuary differentiation along an upstream-downstream gradient was
detected but only for small-bodied organisms, which further adds credence
of eDNA approaches as an ecologically relevant tool for monitoring
fine-scale biodiversity patterns even in profoundly dynamic environments.
Finally, the different communities exhibited contrasting response
patterns, in terms of diversity, composition and uniqueness, to the
anthropogenic gradient. Hence, our findings emphasize the need for
multi-taxonomic assessments, for which eDNA is well-suited, to better
understand the impacts of multiple stressors on biodiversity, and thereby
assist decision makers in the protection and management of tropical
estuaries.

热带河口是兼具超高生物多样性的生态系统，为淡水、广盐性及海洋生物提供了关键栖息生境。长期以来，由于其固有的动态特性，以及其所承受的多种相互作用的自然压力与人为干扰因素，解析生物群落在这类系统中的分布模式始终是一项挑战。本研究采用环境DNA（eDNA）元条形码（metabarcoding）技术，对澳大利亚昆士兰州中部大堡礁沿岸三处受干扰程度不同的河口生态系统中的多分类群群落（包括硅藻、甲壳类、鱼类及整体真核生物）结构及其与环境驱动因子的关联进行了分析。我们首先证实，沉积物与水体基质中的eDNA信号可提供互补信息，若要全面解析受人为干扰的水生环境中的群落动态轨迹，需同时对二者进行监测。研究同时发现，无论所关注的分类群类别如何，群落结构主要由河口的生态环境条件所决定。此外，研究仅在小型生物类群中检测到了河口内部沿上下游梯度的群落分化，这进一步佐证了eDNA技术作为一种具备生态学适用性的工具，即便在高度动态的环境中，也可用于监测精细尺度的生物多样性格局。最后，不同群落的多样性、组成及独特性对人为干扰梯度呈现出各异的响应模式。因此，本研究结果强调，需采用适配eDNA技术的多分类群评估手段，以更深入解析多重干扰对生物多样性的影响，进而为决策者开展热带河口的保护与管理工作提供支撑。