Pacific Northwest Research Station, U.S. Department of Agriculture, Forest Service, Corvallis, OR, USA.
Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
PeerJ. 2023 Apr 3;11:e15127. doi: 10.7717/peerj.15127. eCollection 2023.
The use of environmental DNA (eDNA) to assess aquatic biodiversity is a growing field with great potential for monitoring and managing threatened species, like freshwater mussel (Unionidae) populations. Freshwater mussels are globally imperiled and serve essential roles in aquatic systems as a food source and as a natural water filter making their management essential for ecosystem health. Unfortunately, mussel populations are often understudied, and challenges exist to accurately and efficiently describe the full suite of species present. Multispecies eDNA approaches may also be more challenging where freshwater mussel populations are most diverse due to ongoing and significant taxonomic restructuring that has been further complicated by molecular phylogenies using mitochondrial genes. For this study, we developed a microfluidic metabarcoding array that targets a wide range of species, from invertebrates to fishes, with an emphasis on detecting unionid mussels known to be present in the Sipsey River, Alabama. We compared mussel species diversity across six sites with well-studied mussel assemblages using eDNA surveys and traditional quadrat surveys in 2016. We examined how factors such as mussel population density, biomass and location in the river substrate impacted our ability to detect certain species; and investigated unexpected eDNA detections through phylogenetic analysis. Our eDNA results for fish and mussel species were broadly consistent with the data from traditional electrofishing and quadrat-based field surveys, although both community eDNA and conventional sampling detected species unique to that method. Our phylogenetic analysis agreed with other studies that treat and as synonymous species; however, they are still listed as unique species in molecular databases which complicates their identity in a metabarcoding assay. We also found that and are indistinguishable from one another using a portion of the NADH dehydrogenase Subunit 1 (ND1) marker, which may warrant further investigation into whether or not they are synonymous. Our results show that many factors impacted our ability to detect and correctly identify Unionidae mussel species. Here we describe the obstacles we faced, including the murky phylogeny of Unionidae mussels and turbid river conditions, and our development of a potentially impactful freshwater mussel monitoring eDNA assay.
利用环境 DNA（eDNA）评估水生生物多样性是一个具有巨大潜力的领域，可用于监测和管理受威胁物种，如淡水贻贝（贻贝科）种群。淡水贻贝在全球范围内受到威胁，它们在水生系统中作为食物来源和天然水过滤器发挥着重要作用，因此对其进行管理对于生态系统的健康至关重要。不幸的是，贻贝种群往往研究不足，并且在准确和有效地描述所有存在的物种方面存在挑战。在淡水贻贝种群最为多样化的地方，多物种 eDNA 方法可能也更具挑战性，因为正在进行并具有重大分类学结构重组，这进一步因使用线粒体基因的分子系统发育而变得复杂。在这项研究中，我们开发了一种微流控代谢组学芯片，该芯片针对从无脊椎动物到鱼类的广泛物种，重点检测已知存在于阿拉巴马州锡普斯河的贻贝。我们在 2016 年使用 eDNA 调查和传统的四分体调查，比较了六个具有研究良好的贻贝组合的地点的贻贝物种多样性。我们研究了贻贝种群密度、生物量和在河底基质中的位置等因素如何影响我们检测某些物种的能力；并通过系统发育分析研究了意外的 eDNA 检测。我们的鱼类和贻贝物种的 eDNA 结果与传统电捕鱼和基于四分体的实地调查数据大致一致，尽管两个社区的 eDNA 和常规采样都检测到了该方法特有的物种。我们的系统发育分析与其他将 和 视为同义物种的研究结果一致；然而，它们在分子数据库中仍被列为独特的物种，这使得它们在代谢组学分析中的身份变得复杂。我们还发现， 使用 NADH 脱氢酶亚单位 1（ND1）标记的一部分，与 无法区分，这可能需要进一步研究它们是否同义。我们的结果表明，许多因素影响了我们检测和正确识别贻贝科贻贝物种的能力。在这里，我们描述了我们面临的障碍，包括贻贝科贻贝的模糊系统发育和浑浊的河流条件，以及我们开发的一种潜在的有影响力的淡水贻贝监测 eDNA 分析。
