有害海洋巨藻环境DNA检测中的导航不确定性。

IF 2.6 3区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES
PLoS ONE Pub Date : 2025-02-04 eCollection Date: 2025-01-01 DOI:10.1371/journal.pone.0318414
Patrick K Nichols, Kaʻuaʻoa M S Fraiola, Alison R Sherwood, Brian B Hauk, Keolohilani H Lopes, Colt A Davis, James T Fumo, Chelsie W W Counsell, Taylor M Williams, Heather L Spalding, Peter B Marko
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引用次数: 0

摘要

早期发现有害物种对于管理受威胁的生态系统和防止其广泛建立至关重要。环境DNA (eDNA)数据可以增加生物监测程序的灵敏度,通常以最小的成本和努力。然而,eDNA分析容易出错,这可能使其在管理框架中的使用复杂化。为了解决这个问题,eDNA研究必须考虑不完美的检测并估计错误率。以最小的不确定性检测低丰度的有害物种对于成功遏制和根除至关重要。我们开发了一种新的eDNA检测方法,利用世界上最大的海洋保护区之一Papahānaumokuākea海洋国家纪念碑(PMNM)的表层海水样本检测其殖民前沿的有害海洋巨藻。软骨藻是一种具有入侵特性的隐生红藻,在PMNM形成密集的草席,覆盖珊瑚礁,使本地动植物窒息。我们利用定量聚合酶链反应(qPCR)数据的位点占用检测模型验证了eDNA分析,并根据瘤胃C.底栖生物覆盖范围从< 1%到95%的视觉估计进行了校准。结果随后通过扩增eDNA和阴性对照样品的高通量测序进行验证。总的来说,当多个qPCR重复为阳性时,在占位位点检测到瘤芽胞杆菌的概率至少为92%。假阳性率为3%或更少,假阴性错误率为11%或更少。实验证明,即使在肿瘤梭菌丰度低于1%的情况下,该方法对浅层地点(小于10米)的常规监测也是有效的。eDNA工具在保护决策中的成功实施需要平衡视觉和分子检测方法的不确定性。我们的研究结果和模型证明了该方法对肿瘤弧菌的高敏感性,我们概述了从分子数据推断生态存在-缺失的步骤。这一可靠、经济的工具增强了对低丰度物种的检测,并支持及时的管理干预。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Navigating uncertainty in environmental DNA detection of a nuisance marine macroalga.

Early detection of nuisance species is crucial for managing threatened ecosystems and preventing widespread establishment. Environmental DNA (eDNA) data can increase the sensitivity of biomonitoring programs, often at minimal cost and effort. However, eDNA analyses are prone to errors that can complicate their use in management frameworks. To address this, eDNA studies must consider imperfect detections and estimate error rates. Detecting nuisance species at low abundances with minimal uncertainty is vital for successful containment and eradication. We developed a novel eDNA assay to detect a nuisance marine macroalga across its colonization front using surface seawater samples from Papahānaumokuākea Marine National Monument (PMNM), one of the world's largest marine reserves. Chondria tumulosa is a cryptogenic red alga with invasive traits, forming dense mats that overgrow coral reefs and smother native flora and fauna in PMNM. We verified the eDNA assay using site-occupancy detection modeling from quantitative polymerase chain reaction (qPCR) data, calibrated with visual estimates of benthic cover of C. tumulosa that ranged from < 1% to 95%. Results were subsequently validated with high-throughput sequencing of amplified eDNA and negative control samples. Overall, the probability of detecting C. tumulosa at occupied sites was at least 92% when multiple qPCR replicates were positive. False-positive rates were 3% or less and false-negative errors were 11% or less. The assay proved effective for routine monitoring at shallow sites (less than 10 m), even when C. tumulosa abundance was below 1%. Successful implementation of eDNA tools in conservation decision-making requires balancing uncertainties in both visual and molecular detection methods. Our results and modeling demonstrated the assay's high sensitivity to C. tumulosa, and we outline steps to infer ecological presence-absence from molecular data. This reliable, cost-effective tool enhances the detection of low-abundance species, and supports timely management interventions.

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来源期刊
PLoS ONE
PLoS ONE 生物-生物学
CiteScore
6.20
自引率
5.40%
发文量
14242
审稿时长
3.7 months
期刊介绍: PLOS ONE is an international, peer-reviewed, open-access, online publication. PLOS ONE welcomes reports on primary research from any scientific discipline. It provides: * Open-access—freely accessible online, authors retain copyright * Fast publication times * Peer review by expert, practicing researchers * Post-publication tools to indicate quality and impact * Community-based dialogue on articles * Worldwide media coverage
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