Data from: The utility of environmental DNA from sediment and water samples for recovery of observed plant and animal species from four Mojave Desert springs

Background: Mojave Desert springs are fragile ecosystems, hosting endemic plants and animals, which are threatened by the increasing human demand for water and climate change. To develop management practices that will protect the groundwater-dependent ecosystems at Mojave Desert springs, real-time, low cost biodiversity monitoring and assessments are required. Environmental DNA (eDNA) metabarcoding uses DNA shed from organisms (e.g. skin cells, feces, pollen, etc.) that is present in water, air, soil, or sediment samples to assess community composition. This approach can increase the detection sensitivity for rare and elusive species, compared to expensive and time-consuming conventional methods, which also require taxonomic expertise. Aims: This study tests the effectiveness of eDNA techniques in capturing the observed Mojave Desert spring biodiversity in the winter and spring of 2019 at four distinct, naturally occurring springs. We also test the utility of sample types (water versus sediment) for capturing biodiversity. Results: We found that each of the four Mojave Desert springs supports a unique biological community. Sediment samples contained the greatest biodiversity, but all sample types captured species observed in the field by humans or camera-traps. We also found no statistical difference in species richness captured in winter and spring except for the Cytochrome Oxidase I marker, for which winter had greater biodiversity. Conclusion: This study supports the use of eDNA metabarcoding as an effective tool to mirror observation by human observers of ecological communities in desert springs. It demonstrates the importance of appropriately timing eDNA field sampling, primer selection, and using field-based surveys of wildlife and plants in addition to eDNA detection. This study also identified gaps in reference sequence databases for Mojave biodiversity and encourages collaboration of eDNA researchers with managers for effective conservation management plans.

背景：莫哈韦沙漠泉水属于脆弱生态系统，栖息着特有动植物类群，正面临日益增长的人类水资源需求与气候变化的双重威胁。为制定保护莫哈韦沙漠泉水依赖地下水的生态系统的管理方案，亟需开展实时、低成本的生物多样性监测与评估工作。环境DNA（environmental DNA, eDNA）元条形码（metabarcoding）技术通过提取存在于水、空气、土壤或沉积物样本中的生物体脱落DNA（如皮肤细胞、粪便、花粉等），实现对群落组成的评估。相较于成本高昂、耗时良久且需分类学专业知识的传统监测方法，该技术可提升对稀有及隐匿物种的检测灵敏度。
研究目的：本研究于2019年冬春两季，在四处独立的天然莫哈韦沙漠泉水中开展实验，旨在验证eDNA技术对当地泉水生物多样性的捕获效果；同时测试不同样本类型（水样与沉积物样）在捕获生物多样性方面的应用潜力。
研究结果：研究发现，四处莫哈韦沙漠泉水各自拥有独特的生物群落。沉积物样本的生物多样性最为丰富，但所有样本类型均能捕获到人类野外调查或红外相机监测到的物种。此外，除细胞色素氧化酶I（Cytochrome Oxidase I, COI）分子标记外，冬季与春季捕获的物种丰富度无统计学差异；使用该标记物时，冬季样本的生物多样性更高。
结论：本研究证实，eDNA元条形码技术可作为有效工具，复刻人类观察者对沙漠泉水生态群落的调查结果。研究明确了合理规划eDNA野外采样时机、选择引物，并结合野生动植物实地调查与eDNA检测的重要性。此外，本研究还发现莫哈韦地区生物多样性参考序列数据库存在覆盖缺口，并呼吁eDNA研究人员与生态管理者开展合作，以制定高效的保护管理方案。