Department of Plant and Soil Sciences, University of Delaware, 264 Townsend Hall, Newark, DE, 19716, USA.
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA.
Sci Rep. 2021 Jan 15;11(1):1629. doi: 10.1038/s41598-020-80602-9.
We investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.
我们研究了利用雨水过滤森林冠层和林下植被（即穿透雨）进行陆地环境中环境 DNA（eDNA）的新兴应用和功效。我们展示了这种方法在测量微生物群落和森林生物多样性方面的实用性和潜力。我们收集了纯净的雨水（开阔天空）和穿透雨，成功提取了 DNA，并生成了超过 5000 个独特的扩增子序列变体。我们发现了一些仅存在于穿透雨样本中的分类群，包括支原体属、螺菌属、玫瑰单胞菌属和乳球菌属。螺旋体属、甲基杆菌属、马西利亚菌属、泛菌属和鞘氨醇单胞菌属存在于两种类型的样本中，但在穿透雨中比在雨水中更为丰富。穿透雨样本中含有已被发现与植物相关的γ-变形菌，可能对重要的功能角色做出贡献。我们说明了这种新方法如何用于测量森林生态系统中的微生物生物多样性，预示着用于量化原核和真核生物形态的方法的实用性。利用这些方法将提高我们检测现存物种、描述新物种以及提高我们对森林生态系统中生态群落动态的整体理解的能力。
