A quantitative analysis of vertebrate environmental DNA degradation in soil in response to time, UV light and temperature

Environmental DNA (eDNA) degradation influences the effectiveness of eDNA-based biodiversity monitoring, but the factors that determine the rate of decay of eDNA in terrestrial environments are poorly understood. We assessed the persistence of vertebrate eDNA from a mock vertebrate community created with soil from zoo enclosures holding ten target species from different taxonomic classes (e.g. reptiles, birds and mammals) and of different biomass (e.g. little penguin and giraffe). We examined species detection rates resulting from eDNA metabarcoding, as well as relative eDNA concentrations via qPCR, from soil samples over eight time points (0 to 12 weeks), during exposure to three ambient temperatures (10, 25 and 40 °C) and three levels of ultraviolet B (UV-B) radiation (0%, 50% and 100% intensity). We recorded considerable variation in detectability between species, independent of temperature and UV-B effects. Quantitative PCR indicated degradation of eDNA over time for all temperature..., Sample source
Soil was collected in mid-July 2021 from the enclosures of ten species at the Perth Zoo, South Perth, Western Australia. Soil samples (1.5 L), consisting of five equal subsamples from areas of recent animal activity (as determined by zoo staff) to maximise the likelihood of eDNA presence in a sample, were collected from each of four mammal, three bird and three reptile enclosures (Table 1): approximately 15 L of soil in total. Samples were taken from a depth of 0-50 mm, using sterilised sampling equipment and disposable nitrile gloves. Soil texture varied from sand (e.g. Cape porcupine) to sandy clay loam (e.g. Galápagos tortoise).
Target species (Table 1) did not occur in the Perth metropolitan region, meaning that any DNA detected from species in the samples must be derived from the original soil samples, not reintroduced through subsequent contamination. The emu (Dromaius novaehollandiae) was a possible exception, though contact with DNA from this species was deemed to ..., , # A quantitative analysis of vertebrate environmental DNA degradation in soil in response to time, UV light and temperature

[https://doi.org/10.5061/dryad.1vhhmgqtx](https://doi.org/10.5061/dryad.1vhhmgqtx)

## Description of the data and file structure

There are six files included:

**MSRun480-FTP360_S1_L001_R1_001.fastq.gz** - Compressed sequencing file containing raw sequences from the Illumina MiSeq run

**MSRun485-FTP365_S1_L001_R1_001.fastq.gz** - Compressed sequencing file containing raw sequences from the Illumina MiSeq run

**MSRun504-FTP375_S1_L001_R1_001.zip** - Compressed sequencing file containing raw sequences from the Illumina MiSeq run

**Sample_barcode_eDNA_degradation.csv** - sample metadata including information required to demultiplex raw sequences

**Sample_CT_values.csv** - CT values recorded for soil samples

**filtered_ZOTU_table_Zoo.csv** - Final ZOTU table produced using eDNAFLow bioinformatics pipeline for sequence analysis. Taxonomy included in this file an...,

环境DNA（Environmental DNA，以下简称eDNA）的降解会影响基于eDNA的生物多样性监测效果，但目前学界对陆地环境中eDNA降解速率的决定因子仍知之甚少。本研究针对由动物园圈养动物笼舍土壤构建的模拟脊椎动物群落，对其eDNA留存情况进行了评估；该模拟群落包含10个源自不同分类类群（如爬行类、鸟类和哺乳类）且生物量各异的目标物种（例如小企鹅与长颈鹿）。我们针对8个时间节点（0至12周）采集的土壤样本，分别通过eDNA元条形码测序（metabarcoding）与实时定量聚合酶链反应（quantitative PCR，qPCR）检测了物种检出率与eDNA相对浓度；实验设置了3种环境温度（10℃、25℃与40℃）以及3个紫外B（UV-B）辐射水平（0%、50%与100%强度）。研究发现，不受温度与UV-B辐射影响的前提下，不同物种的eDNA检出率存在显著差异。实时定量PCR结果显示，所有温度条件下的eDNA均随时间发生降解……

样本来源：本研究于2021年7月中旬，从澳大利亚西澳大利亚州南珀斯的珀斯动物园10个物种的笼舍中采集土壤样本。每个笼舍的土壤样本（1.5升）由5份等份子样本混合而成，子样本采自动物园工作人员认定的近期有动物活动的区域，以最大化样本中存在eDNA的概率；本次共采集了4个哺乳类、3个鸟类与3个爬行类笼舍的土壤样本（详见表1），总土壤量约15升。采样时使用灭菌采样设备与一次性丁腈手套，采集深度为0至50毫米的土壤样本。土壤质地涵盖砂土（如南非豪猪）至砂质壤土（如加拉帕戈斯陆龟）的范围。本研究选取的目标物种（详见表1）均未在珀斯都会区自然分布，这意味着样本中检测到的任何物种DNA均源自原始土壤样本，而非后续污染引入。唯有鸸鹋（Dromaius novaehollandiae）可能为例外，不过该物种DNA的接触风险被认定为……

# 土壤中脊椎动物环境DNA降解的定量分析：响应时间、紫外辐射与温度变化

https://doi.org/10.5061/dryad.1vhhmgqtx

## 数据与文件结构说明
本数据集包含6个文件：
1. **MSRun480-FTP360_S1_L001_R1_001.fastq.gz**：压缩格式测序文件，包含Illumina MiSeq测序得到的原始序列数据
2. **MSRun485-FTP365_S1_L001_R1_001.fastq.gz**：压缩格式测序文件，包含Illumina MiSeq测序得到的原始序列数据
3. **MSRun504-FTP375_S1_L001_R1_001.zip**：压缩格式测序文件，包含Illumina MiSeq测序得到的原始序列数据
4. **Sample_barcode_eDNA_degradation.csv**：样本元数据文件，包含原始序列解复用所需的相关信息
5. **Sample_CT_values.csv**：土壤样本的CT值记录文件
6. **filtered_ZOTU_table_Zoo.csv**：使用eDNAFLow生物信息学流程进行序列分析后得到的最终零半径操作分类单元（ZOTU）表，文件中包含物种分类学信息……