Table_2_Capturing marine microbiomes and environmental DNA: A field sampling guide.xlsx

The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.

随着海洋微生物组（marine microbiome）与环境DNA（eDNA）测序数据的研究热度日益高涨，学界亟需标准化的样本采集与保存规范，以实现不同研究间结果的横向对比，并推动元分析（meta-analyses）的开展。本研究基于已发表的方法学成果与野外采样经验梳理形成相关指南，以期助力该项标准化工作的推进。本次指南涵盖四大核心板块：环境与资源考量要点、样本处理策略、样本保存方案以及eDNA提取流程。鉴于eDNA应用场景覆盖范围极广，无法提供普适性建议；因此本指南仅提供相关参考信息，以帮助研究者设计适配自身研究需求的实验方案。为限定研究边界，本次指南的聚焦对象为原核生物与微真核生物的eDNA样本采集与保存工作。即便限定了研究边界，任一方法的实际应用效果仍受多重因素影响，包括生境类型、可用资源以及实验目标。我们总体建议采用严格的去污流程、开展预实验以确定目标物种表征所需的过滤体积，并尽可能减少PCR抑制剂的富集；同时优先选择样本冷冻保存，而非仅添加保存缓冲液。本指南还附上了针对上述参数开展验证的研究的注释列表，以供研究者对具体步骤进行更深入的探究。为展示适配研究需求的方法学应用路径，我们提供了一套适用于海洋科考船的eDNA采样流程方案。本指南可为有意开展海洋微生物组与/或eDNA采样及测序工作的科研人员提供决策参考。