A deep continental aquifer downhole sampler for microbiological studies

In order to be effective, microbiological studies of deep aquifers must be free from surface microbial contaminants (atmosphere/ soil) and infrastructures allowing access to formation water (wellheads, well completions). Many microbiological studies are based on water samples obtained after more or less rinsing of the well without guaranteeing the absence of contaminants (biofilms). The protocol described in this paper presents the adaptation for microbiological studies of deep aquifers of a commercial downhole sampler (Positive Displacement Sampler, PDSshort, Leutert, Germany) used until now for physicochemical and analytical chemistry studies (determination of dissolved gases, isotopy, etc.). Analyzes of taxonomic diversity based on high-throughput sequencing of the bacterial 16S rRNA gene were compared and discussed for different water samples taken at the surface at the wellhead (WHS) or at depth using the downhole sampler (DS). Here, the results show that even after extensive rinsing, the water collected at the wellhead is not free of microbial contaminants and the downhole sampler procedure is the only way to ensure the purity of the sampled water samples. In addition, the downhole sampler allows the formation water and the autochthonous microbial community to be maintained at pressure in situ up to the laboratory. With the advent of metagenomics and metatranscriptomics methods, the non-contamination of the sample and its representativeness are key to guarantee the best results and their interpretations which will allow us to understand the functioning of deep biosphere.

为保障研究有效性，深层含水层（deep aquifers）的微生物学研究必须规避地表微生物污染物（大气/土壤）以及用于获取地层水的配套设施（井口、完井装置）带来的污染。当前多数微生物学研究以经不同程度洗井后获取的水样为研究对象，但此类方法无法确保样本未受污染物（生物膜）污染。本文所述实验方案将一款此前仅用于物理化学与分析化学研究（如溶解气体测定、同位素分析等）的商用井下正位移采样器（Positive Displacement Sampler，简称PDSshort，德国Leutert公司）适配应用于深层含水层微生物学研究。本研究针对两类水样开展基于细菌16S rRNA基因高通量测序的分类多样性分析并展开对比讨论：一类为井口采集的地表水样（WHS），另一类为采用井下采样器获取的深层水样（DS）。研究结果显示，即便经彻底洗井，井口采集的水样仍无法完全摆脱微生物污染物；唯有采用井下采样器流程，方可确保采集水样的纯度。此外，井下采样器可将地层水与原位土著微生物群落维持原位压力，直至运送至实验室。随着宏基因组学（metagenomics）与宏转录组学（metatranscriptomics）技术的发展，样本的无污染物性及其代表性成为保障研究结果可靠性与解读准确性的核心要素，这将助力我们解析深层生物圈（deep biosphere）的运作机制。