Dissecting the deep biosphere: retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones

Abstract

Deep fracture zones in Finnish crystalline bedrock have been isolated for long, the oldest fluids being tens of millions of years old. To accurately measure the native microbial diversity in fracture-zone fluids, water samples were obtained by isolating the borehole fraction spanning a deep subsurface aquifer fracture zone with inflatable packers (500 and 967 m) or by pumping fluids directly from the fracture zone. Sampling frequency was examined to establish the time required for the space between packers to be flushed and replaced by indigenous fracture fluids. Chemical parameters of the fluid were monitored continuously, and samples were taken at three points during the flushing process. Microbial communities were characterized by comparison of 16S ribosomal genes and transcripts and quantification of dsrB (dissimilatory sulfate reduction) gene. Results suggest that fracture-zones host microbial communities with fewer cells and lower diversity than those in the drill hole prior to flushing. In addition, each fracture zone showed a community composition distinct from that inhabiting the drill hole at corresponding depth. The highest diversity was detected from the 967-m fracture zone. We conclude that the applied packer method can successfully isolate and sample authentic microbial fracture-zone communities of deep bedrock environments.

Evaluation of Molecular Techniques in Characterization of Deep Terrestrial Biosphere

“…Earlier research of the Fennoscandian deep subsurface has demonstrated its potential for monitoring changes in microbial community composition at different depths over time and for screening samples prior to the construction of clone libraries or metagenomic work [2] [5] [13]. However, despite use of two universal bacteria primer pairs, DGGE appeared to be biased towards Proteobacteria, especially the γ-and β-groups.…”

“…The greatest part of the archaeal 16S rRNA gene sequences (52%, 81% and 58% in OL-KR40/385m, OL-KR49/532m and OL-KR40/ 609m, respectively) belonged to uncultured Thermoplasmatales (Table 3(b)). 13.7% of the archaeal community in OL-KR40/385m clustered with cultured Thermoplasma species. Pendant 33/DHVE3, 4, 6 archaea was a major group in OL-KR40/609m (47.3%), but was only minor or absent in the other samples.…”

“…Analysis of phylogenetic marker genes using molecular methods offers a way to detect and identify the microbial taxa present in fracture fluids and can thereby be used to generate estimates of community diversity and composition [4] [13]. Gene for ribosomal 16S subunit (16S rRNA) is commonly used as a taxonomic marker because it is highly conserved, found in all bacteria and archaea, and a rich 16S rRNA database has been generated by systematists and evolutionary biologists against which sequences from fracture fluids can be compared and identified [14] [15].…”

“…Molecular techniques such as denaturing gradient gel electrophoresis (DGGE) and clone library construction [2]- [5] [13] most frequently detect Actinobacteria, Firmicutes and various Proteobacteria in deep subsurface fracture fluids of the Fennoscandian Shield. Furthermore, Bacteroidetes, Green non-sulphur bacteria, Candidate Divisions JS1, TM7, OP3, OP8, OP10, OP11, Deinococcus/Thermus, Verrucomicrobia, Bacilli and even Cyanobacteria are often detected in terrestrial subsurface, although in lower abundance [8] [16]- [18].…”

Trends and future challenges in sampling the deep terrestrial biosphere

“…Once a well has been developed, U -tube borehole fluid samplers can be used to remove the drilling fluid or monitor its dilution over time with ground water flow and then collect true formation fluids and gasses at near in situ conditions (Freifeld, 2009; Stotler et al, 2011). Further, geochemical conditions and microbial community structures for specific fractures can be determined through the use of packers that isolate those fractures within a borehole for sampling (Haveman et al, 1999; Shimizu et al, 2006; Purkamo et al, 2013). Finally, significant understanding of the mineralogy and geochemistry of a subsurface environment can be derived from the effective utilization of well log data (Onstott et al, 1998).…”