New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome

Abstract

Background: Hydraulically fractured shales offer a window into the deep biosphere, where hydraulic fracturing creates new microbial ecosystems kilometers beneath the surface of the Earth. Studying the microbial communities from flowback fluids that are assumed to inhabit these environments provides insights into their ecophysiology, and in particular their ability to survive in these extreme environments as well as their influence on site operation e.g. via problematic biofouling processes and/or biocorrosion. Over the past decade, research on fractured shale microbiology has focused on wells in North America, with a few additional reported studies conducted in China. To extend the knowledge in this area, we characterized the geochemistry and microbial ecology of two exploratory shale gas wells in the Bowland Shale, UK. We then employed a meta-analysis approach to compare geochemical and 16S rRNA gene sequencing data from our study site with previously published research from geographically distinct formations spanning China, Canada and the USA.

Results: Our findings revealed that fluids recovered from exploratory wells in the Bowland are characterized by moderate salinity and high microbial diversity. The microbial community was dominated by lineages known to degrade hydrocarbons, including members of Shewanellaceae, Marinobacteraceae, Halomonadaceae and Pseudomonadaceae. Moreover, UK fractured shale communities lacked the usually dominant Halanaerobium lineages. From our meta-analysis, we infer that chloride concentrations play a dominant role in controlling microbial community composition. Spatio-temporal trends were also apparent, with different shale formations giving rise to communities of distinct diversity and composition.

Conclusions: These findings highlight an unexpected level of compositional heterogeneity across fractured shale formations, which is not only relevant to inform management practices but also provides insight into the ability of diverse microbial consortia to tolerate the extreme conditions characteristic of the engineered deep subsurface.

Fig. 1

Microbial community composition of flowback fluids derived from the Bowland shale exploration wells. A Relative abundance of microbial classes in flowback fluids from the Bowland shale. All classes that represent ≥ 5% of sequences from any sample are listed on the bar plot, the rest are grouped as “Other”. B Temporal changes in chloride (ppm) concentration in the Bowland-1 (green) and Bowland-2 (purple) flowback fluids. C Venn diagram depicting the number of shared and unique ASVs (percentage of the total number of sequences) in each well. Relevant shared taxa at family level, i.e., organisms associated with shale systems and hydrocarbon reservoirs reported in previous studies, are indicated in the box

Fig. 2

Map of the location of the datasets examined in the meta-analysis. Number of samples per formation are indicated in parentheses and corresponding references in square brackets. [54] Stemple et al., 2021; [41] Tinker et al., 2020; [ Zhong et al., 2019; [14] Cluff et al., 2014; [55, 13] Rosenblum et al. 2017, Harris et al., 2018; [15, 16] Zhang et al., 2017, 2020

Fig. 3

Temporal and geographical patterns across shale formations. A Chloride concentration in flowback and produced fluids across shales. B Observed ASVs and C Shannon values variation in function of chloride concentration. D Boxplot comparison of observed ASVs and E Shannon (H′)

Fig. 4

Heatmap displaying the top 30 most abundant families across all shale formations. Samples from different wells are indicated with separations within the facets. Annotations indicate the time of the sampling in a range of days after hydraulic fracturing and the salinity level following these categories saline (2000–10,000 mg/L), highly saline (10,000–60,000 mg/L) and brine (over 60,000 mg/L))

Fig. 5

RDA biplot linking microbial composition and geochemistry in the fractured shale microbiome. Dots represent samples, black arrows environmental parameters and red arrows microbial families. The arrows indicate the direction of environmental variables associated with the different bacterial families

Fig. 6

Network analysis of ASVs with abundance of ≥ 1% of the sequences in each given sample based on SPIEC-EASI. A Microbial co-occurrence network. Node’s size represents betweenness centrality. Nodes with betweenness centrality ≥ 1000 are annotated at phylum level. Distinct colors indicate distinct modules. Edges represent interactions between ASVs. B Classification of nodes based on among-module and within-module connectivity, network hubs (purple) and module hubs (orange) in the fractured shale microbiome