An official website of the United States government
Abstract Background Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. Results We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK ( S ooner T rend A nadarko Basin, C anadian and K ingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. Conclusions These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells.
more »
« less
Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer
The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter , Methyloversatilis , and Pseudomonas . Subsequent experimental deployments included a methanogen-dominated stage ( Methanobacteriales and Methanomicrobiales ) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.
more »
« less
- Award ID(s):
- 1826734
- PAR ID:
- 10325473
- Date Published:
- Journal Name:
- Frontiers in Microbiology
- Volume:
- 11
- ISSN:
- 1664-302X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The Chicxulub crater, Mexico, is the site of the asteroid impact that led to the end-Cretaceous mass extinction. While impact events are known to be able to cause severe disruption to surface-dwelling organisms, the effects of such catastrophic perturbations on the deep biosphere are not known. Deep ocean drilling into the peak ring of the Chicxulub impact crater (IODP expedition 364) in 2016 allowed us to study the modern deep biosphere within the (a) high-porosity melt-bearing impact breccia/suevite (617-740 mbsf) emplaced within a day or so of the Cenozoic, (b) the overlying low porosity post-impact marine Cenozoic carbonates (504-617mbsf), and the impacted and fractured granitic basement (740-1334 mbsf). The microbial biomass (~10 cells/g wet weight) was highest in the upper suevite, in underlying non-granitic subvolcanic pre-impact basanite, and at the intercalation of suevite and impact melt rock. Pre-impact sterile conditions of the uplifted granitic basement rocks and mineralogical evidence of impact-induced sterilization suggest that the basement rocks have only been amenable to microbial colonization for less than 66 Myr. Enrichments at in situ 50-60 °C show the presence of heterotrophic lifestyles in the suevite and bacterial sulfate reduction extending into the top of the granitic basement. Cultivation-independent 16S diversity profiling revealed the presence of heterotrophic (fermentative) as well as autotrophic C-fixing thermophilic bacteria in the organic-rich (up to 4 wt % total organic carbon; TOC) Cenozoic sediments. The organic-lean suevite (< 0.1% TOC) showed the unique presence of sequences related to thermophilic Synechococcus (cyanobacteria) and S-oxidizing green sulfur bacteria (chlorobi), and Chloroflexi often associated with organic-poor deep-sea sediments. Alphaproteobacteria, predominated in the upper part of the granitic basement (<1000 mbsf), while putative manganeseoxidising Bacilli (Firmicutes) predominated in the melt-rich granitic basement (>1200 mbsf). Our data suggest that the catastrophe that led to the end-Cretaceous mass extinction caused geological disruption and recolonization of microbial life in the deep subsurface biosphere at the Chicxulub impact site.more » « less
-
Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes (MAGs) representing the most abundant populations. None of the MAGs were closely related to either cultured or non-cultured organisms from the Genome Taxonomy or NCBI databases (none with average nucleotide identity >95%). Despite oxygen concentrations that are consistently below detection in the deep layer, some archaeal and bacterial MAGs mapped transcripts of genes for sulfide oxidation coupled with oxygen reduction. Among these microaerophilic sulfide oxidizers, mixotrophic Thermoplasmatales archaea were the most numerous and represented 24% of the total community. Populations associated with the highest predicted in situ activity for sulfate reduction were affiliated with Actinobacteria, Chloroflexi, and Nitrospirae phyla, and together represented about 9% of the total community. These MAGs, in addition to a less abundant Proteobacteria MAG in the genus Desulfomonile, contained transcripts of genes in the Wood-Ljungdahl pathway. All MAGs had significant genetic potential for organic carbon oxidation. Our results indicate that novel acidophiles are contributing to biosulfidogenesis in the deep layer of Cueva de la Mora, and that in situ sulfide production is limited by organic carbon availability and sulfur oxidation.more » « less
-
Srivastava, Abhishek (Ed.)IntroductionMarine particles form in the ocean surface sink through the water column into the deep ocean, sequestering carbon. Microorganisms inhabit and consume carbon in these particles. The East Pacific Rise (EPR) harbors both an Oxygen Deficient Zone (ODZ) and a non-buoyant plume region formed from hydrothermal vents located on the ocean floor, allowing us to explore relationships between microbial community and particle size between a range of environments. MethodsIn this study, we quantified microbial diversity using a fractionation method that separated particles into seven fine scale fractions (0.2–1.2, 1.2–5, 5–20, 20–53, 53–180,180–500, >500 μm), and included a spike-in standard for sequencing the 16S rRNA gene. Size fractionated organic carbon into the same fractions enabled the calculation of bacterial 16S rRNA copies per μg C and per liter. ResultsThere was a large increase in the bacterial 16S rRNA copies/ug C and copies/L on particles >180 μm between the upper water column and the deep water column. Though the total concentration of organic C in particles decreased in the deep water column, the density of bacteria on large particles increased at depth. The microbial community varied statistically significantly as a function of particle size and depth. Quantitative abundance estimates found that ostensibly obligate free-living microbes, such as SAR11 and Thaumarcheota, were more abundant in the free-living fraction but also common and abundant in the particulate size fractions. Conversely, ostensibly obligate particle attached bacteria such as members of Bacteroidetes and Planctomycetes, while most abundant on particles, were also present in the free living fraction. Total bacterial abundance, and the abundance of many taxonomic groups, increased in the ODZ region, particularly in the free-living fraction. Contrastingly, in the non-buoyant plume, there were highly abundant bacteria in the 5–20 and 20–53 μm fractions but reduced bacteria present in the 53–180 and 180–500 μm fractions. ConclusionQuantitative examination of microbial communities highlights the distribution of microbial taxa unburdened by compositional effects. These data are congruent with existing models which suggest high levels of exchange between particle-attached and free-living communities.more » « less
-
Previous ichnological analysis at the Chicxulub impact crater, Yucatán Peninsula, México (International Ocean Discovery Program [IODP]/International Continental Scientific Drilling Program [ICDP] Site M0077), showed a surprisingly rapid initial tracemaker community recovery after the end-Cretaceous (Cretaceous-Paleogene [K-Pg]) mass extinction event. Here, we found that full recovery was also rapid, with the establishment of a well-developed tiered community within ~700 k.y. Several stages of recovery were observed, with distinct phases of stabilization and diversification, ending in the development of a trace fossil assemblage mainly consisting of abundant Zoophycos, Chondrites, and Planolites, assigned to the Zoophycos ichnofacies. The increase in diversity is associated with higher abundance, larger forms, and a deeper and more complex tiering structure. Such rapid recovery suggests that favorable paleoenvironmental conditions were quickly reestablished within the impact basin, enabling colonization of the substrate. Comparison with the end-Permian extinction reveals similarities during recovery, yet postextinction recovery was significantly faster after the K-Pg event. The rapid recovery has significant implications for the evolution of macrobenthic biota after the K-Pg event. Our results have relevance in understanding how communities recovered after the K-Pg impact and how this event differed from other mass extinction events.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/fmicb.2020.536535
