Subsurface Communities Research Articles

Climate variability shifts the vertical structure of phytoplankton in the Sargasso Sea

AbstractMarine phytoplankton are essential to ocean biogeochemical cycles. However, our understanding of changes in phytoplankton rely largely on satellite data, which can only assess changes in surface phytoplankton. How climate variability is impacting their vertical structure remains unclear. Here we use 33 years’ worth of data from the Sargasso Sea to show distinct seasonal and long-term phytoplankton climate responses in the surface mixed layer compared with the subsurface. Seasonally, the surface community alters their carbon-to-chlorophyll ratio without changing their carbon biomass, whereas the chlorophyll a and carbon of the subsurface community covaries with no change in their carbon-to-chlorophyll ratio. Over the last decade, the subsurface phytoplankton biomass has increased in response to warming, whereas the surface phytoplankton have altered their carbon-to-chlorophyll ratio with minimal change in their carbon biomass. Given that satellites can only view the surface ocean, sustained subsurface monitoring is required to provide a full understanding of how phytoplankton are responding to climate change.

Deep subseafloor sediments in Guaymas Basin harbor cosmopolitan microbiota and traces of hydrothermal populations

Environmental factors shape subsurface microbial ecosystems, and well-characterized sites are ideal for determining how environmental parameters shape sediment communities. Sediments from eight geologically and thermally distinct sites were drilled during International Ocean Discovery Program Expedition 385 in Guaymas Basin, an expedition focused on the hydrothermal deep biosphere. Using high-throughput 16S ribosomal nucleic acid sequencing, cell counts, phylogenetics, metatranscriptomics, and mineralogical/elemental X-ray spectroscopy, we examine linkages and feedbacks between mineral composition, temperature, geochemistry, and microbial populations. We show subsurface life is dominated by heterotrophic, cosmopolitan prokaryotes that thrive within a range of sediments and temperature conditions across Guaymas Basin. Hydrothermally-affiliated lineages are detected in low numbers at sites with steepest temperature gradients, within communities of mesophilic taxa that occur throughout Guaymas Basin and in other marine subsurface habitats. Thus, hydrothermal lineages do not replace the cosmopolitan, mesophilic subsurface community, but remain specific to sites where volcanic intrusions drive hydrothermal circulation.

Microbial ecology of the deep terrestrial subsurface.

The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.

Experimental seabed disturbance effects on Chatham Rise deep-sea meiofaunal communities, Southwest Pacific

ABSTRACT Growing global demand for deep-sea resources may lead to increased pressure on benthic ecosystems. Here we examined changes in meiofaunal communities following an in situ physical disturbance experiment. A significant change in meiofaunal community structure in surface (0-1 cm) and subsurface (1-5 cm) sediments was observed immediately following the disturbance at both the directly and indirectly disturbed sites and adjacent potentially undisturbed/indirectly disturbed sites, reflecting a decrease in the abundance of several meiofaunal taxa. Abundance, taxon richness and diversity also decreased immediately following disturbance across all sites. Surface community parameters returned to pre-disturbance values one year post-disturbance, but only a partial recovery was observed for the subsurface community over the same period. The accumulation of recently resuspended and deposited sediment could have led to lower meiofaunal density and shifts in community structure. Passive dispersal and recolonisation from outside the study area may explain why the surface community recovered more fully than the subsurface community. We show that meiofauna were negatively affected by a relatively minor disturbance compared to proposed commercial seabed mining operations, but the finding that communities had largely recovered one year after disturbance has implications for resilience of fauna to much more pronounced impacts of potential large-scale mining.

Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis.

Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.

Hydrogeological controls on microbial activity and habitability in the Precambrian continental crust.

Earth's deep continental subsurface is a prime setting to study the limits of life's relationship with environmental conditions and habitability. In Precambrian crystalline rocks worldwide, deep ancient groundwaters in fracture networks are typically oligotrophic, highly saline, and locally inhabited by low-biomass communities in which chemolithotrophic microorganisms may dominate. Periodic opening of new fractures can lead to penetration of surface water and/or migration of fracture fluids, both of which may trigger changes in subsurface microbial composition and activity. These hydrogeological processes and their impacts on subsurface communities may play a significant role in global cycles of key elements in the crust. However, to date, considerable uncertainty remains on how subsurface microbial communities may respond to these changes in hydrogeochemical conditions. To address this uncertainty, the biogeochemistry of Thompson mine (Manitoba, Canada) was investigated. Compositional and isotopic analyses of fracture waters collected here at ~1 km below land surface revealed different extents of mixing between subsurface brine and (paleo)meteoric waters. To investigate the effects this mixing may have had on microbial communities, the Most Probable Number technique was applied to test community response for a total of 13 different metabolisms. The results showed that all fracture waters were dominated by viable heterotrophic microorganisms which can utilize organic materials associated with aerobic/facultative anaerobic processes, sulfate reduction, or fermentation. Where mixing between subsurface brines and (paleo)meteoric waters occurs, the communities demonstrate higher cell densities and increased viable functional potentials, compared to the most saline sample. This study therefore highlights the connection between hydrogeologic heterogeneity and the heterogeneity of subsurface ecosystems in the crystalline rocks, and suggests that hydrogeology can have a considerable impact on the scope and scale of subsurface microbial communities on Earth and potentially beyond.

Viruses, Vesicles, and other Biological Nanoparticles: The Sub-cellular Biosphere of a Deeply Buried 2km-Deep, 20-Million-Year-Old Coalbed Community

Horizontal gene transfer is an important driver of adaptation and evolution in microorganisms. Transducing biological nanoparticles such as viral particles are believed to be key facilitators of horizontal gene transfer. In deep subseafloor sediments, energy can be highly limiting, supporting only extremely slow metabolisms. In such low-energy, isolated environments where communities may subsist for millions of years, the mechanisms of subsurface microbial adaptation and evolution remain a mystery. Virus particles have been found everywhere that life has been found, including deep subsurface environments. Although microorganisms are abundant and active in the Earth's subsurface, the role of viruses in shaping and influencing these slow-growing communities is only recently starting to be explored. Here, we analyzed the deeply buried microbial community from a lignite coalbed layer 2km below the seafloor offshore Shimokita, Japan (IODP Expedition 337) that had been buried for 20 million years. We harvested cells (>0.2µm) and biological nanoparticles (<0.2µm) from a bioreactor enrichment seeded by lignite core samples. We sequenced DNA from the cells and nanoparticles and subsequently analyzed the metagenomes. Within the nanoparticle metagenome, numerous complete novel virus genomes were reconstructed. Comparison of the virus genomes to the prokaryotic MAGs (metagenome assembled genomes) revealed that many of the virus genomes had been integrated prophage within bacterial genomes, suggesting the potential for virus-host interactions to occur in the deep subseafloor. Additionally, lysogeny may be an important survival mechanism for viruses in deeply buried, low-energy environments. Host genes were found to be packaged by viral particles, demonstrating the potential for specialized and general transduction by viruses. Not only viral particles, but there was also evidence that membrane vesicles and gene transfer agents may participate in transduction in this deep subsurface community. Horizontal gene transfer mediated by biological nanoparticles may be an important mechanism of adaptation for deep subsurface microbial communities and may provide insight into possible evolutionary processes shaping microbial communities in the deep subsurface. These results may also shed some light onto the nature of viral infection in the subsurface, potentially revealing insights about the long-term persistence of life under extreme energy limitation and how viruses may survive this over geological timescales.

A simplified bacterial community found within the epidermis than at the epidermal surface of atopic dermatitis patients and healthy controls

There has been considerable research into the understanding of the healthy skin microbiome. Similarly, there is also a considerable body of research into whether specific microbes contribute to skin disorders, with atopic dermatitis (AD) routinely linked to increased Staphylococcus aureus (S. aureus) colonisation. In this study, the epidermal surface of participants was sampled using swabs, while serial tape-stripping (35 tapes) was performed to sample through the stratum corneum. Samples were taken from AD patients and healthy controls, and the bacterial communities were profiled by metabarcoding the universal V3-V4 16S rRNA region. Results show that the majority of bacterial richness is located within the outermost layers of the stratum corneum, however there were many taxa that were found almost exclusively at the very outermost layer of the epidermis. We therefore hypothesise that tape-stripping can be performed to investigate the ‘core microbiome’ of participants by removing environmental contaminants. Interestingly, significant community variation between AD patients and healthy controls was only observable at the epidermal surface, yet a number of individual taxa were found to consistently differ with AD status across the entire epidermis (i.e. both the epidermal surface and within the epidermis). Sampling strategy could therefore be tailored dependent on the hypothesis, with sampling for forensic applications best performed using surface swabs and outer tapes, while profiling sub-surface communities may better reflect host genome and immunological status.

Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales

Continental slopes can play a significant contribution to marine productivity and carbon cycling. These regions can harbour distinct geological features, such as salt diapirs and pockmarks, in which their depressions may serve as natural sediment traps where different compounds can accumulate. We investigated the prokaryotic communities in surface (0–2 cm) and subsurface (18–20 or 22–24 cm) sediments from a salt diapir and pockmark field in Santos Basin, Southwest Atlantic Ocean. Metabarcoding of 16 samples revealed that surface sediments were dominated by the archaeal class Nitrososphaeria, while the bacterial class Dehalococcoidia was the most prevalent in subsurface samples. Sediment strata were found to be a significant factor explaining 27% of the variability in community composition. However, no significant difference was observed among geomorphological features. We also performed a metagenomic analysis of three surface samples and analysed the highest quality metagenome-assembled genome retrieved, which belonged to the family CSP1–5, phylum Methylomirabilota. This non-methanotrophic methylotroph contains genes encoding for methanol oxidation and Calvin Cycle pathways, along with diverse functions that may contribute to its adaptation to deep-sea habitats and to oscillating environmental conditions. By integrating metabarcoding and metagenomic approaches, we reported that CSP1–5 is prevalent in the sediment samples from Santos Basin slope, indicating the potential importance of methanol metabolism in this region. Finally, using a phylogenetic approach integrating 16S rRNA sequences assigned to Methylomirabilota in this study with those from a public database, we argued that CSP1–5 public sequences might be misclassified as Methylomirabilaceae (the methanotrophic clade) and, therefore, the role of these organisms and the methanol cycling could also be neglected in other environments.

Phytoplankton diversity explained by connectivity across a mesoscale frontal system in the open ocean

Phytoplankton community composition is important in establishing ecosystem structure and function. Intuitively, we recognize that water movements must be important for modifying spatial gradients and plankton diversity. However, identifying boundaries and exchange between habitats in the open ocean is not straightforward. Here, we use the abundance of nine phytoplankton species closely sampled in a mesoscale frontal system in the northeastern North Sea as a proxy for community composition and explore the relationship between phytoplankton biogeography and transport patterns. Subsurface community distributions could be related to modeled patterns in water movement. A methodology for analyzing pelagic diversity that includes a representation of plankton community composition and an Eulerian connectivity tracer was developed, and the relative importance of connectivity and geographical distance for phytoplankton species composition analyzed. The connectivity tracer identifies timescales and dispersal barriers in the open ocean. Connectivity was found to be superior in explaining pelagic plankton diversity and found to be a prerequisite for understanding the pelagic phytoplankton composition. This approach is a valuable tool for establishing the link between ocean transports, ecosystem structure and biodiversity and for informing the placement of marine protected areas.

Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities.

Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.

The role of subsurface ice in sustaining bacteria in continental and maritime glaciers

In supraglacial environments, surface and subsurface ices are two distinct and connected microhabitats in terms of physicochemical and biological aspects. At the frontline of climate change, glaciers lose tremendous ice masses to downstream ecosystems, serving as crucial sources of both biotic and abiotic materials. In this study, we studied the disparities and relationships of microbial communities between surface and subsurface ices collected from a maritime and a continental glacier during summer. The results showed that surface ices had significantly higher nutrients and were more physiochemically different than subsurface ices. Despite lower nutrients, subsurface ices had higher alpha-diversity with more unique and enriched operational taxonomic units (OTUs) than surface ices, indicating the potential role of subsurface as a bacterial refuge. Sorensen dissimilarity between bacterial communities in surface ices and subsurface ices was mainly contributed by the turnover component, suggesting strong species replacement from surface to subsurface ices due to large environmental gradients. For different glaciers, the maritime glacier had significantly higher alpha-diversity than the continental glacier. The difference between surface and subsurface communities was more pronounced in the maritime glacier than in the continental glacier. The network analysis revealed that surface-enriched and subsurface-enriched OTUs formed independent modules, with surface-enriched OTUs having closer interconnections and greater importance in the network of the maritime glacier. This study highlights the important role of subsurface ice as a bacterial refuge and enriches our knowledge of microbial properties in glaciers.

Estimation of heterogeneous permeability using pressure derivative data through an inversion neural network inspired by the Fast Marching Method

Reservoir heterogeneity significantly impacts the fluid flow behavior in porous media. In subsurface communities including hydrocarbon or geothermal recovery, geological storage of CO2 or H2, and hydrology, transient pressure data are often used to infer the subsurface rock properties (e.g., permeability field) due to its ready availability and quick response. The accurate estimation of such properties is critical to accurately predict fluid flow in porous media.In this work, we propose a deep learning (DL) approach inspired by the Fast Marching Method (FMM), namely the Inversion Neural Network (INN), to inversely infer heterogeneous reservoir model parameters using transient pressure data. The forward model used to generate training data for the INN is established based on a semi-analytic asymptotic solution to the diffusivity equation using the diffusive time of flight (DTOF). The FMM solves the Eikonal equation for the DTOF and provides the partial derivative of pressure drop to the natural logarithm of time (hereafter pressure derivative). The pressure derivative data are then used to predict reservoir model parameters by the INN. In the homogeneous scenario, the INN architecture is a relatively simple fully connected neural network as a proof-of-concept to validate the feasibility, and it directly correlates the permeability value with the pressure derivative. In the heterogeneous scenario, as the heterogeneous permeability field is estimated based on sparse observational data of pressure derivatives, we adopt the convolutional neural network (CNN) to flexibly deal with the image-based properties, and leverage transfer learning to efficiently train a robust INN in the heterogeneous scenario.We first validated that INN can infer the homogeneous permeability fields through numerical experiments by testing root-mean-square-error (RMSE) around 1.086 md. Inspired by that, observational data with different sparsity are used to train convolutional INN and predict heterogeneous permeability fields. As the number of observational locations (nobs) increases from 3 × 3 to 48 × 48, the testing RMSE in heterogeneous scenarios decreases from 187.510 md to 18.080 md. Besides, we found that transfer learning significantly improves the predictive accuracy at low nobs, with relative error decreased by 17.25%. Finally, noisy pressure derivative data under different nobs are used to history match the heterogeneous reservoir model, and INN can infer the permeability field with a low error of 9.6% at nobs=7×7. Without an iterative procedure for parameter estimation, the INN demonstrates to perform permeability inversion with CPU time in the magnitude of 9.2×10−4 s on a single GPU (NVIDIA Quadro P2200). The FMM-inspired INN sets up the basis for the accurate characterization of reservoir model heterogeneity by inverting pressure derivative data with both decent predictive accuracy and computational efficiency.

A global perspective on bacterial diversity in the terrestrial deep subsurface.

While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

Guest Editorial: Why Starting or Continuing a Career in Upstream Oil and Gas Is Still a Good Idea

It has been almost 30 years since I decided to join the oil industry. In the 1990s, it wasn’t an obvious decision for a young woman with a general mathematics degree, studying in London but originally from rural Derbyshire with two teacher parents. And in a time when Shell’s decision to dispose of Brent Spar was a hot topic, and Brent price had subsided to around $20/bbl after an infamous boom in the 1980s. An international oil and gas career was not what I had thought about when I imagined cycling to work along the Thames. But the oil industry still had a long future ahead of it, and the idea of combining technical problem-solving in an international setting had great appeal. I didn’t join Shell with the definite intention of staying with the company, or even in the oil industry, for all of my career. But the initial opportunities to learn and develop, while working on worthwhile and challenging problems with talented colleagues, were clear. And when I reflect on it, regardless of the noise, particularly in Western media, the same value proposition is there. Joining the upstream subsurface community means starting a career full of creative opportunities and a chance to contribute to solving the world’s energy problems. The energy landscape as we know it is shifting. Forecasts indicate that the energy mix is going to change at varying rates and degrees of complexity across the globe in the coming years. Alongside a rapid growth of renewable sources like wind, solar, and low-emission fuels, there will be a continued and long-term global demand for oil and gas. Working in upstream doesn’t necessarily mean staying in upstream, and many of the challenges faced in developing oil and gas are very similar to those faced in developing nonfossil-fuel energy sources, which allows for exciting opportunities to develop transferable skills that would be an asset to many new energies’ projects. What sort of similar challenges are we talking about? Well, the most obvious are those in carbon capture and storage, or CCS. In oil and gas development, we study reservoirs to analyze where to drill, to determine what will be recovered, and to decide whether we should inject water or gas to increase production rates. We drill wells to produce oil or gas, we monitor production and decide whether to optimize production through higher or lower rates, we decide whether to open or close zones, we decide whether to drill infill wells, we decide when to cease production from individual wells or from an entire field, and we decide how to safely abandon the reservoirs and wells. For CCS, we do a subset of this; we work out where we can safely store CO2, we decide how many wells to drill, we determine how to monitor to ensure the CO2 is being safely sequestered, and we decide how to we will eventually safely abandon the storage, leaving the CO2 trapped eternally in the subsurface. Many of our traditional subsurface skills are immediately translated for these types of projects—and equally all of the integration skills that subsurface engineers develop in their oil and gas production roles are immediately translatable for CCS projects.

Chemistry of springs across the Mariana forearc: Carbon flux from the subducting plate triggered by the lawsonite-to-epidote transition?

Low-chlorinity springs sampled from ten sites on nine serpentinite mud volcanoes show systematic chemical gradients across the outer Mariana forearc that result from progressive devolatilization of the subducting Pacific plate. Sites range from 50 to 90 km from the trench axis corresponding to depths to the top of the plate of ∼15–29 km. Dissolved sulfate, Na/Cl, K, Rb, Cs, and B in the springs all increase regularly with distance from the trench, leached from subducting sediment and altered basalt in response to increasing temperature at depth from ∼80 to 350 °C. Sites nearer the trench have high Ca (up to 76 mmol/kg) and Sr, low alkalinity, and pH 10.7, whereas sites farther from the trench have almost no Ca and Sr, alkalinity (some carbonate but mostly hydroxyl) as high as 69 meq/kg, and pH 12.5. Springs with high alkalinity also have high methane (>44 mmol/kg) that feeds sulfate-reducing archaeal communities in the shallow subsurface and macrofauna at the seafloor. These distal springs form chimneys and crusts of CaCO3, whereas the proximal springs form chimneys of brucite. High alkalinity at the distal sites apparently results from carbonate dissolution at the top of the subducting plate; because serpentinization during ascent generates both high pH and H2, the resulting dissolved carbonate is reduced to methane such that carbonate alkalinity is replaced by hydroxyl alkalinity: 4H2 + HCO3– → CH4 + 2H2O + OH–. This reaction can account for the much higher pH of the distal springs. Chlorinity of the springs varies from 234 to 546 mmol/kg and is related to latitude NS rather than distance from the trench. Distal springs have otherwise similar compositions over this entire range of chlorinity, implying that chloride derives from depth rather than from mixing with seawater within the seamounts themselves. The range in chlorinity can readily be explained by serpentinization at reasonable water/rock mass ratios of 0.2–1.0 if 30–40% of the spring water originates as residual pore water in subducted sediment and basalt rather than as H2O+ of dehydration.The pH, alkalinity, and methane content of the springs increase abruptly, while Ca and Sr decrease, because carbonate dissolution joins dehydration as a major process at the top of the subducting plate at ∼70 km from the trench, where metabasites recovered from the serpentinite mud indicate the transition from lawsonite blueschist facies to epidote blueschist facies also occurs. Replacement of lawsonite by epidote drastically depletes the solution in Ca and shifts the equilibrium toward massive dissolution of subducted carbonate. Fluxes of sulfate, C, Na, K, Rb, Cs, B, Ca, and Sr in the forearc springs represent only a few percent of the amounts subducted, consistent with continued supply at greater depth.

The fascinating biology of stinky caves

The discovery of Movile Cave in 1986, similarly to the discovery of the deep-sea vents 9 years earlier, showed that, when redox interfaces are present in subsurface ecosystems, diverse and abundant biological communities can thrive based primarily on autochthonous food produced in situ by chemosynthesis. Additional caves, partially flooded by sulfidic water have been discovered, i.e. the Frasassi caves in Italy, Ein-Nur Cave and Ayyalon Cave in Israel, Melissotrypa Cave in Greece, Tashan Cave in Iran, caves in the Sharo-Argun Valley in the Caucasus Mountains, etc. All of these are inhabited by numerous endemic cave-adapted organisms present in dense populations sustained by a rich food base generated within the subterranean environment by microorganisms that use atmospheric oxygen to oxidize the reduced chemical compounds present in the water (H2S, NH4+, CH4). Stable isotope data has shown that the biological communities found in sulfidic caves are not dependent on carbon fixation in green plants that use light energy in the process of photosynthesis. Special adaptations have been identified in some of these inhabitants that allow them to cope with the adverse environmental conditions such as toxicity of H2S, hypoxia, and extreme pH values. Symbiotic associations between crustaceans, protozoa, and sulfide oxidizing bacteria were discovered in several sulfidic caves. New species of microorganisms have also been described from these unusual subsurface environments. Unusual microbiomes have recently been discovered in dry caves that contain chemoclines between heavy volcanic gasses dominated by CO2, but also containing H2S and CH4, and atmospheric air that floats on top of the volcanic gas emissions. Unique sulfur mineralization, microbial biofilms containing new species of bacteria that thrive at extremely pH values, symbiotic relationships between bacteria and fungi have been discovered in Sulfur Cave in Romania, Bosoletto Cave in Italy, and Sousaki caves in Greece. The extreme life conditions encountered in these caves are of special interest to astrobiologists using these caves as a model for better understanding conditions that life may be present in on other planets and celestial bodies in our Solar System and beyond.

Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow

Subsurface microbial community distribution patterns are influenced by biogeochemical and groundwater fluxes and may inform hydraulic connections along groundwater-flow paths. This study examined the regional-scale microbial community of the Death Valley Regional Flow System and evaluated whether subsurface communities can be used to identify groundwater-flow paths between recharge and discharge areas. Samples were collected from 36 sites in three groundwater basins: Pahute Mesa–Oasis Valley (PMOV), Ash Meadows (AM), and Alkali Flat–Furnace Creek Ranch (AFFCR). Microbial diversity within and between communities varied by location, and communities were separated into two overall groups that affiliated with the AM and PMOV/AFFCR basins. Network analysis revealed patterns between clusters of common microbes that represented groundwaters with similar geochemical conditions and largely corroborated hydraulic connections between recharge and discharge areas. Null model analyses identified deterministic and stochastic ecological processes contributing to microbial community assemblages. Most communities were more different than expected and governed by dispersal limitation, geochemical differences, or undominating processes. However, certain communities from sites located within or near the Nevada National Security Site were more similar than expected and dominated by homogeneous dispersal or selection. Overall, the (dis)similarities between the microbial communities of DVRFS recharge and discharge areas supported previously documented hydraulic connections between: (1) Spring Mountains and Ash Meadows; (2) Frenchman and Yucca Flat and Amargosa Desert; and (3) Amargosa Desert and Death Valley. However, only a portion of the flow path between Pahute Mesa and Oasis Valley could be supported by microbial community analyses, likely due to well-associated artifacts in samples from the two Oasis Valley sites. This study demonstrates the utility of combining microbial data with hydrologic, geologic, and water-chemistry information to comprehensively characterize groundwater systems, highlighting both strengths and limitations of this approach.

Part 2: Oil displacement by foam injection in Hele-Shaw cell with a pattern of impermeable regions

Foam flooding is an enhanced oil recovery (EOR) technique that is used to control gas mobility, particularly in heterogeneous and fractured reservoirs. This paper aims to numerically investigate the effect of foam flooding on oil displacement efficiency at the fracture scale. Also, an empirical model for relative permeability, which remains difficult and troublesome to measure, is proposed and implemented in the numerical model. The experimental data used in this study include five injection methods that are water, gas, tertiary gas, foam, and tertiary foam. Fluid injection was performed through 2D-printed models of an actual rock cross-section, which was obtained from high-resolution micro-computed tomography. In the numerical model used, pressure and saturation equations of injected fluids were solved using the COMSOL software.Based on the findings, both experimental data and numerical simulation results of the five injection methods were in good agreement, which shows the robustness of the proposed relative permeability model with a single fitting parameter. The oil recovery factor predicted using the proposed model outperformed that of the Buckley-Leverett and Brooks-Corey models. Also, the relative permeability model was further tested against coreflooding experimental data from the literature. This study provides more insight into numerical modeling of foam flooding at the fracture scale. Moreover, we believe that the proposed relative permeability model is robust and capable of capturing the evolution of relative permeability with saturation along the injection process, which encourages further investigation and improvement by the subsurface community. Further field-scale studies, including sensitivity and optimization, can be performed based on this work.

Microbial Hydrocarbon Degradation in Guaymas Basin-Exploring the Roles and Potential Interactions of Fungi and Sulfate-Reducing Bacteria.

Hydrocarbons are degraded by specialized types of bacteria, archaea, and fungi. Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions, using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system. This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments, and thus selects for diverse hydrocarbon-degrading communities of which methane, alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied. Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments, and draw attention to possible fungal-bacterial interactions. In this Hypothesis and Theory article, we report on background, recent results and outcomes, and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021, and that we will revisit during our ongoing investigations of bacterial, archaeal, and fungal communities in the deep sedimentary subsurface of Guaymas Basin.