Microbial growth under supercritical CO2

Microbial biosurfactants: Multifarious applications in sustainable agriculture

Agriculture in the 21st century faces grave challenges to meet the unprecedented food demand of the burgeoning population as well as reduce the ecological footprint for achieving sustainable development goals. The extensive use of harsh synthetic surfactants in pesticides and the agrochemical industry has substantial adverse impacts on the soil and environment due to their toxic and non-biodegradable nature. Biosurfactants derived from plant, animal, and microbial sources can be an eco-friendly alternative to chemical surfactants. Microbes producing biosurfactants play a noteworthy role in biofilm formation, plant pathogen elimination, biodegradation, bioremediation, improving nutrient bioavailability, and can thrive well under stressful environments. Microbial biosurfactants are well suited for heavy metal and organic contaminants remediation in agricultural soil due to their low toxicity, high activity at fluctuating temperatures, biodegradability, and stability over a wide array of environmental conditions. This green technology will improve the agricultural soil quality by increasing the soil flushing efficiency, mobilization, and solubilization of nutrients by forming metal-biosurfactant complexes, and through the dissemination of complex nutrients. Such characteristics help it to play a pivotal role in environmental sustainability in the foreseeable future, which is required to increase the viability of biosurfactants for extensive commercial uses, making them accessible, affordable, and economically sustainable.

Identifying and Understanding Microbial Methanogenesis in CO2 Storage

Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO₂ can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO₂, yet there has been little consideration of the subsurface microbial impact on CO₂ storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO₂ that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO₂ storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H₂ generation. We expect that the bioavailability of H₂ (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO₂ storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO₂ storage sites and its potential impact.

Effect of CO2 on biogeochemical reactions and microbial community composition in bioreactors with deep groundwater and basalt

Changes in subsurface microbiology following CO₂ injection have the potential to impact carbon trapping in CO₂ storage reservoirs. However, much remains to be learned about responses of natural microbial consortia to elevated CO₂ in basaltic systems. This study asks: how will microbes from deep (700 m) groundwater change along a gradient in CO₂ (0-20 psi) in batch reactor systems containing basalt chips and groundwater amended with lactate? Reactors incubated for 87 days at 23 °C. Results for reactors with low CO₂ (0 and 3 psi) differed considerably from those with high CO₂ (10 and 20 psi). In reactors with low CO₂, pH was >6.5 and lactate started to be used within 24 days. By 40 days, lactate was completely consumed and acetate increased to ~4 mM. As lactate was consumed, sulfate decreased from 0.16 to 0 mM after 40 days. In contrast, in reactors with high CO₂, pH was <6.5, lactate and sulfate concentrations varied little and acetate was not produced. Biogeochemical modeling and community analyses indicate that differences between reactors with low and high CO₂ reflect tolerances of reactor microbes to CO₂ exposure. Communities in the low CO₂ reactors carried out syntrophic lactate oxidation coupled with methanogenesis and sulfate reduction. Bacteroidota and Firmicutes became dominant phyla after 24 days and groups capable of sulfate reduction and methanogenesis were detected. In reactors with high CO₂, however, biogeochemical activity was insignificant, no groups capable of sulfate reducion or methanogenesis were observed, and the community became less diverse during the incubation. These findings show that the response of microbial consortia can vary sharply along a CO₂ gradient, creating significant differences in community composition and biogeochemistry, and that the timescale of basalt weathering is likely not rapid enough to prevent significant stress following a rapid increase in CO₂ abundance.

Evaluation of supercritical CO2 sterilization efficacy for sanitizing personal protective equipment from the coronavirus SARS-CoV-2

The purpose of this research is to evaluate the supercritical carbon dioxide (scCO₂) sterilization-based NovaClean process for decontamination and reprocessing of personal protective equipment (PPE) such as surgical masks, cloth masks, and N95 respirators. Preliminarily, Bacillus atrophaeus were inoculated into different environments (dry, hydrated, and saliva) to imitate coughing and sneezing and serve as a "worst-case" regarding challenged PPE. The inactivation of the microbes by scCO₂ sterilization with NovaKill or H₂O₂ sterilant was investigated as a function of exposure times ranging from 5 to 90 min with a goal of elucidating possible mechanisms. Also, human coronavirus SARS-CoV-2 and HCoV-NL63 were inoculated on the respirator material, and viral activity was determined post-treatment. Moreover, we investigated the reprocessing ability of scCO₂-based decontamination using wettability testing and surface mapping. Different inactivation mechanisms have been identified in scCO₂ sanitization, such as membrane damage, germination defect, and dipicolinic acid leaks. Moreover, the viral sanitization results showed a complete inactivation of both coronavirus HCoV-NL63 and SARS-CoV-2. We did not observe changes in PPE morphology, topographical structure, or material integrity, and in accordance with the WHO recommendation, maintained wettability post-processing. These experiments establish a foundational understanding of critical elements for the decontamination and reuse of PPE in any setting and provide a direction for future research in the field.

Effect of Fluid-Rock Interactions on In Situ Bacterial Alteration of Interfacial Properties and Wettability of CO2-Brine-Mineral Systems for Geologic Carbon Storage

This study explored the feasibility of biosurfactant amendment in modifying the interfacial characteristics of carbon dioxide (CO₂) with rock minerals under high-pressure conditions for GCS. In particular, while varying the CO₂ phase and the rock mineral, we quantitatively examined the production of biosurfactants by Bacillus subtilis and their effects on interfacial tension (IFT) and wettability in CO₂-brine-mineral systems. The results demonstrated that surfactin produced by B. subtilis caused the reduction of CO₂-brine IFT and modified the wettability of both quartz and calcite minerals to be more CO₂-wet. The production yield of surfactin was substantially greater with the calcite mineral than with the quartz mineral. The calcite played the role of a pH buffer, consistently maintaining the brine pH above 6. By contrast, an acidic condition in CO₂-brine-quartz systems caused the precipitation of surfactin, and hence surfactin lost its ability as a surface-active agent. Meanwhile, the CO₂-driven mineral dissolution and precipitation in CO₂-brine-calcite systems under a non-equilibrium system altered the solid substrates, produced surface roughness, and caused contact angle variations. These results provide unique experimental data on biosurfactant-mediated interfacial properties and wettability in GCS-relevant conditions, which support the exploitation of in situ biosurfactant production for biosurfactant-aided CO₂ injection.

Use of supercritical carbon dioxide technology for fabricating a tissue engineering scaffold for anterior cruciate ligament repair

Tissue-engineered grafts may be useful in Anterior Cruciate Ligament (ACL) repair and provide a novel, alternative treatment to clinical complications of rupture, harvest site morbidity and biocompatibility associated with autografts, allografts and synthetic grafts. We successfully used supercritical carbon dioxide (Sc-CO₂) technology for manufacturing a “smart” biomaterial scaffold, which retains the native protein conformation and tensile strength of the natural ACL but is decellularized for a decreased immunogenic response. We designed and fabricated a new scaffold exhibiting (1) high tensile strength and biomechanical properties comparable to those of the native tissue, (2) thermodynamically-stable extra-cellular matrix (ECM), (3) preserved collagen composition and crosslinking, (4) a decellularized material milieu with potential for future engineering applications and (5) proven feasibility and biocompatibility in an animal model of ligament reconstruction. Because of the “smart” material ECM, this scaffold may have the potential for providing a niche and for directing stem cell growth, differentiations and function pertinent to new tissue formation. Sc-CO₂-related technology is advanced and has the capability to provide scaffolds of high strength and durability, which sustain a lifetime of wear and tear under mechanical loading in vivo.

Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review

Before the industrial revolution, the atmospheric CO₂ concentration was 180-330 ppm; however, fossil-fuel combustion and forest destruction have led to increased atmospheric CO₂ concentration. CO₂ capture and storage is regarded as a promising strategy to prevent global warming and ocean acidification and to alleviate elevated atmospheric CO₂ concentration, but the leakage of CO₂ from storage system can lead to rapid acidification of the surrounding circumstance, which might cause negative influence on environmental microbes. The effects of elevated CO₂ on microbes have been reported extensively, but the review regarding CO₂ affecting different environmental microorganisms has never been done previously. Also, the mechanisms of CO₂ affecting environmental microorganisms are usually contributed to the change of pH values, while the direct influences of CO₂ on microorganisms were often neglected. This paper aimed to provide a systematic review of elevated CO₂ affecting environmental microbes and its mechanisms. Firstly, the influences of elevated CO₂ and potential leakage of CO₂ from storage sites on community structures and diversity of different surrounding environmental microbes were assessed and compared. Secondly, the adverse impacts of CO₂ on microbial growth, cell morphology and membranes, bacterial spores, and microbial metabolism were introduced. Then, based on biochemical principles and knowledge of microbiology and molecular biology, the fundamental mechanisms of the influences of carbon dioxide on environmental microbes were discussed from the aspects of enzyme activity, electron generation and transfer, and key gene and protein expressions. Finally, key questions relevant to the environmental effect of CO₂ that need to be answered in the future were addressed.

Engineered microbial biofuel production and recovery under supercritical carbon dioxide

Culture contamination, end-product toxicity, and energy efficient product recovery are long-standing bioprocess challenges. To solve these problems, we propose a high-pressure fermentation strategy, coupled with in situ extraction using the abundant and renewable solvent supercritical carbon dioxide (scCO₂), which is also known for its broad microbial lethality. Towards this goal, we report the domestication and engineering of a scCO₂-tolerant strain of Bacillus megaterium, previously isolated from formation waters from the McElmo Dome CO₂ field, to produce branched alcohols that have potential use as biofuels. After establishing induced-expression under scCO₂, isobutanol production from 2-ketoisovalerate is observed with greater than 40% yield with co-produced isopentanol. Finally, we present a process model to compare the energy required for our process to other in situ extraction methods, such as gas stripping, finding scCO₂ extraction to be potentially competitive, if not superior.

End-product toxicity, culture contamination, and energy efficient product recovery are long-standing issues in bioprocessing. Here, the authors address these problems using a fermentation strategy that combines microbial production of branched alcohols with supercritical carbon dioxide extraction.

Microbial community composition of a hydrocarbon reservoir 40 years after a CO2 enhanced oil recovery flood

Injecting CO₂ into depleted oil reservoirs to extract additional crude oil is a common enhanced oil recovery (CO₂-EOR) technique. However, little is known about how in situ microbial communities may be impacted by CO₂ flooding, or if any permanent microbiological changes occur after flooding has ceased. Formation water was collected from an oil field that was flooded for CO₂-EOR in the 1980s, including samples from areas affected by or outside of the flood region, to determine the impacts of CO₂-EOR on reservoir microbial communities. Archaea, specifically methanogens, were more abundant than bacteria in all samples, while identified bacteria exhibited much greater diversity than the archaea. Microbial communities in CO₂-impacted and non-impacted samples did not significantly differ (ANOSIM: Statistic R = -0.2597, significance = 0.769). However, several low abundance bacteria were found to be significantly associated with the CO₂-affected group; very few of these species are known to metabolize CO₂ or are associated with CO₂-rich habitats. Although this study had limitations, on a broad scale, either the CO₂ flood did not impact the microbial community composition of the target formation, or microbial communities in affected wells may have reverted back to pre-injection conditions over the ca. 40 years since the CO₂-EOR.

Isolation, Development, and Genomic Analysis of Bacillus megaterium SR7 for Growth and Metabolite Production Under Supercritical Carbon Dioxide

Supercritical carbon dioxide (scCO2) is an attractive substitute for conventional organic solvents due to its unique transport and thermodynamic properties, its renewability and labile nature, and its high solubility for compounds such as alcohols, ketones, and aldehydes. However, biological systems that use scCO2 are mainly limited to in vitro processes due to its strong inhibition of cell viability and growth. To solve this problem, we used a bioprospecting approach to isolate a microbial strain with the natural ability to grow while exposed to scCO2. Enrichment culture and serial passaging of deep subsurface fluids from the McElmo Dome scCO2 reservoir in aqueous media under scCO2 headspace enabled the isolation of spore-forming strain Bacillus megaterium SR7. Sequencing and analysis of the complete 5.51 Mbp genome and physiological characterization revealed the capacity for facultative anaerobic metabolism, including fermentative growth on a diverse range of organic substrates. Supplementation of growth medium with L-alanine for chemical induction of spore germination significantly improved growth frequencies and biomass accumulation under scCO2 headspace. Detection of endogenous fermentative compounds in cultures grown under scCO2 represents the first observation of bioproduct generation and accumulation under this condition. Culturing development and metabolic characterization of B. megaterium SR7 represent initial advancements in the effort toward enabling exploitation of scCO2 as a sustainable solvent for in vivo bioprocessing.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO₂ that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO₂ leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO₂ levels (sample groups I and II) and one control site with low CO₂ content (group III). Samples from sites with elevated CO₂ had pH ranging from 6.2 to 4.5 and samples from the low-CO₂ control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO₂ content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO₂ conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO₂ leakage from geologic storage sites.

Dynamic pathway regulation: recent advances and methods of construction

Microbial cell factories are a renewable source for the production of biofuels and valuable chemicals. Dynamic pathway regulation has proved successful in improving production of molecules by balancing flux between growth of cells and production of metabolites. Systems for autonomous induction of pathway regulation are increasingly being developed, which include metabolite responsive promoters, biosensors, and quorum sensing systems. Since engineering such systems are dependent on the available methods for controlling protein abundance in the desired host, we review recent tools used for gene repression at the transcriptional, post-transcriptional and post-translational levels in Escherichia coli and Saccharomyces cerevisiae. These approaches may facilitate pathway engineering for biofuel and biochemical production.

Biosurfactant as an Enhancer of Geologic Carbon Storage: Microbial Modification of Interfacial Tension and Contact Angle in Carbon dioxide/Water/Quartz Systems

Injecting and storing of carbon dioxide (CO₂) in deep geologic formations is considered as one of the promising approaches for geologic carbon storage. Microbial wettability alteration of injected CO₂ is expected to occur naturally by microorganisms indigenous to the geologic formation or microorganisms intentionally introduced to increase CO₂ storage capacity in the target reservoirs. The question as to the extent of microbial CO₂ wettability alteration under reservoir conditions still warrants further investigation. This study investigated the effect of a lipopeptide biosurfactant—surfactin, on interfacial tension (IFT) reduction and contact angle alteration in CO₂/water/quartz systems under a laboratory setup simulating in situ reservoir conditions. The temporal shifts in the IFT and the contact angle among CO₂, brine, and quartz were monitored for different CO₂ phases (3 MPa, 30°C for gaseous CO₂; 10 MPa, 28°C for liquid CO₂; 10 MPa, 37°C for supercritical CO₂) upon cultivation of Bacillus subtilis strain ATCC6633 with induced surfactin secretion activity. Due to the secreted surfactin, the IFT between CO₂ and brine decreased: from 49.5 to 30 mN/m, by ∼39% for gaseous CO₂; from 28.5 to 13 mN/m, by 54% for liquid CO₂; and from 32.5 to 18.5 mN/m, by ∼43% for supercritical CO₂, respectively. The contact angle of a CO₂ droplet on a quartz disk in brine increased: from 20.5° to 23.2°, by 1.16 times for gaseous CO₂; from 18.4° to 61.8°, by 3.36 times for liquid CO₂; and from 35.5° to 47.7°, by 1.34 times for supercritical CO₂, respectively. With the microbially altered CO₂ wettability, improvement in sweep efficiency of injected and displaced CO₂ was evaluated using 2-D pore network model simulations; again the increment in sweep efficiency was the greatest in liquid CO₂ phase due to the largest reduction in capillary factor. This result provides novel insights as to the role of naturally occurring biosurfactants in CO₂ storage and suggests that biostimulation of biosurfactant production may be a feasible technique for enhancement of CO₂ storage capacity.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO2 -water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling.

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2

Geological carbon sequestration captures CO₂ from industrial sources and stores the CO₂ in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO₂ concentration. This study uses biogeochemical modeling to explore the influence of CO₂ on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO₂ levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO₂ partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO₂ has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO₂ abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses.

Draft Genome Sequences of Supercritical CO2-Tolerant Bacteria Bacillus subterraneus MITOT1 and Bacillus cereus MIT0214

We report draft genome sequences of Bacillus subterraneus MITOT1 and Bacillus cereus MIT0214 isolated through enrichment of samples from geologic sequestration sites in pressurized bioreactors containing a supercritical (sc) CO₂ headspace. Their genome sequences expand the phylogenetic range of sequenced bacilli and allow characterization of molecular mechanisms of scCO₂ tolerance.