Geology topics
Publications and source records attributed to Denise M. Akob.
Here, we present the draft genome sequence of Bordetella sp. strain FB-8, a mixotrophic iron-oxidizing bacterium isolated from creek sediment in the former uranium-mining district of Ronneburg, Germany. To date, iron oxidation has not been reported in Bordetella species, indicating that FB-8 may be an environmentally important Bordetella sp.
Studies of naturally occurring subsurface carbon dioxide (CO 2 ) accumulations can provide useful information for potential CO 2 injection projects; however, the microbial communities and formation water geochemistry of most reservoirs are understudied. Formation water and microbial biomass were sampled at four CO 2 -rich reservoir sites: two within Bravo Dome, a commercial CO 2 field in New Mexico; one northwest of Bravo Dome in Colorado (Oakdale Field); and one southwest of Bravo Dome in New Mexico (Rafter “K” Ranch). Aside from the Rafter “K” Ranch site, minor differences were observed in the geochemistry of formation water collected from these sites compared to historical data. No organisms were significantly associated with Oakdale Field compared to the other three sites, nor were any hydrogeochemical or gas geochemical parameters (for example, CO 2 concentration) found to have significant associations with the microbial ecology of these four sites. Microorganisms from these sites were metabolically diverse and had the potential to (1) generate methane, (2) produce corrosive hydrogen sulfide (H 2 S), and (3) rapidly biofoul and (or) clog pore spaces by shifting microbial communities with changes in salinity or nutrient supply. This study demonstrates that high concentrations of CO 2 in subsurface reservoirs apparently have not imparted a distinct geochemical or microbiological signature on the associated formation waters and that the microorganisms in these reservoirs are metabolically diverse and could adapt to geochemical changes in the subsurface.
The number of horizontally drilled shale oil and gas wells in the United States has increased from nearly 28,000 in 2007 to nearly 127,000 in 2017, and research has suggested the potential for the development of shale resources to affect nearby stream ecosystems. However, the ability to generalize current studies is limited by the small geographic scope as well as limited breadth and integration of measured chemical and biological indicators parameters. This study tested the hypothesis that a quantifiable, significant relationship exists between the density of oil and gas (OG) development, increasing streamwater concentrations of known geochemical tracers of OG extraction, and the composition of benthic macroinvertebrate and microbial communities. 25 headwater streams that drain lands across a gradient of shale gas development intensity were sampled. Our strategy included comprehensive measurements across multiple seasons of sampling to account for temporal variability of geochemical parameters, including known shale OG geochemical tracers, and microbial and benthic macroinvertebrate communities. No significant relationships were found between the intensity of OG development, shale OG geochemical tracers, or benthic macroinvertebrate or microbial community composition, whereas significant seasonal differences in stream chemistry were observed. These results highlight the importance of considering spatial and temporal variability in stream chemistry and biota and not only the presence of anthropogenic activities in a watershed. This comprehensive, integrated study of geochemical and biological variability of headwater streams in watersheds undergoing OG development provides a robust framework for examining the effects of energy development at a regional scale.
Natural attenuation of heavy metals occurs via coupled microbial iron cycling and metal precipitation in creeks impacted by acid mine drainage (AMD). Here, we describe the isolation, characterization, and genomic sequencing of two iron-oxidizing bacteria (FeOB) species: Thiomonas ferrovorans FB-6 and Thiomonas metallidurans FB-Cd, isolated from slightly acidic (pH 6.3), Fe-rich, AMD-impacted creek sediments. These strains precipitated amorphous iron oxides, lepidocrocite, goethite, and magnetite or maghemite and grew at a pH optimum of 5.5. While Thiomonas spp. are known as mixotrophic sulfur oxidizers and As oxidizers, the FB strains oxidized Fe, which suggests they can efficiently remove Fe and other metals via coprecipitation. Previous evidence for Thiomonas sp. Fe oxidation is largely ambiguous, possibly because of difficulty demonstrating Fe oxidation in heterotrophic/mixotrophic organisms. Therefore, we also conducted a genomic analysis to identify genetic mechanisms of Fe oxidation, other metal transformations, and additional adaptations, comparing the two FB strain genomes with 12 other Thiomonas genomes. The FB strains fall within a relatively novel group of Thiomonas strains that includes another strain (b6) with solid evidence of Fe oxidation. Most Thiomonas isolates, including the FB strains, have the putative iron oxidation gene cyc2 , but only the two FB strains possess the putative Fe oxidase genes mtoAB . The two FB strain genomes contain the highest numbers of strain-specific gene clusters, greatly increasing the known Thiomonas genetic potential. Our results revealed that the FB strains are two distinct novel species of Thiomonas with the genetic potential for bioremediation of AMD via iron oxidation.
The American Society for Microbiology (ASM) national conference, Microbe, is the flagship meeting for microbiologists across the globe. The presence of roughly 10,000 attendees provides enormous opportunities for networking and learning. However, such a large meeting can be intimidating to many, especially early career scientists, students, those attending alone, and those from historically underrepresented groups. While mentorship is widely valued by ASM and its members, finding concrete ways to develop new and diverse mentoring opportunities can be a challenge. We recognized the need for an initiative aimed at expanding peer-to-peer mentoring, facilitating networking, and providing support for Microbe attendees; therefore, we created the program Binning Singletons for ASM Microbe 2019. The program consisted of five steps named after tools or phenomena in the profession of microbiology: (i) Identify the Singletons (e.g., individuals attending alone), (ii) Bin the Singletons, (iii) Horizontal Transfer, (iv) Quorum Sensing, and (v) Exponential Growth. These steps resulted in the matching of participants unsure of how to get the most out of their conference experience (e.g., singletons) with mentors who assisted with meeting planning, networking, and/or impostor syndrome. Started on social media only a month before ASM Microbe 2019, the program successfully launched despite limited time and resources. Binning Singletons improved inclusivity and networking opportunities for participants at the conference. Here, we discuss what worked, and what can be improved, with an eye toward development of the Binning Singletons model for future conferences to provide opportunities to increase inclusivity, networking, and accessibility for singletons and build a stronger scientific community.
Water and sediment extracts samples were analyzed for extractable hydrocarbons by gas chromatography/mass spectrometry (GC/MS) using an Agilent (Agilent Technologies, Palo Alto, CA, USA) 7890 series GC and 5975 electron ionization (EI) mass selective detector (MSD) operated in scan mode. Agilent ChemStation software was used for data acquisition and analysis (version E.02.00.493 on GC/MS computer and version F.01.03.2357 on laptop for data workup). A 30 m x 250 m x 0.25 m HP-5MS column (95% dimethyl 5% diphenyl polydimethylsiloxane) was used for GC/MS under the following conditions: 1.0 L splitless injection, constant flow of 0.7 mL/min, solvent delay of 7.5 min, injector temperature of 280C, interface at 300C, temperature program of 50-150C at 7C/min, 150-230C at 6C/min, and 230-300C at 3C/min with mass scanned from 35-500 Da.
Barite dissolution rates and features were investigated under conditions that combine a variety of organic ligands with different background electrolyte solutions. The organic ligands included low molecular weight organic compounds (LMWO) that can be produced by halophilic bacteria and are common in natural environments, as well as synthetic chelators that were previously studied in barite dissolution. Background electrolyte solutions included deionized water, 0.72 M NaCl and 2 M NaCl solutions designed to simulate freshwater, seawater, and brine fluids, respectively. Barite dissolution rates and corresponding rate constants normalized for saturation states were calculated for most experiments. Equal or lower rates and rate constants for pure LMWO relative to controls at all background electrolyte concentrations and pH values indicated that LMWO do not promote barite dissolution. Synthetic chelators showed higher rates and rate constants at pH 10 at static conditions than controls, indicating enhanced barite dissolution. Distinctive etch pit morphologies on the barite (0 0 1) face were observed in the presence of synthetic chelators, suggesting a direct contact dissolution mechanism by synthetic chelators. The effect of synthetic chelators on barite dissolution was significantly reduced in the presence of 2 M NaCl and/or at pH 6.5 due to salting out effects. Under hypersaline conditions, barite dissolution rates and rate constants by bacterial activities were up to four times higher than those of synthetic chelators. The wide range of conditions studied in this work provides insights into prediction of barite dissolution behavior in various natural environments as well as in industrial treatment procedures.
Molecular biological techniques have revolutionized the field of geomicrobiology by providing researchers with robust techniques for identifying microorganisms and characterizing microbial communities in a wide variety of environments. These techniques have freed researchers from the constraints of classical culture-based microbiology and allowed the discovery of previously unknown phylogenetic diversity of microorganisms. In this chapter, we discuss the theory, methods, and workflow for applying molecular techniques to identify and characterize microbial populations. Our chapter focuses on SSU rRNA gene-based approaches, guiding the reader from sample collection and gene amplification through bioinformatics and statistical analysis. The workflow presented has been successfully used to identify microbial populations and community dynamics in a wide variety of habitats to understand the interactions between microbes and their environment.
Biological Mn(II) oxidation produces reactive manganese oxides that help to mitigate metal contamination in the environment. Here we present the genome of Oxalobacteraceae sp. AB_14, a species of Mn(II)-oxidizing bacteria (MOB) notable for its ability to catalyze Mn oxidation at low pH (5.5).
A study conducted by the U.S. Geological Survey, in cooperation with the New Jersey Pinelands Commission and Montclair State University, was designed to compare pesticide concentrations and the presence and prevalence of amphibian pathogens between natural ponds and two types of created wetlands, excavated ponds and stormwater basins, throughout the New Jersey Pinelands. The study described herein is part of a larger study by the New Jersey Pinelands Commission designed to compare the functional equivalency of natural and created wetlands throughout the New Jersey Pinelands. Sites were selected on the basis of land-use classifications within a 500-meter radius around each wetland from a pool of natural ponds, excavated ponds, and stormwater basins determined by the New Jersey Pinelands Commission. Water, bed-sediment, anuran-food, and composite larval-anuran-tissue samples were collected from four reference (minimum land-use effects) and four degraded (maximum land-use effects) sites from each wetland type for a total of 24 ponds or basins throughout the New Jersey Pinelands during 2014–16. Prevalence of Ranavirus was determined on the basis of tail clips collected from 60 individual larval anurans in each wetland, and 10 animals from each wetland also were swabbed for the presence of Batrachochytrium dendrobatidis (Bd). Other constituents measured included turbidity, pH, specific conductance, dissolved oxygen, dissolved organic carbon, percent organic carbon in sediment, and composite larval-anuran lipid content. The amount of altered land (percent agricultural plus percent developed) ranged from 0 to 62.4 percent for the natural ponds, 0 to 63.6 percent for the excavated ponds, and 23.3 to 80.2 percent for the stormwater basins. The herbicides atrazine and metolachlor were observed in 60 and 89 percent of the water samples, respectively. The insecticide bifenthrin was the most frequently detected current-use pesticide (greater than 25 percent of the samples) in bed-sediment, anuran-food, and composite larval-anuran-tissue samples. The legacy insecticide p,p' -DDT and its primary degradates p,p' -DDD and p,p' -DDE were the most frequently detected compounds in bed-sediment and anuran-food samples (32–76 percent in sediment samples and 24–72 percent in anuran-food samples). Significantly, greater numbers of pesticides and higher total pesticide concentrations were observed in stormwater basins than in natural and excavated ponds. Reference wetlands had fewer pesticides and lower total pesticide concentrations compared to degraded wetlands, indicating a positive relation between percent altered land and pesticides throughout the New Jersey Pinelands. Ranavirus was observed in larvae from 4 wetlands, including 1 reference natural pond, 1 degraded natural pond, and 2 degraded stormwater basins, with prevalence ranging from 3 to 43 percent. Bd was detected in swabs from 18 animals and in 4 natural ponds (1 reference and 3 degraded), 3 excavated ponds (all reference), and 2 stormwater basins (1 reference and 1 degraded); however, detection probability was low. In the wetlands with Bd detections, between 10 and 30 percent (between 1 and 3) of the animal’s swabbed tested positive for Bd. Owing to the limited number of positive detections for both Bd and Ranavirus , no statistical comparisons between wetland types and land-use classifications were possible.
Injecting CO 2 into depleted oil reservoirs to extract additional crude oil is a common enhanced oil recovery (CO 2 -EOR) technique. However, little is known about how in situ microbial communities may be impacted by CO 2 flooding, or if any permanent microbiological changes occur after flooding has ceased. Formation water was collected from an oil field that was flooded for CO 2 -EOR in the 1980s, including samples from areas affected by or outside of the flood region, to determine the impacts of CO 2 -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 CO 2 -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 CO 2 -affected group; very few of these species are known to metabolize CO 2 or are associated with CO 2 -rich habitats. Although this study had limitations, on a broad scale, either the CO 2 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 CO 2 -EOR.
Acetylene (IUPAC name: ethyne) is a colorless, gaseous hydrocarbon, composed of two triple bonded carbon atoms attached to hydrogens (C 2 H 2 ). When microbiologists and biogeochemists think of acetylene, they immediately think of its use as an inhibitory compound of certain microbial processes and a tracer for nitrogen fixation. However, what is less widely known is that anaerobic and aerobic microorganisms can degrade acetylene, using it as a sole carbon and energy source and providing the basis of a microbial food web. Here, we review what is known about acetylene degrading organisms and introduce the term 'acetylenotrophs' to refer to the microorganisms that carry out this metabolic pathway. In addition, we review the known environmental sources of acetylene and postulate the presence of an hidden acetylene cycle. The abundance of bacteria capable of using acetylene and other alkynes as an energy and carbon source suggests that there are energy cycles present in the environment that are driven by acetylene and alkyne production and consumption that are isolated from atmospheric exchange. Acetylenotrophs may have developed to leverage the relatively high concentrations of acetylene in the pre-Cambrian atmosphere, evolving later to survive in specialized niches where acetylene and other alkynes were produced.
The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C 3 H 6 BrNO 4 ). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills.
In January 2014, approximately 37 800 L of crude 4-methylcyclohexanemethanol (crude MCHM) spilled into the Elk River, West Virginia. To understand the long-term fate of 4-MCHM, we conducted experiments under environmentally relevant conditions to assess the potential for the 2 primary compounds in crude MCHM (1) to undergo biodegradation and (2) for sediments to serve as a long-term source of 4-MCHM. We developed a solid phase microextraction (SPME) method to quantify the cis - and trans -isomers of 4-MCHM. Autoclaved Elk River sediment slurries sorbed 17.5% of cis -4-MCHM and 31% of trans -4-MCHM from water during the 2-week experiment. Sterilized, impacted, spill-site sediment released minor amounts of cis - and up to 35 μg/L of trans -4-MCHM into water, indicating 4-MCHM was present in sediment collected 10 months post spill. In anoxic microcosms, 300 μg/L cis - and 150 μg/L trans -4-MCHM degraded to nondetectable levels in 8–13 days in both impacted and background sediments. Under aerobic conditions, 4-MCHM isomers degraded to nondetectable levels within 4 days. Microbial communities at impacted sites differed in composition compared to background samples, but communities from both sites shifted in response to crude MCHM amendments. Our results indicate that 4-MCHM is readily biodegradable under environmentally relevant conditions.
Fluids injected into shale formations during hydraulic fracturing of black shale return with extraordinarily high total-dissolved-solids (TDS) and high concentrations of barium (Ba) and radium (Ra). Barite, BaSO 4 , has been implicated as a possible source of Ba as well as a problematic mineral scale that forms on internal well surfaces, often in close association with radiobarite, (Ba,Ra)SO 4 . The dissolution of barite by abiotic processes is well quantified. However, the identification of microbial communities in flowback and produced water necessitates the need to understand barite dissolution in the presence of bacteria. Therefore, we evaluated the rates and mechanisms of abiotic and microbially-mediated barite dissolution under anoxic and hypersaline conditions in the laboratory. Barite dissolution experiments were conducted with bacterial enrichment cultures established from produced water from Marcellus Shale wells located in northcentral Pennsylvania. These cultures were dominated by anaerobic halophilic bacteria from the genus Halanaerobium . Dissolved Ba was determined by ICP-OES and barite surfaces were investigated by SEM and AFM. Our results reveal that: 1) higher amounts of barium (up to ∼5 × ) are released from barite in the presence of Halanaerobium cultures compared to brine controls after 30 days of reaction, 2) etch pits that develop on the barite (001) surface in the presence of Halanaerobium exhibit a morphology that is distinct from those that form during control experiments without bacteria, 3) etch pits that develop in the presence of Halanaerobium exhibit a morphology that is similar to the morphology of etch pits formed in the presence of strong organic chelators, EDTA and DTPA, and 4) experiments using dialysis membranes to separate barite from bacteria suggest that direct contact between the two is not required in order to promote dissolution. These results suggest that Halanaerobium increase the rate of barite dissolution in anoxic and high ionic strength solutions. Additionally, the increase in rate occurs without direct microbe-mineral contact suggesting that metabolites secreted by the bacteria may be responsible for promotion of dissolution. The findings of this study have implications for understanding barium cycling in marine/hypersaline environments, release of barium (and associated radium) from waste solids generated from energy and mining industries, as well as potential for developing new anti-scaling chemicals.
Wastewaters from oil and gas development pose largely unknown risks to environmental resources. In January 2015, 11.4 M L (million liters) of wastewater (300 g/L TDS) from oil production in the Williston Basin was reported to have leaked from a pipeline, spilling into Blacktail Creek, North Dakota. Geochemical and biological samples were collected in February and June 2015 to identify geochemical signatures of spilled wastewaters as well as biological responses along a 44-km river reach. February water samples had elevated chloride (1030 mg/L) and bromide (7.8 mg/L) downstream from the spill, compared to upstream levels (11 mg/L and < 0.4 mg/L, respectively). Lithium (0.25 mg/L), boron (1.75 mg/L) and strontium (7.1 mg/L) were present downstream at 5–10 times upstream concentrations. Light hydrocarbon measurements indicated a persistent thermogenic source of methane in the stream. Semi-volatile hydrocarbons indicative of oil were not detected in filtered samples but low levels, including tetramethylbenzenes and di-methylnaphthalenes, were detected in unfiltered water samples downstream from the spill. Labile sediment-bound barium and strontium concentrations (June 2015) were higher downstream from the Spill Site. Radium activities in sediment downstream from the Spill Site were up to 15 times the upstream activities and, combined with Sr isotope ratios, suggest contributions from the pipeline fluid and support the conclusion that elevated concentrations in Blacktail Creek water are from the leaking pipeline. Results from June 2015 demonstrate the persistence of wastewater effects in Blacktail Creek several months after remediation efforts started. Aquatic health effects were observed in June 2015; fish bioassays showed only 2.5% survival at 7.1 km downstream from the spill compared to 89% at the upstream reference site. Additional potential biological impacts were indicated by estrogenic inhibition in downstream waters. Our findings demonstrate that environmental signatures from wastewater spills are persistent and create the potential for long-term environmental health effects.
Unconventional oil and gas (UOG) production produces large quantities of wastewater with complex geochemistry and largely uncharacterized impacts on surface waters. In this study, we assessed shifts in microbial community structure and function in sediments and waters upstream and downstream from a UOG wastewater disposal facility. To do this, quantitative PCR for 16S rRNA and antibiotic resistance genes along with metagenomic sequencing were performed. Elevated conductivity and markers of UOG wastewater characterized sites sampled downstream from the disposal facility compared to background sites. Shifts in overall high level functions and microbial community structure were observed between background sites and downstream sediments. Increases in Deltaproteobacteria and Methanomicrobia and decreases in Thaumarchaeota were observed at downstream sites. Genes related to dormancy and sporulation and methanogenic respiration were 18–86 times higher at downstream, impacted sites. The potential for these sediments to serve as reservoirs of antimicrobial resistance was investigated given frequent reports of the use of biocides to control the growth of nuisance bacteria in UOG operations. A shift in resistance profiles downstream of the UOG facility was observed including increases in acr B and mex B genes encoding for multidrug efflux pumps, but not overall abundance of resistance genes. The observed shifts in microbial community structure and potential function indicate changes in respiration, nutrient cycling, and markers of stress in a stream impacted by UOG waste disposal operations.
Acetylene (C2H2) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during C2H2 block assays of N2O reductase, and Pelobacter acetylenicus was shown to grow on C2H2 via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (N2ase), is specific for acetylene. Acetylene fermentation is a rare metabolic process that is well characterized only in P. acetylenicus DSM3246 and DSM3247 and Pelobacter sp. strain SFB93. To better understand the genetic controls for AH activity, we sequenced the genomes of the three acetylene-fermenting Pelobacter strains. Genome assembly and annotation produced three novel genomes containing gene sequences for AH, with two copies being present in SFB93. In addition, gene sequences for all five compulsory genes for iron-molybdenum N2ase were also present in the three genomes, indicating the cooccurrence of two acetylene transformation pathways. Nitrogen fixation growth assays showed that DSM3426 could ferment acetylene in the absence of ammonium, but no ethylene was produced. However, SFB93 degraded acetylene and, in the absence of ammonium, produced ethylene, indicating an active N2ase. Diazotrophic growth was observed under N2 but not in experimental controls incubated under argon. SFB93 exhibits acetylene fermentation and nitrogen fixation, the only known biochemical mechanisms for acetylene transformation. Our results indicate complex interactions between N2ase and AH and suggest novel evolutionary pathways for these relic enzymes from early Earth to modern days.