Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes (MAGs) to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin (AppB). Our analyses resulted in the recovery of over 40 MAGs from 8 coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. The data presented herein provides novel insights into AppB coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.

Melanoma is the fifth most common type of cancer with an incidence of 22.2 cases out of 100 000 men and women. There were 96 480 new cases diagnosed in 2019 and the total cases diagnosed per year continues to increase. These statistics were based on information provided by the National Cancer Institute in Bethesda, Maryland. Given the prevalence of melanoma, it becomes imperative that physicians remain up to date on evolving diagnosis and treatment standards. In January of 2018, the National Comprehensive Cancer Network (NCCN) published updated guidelines, in accordance to the American Joint Committee on Cancer, releasing the 8th edition of the staging criteria. Previous studies have shown a lack of adherence to these guidelines leads to increased adverse outcomes. In addition, deficient documentation may lead to inaccurate diagnoses and subsequent inappropriate surgical management. Therefore, collaboration between surgeon and pathologist is paramount for the appropriate management of patients with thin melanoma, aided by clear communication through comprehensive documentation. The purpose of this study was to evaluate surgical and pathological compliance with consensus guidelines in patients with thin melanoma, compare overall compliance between surgical subspecialties, and assess the quality and consistency of documentation among surgeons and pathologists in our community teaching hospital.

Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl coenzyme A (acetyl-CoA) and ultimately acetate using the Wood-Ljungdahl pathway (WLP). Acetobacterium woodii is the type strain of the Acetobacterium genus and has been critical for understanding the biochemistry and energy conservation in acetogens. Members of the Acetobacterium genus have been isolated from a variety of environments or have had genomes recovered from metagenome data, but no systematic investigation has been done on the unique and various metabolisms of the genus. To gain a better appreciation for the metabolic breadth of the genus, we sequenced the genomes of 4 isolates (A. fimetarium, A. malicum, A. paludosum, and A. tundrae) and conducted a comparative genome analysis (pan-genome) of 11 different Acetobacterium genomes. A unifying feature of the Acetobacterium genus is the carbon-fixing WLP. The methyl (cluster II) and carbonyl (cluster III) branches of the Wood-Ljungdahl pathway are highly conserved across all sequenced Acetobacterium genomes, but cluster I encoding the formate dehydrogenase is not. In contrast to A. woodii, all but four strains encode two distinct Rnf clusters, Rnf being the primary respiratory enzyme complex. Metabolism of fructose, lactate, and H-2:CO2 was conserved across the genus, but metabolism of ethanol, methanol, caffeate, and 2,3-butanediol varied. Additionally, clade-specific metabolic potential was observed, such as amino acid transport and metabolism in the psychrophilic species, and biofilm formation in the A. wieringae clade, which may afford these groups an advantage in low-temperature growth or attachment to solid surfaces, respectively. IMPORTANCE Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl-CoA and ultimately acetate using the Wood-Ljungdahl pathway (WLP). This autotrophic metabolism plays a major role in the global carbon cycle and, if harnessed, can help reduce greenhouse gas emissions. Overall, the data presented here provide a framework for examining the ecology and evolution of the Acetobacterium genus and highlight the potential of these species as a source for production of fuels and chemicals from CO2 feedstocks.

The specific questionnaire Liver Disease Quality of Life (LDQOL) is a valid tool for measuring quality of life (QOL) and has been used to show that liver transplantation (LT), which is an effective treatment for end-stage liver disease, may improve QOL.This study aims to identify aspects of QOL that improve after LT and those that do not.Patients accepted for LT were invited to answer the LDQOL at baseline and after transplantation at 6 and 12 months. LDQOL contains the 36-item Short Form Health Survey (SF-36) and 12 specific dimensions. Responsiveness was assessed using the paired Student t test.The study included a cohort of 156 patients, 73% males, of an average age of 53 (26–67) years, with the following common indications: tumor (35%), hepatitis C (23%), and alcohol-related (21%) liver disease. Mean scores showed a statistically significant (P < .05) improvement after 1 year in 6 of 8 SF-36 dimensions, in the physical component summary score, and in 7 of 12 disease-specific dimensions. The two dimensions that showed no improvement in the SF-36 dimensions were “social functioning” and “vitality,” whereas the specific dimensions to not improve were “sleep problems,” “social interaction,” “activities of daily living,” and “concerns about the future.”Findings suggest that perceived QOL after LT improves but could be further enhanced with the use of specific programs for amending sleep disorders and physical aspects.

Non-contrast magnetic resonance imaging (MRI) and ultrasound studies in pediatric patients with suspected appendicitis are often non-diagnostic. The primary objective of this investigation was to determine if combining these non-diagnostic imaging results with white blood cell (WBC) cutoffs improves their negative predictive values (NPVs).A retrospective chart review was conducted including patients ≤18 years old with suspected appendicitis who had MRI performed with or without a preceding ultrasound study in a pediatric emergency department. Imaging results were sorted into 2 diagnostic and 5 non-diagnostic categories. NPVs were calculated for the non-diagnostic MRI and ultrasound categories with and without combining them with WBC cutoffs of <10.0 and <7.5 × 109/L.Of the 612 patients with MRI studies included, 402 had ultrasound studies performed. MRI with incomplete visualization of a normal appendix without secondary signs of appendicitis had an NPV of 97.9% that changed to 98.1% and 98.2% when combined with WBC cutoffs of <10.0 and <7.5, respectively. Ultrasound studies with incomplete visualization of a normal appendix without secondary signs had an NPV of 85.3% that improved to 94.8% and 96.5% when combined with WBC cutoffs of <10.0 and <7.5, respectively.In pediatric patients with suspected appendicitis, MRI studies with incomplete visualization of a normal appendix without secondary signs have a high NPV that does not significantly change with the use of these WBC cutoffs. In contrast, combining WBC cutoffs with ultrasound studies with the same interpretation identifies low-risk groups.

The Bakken Shale has become one of the United States' most important oil and gas producing regions. This study examined the microbiology and geochemical characteristics of Bakken region produced water from 17 well sites sampled from the three-phase separator and produced water holding tank over a 6-month time frame. Produced water samples had high total dissolved solids (220 000-350 000 mg/L) and low dissolved organic carbon concentrations (41-132 mg/L). Microbial abundances varied between 101 and 104 16S rRNA gene copies/mL, approximately four orders of magnitude below those observed for produced waters from other hydraulic fracturing regions. The most abundant bacterial orders found in produced water samples were Bacillales, Halanaerobiales and Pseudomonadales, consistent with observations from other unconventional resource plays. Our observations suggest temporal community structuring, as produced waters sampled early in our sampling period were dominated by Halanaerobiales, and produced waters sampled at the remaining winter sampling time points were characterized by high relative abundances of Bacillales and Pseudomonadales. Data from this study extends the current available knowledge of the microbiology and chemistry associated with produced water from the Bakken region and provides insights into microbial community dynamics in hypersaline subsurface fluids.

Geological carbon storage is likely to be a part of a comprehensive strategy to minimize the atmospheric release of carbon dioxide (CO2 ), raising concerns that injected CO2 will leak into overlying freshwater aquifers. CO2(aq) leakage may impact the dominant microbial community responsible for important ecosystem functions such as nutrient cycling, metal cycling and carbon conversion. Here, we examined the impact of an experimental in situ CO2 -leakage on a freshwater aquifer microbial community. High-throughput 16S rRNA gene sequencing demonstrated lower microbial diversity in freshwater wells with CO2 concentrations above 1.15 g l-1 . Metagenomic sequencing and population genome binning were used to evaluate the metabolic potential of microbial populations across four CO2 exposed samples and one control sample. Population genome binning resulted in the recovery and annotation of three metagenome assembled genomes (MAGs). Two of the MAGs, most closely related to Curvibacter and Sulfuricurvum, had the functional capacity for CO2 utilization via carbon fixation coupled to sulfur and iron oxidation. The third draft genome was an Archaea, most closely related to Methanoregula, characterized by the metabolic potential for methanogenesis. Together, these findings show that CO2 leakage in a freshwater aquifer poses a strong selection, driving both microbial community structure and metabolic function.

Natural gas is a major source of global energy, and a large fraction is generated in subsurface coalbed deposits. Microbial communities within coalbed deposits impact methane production, and as a result contribute to global carbon cycling. The process of biogenic coal-to-methane conversion is not well understood. Here we demonstrate the first read- and assembly-based metagenome profiling of coal-associated formation waters, resulting in the recovery of over 40 metagenome-assembled genomes (MAGs) from eight individual coalbed methane wells in the Appalachian Basin. The majority of samples contained hydrogenotrophic methanogens, which were present in higher relative abundances than was previously reported for other coalbed basins. The abundance of Archaea and salinity were positively correlated, suggesting that salinity may be a controlling factor for biogenic coalbed methane. Low-abundance coalbed microbial populations were functionally diverse, while the most dominant organisms exhibit a high degree of genomic and functional similarities. Basin-specific pan-metagenome clustering suggests lower abundant and diverse bacterial communities are shaped by local basin parameters. Our analyses show Appalachian Basin coalbed microbial communities encode for the potential to convert coal into methane, which may be used as an indicator of potential biogenic methane production for future well performance and increased well longevity.

ABSTRACT Draft genome sequences of Acetobacterium sp. strain MES1 and Desulfovibrio sp. strain MES5 were obtained from the metagenome of a cathode-associated community enriched within a microbial electrosynthesis system (MES). The draft genome sequences provide insight into the functional potential of these microorganisms within an MES and a foundation for future comparative analyses.

ABSTRACTMicrobial activity in the produced water from hydraulically fractured oil and gas wells may potentially interfere with hydrocarbon production and cause damage to the well and surface infrastructure via corrosion, sulfide release, and fouling. In this study, we surveyed the microbial abundance and community structure of produced water sampled from 42 Marcellus Shale wells in southwestern Pennsylvania (well age ranged from 150 to 1,846 days) to better understand the microbial diversity of produced water. We sequenced the V4 region of the 16S rRNA gene to assess taxonomy and utilized quantitative PCR (qPCR) to evaluate the microbial abundance across all 42 produced water samples. Bacteria of the orderHalanaerobialeswere found to be the most abundant organisms in the majority of the produced water samples, emphasizing their previously suggested role in hydraulic fracturing-related microbial activity. Statistical analyses identified correlations between well age and biocide formulation and the microbial community, in particular, the relative abundance ofHalanaerobiales. We further investigated the role of members of the orderHalanaerobialesin produced water by reconstructing and annotating aHalanaerobiumdraft genome (named MDAL1), using shotgun metagenomic sequencing and metagenomic binning. The recovered draft genome was found to be closely related to the speciesH. congolense, an oil field isolate, andHalanaerobiumsp. strain T82-1, also recovered from hydraulic fracturing produced water. Reconstruction of metabolic pathways revealedHalanaerobiumsp. strain MDAL1 to have the potential for acid production, thiosulfate reduction, and biofilm formation, suggesting it to have the ability to contribute to corrosion, souring, and biofouling events in the hydraulic fracturing infrastructure.IMPORTANCEThere are an estimated 15,000 unconventional gas wells in the Marcellus Shale region, each generating up to 8,000 liters of hypersaline produced water per day throughout its lifetime (K. Gregory, R. Vidic, and D. Dzombak, Elements 7:181–186, 2011,https://doi.org/10.2113/gselements.7.3.181; J. Arthur, B. Bohm, and M. Layne, Gulf Coast Assoc Geol Soc Trans 59:49–59, 2009;https://www.marcellusgas.org/index.php). Microbial activity in produced waters could lead to issues with corrosion, fouling, and souring, potentially interfering with hydraulic fracturing operations. Previous studies have found microorganisms contributing to corrosion, fouling, and souring to be abundant across produced water samples from hydraulically fractured wells; however, these findings were based on a limited number of samples and well sites. In this study, we investigated the microbial community structure in produced water samples from 42 unconventional Marcellus Shale wells, confirming the dominance of the genusHalanaerobiumin produced water and its metabolic potential for acid and sulfide production and biofilm formation.

Microbial electrosynthesis is a renewable energy and chemical production platform that relies on microbial cells to capture electrons from a cathode and fix carbon. Yet despite the promise of this technology, the metabolic capacity of the microbes that inhabit the electrode surface and catalyze electron transfer in these systems remains largely unknown. We assembled thirteen draft genomes from a microbial electrosynthesis system producing primarily acetate from carbon dioxide, and their transcriptional activity was mapped to genomes from cells on the electrode surface and in the supernatant. This allowed us to create a metabolic model of the predominant community members belonging to Acetobacterium, Sulfurospirillum, and Desulfovibrio. According to the model, the Acetobacterium was the primary carbon fixer, and a keystone member of the community. Transcripts of soluble hydrogenases and ferredoxins from Acetobacterium and hydrogenases, formate dehydrogenase, and cytochromes of Desulfovibrio were found in high abundance near the electrode surface. Cytochrome c oxidases of facultative members of the community were highly expressed in the supernatant despite completely sealed reactors and constant flushing with anaerobic gases. These molecular discoveries and metabolic modeling now serve as a foundation for future examination and development of electrosynthetic microbial communities.

ABSTRACT We report the 5,425,832 bp draft genome of Pseudomonas sp. strain BDAL1, recovered from a Bakken shale hydraulic fracturing-produced water tank metagenome. Genome annotation revealed several key biofilm formation genes and osmotic stress response mechanisms necessary for survival in hydraulic fracturing-produced water.

We report here the 1,882,100-bp draft genome sequence of Methanohalophilus mahii strain DAL1, recovered from Marcellus Shale hydraulic fracturing-produced water using metagenomic contig binning. Genome annotation revealed several key methanogenesis genes and provides valuable information on archaeal activity associated with hydraulic fracturing-produced water environments.

The draft genome sequence of Pseudomonas stutzeri strain K35 was separated from a metagenome derived from a produced water microbial community of a coalbed methane well. The genome encodes a complete nitrogen fixation pathway and the upper and lower naphthalene degradation pathways.