CRISPR-Cas9-mediated barcode insertion into for surrogate tracking.

Unlabelled: The use of surrogate organisms can enable researchers to safely conduct research on pathogens and in a broader set of conditions. Being able to differentiate between the surrogates used in the experiments and background contamination as well as between different experiments will further improve research efforts. One effective approach is to introduce unique genetic barcodes into the surrogate genome and track their presence using the quantitative polymerase chain reaction (qPCR).

COVID-19 trends at the University of Tennessee: predictive insights from raw sewage SARS-CoV-2 detection and evaluation and PMMoV as an indicator for human waste.

Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring the prevalence of SARS-CoV-2 on university campuses. However, concerns about effectiveness of raw sewage as a COVID-19 early warning system still exist, and it's not clear how useful normalization by simultaneous comparison of Pepper Mild Mottle Virus (PMMoV) is in addressing variations resulting from fecal discharge dilution. This study aims to contribute insights into these aspects by conducting an academic-year field trial at the student residences on the University of Tennessee, Knoxville campus, raw sewage.

Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback.

Methane (CH4) and nitrous oxide (N2O) are major greenhouse gases that are predominantly generated by microbial activities in anoxic environments. N2O inhibition of methanogenesis has been reported, but comprehensive efforts to obtain kinetic information are lacking. Using the model methanogen Methanosarcina barkeri strain Fusaro and digester sludge-derived methanogenic enrichment cultures, we conducted growth yield and kinetic measurements and showed that micromolar concentrations of N2O suppress the growth of methanogens and CH4 production from major methanogenic substrate classes.

Integrated Advanced Molecular Tools Predict In Situ cVOC Degradation Rates: Field Demonstration.

Chlorinated volatile organic compound (cVOC) degradation rate constants are crucial information for site management. Conventional approaches generate rate estimates from the monitoring and modeling of cVOC concentrations. This requires time series data collected along the flow path of the plume.

Genome-Wide Expression Analysis Unravels Fluoroalkane Metabolism in sp. Strain 273.

sp. strain 273 grows with medium-chain terminally fluorinated alkanes under oxic conditions, releases fluoride, and synthesizes long-chain fluorofatty acids. To shed light on the genes involved in fluoroalkane metabolism, genome, and transcriptome sequencing of strain 273 grown with 1,10-difluorodecane (DFD), decane, and acetate were performed.

sp. nov., a formate-oxidizing, organohalide-respiring bacterium isolated from grape pomace.

A strictly anaerobic, organohalide-respiring bacterium, designated strain GP, was characterized using a polyphasic approach. GP is Gram-stain-negative, non-spore-forming and non-motile. Cells are irregular cocci ranging between 0.

Metabolome patterns identify active dechlorination in bioaugmentation consortium SDC-9™.

Ultra-high performance liquid chromatography-high-resolution mass spectrometry (UPHLC-HRMS) is used to discover and monitor single or sets of biomarkers informing about metabolic processes of interest. The technique can detect 1000's of molecules (i.e.

Dehalogenation of Chlorinated Ethenes to Ethene by a Novel Isolate, " Dehalogenimonas etheniformans".

Dehalococcoides mccartyi strains harboring vinyl chloride (VC) reductive dehalogenase (RDase) genes are keystone bacteria for VC detoxification in groundwater aquifers, and bioremediation monitoring regimens focus on D. mccartyi biomarkers. We isolated a novel anaerobic bacterium, " Dehalogenimonas etheniformans" strain GP, capable of respiratory dechlorination of VC to ethene.

Identification and widespread environmental distribution of a gene cassette implicated in anaerobic dichloromethane degradation.

Anthropogenic activities and natural processes release dichloromethane (DCM, methylene chloride), a toxic chemical with substantial ozone-depleting capacity. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of the three known anaerobic DCM-degrading bacterial species revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising 8-10 genes encoding proteins with 79.

Ultrastructure of Organohalide-Respiring Revealed by Cryo-Electron Tomography.

Dehalococcoides mccartyi () and spp. () are members of the class , phylum Chloroflexi, characterized by streamlined genomes and a strict requirement for organohalogens as electron acceptors. Here, we used cryo-electron tomography to reveal morphological and ultrastructural features of strain BAV1 and " Dehalogenimonas etheniformans" strain GP cells at unprecedented resolution.

Anaerobic Microbial Metabolism of Dichloroacetate.

Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising " Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway.

Genome Sequence of " Dehalogenimonas etheniformans" Strain GP, a Vinyl Chloride-Respiring Anaerobe.

" Dehalogenimonas etheniformans" strain GP couples growth with the reductive dechlorination of vinyl chloride and several polychlorinated ethenes. The genome sequence comprises a circular 2.07-Mb chromosome with a G+C content of 51.

Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the -Containing Consortium SDC-9.

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as (). Metagenome sequencing of the commercial, -containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including (two copies), , and , and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS).

Nitrous Oxide Is a Potent Inhibitor of Bacterial Reductive Dechlorination.

Organohalide-respiring bacteria are key players for the turnover of organohalogens. At sites impacted with chlorinated ethenes, bioremediation promotes reductive dechlorination; however, stoichiometric conversion to environmentally benign ethene is not always achieved. We demonstrate that nitrous oxide (NO), a compound commonly present in groundwater, inhibits organohalide respiration.

Investigation of nonylphenol and nonylphenol ethoxylates in sewage sludge samples from a metropolitan wastewater treatment plant in Turkey.

Nonylphenol ethoxylates (NPEOs) have drawn significant attention within the last decade for both scientific and legislative reasons. In Turkey, the Regulation Regarding the Use of Domestic and Urban Sludges on Land states a limit value for the sum of nonylphenol (NP), nonylphenol monoethoxylate (NP1EO) and nonylphenol diethoxylate (NP2EO) as NPE (NPE=NP+NP1EO+NP2EO). Unfortunately a standard method for the determination of these chemicals has not been yet set by the authorities and no data exists about the concentrations of NP and NPEOs in sewage sludge in Turkey.