Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost.

Plasmids play a major role in rapid adaptation of bacteria by facilitating horizontal transfer of diverse genes, most notably those conferring antibiotic resistance. While most plasmids that replicate in a broad range of bacteria also persist well in diverse hosts, there are exceptions that are poorly understood. We investigated why a broad-host range plasmid, pBP136, originally found in clinical isolates, quickly became extinct in laboratory populations.

Compound-specific isotope analysis (CSIA) evaluation of degradation of chlorinated benzenes (CBs) and benzene in a contaminated aquifer.

Compound-specific isotope analysis (CSIA) has become a valuable tool in understanding the fate of organic contaminants at field sites. However, its application to chlorinated benzenes (CBs), a group of toxic and persistent groundwater contaminants, has received less attention. This study employed CSIA to investigate the occurrence of natural degradation of various CBs and benzene in a contaminated aquifer.

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.

Multi-element isotopic evidence for monochlorobenzene and benzene degradation under anaerobic conditions in contaminated sediments.

Industrial chemicals are frequently detected in sediments due to a legacy of chemical spills. Globally, site remedies for groundwater and sediment decontamination include natural attenuation by in situ abiotic and biotic processes. Compound-specific isotope analysis (CSIA) is a diagnostic tool to identify, quantify, and characterize degradation processes in situ, and in some cases can differentiate between abiotic degradation and biodegradation.

Application of biochar prepared from ethanol refinery by-products for Hg stabilization in floodplain soil: Impacts of drying and rewetting.

This study evaluated three biochars derived from bioenergy by-products - manure-based anaerobic digestate (DIG), distillers' grains (DIS), and a mixture thereof (75G25S) - as amendments to stabilize Hg in contaminated floodplain soil under long-term saturated (up to 200 d) and cyclic drying and rewetting conditions. Greater total Hg (THg) removal (72 to nearly 100%) and limited MeHg production (<65 ng L) were observed in digestate-based biochar-amended systems under initial saturated conditions. Drying and rewetting resulted in limited THg release, increased aqueous MeHg, and decreased solid MeHg in digestate-based biochar-amended systems.

Babesia bovis Rad51 ortholog influences switching of ves genes but is not essential for segmental gene conversion in antigenic variation.

The tick-borne apicomplexan parasite, Babesia bovis, a highly persistent bovine pathogen, expresses VESA1 proteins on the infected erythrocyte surface to mediate cytoadhesion. The cytoadhesion ligand, VESA1, which protects the parasite from splenic passage, is itself protected from a host immune response by rapid antigenic variation. B.

Impact of multiple drying and rewetting events on biochar amendments for Hg stabilization in floodplain soil from South River, VA.

Frequent drying and rewetting due to flooding/precipitation and drainage events in floodplains induces changes in biogeochemical conditions that may influence the effectiveness of in situ Hg stabilization using biochars as soil amendments. This study evaluated two selected biochars anaerobic digestate (DIG) and sulfurized hardwood (MOAK)) as potential amendment materials in moderately reduced floodplain soil under repeated drying and rewetting events using a modified humidity cell protocol. Enhanced release of filter-passing (0.

Use of hardwood and sulfurized-hardwood biochars as amendments to floodplain soil from South River, VA, USA: Impacts of drying-rewetting on Hg removal.

Periodic flooding and drying conditions in floodplains affect the mobility and bioavailability of Hg in aquatic sediments and surrounding soils. Sulfurized materials have been recently proposed as Hg sorbents due to their high affinity to bind Hg, while sulfurizing organic matter may enhance methylmercury (MeHg) production, offsetting the beneficial aspects of these materials. This study evaluated hardwood biochar (OAK) and sulfurized-hardwood biochar (MOAK) as soil amendments for controlling Hg release in a contaminated floodplain soil under conditions representative of periodic flooding and drying in microcosm experiments in three stages: (1) wet biochar amended-systems with river water in an anoxic environment up to 200 d; (2) dry selected reaction vessels in an oxic environment for 90 d; (3) rewet such vessels with river water in an anoxic environment for 90 d.

Mineralization versus fermentation: evidence for two distinct anaerobic bacterial degradation pathways for dichloromethane.

Dichloromethane (DCM) is an anthropogenic pollutant with ozone destruction potential that is also formed naturally. Under anoxic conditions, fermentation of DCM to acetate and formate has been reported in axenic culture Dehalobacterium formicoaceticum, and to acetate, H and CO in mixed culture RM, which harbors the DCM degrader 'Candidatus Dichloromethanomonas elyunquensis'. RM cultures produced 28.

Transformation of Chlorofluorocarbons Investigated via Stable Carbon Compound-Specific Isotope Analysis.

Compound-specific isotope analysis (CSIA) is a valuable tool in contaminant remediation studies. Chlorofluorocarbons (CFCs) are ozone-depleting substances previously thought to be persistent in groundwater under most geochemical conditions but more recently have been found to (bio)transform in some laboratory experiments. To date, limited applications of CSIA to CFCs have been undertaken.

Biotic and Abiotic Dehalogenation of 1,1,2-Trichloro-1,2,2-trifluoroethane (CFC-113): Implications for Bacterial Detoxification of Chlorinated Ethenes.

Chlorofluorocarbons including 1,1,2-trichloro-1,2,2-trifluoroethane (CFC-113) often occur in groundwater plumes comingled with chlorinated solvents such as trichloroethene (TCE). We show that CFC-113 inhibits reductive dechlorination by () in a concentration-dependent manner, causing -1,2-dichloroethene (-DCE) stalls. Following a 17-day exposure of -containing consortium SDC-9 to 76 μM CFC-113, -DCE dechlorination activity did not recover after CFC-113 removal.

Knockout of Babesia bovis rad51 ortholog and its complementation by expression from the BbACc3 artificial chromosome platform.

Babesia bovis establishes persistent infections of long duration in cattle, despite the development of effective anti-disease immunity. One mechanism used by the parasite to achieve persistence is rapid antigenic variation of the VESA1 cytoadhesion ligand through segmental gene conversion (SGC), a phenomenon thought to be a form of homologous recombination (HR). To begin investigation of the enzymatic basis for SGC we initially identified and knocked out the Bbrad51 gene encoding the B.

Aerobic biodegradation of 2,3- and 3,4-dichloronitrobenzene.

Dichloronitrobenzenes (DCNB) are intermediates in the production of dichloroanilines, which are key feedstocks for synthesis of diuron and other herbicides. Although DCNB is a major contaminant at certain chemical manufacturing sites, aerobic DCNB biodegradation is poorly understood and such sites have not been candidates for bioremediation. When a bench-scale aerobic fluidized- bed bioreactor was inoculated with samples from a DCNB contaminated site in Brazil 2,3-DCNB, 3,4-DCNB, 1,2-dichlorobenzene (o-DCB), and chlorobenzene (CB) were biodegraded simultaneously.

Nontargeted Analysis of a Non-Aqueous-Phase Liquid From a Chemical Manufacturing Site Using Nuclear Magnetic Resonance Spectroscopy.

Non-aqueous-phase liquids (NAPLs), composed primarily of organic solvents and other immiscible liquids, can be found in the subsurface at many industrial sites. The chemical composition of NAPLs is often complex and, in many instances, difficult to fully characterize using conventional analytical techniques based on targeted compound analysis. Incomplete characterization of NAPLs leaves gaps in the understanding of the chemical profile at an impacted site.

Evaluating a novel permeable reactive bio-barrier to remediate PAH-contaminated groundwater.

Permeable reactive barriers (PRBs) are an environmentally-friendly, cost-effective in-situ technology that can be used to remediate polycyclic aromatic hydrocarbons (PAHs)-contaminated groundwater. In this study, PRBs of two different materials (A and B) that relied on microbes self-domestication mechanism were designed and tested. The materials A and B were the same apart from their carbon source: A was based on wheat straw and B was based on coconut shell biochar.

Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism.

Dichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader " Dichloromethanomonas elyunquensis" strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM.

Determination of in situ biodegradation rates via a novel high resolution isotopic approach in contaminated sediments.

A key challenge in conceptual models for contaminated sites is identification of the multiplicity of processes controlling contaminant concentrations and distribution as well as quantification of the rates at which such processes occur. Conventional protocol for calculating biodegradation rates can lead to overestimation by attributing concentration decreases to degradation alone. This study reports a novel approach of assessing in situ biodegradation rates of monochlorobenzene (MCB) and benzene in contaminated sediments.

Practical application of H benchtop NMR spectroscopy for the characterization of a nonaqueous phase liquid from a contaminated environment.

Nonaqueous phase liquids (NAPLs) located at the surface of the water table and/or below the water table are often a significant source for groundwater contamination near current or former commercial/industrial facilities. Due to the complex and long history of many industrial sites, these NAPLs often contain a complex mixture of contaminants and as such can be difficult to fully characterize using conventional analytical methods. Remediation and risk assessment activities at sites containing NAPLs may, subsequently, be hindered as the contamination profile may not be fully understood.

A Dehalogenimonas Population Respires 1,2,4-Trichlorobenzene and Dichlorobenzenes.

Chlorobenzenes are ubiquitous contaminants in groundwater and soil at many industrial sites. Previously, we demonstrated the natural attenuation of chlorobenzenes and benzene at a contaminated site inferred from a 5 year site investigation and parallel laboratory microcosm studies. To identify the microbes responsible for the observed dechlorination of chlorobenzenes, the microbial community was surveyed using 16S rRNA gene amplicon sequencing.

Using positive matrix factorization to investigate microbial dehalogenation of chlorinated benzenes in groundwater at a historically contaminated site.

Chlorinated benzenes are common groundwater contaminants in the United States, so demonstrating whether they undergo degradation in the subsurface is important in determining the best remedy for this contamination. The purpose of this work was to use a new data mining approach to investigate chlorinated benzene degradation pathways in the subsurface. Positive Matrix Factorization (PMF) was used to analyze long-term measurements of chlorinated benzene concentrations in groundwater at a contaminated site in New Jersey.

Dual Carbon-Chlorine Isotope Analysis Indicates Distinct Anaerobic Dichloromethane Degradation Pathways in Two Members of Peptococcaceae.

Dichloromethane (DCM) is a probable human carcinogen and frequent groundwater contaminant and contributes to stratospheric ozone layer depletion. DCM is degraded by aerobes harboring glutathione-dependent DCM dehalogenases; however, DCM contamination occurs in oxygen-deprived environments, and much less is known about anaerobic DCM metabolism. Some members of the Peptococcaceae family convert DCM to environmentally benign products including acetate, formate, hydrogen (H), and inorganic chloride under strictly anoxic conditions.

Identification of Degradation Pathways of Chlorohydrocarbons in Saturated Low-Permeability Sediments Using Compound-Specific Isotope Analysis.

This study aims to investigate whether compound-specific carbon isotope analysis (CSIA) can be used to differentiate the degradation pathways of chlorohydrocarbons in saturated low-permeability sediments. For that purpose, a site was selected, where a complex mixture of chlorohydrocarbons contaminated an aquifer-aquitard system. Almost 50 years after contaminant releases, high-resolution concentration, CSIA, and microbial profiles were determined.

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture.

The microbial mixed culture RM grows with dichloromethane (DCM) as the sole energy source generating acetate, methane, chloride and biomass as products. Chloromethane (CM) was not an intermediate during DCM utilization consistent with the observation that CM could not replace DCM as a growth substrate. Interestingly, cultures that received DCM and CM together degraded both compounds concomitantly.