scholarly journals Acetylene-Fueled Trichloroethene Reductive Dechlorination in a Groundwater Enrichment Culture

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sara Gushgari-Doyle ◽  
Ronald S. Oremland ◽  
Ray Keren ◽  
Shaun M. Baesman ◽  
Denise M. Akob ◽  
...  
Keyword(s):  
Microbial Community ◽  
Reductive Dechlorination ◽  
Enrichment Culture ◽  
The United States ◽  
Degradation Pathway ◽  
Content Type ◽  
Dehalococcoides Mccartyi ◽  
Abiotic Degradation ◽  
Laboratory Microcosm ◽  
Microcosm Studies

ABSTRACT In aquifers, acetylene (C2H2) is a product of abiotic degradation of trichloroethene (TCE) catalyzed by in situ minerals. C2H2 can, in turn, inhibit multiple microbial processes including TCE dechlorination and metabolisms that commonly support dechlorination, in addition to supporting the growth of acetylenotrophic microorganisms. Previously, C2H2 was shown to support TCE reductive dechlorination in synthetic, laboratory-constructed cocultures containing the acetylenotroph Pelobacter sp. strain SFB93 and Dehalococcoides mccartyi strain 195 or strain BAV1. In this study, we demonstrate TCE and perchloroethene (PCE) reductive dechlorination by a microbial community enriched from contaminated groundwater and amended with C2H2 as the sole electron donor and organic carbon source. The metagenome of the stable, enriched community was analyzed to elucidate putative community functions. A novel anaerobic acetylenotroph in the phylum Actinobacteria was identified using metagenomic analysis. These results demonstrate that the coupling of acetylenotrophy and reductive dechlorination can occur in the environment with native bacteria and broaden our understanding of biotransformation at contaminated sites containing both TCE and C2H2. IMPORTANCE Understanding the complex metabolisms of microbial communities in contaminated groundwaters is a challenge. PCE and TCE are among the most common groundwater contaminants in the United States that, when exposed to certain minerals, exhibit a unique abiotic degradation pathway in which C2H2 is a product. C2H2 can act as both an inhibitor of TCE dechlorination and of supporting metabolisms and an energy source for acetylenotrophic bacteria. Here, we combine laboratory microcosm studies with computational approaches to enrich and characterize an environmental microbial community that couples two uncommon metabolisms, demonstrating unique metabolic interactions only yet reported in synthetic, laboratory-constructed settings. Using this comprehensive approach, we have identified the first reported anaerobic acetylenotroph in the phylum Actinobacteria, demonstrating the yet-undescribed diversity of this metabolism that is widely considered to be uncommon.

scholarly journals Unexpected Specificity of Interspecies Cobamide Transfer from Geobacter spp. to Organohalide-Respiring Dehalococcoides mccartyi Strains

2012 ◽  
Vol 78 (18) ◽  
pp. 6630-6636 ◽  
Author(s):  
Jun Yan ◽  
Kirsti M. Ritalahti ◽  
Darlene D. Wagner ◽  
Frank E. Löffler
Keyword(s):  
Reductive Dechlorination ◽  
De Novo ◽  
Synthetic Medium ◽  
Geobacter Sulfurreducens ◽  
Rrna Gene ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Gene Copies ◽  
Pure Cultures

ABSTRACTDehalococcoides mccartyistrains conserve energy from reductive dechlorination reactions catalyzed by corrinoid-dependent reductive dehalogenase enzyme systems.Dehalococcoideslacks the ability forde novocorrinoid synthesis, and pure cultures require the addition of cyanocobalamin (vitamin B12) for growth. In contrast,Geobacter lovleyi, which dechlorinates tetrachloroethene tocis-1,2-dichloroethene (cis-DCE), and the nondechlorinating speciesGeobacter sulfurreducenshave complete sets of cobamide biosynthesis genes and produced 12.9 ± 2.4 and 24.2 ± 5.8 ng of extracellular cobamide per liter of culture suspension, respectively, during growth with acetate and fumarate in a completely synthetic medium.G. lovleyi-D. mccartyistrain BAV1 or strain FL2 cocultures provided evidence for interspecies corrinoid transfer, andcis-DCE was dechlorinated to vinyl chloride and ethene concomitant withDehalococcoidesgrowth. In contrast, negligible increase inDehalococcoides16S rRNA gene copies and insignificant dechlorination occurred inG. sulfurreducens-D. mccartyistrain BAV1 or strain FL2 cocultures. Apparently,G. lovleyiproduces a cobamide that complementsDehalococcoides' nutritional requirements, whereasG. sulfurreducensdoes not. Interestingly,Dehalococcoidesdechlorination activity and growth could be restored inG. sulfurreducens-Dehalococcoidescocultures by adding 10 μM 5′,6′-dimethylbenzimidazole. Observations made with theG. sulfurreducens-Dehalococcoidescocultures suggest that the exchange of the lower ligand generated a cobalamin, which supportedDehalococcoidesactivity. These findings have implications forin situbioremediation and suggest that the corrinoid metabolism ofDehalococcoidesmust be understood to faithfully predict, and possibly enhance, reductive dechlorination activities.

scholarly journals Complete Genome Sequence of Dehalococcoides mccartyi Strain FL2, a Trichloroethene-Respiring Anaerobe Isolated from Pristine Freshwater Sediment

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Jun Yan ◽  
Yi Yang ◽  
Xiuying Li ◽  
Frank E. Löffler
Keyword(s):  
Complete Genome Sequence ◽  
Reductive Dechlorination ◽  
Complete Genome ◽  
Hydrogen Oxidation ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Reductive Dehalogenase Genes

Dehalococcoides mccartyi strain FL2 couples growth to hydrogen oxidation and reductive dechlorination of trichloroethene and cis- and trans-1,2-dichloroethenes. Strain FL2 has a 1.42-Mb genome with a G+C content of 47.0% and carries 1,465 protein-coding sequences, including 24 reductive dehalogenase genes.

scholarly journals A Pilot Study of Chicago Waterways as Reservoirs of Multidrug-Resistant Enterobacteriaceae (MDR-Ent) in a High-Risk Region for Community-Acquired MDR-Ent Infection in Children

2020 ◽  
Vol 64 (4) ◽  
Author(s):  
Latania K. Logan ◽  
Liqing Zhang ◽  
Stefan J. Green ◽  
Samuel Dorevitch ◽  
Gustavo A. Arango-Argoty ◽  
...  
Keyword(s):  
Microbial Community ◽  
Pilot Study ◽  
Microbial Community Composition ◽  
Antibiotic Resistance Genes ◽  
The United States ◽  
Multidrug Resistant ◽  
Most Probable Number ◽  
Metagenomic Sequencing ◽  
Probable Number ◽  
Content Type

ABSTRACT Community-acquired multidrug resistant Enterobacteriaceae (MDR-Ent) infections continue to increase in the United States. In prior studies, we identified neighboring regions in Chicago, Illinois, where children have 5 to 6 times greater odds of MDR-Ent infections. To prevent community spread of MDR-Ent, we need to identify the MDR-Ent reservoirs. A pilot study of 4 Chicago waterways for MDR-Ent and associated antibiotic resistance genes (ARGs) was conducted. Three waterways (A1 to A3) are labeled safe for “incidental contact recreation” (e.g., kayaking), and A4 is a nonrecreational waterway that carries nondisinfected water. Surface water samples were collected and processed for standard bacterial culture and shotgun metagenomic sequencing. Generally, A3 and A4 (neighboring waterways which are not hydraulically connected) were strikingly similar in bacterial taxa, ARG profiles, and abundances of corresponding clades and genera within the Enterobacteriaceae. Additionally, total ARG abundances recovered from the full microbial community were strongly correlated between A3 and A4 (R2 = 0.97). Escherichia coli numbers (per 100 ml water) were highest in A4 (783 most probable number [MPN]) and A3 (200 MPN) relative to A2 (84 MPN) and A1 (32 MPN). We found concerning ARGs in Enterobacteriaceae such as MCR-1 (colistin), Qnr and OqxA/B (quinolones), CTX-M, OXA and ACT/MIR (beta-lactams), and AAC (aminoglycosides). We found significant correlations in microbial community composition between nearby waterways that are not hydraulically connected, suggesting cross-seeding and the potential for mobility of ARGs. Enterobacteriaceae and ARG profiles support the hypothesized concerns that recreational waterways are a potential source of community-acquired MDR-Ent.

scholarly journals Complete Genome Sequence of Dehalococcoides mccartyi Strain WBC-2, Capable of Anaerobic Reductive Dechlorination of Vinyl Chloride

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Olivia Molenda ◽  
Shuiquan Tang ◽  
Elizabeth A. Edwards
Keyword(s):  
Vinyl Chloride ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Reductive Dechlorination ◽  
Complete Genome ◽  
Microbial Consortium ◽  
Enrichment Culture ◽  
Metagenomic Sequencing ◽  
The West ◽  
Dehalococcoides Mccartyi

Dehalococcoides mccartyi strain WBC-2 dechlorinates carcinogen vinyl chloride to ethene in the West Branch Canal Creek (WBC-2) microbial consortium used for bioaugmentation. We assembled and closed the complete genome sequence of this prokaryote using metagenomic sequencing from an enrichment culture.

The formation and fate of organoarsenic species in marine ecosystems: do existing experimental approaches appropriately simulate ecosystem complexity?

2015 ◽  
Vol 12 (2) ◽  
pp. 149 ◽  
Author(s):  
Elliott G. Duncan ◽  
William A. Maher ◽  
Simon D. Foster
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Inorganic Arsenic ◽  
Arsenic Species ◽  
Marine Ecosystems ◽  
Degradation Pathway ◽  
Marine Environments ◽  
Experimental Approaches ◽  
Microcosm Studies ◽  
Macro Algae

Environmental context In marine environments, inorganic arsenic present in seawater is transformed to organoarsenic species, mainly arsenoribosides in algae and arsenobetaine in animals. These transformations decrease the toxicity of arsenic, yet the fate of arsenoribosides and arsenobetaine when marine organisms decompose is unknown. We review the current literature on the degradation of these organoarsenic species in marine systems detailing the drivers behind their degradation, and also discuss the environmental relevance of laboratory-based experiments. Abstract Despite arsenoribosides and arsenobetaine (AB) being the major arsenic species in marine macro-algae and animals they have never been detected in seawater. In all studies reviewed arsenoribosides from marine macro-algae were degraded to thio-arsenoribosides, dimethylarsinoylethanol (DMAE), dimethylarsenate (DMA), methylarsenate (MA) with arsenate (AsV) the final product of degradation. The use of different macro-algae species and different experimental microcosms did not influence the arsenoriboside degradation pathway. The use of different experimental approaches, however, did influence the rate and extent at which arsenoriboside degradation occurred. This was almost certainly a function of the complexity of the microbial community within the microcosm, with greater complexity resulting in rapid and more complete arsenoriboside degradation. AB from decomposing animal tissues is degraded to trimethylarsine oxide (TMAO) or dimethylarsenoacetate (DMAA), DMA and finally AsV. The degradation of AB unlike arsenoribosides occurs via a dual pathway with environmental or microbial community variability influencing the pathway taken. The environmental validity of different experimental approaches used to examine the fate of organoarsenic species was also reviewed. It was evident that although liquid culture incubation studies are cheap and reproducible they lack the ability to culture representative microbial communities. Microcosm studies that include sand and sediment are more environmentally representative as they are a better simulation of marine ecosystems and are also likely to facilitate complex microbial communities. An added benefit of microcosm studies is that they are able to be run in parallel with field-based research to provide a holistic assessment of the degradation of organoarsenic species in marine environments.

scholarly journals Effects of Sulfate Reduction on Trichloroethene Dechlorination by Dehalococcoides-Containing Microbial Communities

2017 ◽  
Vol 83 (8) ◽  
Author(s):  
Xinwei Mao ◽  
Alexandra Polasko ◽  
Lisa Alvarez-Cohen
Keyword(s):  
Microbial Communities ◽  
Sulfate Reduction ◽  
Electron Donor ◽  
Reductive Dechlorination ◽  
Sulfate Reducer ◽  
Content Type ◽  
Dehalococcoides Mccartyi ◽  
Sulfide Inhibition ◽  
Genes Encoding ◽  
High Sulfate

ABSTRACT In order to elucidate interactions between sulfate reduction and dechlorination, we systematically evaluated the effects of different concentrations of sulfate and sulfide on reductive dechlorination by isolates, constructed consortia, and enrichments containing Dehalococcoides sp. Sulfate (up to 5 mM) did not inhibit the growth or metabolism of pure cultures of the dechlorinator Dehalococcoides mccartyi 195, the sulfate reducer Desulfovibrio vulgaris Hildenborough, or the syntroph Syntrophomonas wolfei. In contrast, sulfide at 5 mM exhibited inhibitory effects on growth of the sulfate reducer and the syntroph, as well as on both dechlorination and growth rates of D. mccartyi. Transcriptomic analysis of D. mccartyi 195 revealed that genes encoding ATP synthase, biosynthesis, and Hym hydrogenase were downregulated during sulfide inhibition, whereas genes encoding metal-containing enzymes involved in energy metabolism were upregulated even though the activity of those enzymes (hydrogenases) was inhibited. When the electron acceptor (trichloroethene) was limiting and an electron donor (lactate) was provided in excess to cocultures and enrichments, high sulfate concentrations (5 mM) inhibited reductive dechlorination due to the toxicity of generated sulfide. The initial cell ratio of sulfate reducers to D. mccartyi (1:3, 1:1, or 3:1) did not affect the dechlorination performance in the presence of sulfate (2 and 5 mM). In contrast, under electron donor limitation, dechlorination was not affected by sulfate amendments due to low sulfide production, demonstrating that D. mccartyi can function effectively in anaerobic microbial communities containing moderate sulfate concentrations (5 mM), likely due to its ability to outcompete other hydrogen-consuming bacteria and archaea. IMPORTANCE Sulfate is common in subsurface environments and has been reported as a cocontaminant with chlorinated solvents at various concentrations. Inconsistent results for the effects of sulfate inhibition on the performance of dechlorination enrichment cultures have been reported in the literature. These inconsistent findings make it difficult to understand potential mechanisms of sulfate inhibition and complicate the interpretation of bioremediation field data. In order to elucidate interactions between sulfate reduction and reductive dechlorination, this study systematically evaluated the effects of different concentrations of sulfate and sulfide on reductive dechlorination by isolates, constructed consortia, and enrichments containing Dehalococcoides sp. This study provides a more fundamental understanding of the competition mechanisms between reductive dechlorination by Dehalococcoides mccartyi and sulfate reduction during the bioremediation process. It also provides insights on the significance of sulfate concentrations on reductive dechlorination under electron donor/acceptor-limiting conditions during in situ bioremediation applications. For example, at a trichloroethene-contaminated site with a high sulfate concentration, proper slow-releasing electron donors can be selected to generate an electron donor-limiting environment that favors reductive dechlorination and minimizes the sulfide inhibition effect.

scholarly journals The Periodontal Pathogen Porphyromonas gingivalis Induces Expression of Transposases and Cell Death of Streptococcus mitis in a Biofilm Model

2014 ◽  
Vol 82 (8) ◽  
pp. 3374-3382 ◽  
Author(s):  
Ana E. Duran-Pinedo ◽  
Vinesha D. Baker ◽  
Jorge Frias-Lopez
Keyword(s):  
Cell Death ◽  
Microbial Community ◽  
Porphyromonas Gingivalis ◽  
Bacterial Species ◽  
The United States ◽  
Oral Microbiome ◽  
Microbial Pathogens ◽  
Periodontal Pathogen ◽  
Streptococcus Mitis ◽  
Content Type

ABSTRACTOral microbial communities are extremely complex biofilms with high numbers of bacterial species interacting with each other (and the host) to maintain homeostasis of the system. Disturbance in the oral microbiome homeostasis can lead to either caries or periodontitis, two of the most common human diseases. Periodontitis is a polymicrobial disease caused by the coordinated action of a complex microbial community, which results in inflammation of tissues that support the teeth. It is the most common cause of tooth loss among adults in the United States, and recent studies have suggested that it may increase the risk for systemic conditions such as cardiovascular diseases. In a recent series of papers, Hajishengallis and coworkers proposed the idea of the “keystone-pathogen” where low-abundance microbial pathogens (Porphyromonas gingivalis) can orchestrate inflammatory disease by turning a benign microbial community into a dysbiotic one. The exact mechanisms by which these pathogens reorganize the healthy oral microbiome are still unknown. In the present manuscript, we present results demonstrating thatP. gingivalisinducesS. mitisdeath and DNA fragmentation in anin vitrobiofilm system. Moreover, we report here the induction of expression of multiple transposases in aStreptococcus mitisbiofilm when the periodontopathogenP. gingivalisis present. Based on these results, we hypothesize thatP. gingivalisinducesS. mitiscell death by an unknown mechanism, shaping the oral microbiome to its advantage.

scholarly journals Geographical Location Determines the Population Structure in Phyllosphere Microbial Communities of a Salt-Excreting Desert Tree

2011 ◽  
Vol 77 (21) ◽  
pp. 7647-7655 ◽  
Author(s):  
Omri M. Finkel ◽  
Adrien Y. Burch ◽  
Steven E. Lindow ◽  
Anton F. Post ◽  
Shimshon Belkin
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Geographical Location ◽  
Geographic Location ◽  
The United States ◽  
Dead Sea ◽  
Content Type ◽  
Extreme Stress ◽  
Diverse Community ◽  
The Mediterranean

ABSTRACTThe leaf surfaces ofTamarix, a salt-secreting desert tree, harbor a diverse community of microbial epiphytes. This ecosystem presents a unique combination of ecological characteristics and imposes a set of extreme stress conditions. The composition of the microbial community along ecological gradients was studied from analyses of microbial richness and diversity in the phyllosphere of threeTamarixspecies in the Mediterranean and Dead Sea regions in Israel and in two locations in the United States. Over 200,000 sequences of the 16S V6 and 18S V9 hypervariable regions revealed a diverse community, with 788 bacterial and 64 eukaryotic genera but only one archaeal genus. Both geographic location and tree species were determinants of microbial community structures, with the former being more dominant. Tree leaves of all three species in the Mediterranean region were dominated byHalomonasandHalobacteria, whereas trees from the Dead Sea area were dominated byActinomycetalesandBacillales. Our findings demonstrate that microbial phyllosphere communities on differentTamarixspecies are highly similar in the same locale, whereas trees of the same species that grow in different climatic regions host distinct microbial communities.

scholarly journals Multicenter Clinical and Molecular Epidemiological Analysis of Bacteremia Due to Carbapenem-Resistant Enterobacteriaceae (CRE) in the CRE Epicenter of the United States

2017 ◽  
Vol 61 (4) ◽  
Author(s):  
Michael J. Satlin ◽  
Liang Chen ◽  
Gopi Patel ◽  
Angela Gomez-Simmonds ◽  
Gregory Weston ◽  
...  
Keyword(s):  
New York ◽  
Empirical Therapy ◽  
Carbapenem Resistance ◽  
The United States ◽  
Resistance Mechanisms ◽  
Rapid Diagnostics ◽  
Multicenter Studies ◽  
Content Type ◽  
Medical Centers ◽  
Carbapenem Resistant

ABSTRACT Although the New York/New Jersey (NY/NJ) area is an epicenter for carbapenem-resistant Enterobacteriaceae (CRE), there are few multicenter studies of CRE from this region. We characterized patients with CRE bacteremia in 2013 at eight NY/NJ medical centers and determined the prevalence of carbapenem resistance among Enterobacteriaceae bloodstream isolates and CRE resistance mechanisms, genetic backgrounds, capsular types (cps), and antimicrobial susceptibilities. Of 121 patients with CRE bacteremia, 50% had cancer or had undergone transplantation. The prevalences of carbapenem resistance among Klebsiella pneumoniae, Enterobacter spp., and Escherichia coli bacteremias were 9.7%, 2.2%, and 0.1%, respectively. Ninety percent of CRE were K. pneumoniae and 92% produced K. pneumoniae carbapenemase (KPC-3, 48%; KPC-2, 44%). Two CRE produced NDM-1 and OXA-48 carbapenemases. Sequence type 258 (ST258) predominated among KPC-producing K. pneumoniae (KPC-Kp). The wzi154 allele, corresponding to cps-2, was present in 93% of KPC-3-Kp, whereas KPC-2-Kp had greater cps diversity. Ninety-nine percent of CRE were ceftazidime-avibactam (CAZ-AVI)-susceptible, although 42% of KPC-3-Kp had an CAZ-AVI MIC of ≥4/4 μg/ml. There was a median of 47 h from bacteremia onset until active antimicrobial therapy, 38% of patients had septic shock, and 49% died within 30 days. KPC-3-Kp bacteremia (adjusted odds ratio [aOR], 2.58; P = 0.045), cancer (aOR, 3.61, P = 0.01), and bacteremia onset in the intensive care unit (aOR, 3.79; P = 0.03) were independently associated with mortality. Active empirical therapy and combination therapy were not associated with survival. Despite a decade of experience with CRE, patients with CRE bacteremia have protracted delays in appropriate therapies and high mortality rates, highlighting the need for rapid diagnostics and evaluation of new therapeutics.

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