Chlorinated electron acceptor availability selects for specificDehalococcoidespopulations in dechlorinating enrichment cultures and in groundwater

AbstractIndividualDehalococcoides mccartyi (Dhc)strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes contained within their respective genomes. While thousands ofrdhAgenes have been sequenced, the activity of the corresponding proteins have been identified in only a handful of cases. Most effort has focused on identifying the enzymes that dechlorinate substrates including trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC) relevant to groundwater remediation. The associatedrdhAgenes, namelytceA, bvcA,andvcrA, along with theD. mccartyi16S rRNA gene are often used to track growth and dechlorinating activity in DNA extracted from field samples. In this study, we augmented the typical suite of three characterizedrdhAgenes to include an additional 12 uncharacterizedrdhAsequences identified in the metagenome in the mixedDhc-containing culture KB-1 to track population shifts within the culture and at two bioaugmented field sites. Quantitative PCR assays were developed for the 15 selectedD. mccartyi rdhAgenes and evaluated using 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion ofrdhAgene copies relative toDhc16S gene copies indicated the presence of multiple distinctDhcpopulations in each culture. The specific electron acceptor amended to each culture had a major influence on the distribution ofD. mccartyipopulations and their associatedrdhAgenes. We also surveyed the abundance ofrdhAgenes in samples obtained from two bioaugmented field sites. Growth of the dominantD. mccartyipopulation in the KB-1 inoculum was detected in the UK site samples. At both field sites, the measurement of relativerdhAabundances revaled significantD. mccartyipopulation shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene, indicating that the selective pressure of the most abundant chlorinated electron acceptor that was observed in lab cultures was also occurring in the populations in the field. Understanding driving forces behindD. mccartyipopulation selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.

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

Applied and Environmental Microbiology ◽

10.1128/aem.01535-12 ◽

2012 ◽

Vol 78 (18) ◽

pp. 6630-6636 ◽

Cited By ~ 80

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.

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Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds

Applied and Environmental Microbiology ◽

10.1128/aem.02597-14 ◽

2014 ◽

Vol 81 (2) ◽

pp. 587-596 ◽

Cited By ~ 36

Author(s):

Marlén Pöritz ◽

Christian L. Schiffmann ◽

Gerd Hause ◽

Ulrike Heinemann ◽

Jana Seifert ◽

...

Keyword(s):

Electron Acceptor ◽

Aromatic Compounds ◽

Lag Phase ◽

Organohalide Respiration ◽

Content Type ◽

Reductive Dehalogenase ◽

Dehalococcoides Mccartyi ◽

Type Iv ◽

Transmission Electron ◽

Almost All

ABSTRACTPolyhalogenated aromatic compounds are harmful environmental contaminants and tend to persist in anoxic soils and sediments.Dehalococcoides mccartyistrain DCMB5, a strain originating from dioxin-polluted river sediment, was examined for its capacity to dehalogenate diverse chloroaromatic compounds. Strain DCMB5 used hexachlorobenzenes, pentachlorobenzenes, all three tetrachlorobenzenes, and 1,2,3-trichlorobenzene as well as 1,2,3,4-tetra- and 1,2,4-trichlorodibenzo-p-dioxin as electron acceptors for organohalide respiration. In addition, 1,2,3-trichlorodibenzo-p-dioxin and 1,3-, 1,2-, and 1,4-dichlorodibenzo-p-dioxin were dechlorinated, the latter to the nonchlorinated congener with a remarkably short lag phase of 1 to 4 days following transfer. Strain DCMB5 also dechlorinated pentachlorophenol and almost all tetra- and trichlorophenols. Tetrachloroethene was dechlorinated to trichloroethene and served as an electron acceptor for growth. To relate selected dechlorination activities to the expression of specific reductive dehalogenase genes, the proteomes of 1,2,3-trichlorobenzene-, pentachlorobenzene-, and tetrachloroethene-dechlorinating cultures were analyzed. Dcmb_86, an ortholog of the chlorobenzene reductive dehalogenase CbrA, was the most abundant reductive dehalogenase during growth with each electron acceptor, suggesting its pivotal role in organohalide respiration of strain DCMB5. Dcmb_1041 was specifically induced, however, by both chlorobenzenes, whereas 3 putative reductive dehalogenases, Dcmb_1434, Dcmb_1339, and Dcmb_1383, were detected only in tetrachloroethene-grown cells. The proteomes also harbored a type IV pilus protein and the components for its assembly, disassembly, and secretion. In addition, transmission electron microscopy of DCMB5 revealed an irregular mode of cell division as well as the presence of pili, indicating that pilus formation is a feature ofD. mccartyiduring organohalide respiration.

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Coupled Adsorption and Biodegradation of Trichloroethylene on Biochar from Pine Wood Wastes: A Combined Approach for a Sustainable Bioremediation Strategy

Microorganisms ◽

10.3390/microorganisms10010101 ◽

2022 ◽

Vol 10 (1) ◽

pp. 101

Author(s):

Marta M. Rossi ◽

Bruna Matturro ◽

Neda Amanat ◽

Simona Rossetti ◽

Marco Petrangeli Papini

Keyword(s):

Reductive Dechlorination ◽

Adsorption Mechanism ◽

Biological Process ◽

Chlorinated Solvents ◽

Biofilm Reactor ◽

Rrna Gene ◽

Pine Wood ◽

Dehalococcoides Mccartyi ◽

Gene Copies ◽

Physical Treatments

Towards chlorinated solvents, the effectiveness of the remediation strategy can be improved by combining a biological approach (e.g., anaerobic reductive dechlorination) with chemical/physical treatments (e.g., adsorption). A coupled adsorption and biodegradation (CAB) process for trichloroethylene (TCE) removal is proposed in a biofilm–biochar reactor (BBR) to assess whether biochar from pine wood (PWB) can support a dechlorinating biofilm by combining the TCE (100 µM) adsorption. The BBR operated for eight months in parallel with a biofilm reactor (BR)—no PWB (biological process alone), and with an abiotic biochar reactor (ABR)—no dechlorinating biofilm (only an adsorption mechanism). Two flow rates were investigated. Compared to the BR, which resulted in a TCE removal of 86.9 ± 11.9% and 78.73 ± 19.79%, the BBR demonstrated that PWB effectively adsorbs TCE and slows down the release of its intermediates. The elimination of TCE was quantitative, with 99.61 ± 0.79% and 99.87 ± 0.51% TCE removal. Interestingly, the biomarker of the reductive dechlorination process, Dehalococcoides mccartyi, was found in the BRR (9.2 × 105 16S rRNA gene copies/g), together with the specific genes tceA, bvcA, and vcrA (8.16 × 106, 1.28 × 105, and 8.01 × 103 gene copies/g, respectively). This study suggests the feasibility of biochar to support the reductive dechlorination of D. mccartyi, opening new frontiers for field-scale applications.

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Correlations between maximum reductive dechlorination rates and specific biomass parameters in Dehalococcoides mccartyi consortia enriched on chloroethenes PCE, TCE, and cis-1,2-DCE

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab064 ◽

2021 ◽

Author(s):

B Matturro ◽

M Majone ◽

F Aulenta ◽

S Rossetti

Keyword(s):

16S Rrna ◽

Reductive Dechlorination ◽

Correlation Factor ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Activity Levels ◽

Dehalococcoides Mccartyi ◽

Gene Copies ◽

Specific Biomass

Abstract One of the challenges to implementing the modeling of the biological reductive dechlorination (RD) process is the evaluation of biological parameters that represent the abundance/activity levels of the microorganisms involved in the biodegradation of chloroethenes. Here we report a combined analysis of kinetic and specific biomass parameters conducted on three dechlorinating consortia enriched on PCE, TCE, and cis-1,2-DCE. In these consortia, Dehalococcoides mccartyi (Dhc) represented ≥ 70% of the bacterial population identified via 16S rRNA gene amplicon sequencing. Quantitative biomolecular methods were used to generate specific biomass parameters targeting either the Dhc population (16S rRNA genes or cells) or specific genes encoding RD process-involved reductive dehalogenases. The correlation factor between the abundance of active Dhc cells or tceA gene copies and maximum RD rates allowed to predict an increment of 7E+09 of active Dhc cells or 5E+09 tceA gene copies L−1 under controlled conditions. Diversely, the utilization of gene transcripts as biomass parameters for RD modeling did not provide reliable correlations with kinetic performances. This study provides valuable insights for further modeling of the RD process through the utilization of specific biomass parameters.

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Monitoring Abundance and Expression of “Dehalococcoides” Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column

Applied and Environmental Microbiology ◽

10.1128/aem.00926-08 ◽

2008 ◽

Vol 74 (18) ◽

pp. 5695-5703 ◽

Cited By ~ 94

Author(s):

Sebastian Behrens ◽

Mohammad F. Azizian ◽

Paul J. McMurdie ◽

Andrew Sabalowsky ◽

Mark E. Dolan ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Reductive Dehalogenation ◽

Gene Copy ◽

Rrna Gene ◽

Reductive Dehalogenase ◽

Gene Copies ◽

Donor And Acceptor ◽

Rdase Genes

ABSTRACT We investigated the distribution and activity of chloroethene-degrading microorganisms and associated functional genes during reductive dehalogenation of tetrachloroethene to ethene in a laboratory continuous-flow column. Using real-time PCR, we quantified “Dehalococcoides” species 16S rRNA and chloroethene-reductive dehalogenase (RDase) genes (pceA, tceA, vcrA, and bvcA) in nucleic acid extracts from different sections of the column. Dehalococcoides 16S rRNA gene copies were highest at the inflow port [(3.6 ± 0.6) × 106 (mean ± standard deviation) per gram soil] where the electron donor and acceptor were introduced into the column. The highest transcript numbers for tceA, vcrA, and bvcA were detected 5 to 10 cm from the column inflow. bvcA was the most highly expressed of all RDase genes and the only vinyl chloride reductase-encoding transcript detectable close to the column outflow. Interestingly, no expression of pceA was detected in the column, despite the presence of the genes in the microbial community throughout the column. By comparing the 16S rRNA gene copy numbers to the sum of all four RDase genes, we found that 50% of the Dehalococcoides population in the first part of the column did not contain either one of the known chloroethene RDase genes. Analysis of 16S rRNA gene clone libraries from both ends of the flow column revealed a microbial community dominated by members of Firmicutes and Actinobacteria. Higher clone sequence diversity was observed near the column outflow. The results presented have implications for our understanding of the ecophysiology of reductively dehalogenating Dehalococcoides spp. and their role in bioremediation of chloroethenes.

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Characterization of a Dehalobacter Coculture That Dechlorinates 1,2-Dichloroethane to Ethene and Identification of the Putative Reductive Dehalogenase Gene

Applied and Environmental Microbiology ◽

10.1128/aem.02037-08 ◽

2009 ◽

Vol 75 (9) ◽

pp. 2684-2693 ◽

Cited By ~ 64

Author(s):

Ariel Grostern ◽

Elizabeth A. Edwards

Keyword(s):

Enrichment Culture ◽

Growth Yield ◽

Individual Species ◽

Rrna Gene ◽

Degenerate Primers ◽

Reductive Dehalogenase ◽

Gene Copies ◽

Parent Culture ◽

Dehalogenase Gene

ABSTRACT Dehalobacter and “Dehalococcoides” spp. were previously shown to be involved in the biotransformation of 1,1,2-trichloroethane (1,1,2-TCA) and 1,2-dichloroethane (1,2-DCA) to ethene in a mixed anaerobic enrichment culture. Here we report the further enrichment and characterization of a Dehalobacter sp. from this mixed culture in coculture with an Acetobacterium sp. Through a series of serial transfers and dilutions with acetate, H2, and 1,2-DCA, a stable coculture of Acetobacterium and Dehalobacter spp. was obtained, where Dehalobacter grew during dechlorination. The isolated Acetobacterium strain did not dechlorinate 1,2-DCA. Quantitative PCR with specific primers showed that Dehalobacter cells did not grow in the absence of a chlorinated electron acceptor and that the growth yield with 1,2-DCA was 6.9 (±0.7) × 107 16S rRNA gene copies/μmol 1,2-DCA degraded. PCR with degenerate primers targeting reductive dehalogenase genes detected three distinct Dehalobacter/Desulfitobacterium-type sequences in the mixed-parent culture, but only one of these was present in the 1,2-DCA-H2 coculture. Reverse transcriptase PCR revealed the transcription of this dehalogenase gene specifically during the dechlorination of 1,2-DCA. The 1,2-DCA-H2 coculture could dechlorinate 1,2-DCA but not 1,1,2-TCA, nor could it dechlorinate chlorinated ethenes. As a collective, the genus Dehalobacter has been show to dechlorinate many diverse compounds, but individual species seem to each have a narrow substrate range.

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Metagenomic Analysis Reveals Microbial Interactions at the Biocathode of a Bioelectrochemical System Capable of Simultaneous Trichloroethylene and Cr(VI) Reduction

Frontiers in Microbiology ◽

10.3389/fmicb.2021.747670 ◽

2021 ◽

Vol 12 ◽

Author(s):

Bruna Matturro ◽

Marco Zepilli ◽

Agnese Lai ◽

Mauro Majone ◽

Simona Rossetti

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Microbial Interactions ◽

Metagenomic Analysis ◽

Rrna Gene ◽

Shotgun Metagenomics ◽

Dehalococcoides Mccartyi ◽

Hydrogenotrophic Methanogenesis ◽

Gene Copies

Bioelectrochemical systems (BES) are attractive and versatile options for the bioremediation of organic or inorganic pollutants, including trichloroethylene (TCE) and Cr(VI), often found as co-contaminants in the environment. The elucidation of the microbial players’ role in the bioelectroremediation processes for treating multicontaminated groundwater is still a research need that attracts scientific interest. In this study, 16S rRNA gene amplicon sequencing and whole shotgun metagenomics revealed the leading microbial players and the primary metabolic interactions occurring in the biofilm growing at the biocathode where TCE reductive dechlorination (RD), hydrogenotrophic methanogenesis, and Cr(VI) reduction occurred. The presence of Cr(VI) did not negatively affect the TCE degradation, as evidenced by the RD rates estimated during the reactor operation with TCE (111±2 μeq/Ld) and TCE/Cr(VI) (146±2 μeq/Ld). Accordingly, Dehalococcoides mccartyi, the primary biomarker of the RD process, was found on the biocathode treating both TCE (7.82E+04±2.9E+04 16S rRNA gene copies g−1 graphite) and TCE/Cr(VI) (3.2E+07±2.37E+0716S rRNA gene copies g−1 graphite) contamination. The metagenomic analysis revealed a selected microbial consortium on the TCE/Cr(VI) biocathode. D. mccartyi was the sole dechlorinating microbe with H2 uptake as the only electron supply mechanism, suggesting that electroactivity is not a property of this microorganism. Methanobrevibacter arboriphilus and Methanobacterium formicicum also colonized the biocathode as H2 consumers for the CH4 production and cofactor suppliers for D. mccartyi cobalamin biosynthesis. Interestingly, M. formicicum also harbors gene complexes involved in the Cr(VI) reduction through extracellular and intracellular mechanisms.

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Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella

Microbiology ◽

10.1099/mic.0.038224-0 ◽

2010 ◽

Vol 156 (7) ◽

pp. 2080-2091 ◽

Cited By ~ 28

Author(s):

Anne-Laure Michon ◽

Fabien Aujoulat ◽

Laurent Roudière ◽

Olivier Soulier ◽

Isabelle Zorgniotti ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Diversity ◽

Natural Populations ◽

Variable Region ◽

Housekeeping Gene ◽

Single Copy ◽

Population Based ◽

Rrna Gene ◽

Gene Copies

As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel electrophoresis (TTGE). 16S rRNA gene diversity was high in the studied population, as 45 different banding patterns were observed. Intragenomic heterogeneity was demonstrated for 110 (74 %) isolates and 8 (61.5 %) type or reference strains displaying two or three different gene copies. Polymorphic nucleotide positions accounted for 0.5–2.5 % of the sequence and were scattered in helices H16 and H17 of the rRNA molecule. Some of them changed the secondary structure of H17. Phylotaxonomic structure of the population based on the single-copy housekeeping gene rpoB was compared with TTGE patterns. The intragenomic V3 heterogeneity, as well as recombination events between strains or isolates of different rpoB clades, impaired the 16S rRNA-based identification for some Veillonella species. Such approaches should be conducted in other bacterial populations to optimize the interpretation of 16S rRNA gene sequences in taxonomy and/or diversity studies.

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Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium ( Alphaproteobacteria : Rhodospirillaceae ) isolated from a salt marsh

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.044453-0 ◽

2013 ◽

Vol 63 (Pt_5) ◽

pp. 1824-1833 ◽

Cited By ~ 52

Author(s):

Dennis A. Bazylinski ◽

Timothy J. Williams ◽

Christopher T. Lefèvre ◽

Denis Trubitsyn ◽

Jiasong Fang ◽

...

Keyword(s):

Salt Marsh ◽

Electron Acceptor ◽

Anaerobic Growth ◽

Rrna Gene ◽

Magnetotactic Bacterium ◽

Single Chain ◽

Circular Chromosome ◽

Terminal Electron Acceptor ◽

Content Type ◽

Link Type

A magnetotactic bacterium, designated strain MV-1T, was isolated from sulfide-rich sediments in a salt marsh near Boston, MA, USA. Cells of strain MV-1T were Gram-negative, and vibrioid to helicoid in morphology. Cells were motile by means of a single polar flagellum. The cells appeared to display a transitional state between axial and polar magnetotaxis: cells swam in both directions, but generally had longer excursions in one direction than the other. Cells possessed a single chain of magnetosomes containing truncated hexaoctahedral crystals of magnetite, positioned along the long axis of the cell. Strain MV-1T was a microaerophile that was also capable of anaerobic growth on some nitrogen oxides. Salinities greater than 10 % seawater were required for growth. Strain MV-1T exhibited chemolithoautotrophic growth on thiosulfate and sulfide with oxygen as the terminal electron acceptor (microaerobic growth) and on thiosulfate using nitrous oxide (N2O) as the terminal electron acceptor (anaerobic growth). Chemo-organoautotrophic and methylotrophic growth was supported by formate under microaerobic conditions. Autotrophic growth occurred via the Calvin–Benson–Bassham cycle. Chemo-organoheterotrophic growth was supported by various organic acids and amino acids, under microaerobic and anaerobic conditions. Optimal growth occurred at pH 7.0 and 26–28 °C. The genome of strain MV-1T consisted of a single, circular chromosome, about 3.7 Mb in size, with a G+C content of 52.9–53.5 mol%.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MV-1T belongs to the family Rhodospirillaceae within the Alphaproteobacteria , but is not closely related to the genus Magnetospirillum . The name Magnetovibrio blakemorei gen. nov., sp. nov. is proposed for strain MV-1T. The type strain of Magnetovibrio blakemorei is MV-1T ( = ATCC BAA-1436T = DSM 18854T).

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Intellectual property information services and the impacts on academic libraries’ transformation from the perspective of Chinese university libraries

IFLA Journal ◽

10.1177/03400352211025552 ◽

2021 ◽

pp. 034003522110255

Author(s):

Wei Yang ◽

Tianlin Liu

Keyword(s):

Intellectual Property ◽

Driving Forces ◽

Information Service ◽

Information Services ◽

University Libraries ◽

Chinese University ◽

The Usa ◽

The Uk ◽

Library Transformation ◽

Information Providers

Approximately 100 Intellectual Property Information Services Centres have been established in Chinese university libraries, more than 80% of them since 2017. The context of this boom in Intellectual Property Information Services Centres is the rapidly increasing number of patent applications in China, as well as an unacceptably low transfer ratio. Do Intellectual Property Information Services Centres represent a promising direction for university library transformation? This is the central issue addressed in this article. The characteristics of the Chinese evolutionary path and driving forces are discussed, and distinctive intellectual property information service practices are studied and summarized. Comparisons are made with the USA, the UK, Europe and India. With Intellectual Property Information Services Centres, university libraries can evolve from information providers to innovation catalysts, and establish closer connections between universities, communities and industries. The impacts of Intellectual Property Information Services Centres on university librarianship are multifaceted. The trends and challenges of intellectual property information services are also discussed in the article.

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