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

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.

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Jun Yan ◽  
Yi Yang ◽  
Xiuying Li ◽  
Frank E. Löffler

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.


2022 ◽  
Vol 10 (1) ◽  
pp. 101
Author(s):  
Marta M. Rossi ◽  
Bruna Matturro ◽  
Neda Amanat ◽  
Simona Rossetti ◽  
Marco Petrangeli Papini

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.


Author(s):  
B Matturro ◽  
M Majone ◽  
F Aulenta ◽  
S Rossetti

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.


2017 ◽  
Author(s):  
A. Pérez-de-Mora ◽  
A. Lacourt ◽  
M.L. McMaster ◽  
X. Liang ◽  
S.M. Dworatzek ◽  
...  

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.


2012 ◽  
Vol 78 (22) ◽  
pp. 8025-8032 ◽  
Author(s):  
Anika Reinhold ◽  
Martin Westermann ◽  
Jana Seifert ◽  
Martin von Bergen ◽  
Torsten Schubert ◽  
...  

ABSTRACTCorrinoids are essential cofactors of reductive dehalogenases in anaerobic bacteria. Microorganisms mediating reductive dechlorination as part of their energy metabolism are either capable ofde novocorrinoid biosynthesis (e.g.,Desulfitobacteriumspp.) or dependent on exogenous vitamin B12(e.g.,Dehalococcoidesspp.). In this study, the impact of exogenous vitamin B12(cyanocobalamin) and of tetrachloroethene (PCE) on the synthesis and the subcellular localization of the reductive PCE dehalogenase was investigated in the Gram-positiveDesulfitobacterium hafniensestrain Y51, a bacterium able to synthesize corrinoidsde novo. PCE-depleted cells grown for several subcultivation steps on fumarate as an alternative electron acceptor lost the tetrachloroethene-reductive dehalogenase (PceA) activity by the transposition of thepcegene cluster. In the absence of vitamin B12, a gradual decrease of the PceA activity and protein amount was observed; after 5 subcultivation steps with 10% inoculum, more than 90% of the enzyme activity and of the PceA protein was lost. In the presence of vitamin B12, a significant delay in the decrease of the PceA activity with an ∼90% loss after 20 subcultivation steps was observed. This corresponded to the decrease in thepceAgene level, indicating that exogenous vitamin B12hampered the transposition of thepcegene cluster. In the absence or presence of exogenous vitamin B12, the intracellular corrinoid level decreased in fumarate-grown cells and the PceA precursor formed catalytically inactive, corrinoid-free multiprotein aggregates. The data indicate that exogenous vitamin B12is not incorporated into the PceA precursor, even though it affects the transposition of thepcegene cluster.


mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Pravin Malla Shrestha ◽  
Kelly P. Nevin ◽  
Minita Shrestha ◽  
Derek R. Lovley

ABSTRACTGeobacter sulfurreducensstrain KN400 was recovered in previous studies in which a culture of the DL1 strain ofG. sulfurreducensserved as the inoculum in investigations of microbial current production at low anode potentials (−400 mV versus Ag/AgCl). Differences in the genome sequences of KN400 and DL1 were too great to have arisen from adaptive evolution during growth on the anode. Previous deep sequencing (80-fold coverage) of the DL1 culture failed to detect sequences specific to KN400, suggesting that KN400 was an external contaminant inadvertently introduced into the anode culturing system. In order to evaluate this further, a portion of the gene for OmcS, ac-type cytochrome that both KN400 and DL1 possess, was amplified from the DL1 culture. HiSeq-2000 Illumina sequencing of the PCR product detected the KN400 sequence, which differs from the DL1 sequence at 14 bp, at a frequency of ca. 1 in 105copies of the DL1 sequence. A similar low frequency of KN400 was detected with quantitative PCR of a KN400-specific gene. KN400 persisted at this frequency after intensive restreaking of isolated colonies from the DL1 culture. However, a culture in which KN400 could no longer be detected was obtained by serial dilution to extinction in liquid medium. The KN400-free culture could not grow on an anode poised at −400 mV. Thus, KN400 cryptically persisted in the culture dominated by DL1 for more than a decade, undetected by even deep whole-genome sequencing, and was only fortuitously uncovered by the unnatural selection pressure of growth on a low-potential electrode.IMPORTANCERepeated streaking of isolated colonies on solidified medium remains a common strategy for obtaining pure cultures, especially of difficult-to-cultivate microorganisms such as strict anaerobes. The results presented here demonstrate that verifying the purity of cultures obtained in this manner may be difficult because extremely rare variants can persist, undetectable with even deep genomic DNA sequencing. The only way to ensure that a culture is pure is to cultivate it from an initial single cell, which may be technically difficult for many environmentally significant microbes.


2012 ◽  
Vol 78 (21) ◽  
pp. 7745-7752 ◽  
Author(s):  
Shan Yi ◽  
Erica C. Seth ◽  
Yu-Jie Men ◽  
Sally P. Stabler ◽  
Robert H. Allen ◽  
...  

ABSTRACTCorrinoids are cobalt-containing molecules that function as enzyme cofactors in a wide variety of organisms but are produced solely by a subset of prokaryotes. Specific corrinoids are identified by the structure of their axial ligands. The lower axial ligand of a corrinoid can be a benzimidazole, purine, or phenolic compound. Though it is known that many organisms obtain corrinoids from the environment, the variety of corrinoids that can serve as cofactors for any one organism is largely unstudied. Here, we examine the range of corrinoids that function as cofactors for corrinoid-dependent metabolism inDehalococcoides mccartyistrain 195.Dehalococcoidesbacteria play an important role in the bioremediation of chlorinated solvents in the environment because of their unique ability to convert the common groundwater contaminants perchloroethene and trichloroethene to the innocuous end product ethene. All isolatedD. mccartyistrains require exogenous corrinoids such as vitamin B12for growth. However, like many other corrinoid-dependent bacteria, none of the well-characterizedD. mccartyistrains has been shown to be capable of synthesizing corrinoidsde novo. In this study, we investigate the ability ofD. mccartyistrain 195 to use specific corrinoids, as well as its ability to modify imported corrinoids to a functional form. We show that strain 195 can use only specific corrinoids containing benzimidazole lower ligands but is capable of remodeling other corrinoids by lower ligand replacement when provided a functional benzimidazole base. This study of corrinoid utilization and modification byD. mccartyiprovides insight into the array of strategies that microorganisms employ in acquiring essential nutrients from the environment.


2012 ◽  
Vol 79 (3) ◽  
pp. 974-981 ◽  
Author(s):  
Shuiquan Tang ◽  
Winnie W. M. Chan ◽  
Kelly E. Fletcher ◽  
Jana Seifert ◽  
Xiaoming Liang ◽  
...  

ABSTRACTDehalococcoides mccartyistrains are obligate organohalide-respiring bacteria harboring multiple distinct reductive dehalogenase (RDase) genes within their genomes. A major challenge is to identify substrates for the enzymes encoded by these RDase genes. We demonstrate an approach that involves blue native polyacrylamide gel electrophoresis (BN-PAGE) followed by enzyme activity assays with gel slices and subsequent identification of proteins in gel slices using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). RDase expression was investigated in cultures ofDehalococcoides mccartyistrain BAV1 and in the KB-1 consortium growing on chlorinated ethenes and 1,2-dichloroethane. In cultures of strain BAV1, BvcA was the only RDase detected, revealing that this enzyme catalyzes the dechlorination not only of vinyl chloride, but also of all dichloroethene isomers and 1,2-dichloroethane. In cultures of consortium KB-1, five distinctDehalococcoidesRDases and oneGeobacterRDase were expressed under the conditions tested. Three of the five RDases included orthologs to the previously identified chlorinated ethene-dechlorinating enzymes VcrA, BvcA, and TceA. This study revealed substrate promiscuity for these three enzymes and provides a path forward to further explore the largely unknown RDase protein family.


2014 ◽  
Vol 81 (2) ◽  
pp. 587-596 ◽  
Author(s):  
Marlén Pöritz ◽  
Christian L. Schiffmann ◽  
Gerd Hause ◽  
Ulrike Heinemann ◽  
Jana Seifert ◽  
...  

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.


2016 ◽  
Vol 198 (23) ◽  
pp. 3130-3141 ◽  
Author(s):  
Lydia Krasper ◽  
Hauke Lilie ◽  
Anja Kublik ◽  
Lorenz Adrian ◽  
Ralph Golbik ◽  
...  

ABSTRACTReductive dehalogenases are essential enzymes in organohalide respiration and consist of a catalytic subunit A and a membrane protein B, encoded byrdhABgenes. Thirty-twordhABgenes exist in the genome ofDehalococcoides mccartyistrain CBDB1. To gain a first insight into the regulation ofrdhoperons, the control of gene expression of twordhABgenes (cbdbA1453/cbdbA1452 and cbdbA1455/cbdbA1454) by the MarR-type regulator Rdh2R (cbdbA1456) encoded directly upstream was studied using heterologous expression andin vitrostudies. Promoter-lacZreporter fusions were generated and integrated into the genome of theEscherichia colihost. ThelacZreporter activities of bothrdhApromoters decreased upon transformation of the cells with a plasmid carrying therdh2Rgene, suggesting that Rdh2R acts as repressor, whereas thelacZreporter activity of therdh2Rpromoter was not affected. The transcriptional start sites of bothrdhAgenes in strain CBDB1 and/or the heterologous host mapped to a conserved direct repeat with 11- to 13-bp half-sites. DNase I footprinting revealed binding of Rdh2R to a ∼30-bp sequence covering the complete direct repeat in both promoters, including the transcriptional start sites. Equilibrium sedimentation ultracentrifugation revealed that Rdh2R binds as tetramer to the direct-repeat motif of therdhA(cbdbA1455) promoter. Using electrophoretic mobility shift assays, a similar binding affinity was found for bothrdhApromoters. In the presence of only one half-site of the direct repeat, the interaction was strongly reduced, suggesting a positive cooperativity of binding, for which unusual short palindromes within the direct-repeat half-sites might play an important role.IMPORTANCEDehalococcoides mccartyistrains are obligate anaerobes that grow by organohalide respiration. They have an important bioremediation potential because they are capable of reducing a multitude of halogenated compounds to less toxic products. We are now beginning to understand how these organisms make use of this large catabolic potential, wherebyD. mccartyiexpresses dehalogenases in a compound-specific fashion. MarR-type regulators are often encoded in the vicinity of reductive dehalogenase genes. In this study, we made use of heterologous expression andin vitrostudies to demonstrate that the MarR-type transcription factor Rdh2R acts as a negative regulator. We identify its binding site on the DNA, which suggests a mechanism by which it controls the expression of two adjacent reductive dehalogenase operons.


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