Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes

Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.

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Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater

Applied Microbiology and Biotechnology ◽

10.1007/s00253-017-8203-y ◽

2017 ◽

Vol 101 (11) ◽

pp. 4827-4835 ◽

Cited By ~ 6

Author(s):

Yogendra H. Kanitkar ◽

Robert D. Stedtfeld ◽

Paul B. Hatzinger ◽

Syed A. Hashsham ◽

Alison M. Cupples

Keyword(s):

Inexpensive Method ◽

Reductive Dehalogenase ◽

Reductive Dehalogenase Genes ◽

User Friendly

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Concurrent Ethene Generation and Growth ofDehalococcoidesContaining Vinyl Chloride Reductive Dehalogenase Genes During an Enhanced Reductive Dechlorination Field Demonstration

Environmental Science & Technology ◽

10.1021/es800764t ◽

2008 ◽

Vol 42 (24) ◽

pp. 9302-9309 ◽

Cited By ~ 91

Author(s):

Charlotte Scheutz ◽

Neal d. Durant ◽

Philip Dennis ◽

Maria Heisterberg Hansen ◽

Torben Jørgensen ◽

...

Keyword(s):

Vinyl Chloride ◽

Reductive Dechlorination ◽

Reductive Dehalogenase ◽

Reductive Dehalogenase Genes ◽

Enhanced Reductive Dechlorination

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

Microbiology Resource Announcements ◽

10.1128/mra.00558-19 ◽

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.

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Multiple Nonidentical Reductive-Dehalogenase-Homologous Genes Are Common in Dehalococcoides

Applied and Environmental Microbiology ◽

10.1128/aem.70.9.5290-5297.2004 ◽

2004 ◽

Vol 70 (9) ◽

pp. 5290-5297 ◽

Cited By ~ 98

Author(s):

Tina Hölscher ◽

Rosa Krajmalnik-Brown ◽

Kirsti M. Ritalahti ◽

Friedrich von Wintzingerode ◽

Helmut Görisch ◽

...

Keyword(s):

Amino Acid ◽

Restriction Analysis ◽

Sequence Similarity ◽

Comparative Sequence Analysis ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

Degenerate Primers ◽

Reductive Dehalogenase ◽

Genes Encoding ◽

Reductive Dehalogenase Genes

ABSTRACT Degenerate primers were used to amplify large fragments of reductive-dehalogenase-homologous (RDH) genes from genomic DNA of two Dehalococcoides populations, the chlorobenzene- and dioxin-dechlorinating strain CBDB1 and the trichloroethene-dechlorinating strain FL2. The amplicons (1,350 to 1,495 bp) corresponded to nearly complete open reading frames of known reductive dehalogenase genes and short fragments (approximately 90 bp) of genes encoding putative membrane-anchoring proteins. Cloning and restriction analysis revealed the presence of at least 14 different RDH genes in each strain. All amplified RDH genes showed sequence similarity with known reductive dehalogenase genes over the whole length of the sequence and shared all characteristics described for reductive dehalogenases. Deduced amino acid sequences of seven RDH genes from strain CBDB1 were 98.5 to 100% identical to seven different RDH genes from strain FL2, suggesting that both strains have an overlapping substrate range. All RDH genes identified in strains CBDB1 and FL2 were related to the RDH genes present in the genomes of Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain BAV1; however, sequence identity did not exceed 94.4 and 93.1%, respectively. The presence of RDH genes in strains CBDB1, FL2, and BAV1 that have no orthologs in strain 195 suggests that these strains possess dechlorination activities not present in strain 195. Comparative sequence analysis identified consensus sequences for cobalamin binding in deduced amino acid sequences of seven RDH genes. In conclusion, this study demonstrates that the presence of multiple nonidentical RDH genes is characteristic of Dehalococcoides strains.

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Quantitative Analysis of the Relative Transcript Levels of Four Chlorophenol Reductive Dehalogenase Genes in Desulfitobacterium hafniense PCP-1 Exposed to Chlorophenols

Applied and Environmental Microbiology ◽

10.1128/aem.00390-11 ◽

2011 ◽

Vol 77 (17) ◽

pp. 6261-6264 ◽

Cited By ~ 16

Author(s):

Ariane Bisaillon ◽

Réjean Beaudet ◽

François Lépine ◽

Richard Villemur

Keyword(s):

Quantitative Analysis ◽

Transcript Levels ◽

Content Type ◽

Reductive Dehalogenase ◽

Reductive Dehalogenase Genes ◽

Desulfitobacterium Hafniense

ABSTRACTRelative to those of unexposed cultures, the transcript levels of the four CprA-type reductive dehalogenase genes (cprA2,cprA3,cprA4, andcprA5) inDesulfitobacterium hafniensePCP-1 were measured in cultures exposed to chlorophenols. In 2,4,6-trichlorophenol-amended cultures,cprA2andcprA3were upregulated, as wascprA5, but concomitantly with the appearance of 2,4-dichlorophenol (DCP). In 3,5-DCP-amended cultures, onlycprA5was upregulated. In pentachlorophenol-amended cultures grown for 12 h,cprA2andcprA3were upregulated but notcprA5. cprA4was not upregulated significantly in cultures containing any tested chlorophenols.

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