Complete Genome Sequence of the Dehalorespiring Bacterium Desulfitobacterium hafniense Y51 and Comparison with Dehalococcoides ethenogenes 195

Abstract

Desulfitobacterium strains have the ability to dechlorinate halogenated compounds under anaerobic conditions by dehalorespiration. The complete genome of the tetrachloroethene (PCE)-dechlorinating strain Desulfitobacterium hafniense Y51 is a 5,727,534-bp circular chromosome harboring 5,060 predicted protein coding sequences. This genome contains only two reductive dehalogenase genes, a lower number than reported in most other dehalorespiring strains. More than 50 members of the dimethyl sulfoxide reductase superfamily and 30 paralogs of the flavoprotein subunit of the fumarate reductase are encoded as well. A remarkable feature of the genome is the large number of O-demethylase paralogs, which allow utilization of lignin-derived phenyl methyl ethers as electron donors. The large genome reveals a more versatile microorganism that can utilize a larger set of specialized electron donors and acceptors than previously thought. This is in sharp contrast to the PCE-dechlorinating strain Dehalococcoides ethenogenes 195, which has a relatively small genome with a narrow metabolic repertoire. A genomic comparison of these two very different strains allowed us to narrow down the potential candidates implicated in the dechlorination process. Our results provide further impetus to the use of desulfitobacteria as tools for bioremediation.Halogenated organic compounds are released into the environment from natural and anthropogenic sources. Many anthropogenic halogenated chemicals, like chlorinated haloalkenes (7, 10, 46), benzenes (1), and dioxins (5), are of particular concern due to their toxicity to humans and other forms of life. This toxicity is often paired with high recalcitrance to degradation, especially in anaerobic environments, leading to persistent contamination.Anaerobic environments are frequently characterized by limited availability of electron acceptors. Theoretical calculations have shown that coupling the reduction of many halogenated organic compounds to the oxidation of suitable substrates is a way to harness energy (46). As determined two decades ago, this source of energy is utilized by the microbial community. The oxidation of available electron donors coupled to the reduction of halogenated organic compounds while energy is conserved is called dehalorespiration (7,10,46). Dehalorespiring strains have been isolated independently from contaminated sites around the world. The two most prominent genera resulting from these isolation efforts are Dehalococcoides (29) and Desulfitobacterium (51), and various strains of these genera are used as model systems to study dehalorespiration (8,11,51).Dehalococcoides ethenogenes 195 is one of the few strains isolated to date which can dechlorinate tetrachloroethene (PCE) to ethene (29). D. ethenogenes 195 can use only hydrogen as an electron donor and chlorinated compounds as electron acceptors (29).Desulfitobacterium strains are also known to dechlorinate a wide variety of substrates, including halophenolic compounds and chloroalkenes (7,10,46). Although several s...

Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases

“…E1 was recently elucidated based on metagenome analysis of a defined co-culture [22]. The availability of OHRB genomes has allowed comparative genomic studies within genera [15,23] as well as across phyla [6]. Genome sequences of the Dehalococcoides have revealed specific metabolic requirements, including corrinoid auxotrophy for the majority of sequenced strains [13][14][15].…”

“…OHRB have been identified from diverse bacterial phyla, including the Proteobacteria, Firmicutes and Chloroflexi [5][6][7][8]. The known OHRB can be grouped as either obligate or non-obligate organohalide respirers [9].…”

“…Genome sequences exist for several OHRB, including five Dehalococcoides mccartyi strains [13][14][15][16] and Dehalogenimonas lykanthroporepellens strain BL-DC-9 [17] within the Chloroflexi; Geobacter lovleyi strain SZ [18] and Anaeromyxobacter dehalogenans strains 2CP-C and 2CP-1 [19] from the Proteobacteria; and Desulfitobacterium hafniense strains Y51 and DCB-2 [6,20], Desulfitobacterium dehalogenans (NC_018017), Desulfitobacterium dichloroeliminans (NZ_AGJE00000000) and most recently two Dehalobacter strains [21] from the Firmicutes. Given the low cost and broad availability of sequencing from pure or mixed cultures, the number of OHRB genomes will increase rapidly.…”

Application of molecular techniques to evaluate the methanogenic archaea and anaerobic bacteria in the presence of oxygen with different COD:Sulfate ratios in a UASB reactor

“…Uncultured bacterium (AY945891) was previously identified from the secondary sedimentation tank of wastewater from a coking and chemical treatment plant (Shangai, China) that was studied in a denitrifying quinoline-removal bioreactor [40]. D. hafniense (AP008230) were previously isolated from an environment contaminated with dechlorinate tetrachloroethene (PCE) [41]. Suyama et al [42] observed that D. hafniense were capable of reducing either sulfate or nitrate when pyruvate was the electron donor.…”

Desulfitobacterium contributes to the microbial transformation of 2,4,5‐T by methanogenic enrichment cultures from a Vietnamese active landfill

“…The resulting reducing equivalents allow growth using terminal electron acceptors such as fumarate (Kreher et al ., 2010; Studenik et al ., 2012). Despite the presence of several O‐demethylases encoded in the genomes of Desulfitobacterium (Nonaka et al ., 2006; Kim et al ., 2012), none of these proteins was detected in the metaproteome (Tables S3 and S6), strongly suggesting that they do not play a role in 2,4,5‐T ether cleavage.…”