Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

Abstract

BackgroundGeobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE) reductive dechlorination to cis-1,2-dichloroethene (cis-DCE) with energy conservation and growth (i.e., organohalide respiration). Strain SZ also reduces U(VI) to U(IV) and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae.ResultsSequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs) and cytosines (Cs) among the four bases within the genome), and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC), with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. A plasmid with 99% sequence identity to pSZ77 was subsequently detected in the PCE-dechlorinating G. lovleyi strain KB-1 present in the PCE-to-ethene-dechlorinating consortium KB-1. Additional PCE-to-cis-DCE-dechlorinating G. lovleyi strains obtained from the PCE-contaminated Fort Lewis, WA, site did not carry a plasmid indicating that pSZ77 is not a requirement (marker) for PCE respiration within this species. Chromosomal genomic islands found within the G. lovleyi strain SZ genome encode two reductive dehalogenase (RDase) homologs and a putative conjugative pilus system. Despite the loss of many c-type cytochrome and oxidative-stress-responsive genes, strain SZ retained the majority of Geobacter core metabolic capabilities, including U(VI) respiration.ConclusionsGene acquisitions have expanded strain SZ’s respiratory capabilities to include PCE and TCE as electron acceptors. Respiratory processes core to the Geobacter genus, such as metal reduction, were retained despite a substantially reduced number of c-type cytochrome genes. pSZ77 is stably maintained within its host strains SZ and KB-1, likely because the replicon carries essential genes including genes involved in cobalamin biosynthesis and possibly corrinoid transport. Lateral acquisition of the plasmid replicon and the RDase genomic island represent unique genome features of the PCE-respiring G. lovleyi strains SZ and KB-1, and at least the latter signifies adaptation to PCE contamination.

Identity and Substrate Specificity of Reductive Dehalogenases Expressed in Dehalococcoides-Containing Enrichment Cultures Maintained on Different Chlorinated Ethenes

“…The KB-1 parent enrichment culture was originally derived over 15 years ago from sediment from a TCEcontaminated site in southern Ontario, Canada, and has been maintained with TCE as terminal electron acceptor and methanol as electron donor in a defined prereduced mineral medium supplemented with vitamins (33). This consortium contains multiple D. mccartyi strains that comprise more than 50% of the culture that are able to dechlorinate PCE and TCE to ethene (34) and a Geobacter lovleyi strain that makes up 10 to 20% of the culture that dechlorinates PCE and TCE to cis-DCE (35,36). This parent culture is referred to here as TCE/M_1998, with the naming convention indicating that TCE and methanol ("M") were added as the electron acceptor and donor, respectively, and that the culture was first established in 1998.…”

Functional Characterization of Reductive Dehalogenases by Using Blue Native Polyacrylamide Gel Electrophoresis

“…KB-1 was enriched from sediment from a contaminated site in Ontario (Canada) and contains multiple D. mccartyi strains (23). KB-1 also contains a PCE-and TCE-dechlorinating Geobacter lovleyi strain KB-1 (24). The KB-1 consortium was routinely maintained with TCE as an electron acceptor and methanol and ethanol as electron donors in a defined mineral salts medium (25).…”

“…The KB-1 metagenome was obtained from shotgun sequencing of the KB-1 culture DNA using Sanger sequencing (10). The assembly and annotation of the KB-1 metagenome were performed using the in-house pipelines of the Department of Energy (DoE) Joint Genome Institute (JGI) (Walnut Creek, CA) (10) Geobacter rdhA gene (KB1_GeobRD) (24). Because this collection of 36 rdhA sequences from the KB-1 culture was from metagenomic data, it may not cover all rdhA sequences in KB-1 cultures.…”

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment

“…The presence of Desulfovibrio in dechlorinating microcosms suggests its possible indirect role in dechlorination via syntrophic association with existing dehalorespiring bacteria (Drzyzga et al, 2001). Geobacter, as well as being detected in established dechlorinating microcosms, has also been suggested to play a role in organohalide respiration (Wagner et al, 2012). Cultures devoid of the distinct DGGE band assigned to Desulfitobacterium, lack any dechlorination activity, providing clear evidence that Desulfitobacterium sp.…”