Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi

Abstract

Six obligately anaerobic bacterial isolates (195T, CBDB1, BAV1, VS, FL2 and GT) with strictly organohalide-respiring metabolisms were obtained from chlorinated solvent-contaminated aquifers, contaminated and uncontaminated river sediments or anoxic digester sludge. Cells were non-motile with a disc-shaped morphology, 0.3–1 µm in diameter and 0.1–0.2 µm thick, and characteristic indentations on opposite flat sides of the cell. Growth occurred in completely synthetic, reduced medium amended with a haloorganic electron acceptor (mostly chlorinated but also some brominated compounds), hydrogen as electron donor, acetate as carbon source, and vitamins. No other growth-supporting redox couples were identified. Aqueous hydrogen consumption threshold concentrations were <1 nM. Growth ceased when vitamin B12 was omitted from the medium. Addition of sterile cell-free supernatant of Dehalococcoides-containing enrichment cultures enhanced dechlorination and growth of strains 195 and FL2, suggesting the existence of so-far unidentified stimulants. Dechlorination occurred between pH 6.5 and 8.0 and over a temperature range of 15–35 °C, with an optimum growth temperature between 25 and 30 °C. The major phospholipid fatty acids were 14 : 0 (15.7 mol%), br15 : 0 (6.2 mol%), 16 : 0 (22.7 mol%), 10-methyl 16 : 0 (25.8 mol%) and 18 : 0 (16.6 mol%). Unusual furan fatty acids including 9-(5-pentyl-2-furyl)-nonanoate and 8-(5-hexyl-2-furyl)-octanoate were detected in strains FL2, BAV1 and GT, but not in strains 195T and CBDB1. The 16S rRNA gene sequences of the six isolates shared more than 98 % identity, and phylogenetic analysis revealed an affiliation with the phylum Chloroflexi and more than 10 % sequence divergence from other described isolates. The genome sizes and G+C contents ranged from 1.34 to 1.47 Mbp and 47 to 48.9 mol% G+C, respectively. Based on 16S rRNA gene sequence comparisons, genome-wide average nucleotide identity and phenotypic characteristics, the organohalide-respiring isolates represent a new genus and species, for which the name Dehalococcoides mccartyi gen. nov., sp. nov. is proposed. Isolates BAV1 ( = ATCC BAA-2100 = JCM 16839 = KCTC 5957), FL2 ( = ATCC BAA-2098 = DSM 23585 = JCM 16840 = KCTC 5959), GT ( = ATCC BAA-2099 = JCM 16841 = KCTC 5958), CBDB1, 195T ( = ATCC BAA-2266T = KCTC 15142T) and VS are considered strains of Dehalococcoides mccartyi, with strain 195T as the type strain. The new class Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov. are described to accommodate the new taxon.

Dechlorination and organohalide-respiring bacteria dynamics in sediment samples of the Yangtze Three Gorges Reservoir

“…were observed. The D. mccartyi group encompasses the six bacterial isolates of strains 195, BAV1, CBDB1, FL2, GT, and VS (Löffler et al 2012). Most probably, different strains of the genus Dehalococcoides spp.…”

“…Microorganisms which are known to be able to reductively dechlorinate pollutants are Desulfomonile spp., Desulfitobacterium spp., Dehalobacter spp., Desulfuromonas spp., and Dehalococcoides spp., but only bacteria belonging to Dehalococcoides spp. are capable of complete dehalogenation of tetrachloroethene (PCE) to ethene (Holliger et al 1993;Smidt and de Vos 2004;Schmidt et al 2006;Aktaş et al 2012;Löffler et al 2012).…”

“…(Lohner and Tiehm 2009), Desulfitobacterium dehalogenans and Desulfomonile tiedjei (El Fantroussi et al 1997), Desulfuromonas spp. and Dehalococcoides mccartyi (Löffler et al 2000;Löffler et al 2012), Dehalobacter spp. and Dehalococcoides spp.…”

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

“…From the Dehalococcoides mccartyi genomes, the current minimum number of rdhA genes per genome is 10 [15], with up to 36 rdhA genes present on a single genome [15]. The genome of Dehalococcoides mccartyi (formerly ethenogenes) strain 195 [65] harbours 17 different rdhA genes [14], while strain CBDB1 0 s genome contains 32 rdhAs [13]. The genome of Dehalogenimonas lykanthroporepellens strain BL-DC-9, the only sequenced Dehalogenimonas, contains 19 rdhA genes [17,66].…”

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

“…To date, our knowledge about the metabolic properties of members of this clade is derived from several closely related cultivated strains, that is, Dehalococcoides mccartyi strains (Lö ffler et al, 2012), Dehalogenimonas lykanthroporepellens strains (Moe et al, 2009), Dehalogenimonas alkenigignens strains (Bowman et al, 2012) and 'Dehalobium chlorocoercia' strain DF-1 (May et al, 2008). These isolates are unified by their ability to grow via organohalide respiration, that is, they use halogenated organic compounds as terminal electron acceptors while using hydrogen as an electron donor in an anaerobic respiration (Tas et al, 2010).…”