Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type strain (IP3-3(T))

Abstract

Dehalogenimonas alkenigignens IP3-3(T) is a strictly anaerobic, mesophilic, Gram negative staining bacterium that grows by organohalide respiration, coupling the oxidation of H2 to the reductive dehalogenation of polychlorinated alkanes. Growth has not been observed with any non-polyhalogenated alkane electron acceptors. Here we describe the features of strain IP3-3(T) together with genome sequence information and its annotation. The 1,849,792 bp high-quality-draft genome contains 1936 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S) locus. The genome contains 29 predicted reductive dehalogenase genes, a large majority of which lack cognate genes encoding membrane anchoring proteins.

Keywords: 1,2,3-trichloropropane; 1,2-dichloroethane; 1,2-dichloropropane; Chloroflexi; Dehalococcoidia; Reductive dechlorination.

Fig. 1

Phylogenetic tree showing the position of D. alkenigignens IP3-3^T (shown in bold) relative to the other species of the genus Dehalogenimonas and type species of other genera within the phylum Chloroflexi. The tree was inferred from 1392 aligned nucleotide positions of the 16S rRNA gene sequence using the Neighbor-Joining method within the MEGA v4.0.2 package [60]. Scale bar represents 2 substitutions per 100 nucleotide positions. Numbers at branching points denote support values from 1000 bootstrap replicates if larger than 70 %. Lineages with published genomes are: Anaerolinea thermophila UNI-1^T (AP012029), Ardenticatena maritima 110S^T (LGKN00000000), Bellilinea caldifistulae GOMI-1^T (BBXX00000000), Caldilinea aerophila STL-6-O1^T (AP012337), Chloroflexus aurantiacus J-10-fl^T (CP000909), Dehalococcoides mccartyi 195 ^T (CP000027), Dehalogenimonas alkenigignens IP3-3^T (LFDV00000000), Dehalogenimonas lykanthroporepellens BL-DC-9^T (CP002084), Herpetosiphon aurantiacus DSM 785^T (CP000875), Kallotenue papyrolyticum JKG1^T (JAGA00000000), Ktedonobacter racemifer SOSP1-21^T (ADVG00000000), Leptolinea tardivitalis YMTK-2^T (LGCK00000000), Levilinea saccharolytica KIBI-1 T (BBXZ00000000), Longilinea arvoryzae KOME-1^T (BBXY00000000), Nitrolancea hollandica Lb^T (CAGS00000000), Ornatilinea apprima P3M-1^T (LGCL00000000), Oscillochloris trichoides DG-6^T (ADVR00000000), Roseiflexus castenholzii DSM 13941^T (CP000804), Sphaerobacter thermophiles DSM 20745^T (CP001823), “Thermanaerothrix daxensis” GNS-1 (LGKO00000000), “Thermobaculum terrenum” YNP1 (CP001825), Thermomicrobium roseum DSM 5159^T (CP001275), and Thermorudis peleae KI4 ^T (JQMP00000000)

Fig. 2

Scanning electron micrograph of cells of D. alkenigignens strain IP3-3^T

Fig. 3

Graphical circular map of the largest contig. From the outside to the center: RNA genes (rRNAs in red and tRNAs in blue), genes on the reverse strand (colored according to the COGs categories), genes on the forward strand (colored according to the COGs categories), GC skew (where yellow indicates positive values and blue indicates negative values), GC ratio (shown in red/green, which indicates positive/negative, respectively)