First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327).

We report the draft genome sequence of the Acidovorax caeni type strain R-24608 that was isolated from activated sludge of an aerobic-anaerobic wastewater treatment plant. The closest strain to Acidovorax caeni strain R-24608 is Acidovorax sp. strain MR-S7 with a 55.4% (amino-acid sequence) open reading frames (ORFs) average similarity.

GENOME ANNOUNCEMENT

Acidovorax isolates (Comamonadaceae family) are Gram-negative, aerobic bacteria with a polar flagellum and 62 to 70% G+C (1). Acidovorax species have been isolated from soil or water (1, 2), infected plants (3, 4), activated sludge (5–7), and clinical samples (1, 8–10). Acidovorax radicis N35 was identified as a root-colonizing bacterium without phytopathogenic potential, which showed plant-growth-promoting activity (11). Autotrophic growth with hydrogen as an electron donor was found in Acidovorax facilis and some strains of Acidovorax delafieldii (1). Denitrification in wastewater treatment plants has been proposed to be catalyzed by members of the Acidovorax genus (6, 12, 13) and based on 16S rRNA gene sequence analysis, 19 denitrifiers were recently identified as Acidovorax avenae, A. defluvii, and A. temperans species (5).

Four novel denitrifyers were characterized as belonging to a new species termed Acidovorax caeni sp. nov. Here, we announce the first draft genome sequence of the Acidovorax caeni sp. nov. type strain R-24608 (14).

The genome was sequenced using the Illumina MiSeq platform, which generated pair-end read sequences of 250 bp. Assemblage using Edena (15, 16) produced 152 contigs with a total genome size of 4,190,928 bs (63.2% G+C content, N50: 78.99 Kbp, mean: 27.43 Kb) and an average of 83.9-fold coverage. Automatic annotation was performed using the RAST server version 4.0 (17), generating 3,904 features potentially assigned to protein-encoding genes (open reading frames [ORFs]).

A comparison between the draft genome of Acidovorax caeni strain R-24608 and the 17 genomes or draft genomes currently available for Acidovorax isolates, Acidovorax sp. JHL-3 (PRJNA195669), JHL-9 (PRJNA195668), NO-1 (18), CF 316 (19), MR-S7 (20), JS42 (PRJNA15685), KKS102 (21) and A. citrulli AAC00-1 (PRJNA15708), A. citrulli ZJU1106 (PRJNA175738), A. avenae ATCC 19860 (PRJNA37867), A. avenae RS-1 (22), A. radices N35 (PRJNA64465), A. radices N35v (PRJNA64471), A. ebreus TPSY (23), A. delafieldii 2AN (PRJNA32605), A. oryzae ATCC 19882 (PRJNA223028), and A. temperans KY4 (PRJNA270288) indicated Acidovorax sp. strain MR-S7 with a 55.4% (amino-acid sequence) of ORFs average similarity to be the most closely related to strain R-24608. Both strains share 1,318 ORFs with >80% similarity and 934 ORFs observed in the genome of R-24608 were absent in the genome of the strain MR-S7.

Genes involved in denitrification are encoded by nitrate respiration (nar), nitrite respiration (nir), nitric oxide respiration (nor), and nitrous oxide respiration (nos) genes (24). Strain R-24608 harbors the operon narGHJI and upstream two narK genes encoding nitrate transporter proteins as previously described (25). Nitrite respiration, encoded by the nirSCFDLHJN operon was found in R-24608 and we observed that this genomic organization was spread in most of the Acidovorax species. The operon involved in nitric oxide respiration, norEFCBQD, was identified downstream from the nir operon as previously observed in Brucella suis 1330 (26). Nitrous oxide respiration, encoded by the nosDFYL operon, was located upstream of the nosR gene and the catabolic subunit nosZ was eliminated as previously found in Neisseria meningitidis MC58 (27).

Nucleotide sequence accession numbers.

This draft genome sequencing project has been deposited at the EMBL-EBI European Nucleotide Archive under accession numbers CYIG0100000001 to CYIG0100000152.