Genome Sequences of Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R, Two Efficient Carbazole-Degrading Strains

Abstract

Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R are two efficient carbazole-degrading pseudomonad strains. Here we present 4.63-and 4.70-Mb assemblies of their genomes. Their annotated key genes for carbazole catabolism are similar, which may provide further insights into the molecular mechanism of carbazole degradation in Pseudomonas. Carbazole and its derivatives in N-heterocyclic compounds have a dioxin-like structure, and some of them are toxic and mutagenic (5). They are most common in creosote, crude oil, and shale oil and are environmental pollutants and recalcitrant molecules, as well as raw materials for dyes, reagents, explosives, insecticides, lubricants, etc. (11). Microbial degradation is an effective way to remove such pollutants from the environment (1, 13). The genus Pseudomonas is a diverse group and has the ability to degrade various aromatic compounds, including carbazole (2, 12). Moreover, some strains of this genus have drawn much attention because of their denitrification and nitrogen fixation abilities (6).We have previously isolated Pseudomonas luteola XLDN4-9 (CCTCC M 205094) and Pseudomonas stutzeri XLDN-R (CCTCC AB 2012149) from soil samples on the basis of their abilities to utilize carbazole as their sole source of carbon and nitrogen. They can degrade 99 and 97% of the carbazole present (500 mg/liter) in 16 and 13 h, respectively. It was reported that the carbazole degradation ability of strain XLDN4-9 could be enhanced in the presence of a nonaqueous-phase liquid (8). The derivatives of carbazole were also biodegradable by this strain (7).The genomes of strains XLDN4-9 and XLDN-R were sequenced using the Illumina HiSeq 2000 system. The reads were assembled into 232 and 167 contigs, respectively, using Velvet 1.2.03. The largest contigs of strains XLDN4-9 and XLDN-R are 265,571 and 235,018 bp. The draft genome sequence of strain XLDN4-9 consists of 4,627,073 bases with a GϩC content of 54.2%, while the draft genome sequence of strain XLDN-R contains 4,695,416 bases with a GϩC content of 63.9%, which is in accordance with other P. stutzeri strains (6, 14, 15). There were 45 and 58 predicted tRNAs, 4,454 and 4,247 coding sequences, and 444 and 496 subsystems in strains XLDN4-9 and XLDN-R, respectively.As expected, the genomes of strains XLDN4-9 and XLDN-R encode a diverse array of related proteins with predicted roles in the metabolism of aromatic compounds, such as biphenyl, benzoate, and chloroaromatic compounds. With respect to carbazole degradation, the car genes in strains XLDN4-9 and XLDN-R were found to be clustered in an arrangement similar to that of the car cluster in Pseudomonas sp. strain CA10 (10), which is different from that of Sphingobium yanoikuyae 4).The genomes of strains XLDN4-9 and XLDN-R contain 59 and 69 contigs involved in the degradation of aromatic compounds and multiple predicted pathways of protection against environmental stress. In our previous study, we found that carotenoids produced by strain XLDN2-5 might play a positive role in the degrad...

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

“…fluorescens, putida, alcaligenes ) have been reported to degrade the fatty acid derivatives, its implicit presence in RL indicates at its differential capacity to use α-linoleic acid as carbon source [ 75 ]. Similarly, when compared to the other genomes (n = 17), P. stutzeri XLDN-R was found to exclusively possess the carbazole degradation pathway which was further supported by the fact that this particular strain was isolated from soil for its differential ability to utilize carbazole as sole source of both carbon and nitrogen [ 69 ]. 3-chloroacrylic acid degradation pathway was found uniquely in P. stutzeri CCUG 29243 indicating at its capability of using 3-chloroacrylic acid as carbon source [ 76 ].…”

“…However, two sub-groups were identified for P. stutzeri clade, first with P. stutzeri CCUG 29243 and ATCC 14405, and second containing P. stutzeri A1501, T13 and XLDN-R (Figure 1 A). This distinct deviation could be accredited to the ecotype status resulting from the niche specific adaptations, as P. stutzeri ATCC 14405 and CCUG 29243 both are marine isolates [ 66 , 67 ] however, A1501, T13, and XLDN-R, are well-known soil/sludge dwellers [ 68 , 69 ]. ANI values for P. stutzeri group (≤88.2%) were also not in accordance with species demarcation value of 95-96% [ 65 ] indicating towards intra species level divergence (Figure 1 B).…”

Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas stutzeri KF716 (NBRC 110668)

“…The coding sequences were classified into 2,965 subsystems, the most abundant of which were metabolism of amino acids derivatives ( n = 314 CDSs) and carbohydrates ( n = 273); cofactors, vitamins, prosthetic groups, and pigments ( n = 258); and protein metabolism ( n = 250). A comparison of genome sequences available in the RAST data sets revealed that P. stutzeri A1501 ( 11 ) is the closest neighbor of the KF716 strain with a score of 534, followed by P. stuzeri XLDN-R with a score of 462 ( 12 ). The bph-sal element, similar to that of P. putida KF715 identified previously ( 2 ), was found in a single contig.…”

Draft Genome of the Nitrogen-Fixing Bacterium Pseudomonas stutzeri Strain KOS6 Isolated from Industrial Hydrocarbon Sludge

“…Genome assemblies for ten strains of P. stutzeri , including one type strain (clinic CGMCC 1.1803 [3]), one naphthalene-degrading strain (CCUG 29243 [4]), two nitrogen-fixing strains (A1501 [5], DSM 4166 [6]), one carbazole-degrading (XLDN-R [7]), one arsenite-oxidizing strain (TS44 [8]), some model strains (denitrification CCUG 16156 [9], T13 [10]), a natural transformation strain (DSM 10701 [11]), and a lactate utilization strain (SDM-LAC [12]), are already available at GenBank. We used them for comparison with the genome of strain KOS6.…”