Polaromonas naphthalenivorans

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A Microbial Biorealm page on the genus Polaromonas naphthalenivorans


Higher order taxa

Bacteria; Protobacteria; Betaprotobacteria; Burkholderiales; Comamonadaceae, Polaromonas


NCBI: Taxonomy

Polaramonas napthalenivorans CJ2

Description and significance

P. naphthalenivorans is an aquatic gram-negative, non-spore forming, non-motile coccus that is capable of growth with naphthalene as its sole carbon and energy source. (2)

The genus Polaromonas was proposed in 1996 and contained only one species, P. vacuolata, until 2004 when P. naphthalenivorans was discovered. (3) Strain CJ2 was isolated from coal-tar-contaminated freshwater sediment in South Glens Falls, New York, USA. (1) It was discovered using stable isotope probing (SIP), a technique that enabled researchers to follow the flow of labeled carbon atoms from naphthalene to the DNA of naturally occurring microbial populations in the environment such as P. naphthalenivorans. (4)

It is important to have the genome of P. naphthalenivorans sequenced because of its ability to efficiently remove naphthalene from solution. Naphthalene is a polycyclic aromatic hydrocarbon (PAH) that can cause contamination of soil, water or sediment and can be toxic and/or carcinogenic. (2)

Genome structure

The complete genome of P. naphthalenivorans is 4,410,291 base pairs long, with a G+C content of 61.5%. (2,5) It consists of a circular chromosome that is 4.4Mbp long and encodes 4084 proteins and eight circular plasmids that collectively encode 2195 proteins. pPNAP01 is .35Mbp long and encodes 205 proteins. pPNAP02 is .19Mbp long and encodes 161 proteins. pPNAP03 is .17Mbp long and encodes 155 proteins. pPNAP04 is .14Mbp long and encodes 136 proteins. pPNAP05 is .059Mbp long and encodes 52 proteins. pPNAP06 is .022Mbp long and encodes 20 proteins. pPNAP07 is .0099Mbp long and encodes 11 proteins. pPNAP08 is .0065Mbp long and encodes 5 proteins. (6)

Comparative 16S rDNA analysis showed that P. naphthalenivorans is related to the family Comamonadaceae, with its nearest phylogenetic relative being P. vacuolata (97.1% similar). (2)

The naphthalene catabolic genes of P. naphthalenivorans are separated into a large cluster (25,748bp) and small cluster (14,217bp) and many of these genes are homologous to the catabolic genes of Ralstonia U2, an organism that uses the gentisate pathway to convert naphthalene to central metabolites. Three open reading frames present in Ralstonia U2 (nagY, nagM and nagN) are missing in P. naphthalenivorans. (6)

Cell structure and metabolism

Unlike other species from the genus Polaromonas, P. naphthalenivorans does not have flagella. (2)

P. naphthalenivorans grows optimally at a temperature of 20oC (can grow between 4oC and 35oC) and pH of 7.0-7.5 (can grow between pH 6.0 and pH 9.0). It can be found as individual organisms that are 1-4um in diameter or in small clusters of loosely adherent cells. Colonies appear circular and convex, with a smooth surface and no pigment production. (2)

P. naphthalenivorans has the unusual ability to store all three common types of prokaryotic cellular reserve materials (PHA, polyglucose and polyphosphate granules) during its exponential growth phase. (2)

P. naphthalenivorans is an aerobic heterotroph that is capable of utilizing glucose and other simple sugars, and can grow with naphthalene as its sole carbon source. (2) Naphthalene degradation occurs through two pathways, both of which are chromosomally encoded. These two pathways are the naphthalene degradation upper pathway and naphthalene degradation lower pathway. The upper pathway converts naphthalene to salicylate and the lower pathway converts salicylate to pyruvate and acetyl coenzyme A via meta cleavage. (6)


This organism is found in aquatic environments that are between 4oC and 25oC, and at a pH of 6.0 and 9.0. (2)

P. naphthalenivorans has no known interactions with eukaryotes and is not known to be pathogenic.

There is potential for the use of P. naphthalenivorans for bioremediation at sites of contamination by polycyclic aromatic hydrocarbons (PAHs) such as naphthalene because of its ability to efficiently remove naphthalene from solution. This is important because polycyclic aromatic hydrocarbons can cause contamination of soil, water or sediment and can be toxic and/or carcinogenic. (2)


There are no known diseases caused by P. naphthalenivorans CJ2.


(1) NCBI: Polaromonas naphthalenivorans. <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=365044&lvl=3&lin=f&keep=1&srchmode=1&unlock>

(2) Jeon CO, Park W, Ghiorse WC, Madsen EL. "Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment". International Journal of Systematic and Evolutionary Microbiology. 2004. Volume 54. p. 93-97.

(3) Kampfer P, Busse HJ, Falsen E. "Polaromonas aquatica sp. nov., isolated from tap water". International Journal of Systematic and Evolutionary Microbiology. 2006. Volume 56. p. 605-608.

(4) Jeon CO, et al. "Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc. Natl Acad. Sci. USA. 2003. Volume 100. p. 13591–13596

(5) NCBI: Polaromonas naphthalenivorans CJ2, complete genome. <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=121602919>

(6) Jeon CO, Park M, Ro HS, Park W, Madsen EL. "The Naphthalene Catabolic (nag) Genes of Polaromonas naphthalenivorans CJ2: Evolutionary Implications for Two Gene Clusters and Novel Regulatory Control". Applied and Environmental Microbiology. 2006. Volume 72. p. 1086-1095.

Edited by Christina Hopson, student of Rachel Larsen

Edited by KLB