Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants

Abstract

In this study, following its isolation from contaminated soil, the genomic sequence of Pseudomonas alcaliphila strain JAB1 (=DSM 26533), a biphenyl-degrading bacterium, is reported and analyzed in relation to its extensive degradative capabilities. The P. alcaliphila JAB1 genome (GenBank accession no. CP016162) consists of a single 5.34 Mbp-long chromosome with a GC content of 62.5%. Gene function was assigned to 3816 of the 4908 predicted genes. The genome harbors a bph gene cluster, permitting degradation of biphenyl and many congeners of polychlorinated biphenyls (PCBs), a ben gene cluster, enabling benzoate and its derivatives to be degraded, and phe gene cluster, which permits phenol degradation. In addition, P. alcaliphila JAB1 is capable of cometabolically degrading cis-1,2-dichloroethylene (cDCE) when grown on phenol. The strain carries both catechol and protocatechuate branches of the β-ketoadipate pathway, which is used to funnel the pollutants to the central metabolism. Furthermore, we propose that clustering of MALDI-TOF MS spectra with closest phylogenetic relatives should be used when taxonomically classifying the isolated bacterium; this, together with 16S rRNA gene sequence and chemotaxonomic data analyses, enables more precise identification of the culture at the species level.Electronic supplementary materialThe online version of this article (10.1186/s40793-017-0306-7) contains supplementary material, which is available to authorized users.

Assessment of Biodegradation Efficiency of Polychlorinated Biphenyls (PCBs) and Petroleum Hydrocarbons (TPH) in Soil Using Three Individual Bacterial Strains and Their Mixed Culture

“…Alkanes with chain length C 10 -C 22 are substances most willingly used by bacteria in metabolic processes [39,46,66,67]. For the most effective bacterial Mycolicibacterium frederiksbergense IN53, the content of aliphatic hydrocarbons with carbon chain length nC 10 -nC 22 was reduced by 46.9%, and in the case of hydrocarbons with longer chains (nC 23 -nC 40 ), the degree of their reduction was around 39.5%, which proves a high degree of their biodegradation [39,51].…”

“…Moreover, the obtained results of chromatographic analyses enabled determination of biodegradability of individual hydrocarbon groups (Table S2). The rate of individual hydrocarbon groups removal was arranged in a decreasing order nC 10 -nC 22 > nC 23 -nC 28 > nC 29 -nC 40 . This removal scheme is probably related to the chemical structure of alkanes.…”

“…The TPH content in Soil B samples inoculated with IN129 and IN306 strains was reduced by 28.5% and 24.9%, respectively. The easiest to degrade were aliphatic hydrocarbons with chain lengths nC 10 -nC 22 A satisfactory effect of n-alkanes biodegradation as a result of Soil B inoculation is proven by indices of C 17 /Pr and C 18 /Ph biodegradation, which were substantially reduced (Table S2). The highest reduction was recorded during inoculation with the IN53 strain (C 17 /Pr from 0.818 to 0.473 and C 18 /Ph from 1.675 to 0.985) and with mixed culture M1 (C 17 /Pr from 0.818 to 0.522 and C 18 /Ph from 1.675 to 1.029).…”

“…IN306, and mixed culture M1, which showed that the strain Mycolicibacterium frederiksbergense IN53 features the highest biodegradation potential with respect to TPH. Table S2 and Figure 4 present a comparison of the content reduction for TPH; unidentified hydrocarbons; alkanes; ΣnC 10 -nC 22 , ΣnC 23 -nC 40 ; and individual n-alkanes in Soil B after inoculation with strains IN53, IN129, IN306, and mixed culture M1.…”

“…Individual coefficients of equation (2): k, (C/C x ) 0 , and the correlation coefficient (r 2 ) are specified in Table S3. A comparison of the biodegradation course is presented in a graphical form for PCBs, TriCBs, TetraCBs, PentaCBs, HexaCBs, HeptaCBs (Figure 7a), and for TPH, ΣnC 10 -nC 22 , and ΣnC 23 -nC 40 (Figure 7b). The first-order biodegradation constants (k) during inoculation of non-sterile Soil D with mixed culture M1 are as follows: PCBs (0.0109 d −1 ), TriPCB (0.0170 d −1 ), TetraCBs (0.0110 d −1 ), PentaCBs (0.0095 d −1 ), Hexa CBs (0.0082 d −1 ), and HeptaCBs (0.0050 d −1 ).…”