Functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation from Sphingomonas sp. strain A4

Evaluation of the application potential of bentonites in phenanthrene bioremediation by characterizing the biofilm community

Application of clay minerals in bioremediation has emerged as a new and promising research field. In this study, the application of calcinated bentonite (CB) and calcinated organobentonite (COB) in phenanthrene (Phe) bioremediation showed high Phe removal efficiency. Clone libraries based on 16S rRNA gene and scanning electronic microscopy showed that diverse taxa of bacteria formed biofilms on both COB and CB particles. The family Sphingomonadaceae was the major group and made up 18% and 23% of the COB and CB biofilm composition, respectively. All and 80% of dioxygenase genes from COB and CB biofilms were closely related to that of Sphingomonas sp., and others matched to that of Comamonas and Mycobacterium. The selective effect of COB on bacterial community was also evident. This study characterized for the first time the bacterial diversity of biofilm community and functional Phe degrading groups on bentonites particles, and provided useful information for future applications.

Characterization of the metabolic pathway involved in assimilation of acenaphthene in Acinetobacter sp. strain AGAT-W

Utilization of an enrichment technique led to isolation of a bacterium from municipal waste-contaminated soil in which acenaphthene was used as the sole source of carbon and energy. The isolate was identified as Acinetobacter sp. strain AGAT-W based on morphological, nutritional and biochemical characteristics and 16S rRNA sequence analysis. Characterization of metabolites by HPLC and GC-MS suggested hydroxylation of acenaphthene to 1-acenaphthenol, which was subsequently transformed to catechol via acenaphthenequinone, naphthalene-1,8-dicarboxylic acid, 1-naphthoic acid and salicylic acid before entering into the tricarboxylic acid cycle. Detection of key enzymes, viz., 1-acenaphthenol dehydrogenase, salicylaldehyde dehydrogenase and catechol 1,2-dioxygenase, in the cell-free extract of Acinetobacter sp. further supported the proposed degradation pathway. This study proposes a metabolic pathway involved in acenaphthene assimilation in strain AGAT-W.

The development of a liquid formulation of Pseudoxanthomonas sp. RN402 and its application in the treatment of pyrene-contaminated soil

AIM

To develop a liquid formulation of Pseudoxanthomonas sp. RN402 for prolonged storage and maintaining high survival rates and pyrene biodegradability.

METHODS AND RESULTS

Liquid formulations of RN402, designated as L-RN402, were prepared by suspending bacterial cells (10⁹ CFU ml⁻¹) in various buffers. Analysis found that phosphate buffer containing glycerol maintained high survival rate (94%) as well as pyrene biodegradability of bacteria after a 30-day storage. This L-RN402 could be stored at 30°C for at least 6 months. Bioaugmentation treatment with stored L-RN402 resulted in the complete degradation of pyrene (300 mg kg⁻¹) in soil microcosms within 4 weeks. RN402 could be detected by denaturing gradient gel electrophoresis throughout the period; moreover, real-time PCR indicated the presence of high number of nidA-containing bacteria.

CONCLUSIONS

A liquid formulation of RN402, an effective pyrene degrader, was developed by suspending RN402 in phosphate buffer containing 1% glycerol. This formulation could be stored at 30°C for at least 6 months and maintain high efficacy in the treatment of pyrene-contaminated soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work is the first description of a liquid formulation of pyrene-degrading bacteria for prolonged storage that retains biological activity for the treatment of environmental pollutants.

Molecular characteristics of xenobiotic-degrading sphingomonads

The genus Sphingomonas (sensu latu) belongs to the alpha-Proteobacteria and comprises strictly aerobic chemoheterotrophic bacteria that are widespread in various aquatic and terrestrial environments. The members of this genus are often isolated and studied because of their ability to degrade recalcitrant natural and anthropogenic compounds, such as (substituted) biphenyl(s) and naphthalene(s), fluorene, (substituted) phenanthrene(s), pyrene, (chlorinated) diphenylether(s), (chlorinated) furan(s), (chlorinated) dibenzo-p-dioxin(s), carbazole, estradiol, polyethylene glycols, chlorinated phenols, nonylphenols, and different herbicides and pesticides. The metabolic versatility of these organisms suggests that they have evolved mechanisms to adapt quicker and/or more efficiently to the degradation of novel compounds in the environment than members of other bacterial genera. Comparative analyses demonstrate that sphingomonads generally use similar degradative pathways as other groups of microorganisms but deviate from competing microorganisms by the existence of multiple hydroxylating oxygenases and the conservation of specific gene clusters. Furthermore, there is increasing evidence for the existence of plasmids that only can be disseminated among sphingomonads and which undergo after conjugative transfer pronounced rearrangements.

The Sphingomonas plasmid pCAR3 is involved in complete mineralization of carbazole

We determined the complete 254,797-bp nucleotide sequence of the plasmid pCAR3, a carbazole-degradative plasmid from Sphingomonas sp. strain KA1. A region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pNL1 isolated from the aromatic-degrading Novosphingobium aromaticivorans strain F199. The presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. Although pCAR3 is thought to carry clustered genes for conjugative transfer, a filter-mating assay between KA1 and a pCAR3-cured strain (KA1W) was unsuccessful, indicating that pCAR3 might be deficient in conjugative transfer. Several degradative genes were found on pCAR3, including two kinds of carbazole-degradative gene clusters (car-I and car-II), and genes for electron transfer components of initial oxygenase for carbazole (fdxI, fdrI, and fdrII). Putative genes were identified for the degradation of anthranilate (and), catechol (cat), 2-hydroxypenta-2,4-dienoate (carDFE), dibenzofuran/fluorene (dbf/fln), protocatechuate (lig), and phthalate (oph). It appears that pCAR3 may carry clustered genes (car-I, car-II, fdxI, fdrI, fdrII, and, and cat) for the degradation of carbazole into tricarboxylic acid cycle intermediates; KA1W completely lost the ability to grow on carbazole, and the carbazole-degradative genes listed above were all expressed when KA1 was grown on carbazole. Reverse transcription-PCR analysis also revealed that the transcription of car-I, car-II, and cat genes was induced by carbazole or its metabolic intermediate. Southern hybridization analyses with probes prepared from car-I, car-II, repA, parA, traI, and traD genes indicated that several Sphingomonas carbazole degraders have DNA regions similar to parts of pCAR3.