Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp.

Heavy metal acclimation of bacteria is of particular interest in many aspects. It could add to our understanding of adaptation strategies applied by bacteria, as well as help us in devising ways to use such adaptive bacteria for bioremediation. In this study, we have explored the changes in the DNA of an aquatic Gordonia sp. acclimated to silver, cadmium, and lead. We have measured the changes in the DNA extracted from the acclimated bacteria by using ATR-FTIR coupled with unsupervised and supervised pattern recognition algorithms. Although whole-cell FTIR studies do reveal nucleic acid changes, the special care should be taken when considering marker nucleic acid bands in such spectra, as various other cell or tissue constituents also yield IR bands in the same region. An FTIR study on isolated DNA can be used to avoid this problem. The IR spectral profiles of the DNA molecules revealed significant changes in the backbone and sugar conformations of upon acclimation. We then further analyzed the DNA's global cytosine-methylation patterns of the heavy metal-acclimated bacteria. We aimed to find out whether epigenetic mechanisms operate in bacteria for survival and growth in inhibitory heavy metal concentrations or not. We found hypermethylation in Cd acclimation but hypomethylation for both Pb and Ag in Gordonia sp. Our results imply that changes in the conformational and methylation states of DNA seem to let bacteria to thrive in otherwise inhibitory conditions and mark the involvement of epigenetic modulation in acclimation processes.

Impact of additives of commercial rubber compounds on the microbial and enzymatic degradation of poly(cis-1,4-isoprene).

Much fundamental research has already been performed to understand the mechanism of microbial rubber degradation. Due to the increasing amount of rubber waste, biotechnical methods to degrade that particular waste are strongly needed. The present study evaluates whether a microbial or an enzymatic process is more suitable for efficient biodegradation, due to less sensitivity towards rubber additives. Therefore we investigated the impact of 15 different frequently used rubber additives on cells of the potent rubber degrader Gordonia polyisoprenivorans VH2 and the enzyme Lcp1VH2. For this, cells were grown on poly(cis-1,4-isoprene) in presence of these rubber additives. Furthermore, the effect of those additives on the enzymatic cleavage of poly(cis-1,4-isoprene) by Lcp1VH2 was determined by in vitro studies. It was observed that additives, used to accelerate the vulcanization process, like N-cyclohexyl-2-benzothiazolesulfenamide and zinc-bis(N,N-dibenzyl-dithiocarbamate), are diminishing the growth of the microorganism depending on their concentration-higher toxicity with increasing concentration. In contrast, sulfur prevents cell growth, but does not affect Lcp1VH2. Stearic acid and paraffin wax were found to be consumed by G. polyisoprenivorans VH2. Plasticizers mainly prevent growth, but do not interfere with the enzyme activity. This study identified antioxidants as the most interfering group of additives for microbial and enzymatic rubber degradation. It was found that the in vitro degradation by Lcp1VH2 is much more resistant and less sensitive towards the investigated rubber additives, when compared to the in vivo approach. Therefore, an enzymatic process might be a promising method to enhance rubber degradation.

RDX degradation in bioaugmented model aquifer columns under aerobic and low oxygen conditions.

Degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in laboratory columns following biostimulation and bioaugmentation was investigated using sediment and groundwater from a contaminated aquifer at a US Navy facility. No RDX degradation was observed following aerobic biostimulation with either fructose or lactate (both 0.1 mM) prior to bioaugmentation. Replicate columns were then bioaugmented with either Gordonia sp. KTR9, Pseudomonas fluorescens I-C (Ps I-C), or both strains. Under aerobic conditions (influent dissolved oxygen (DO) >6 mg/L), RDX was degraded following the addition of fructose, and to a lesser extent with lactate, in columns bioaugmented with KTR9. No degradation was observed in columns bioaugmented with only Ps I-C under aerobic conditions, consistent with the known anaerobic RDX degradation pathway for this strain. When influent DO was reduced to <2 mg/L, good RDX degradation was observed in the KTR9-bioaugmented column, and some degradation was also observed in the Ps I-C-bioaugmented column. After DO levels were kept below 1 mg/L for more than a month, columns bioaugmented with KTR9 became unresponsive to fructose addition, while RDX degradation was still observed in the Ps I-C-bioaugmented columns. These results indicate that bioaugmentation with the aerobic RDX degrader KTR9 could be effective at sites where site geology or geochemistry allow higher DO levels to be maintained. Further, inclusion of strains capable of anoxic RDX degradation such as Ps I-C may facilitate bimodal RDX removal when DO levels decrease.

Effects of solution chemistry on antimicrobial activities of silver nanoparticles against Gordonia sp.

Silver nanoparticles (NPs) are the largest and fastest growing category of nanotechnology-based medicines and consumer products. Silver can have great toxicity to some aquatic organisms and, as a biocidal agent, may also damage or alter the most abundant and vulnerable beneficial microorganisms in the environment, such as Gordonia sp. However, considering the complex chemical background of natural waters, silver NPs can have complicated interactions with background chemicals such as chloride, surfactants, and dissolved natural organic matters (NOM). The results of this study show that the average particle size and dispersivity of silver NPs and the surface characteristics play an important role in the toxicity of silver NPs. Aggregation was enhanced for silver NPs in 10mM NaNO3, but not much in 10mM NaCl due to reactions with chloride. However, the presence of 3mM sodium dodecyl sulfate (SDS) or 8mgC/L Suwannee River (SR) NOM appeared to reduce the aggregation of silver NPs. Regarding the bactericidal effect of silver NPs, solubility analysis suggests silver NPs inactivate Gordonia sp. differently from Ag(+) and/or a slow release of Ag(+) from silver NPs. When the silver NP concentration was raised from 7.3 to 29.2mg/L in DI water, the log inactivation rate of Gordonia sp. increased from 0.16±0.04 to 0.45±0.13. However, with 29.2mg/L silver NPs the log inactivation rate reached 1.40±0.26 in 3mM SDS. The presence of SRNOM mitigated the bactericidal efficacy of silver NPs due to surface coating/adsorption. On the other hand, 10mM NaCl reduced the log inactivation rate to 0.07±0.07 due to the formation of likely less toxic silver chloride species, such as AgCl, AgCl2(-), AgCl3(2-), and AgCl4(3-).

Peritoneal-dialysis related peritonitis caused by Gordonia species: report of four cases and literature review.

AIM: To investigate the clinical course and outcome of peritoneal dialysis-associated peritonitis secondary to Gordonia species. METHOD: We reviewed all Gordonia peritonitis episodes occurring in a single dialysis unit from 1994 to 2013. RESULTS: During the study period, four episodes of Gordonia peritonitis were recorded. All were male patients. One patient responded to vancomycin therapy. One patient had refractory peritonitis despite vancomycin, but responded to imipenem and amikacin combination therapy. One patient had relapsing peritonitis and required catheter removal. The fourth patient had an elective Tenckhoff catheter exchange. No patient died of peritonitis. Causative organism was not fully identified until 7 to 18 days of peritonitis. CONCLUSION: Gordonia species is increasingly recognized to cause serious infections. In patients undergoing peritoneal dialysis, Gordonia peritonitis should be considered in case of refractory Gram-positive bacilli peritonitis, especially when the exact organism could not be identified one week after the onset of peritonitis. A close liaison with a microbiologist is needed for a timely diagnosis.

Analysis of petroleum biodesulfurization in an airlift bioreactor using response surface methodology.

For the first time, growing cells of Gordonia alkanivorans RIPI90A were used for biodesulfurization (BDS) of diesel. This process was carried out in an internal airlift bioreactor. BDS parameters (oil/water phase ratio and initial sulfur concentration) were optimized in flasks using response surface methodology. Predicted results were found to be in good agreement with experimental results. Initial sulfur concentration had a remarkable effect on BDS process. Maximum removal of sulfur (21 mg/l) can be achieved at oil/water phase ratio of 25% (v/v) and initial sulfur concentration of 28 mg/l. Moreover, effect of superficial gas velocity (Ug) and working volume (v) on volumetric gas liquid mass transfer coefficient was studied in an airlift bioreactor for BDS of diesel. The best results were achieved at Ug and v of 2.5l/min and 6.6l, respectively. Subsequently, BDS of diesel was investigated in an airlift bioreactor under optimized conditions. Sulfur reduction after 30 h was 14 mg/l.

Toxicity evaluation of 2-hydroxybiphenyl and other compounds involved in studies of fossil fuels biodesulphurisation.

The acute toxicity of some compounds used in fossil fuels biodesulphurisation studies, on the respiration activity, was evaluated by Gordonia alkanivorans and Rhodococcus erythropolis. Moreover, the effect of 2-hydroxybiphenyl on cell growth of both strains was also determined, using batch (chronic bioassays) and continuous cultures. The IC50 values obtained showed the toxicity of all the compounds tested to both strains, specially the high toxicity of 2-HBP. These results were confirmed by the chronic toxicity data. The toxicity data sets highlight for a higher sensitivity to the toxicant by the strain presenting a lower growth rate, due to a lower cells number in contact with the toxicant. Thus, microorganisms exhibiting faster generation times could be more resistant to 2-HBP accumulation during a BDS process. The physiological response of both strains to 2-HBP pulse in a steady-state continuous culture shows their potential to be used in a future fossil fuel BDS process.

Characterization of clinical isolates of Gordonia species in Japanese clinical samples during 1998-2008.

During 1998-2008, there were 31 strains of Gordonia species isolated from clinical specimens in our laboratory. Our identification of the 31 strains of Gordonia species showed that major pathogenic Gordonia species in Japan were classifiable, respectively into 14 and 13 strains of Gordonia sputi and Gordonia bronchialis. The four remaining strains were identified as three Gordonia species: G. aichiensis (2 strains), and G. terrae (1 strain), and G. otitidis (1 strain). Results of drug susceptibility tests for these 31 strains of Gordonia isolates are reported herein.

Evidence for the role of zinc on the performance of dibenzothiophene desulfurization by Gordonia alkanivorans strain 1B.

Gordonia alkanivorans strain 1B is able to desulfurize dibenzothiophene (DBT) to 2-hydroxybiphenyl (2-HBP), the final product of the 4S pathway. However, both the cell growth and the rate of desulfurization can be largely affected by the nutrient composition of the growth medium due to cofactor requirements of many enzymes involved in the biochemical pathways. In this work, the effect of several metal ions on the growth and DBT desulfurization by G. alkanivorans was studied. From all the metal ions tested, only the absence of zinc significantly affected the cell growth and the desulfurization rate. By increasing the concentration of Zn from 1 to 10 mg L(-1), 2-HBP productivity was improved by 26%. The absence of Zn(2+), when sulfate was also used as the only sulfur source, did not cause any difference in the bacterial growth. Resting cells grown in the presence of Zn(2+) exhibited a 2-HBP specific productivity of 2.29 micromol g(-1) (DCW) h(-1), 7.6-fold higher than the specific productivity obtained by resting cells grown in the absence of Zn(2+) (0.30 micromol g(-1) (DCW) h(-1)). These data suggests that zinc might have a key physiological role in the metabolism of DBT desulfurization.

Effect of hypochloride on microbial ecology of bulking and foaming activated sludge treatment for tannery wastewater.

This study investigates the effect of hypochloride application for controlling bulking and foaming on the microbial ecology of an activated sludge system treating tannery wastewater. Detailed characterization of the wastewater treatment influent and effluent is also reported for the study period. During the study, bulking and foaming are first monitored with a sudden burst in the sludge volume index over 250 mL g(-1), creating a significant deterioration of the effluent quality. The corresponding upset in the microbial ecology is the combined excessive proliferation of M. parvicella, N. limicola II and Gordona (Nocardia) spp., but mainly triggered by Gordona contamination of the floc structure and the rapid outward growth of this filamentous microorganism extending to adjacent flocs. Chlorine application at an average rate of 3 g Cl(-1)(kg MLSS.day)(-1) for 12 days provide an effective solution for bulking and foaming, restoring the effluent quality. It destroys filamentous texture between the flocs, leaving only a lot of loose and chopped filament fragments and, totally removes the Gordona spp. from solution which retrieves back into the flocs. Therefore, chlorine remediation of bulking and foaming, although temporarily effective, is only superficial as the Gordona seeding inside the floc remains intact and potentially available for excessive growth in the next favorable conditions.

Proposal of a method for the genetic transformation of Gordonia jacobaea.

AIMS: Gordonia jacobaea is a recently isolated bacterial species with potential industrial application on account of its ability to store large quantities of trans-canthaxanthin. Its genetic manipulation is, however, difficult and cumbersome owing to the presence of mycolic acids in the cell wall and, especially, because of current lack of knowledge about its basic genetics. The present work describes a method for the genetic transformation of G. jacobaea. METHODS AND RESULTS: Gordonia jacobaea was grown in media supplemented with different glycine, penicillin G and isoniazid concentrations. The temperature, carbon source, growth phase and ultrasounds were analyzed for improving the method efficiency. The cells were finally transformed by electroporation. Finally, the method was applied to Brevibacteriumlactofermentum and Gordonia bronchialis. CONCLUSIONS: The growth of G. jacobaea in the presence of glycine and isoniazid is essential for obtaining electrocompetents cells. The temperature, growth phase and ultrasounds appeared as the main factors for increasing the transformation efficiency. The use of shuttle plasmids became necessary. The method described can be used with other Corynebacteria species. SIGNIFICANCE AND IMPACT OF THE STUDY: Because of the importance of the CNM group (Corynebacteria, Nocardia and Mycobacteria genera) in different areas such as industry, bioremediation improve the knowledge of their molecular mechanisms are becoming essential. The method described here improves the genetic manipulation of this group of bacteria.