Purification and characterization of a novel medium-chain ribitol dehydrogenase from a lichen-associated bacterium Sphingomonas sp

Sugar alcohols (polyols) are abundant carbohydrates in lichen-forming algae and transported to other lichen symbionts, fungi, and bacteria. Particularly, ribitol is an abundant polyol in the lichen Cetraria sp. Polyols have important physiological roles in lichen symbiosis, but polyol utilization in lichen-associated bacteria has been largely unreported. Herein, we purified and characterized a novel ribitol dehydrogenase (RDH) from a Cetraria sp.-associated bacterium Sphingomonas sp. PAMC 26621 grown on a minimal medium containing D-ribitol (the RDH hereafter referred to as SpRDH). SpRDH is present as a trimer in its native form, and the molecular weight of SpRDH was estimated to be 39 kDa by SDS-PAGE and 117 kDa by gel filtration chromatography. SpRDH converted D-ribitol to D-ribulose using NAD+ as a cofactor. As far as we know, SpRDH is the first RDH belonging to the medium-chain dehydrogenase/reductase family. Multiple sequence alignments indicated that the catalytic amino acid residues of SpRDH consist of Cys37, His65, Glu66, and Glu157, whereas those of short-chain RDHs consist of Ser, Tyr, and Lys. Furthermore, unlike other short-chain RDHs, SpRDH did not require divalent metal ions for its catalytic activity. Despite SpRDH originating from a psychrophilic Arctic bacterium, Sphingomonas sp., it had maximum activity at 60°C and exhibited high thermal stability within the 4-50°C range. Further studies on the structure/function relationship and catalytic mechanism of SpRDH will expand our understanding of its role in lichen symbiosis.

Growth, Viability, and Death of Planktonic and Biofilm Sphingomonas desiccabilis in Simulated Martian Brines

Aqueous solutions on Mars are theorized to contain very different ion compositions than those on Earth. To determine the effect of such solutions on typical environmental micro-organisms, which could be released from robotic spacecraft or human exploration activity, we investigated the resistance of Sphingomonas desiccabilis to brines that simulate the composition of martian aqueous environments. S. desiccabilis is a desiccation-resistant, biofilm-forming microbe found in desert crusts. The viability of cells in both planktonic and biofilm forms was measured after exposure to simulated martian brines. Planktonic cells showed a loss of viability over the course of several hours in almost all of the seven brines tested. Biofilms conferred greater resistance to all the brines, including those with low water activity and pH, but even cells in biofilms showed a complete loss of viability in <6 h in the harsher brines and in <2 days in the less harsh brines. One brine, however, allowed the microbes to maintain viability over several days, despite having a water activity and pH lower and ionic strength higher than brines that reduced viability over the same timescales, suggesting important ion-specific effects. These data show that biofilm-forming cells have a greater capacity to resist martian aqueous extremes, but that evaporative or deliquescent brines are likely to be destructive to many organisms over relatively short timescales, with implications for the habitability of Mars and for micro-organisms dispersed by robotic or human explorers.

Stereoselective accumulations of hexachlorocyclohexanes (HCHs) are correlated with Sphingomonas spp. in agricultural soils across China

The wide usage of hexachlorocyclohexanes (HCHs) as pesticides has caused soil pollution and adverse health effects through direct contact or bioaccumulation in the food chain. This study quantified major HCH isomers in farmland topsoils across China, and evaluated their correlations with microbial community structure, function, and abiotic variables (e.g., moisture, pH, and temperature). Recalcitrant β-HCH was more abundant than α-, γ-, and δ-HCHs, and α-HCH enantiomeric fractions (EF) were larger than 0.5, indicating preferential degradation of (-)-α-HCH. Sphingomonas was not only a predominant population (especially in samples collected in the south), but also a promising biomarker indicating total- and β-HCH residuals, and EF values of α-HCH. Soil moisture and temperature were among the most influential factors that structured the diversity and function of soil microbial communities. The results suggested that increasing soil moisture (in the range of 5-45%) would benefit the growth of HCH-degrading populations and the enrichment of HCH-degradation related pathways. Revealing the site-specific relationships between topsoil physical, chemical, and microbial properties will benefit the in situ bioremediation of farmlands with relatively low HCH residuals across the world.

Differential regulation of phenanthrene biodegradation process by kaolinite and quartz and the underlying mechanism

Natural and cost-effective materials such as minerals can serve as supportive matrices to enhance biodegradation of polycyclic aromatic hydrocarbons (PAHs). In this study we evaluated and compared the regulatory role of two common soil minerals, i.e. kaolinite and quartz in phenanthrene (a model PAH) degradation by a PAH degrader Sphingomonas sp. GY2B and investigated the underlying mechanism. Overall kaolinite was more effective than quartz in promoting phenanthrene degradation and bacterial growth. And it was revealed that a more intimate association was established between GY2B and kaolinite. Si and O atoms on mineral surface were demonstrated to be involved in GY2B-mineral interaction. There was an higher polysaccharide/lipid content in the EPS (extracellular polymeric substances) secreted by GY2B on kaolinite than on quartz. Altogether, these results showed that differential bacterial growth, enzymatic activity, EPS composition as well as the interface interaction may explain the effects minerals have on PAH biodegradation. It was implicated that different interface interaction between different minerals and bacteria can affect microbial behavior, which ultimately results in different biodegradation efficiency.

Inoculation of soil with an Isoproturon degrading microbial community reduced the pool of "real non-extractable" Isoproturon residues

During pesticides degradation, biogenic non-extractable residues ("apparent NER") may not share the same environmental fate and risks with the "real NER" that are bound to soil matrix. It is not clear how microbial community (MC) inoculation for pesticides degradation would influence the NER composition. To investigate degradation efficiency of pesticides Isoproturon (IPU) and NER composition following MC inoculation, clay particles harboring MC that contains the IPU degrading strain, Sphingomonas sp., were inoculated into soil receiving ¹⁴C-labeled IPU addition. Mineralization of IPU was greatly enhanced with MC inoculation that averagely 55.9% of the applied ¹⁴C-IPU was consumed up into ¹⁴CO₂ during 46 days soil incubation. Isoproturon degradation was more thorough with MC than that in the control: much less amount of metabolic products (4.6% of applied IPU) and NER (35.4%) formed in MC treatment, while the percentages were respectively 30.3% for metabolites and 49.8% for NER in the control. Composition of NER shifted with MC inoculation, that relatively larger amount of IPU was incorporated into the biogenic "apparent NER" in comparison with "real NER". Besides its well-recognized role on enhancing mineralization, MC inoculation with clay particles benefits soil pesticides remediation in term of reducing "real NER" formation, which has been previously underestimated.

Biofilm forming ability of Sphingomonas paucimobilis isolated from community drinking water systems on plumbing materials used in water distribution

Sphingomonas paucimobilis, an oligotroph, is well recognized for its potential for biofilm formation. The present study explored the biofilm forming ability of a strain isolated from municipal drinking water on plumbing materials. The intensity of biofilm formation of this strain on different plumbing materials was examined by using 1 × 1 cm² pieces of six different pipe materials, i.e. polyvinyl chloride (PVC), polypropylene (PP), polyethylene (PE), aluminium (Al), copper (Cu) and rubber (R) and observing by staining with the chemical chromophore, Calcofluor. To understand whether biofilm formation occurs under flow through conditions, a laboratory-scale simulated distribution system, comprised of the above materials was fabricated. Biofilm samples were collected from the designed system at different biofilm ages (10, 40 and 90 hours old) and enumerated. The results indicated that the biofilm formation occurred on all plumbing materials with Cu and R as exceptions. The intensity of biofilm formation was found to be maximum on PVC followed by PP and PE. We also demonstrated the chemical chromophore (Calcofluor) successfully for rapid and easy visual detection of biofilms, validated by scanning electron microscope (SEM) analysis of the plumbing materials. Chlorination has little effect in preventing biofilm development.

Effects of synthetic iron and aluminium oxide surface charge and hydrophobicity on the formation of bacterial biofilm

In this research, bacterial cell attachments to hematite, goethite and aluminium hydroxide were investigated. The aim was to study the effects of these minerals' hydrophobicity and pH-dependent surface charge on the extent of biofilm formation using six genetically diverse bacterial strains: Rhodococcus spp. (RC92 & RC291), Pseudomonas spp. (Pse1 & Pse2) and Sphingomonas spp. (Sph1 & Sph2), which had been previously isolated from contaminated environments. The surfaces were prepared in a way that was compatible with the naturally occurring coating process in aquifers: deposition of colloidal particles from the aqueous phase. The biofilms were evaluated using a novel, in situ and non-invasive technique developed for this purpose. A manufactured polystyrene 12-well plate was used as the reference surface to be coated with synthesized minerals by deposition of their suspended particles through evaporation. Planktonic phase growth indicates that it is independent of the surface charge and hydrophobicity of the studied surfaces. The hydrophobic similarities failed to predict biofilm proliferation. Two of the three hydrophilic strains formed extensive biofilms on the minerals. The third one, Sph2, showed anomalies in contrast to the expected electrostatic attraction between the minerals and the cell surface. Further research showed how the solution's ionic strength affects Sph2 surface potential and shapes the extent of its biofilm formation; reducing the ionic strength from ≈200 mM to ≈20 mM led to a tenfold increase in the number of cells attached to hematite. This study provides a technique to evaluate biofilm formation on metal-oxide surfaces, under well-controlled conditions, using a simple yet reliable method. The findings also highlight that cell numbers in the planktonic phase do not necessarily show the extent of cell attachment, and thorough physicochemical characterization of bacterial strains, substrata and the aquifer medium is fundamental to successfully implementing any bioremediation projects.

Ecological succession of the microbial communities of an air-conditioning cooling coil in the tropics

Air-conditioning systems harbor microorganisms, potentially spreading them to indoor environments. While air and surfaces in air-conditioning systems are periodically sampled as potential sources of indoor microbes, little is known about the dynamics of cooling coil-associated communities and their effect on the downstream airflow. Here, we conducted a 4-week time series sampling to characterize the succession of an air-conditioning duct and cooling coil after cleaning. Using an universal primer pair targeting hypervariable regions of the 16S/18S ribosomal RNA, we observed a community succession for the condensed water, with the most abundant airborne taxon Agaricomycetes fungi dominating the initial phase and Sphingomonas bacteria becoming the most prevalent taxa toward the end of the experiment. Duplicate air samples collected upstream and downstream of the coil suggest that the system does not act as ecological filter or source/sink for specific microbial taxa during the duration of the experiment.

The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health

Plants are colonized by a variety of bacteria, most of which are not pathogenic. Currently, the plant responses to phyllosphere commensals or to pathogen infection in the presence of commensals are not well understood. Here, we examined the transcriptional response of Arabidopsis thaliana leaves to colonization by common commensal bacteria in a gnotobiotic system using RNA sequencing and conducted plant mutant assays. Arabidopsis responded differently to the model bacteria Sphingomonas melonis Fr1 (S.Fr1) and Methylobacterium extorquens PA1 (M.PA1). Whereas M.PA1 only marginally affected the expression of plant genes (< 10), S.Fr1 colonization changed the expression of almost 400 genes. For the latter, genes related to defense responses were activated and partly overlapped with those elicited by the pathogen Pseudomonas syringae DC3000 (Pst). As S.Fr1 is able to mediate plant protective activity against Pst, we tested plant immunity mutants and found that the pattern-recognition co-receptor mutant bak1/bkk1 showed attenuated S.Fr1-dependent plant protection. The experiments demonstrate that the plant responds differently to members of its natural phyllosphere microbiota. A subset of commensals trigger expression of defense-related genes and thereby may contribute to plant health upon pathogen encounter.

Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay

Sphingomonas wittichii strain RW1 (RW1) is one of the few strains that can grow on dibenzo-p-dioxin (DD). We conducted a transcriptomic study of RW1 using RNA-Seq to outline transcriptional responses to DD, dibenzofuran (DF), and the smectite clay mineral saponite with succinate as carbon source. The ability to grow on DD is rare compared to growth on the chemically similar DF even though the same initial dioxygenase may be involved in oxidation of both substrates. Therefore, we hypothesized the reason for this lies beyond catabolic pathways and may concern genes involved in processes for cell-substrate interactions such as substrate recognition, transport, and detoxification. Compared to succinate (SUC) as control carbon source, DF caused over 240 protein-coding genes to be differentially expressed, whereas more than 300 were differentially expressed with DD. Stress response genes were up-regulated in response to both DD and DF. This effect was stronger with DD than DF, suggesting a higher toxicity of DD compared to DF. Both DD and DF caused changes in expression of genes involved in active cross-membrane transport such as TonB-dependent receptor proteins, but the patterns of change differed between the two substrates. Multiple transcription factor genes also displayed expression patterns distinct to DD and DF growth. DD and DF induced the catechol ortho- and the salicylate/gentisate pathways, respectively. Both DD and DF induced the shared down-stream aliphatic intermediate compound pathway. Clay caused category-wide down-regulation of genes for cell motility and chemotaxis, particularly those involved in the synthesis, assembly and functioning of flagella. This is an environmentally important finding because clay is a major component of soil microbes’ microenvironment influencing local chemistry and may serve as a geosorbent for toxic pollutants. Similar to clay, DD and DF also affected expression of genes involved in motility and chemotaxis.

Enhanced degradation of phenol by Sphingomonas sp. GY2B with resistance towards suboptimal environment through adsorption on kaolinite

The effects of clay minerals on microbial degradation of phenol under unfavorable environmental conditions were investigated. Degradation of phenol by Sphingomonas sp. GY2B adsorbed on kaolinite, montmorillonite, and vermiculite were evaluated in comparison with free bacteria under optimal conditions. Kaolinite was found to be the most effective in accelerating degradation rate (reducing the degradation time) as well as improving degradation efficiency (increasing the percentage of phenol degraded), with GY2B/kaolinite complex achieving a degradation efficiency of 96% within 6 h. GY2B adsorbed on kaolinite was more competent than free GY2B in degradation under conditions with high phenol concentrations and at alkaline pH. Kaolinite reduced the time required for degradation by 8-12 h and improved the degradation efficiency by as much as 82% at high phenol concentrations. Meanwhile, the GY2B/kaolinite complex reduced the degradation time by 24 h and improved the degradation efficiency by 46% at pH 12. The improvement was partially due to the buffering effects of kaolinite. It was also shown that Cr(VI) and kaolinite synergistically enhanced the degradation by GY2B, with Cr(VI) and kaolinite both increasing the degradation rate and kaolinite being primarily responsible for enhanced degradation efficiency. These results showed one of the common clay minerals, kaolinite, is able to significantly improve the microbial degradation performance, and protect microorganisms against unfavorable environment. Kaolinite can collaborate with Cr(VI) to further improve the microbial degradation performance. It is implied that clay minerals have great potential to be applied in enhancing the biodegradation of phenol.

Effects of nano bamboo charcoal on PAHs-degrading strain Sphingomonas sp. GY2B

Nano bamboo charcoal (NBC) has been commonly used in the production of textiles, plastics, paint, etc. However, little is known regarding their effects towards the microorganisms. The effects of NBC on phenanthrene degrading strain Sphingomonas sp. GY2B were investigated in the present study. Results showed that the addition of NBC could improve the phenanthrene removal by Sphingomonas sp. GY2B, with removal efficiencies increased by 10.29-18.56% in comparison to the control at 24h, and phenanthrene was almost completely removed at 48h. With the presence of low dose of NBC (20 and 50mgL(-1)), strain GY2B displayed a better growth at 6h, suggesting that NBC was beneficial to the growth of GY2B and thus resulting in the quick removal of phenanthrene from water. However, the growth of strain GY2B in high dose of NBC (200mgL(-1)) was inhibited at 6h, and the inhibition could be attenuated and eliminated after 12h. NBC-effected phenanthrene solubility experiment suggested that NBC makes a negligible contribution to the solubilization of phenanthrene in water. Results of electronic microscopy analysis (SEM and TEM) indicated NBC may interact with the cell membrane, causing the enhanced membrane permeability and then NBC adsorbed on the membrane would enter into the cells. The findings of this work would provide important information for the future usage and long-term environmental risk assessment of NBC.

Degradation of triclocarban by a triclosan-degrading Sphingomonas sp. strain YL-JM2C

Bacterial degradation plays a vital role in determining the environmental fate of micropollutants like triclocarban. The mechanism of triclocarban degradation by pure bacterium is not yet explored. The purpose of this study was to identify metabolic pathway that might be involved in bacterial degradation of triclocarban. Triclosan-degrading Sphingomonas sp. strain YL-JM2C was first found to degrade up to 35% of triclocarban (4 mg L(-1)) within 5 d. Gas chromatography-mass spectrometry detected 3,4-dichloroaniline, 4-chloroaniline and 4-chlorocatechol as the major metabolites of the triclocarban degradation. Furthermore, total organic carbon results confirmed that the intermediates, 3,4-dichloroaniline (4 mg L(-1)) and 4-chloroaniline (4 mg L(-1)) could be degraded up to 77% and 80% by strain YL-JM2C within 5 d.

Removal of environmental estrogens by bacterial cell immobilization technique

Contamination of steroidal estrogens in the environment has raised a great public concern, and therefore, developing an effective method for removal of trace amount of environmental estrogens is necessary. In this study, two estrogen-degrading bacteria were isolated from activated sludge and were identified as strain Sphingomonas sp. AHC-F and strain Sphingobium sp. AX-B. They were capable of utilizing estrone (E1) and 17ß-estradiol (E2) as sole carbon and energy source. Cell immobilization technique was applied to these two estrogen-degrading bacteria. Confocal laser-scanning microscopy images with live and dead staining of entrapped bacterial cells showed that most bacteria were present inside the porous structure and were mostly viable after immobilization procedures. Batch estrogen degradation study showed that immobilized strains AHC-F and AX-B could effectively degrade 2 mg/L of E2 and its metabolite E1. Immobilized bacteria column reactors using pure culture of strain AHC-F were set up for continuous-flow removal of 850 ng/L of E2 in the influent. The removal efficiency of E2 and equivalent estrogenic quantity of E2 (EEQ) could achieve 94 and 87% under 12 h hydraulic retention time (HRT), respectively. Increasing HRT could further improve the removal efficiency of EEQ. When the HRT increased to 72 h, the effluent concentrations of E2 and E1 were not detectable by gas chromatography-mass spectrometry. Our results also proved that most of the estrogen removal was due to biodegradation. This study has demonstrated the potential use of immobilized bacteria technique for the removal of environmental estrogens.

The biosorption capacity of biochar for 4-bromodiphengl ether: study of its kinetics, mechanism, and use as a carrier for immobilized bacteria

Polybrominated diphenyl ethers (PBDEs) are known as ubiquitous pollutants in ecological systems and thus pose a great threat to the health of humans and other organisms due to their bioamplification and bioaccumulation along the food chain. The present study was designed to investigate the biosorption capacity of biochar for the removal of 4-monobromodiphengl ether and its synergistic effect when used as a carrier to immobilize the 4-monobromodiphengl ether-degrading strain Sphingomonas sp. DZ3. The raw biochar material was prepared by pyrolyzing maize straw at 350 °C under oxygen-limited conditions. The maximum biosorption capacity of biochar for 4-bromodiphengl ether was determined to be 50.23 mg/L under an initial concentration of 800 mg/L at pH 7.0 and 40 °C. The data obtained from the biosorption studies were fitted successfully with the pseudo-first-order kinetic and Freundlich isotherm models. The Weber-Morris model analysis indicated that intraparticle diffusion was the limiting step in the biosorption of 4-bromodiphengl ether onto the biosorbent. The values of thermodynamic parameters △G0 were calculated as -24.61 kJ/mol (20 °C), -24.35 kJ/mol (30 °C), and -23.98 kJ/mol (40 °C), △S(0) was -8.45 kJ/mol/K, and △H(0) was 21.36 kJ/mol. The artificial neural network analysis indicated that the initial concentration appeared to be the most influential parameter on the biosorption processes. The removal rate of 4-bromodiphengl ether achieved using the biochar-microorganism system was increased by 63 and 83% compared with the rates obtained with biochar and the strain individually, respectively. The morphology of the biochar and immobilized strain was determined using a scanning electron microscope, and information of the surface functional groups of biochar was obtained through an infrared spectra study.

Sphingomonas wittichii RW1 gene reporters interrogating the dibenzofuran metabolic network highlight conditions for early successful development in contaminated microcosms

In order to better understand the fate and activity of bacteria introduced into contaminated material for the purpose of enhancing biodegradation rates, we constructed Sphingomonas wittichii RW1 variants with gene reporters interrogating dibenzofuran metabolic activity. Three potential promoters from the dibenzofuran metabolic network were selected and fused to the gene for enhanced green fluorescent protein (EGFP). The stability of the resulting genetic constructions in RW1 was examined, with plasmids based on the broad-host range vector pME6012 being the most reliable. One of the selected promoters, upstream of the gene Swit_4925 for a putative 2-hydroxy-2,4-pentadienoate hydratase, was inducible by growth on dibenzofuran. Sphingomonas wittichii RW1 equipped with the Swit_4925 promoter egfp fusion grew in a variety of non-sterile sandy microcosms contaminated with dibenzofuran and material from a former gasification site. The strain also grew in microcosms without added dibenzofuran but to a very limited extent, and EGFP expression indicated the formation of consistent small subpopulations of cells with an active inferred dibenzofuran metabolic network. Evidence was obtained for competition for dibenzofuran metabolites scavenged by resident bacteria in the gasification site material, which resulted in a more rapid decline of the RW1 population. Our results show the importance of low inoculation densities in order to observe the population development of the introduced bacteria and further illustrate that the limited availability of unique carbon substrate may be the most important factor impinging growth.

Experimental results and integrated modeling of bacterial growth on an insoluble hydrophobic substrate (phenanthrene)

Metabolism of a low-solubility substrate is limited by dissolution and availability and can hardly be determined. We developed a numerical model for simultaneously calculating dissolution kinetics of such substrates and their metabolism and microbial growth (Monod kinetics with decay) and tested it with three aerobic phenanthrene (PHE) degraders: Novosphingobium pentaromativorans US6-1, Sphingomonas sp. EPA505, and Sphingobium yanoikuyae B1. PHE was present as microcrystals, providing non-limiting conditions for growth. Total PHE and protein concentration were tracked over 6-12 days. The model was fitted to the test results for the rates of dissolution, metabolism, and growth. The strains showed similar efficiency, with vmax values of 12-18 g dw g(-1) d(-1), yields of 0.21 g g(-1), maximum growth rates of 2.5-3.8 d(-1), and decay rates of 0.04-0.05 d(-1). Sensitivity analysis with the model shows that (i) retention in crystals or NAPLs or by sequestration competes with biodegradation, (ii) bacterial growth conditions (dissolution flux and resulting chemical activity of substrate) are more relevant for the final state of the system than the initial biomass, and (iii) the desorption flux regulates the turnover in the presence of solid-state, sequestered (aged), or NAPL substrate sources.

Bacterial pyruvate production from alginate, a promising carbon source from marine brown macroalgae

Marine brown macroalgae is a promising source of material for biorefining, and alginate is one of the major components of brown algae. Despite the huge potential availability of alginate, no system has been reported for the production of valuable compounds other than ethanol from alginate, hindering its further utilization. Here we report that a bacterium, Sphingomonas sp. strain A1, produces pyruvate from alginate and secretes it into the medium. High aeration and deletion of the gene for d-lactate dehydrogenase are critical for the production of high concentrations of pyruvate. Pyruvate concentration and productivity were at their maxima (4.56 g/l and 95.0 mg/l/h, respectively) in the presence of 5% (w/v) initial alginate, whereas pyruvate produced per alginate consumed and % of theoretical yield (0.19 g/g and 18.6%, respectively) were at their maxima at 4% (w/v) initial alginate. Concentration of pyruvate decreased after it reached its maximum after cultivations for 2 or 3 days at 145 strokes per minute. Our study is the first report to demonstrate the production of other valuable compounds than ethanol from alginate, a promising marine macroalgae carbon source.

Proposal for a method to estimate nutrient shock effects in bacteria

BACKGROUND

Plating methods are still the golden standard in microbiology; however, some studies have shown that these techniques can underestimate the microbial concentrations and diversity. A nutrient shock is one of the mechanisms proposed to explain this phenomenon. In this study, a tentative method to assess nutrient shock effects was tested.

FINDINGS

To estimate the extent of nutrient shock effects, two strains isolated from tap water (Sphingomonas capsulata and Methylobacterium sp.) and two culture collection strains (E. coli CECT 434 and Pseudomonas fluorescens ATCC 13525) were exposed both to low and high nutrient conditions for different times and then placed in low nutrient medium (R2A) and rich nutrient medium (TSA).The average improvement (A.I.) of recovery between R2A and TSA for the different times was calculated to more simply assess the difference obtained in culturability between each medium. As expected, A.I. was higher when cells were plated after the exposition to water than when they were recovered from high-nutrient medium showing the existence of a nutrient shock for the diverse bacteria used. S. capsulata was the species most affected by this phenomenon.

CONCLUSIONS

This work provides a method to consistently determine the extent of nutrient shock effects on different microorganisms and hence quantify the ability of each species to deal with sudden increases in substrate concentration.

Characterization of the propanil biodegradation pathway in Sphingomonas sp. Y57 and cloning of the propanil hydrolase gene prpH

In our previous study, the isoproturon-degrading strain Sphingomonas sp. Y57 was isolated from the wastewater treatment system of an herbicide factory. Interestingly, this strain also showed the ability to degrade propanil (3,4-dichloropropionamilide). The present work reveals that Y57 degrades propanil via the following pathway: propanil was initially hydrolyzed to 3,4-dichloroaniline (3,4-DCA) and then converted to 4,5-dichlorocatechol, which was then subjected to aromatic ring cleavage and further processing. N-acylation and N-deacylation of 3,4-DCA also occurred, and among N-acylation products, 3,4-dichloropropionanilide was found for the first time. The gene encoding the propanil hydrolase responsible for transforming propanil into 3,4-DCA was cloned from Y57 and was designated as prpH. PrpH was expressed in Escherichia coli BL21 and purified using Ni-nitrilotriacetic acid affinity chromatography. PrpH displayed the highest activity against propanil at 40°C and at pH 7.0. The effect of metal ions on the propanil-degrading activity of PrpH was also determined. To our knowledge, this is the first report of a strain that can degrade both propanil and 3,4-DCA and the first identification of a gene encoding a propanil hydrolase in bacteria.

Effect of Fe-Pd bimetallic nanoparticles on Sphingomonas sp. PH-07 and a nano-bio hybrid process for triclosan degradation

In this study, we have evaluated the effect of palladium-iron bimetallic nanoparticles (nFe-Pd) on diphenyl ether (DE) degrading bacterial strain Sphingomonas sp. PH-07 as well as a sequential nano-bio hybrid process with nFe-Pd as catalytic reductant and PH-07 as biocatalyst for degradation of triclosan. Strain PH-07 grew well in the presence of nFe-Pd up to 0.1g/L in minimal salts medium with DE as carbon source. In aqueous system, TCS (17.3 μM) was completely dechlorinated within 2h by nFe-Pd (0.1g/L) with concomitant release of 2-phenoxyphenol (16.8 μM) and chloride ions (46 μM). All possible dichloro- and monochloro-2-phenoxyphenol intermediates were identified by HPLC and GC-MS analyses, and the dechlorination pathway was proposed. Addition of PH-07 cells into the reactor effectively degraded the 2-phenoxyphenol. Our results reveal that strain PH-07 survives well in the presence of nFe-Pd and nFe-Pd/PH-07 hybrid treatment could be a potential strategy for degradation of TCS.

Interaction of Legionella pneumophila and Helicobacter pylori with bacterial species isolated from drinking water biofilms

BACKGROUND

It is well established that Legionella pneumophila is a waterborne pathogen; by contrast, the mode of Helicobacter pylori transmission remains unknown but water seems to play an important role. This work aims to study the influence of five microorganisms isolated from drinking water biofilms on the survival and integration of both of these pathogens into biofilms.

RESULTS

Firstly, both pathogens were studied for auto- and co-aggregation with the species isolated from drinking water; subsequently the formation of mono and dual-species biofilms by L. pneumophila or H. pylori with the same microorganisms was investigated. Neither auto- nor co-aggregation was observed between the microorganisms tested. For biofilm studies, sessile cells were quantified in terms of total cells by SYTO 9 staining, viable L. pneumophila or H. pylori cells were quantified using 16 S rRNA-specific peptide nucleic acid (PNA) probes and cultivable cells by standard culture techniques. Acidovorax sp. and Sphingomonas sp. appeared to have an antagonistic effect on L. pneumophila cultivability but not on the viability (as assessed by rRNA content using the PNA probe), possibly leading to the formation of viable but noncultivable (VBNC) cells, whereas Mycobacterium chelonae increased the cultivability of this pathogen. The results obtained for H. pylori showed that M. chelonae and Sphingomonas sp. help this pathogen to maintain cultivability for at least 24 hours.

CONCLUSIONS

It appears that M. chelonae may have an important role in the survival of both pathogens in drinking water. This work also suggests that the presence of some microorganisms can decrease the cultivability of L. pneumophila but not the viability which indicates that the presence of autochthonous microorganisms can lead to misleading results when the safety of water is assessed by cultivable methods alone.

Population dynamics in bioaugmented membrane bioreactor for treatment of bromoamine acid wastewater

The performances and microbial population changes in laboratory-scale membrane bioreactor (MBR) augmented with Sphingomonas xenophaga QYY were investigated in the present study. It was demonstrated that after 30 days acclimation, the non-augmented MBR system were able to degrade bromoamine acid (BAA) well. However, the efficiency of the system decreased with BAA concentration increasing. While the augmented MBR showed higher capability, in which the color and COD removal were more than 90% and 50%, respectively. By ribosomal intergenic spacer analysis (RISA), it was found that BAA-utilizing populations gradually increased to become the dominant species in the non-augmented MBR. However, the augmented MBR possessed relatively stable treatment abilities, in which the introduced strain QYY could be persistent and co-exist well with the indigenous populations.

Metabolism of nitrodiphenyl ether herbicides by dioxin-degrading bacterium Sphingomonas wittichii RW1

Nitrodiphenyl ether herbicides, including chlomethoxyfen, nitrofen, and oxyfluorfen are potent herbicides. Some metabolites and parent compounds are considered as possible mutagens and endocrine disruptors. Both properties pose serious hygienic and environmental risks. Sphingomonas wittichii RW1 is a well-known degrader of polychlorinated dibenzo- p-dioxins, dibenzofurans, and diphenyl ethers. However, no detailed research of its metabolic activity has been performed against pesticides with a diphenyl ether scaffold. In this study, we report S. wittichii RW1 as a very potent diphenyl ether herbicide-metabolizing bacterium with broad substrate specificity. The structures of metabolites were determined by instrumental analysis and synthetic standards. Most pesticides were rapidly removed from the culture medium in the order of nitrofen > oxyfluorfen > chlomethoxyfen. In general, herbicides were degraded through the initial reduction and N-acetylation of nitro groups, followed by ether bond cleavage. Relatively low concentrations of phenolic and catecholic metabolites throughout the study suggested that these metabolites were rapidly metabolized and incorporated into primary metabolism. These results indicate that strain RW1 has very versatile metabolic activities over a wide range of environmental contaminants.

Isomer-specific biodegradation of methylphenanthrenes by soil bacteria

It is assumed that bacteria generally degrade 2-methylphenanthrene (2MPhe) in preference to 1-methylphenanthrene (1MPhe), and that environmental biodegradation of methylated PAHs therefore can be described qualitatively by changes in relative concentrations of these isomers. Our objective was to investigate whether microbial phenanthrene degraders (Sphingomonas and Mycobacterium) show such isomer-specific PAH degradation. Eleven out of twenty-nine phenanthrene degraders could grow on methylphenanthrene. The mycobacteria grew only on 2MPhe, the sphingomonads grew mostly on 1MPhe, and one sphingomonad could utilize both substrates. Seven strains were tested in a two-phase system where 1MPhe and 2MPhe were supplied in heptamethylnonane. For these strains, a consistent description of biodegradation based on the 2MPhe/1MPhe diagnostic ratio would not be possible because three Mycobacterium and one Sphingomonas degraded 2MPhe faster than 1MPhe, another Sphingomonas degraded 1MPhe and 2MPhe at almost equal rates, and two Sphingomonas degraded 1MPhe faster than 2MPhe. Thus, environmental biodegradation of phenanthrenes may theoretically proceed with only minor changes in 2MPhe/1MPhe ratios if individual members of the degrader community have different isomer preferences. However, two soil microcosms polluted with bunker oil confirmed the general decline in 2MPhe/1MPhe ratio during oil biodegradation.

[Relationship between soil fungistasis and bacterial community structure]

As a natural attribute of clean and healthy soil, fungistasis is an important indicator of soil quality, and has positive ecological significance to the inhibition of plant disease eruption caused by soil-borne fungal pathogens. In this study, soil samples (0-15 cm) were collected from the abandoned land at Shenyang Experimental Station of Ecology, Chinese Academy of Sciences, to which pesticides and fertilizers have never been applied for nearly 10 years. A series of soil samples with gradient fungistasis was obtained by heating (CK, 100 degrees C, 110 degrees C, and 121 degrees C for 4 min, respectively), and bacterial community structure was analyzed by Polymerase Chain Reaction coupled with Denaturing Gradient Gel Electrophoresis method (PCR-GGGE). The results showed that there was a significant correlation between soil fungistasis and bacterial community composition. Treatment CK showed the strongest capacity to control the growth of target soil-borne pathogenic fungi. The further the bacterial community structure of treated soil deviated from that of CK, the lower the soil fungistasis was. Sequencing and the following phylogenetic analysis of special bands in DGGE indicated that Sphingomonas asaccharolytica, Nitrospira sp., Hyphomicrobiaceae sp., Bacillus megaterium, and Micrococcus sp. could be involved in soil fungistasis.

Microbial diversity of soil bacteria in agricultural field contaminated with heavy metals

In this study we evaluated the bacterial diversity in a soil sample from a site next to a chemical industrial factory previously contaminated with heavy metals. Analysis of 16S rDNA sequences amplified from DNA directly extracted from the soil revealed 17 different bacterial types (genera and/or species). They included Polyangium spp., Sphingomonas spp., Variovorax spp., Hafina spp., Clostridia, Acidobacteria, the enterics and some uncultured strains. Microbes able to tolerate high concentrations of cadmium (500 micromol/L and above) were also isolated from the soil. These isolates included strains of Acinetobacter (strain CD06), Enterobacter sp. (strains CD01, CD03, CD04 and CD08) (similar strains also identified in culture-independent approach) and a strain of Stenotrophomonas sp. The results indicated that the species identified from direct analysis of 16S rDNA of the soil can be quite different from those strains obtained from enrichment cultures and the microbial activities for heavy metal resistance might be more appropriately addressed by the actual isolates.

Parameters controlling the gene-targeting frequency at the Sphingomonas species rrn site and expression of the methyl parathion hydrolase gene

AIMS

To investigate the key parameters controlling the exogenous methyl parathion hydrolase (MPH) gene mpd-targeting frequency at the ribosomal RNA operon (rrn) site of Sphingomonas species which has a wide range of biotechnological applications.

METHODS AND RESULTS

Targeting vectors with different homology lengths and recipient target DNA with different homology identities were used to investigate the parameters controlling the targeting frequency at the Sphingomonas species rrn site. Targeting frequency decreased with the reduction of homology length, and the minimal size for normal homologous recombination was >100 bp. Homologous recombination could succeed even if there were 3-4% mismatches; however, targeting frequency decreased with increasing sequence divergence. The Red recombination system could increase the targeting frequency to some extent. Targeting of the mpd gene to the rrn site did not affect cell viability and resulted in an increase of MPH-specific activity in recombinants.

CONCLUSIONS

Targeting frequency was affected by homology length, identity and the Red recombination system. The rrn site is a good target site for the expression of exogenous genes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work is useful as a foundation for a better understanding of recombination events involving homologous sequences and for the improved manipulation of Sphingomonas genes in biotechnological applications.

Degradation of carbazole by microbial cells immobilized in magnetic gellan gum gel beads

Polycyclic aromatic heterocycles, such as carbazole, are environmental contaminants suspected of posing human health risks. In this study, we investigated the degradation of carbazole by immobilized Sphingomonas sp. strain XLDN2-5 cells. Four kinds of polymers were evaluated as immobilization supports for Sphingomonas sp. strain XLDN2-5. After comparison with agar, alginate, and kappa-carrageenan, gellan gum was selected as the optimal immobilization support. Furthermore, Fe(3)O(4) nanoparticles were prepared by a coprecipitation method, and the average particle size was about 20 nm with 49.65-electromagnetic-unit (emu) g(-1) saturation magnetization. When the mixture of gellan gel and the Fe(3)O(4) nanoparticles served as an immobilization support, the magnetically immobilized cells were prepared by an ionotropic method. The biodegradation experiments were carried out by employing free cells, nonmagnetically immobilized cells, and magnetically immobilized cells in aqueous phase. The results showed that the magnetically immobilized cells presented higher carbazole biodegradation activity than nonmagnetically immobilized cells and free cells. The highest biodegradation activity was obtained when the concentration of Fe(3)O(4) nanoparticles was 9 mg ml(-1) and the saturation magnetization of magnetically immobilized cells was 11.08 emu g(-1). Additionally, the recycling experiments demonstrated that the degradation activity of magnetically immobilized cells increased gradually during the eight recycles. These results support developing efficient biocatalysts using magnetically immobilized cells and provide a promising technique for improving biocatalysts used in the biodegradation of not only carbazole, but also other hazardous organic compounds.

Microbial degradation of the biocide polyhexamethylene biguanide: isolation and characterization of enrichment consortia and determination of degradation by measurement of stable isotope incorporation into DNA

AIMS

To isolate micro-organisms capable of utilizing polyhexamethylene biguanide (PHMB) as a sole source of nitrogen, and to demonstrate biodegradation of the biocide.

METHODS AND RESULTS

Two consortia of bacteria were successfully enriched at the expense of PHMB, using sand from PHMB-treated swimming pools as inoculum. Both consortia were shown to contain bacteria belonging to the genera Sphingomonas, Azospirillum and Mesorhizobium. It was shown that the presence of both Sphingomonas and Azospirillum spp. was required for extensive growth of the consortia. In addition, the Sphingomonads were the only isolates capable of growth in axenic cultures dosed with PHMB. Using a stable isotope (15N)-labelled PHMB, metabolism of the biocide by both consortia was demonstrated. By comparing the level of 15N atom incorporation into bacterial DNA after growth on either 15N-PHMB or 15N-labelled NH4Cl, it was possible to estimate the percentage of PHMB biodegradation.

CONCLUSIONS

The microbial metabolism of nitrogen from the biguanide moiety of PHMB has been demonstrated. It was revealed that Sphingomonas and Azospirillum spp. are the principal organisms responsible for growth at the expense of PHMB.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to demonstrate the microbial metabolism of PHMB.

Identification of opdA, a gene involved in biodegradation of the endocrine disrupter octylphenol

Octylphenol (OP) is an estrogenic detergent breakdown product. Structurally similar nonylphenols are transformed via type II ispo substitution, resulting in the production of hydroquinone and removal of the branched side chain. Nothing is known, however, about the gene(s) encoding this activity. We report here on our efforts to clone the gene(s) encoding OP degradation activity from Sphingomonas sp. strain PWE1, which we isolated for its ability to grow on OP. A fosmid library of PWE1 DNA yielded a single clone, aew4H12, which accumulated a brown polymerization product in the presence of OP. Sequence analysis of loss-of-function transposon mutants of aew4H12 revealed a single open reading frame, opdA, that conferred OP degradation activity. Escherichia coli subclones expressing opdA caused OP disappearance, with the concomitant production of hydroquinone and 2,4,4-trimethyl-1-pentene as well as small amounts of 2,4,4-trimethyl-2-pentanol. These metabolites are consistent with a type II ipso substitution reaction, the same mechanism described for nonylphenol biodegradation in other sphingomonads. Based on opdA's sequence homology to a unique group of putative flavin monooxygenases and the recovery of hydroxylated OP intermediates from E. coli expressing opdA, we conclude that this gene encodes the observed type II ipso substitution activity responsible for the initial step in OP biodegradation.

Degradation pathway of bisphenol A: does ipso substitution apply to phenols containing a quaternary alpha-carbon structure in the para position?

The degradation of bisphenol A and nonylphenol involves the unusual rearrangement of stable carbon-carbon bonds. Some nonylphenol isomers and bisphenol A possess a quaternary alpha-carbon atom as a common structural feature. The degradation of nonylphenol in Sphingomonas sp. strain TTNP3 occurs via a type II ipso substitution with the presence of a quaternary alpha-carbon as a prerequisite. We report here a new degradation pathway of bisphenol A. Consequent to the hydroxylation at position C-4, according to a type II ipso substitution mechanism, the C-C bond between the phenolic moiety and the isopropyl group of bisphenol A is broken. Besides the formation of hydroquinone and 4-(2-hydroxypropan-2-yl)phenol as the main metabolites, further compounds resulting from molecular rearrangements consistent with a carbocationic intermediate were identified. Assays with resting cells or cell extracts of Sphingomonas sp. strain TTNP3 under an (18)O(2) atmosphere were performed. One atom of (18)O(2) was present in hydroquinone, resulting from the monooxygenation of bisphenol A and nonylphenol. The monooxygenase activity was dependent on both NADPH and flavin adenine dinucleotide. Various cytochrome P450 inhibitors had identical inhibition effects on the conversion of both xenobiotics. Using a mutant of Sphingomonas sp. strain TTNP3, which is defective for growth on nonylphenol, we demonstrated that the reaction is catalyzed by the same enzymatic system. In conclusion, the degradation of bisphenol A and nonylphenol is initiated by the same monooxygenase, which may also lead to ipso substitution in other xenobiotics containing phenol with a quaternary alpha-carbon.

Cyclodextrin-linked alginate beads as supporting materials for Sphingomonas cloacae, a nonylphenol degrading bacteria

Calcium alginate beads covalently linked with alpha-cyclodextrin (alpha-CD-alginate beads) were prepared and examined for their ability to serve as a supporting matrix for bacterial degradation of nonylphenol, an endocrine disruptor. Column chromatographic experiment using alpha-CD-alginate beads with diameter of 657+/-82 microm and with degree of CD substitution of 0.16 showed a strong affinity for nonylphenol adsorption. Although addition of alpha-CD (2.7-27 mM) to the culture broth of Sphingomonas cloacae retarded nonylphenol degradation, the immobilized bacteria on the CD-alginate beads were effective for the degradation. Batch degradation tests using the immobilized bacteria on alpha-CD-alginate-beads showed 46% nonylphenol recovery after 10-day incubation at 25+/-2 degrees C, and the recovery reached to about 17% when wide and shallow incubation tubes were used to facilitate uptake of the viscous liquid of nonylphenol on the surface of the medium. Scanning electron microscopic photographs revealed that multiplicated bacteria was present both on the surface and inside the beads and the matrix of CD-alginate was stable and suitable during 10-day incubation.

Novel aspects of symbiotic (polyvinyl alcohol) biodegradation

A new polyvinyl alcohol (PVA)-degrading bacterium was isolated from activated sludge sampled during a waste water treatment process and identified as Sphingomonas sp. Its PVA oxidase activity and alcohol dehydrogenase activity for various low-molecular-weight secondary alcohols were detected. Both activities were associated with cells of the degrader, and they were not extracellular. Under optimal conditions, the isolate was able to degrade 500 mg of PVA per litre in 2 weeks. The strain required pyrroloquinoline quinone (PQQ) and another growth factor, the later could be supplied by a co-isolated Rhodococcus erythropolis strain. The findings stressed the complex nature of environmental PVA degradation and proved that other factors different from PQQ could be important in symbiotic biodegradation of PVA with some sphingomonads.

[Bioremediation of fenpropathrin-contaminated soil by Sphingomonas sp.JQL4-5]

JQL4-5 (Sphingomonas sp.), a fenpropathrin-degrading strain isolated from soils exposed to repeated pesticides contamination, was used in this work to study factors affecting its degrading capacity of fenpropathrin in soil microcosms. In sterilized soil, the degradation rates of fenpropathrin by JQL4-5 were faster than those in unsterilized soil. Various factors, including soil pH, temperature, initial fenitrothion concentration, and inoculum size influenced its degradation efficiency. The addition of 10(6) CFU x g(-1) was able to degrade varying concentrations (10-200 mg x kg(-1) soil) of fenpropathrin over a temperature range of 20-40 degrees C and pH range (6.5 - 7.5). The results indicated that strain JQL4-5 has potential use in bioremediation of fenpropathrin-contaminated soil.

Influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons by Sphingomonas sp. strain PheB4

The influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated when Sphingomonas sp. strain PheB4 isolated from surface mangrove sediments was grown in either phenanthrene-containing mineral salts medium (PMSM) or nutrient broth (NB). The NB-grown culture exhibited a more rapid cometabolic degradation of single and mixed non-growth substrate PAHs compared to the PMSM-grown culture. The concentrations of PAH metabolites were also lower in NB-grown culture than in PMSM-grown culture, suggesting that NB-grown culture removed metabolites at a faster rate, particularly, for metabolites produced from cometabolic degradation of a binary mixture of PAHs. Cometabolic pathways of single PAH (anthracene, fluorene, or fluoranthene) in NB-grown culture showed similarity to that in PMSM-grown culture. However, cometabolic pathways of mixed PAHs were more diverse in NB-grown culture than that in PMSM-grown culture. These results indicated that nutrient rich medium was effective in enhancing cometabolic degradation of mixed PAHs concomitant with a rapid removal of metabolites, which could be useful for the bioremediation of mixed PAHs contaminated sites using Sphingomonas sp. strain PheB4.

Elucidation of the ipso-substitution mechanism for side-chain cleavage of alpha-quaternary 4-nonylphenols and 4-t-butoxyphenol in Sphingobium xenophagum Bayram

Recently we showed that degradation of several nonylphenol isomers with alpha-quaternary carbon atoms is initiated by ipso-hydroxylation in Sphingobium xenophagum Bayram (F. L. P. Gabriel, A. Heidlberger, D. Rentsch, W. Giger, K. Guenther, and H.-P. E. Kohler, J. Biol. Chem. 280:15526-15533, 2005). Here, we demonstrate with 18O-labeling experiments that the ipso-hydroxy group was derived from molecular oxygen and that, in the major pathway for cleavage of the alkyl moiety, the resulting nonanol metabolite contained an oxygen atom originating from water and not from the ipso-hydroxy group, as was previously assumed. Our results clearly show that the alkyl cation derived from the alpha-quaternary nonylphenol 4-(1-ethyl-1,4-dimethyl-pentyl)-phenol through ipso-hydroxylation and subsequent dissociation of the 4-alkyl-4-hydroxy-cyclohexadienone intermediate preferentially combines with a molecule of water to yield the corresponding alcohol and hydroquinone. However, the metabolism of certain alpha,alpha-dimethyl-substituted nonylphenols appears to also involve a reaction of the cation with the ipso-hydroxy group to form the corresponding 4-alkoxyphenols. Growth, oxygen uptake, and 18O-labeling experiments clearly indicate that strain Bayram metabolized 4-t-butoxyphenol by ipso-hydroxylation to a hemiketal followed by spontaneous dissociation to the corresponding alcohol and p-quinone. Hydroquinone effected high oxygen uptake in assays with induced resting cells as well as in assays with cell extracts. This further corroborates the role of hydroquinone as the ring cleavage intermediate during degradation of 4-nonylphenols and 4-alkoxyphenols.

Dominance of sphingomonads in a copper-exposed biofilm community for groundwater treatment

The structure, biological activity and microbial biodiversity of a biofilm used for the removal of copper from groundwater were studied and compared with those of a biofilm grown under copper-free conditions. A laboratory-scale submerged fixed biofilter was fed with groundwater (2.3 l h(-1)) artificially polluted with Cu(II) (15 mg l(-1)) and amended with sucrose (150 mg l(-1)) as carbon source. Between 73 and 90 % of the Cu(II) was removed from water during long-term operation (over 200 days). The biofilm was a complex ecosystem, consisting of eukaryotic and prokaryotic micro-organisms. Scanning electron microscopy revealed marked structural changes in the biofilm induced by Cu(II), compared to the biofilm grown in absence of the heavy metal. Analysis of cell-bound extracellular polymeric substances (EPS) demonstrated a significant modification of the composition of cell envelopes in response to Cu(II). Transmission electron microscopy and energy-dispersive X-ray microanalysis (EDX) showed that copper bioaccumulated in the EPS matrix by becoming bound to phosphates and/or silicates, whereas copper accumulated only intracytoplasmically in cells of eukaryotic microbes. Cu(II) also decreased sucrose consumption, ATP content and alkaline phosphatase activity of the biofilm. A detailed study of the bacterial community composition was conducted by 16S rRNA-based temperature gradient gel electrophoresis (TGGE) profiling, which showed spatial and temporal stability of the species diversity of copper-exposed biofilms during biofilter operation. PCR reamplification and sequencing of 14 TGGE bands showed the prevalence of alphaproteobacteria, with most sequences (78 %) affiliated to the Sphingomonadaceae. The major cultivable colony type in plate counts of the copper-exposed biofilm was also identified as that of Sphingomonas sp. These data confirm a major role of these organisms in the composition of the Cu(II)-removing community.

Endogenous sphingolipid metabolites related to the growth inSphingomonas chungbukensis

Sphingolipids are present in animals, plants, fungi, yeasts and some bacteria. In mammalian cells sphingolipids act as lipid mediators for cell growth, differentiation, apoptosis and angiogenesis. In contrast, in bacteria the biological significance of sphingolipids has not been fully elucidated and sphingolipid metabolism has not been investigated. The aim of this study was to compare the pattern of sphingolipid metabolites in HIT-T15 beta cells originating from hamster pancreas to that in the bacterial strain Sphingomonas chungbukensis DJ77, under various culture conditions. It was found that the concentration of cellular sphinganine (Sa) in S. chungbukensis was higher than that of sphingosine (So), while the level of cellular So in HIT-T15 cells was higher than that of Sa. Aeration and shaking during culture increased bacterial growth in S. chungbukensis, and the contents of So and Sa were also elevated. These results indicate that a de novo sphingolipid pathway appeared to be active in bacteria and that bacterial growth may be closely related to Sa levels.

Effect of heavy metals on the biodegradation of dibenzofuran in liquid medium

The effect of heavy metals on the degradation of dibenzofuran by Sphingomonas wittichii RW1 was determined in liquid cultures. The results showed that 10mg/L cadmium, mercury and copper not only affected the growth of RW1 with dibenzofuran but also the ability of resting cells to degrade this compound. Growth and degradation were strongly inhibited by mercury, even at 1mg/L, while the inhibitory effect of cadmium and copper at the same concentration or at 5mg/L were negligible. In contrast, arsenic and lead did not affect degradation or growth, even at very high concentrations of 100mg/L. Subsequent analyses additionally revealed that concentrations of arsenic and lead remained unchanged following incubation, while those of cadmium, mercury and copper decreased significantly.

Bacterial contamination of water in dental unit reservoirs

The aim of this study was bacteriological assessment of water in dental unit reservoirs--concentration and composition of the aerobe and facultative anaerobe bacterial microflora. Reservoir water samples were taken from 25 units. Bacterial flora were determined with the plate culture method. Bacteria were identified with biochemical microtests: API 20E, API 20NE (bioMérieux, France) and GP2 MicroPlateTM (BIOLOG, USA). The concentration of total bacteria isolated from one site was 201,039 cfu/ml, on average; the minimum was 22,300 cfu/ml, and the maximum - 583,000 cfu/ml. The following bacteria were identified: Gram-negative bacteria--Brevundimonas vesicularis, Moraxella lacunata, Moraxella spp., Ralstonia pickettii, Sphingomonas paucimobilis, Stenotrophomonas maltophilia; Gram-positive cocci--Micrococcus luteus, Micrococcus lylae, Staphylococcus cohnii, Staphylococcus hominis ss novobiosepticus, Staphylococcus spp., Streptococcus spp.; actinomycetes--Streptomyces albus. The prevailing bacteria were: Ralstonia pickettii (96.46%), found in all the units. Sphingomonas paucimobilis (1.32%) and Brevundimonas vesicularis (1.07%) were the next most frequently occurring bacteria. Bacteria concentration in dental unit reservoirs reached excessive values, and the bacterial flora were composed of the bacteria characteristic for water supply systems, opportunistic pathogens, and bacteria of the oral cavity flora. Continuous microbiological monitoring of the DUWL water, including application of a disinfecting procedure, is necessary.

Limits of propidium iodide as a cell viability indicator for environmental bacteria

BACKGROUND

Viability measurements of individual bacteria are applied in various scopes of research and industry using approaches where propidium iodide (PI) serves as dead cell indicator. The reliability of PI uptake as a cell viability indicator for dead (PI permeable) and viable (PI impermeable) bacteria was tested using two soil bacteria, the gram(-) Sphingomonas sp. LB126 and the gram(+) Mycobacterium frederiksbergense LB501T.

METHODS

Bacterial proliferation activities observed viaDAPI and Hoechst 33342 staining were linked to the energy charge and the proportion of dead cells as obtained by diOC(6) (3)-staining and PI-uptake, respectively. Calibration and verification experiments were performed using batch cultures grown on different substrates.

RESULTS

PI uptake depended on the physiological state of the bacterial cells. Unexpectedly, up to 40% of both strains were stained by PI during early exponential growth on glucose when compared to 2-5% of cells in the early stationary phase of growth.

CONCLUSIONS

The results question the utility of PI as a universal indicator for the viability of (environmental) bacteria. It rather appears that in addition to nonviable cells, PI also stains growing cells of Sphingomonas sp. and M. frederiksbergense during a short period of their life cycle.

Statistical approach to optimization of fermentative production of gellan gum from Sphingomonas paucimobilis ATCC 31461

Gellan gum, a high-molecular-weight anionic linear polysaccharide produced by pure-culture fermentation from Sphingomonas paucimobilis ATCC 31461, has elicited industrial interest in recent years as a high-viscosity biogum, a suspending agent, a gelling agent, and an agar substitute in microbial media. In this paper we report on the optimization of gellan gum production using a statistical approach. In the first step, the one factor-at-a-time method was used to investigate the effect of medium constituents such as carbon and nitrogen sources; subsequently, the intuitive analysis based on statistical calculations carried out using the L16 -orthogonal array method. The design for the L16 -orthogonal array was developed and analyzed using MINITAB 13.30 software. All the fermentation runs were carried out at 30+/-2 degrees C on a rotary orbital shaker at 180 rpm for 48 h. In the second step, the effects of amino acids and gellan precursors such as uridine-5'-diphospate (UDP) and adenosine-5'-diphospate (ADP) on the fermentative production of gellan gum were studied. Media containing 4% soluble starch, 0.025% yeast extract, 1.0 mM ADP and 0.05% tryptophan gave a maximum yield of 43.6 g l(-1) starch-free gellan gum, which was significantly higher than reported values in the literature.

Distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from Spain

Hexachlorocyclohexane (HCH)-degrading bacteria are believed to mediate natural attenuation of HCH contamination and have potential for active bioremediation processes. This study addressed the very limited understanding of the distribution, diversity and substrate specificity of such bacteria from 13 soil samples, varying in levels of HCH contamination, from four sites in Spain. Hexachlorocyclohexane removal occurred in 16 of 36 enrichment cultures. Hexachlorocyclohexane-degrading populations were clearly associated with HCH-contaminated soils, and populations growing on the delta-HCH isomer were only found in soil contaminated with delta-HCH. beta-Hexachlorocyclohexane was persistent in enrichment cultures, and there was no evidence for populations growing on beta-HCH. From alpha- and gamma-HCH enrichment cultures, nine HCH-degrading isolates were obtained, which were all Sphingomonas spp. Attempts to isolate organisms from delta-HCH enrichment cultures failed. None of the isolates grew on HCH as a sole organic substrate in pure culture. All isolates degraded alpha- and gamma-HCH, and most degraded beta-HCH. delta-Hexachlorocyclohexane inhibited growth of most isolates, but could be degraded by cell suspensions of at least four strains. Denaturing gradient gel electrophoresis indicated that the isolates represented predominant populations in the enrichment cultures, but additional predominant populations, including some Pseudomonas spp., could not be isolated.

Improvement in Production and Quality of Gellan Gum by Sphingomonas paucimobilis Under High Dissolved Oxygen Tension Levels

The effect of agitation rate and dissolved oxygen tension (DOT) on growth and gellan production by Sphingomonas paucimobilis was studied. Higher cell growth of 5.4 g l(-1) was obtained at 700 rpm but maximum gellan (15 g l(-1)) was produced at 500 rpm. DOT levels above 20% had no effect on cell growth but gellan yield was increased to 23 g l(-1 )with increase in DOT level to 100%. Higher DOT levels improved the viscosity and molecular weight of the polymer with change in acetate and glycerate content of the polymer.

Influence of growth phase on the phospholipidic fatty acid composition of two marine bacterial strains in pure and mixed cultures

This in vitro study was conducted in order to determine the effects of hydrocarbons and growth phase on the phospholipid ester-linked fatty acid composition of two marine sedimentary hydrocarbon-degrading bacteria. These two strains, namely Corynebacterium sp. and Sphingomonas sp. 2MPII, were cultivated on either a simple soluble substrate (ammonium acetate) or a hydrocarbon (respectively n-eicosane and phenanthrene). The incubations were stopped at different times corresponding to point of lag (2 days), exponential (7 days) and stationary phases (21 and 56 days). The effects of growth phase and hydrophobic substrates were successfully demonstrated by a simple index, given as the sum of saturated fatty acids divided by the sum of unsaturated fatty acids ( summation operatorSFA/ summation operatorMUFA), ranging from 1.4 to 3, 0.3 to 0.6, and 0.5 to 1.0 for Corynebacterium sp., Sphingomonas sp. 2MPII, and mixed cultures, respectively. This result was validated by a principal component analysis. In pure cultures, the phospholipid fatty acid (PLFA) composition was strongly influenced by both the carbon source and the growth phase. Nevertheless, the two strains showed different "behaviors". For 2MPII, the main PLFA composition changes were observed at 2 days while they were progressive as a function of time for Corynebacterium sp. These differences could explain the evolution of PLFAs of mixed cultures.

Modeling for gellan gum production by Sphingomonas paucimobilis ATCC 31461 in a simplified medium

Gellan gum production was carried out by Sphingomonas paucimobilis ATCC 31461 in a simplified medium with a short incubation time, and a kinetic model for understanding, controlling, and optimizing the fermentation process was proposed. The results revealed that glucose was the best carbon source and that the optimal concentration was 30 g liter(-1). As for the fermenting parameters, considerably large amounts of gellan gum were yielded by an 8-h-old culture and a 4% inoculum at 200 rpm on a rotary shaker. Under the optimized conditions, the maximum level of gellan gum (14.75 g liter(-1)) and the highest conversion efficiency (49.17%) were obtained in a 30-liter fermentor in batch fermentation. Logistic and Luedeking-Piret models were confirmed to provide a good description of gellan gum fermentation, which gave some support for the study of gellan gum fermentation kinetics. Additionally, this study is the first demonstration that gellan gum production is largely growth associated by analysis of kinetics in its batch fermentation process. Based on model prediction, higher gellan gum production (17.71 g liter(-1)) and higher conversion efficiency (57.12%) were obtained in fed-batch fermentation at the same total glucose concentration (30 g liter(-1)).

Slow-release inoculation allows sustained biodegradation of gamma-hexachlorocyclohexane

This study investigated the feasibility of a slow-release inoculation approach as a bioaugmentation strategy for the degradation of lindane (gamma-hexachlorocyclohexane [gamma-HCH]). Slow-release inoculation of Sphingomonas sp. gamma 1-7 was established in both liquid and soil slurry microcosms using open-ended silicone tubes in which the bacteria are encapsulated in a protective nutrient-rich matrix. The capacity of the encapsulated cells to degrade lindane under aerobic conditions was evaluated in comparison with inoculation of free-living cells. Encapsulation of cells in tubes caused the removal of lindane by adsorption to the silicone tubes but also ensured prolonged biodegradation activity. Lindane degradation persisted 2.2 and 1.4 times longer for liquid and soil slurry microcosms, respectively, than that for inoculation with free cells. While inoculation of free-living cells led to a loss in lindane-degrading activity in limited time intervals, encapsulation in tubes allowed for a more stable actively degrading community. The loss in degrading activity was linked to the loss of the linA gene, encoding gamma-HCH dehydrochlorinase (LinA), which is involved in the initial steps of the lindane degradation pathway. This work shows that a slow-release inoculation approach using a catabolic strain encapsulated in open-ended tubes is a promising bioaugmentation tool for contaminated sites, as it can enhance pollutant removal and can prolong the degrading activity in comparison with traditional inoculation strategies.

Application of stereolithographic custom models for studying the impact of biofilms and mineral precipitation on fluid flow

Here we introduce the use of transparent experimental models fabricated by stereolithography for studying the impacts of biomass accumulation, minerals precipitation, and physical configuration of flow paths on liquid flow in fracture apertures. The internal configuration of the models ranged in complexity from simple geometric shapes to those that incorporate replicated surfaces of natural fractures and computationally derived fracture surfaces. High-resolution digital time-lapse imaging was employed to qualitatively observe the migration of colloidal and soluble dyes through the flow models. In this study, a Sphingomonas sp. and Sporosarcina (Bacillus) pasteurii influenced the fluid dynamics by physically altering flow paths. Microbial colonization and calcite deposition enhanced the stagnant regions adjacent to solid boundaries. Microbial growth and calcite precipitation occurred to a greater extent in areas behind the fabricated obstacles and less in high-velocity orifices.