Sphingobium yanoikuyae Bacteremia, Japan.

We report a case of Sphingobium yanoikuyae bacteremia in an 89-year-old patient in Japan. No standard antimicrobial regimen has been established for S. yanoikuyae infections. However, ceftriaxone and ceftazidime treatments were effective in this case. Increased antimicrobial susceptibility data are needed to establish appropriate treatments for S. yanoikuyae.

Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation.

Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.

Organophosphate hydrolase interacts with ferric-enterobactin and promotes iron uptake in association with TonB-dependent transport system.

Our previous studies have shown the existence of organophosphate hydrolase (OPH) as a part of the inner membrane associated Ton complex (ExbB/ExbD and TonB) of Sphingobium fuliginis. We now show its involvement in iron uptake by establishing direct interactions with ferric-enterobactin. The interactions between OPH and ferric-enterobactin were not affected even when the active site architecture is altered by substituting active site aspartate with either alanine or asparagine. Protein docking studies further substantiated these findings and predicted the existence of ferric-enterobactin binding site that is different from the catalytic site of OPH. A lysine residue (82K) found at the predicted ferric-enterobactin binding site facilitated interactions between OPH and ferric-enterobactin. Substitution of lysine with alanine did not affect triesterase activity, but it abrogated OPH ability to interact with both ferric-enterobactin and ExbD, strengthening further the fact that the catalytic site is not the site for binding of these ligands. In the absence of interactions between OPHK82A and ExbD, OPHK82A failed to target membrane in E. coli cells. The Sphingobium fuliginis TonB-dependent transport (SfTonBDT) system was reconstituted in E. coli GS027 cells generated by deleting the exbD and tonB genes. The E. coli GS030 cells having SfTonBDT system with OPH showed increased iron uptake. Such an increase was not seen in E. coli GS029, cells having SfTonBDT system generated either by omitting OPH or by including its variants, OPHD301A, OPHD301N suggesting a role for OPH in enhanced iron uptake.

Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds.

Iron, an essential element for all organisms, acts as a cofactor of enzymes in bacterial degradation of recalcitrant aromatic compounds. The bacterial family, Sphingomonadaceae comprises various degraders of recalcitrant aromatic compounds; however, little is known about their iron acquisition system. Here, we investigated the iron acquisition system in a model bacterium capable of degrading lignin-derived aromatics, Sphingobium sp. strain SYK-6. Analyses of SYK-6 mutants revealed that FiuA (SLG_34550), a TonB-dependent receptor (TBDR), was the major outer membrane iron transporter. Three other TBDRs encoded by SLG_04340, SLG_04380, and SLG_10860 also participated in iron uptake, and tonB2 (SLG_34540), one of the six tonB comprising the Ton complex which enables TBDR-mediated transport was critical for iron uptake. The ferrous iron transporter FeoB (SLG_36840) played an important role in iron uptake across the inner membrane. The promoter activities of most of the iron uptake genes were induced under iron-limited conditions, and their regulation is controlled by SLG_29410 encoding the ferric uptake regulator, Fur. Although feoB, among all the iron uptake genes identified is highly conserved in Sphingomonad strains, the outer membrane transporters seem to be diversified. Elucidation of the iron acquisition system promises better understanding of the bacterial degradation mechanisms of aromatic compounds.

Cefoperazone induces esterase B expression by EstR and esterase B enhances cefoperazone activity at the periplasm.

The occurrence of antibiotic resistance bacteria has become a major threat to public health. We have recently discovered a transcriptional activator that belongs to MarR family, EstR, and an esterase B (EstB) with a newly proposed de-arenethiolase activity from Sphingobium sp. SM42. De-arenethiolase activity involves the removal of the small aromatic side chain of cephalosporin antibiotics as an excellent leaving group by the enzymatic CS bond cleavage. Here, we report the regulation of estB through EstR as an activator in response to a third generation cephalosporin, cefoperazone, antibiotic. Cefoperazone induced the expression of estB in wild type Sphingobium sp., but not in the estR knockout strain, and the induction was restored in the complemented strain. Moreover, we revealed the importance of EstB localization in periplasm. Since EsB has the ability to inactivate selected ß-lactam antibiotics in vitro, it is possible that the enzyme works at the periplasmic space of Gram negative bacteria similar to ß-lactamases. EstB was genetically engineered by incorporating NlpA binding motif, or OmpA signal sequence, or SpyTag-SpyCatcher to the estB gene to mobilize it to different compartments of periplasm; inner membrane, outer membrane, and periplasmic space, respectively. Surprisingly, we found that Sphingobium sp. SM42 and E. coli expressing EstB at the periplasm were more sensitive to cefoperazone. The possible drug enhancement mechanism by enzyme was proposed. This work might lead to a novel strategy to tackle antibiotic resistance problem.

Role and mechanism of cell-surface hydrophobicity in the adaptation of Sphingobium hydrophobicum to electronic-waste contaminated sediment.

Sphingomonads are isolated at exceptionally high frequency from organic polluted environments and assumed to be more hydrophobic than other Gram-negative bacteria. However, the potential roles of cell-surface hydrophobicity (CSH) in the cell survival in polluted environment, as well as the mechanisms underlying the CSH of sphingomonads, remain unclear. Sphingobium hydrophobicum C1T is a highly hydrophobic sphingomonad isolated from electronic-waste contaminated sediment. In this study, we found that exposure to the typical pollutants in electronic-waste contaminated sediment, such as the heavy metal ion Pb and the organic compound deca-brominated diphenyl ether (deca-BDE), resulted in the development of even higher CSH of the hydrophobic strain C1T; but no significant change was observed in the low CSH of its hydrophilic variant C2. The hydrophobic strain C1T achieved higher biomass yield in standing conditions and adsorbed more amounts of hydrophobic deca-BDE than its hydrophilic variant C2, suggesting that the high CSH potentially enhanced the adaptation of hydrophobic strain to colonize in sediment and adsorb hydrophobic nutrients. The identification of the bacterial cell-surface constituents showed that the high CSH of S. hydrophobicum was contributed greatly by outer-membrane proteins, particularly membrane transporters functioning as enhancers for nutrient uptake and stress sustainment. This study will enhance our understanding of the adaptive strategies of sphingomonads in contaminated environments. It will be of great importance to enhance the CSH of sphingomonads and utilize them in cleaning up the environment from organic pollution.

Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq.

Nickel acts as cofactor for a number of enzymes of many bacteria species. Its homeostasis is ensured by proteins working as ion efflux or accumulation systems. These mechanisms are also generally adopted to counteract life-threatening high extra-cellular Ni2+ concentrations. Little is known regarding nickel tolerance in the genus Sphingobium. We studied the response of the novel Sphingobium sp. ba1 strain, able to adapt to high Ni2+ concentrations. Differential gene expression in cells cultured in 10 mM Ni2+, investigated by RNA-seq analysis, identified 118 differentially expressed genes. Among the 90 up-regulated genes, a cluster including genes coding for nickel and other metal ion efflux systems (similar to either cnrCBA, nccCBA or cznABC) and for a NreB-like permease was found. Comparative analyses among thirty genomes of Sphingobium species show that this cluster is conserved only in two cases, while in the other genomes it is partially present or even absent. The differential expression of genes encoding proteins which could also work as Ni2+-accumulators (HupE/UreJ-like protein, NreA and components of TonB-associated transport and copper-homeostasis systems) was also detected. The identification of Sphingobium sp. ba1 strain adaptive mechanisms to nickel ions, can foster its possible use for biodegradation of poly-aromatic compounds in metal-rich environments.

[Chemotaxis and characteristics of chemotactic genes in Novosphingobium strains].

Objective: The present study aims to analyze the chemotaxis genes and proteins of several PAH-degrading Novosphingobium strains, and the chemotaxis of these strains toward aromatic compounds and intermediates. Methods: Based on genome comparative analysis, we identified the chemotaxis genes organization and proteins distribution. We used drop and swarm plate assays to detect the chemotaxis of these strains toward aromatic compounds and intermediates of TCA cycle. Results: We found that all these Novosphingobium strains showed chemotaxis, but the chemotatic ability varied. The completed genome sequenced strains N. pentaromativorans F2, N. pentaromativorans US6-1, N. pentaromativorans PP1Y, Novosphingobium sp. AP12, Novosphingobium sp. Rr 2-17, and Novosphingobium nitrogenifigens DSM 19370 contained MCP, CheW, CheA, CheB, CheR and CheY. Strain F2, US6-1 and PP1Y, shared a consistent order of chemotaxis genes in "che" cluster. The chemotatic system of these Novosphingobium strains belonged to the Fla chemotactic system. Conclusion: These strains all contained a complete chmotaxis pathway. Their chemotactic ability toward aromatic compounds and intermediates varied, and the chemotaxis of US6-1 was obvious.

Requirement of dark culture condition for enlargement of spheroplasts of the aerobic anoxygenic photosynthetic marine bacterium Erythrobacter litoralis.

In the present study, spheroplasts from the aerobic anoxygenic photosynthetic marine bacterium Erythrobacter litoralis were generated and cultivated. In the presence of penicillin, the spheroplasts grew and enlarged in marine broth without undergoing cell division. However, continuous light inhibited their enlargement, and they were therefore cultivated in the dark. Cellular DNA was quantified at various time points (0, 24, and 48 h) and temperatures (20°C, 25°C, and 30°C) using real-time quantitative PCR. The DNA content was highest at 30°C in the absence of penicillin, whereas there was no observable change with exposure to penicillin at all evaluated temperatures. During growth, larger spheroplasts were more frequently observed at 25°C in the presence of penicillin. These results demonstrate that the optimal culture conditions for the enlargement of spheroplasts in E. litoralis differ from those required for cell division.

Bioremediation potential of a highly mercury resistant bacterial strain Sphingobium SA2 isolated from contaminated soil.

A mercury resistant bacterial strain, SA2, was isolated from soil contaminated with mercury. The 16S rRNA gene sequence of this isolate showed 99% sequence similarity to the genera Sphingobium and Sphingomonas of α-proteobacteria group. However, the isolate formed a distinct phyletic line with the genus Sphingobium suggesting the strain belongs to Sphingobium sp. Toxicity studies indicated resistance to high levels of mercury with estimated EC50 values 4.5 mg L(-1) and 44.15 mg L(-1) and MIC values 5.1 mg L(-1) and 48.48 mg L(-1) in minimal and rich media, respectively. The strain SA2 was able to volatilize mercury by producing mercuric reductase enzyme which makes it potential candidate for remediating mercury. ICP-QQQ-MS analysis of Hg supplemented culture solutions confirmed that almost 79% mercury in the culture suspension was volatilized in 6 h. A very small amount of mercury was observed to accumulate in cell pellets which was also evident according to ESEM-EDX analysis. The mercuric reductase gene merA was amplified and sequenced. The deduced amino acid sequence demonstrated sequence homology with α-proteobacteria and Ascomycota group.

Impact of bioaccessible pyrene on the abundance of antibiotic resistance genes during Sphingobium sp.- and sophorolipid-enhanced bioremediation in soil.

Soils are exposed to various types of chemical contaminants due to anthropogenic activities; however, research on persistent organic pollutants and the existence of antibiotic resistance genes (ARGs) is limited. To our knowledge, the present work for the first time focused on the bioremediation of soil co-contaminated with pyrene and tetracycline/sulfonamide-resistance genes. After 90 days of incubation, the pyrene concentration and the abundance of the four ARGs (tetW, tetM, sulI, and sulII) significantly decreased in different treatment conditions (p<0.05). The greatest pyrene removal (47.8%) and greatest decrease in ARG abundance (from 10(-7) to 10(-8) ARG copies per 16S rRNA copy) were observed in microcosms with a combination of bacterial and sophorolipid treatment. Throughout the incubation, pyrene bioaccessibility constantly declined in the microcosm inoculated with bacteria. However, an increased pyrene bioaccessibility and ARG abundance at day 40 were observed in soil treated with sophorolipid alone. Tenax extraction methods and linear correlation analysis indicated a strong positive relationship between the rapidly desorbing fraction (Fr) of pyrene and ARG abundance. Therefore, we conclude that bioaccessible pyrene rather than total pyrene plays a major role in the maintenance and fluctuation of ARG abundance in the soil.

Draft genome sequence of Sphingobium sp. strain ba1, resistant to kanamycin and nickel ions.

The genome sequence of a Sphingobium strain capable of tolerating high concentrations of Ni ions, and exhibiting natural kanamycin resistance, is presented. The presence of a transposon derived kanamycin resistance gene and several genes for efflux-mediated metal resistance may explain the observed characteristics of the new Sphingobium isolate.

Evaluation of single and joint effect of metabolites isolated from marine sponges, Fasciospongia cavernosa and Axinella donnani on antimicrobial properties.

The biochemical mechanisms that marine sponges have developed as a chemical defense to protect themselves against micro and subsequent macrobiofouling process might comprise a potential alternative for the preventing attack of biofilm forming bacteria. The present study investigated the antimicrobial activity of a series of major secondary metabolites isolated from the sponges Fasciospongia cavernosa and Axinella donnani against fouling bacteria. Secomanoalide (1), dehydromanoalide (2) and cavernosine (3) have been isolated from F. cavernosa. Their structures were determined by MS, (1)H NMR spectra analyses and by comparison with those reported in the literature. The most promising activity was exhibited by the metabolites from A. donnani, that is, cerebroside (5) against three strains Aeromonas hydrophila subsp. salmonicida A449 and Erythrobacter litoralis. Our investigation revealed that combined metabolites 1, 2 and 3 retained strong activity but individual metabolite had moderate activity indicating that activity probably results from synergistic interactions between multiple compounds. The antibacterial screening of compounds 3, 5 and synergistic effect of 1-3 against fouling bacteria has been studied for the first time. Further, isolation of manoalide related compounds and their synergistic screening can be accelerated for the development of new biofilm inhibitors.

Divergent responses of functional gene expression to various nutrient conditions during microcystin-LR biodegradation by Novosphingobium sp. THN1 strain.

To better understand the mechanisms for microcystin-LR (MCLR) biodegradation, the linkage between MCLR-biodegradation kinetics and functional gene expression dynamics was originally investigated with Novosphingobium sp. THN1 as inoculum under various nutrient conditions. Along biodegradation, mlrA gene expression, coupled with mlrD, presented similar trend but was regulated differentially among different conditions. Good positive correlation was observed between MCLR degraded and induction ratios of functional genes until 42h at respective condition. Compared to those under nutrient-free condition, the stimulated or decelerated biodegradation with dipotassium phosphate (DP) or ammonium chloride (AC) (both at 100mg L(-1)) was related to higher or lower up-regulation in mlr gene expression, suggesting that divergent mlr gene expression was one of the reasons for different effects of DP or AC on degradation. However, stimulated degradation with sodium nitrate (100mg L(-1)) might involve other mechanisms where mlr expression was not the decisive prerequisite to govern MCLR-biodegradation.

Genotypic diversity and antibiotic resistance in Sphingomonadaceae isolated from hospital tap water.

The aim of this study was to infer about the modes and extent of dispersion of Sphingomonadaceae via tap water. Sphingomonadaceae isolated from tap water samples in different places of a hospital were compared, based on intra-species genetic variability and antibiotic resistance phenotypes. These isolates were also compared with others isolated before from houses and dental chairs, served by the same municipal water supply system. Sphingomonadaceae from hospital tap water comprised members of the genera Sphingomonas, Sphingobium, Novosphingobium and Blastomonas. In general, distinct genotypes of Sphingomonadaceae were detected in different hospital areas and in tap water outside the hospital, suggesting these bacteria are not persistent or widespread in the urban water distribution system. Possible intrinsic antibiotic resistance, observed in most or all members of the family or of a genus, was observed for colistin in Sphingomonadaceae, aminoglycosides in the genus Blastomonas and beta-lactams in the genus Sphingobium. Possible acquired resistance phenotypes, not common to all members of a given species, comprised fluoroquinolones, cephalosporins and sulphonamides. Although the potential of Sphingomonadaceae as opportunistic pathogens may be low, the capacity of these bacteria to thrive in water supply systems, combined with the intrinsic or acquired antibiotic resistance, may raise the risk associated with their occurrence in hospital tap water.

Proteomic phenotyping of Novosphingobium nitrogenifigens reveals a robust capacity for simultaneous nitrogen fixation, polyhydroxyalkanoate production, and resistance to reactive oxygen species.

Novosphingobium nitrogenifigens Y88(T) (Y88) is a free-living, diazotrophic Alphaproteobacterium, capable of producing 80% of its biomass as the biopolymer polyhydroxybutyrate (PHB). We explored the potential utility of this species as a polyhydroxybutyrate production strain, correlating the effects of glucose, nitrogen availability, dissolved oxygen concentration, and extracellular pH with polyhydroxybutyrate production and changes in the Y88 proteomic profile. Using two-dimensional differential in-gel electrophoresis and tandem mass spectrometry, we identified 217 unique proteins from six growth conditions. We observed reproducible, characteristic proteomic signatures for each of the physiological states we examined. We identified proteins that changed in abundance in correlation with either nitrogen fixation, dissolved oxygen concentration, or acidification of the growth medium. The proteins that correlated with nitrogen fixation were identified either as known nitrogen fixation proteins or as novel proteins that we predict play roles in aspects of nitrogen fixation based on their proteomic profiles. In contrast, the proteins involved in central carbon and polyhydroxybutyrate metabolism were constitutively abundant, consistent with the constitutive polyhydroxybutyrate production that we observed in this species. Three proteins with roles in detoxification of reactive oxygen species were identified in this obligate aerobe. The most abundant protein in all experiments was a polyhydroxyalkanoate granule-associated protein, phasin. The full-length isoform of this protein has a long, intrinsically disordered Ala/Pro/Lys-rich N-terminal segment, a feature that appears to be unique to sphingomonad phasins. The data suggest that Y88 has potential as a PHB production strain due to its aerobic tolerance and metabolic orientation toward polyhydroxybutyrate accumulation, even in low-nitrogen growth medium.

Inhibition of quorum sensing and efflux pump system by trifluoromethyl ketone proton pump inhibitors.

BACKGROUND: One major microbiological problem is the widespread antibiotic resistance. There is an urgent need for new antibiotics and ways to treat multi-drug-resistant infections. Inhibition of bacterial quorum sensing (QS) systems could be an effective alternative in a smuch as they regulate a broad spectrum of cell functions, including, virulence factor production, biofilm organisation and motility. Influx and efflux bacterial systems involved in quorum sensing (QS) are known to depend on the proton motive force (PMF). Thus, a new series of 12 trifluoromethyl ketones (TFs) known to inhibit the PMF, was investigated for effects on the efflux pump of a QS responding bacterium, for its subsequent effect on the response to a QS signal and its direct inhibition of the response to a QS signal. MATERIALS AND METHODS: Chromobacterium violaceum 026 (CV026) was used as the indicator strain to evaluate the QS inhibitory effect of TFs. This strain responds to the presence of short carbon chain acyl-homoserine lactones (AHLs) by the development of a purple pigment. Effect on the QS response of CV026 to externally added AHLs was evaluated. In addition, the specific activity of the TFs on the efflux pump system of the CV026 strain and a wild-type Escherichia coli strain was assessed with the aid of the automated real-time ethidium bromide method. RESULTS: From the 12 compounds, 6 proved to be effective inhibitors of the QS response by CV026, as well as inhibit the efflux pumps of CV026 and Escherichia coli. CONCLUSION: Our results show that TFs have QS inhibitory properties that are mediated through their inhibition of efflux pumps that extrude the noxious QS signal before it reaches its intended target. Because the TFs also inhibit the efflux pump of a pathogenic bacterium, the method used for the evaluation of the TFs in the current study has clinical relevance and may be exploited for the prevention of QS responses of infecting bacteria.

Diversity and antibiotic resistance patterns of Sphingomonadaceae isolates from drinking water.

Sphingomonadaceae (n = 86) were isolated from a drinking water treatment plant (n = 6), tap water (n = 55), cup fillers for dental chairs (n = 21), and a water demineralization filter (n = 4). The bacterial isolates were identified based on analysis of the 16S rRNA gene sequence, and intraspecies variation was assessed on the basis of atpD gene sequence analysis. The isolates were identified as members of the genera Sphingomonas (n = 27), Sphingobium (n = 28), Novosphingobium (n = 12), Sphingopyxis (n = 7), and Blastomonas (n = 12). The patterns of susceptibility to five classes of antibiotics were analyzed and compared for the different sites of isolation and taxonomic groups. Colistin resistance was observed to be intrinsic (92%). The highest antibiotic resistance prevalence values were observed in members of the genera Sphingomonas and Sphingobium and for beta-lactams, ciprofloxacin, and cotrimoxazole. In tap water and in water from dental chairs, antibiotic resistance was more prevalent than in the other samples, mainly due to the predominance of isolates of the genera Sphingomonas and Sphingobium. These two genera presented distinct patterns of association with antibiotic resistance, suggesting different paths of resistance development. Antibiotic resistance patterns were often related to the species rather than to the site or strain, suggesting the importance of vertical resistance transmission in these bacteria. This is the first study demonstrating that members of the family Sphingomonadaceae are potential reservoirs of antibiotic resistance in drinking water.