A mechanism of resistance to hydrogen peroxide in Vibrio rumoiensis S-1

Vibrio ulleungensis sp. nov., isolated from Mytilus coruscus

A Gram-stain-negative, rod-shaped, motile via polar flagellum, facultatively aerobic, light-yellow, bacterium (designated 188UL20-2^T) was isolated from a mussel sample of Mytilus coruscus collected on Ulleung Island, Ulleung-gun, Gyeongsangbuk-do, Republic of Korea. On the basis of 16S rRNA gene sequencing results, strain 188UL20-2^T clustered with species of the genus Vibrio and appeared closely related to Vibrio marisflavi DSM 23086^T (96.59%), Vibrio variabilis DSM 26147^T (96.57%), Vibrio penaeicida DSM 14398^T (96.37%) and Vibrio litoralis DSM 17657^T (95.97%). The average nucleotide identity and digital DNA-DNA hybridization values between strain 188UL20-2^T and its closest related strain were 71.3 and 16.4%, indicating that 188UL20-2^T represents a novel species of the genus Vibrio. Growth occurred at 18-37 °C on MA medium in the presence of 1-4% NaCl (w/v) and at pH 5.0-10.0. The DNA G+C content of the genomic DNA was 45.4 mol%, and ubiquinone-8 (Q-8) was the major respiratory quinone. The major cellular fatty acids (>5%) were C_16:1 ω6c and/or C_16:1 ω7c (summed feature 3), C_18:1 ω7c and/or C_18:1 ω6c (summed feature 8), C_16:0, C_16:0 iso, C_14:0, C_14:0 iso and C_12:0. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, unidentified aminophospholipid, unidentified glycolipid and seven unidentified lipids. Physiological and biochemical characteristics indicated that strain 188UL20-2^T represents a novel species of the genus Vibrio, for which the name Vibrio ulleungensis sp. nov. is proposed. The type strain is 188UL20-2^T (=KACC 22258^T=LMG 32202^T).

Genomic characterization of closely related species in the Rumoiensis clade infers ecogenomic signatures to non-marine environments

Members of the family Vibrionaceae are generally found in marine and brackish environments, playing important roles in nutrient cycling. The Rumoiensis clade is an unconventional group in the genus Vibrio, currently comprising six species from different origins including two species isolated from non-marine environments. In this study, we performed comparative genome analysis of all six species in the clade using their complete genome sequences. We found that two non-marine species, Vibrio casei and Vibrio gangliei, lacked the genes responsible for algal polysaccharide degradation, while a number of glycoside hydrolase genes were enriched in these two species. Expansion of insertion sequences was observed in V. casei and Vibrio rumoiensis, which suggests ongoing genomic changes associated with niche adaptations. The genes responsible for the metabolism of glucosylglycerate, a compound known to play a role as compatible solutes under nitrogen limitation, were conserved across the clade. These characteristics, along with genes encoding species-specific functions, may reflect the habit expansion which has led to the current distribution of Rumoiensis clade species. Genome analysis of all species in a single clade give us valuable insights into the genomic background of the Rumoiensis clade species and emphasize the genomic diversity and versatility of Vibrionaceae.

Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter

Spacecraft assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions. Using cultivation and stable isotope labeling studies, we show that ethanol is a sole carbon source when cultivating in 0.2 × M9 minimal medium containing 26 μM Fe(NH4)2(SO4)2. Although cultures expectedly did not grow solely on 2-propanol, cultivations on mixtures of ethanol and 2-propanol exhibited enhanced plate counts at mole ratios of ≤0.50. In support, enzymology experiments on cellular extracts were consistent with oxidation of ethanol and 2-propanol by a membrane-bound alcohol dehydrogenase. In the presence of Kleenol 30, untargeted metabolite profiling on ultraminimal cultures of Acinetobacter radioresistens 50v1 indicated (1) biodegradation of Kleenol 30 into products including ethylene glycols, (2) the potential metabolism of decanoate (formed during incubation of Kleenol 30 in 0.2 × M9), and (3) decreases in the abundances of several hydroxy- and ketoacids in the extracellular metabolome. In ultraminimal medium (when using ethanol as a sole carbon source), A. radioresistens 50v1 also exhibits a remarkable survival against hydrogen peroxide (∼1.5-log loss, ∼108 colony forming units (cfu)/mL, 10 mM H2O2), indicating a considerable tolerance toward oxidative stress under nutrient-restricted conditions. Together, these results suggest that the spacecraft cleaning reagents may (1) serve as nutrient sources under oligotrophic conditions and (2) sustain extremotolerances against the oxidative stresses associated with low-humidity environments. In perspective, this study provides a plausible biochemical rationale to the observed microbial ecology dynamics of spacecraft-associated environments.

Characterization of hydrogen peroxide-resistant Acinetobacter species isolated during the Mars Phoenix spacecraft assembly

The microbiological inventory of spacecraft and the associated assembly facility surfaces represent the primary pool of forward contaminants that may impact the integrity of life-detection missions. Herein, we report on the characterization of several strains of hydrogen peroxide-resistant Acinetobacter, which were isolated during the Mars Phoenix lander assembly. All Phoenix-associated Acinetobacter strains possessed very high catalase specific activities, and the specific strain, A. gyllenbergii 2P01AA, displayed a survival against hydrogen peroxide (no loss in 100 mM H2O2 for 1 h) that is perhaps the highest known among Gram-negative and non-spore-forming bacteria. Proteomic characterizations reveal a survival mechanism inclusive of proteins coupled to peroxide degradation (catalase and alkyl hydroperoxide reductase), energy/redox management (dihydrolipoamide dehydrogenase), protein synthesis/folding (EF-G, EF-Ts, peptidyl-tRNA hydrolase, DnaK), membrane functions (OmpA-like protein and ABC transporter-related protein), and nucleotide metabolism (HIT family hydrolase). Together, these survivability and biochemical parameters support the hypothesis that oxidative tolerance and the related biochemical features are the measurable phenotypes or outcomes for microbial survival in the spacecraft assembly facilities, where the low-humidity (desiccation) and clean (low-nutrient) conditions may serve as selective pressures. Hence, the spacecraft-associated Acinetobacter, due to the conferred oxidative tolerances, may ultimately hinder efforts to reduce spacecraft bioburden when using chemical sterilants, thus suggesting that non-spore-forming bacteria may need to be included in the bioburden accounting for future life-detection missions.

Investigating catalase activity through hydrogen peroxide decomposition by bacteria biofilms in real time using scanning electrochemical microscopy

Catalase activity through hydrogen peroxide decomposition in a 1 mM bulk solution above Vibrio fischeri (γ-Protebacteria-Vibrionaceae) bacterial biofilms of either symbiotic or free-living strains was studied in real time by scanning electrochemical microscopy (SECM). The catalase activity, in units of micromoles hydrogen peroxide decomposed per minute over a period of 348 s, was found to vary with incubation time of each biofilm in correlation with the corresponding growth curve of bacteria in liquid culture. Average catalase activity for the same incubation times ranging from 1 to 12 h was found to be 0.28 ± 0.07 μmol H2O2/min for the symbiotic biofilms and 0.31 ± 0.07 μmol H2O2/min for the free-living biofilms, suggesting similar catalase activity. Calculations based on Comsol Multiphysics simulations in fitting experimental biofilm data indicated that approximately (3 ± 1) × 10(6) molecules of hydrogen peroxide were decomposed by a single bacterium per second, signifying the presence of a highly active catalase. A 2-fold enhancement in catalase activity was found for both free-living and symbiotic biofilms in response to external hydrogen peroxide concentrations as low as 1 nM in the growth media, implying a similar mechanism in responding to oxidative stress.

Growth-dependent catalase localization in Exiguobacterium oxidotolerans T-2-2T reflected by catalase activity of cells

A psychrotolerant and H₂O₂-resistant bacterium, Exiguobacterium oxidotolerans T-2-2^T, exhibits extraordinary H₂O₂ resistance and produces catalase not only intracellularly but also extracellularly. The intracellular and extracellular catalases exhibited the same enzymatic characteristics, that is, they exhibited the temperature-dependent activity characteristic of a cold-adapted enzyme, their heat stabilities were similar to those of mesophilic enzymes and very high catalytic intensity. In addition, catalase gene analysis indicated that the bacterium possessed the sole clade 1 catalase gene corresponding to intracellular catalase. Hence, intracellular catalase is secreted into the extracellular space. In addition to intracellular and extracellular catalases, the inner circumference of the cells showed the localization of catalase in the mid-stationary growth phase, which was observed by immunoelectron microscopy using an antibody against the intracellular catalase of the strain. The cells demonstrated higher catalase activity in the mid-stationary growth phase than in the exponential growth phase. The catalase localized in the inner circumference can be dissociated by treatment with Tween 60. Thus, the localized catalase is not tightly bound to the inner circumference of the cells and may play a role in the oxidative defense of the cells under low metabolic state.

Insights into the extremotolerance of Acinetobacter radioresistens 50v1, a gram-negative bacterium isolated from the Mars Odyssey spacecraft

The microbiology of the spacecraft assembly process is of paramount importance to planetary exploration, as the biological contamination that can result from remote-enabled spacecraft carries the potential to impact both life-detection experiments and extraterrestrial evolution. Accordingly, insights into the mechanisms and range of extremotolerance of Acinetobacter radioresistens 50v1, a Gram-negative bacterium isolated from the surface of the preflight Mars Odyssey orbiter, were gained by using a combination of microbiological, enzymatic, and proteomic methods. In summary, A. radioresistens 50v1 displayed a remarkable range of survival against hydrogen peroxide and the sequential exposures of desiccation, vapor and plasma phase hydrogen peroxide, and ultraviolet irradiation. The survival is among the highest reported for non-spore-forming and Gram-negative bacteria and is based upon contributions from the enzyme-based degradation of H(2)O(2) (catalase and alkyl hydroperoxide reductase), energy management (ATP synthase and alcohol dehydrogenase), and modulation of the membrane composition. Together, the biochemical and survival features of A. radioresistens 50v1 support a potential persistence on Mars (given an unintended or planned surface landing of the Mars Odyssey orbiter), which in turn may compromise the scientific integrity of future life-detection missions.

Characterization of catalase from psychrotolerant Psychrobacter piscatorii T-3 exhibiting high catalase activity

A psychrotolerant bacterium, strain T-3 (identified as Psychrobacter piscatorii), that exhibited an extraordinarily high catalase activity was isolated from the drain pool of a plant that uses H₂O₂ as a bleaching agent. Its cell extract exhibited a catalase activity (19,700 U·mg protein⁻¹) that was higher than that of Micrococcus luteus used for industrial catalase production. Catalase was approximately 10% of the total proteins in the cell extract of the strain. The catalase (PktA) was purified homogeneously by only two purification steps, anion exchange and hydrophobic chromatographies. The purified catalase exhibited higher catalytic efficiency and higher sensitivity of activity at high temperatures than M. luteus catalase. The deduced amino acid sequence showed the highest homology with catalase of Psycrobacter cryohalolentis, a psychrotolelant bacterium obtained from Siberian permafrost. These findings suggest that the characteristics of the PktA molecule reflected the taxonomic relationship of the isolate as well as the environmental conditions (low temperatures and high concentrations of H₂O₂) under which the bacterium survives. Strain T-3 efficiently produces a catalase (PktA) at a higher rate than Exiguobacterium oxidotolerans, which produces a very strong activity of catalase (EktA) at a moderate rate, in order to adapt to high concentration of H₂O₂.

Hfq regulates anti-oxidative ability in Vibrio parahaemolyticus

Hfq plays a fundamental role in bacterial cell physiology. It can stimulate or repress the expression of certain target genes, and there is a possibility that Hfq regulates the oxidative stress response. However, how Hfq functions that in Vibrio parahaemolyticus remains speculative. In this paper, we explain the functions Hfq plays in V. parahaemolyticus in the gene expression of superoxide dismutase gene and catalase gene, comparing the hfq deletion mutant strain to the parental strain. The results show that the hfq deletion mutant V. parahaemolyticus has a stronger ability to resist H(2)O(2). Superoxide dismutase (SOD) and catalase (CAT) activities in the hfq deletion mutant were remarkably higher than in the parental strain. Genetic experiments indicated that the gene expression of sod and kat was up-regulated in the mutant strain. These results indicate that Hfq down-regulates CAT and SOD activity, and Hfq is associated with the oxidative stress response.

Enhancement of the nitrogen fixation efficiency of genetically-engineered Rhizobium with high catalase activity

The vktA catalase gene, which had been cloned from Vibrio rumoiensis S-1T having extraordinarily high catalase activity, was introduced into the root nodule bacterium, Rhizobium leguminosarum bv. phaseoli USDA 2676. The catalase activity of the vktA-transformed R. leguminosarum cells (free-living) was three orders in magnitude higher than that of the parent cells and this transformant could grow in a higher concentration of exogenous hydrogen peroxide (H2O2). The vktA-transformant was inoculated to the host plant (Phaseolus vulgaris L.) and the nodulation efficiency was evaluated. The results showed that the nitrogen-fixing activity of nodules was increased 1.7 to 2.3 times as compared to the parent. The levels of H2O2 in nodules formed by the vktA-transformant were decreased by around 73%, while those of leghemoglobins (Lba and Lbb) were increased by 1.2 (Lba) and 2.1 (Lbb) times compared with the parent. These results indicated that the increase of catalase activity in rhizobia could be useful to improve the nitrogen-fixing efficiency of nodules by the reduction of H2O2 content concomitantly with the enhancement of leghemoglobins contents.

H2O2 tolerance of Vibrio rumoiensis S-1(T) is attributable to the cellular catalase activity

The extraordinarily high level of H2O2 tolerance of Vibrio rumoiensis strain S-1(T) when compared with the tolerance levels of strain S-4, a probable catalase-deficient derivative of strain S-1(T), was demonstrated by the introduction of 0-100 mM H2O2 during the mid-exponential growth phase. The contribution of catalase to the H2O2 tolerance was also demonstrated by comparing the catalase-deficient mutant Escherichia coli strain UM2 with a UM2 strain, harboring the plasmid pBSsa1, which carried the strain S-1(T) catalase gene vktA. The decomposition rates of 23-25 mM H2O2 that was introduced in the culture fluids of strain S-1(T) and E. coli UM2 harboring pBSsa1 corresponded to the calatase activities of the cells by spectrophotometric measurements. The presence of cell surface catalase was observed by immunoelectron microscopy, using an antibody for intracellular catalase in strain S-1(T). The high level of H2O2 tolerance of strain S-1(T) was attributable to the catalase activity of the cells. Cell surface catalase is considered to contribute to the catalase activity of strain S-1(T) cells.

The antioxidative function of eicosapentaenoic acid in a marine bacterium,Shewanella marinintestinaIK-1

When the eicosapentaenoic acid (EPA)-deficient mutant strain IK-1Delta8 of the marine EPA-producing Shewanella marinintestina IK-1 was treated with various concentrations of hydrogen peroxide (H(2)O(2)), its colony-forming ability decreased more than that of the wild type. Protein carbonylation, induced by treating cells with 0.01 mM H(2)O(2) under bacteriostatic conditions, was enhanced only in cells lacking EPA. The amount of cells recovered from the cultures was decreased more significantly by the presence of H(2)O(2) for cells lacking EPA than for those producing EPA. Treatment of the cells with 0.1 mM H(2)O(2) resulted in much lower intracellular concentrations of H(2)O(2) being consistently detected in cells with EPA than in those without EPA. These results suggest that cellular EPA can directly protect cells against oxidative damage by shielding the entry of exogenously added H(2)O(2) in S. marinintestina IK-1.

Study and improvement of the conditions for production of a novel alkali stable catalase

Catalase (CAT) is an enzyme capable of catalyzing the conversion of H(2)O(2) to O(2) and H(2)O. It has recently acquired interest due to its attractive potential application in the textile industries. In a previous study, a bacterium with slight halophilic and alkaliphilic characteristics, Bacillus sp. F26, was isolated and found to produce high-level alkaline CAT. In the present study, the effects of culture conditions on the CAT production were investigated. The results showed that the highest activity of CAT (13.9 U/mg protein) was obtained when glucose (15 g/L) was used as carbon source. The utilization of the mixture of corn steep liquid and beef extract stimulated both bacterial growth and CAT synthesis. The highest biomass (4.5 g/L) and activity of CAT (16.5 U/mg protein) were found synchronously when 10 g/L corn steep liquid and 10 g/L beef extract were used as nitrogen source. The addition of H(2)O(2) as an oxidative stress was used to enhance CAT production in the flasks. It was found that the activity of CAT was increased by 51.3-22.8 U/mg protein compared with the control when 2 mmol/L H(2)O(2) was added at later exponential phases (16 h), although the cell growth was significantly inhibited. Based on the above, an exponential H(2)O(2) feed strategy was developed, in which the feed rate of H(2)O(2) was controlled according to specific cell growth rate (mu). In this way, the maximum CAT production (29.9 U/mL) was obtained, which was 92.8 and 20.7% higher than that in batch and constant rate fed-batch fermentation, respectively.

Recurrent isolation of hydrogen peroxide-resistant spores of Bacillus pumilus from a spacecraft assembly facility

While the microbial diversity of a spacecraft assembly facility at the Jet Propulsion Laboratory (Pasadena, CA) was being monitored, H2O2-resistant bacterial strains were repeatedly isolated from various surface locations. H2O2 is a possible sterilant for spacecraft hardware because it is a low-temperature process and compatible with various modern-day spacecraft materials, electronics, and components. Both conventional biochemical testing and molecular analyses identified these strains as Bacillus pumilus. This Bacillus species was found in both unclassified (entrance floors, anteroom, and air-lock) and classified (floors, cabinet tops, and air) locations. Both vegetative cells and spores of several B. pumilus isolates were exposed to 5% liquid H2O2 for 60 min. Spores of each strain exhibited higher resistance than their respective vegetative cells to liquid H2O2. Results indicate that the H2O2 resistance observed in both vegetative cells and spores is strain-specific, as certain B. pumilus strains were two to three times more resistant than a standard Bacillus subtilis dosimetry strain. An example of this trend was observed when the type strain of B. pumilus, ATCC 7061, proved sensitive, whereas several environmental strains exhibited varying degrees of resistance, to H2O2. Repeated isolation of H2O2-resistant strains of B. pumilus in a clean-room is a concern because their persistence might potentially compromise life-detection missions, which have very strict cleanliness and sterility requirements for spacecraft hardware.

Isolation and characterization of rpoS from a pathogenic bacterium, Vibrio vulnificus: role of sigmaS in survival of exponential-phase cells under oxidative stress

A gene homologous to rpoS was cloned from a fatal human pathogen, Vibrio vulnificus. The functional role of rpoS in V. vulnificus was accessed by using an rpoS knockout mutant strain. This mutant was impaired in terms of the ability to survive under oxidative stress, nutrient starvation, UV irradiation, or acidic conditions. The increased susceptibility of the V. vulnificus mutant in the exponential phase to H2O2 was attributed to the reduced activity of hydroperoxidase I (HPI). Although sigmaS synthesis was induced and HPI activity reached the maximal level in the stationary phase, the mutant in the stationary phase showed the same susceptibility to H2O2 as the wild-type strain in the stationary phase. In addition, HPII activity, which is known to be controlled by sigmaS in Escherichia coli, was not detectable in V. vulnificus strains under the conditions tested. The mutant in the exponential phase complemented with multiple copies of either the rpoS or katG gene of V. vulnificus recovered both resistance to H2O2 and HPI activity compared with the control strain. Expression of the katG gene encoding HPI in V. vulnificus was monitored by using a katG::luxAB transcriptional fusion. The expression of this gene was significantly reduced by deletion of sigmaS in both the early exponential and late stationary phases. Thus, sigmaS is necessary for increased synthesis and activity of HPI, and sigmaS is required for exponentially growing V. vulnificus to develop the ability to survive in the presence of H2O2.

Influence des conditions de culture préalables et de la présence du gènerpoSpour la survie deSalmonella typhimuriumen eau de mer exposée à la lumière solaire

The effect of sunlight exposure on Salmonella typhimurium isogenic strains harboring an rpoS gene functional (rpoS+) or not functional (rpoS–) was investigated in microcosms of sterile sea water at 20 °C. The two strains rapidly lost their ability to produce colonies on solid culture media. The detrimental action of sunlight was more important when the salinity of sea water increased. The survival of stationary phase cells was influenced by RpoS. Bacteria grown in media with high salinity or osmolarity and transferred to sea water in stationary phase were more resistant to irradiation than those grown in media with low salinity. Prior growth under oxidative (0.2 mmol/L of H2O2) or amino acid starved (minimal medium) conditions did not modify the survival of either strain when they were exposed to sunlight. Bacteria were more resistant when cells were incubated in sea water in the dark prior to being exposed to sunlight. The resistance to sunlight irradiation was also greater in clones of both strains isolated from microcosms exposed to sunlight for 90 min, then further inoculated into sea water and reexposed to sunlight.Key words: Salmonella typhimurium, sea water, sunlight, rpoS, σs.

Purification and characterization of a catalase from the facultatively psychrophilic bacterium Vibrio rumoiensis S-1(T) exhibiting high catalase activity

Catalase from the facultatively psychrophilic bacterium Vibrio rumoiensis S-1(T), which was isolated from an environment exposed to H(2)O(2) and exhibited high catalase activity, was purified and characterized, and its localization in the cell was determined. Its molecular mass was 230 kDa, and the molecule consisted of four identical subunits. The enzyme, which was not apparently reduced by dithionite, showed a Soret peak at 406 nm in a resting state. The catalytic activity was 527,500 U. mg of protein(-1) under standard reaction conditions at 40 degrees C, 1.5 and 4.3 times faster, respectively, than those of the Micrococcus luteus and bovine catalases examined under the same reaction conditions, and showed a broad optimum pH range (pH 6 to 10). The catalase from strain S-1(T) is located not only in the cytoplasmic space but also in the periplasmic space. There is little difference in the activation energy for the activity between strain S-1(T) catalase and M. luteus and bovine liver catalases. The thermoinstability of the activity of the former catalase were significantly higher than those of the latter catalases. The thermoinstability suggests that the catalase from strain S-1(T) should be categorized as a psychrophilic enzyme. Although the catalase from strain S-1(T) is classified as a mammal type catalase, it exhibits the unique enzymatic properties of high intensity of enzymatic activity and thermoinstability. The results obtained suggest that these unique properties of the enzyme are in accordance with the environmental conditions under which the microorganism lives.