Generation of reactive oxygen species from conventional laboratory media

Isolation of hitherto-uncultivated microorganisms- Application of radical scavengers

The culture filtrates of the predominant bacterial strains isolated from soil samples have been shown to increase the microbial colony counts on agar plates used for the isolation of uncultured bacteria. One of the factors in the culture filtrates responsible for this increase was identified to be superoxide dismutase (SOD). The generation of reactive oxygen species (O2-, H2O2, and ・OH) was detected from conventional laboratory agar media. The use of agar media supplemented with radical scavengers (SOD, catalase, ascorbic acid, or rutin) effectively increased the colony counts and kinds of microbial strains that grew from soil samples. Taxonomical studies on these isolates revealed new taxa for phylum Actinomycetota; one family, three genera, and nine species were newly described. One of the strains, Patulibacter minatonensis KV-614T belonging to the new family Patulibacteraceae, was isolated on agar medium supplemented with SOD. P. minatonensis KV-614T represents a novel lineage within the phylum Actinomycetota. A polymerase chain reaction (PCR) study using specific primers for the detection of strains related to the genus Patulibacter, order Solirubrobacterales, showed a high distribution frequency, with detection in over 70% of the soil samples tested. These data suggest that the use of radical scavengers may facilitate the isolation of some hitherto-uncultivated microorganisms widely distributed in soil.

Evaluation of distinct modes of oxidative secondary injury generated in heat-treated cells of Escherichia coli with solid/liquid and complex/semi-synthetic media sets

AIMS

To characterize and evaluate oxidative secondary injury generated in heat-treated Escherichia coli cells during recovery cultivation either on agar or in a broth of a semi-synthetic enriched M9 (EM9) medium and a complex Luria broth (LB) medium with different types of antioxidants.

METHODS AND RESULTS

E. coli cells grown in the EM9 and LB broth were heated at 50^o C in a buffer (pH7.0). Heated cells were recovered on the same kind of agar medium as that used for growth, with or without different antioxidants. Although these antioxidants mostly protected the cells from oxidative secondary injury on the recovery media, sodium thiosulfate and sodium pyruvate were most protective on EM9 and LB agars, respectively. Determination of viability using the most probable number and growth delay analysis methods showed significant reductions in the protective effects of antioxidants in the EM9 and LB media.

CONCLUSION

Oxidative secondary injury generated in heated E. coli cells was found to be qualitatively and quantitatively diverse under cellular and environmental conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results suggest that different modes of oxidation should be considered in viability determination and injured cell enumeration of heat-treated cells.

Optimized UV-Spectrophotometric Assay to Screen Bacterial Uricase Activity Using Whole Cell Suspension

Uricase catalyzes the conversion of uric acid into allantoin with concomitant reduction of molecular oxygen to hydrogen peroxide. In humans, uricase is not functional, thereby predisposing individuals to hyperuricemia, a metabolic disturbance associated with gout, chronic kidney disorders, and cardiovascular diseases. The efficacy of current therapies to treat hyperuricemia is limited, and novel approaches are therefore desired, for instance using uricase-expressing probiotic strains. Here, we evaluated UV-spectrophotometric and H₂O₂-based fluorescent assays to enable the rapid identification of uricase activity in a broad panel of lactobacilli, Bacillus, and Bifidobacterium species. We highlighted abiotic (medium composition and mode of sterilization) and biotic (H₂O₂-producing strains) factors impacting the measurements' accuracy, and reported on the stepwise optimization of a simple, fast, and robust high-throughput UV-spectrophotometric method to screen uricase activity using whole bacterial suspension, thereby assessing both cell-associated and extracellular activity. The validity of the optimized assay, based on the monitoring of uric acid degradation at 300 nm, was confirmed via liquid chromatography. Finally, a panel of 319 Qualified Presumption of Safety (QPS) strains of lactobacilli (18 species covering nine genera), Bacillus (three species), and Bifidobacterium (four species) were screened for uricase activity using the optimized method. All 319 strains, but the positive control Bacillus sp. DSM 1306, were uricase-negative, indicating that this activity is rare among these genera, especially in isolates from food or feces. Altogether, the UV-spectrophotometric high-throughput assay based on whole bacterial suspension reported here can be used to rapidly screen large microbial collections, by simultaneously detecting cell-associated and extracellular uricase activity, thereby accelerating the identification of uricolytic strains with therapeutic potential to treat hyperuricemia.

Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges-A Review

The application of high-throughput microbial community profiling as well as "omics" approaches unveiled high diversity and host-specificity of bacteria associated with marine sponges, which are renowned for their wide range of bioactive natural products. However, exploration and exploitation of bioactive compounds from sponge-associated bacteria have been limited because the majority of the bacteria remains recalcitrant to cultivation. In this review, we (i) discuss recent/novel cultivation techniques that have been used to isolate sponge-associated bacteria, (ii) provide an overview of bacteria isolated from sponges until 2017 and the associated culture conditions and identify the bacteria not yet cultured from sponges, and (iii) outline promising cultivation strategies for cultivating the uncultivated majority of bacteria from sponges in the future. Despite intensive cultivation attempts, the diversity of bacteria obtained through cultivation remains much lower than that seen through cultivation-independent methods, which is particularly noticeable for those taxa that were previously marked as "sponge-specific" and "sponge-enriched." This poses an urgent need for more efficient cultivation methods. Refining cultivation media and conditions based on information obtained from metagenomic datasets and cultivation under simulated natural conditions are the most promising strategies to isolate the most wanted sponge-associated bacteria.

Behavior of Salmonella Enteritidis and Shigella flexneri during induction and recovery of the viable but nonculturable state

Bacteria may enter into a viable but nonculturable (VBNC) state as a response to stresses, such as those found in food processing. Cells in the VBNC state lose the ability to grow in a conventional culture medium but man recover culturability. The viability, culturability and intracellular reactive oxygen species (ROS) of Salmonella Enteritidis and Shigella flexneri were evaluated under stress conditions to induce a VBNC state. Cells were maintained under nutritional, osmotic and cold stresses (long-term induction) in Butterfield's phosphate solution plus 1.2 M of NaCl at 4°C and under nutritional and oxidative stresses (short-term induction) in 10 mM of H2O2. Culture media, recovery agents, sterilization methods of media and incubation temperature, were combined and applied to recover the culturability of the VBNC cells. Salmonella entered in the VBNC state after 135 days under long-term induction, while Shigella maintained culturability after 240 days. Under short-term induction, Salmonella and Shigella lose culturability after 135 and 240 min, respectively. Flow cytometric analysis revealed viable cells and intracellular ROS in both species in VBNC. It was not possible to recover the culturability of VBNC cells using the 42 combinations of different factors.

Molecular cloning and functional characterization of a Cu/Zn superoxide dismutase from jellyfish Cyanea capillata

We identified and characterized a novel superoxide dismutase (SOD), designated as CcSOD1, from the cDNA library from the tentacle tissue of the jellyfish Cyanea capillata. The full-length cDNA sequence of CcSOD1 consists of 745 nucleotides with an open reading frame encoding a mature protein of 154 amino acids, sharing a predicted structure similar to the typical Cu/Zn-SODs. The CcSOD1 coding sequence was cloned into the expression vector pET-24a and successfully expressed in Escherichia coli Rosetta (DE3) pLysS. The recombinant protein rCcSOD1 was purified by HisTrap High Performance chelating column chromatography and analyzed for its biological function. Our results showed that the purified rCcSOD1 could inhibit superoxide anion and keep active in a pH interval of 4.5-9 and a temperature interval of 10-70°C. Even when heated at 70°C for 60 min, rCcSOD1 retained 100% activity, indicating a relatively high thermostability. These results suggest that CcSOD1 protein may play an important role in protecting jellyfish from oxidative damage and can serve as a new resource for antioxidant products.

Coping with Reactive Oxygen Species to Ensure Genome Stability in Escherichia coli

The facultative aerobic bacterium Escherichia coli adjusts its cell cycle to environmental conditions. Because of its lifestyle, the bacterium has to balance the use of oxygen with the potential lethal effects of its poisonous derivatives. Oxidative damages perpetrated by molecules such as hydrogen peroxide and superoxide anions directly incapacitate metabolic activities relying on enzymes co-factored with iron and flavins. Consequently, growth is inhibited when the bacterium faces substantial reactive oxygen insults coming from environmental or cellular sources. Although hydrogen peroxide and superoxide anions do not oxidize DNA directly, these molecules feed directly or indirectly the generation of the highly reactive hydroxyl radical that damages the bacterial chromosome. Oxidized bases are normally excised and the single strand gap repaired by the base excision repair pathway (BER). This process is especially problematic in E. coli because replication forks do not sense the presence of damages or a stalled fork ahead of them. As consequence, single-strand breaks are turned into double-strand breaks (DSB) through replication. Since E. coli tolerates the presence of DSBs poorly, BER can become toxic during oxidative stress. Here we review the repair strategies that E. coli adopts to preserve genome integrity during oxidative stress and their relation to cell cycle control of DNA replication.

Improved measurements of scant hydrogen peroxide enable experiments that define its threshold of toxicity for Escherichia coli

Escherichia coli is a model organism that has been exploited to reveal key details of hydrogen peroxide stress: the biomolecules that H₂O₂ most rapidly damages and the defensive tactics that organisms use to fend it off. Much less clear is the amount of exogenous H₂O₂ that is sufficient to injure the bacterium and/or to trigger its stress response. To fill this gap, we need to study the behavior of cells when they are exposed to defined amounts of H₂O₂ on an hours-long time scale. Such experiments are difficult because bacteria rapidly consume H₂O₂ that is added to test cultures. Further, lab media itself can generate H₂O₂, and media components interfere with the quantification of H₂O₂ levels. In this study we describe mechanisms by which media components interfere with H₂O₂ determinations, and we identify simple ways to minimize and correct for this interference. Using these techniques, it was shown that standard media generate so much H₂O₂ that most intracellular H₂O₂ derives from the medium rather than from endogenous metabolism. Indeed, bacteria spread on plates must induce their stress response or else perish. Finally, two straightforward methods were used to sustain low-micromolar steady-state concentrations of H₂O₂. In this way we determined that > 2 μM extracellular H₂O₂ is sufficient to trigger the intracellular OxyR stress response, and > 5 μM begins to impair cell growth in a minimal medium. These concentrations are orders of magnitude lower than the doses that have typically been used in lab experiments. The new approaches should enable workers to study how various organisms cope with natural levels of H₂O₂ stress.

Continuing fascination of exploration in natural substances from microorganisms†

In the search for novel organic compounds, I think it is of paramount importance not to overlook the pursuit of microorganism diversity and the abilities those microorganisms hold as a resource. In commemoration of Professor Satoshi Ōmura’s Nobel Prize in Physiology or Medicine, I will briefly describe the microorganism that produces avermectin and then discuss how innovating isolation methods and pioneering isolation sources have opened the door to numerous new microorganism resources. Furthermore, as exploratory research of substances views the world from many different angles—from biological activity to a compound’s physiochemical properties—it is possible to discover a novel compound from a well-known microorganism. Based on this, I will discuss the future prospects of exploratory research.

New compounds, nanaomycin F and G, discovered by physicochemical screening from a culture broth of Streptomyces rosa subsp. notoensis OS-3966

Two new compounds, nanaomycin F and G, were isolated by physicochemical screening method from cultured broth of Streptomyces rosa subsp. notoensis OS-3966, which is known to produce nanaomycin A, B, C, D, and E. Nanaomycin F is a new nanaomycin analog, a 4a-hydroxyl analog of nanaomycin B. Nanaomycin G has a unique skeleton with 1-indanone infused with a tetrahydropyran ring. Nanaomycin A possesses broad antimicrobial activity but nanaomycin F and G demonstrated no bioactivity against all bacteria and fungi tested in this study. In addition, in both nanaomycin F and G, the production of superoxide radicals was majorly decreased in comparison to nanaomycin A. It was considered that the antimicrobial properties were lost as a result of the decrease in production of the superoxide radicals.

A hidden pitfall in the preparation of agar media undermines microorganism cultivability

Microbiologists have been using agar growth medium for over 120 years. It revolutionized microbiology in the 1890s when microbiologists were seeking effective methods to isolate microorganisms, which led to the successful cultivation of microorganisms as single clones. But there has been a disparity between total cell counts and cultivable cell counts on plates, often referred to as the "great plate count anomaly," that has long been a phenomenon that still remains unsolved. Here, we report that a common practice microbiologists have employed to prepare agar medium has a hidden pitfall: when phosphate was autoclaved together with agar to prepare solid growth media (PT medium), total colony counts were remarkably lower than those grown on agar plates in which phosphate and agar were separately autoclaved and mixed right before solidification (PS medium). We used a pure culture of Gemmatimonas aurantiaca T-27(T) and three representative sources of environmental samples, soil, sediment, and water, as inocula and compared colony counts between PT and PS agar plates. There were higher numbers of CFU on PS medium than on PT medium using G. aurantiaca or any of the environmental samples. Chemical analysis of PT agar plates suggested that hydrogen peroxide was contributing to growth inhibition. Comparison of 454 pyrosequences of the environmental samples to the isolates revealed that taxa grown on PS medium were more reflective of the original community structure than those grown on PT medium. Moreover, more hitherto-uncultivated microbes grew on PS than on PT medium.

Generation of superoxide anions by a glycation reaction in conventional laboratory media

We reported that generation of superoxide anion (O(2)(-)) was detected from conventional laboratory media. The generated O(2)(-) is non-enzymatic converted to hydroxyl radicals, which cause damage to lipids, proteins, and nucleic acids. However, the O(2)(-) generating mechanism from culture media is unclear. We considered that the O(2)(-) generation was implicated in a glycation reaction between reducing sugar and proteins, which is the early stage of Maillard reaction. It has been suggested that the glycated proteins, such as Schiff base and Amadori compounds, undergo a spontaneous autoxidation reaction, catalyzed by transition metal ions, involving the O(2)(-) generation. Therefore, we investigated the effect of Chelex 100 on the O(2)(-) generation from brain-heart-infusion (BHI) medium, which is a nutritional culture medium for bacteria. However, the O(2)(-) generation from the BHI medium treated with Chelex 100 was significantly increased in comparison to it treated without Chelex 100. The quantity of O(2)(-) generation from BHI medium was significantly increased by addition of glucose, and in alkaline environment as well as a glycation reaction model system that autoclaved a mixture solution of glucose and tryptophan. In addition, the O(2)(-) generation from BHI medium was significantly inhibited by pyridoxamine that is a Maillard reaction inhibitor. Therefore, it was suggested that the O(2)(-) generation from BHI medium is closely related to the glycation reaction of amide compounds such as proteins containing in the medium without the transition metals.