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Indigo is a fabric dye that requires reduction by microbial activity or chemical reagents to render it soluble in water. Sources of indigo for fermentation are primarily divided into composted indigo-containing plants and indigo extracted from plants. To elucidate the factors responsible for bacterial diversity, and for sustaining reduced state of indigo in different preparations, this study assessed fermentation-derived fluids using composted plant leaves, sukumo, and extracted indigo (Ryukyu-ai paste, and Indian indigo cake) prepared using different procedures. Regardless of the indigo source, obligate anaerobic bacteria, including the families Proteinivoraceae and Tissierellaceae, predominate (16.9-46.1%), suggesting their high affinity for this fermentation ecosystem (hyperalkaline and low redox potential). Moreover, bacterial communities in sukumo fermentations are more diverse than those from indigo extracts with the diversity tending to increase based on the fermentation period. Our results further suggest that the microbiota composition in sukumo fermentation is associated with the various bacterial nutrients derived from sukumo, including seed microorganisms. In addition, the debris derived from sukumo can reduce the pH stress experienced by the microorganisms. Further, regardless of 5.4 years difference in the fermentation age, the bacterial flora in two Ryukyu-ai batches exhibit similar features with low microbial diversities. The uniformity of the nutrient, along with the simple, yet strong, bacterial network in Ryukyu-ai fluids may be responsible for the stable bacterial flora composition. Taken together, these results indicate that the microbiota in indigo fermentation is highly influenced by the seed culture, the nutrient derived from raw materials, and the fermentation conditions.

The effects of H2O2 under low- and high-aeration-level conditions on growth and catalase activity in Exiguobacterium oxidotolerans T-2-2T were investigated. Continuous addition of 5-200 mM H2O2 to the culture medium from the mid-exponential growth phase enhanced the growth of the strain under the low-aeration-level condition, whereas the addition of 5-50 mM H2O2 decreased intracellular specific catalase activity and extracellular total catalases activity. The detection of extracellular catalase by the cells and the decrease in intracellular specific catalase activity and extracellular total catalase activity under the high-aeration-level condition account for the stimulation of growth by the introduced H2O2 and the decrease in catalase activities induced by O(2) from H2O2 in the medium. On the other hand, the addition of H2O2 to the medium prior to the initiation of growth inhibited the growth but increased the specific activity of intracellular catalase in the stationary growth phase. Strain T-2-2T grew when 10 mM H2O2 was added to the medium prior to growth. However, the growth was completely inhibited by the catalase inhibitor 3-amino-1,2,4-triazole (3-AT). The continuous addition of H2O2 at an appropriate concentration from prior to the initiation of growth to the stationary growth phase under the low-aeration-level condition resulted in higher intracellular specific catalase activity and cell growth rate than single H2O2 addition prior to growth.

A soluble class I cytochrome c of an alkaliphile was purified and characterized, and its primary structure was determined. This is the first example of a soluble class I cytochrome c in alkaliphiles. Cells the alkaliphilic gram-negative bacterium Pseudomonas alcaliphila AL15-21(T) grown at pH 10 had a soluble cytochrome c content that was more than twofold that of strain AL15-21(T) cells grown at pH 7 under air-limited conditions. Cytochrome c-552, a soluble cytochrome c with a low molecular weight, was purified from strain AL15-21(T) cells grown at pH 10 under air-limited conditions. Cytochrome c-552 had a molecular mass of 7.5 kDa and exhibited an almost fully reduced state in the resting form, which exhibited absorption maxima at wavelengths of 552, 523 and 417 nm. In the oxidized state, it exhibited an absorption maximum at 412 nm when it was oxidized by ferricyanide, its isoelectric point (pI) was 4.3 and it contained one heme c as a prosthetic group. Cytochrome c-552 was autoreduced at pH 10, and the autoreduction was reproducible. On the other hand, the autoreduction of cytochrome c-552 was not observed at pH 7.0. When pH was increased from 7.0 to 8.3, its midpoint redox potentials (E(m) values) increased from +228 mV to +276 mV as determined by redox titrations, and from +217 mV to +275 mV as determined by cyclic voltammetric measurements. The amino acid sequence deduced by cytochrome c-552 gene analysis revealed that the sequence consists of 96 residues, including 19 residues as an amino-terminal signal peptide. A phylogenetic tree based on amino acid sequence indicated that the protein belongs to group 4, cytochrome c(5) in class I cytochrome c.

Although a bioenergetic parameter is unfavorable for production of ATP (DeltapH0), the growth rate and yield of alkaliphilic Bacillus strains are higher than those of neutralophilic Bacillus subtilis. This finding suggests that alkaliphiles possess a unique energy-producing machinery taking advantage of the alkaline environment. Expected bioenergetic parameters for the production of ATP (DeltapH and DeltaPsi) do not reflect the actual parameters for energy production. Certain strains of alkaliphilic Bacillus spp. possess large amounts of cytochrome c when grown at a high pH. The growth rate and yield are higher at pH 10 than at pH 7 in facultative alkaliphiles. These findings suggest that a large amount of cytochrome c at high pHs (e.g., pH 10) may be advantageous for sustaining growth. To date, isolated cytochromes c of alkaliphiles have a very low midpoint redox potential (less than +100 mV) compared with those of neutralophiles (approximately +220 mV). On the other hand, the redox potential of the electron acceptor from cytochrome c, that is, cytochrome c oxidase, seems to be normal (redox potential of cytochrome a=+250 mV). This large difference in midpoint redox potential between cytochrome c and cytochrome a concomitant with the configuration (e.g., a larger negative ion capacity at the inner surface membrane than at the outer surface for the attraction of H+ to the intracellular membrane and a large amount of cyrochrome c) supporting H+-coupled electron transfer of cytochrome c may have an important meaning in the adaptation of alkaliphiles at high pHs. This respiratory system includes a more rapid and efficient H+ and e- flow across the membrane in alkaliphiles than in neutralophiles.

A bacterium, Ikeda-3, that was isolated from the wastewater of a winery was found to produce floating and precipitating exopolysaccharides (EPSs) when grown aerobically in a medium containing sucrose as the sole carbon source. The concentrations of floating and precipitating EPSs were approximately 2.7 g/l and 0.6 g/l, respectively, in a mini-jar fermentor after incubations of the bacterium at 15 degrees C for 5 d in a synthetic medium containing 1% sucrose, 0.01% CaCO3, 0.05% MgSO4, 0.05% K2HPO4, 0.0001% Na2MoO4, 0.05% peptone and 0.82% bicine. A component analysis of two types of EPS suggested that they represent a novel type of sphingan composed of glucose, rhamnose, mannose and mannuroic acid. Glucoronic acid, which is commonly found in sphingans, was absent. From physiological, biochemical and chemotaxonomic characterization, phylogenetic analysis and DNA-DNA relatedness, Ikeda-3 was identified as Novosphingobium rosa. To our knowledge the production of EPS by N. rosa is reported here for the first time.

The catalase gene, vktA, of the hydrogen peroxide-resistant bacterium Vibrio rumoiensis S-1 has been isolated and sequenced. Plasmid pBSsa1 was obtained by genome library screening and it complemented a catalase-less mutant, Escherichia coli strain UM2, indicating that pBSsa1 contained the catalase gene (vktA). The vktA gene consisted of an open reading frame of 1530 bp encoding a 508 amino-acid protein with a calculated size of 57657.79 Da. The deduced amino acid sequence showed high homology with that of bacterial group III catalases. Investigation of the subcellular catalase localization using an immuno-electron microscopical technique revealed that a larger amount of VktA catalase is present in the periplasmic space than in the cytoplasm. The periplasmic space of this bacterium can therefore be regarded as a reservoir of VktA catalase in V. rumoiensis S-1.

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.

Cytochrome c-552 from Pseudomonas alcaliphila AL15-21(T), which is a small cytochrome c(5) from Pseudomonas spp., was first purified and characterized in our previous study. Although it has been found that cytochrome c-552 is induced at a high pH under air-limited condition, the physiological role of this cytochrome c has not been clarified yet. Therefore, to understand its physiological role, further characterization of this cytochrome expressed in Escherichia coli was performed. The yield of the recombinant protein reached 2.8 mg/l of culture, which was 76.4-fold larger than that of native cells. Analytical data of the recombinant protein exactly agreed with that of native cytochrome c-552. The recombinant cytochrome c-552 was oxidized by partially purified cb-type cytochrome c oxidase from P. alcaliphila AL15-21(T) at a rate of 9.6 mu mol min(-1) mg oxidase(-1). Unlike reported cytochromes c from other Pseudomonas spp., the E degrees ' values between pHs 5.0 and 10.0 were nearly unchanged. Cytochrome c-552 oxidized very slowly at pHs 8.0 (6.1 x 10(-4) h(-1)), 9.0 (1.4 x 10(-3) h(-1)) and 10.0 (1.6 x 10(-3) h(-1)), whereas it oxidized more rapidly at pH 7.0 (2.5 x 10(-3) h(-1)). On the other hand, horse heart cytochrome c showed higher oxidation rates at pHs 6.0-10.0 than cytochrome c-552. It is considered that the high electron-retaining ability of cytochrome c-552 at high pHs is important for its physiological function in the environmental adaptation of this bacteria for superior growth at high pHs under air-limited conditions.

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.

Alkaliphilic microorganisms are widely distributed in nature. Among them, several aerobic alkaliphilic Bacillus spp. have been studied in terms of their mechanisms of physiological adaptation under an extremely alkaline condition. On the basis of chemiosmotic theories, neutrophiles produce H+ electrochemical potential (deltap), which is the sum of transmembrane pH gradient (deltapH) (alkaline, inside) and membrane potential (deltapsi) (negative, inside), for active transport of solutes, motility, and ATP synthesis. In the case of alkaliphiles, it seems that Mitchell's chemiosmotic theories alone cannot explain clearly their positive H+ electrochemical potential (deltap) across the membrane because these bacteria exhibit deltaph in a direction opposite to that in neutrophiles, which seems to be causing extensively negative to produce energy, theoretically. Nevertheless, it is reported that ATP synthesis is more rapid at high alkaline pH than at near neutral pH in the facultative alkaliphile Bacillus pseudofirmus OF4. The respiratory system of alkaliphilic microorganisms might have an important role in compensating the reversed transmembrane pH gradient by means of ATP synthesis. To understand the function of the respiratory system in alkaliphiles, several respiratory components in alkaliphilic Bacillus spp. were isolated and characterized. In these studies, respiratory components of alkaliphiles exhibiting several unique characteristics are identified. These characteristics may have an important role in obtaining energy in alkaline environments. Information obtained from bioenergetics studies of alkaliphiles will reveal new important findings on general energy coupling phenomena.

A bacterium Tomakomai B-1 that was isolated from the activated sludge of a treatment process for wastewater of the pulp industry was found to produce soluble and insoluble exopolysaccharides (EPSs) when grown aerobically in a medium containing sucrose as the sole carbon source. The sugar component of soluble EPSs consisted of rhamnose, mannose, galactose, glucose, mannuronic acid, galacturonic acid and glucuronic acid, and that of insoluble EPSs consisted of rhamnose, mannose, galactose, glucose, mannuronic acid and glucuronic acid. The concentrations of insoluble and soluble EPS were approximately 1.63 and 2.58 g/l, respectively, by Erlenmeyer flask culture at 20 degrees C for 3 d with a synthetic medium containing 1% sucrose, 0.05% CaCO(3), 0.05% MgSO(4), 0.1% K(2)HPO(4), 0.0001% Na(2)MoO(4), 0.01% urea, 1.07% MES and small amounts of trace metals. Tomakomai B-1 was identified as Rahnella aquatilis. To our knowledge the production of EPSs by R. Aquatilis is reported here for the first time.