Microorganisms in Unamended Soil as Observed by Various Forms of Microscopy and Staining

A light-diffraction microscope was modified to allow sequential viewing of the microorganisms in a soil smear by transmitted, reflected, and reflected-polarized incandescent light and by reflected ultraviolet light. Observations were also made by conventional incandescent and ultraviolet transmitted-light microscopy. All results for the various forms of bright-field microscopy with stained and unstained soils were in agreement, but they differed from the results obtained for two types of ultraviolet-fluorescence microscopy. The latter proved to be nonspecific for in situ soil microorganisms. Capsule-like areas were noted surrounding many of the resident microbial cells of soil when viewed by the various forms of bright-field microscopy. These areas could not be stained or removed by a variety of treatments, but they apparently often did take up stain after in situ soil growth had been initiated. It was concluded that these areas are not capsules but may represent a structural component of nonmultiplying microbial cells in soil.     

New L-Amino Acid Ligases Catalyzing Oligopeptide Synthesis from Various Microorganisms

L-Amino acid ligase synthesizes various peptides from unprotected L-amino acids in an ATP-dependent manner. Known L-amino acid ligases catalyze only dipeptide synthesis, but recently we found that RizB of Bacillus subtilis NBRC 3134 catalyzes oligopeptide synthesis. In the present study, we searched for new members of the L-amino acid ligase group that catalyze oligopeptide synthesis. Several hypothetical proteins possessing the ATP-grasp motif were selected by in silico analysis. These recombinant proteins were assayed for L-amino acid ligase activity. We obtained five L-amino acid ligases showing oligopeptide synthesis activities. These proteins showed low similarity in amino acid sequence, but commonly used branched-chain amino acids, such as RizB, as substrates. Furthermore, the spr0969 protein of Streptococcus pneumoniae synthesized longer peptides than those synthesized by RizB, and the BAD_1200 protein of Bifidobacterium adolescentis showed higher activity toward aromatic amino acids than toward branched-chain ones. We also examined some of their characteristics.     

Microbiological Conversion of Lapachol by Various Microorganisms

Oxydative cyclization of lapachol was attempted by feeding this compound into the culture broth of Beauveria sulfurescens and two ionophore-producing strains of Streptomyces albus and Streptomyces griseus. As a result, three compounds were obtained, lomatiol, lomatic acid and lomatiol acetate, only with B. sulfurescens and S. albus. The structures of these products were determinated by NMR and mass spectrometry. The stereochemistry is given by a comparison with butene analogs.     

Oxidative Cyclization of Linalol by Various Microorganisms

(±) Linalol is cyclized into cis and trans linalol oxides by various microorganisms. This reaction, assuming an intermediate epoxidation step, is analogous to the corresponding step proposed for the biosynthesis of ionophorous antibiotics.     

Characteristics of Cyclodextrin Production Using Cyclodextrin Glucanotransferases from Various Groups of Microorganisms

Cyclodextrin glucanotransferases (CGTases; EC 2.4.1.19) from newly isolated mesophilic, thermophilic, alkalophilic, and halophilic bacilli, as well as from thermoactinomycetes, were purified to homogeneity, and some of their physicochemical and biochemical characteristics (cyclizing, disproportionating, and hydrolytic activities) were studied. Cyclodextrin (CD) production in the presence and absence of compounds favoring formation of complexes had certain specific features. We were able to demonstrate that CGTases of mesophilic and thermophilic strains form mixtures of -, -, and -CDs, whereas the enzymes from halophilic and alkalophilic microorganisms preferentially catalyze the formation of -CD.     

Extradiol Cleavage of 3-Methylcatechol by Catechol 1,2-Dioxygenase from Various Microorganisms

The isofunctional enzymes of catechol 1,2-dioxygenase from species of Acinetobacter, Pseudomonas, Nocardia, Alcaligenes, and Corynebacterium oxidize 3-methylcatechol according to both the intradiol and extradiol cleavage patterns. However, the enzyme preparations from Brevibacterium and Arthrobacter have only the intradiol cleavage activity. Comparison of substrate specificity among these isofunctional dioxygenases shows striking differences in the oxidation of 3-methylcatechol, 4-methylcatechol and pyrogallol.     

多花蔷薇总RNA提取方法

根据总RNA完整性、纯度和得率筛选出适合多花蔷薇幼嫩根、叶总RNA的提取方法。结果表明,以CTAB/酸酚法提取的扦插苗根系总RNA、以LiCl-尿素法提取的扦插苗根、叶总RNA以及采用RNeasyPlantMiniKit试剂盒的改进方法提取的组培苗嫩叶总RNA电泳有清晰明亮的28S、18S条带,无降解;其A260/A280值为1.73~2.04,表明总RNA质量好。RT-PCR结果进一步证实所提取的总RNA能够用于分子生物学的各种下游实验。RNA得率分别为:根系和组培苗嫩叶120-140μg/g(fw),扦插苗嫩叶190-230μg/g(fw)。CTAB/酸酚法提取的嫩叶总RNA、SDS/酸酚法提取的根、叶总RNA有多糖污染,且有明显降解。TotalRNAisolationsystem(Z5111,Promega)试剂盒不适合提取多花蔷薇各组织总RNA。     

Replica Plating Method for Estimating Phenanthrene-Utilizing and Phenanthrene-Cometabolizing Microorganisms

A replica plating method was developed for detecting and enumerating phenanthrene-degrading microorganisms. The method is designed to discriminate between aquatic organisms that utilize phenanthrene as the sole carbon and energy source and organisms that cometabolize phenanthrene. The method was used to demonstrate that phenanthrene utilizers and phenanthrene cometabolizers coexist in estuarine sediments.     

Estimate of the Genome Size of Various Microorganisms

Bacterial genome sizes, determined by deoxyribonucleic acid reassociation kinetics, vary over a 10-fold range. The smallest studied, Chlamydia trachomatis, had a genome of 6 x 10(5) nucleotide pairs compared to 4.5 x 10(6) for Escherichia coli.     

Transfer of Microorganisms, Including Listeria monocytogenes, from Various Materials to Beef

The quantity of microorganisms that may be transferred to a food that comes into contact with a contaminated surface depends on the density of microorganisms on the surface and on the attachment strengths of the microorganisms on the materials. We made repeated contacts between pieces of meat and various surfaces (stainless steel and conveyor belt materials [polyvinyl chloride and polyurethane]), which were conditioned with meat exudate and then were contaminated with Listeria monocytogenes, Staphylococcus sciuri, Pseudomonas putida, or Comamonas sp. Attachment strengths were assessed by the slopes of the two-phase curves obtained by plotting the logarithm of the number of microorganisms transferred against the order number of the contact. These curves were also used to estimate the microbial population on the surface by using the equation of A. Veulemans, E. Jacqmain, and D. Jacqmain (Rev. Ferment. Ind. Aliment. 25:58-65, 1970). The biofilms were characterized according to their physicochemical surface properties and structures. Their exopolysaccharide-producing capacities were assessed from biofilms grown on polystyrene. The L. monocytogenes biofilms attached more strongly to polymers than did the other strains, and attachment strength proved to be weaker on stainless steel than on the two polymers. However, in most cases, it was the population of the biofilms that had the strongest influence on the total number of CFU detached. Although attachment strengths were weaker on stainless steel, this material, carrying a smaller population of bacteria, had a weaker contaminating capacity. In most cases the equation of Veulemans et al. revealed more bacteria than did swabbing the biofilms, and it provided a better assessment of the contaminating potential of the polymeric materials studied here.     

Isolation and Characterization of Four Gram-Positive Nickel-Tolerant Microorganisms from Contaminated Sediments

Microbial communities from riparian sediments contaminated with high levels of Ni and U were examined for metal-tolerant microorganisms. Isolation of four aerobic Ni-tolerant, Gram-positive heterotrophic bacteria indicated selection pressure from Ni. These isolates were identified as Arthrobacter oxydans NR-1, Streptomyces galbus NR-2, Streptomyces aureofaciens NR-3, and Kitasatospora cystarginea NR-4 based on partial 16S rDNA sequences. A functional gene microarray containing gene probes for functions associated with biogeochemical cycling, metal homeostasis, and organic contaminant degradation showed little overlap among the four isolates. Fifteen of the genes were detected in all four isolates with only two of these related to metal resistance, specifically to tellurium. Each of the four isolates also displayed resistance to at least one of six antibiotics tested, with resistance to kanamycin, gentamycin, and ciprofloxacin observed in at least two of the isolates. Further characterization of S. aureofaciens NR-3 and K. cystarginea NR-4 demonstrated that both isolates expressed Ni tolerance constitutively. In addition, both were able to grow in higher concentrations of Ni at pH 6 as compared with pH 7 (42.6 and 8.5 mM Ni at pH 6 and 7, respectively). Tolerance to Cd, Co, and Zn was also examined in these two isolates; a similar pH-dependent metal tolerance was observed when grown with Co and Zn. Neither isolate was tolerant to Cd. These findings suggest that Ni is exerting a selection pressure at this site for metal-resistant actinomycetes.     

Isolation of Arthrobacter Bacteriophage from Soil

Soil was percolated with water and various nutrient solutions, and then the percolates were analyzed for bacteriophages which produced plaques on various Arthrobacter strains. The water percolates did not contain detectable phage. In contrast, phages for A. globiformis strains ATCC 8010 and 4336, and for several recent Arthrobacter species soil isolates, were easily detected in nutrient broth, soil extract, and cation-complete medium percolates. These percolates did not contain phage that produced plaques on A. oxydans and a recent Arthrobacter species soil isolate. Percolation with a selective nicotine-salts solution was required for demonstrating phage for these bacteria. None of the percolates contained phage for five additional named Arthrobacter species. In addition, phages were not detected for A. crystallopoietes in a 2-hydroxypyridine percolate of soil. Based on their lytic spectra, the phage isolates from this soil were relatively host specific.     

Isolation of Saprophytic Basidiomycetes from Soil

A method with the combined advantages of soil particle washing, selective inhibitors, and an indicator substrate was developed to isolate saprophytic basidiomycetes from soil. Organic particles were washed from soil and plated on a medium containing lignin, guaiacol, and benomyl, which reduced mold growth and allowed detection of basidiomycetes producing laccase or peroxidase. The 64 soil samples yielded 67 basidiomycete isolates, representing 51 groups on the basis of morphology and physiology. This method should facilitate investigations into the biodiversity of soil basidiomycetes and yield organisms that are useful in bioremediation of soils contaminated with pesticides or other recalcitrant aromatic compounds.     

Selective-Differential Medium for Isolation and Differentiation of Pectinatus from Other Brewery Microorganisms

An agar medium, LL-agar (lactate-lead acetate) was designed to selectively differentiate members of the genus Pectinatus (S. Y. Lee, M. S. Mabee, and N. O. Jangaard, Int. J. Syst. Bacteriol. 28:582-594, 1978; S. Y. Lee, M. S. Mabee, N. O. Jangaard, and E. K. Horiuchi, J. Inst. Brew. 86:28-30, 1980) from other brewery microorganisms. Selectivity was achieved by the use of sodium lactate as the sole source of carbon and phenylethyl alcohol as an inhibitor for aerobic gram-negative bacteria and yeast. Differentiation was established by the introduction of lead acetate into the medium, which reacted with the H₂S liberated by Pectinatus and resulted in a blackening of the Pectinatus colonies while the other brewery organisms, when present, remained white. In combination with the Lee tube (J. E. Ogg, S. Y. Lee, and B. J. Ogg, Can. J. Microbiol. 25:987-990, 1979) and this medium, isolation of Pectinatus organisms from beer samples was accomplished with convenience and simplicity.     

Isolation of Alkaline Protease Inhibitor Producing Microorganisms

For the purpose of obtaining microorganisms capable of producing alkaline protease inhibitor, screening test was carried out. One strain of microorganisms (No. S–3253) showed strong ability to produce alkaline protease inhibitor.

The morphological and physiological characteristics of strain S–3253 were studied. This strain was found to belong to Streptomyces albogriseolus.

When the strain S–3253 was cultivated at 45°C with a medium containing 4% polypepton, 2% starch, 0.1% yeast extract, 0.1% NaCl, 0.1% K₂HPO₄ and 0.05% MgSO₄-7H₂O in shake-flasks (pH 7.0), the highest activity was obtained after 40~48 hr cultivation.     

Isolation of Acinetobacter from Soil and Water

An enrichment culture procedure for isolating members of the genus Acinetobacter from soil and water is described. It involves the use of vigorously aerated mineral media at relative low pH, supplemented with acetate or other suitable carbon source and nitrate as nitrogen source. With this method, virtually all samples of soil and water yielded representatives of this genus. Semiquantitative comparisons of the numbers of Acinetobacter and of all bacteria capable of aerobic growth in a complex medium revealed that Acinetobacter constituted no less than 0.001% of the total heterotrophic aerobic population in soil and water and was one of the predominant organisms in some water samples.