Studies on the microbial populations of the rhizosphere of big sagebrush (<Emphasis Type="Italic">Artemisia tridentata</Emphasis>)

Prolonged use of broad-spectrum antibiotics has led to the emergence of drug-resistant pathogens, both in medicine and in agriculture. New threats such as biological warfare have increased the need for novel and efficacious antimicrobial agents. Natural habitats not previously examined as sources of novel antibiotic-producing microorganisms still exist. One such habitat is the rhizosphere of desert shrubs. Here, we show that one desert shrub habitat, the rhizosphere of desert big sagebrush (Artemisia tridentata) is a source of actinomycetes capable of producing an extensive array of antifungal metabolites. Culturable microbial populations from both the sagebrush rhizosphere and nearby bulk soils from three different sites were enumerated and compared, using traditional plate-count techniques and antibiotic activity bioassays. There were no statistical differences between the relative numbers of culturable non-actinomycete eubacteria, actinomycetes and fungi in the rhizosphere versus bulk soils, but PCR amplification of the 16S rRNA gene sequences of the total soil DNA and denaturing gradient gel electrophoresis showed that the community structure was different between the rhizosphere and the bulk soils. A high percentage of actinomycetes produced antimicrobials; and the percentage of active producers was significantly higher among the rhizosphere isolates, as compared with the bulk soil isolates. Also, the rhizosphere strains were more active in the production of antifungal compounds than antibacterial compounds. 16S rRNA gene sequence analysis showed that sagebrush rhizospheres contained a variety of Streptomyces species possessing broad spectrum antifungal activity. Scanning electron microscopy studies of sagebrush root colonization by one of the novel sagebrush rhizosphere isolates, Streptomyces sp. strain RG, showed that it aggressively colonized young sagebrush roots, whereas another plant rhizosphere-colonizing strain, S. lydicus WYEC108, not originally isolated from sagebrush, was a poor colonizer of the roots of this plant, as were two other Streptomyces isolates from forest soil. These results support the hypothesis that the rhizosphere of desert big sagebrush is a promising source of habitat-adapted actinomycetes, producing antifungal antibiotics.     

Characterization of Antifungal Chitinase from Marine Streptomyces sp. DA11 Associated with South China Sea Sponge Craniella Australiensis

The gene cloning, purification, properties, kinetics, and antifungal activity of chitinase from marine Streptomyces sp. DA11 associated with South China sponge Craniella australiensis were investigated. Alignment analysis of the amino acid sequence deduced from the cloned conserved 451 bp DNA sequence shows the chitinase belongs to ChiC type with 80% similarity to chitinase C precursor from Streptomyces peucetius. Through purification by 80% ammonium sulfate, affinity binding to chitin and diethylaminoethyl-cellulose anion-exchange chromatography, 6.15-fold total purification with a specific activity of 2.95 Umg⁻¹ was achieved. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) showed a molecular weight of approximately 34 kDa and antifungal activities were observed against Aspergillus niger and Candida albicans. The optimal pH, temperature, and salinity for chitinase activity were 8.0, 50°C, and 45 g‰ psu, respectively, which may contribute to special application of this marine microbe-derived chitinase compared with terrestrial chitinases. The chitinase activity was increased by Mn²⁺, Cu²⁺, and Mg²⁺, while strongly inhibited by Fe²⁺ and Ba²⁺. Meanwhile, SDS, ethyleneglycoltetraacetic acid, urea, and ethylenediaminetetraacetic acid were found to have significantly inhibitory effect on chitinase activity. With colloidal chitin as substrates instead of powder chitin, higher V _max (0.82 mg product/min·mg protein) and lower K _m (0.019 mg/ml) values were achieved. The sponge’s microbial symbiont with chitinase activity may contribute to chitin degradation and antifungal defense. To our knowledge, it was the first time to study sponge-associated microbial chitinase.     

A new actinomycete strain SK4-6 producing secondary metabolite effective against methicillin-resistant Staphylococcus aureus

A new actinomycete strain designated SK4-6, was isolated. This organism exhibited strong activity against bacteria including methicillin-resistant Staphylococcus aureus and Micrococcus luteus, in addition to the causative agents of Candidiasis and Aspergillosis diseases, Candida albicans and Aspergillus species respectively. Morphological and chemical studies indicated that this organism belongs to the genus Streptomyces. Analysis of the 16S rRNA sequence of strain SK4-6 showed a high similarity, 99%, with S. qinlingensis. Optimization of cultural conditions was carried out using Plackett–Burman statistical design where seven variables were examined. Starch, pH and inoculum size showed a positive effect on the production of the active substances, however, sucrose, (NH₄)₂SO₄ and yeast extract repress the production.     

Identification of a lipoarabinomannan-like lipoglycan in the actinomycete Gordonia bronchialis

The cell envelopes of actinomycetes contain lipidated macroamphiphiles, of which the most extensively characterised are the lipoarabinomannans of mycobacteria and related bacteria. We have investigated the mycolic acid-containing actinomycete Gordonia bronchialis and identified the presence of a lipoarabinomannan-like lipoglycan. The extraction and purification procedures recovered a second amphiphilic fraction with properties suggesting a phosphatidylinositol mannoside, consistent with studies of other Gordonia species.Dedicated to the memory of our former colleague Dr. David Bendell.     

Evaluation of Streptomyces sp. strain g10 for suppression of Fusarium wilt and rhizosphere colonization in pot-grown banana plantlets

Streptomyces sp. strain g10 exhibited strong antagonism towards Fusarium oxysporum f.sp. cubense (Foc) races 1, 2 and 4 in plate assays by producing extracellular antifungal metabolites. Treating the planting hole and roots of 4-week-old tissue-culture-derived Novaria banana plantlets with strain g10 suspension (10⁸ cfu/ml), significantly (P<0.05) reduced wilt severity when the plantlets were inoculated with 10⁴ spores/ml Foc race 4. The final disease severity index for leaf symptom (LSI) and rhizome discoloration (RDI) was reduced about 47 and 53%, respectively, in strain g10-treated plantlets compared to untreated plantlets. Reduction in disease incidence was not significant (P<0.05) when plantlets were inoculated with a higher concentration (10⁶ spores/ml) of Foc race 4. Rhizosphere population of strain g10 showed significant (P=0.05) increase of more than 2-fold at the end of the 3rd week compared to the 2nd week after soil amendment with the antagonist. Although the level dropped, the rhizosphere population at the end of the 6th week was still nearly 2-fold higher than the level detected after 2 weeks. In contrast, the root-free population declined significantly (P=0.05), nearly 4-fold after 6 weeks when compared to the level detected after 2 weeks. Neither growth-inhibiting nor growth-stimulating effects were observed in plantlets grown in strain g10-amended soil.     

A PCR-based method for the screening of bacterial strains with antifungal activity in suppressive soybean rhizosphere

Selection and evaluation of microbial strains for their antifungal activity in natural environments is time- and energy-consuming. We have adapted a PCR-based method to avoid these inconveniences. Soils that are naturally suppressive to plant disease were chosen as a source of antibiotic-producing bacteria. The screening was performed by means of PCR amplification using degenerate primers corresponding to peptide synthetase genes. Amplification fragments were obtained using template DNA from the rhizosphere of three different soybean fields. In order to assay their potential utility in pathogen control, several Bacillus strains were analysed for their in vitro antifungal activity by testing growth inhibition of Sclerotinia sclerotiorum. Four Bacillus sp. isolates gave a positive amplification signal, and three of them had an inhibitory effect on S. sclerotiorum growth, whereas two strains that failed to give an amplification signal did not inhibit fungal growth. These results show that PCR-based techniques could be useful to assess the presence of strains with potential use as biocontrol agents.     

Antimicrobial and antiviral activities of an actinomycete (Streptomyces sp.) isolated from a Brazilian tropical forest soil

A promising producer of bioactive compounds isolated from a Brazilian tropical soil was tested for its range of antimicrobial activities. Strain 606, classified as Streptomyces sp., could not be identified up to species level, suggesting a possible new taxon. The supernatant and 10 extracts and fractions, obtained by extraction and chromatographic techniques, presented antimicrobial activity using antibiograms. The methanolic fraction was highly active against pathogenic bacteria, phytopathogenic fungi and the human pathogenic yeast Candida albicans. It also possessed high antiviral activity inhibiting the propagation of an acyclovir-resistant herpes simplex virus type 1 strain on HEp-2 cells at non-cytotoxic concentration. The strong cytotoxic effect suggests an antitumour action. This revised version was published online in August 2006 with corrections to the Cover Date.     

Novel Production of Isochainin by a Strain of <Emphasis Type="Italic">Streptomyces </Emphasis>sp<Emphasis Type="Italic">.</Emphasis> Isolated from Rhizosphere Soil of the Indigenous Moroccan Plant <Emphasis Type="Italic">Argania Spinosa</Emphasis> L

Summary An actinomycete strain (designated Ap1) isolated from the rhizosphere soil of Argania spinosa L. strongly inhibited the growth of two plant pathogens: Fusarium oxysporum f.sp. albedinis and Verticillium dahliae. The spore morphology suggested that the Ap1 strain belonged to the genus Streptomyces. The antifungal compound produced by Ap1 was purified by HPLC and identified as the polyene macrolide, isochainin, by NMR and mass spectroscopy. Ap1 showed normal biosynthesis of isochainin in comparison with S. cellulosae ATTC 12625, in which precursor-directed biosynthesis by feeding ethyl (Z)-16-phenylhexadec-9-enoate to the culture medium is required. In addition, Streptomyces sp. strain Ap1 produces isochainin with a 6.5-fold higher concentration than Streptomyces cellulosae ATTC 12625.     

Ultrastructure of freeze-substitutedFrankia strain HFPCcI 3, the actinomycete isolated from root nodules ofCasuarina cunninghamiana

Summary Frankia strain HFPCcI 3 is an actinomycete isolated from root nodules ofCasuarina cunninghamiana. In culture it exhibits typicalFrankia morphology and may produce three distinct morphological forms: branching septate hyphae, terminal or intercalary sporangia, and specialized structures termed vesicles which are the purported site of nitrogenase activity. An examination of the ultrastructure of all three morphological forms using both conventional chemical fixation (CF) and quick-freezing followed by freeze-substitution (FS) reveals some interesting differences between the two fixation methods. Unique to FS material are: 1. smooth membrane profiles; 2. lack of mesosomes; 3. lack of discernible nucleoid regions with condensed chromatin; 4. clarity of cytoplasmic elements such as ribosomes and granular bodies; 5. large cytoplasmic tubules in hyphae and young sporangia; 6. outer wall layer not widely separated from the spherical portion of the vesicle, and 7. bundles of microfilaments in vesicles. The quality of preservation after FS appears to be far superior to that obtained with CF. Accordingly the structures observed after FS are thought to represent more faithfully the structure of the living cell.     

Diversity of nodule-endophytic agrobacteria-like strains associated with different grain legumes in Tunisia

This study represents the first report describing the genetic diversity of nodule-endophytic agrobacteria isolated from diverse legumes and their phylogenetic relationships with the valid species of agrobacteria, as well as the non-recognized genomospecies of the former Agrobacterium tumefaciens (Rhizobium radiobacter). The genetic diversity of a collection of 18 non-nodulating agrobacteria-like strains, previously isolated from root nodules of Vicia faba, Cicer arietinum and Phaseolus vulgaris from different geographical regions of Tunisia, was studied by REP-PCR and PCR-RFLP of the 16S-23S rDNA IGS, as well as by sequence analysis of the 16S rDNA and the housekeeping genes recA and atpD. The aim of the work was to study the genetic diversity of the different isolates and to check for any host-specificity. The results from the different techniques were congruent and suggested a specific interaction for P. vulgaris, whereas no specific endophytic interaction was observed for V. faba and C. arietinum. The phylogenetic analysis clearly indicated that some isolates were affiliated to R. radiobacter or to its non-recognized genomic species (genomovars G2, G4 and G9). However, the other isolates probably constitute new species within Rhizobium (Agrobacterium) and Shinella.     

Exploiting marine actinomycete biosynthetic pathways for drug discovery

Drug discovery relies on the generation of large numbers of structurally diverse compounds from which a potential candidate can be identified. To this end, actinomycetes have often been exploited because of their ability to biosynthesize an impressive array of novel metabolites particularly polyketides. The genetic organization of polyketide synthases (PKSs) makes them readily amenable to manipulation, and thus re-engineering artificial or hybrid PKSs to produce unnatural natural products is a reality. This review highlights two approaches we have used to generate novel polyketides by manipulating genes responsible for starter unit biosynthesis in the Streptomyces maritimus enterocin type II PKS. Our preliminary investigation into the biosynthesis of neomarinone, a rare marine actinomycete-derived meroterpenoid, is also presented.     

Determining the Suitability of Lactobacilli Antifungal Metabolites for Inhibiting Mould Growth

Summary In recent years, public concern about indoor mould growth has increased dramatically in the United States. In this study, lactic acid bacteria (LAB), which are known to produce antimicrobial compounds important in the biopreservation of food, were evaluated to determine if the same antimicrobial properties can be used to inhibit mould fungi that typically colonize wood. Based on biomass measurement, cell-free supernatants from Lactobacillus casei subsp. rhamnosus and Lactobacillus acidophilus grown in deMan Rogosa Sharpe (MRS) broth inhibited 95–100% growth of three mould fungi and one stain fungus associated with wood-based building materials. Lactic acid and four unknown compounds ⩽ kDa molecular weight were fractionated from the culture supernatant by thin layer chromatography and high-performance liquid chromatography. Antifungal activity, which was attributed to one or more unknown metabolites, was retained during heating and neutralization. A 1:2 dilution of L. casei supernatant inhibited 100% growth of all test fungi.     

Enzyme activities in Chrysosporium strains

390 strains of Chrysosporium were screened for their ability to produce enzymes. All strains produced: catalase, phosphatase, lipase, amylase, DNAse and phosphoamidase. No strains showed: valine arylamidase, oxidase, -galactosidase, urease, pectolase, protease nor RNAse.     

Antifungal activities of origanum oil against Candida albicans

The antimicrobial properties of volatile aromatic oils from medicinal as well as other edible plants has been recognized since antiquity. Origanum oil, which is used as a food flavoring agent, possesses a broad spectrum of in vitro antimicrobial activities attributed to the high content of phenolic derivatives such as carvacrol and thymol. In the present study, antifungal properties of origanum oil were examined both in vitro and in vivo. Using Candida albicans in broth cultures and a micro dilution method, comparative efficacy of origanum oil, carvacrol, nystatin and amphotericin B were examined in vitro. Origanum oil at 0.25 mg/ml was found to completely inhibit the growth of C. albicans in culture. Growth inhibitions of 75% and >50% were observed at 0.125 mg/ml and 0.0625 mg/ml level, respectively. In addition, both the germination and the mycelial growth of C. albicans were found to be inhibited by origanum oil and carvacrol in a dose-dependent manner. Furthermore, the therapeutic efficacy of origanum oil was examined in an experimental murine systemic candidiasis model. Groups of mice (n = 6) infected with C. albicans (5 × LD₅₀) were fed varying amounts of origanum oil in a final vol. of 0.1 ml of olive oil (vehicle). The daily administration of 8.6 mg of origanum oil in 100 l of olive oil/kg body weight for 30 days resulted in 80% survivability, with no renal burden of C. albicans as opposed to the group of mice fed olive oil alone, who died within 10 days. Similar results were obtained with carvacrol. However, mice fed origanum oil exhibited cosmetically better clinical appearance compared to those cured with carvacrol. The results from our study encourage examination of the efficacy of origanum oil in other forms of systemic and superficial fungal infections and exploration of its broad spectrum effect against other pathogenic manifestations including malignancy.     

Antifungal action of human cathelicidin fragment (LL13-37) on Candida albicans

Human cathelicidin LL37 and its fragments LL13–37 and LL17–32 exhibited similar potencies in inhibiting growth of the yeast Candida albicans. After treatment with 0.5 μM and 5 μM LL13–37, the hyphae changed from a uniformly thick to an increasingly slender appearance, with budding becoming less normal in appearance and cell death could be detected. Only the yeast form and no hyphal form could be observed following exposure to 50 μM LL13–37. LL13–37 at a concentration of 5 μM was able to permeabilize the membrane of yeast form as well as hyphal form of C. albicans since the nuclear stain SYTOX Green was localized in both forms. Mycelia treated with LL13–37 stained with SYTOX Green, but did not stain with MitoTracker deep red, indicating that the mitochondria were adversely affected by LL13–37. Bimane-labeled LL13–37 was able to enter some of the hyphae, but not all hyphae were affected, suggesting that LL37impaired membrane permeability characteristics in some of the hyphae. Reactive oxygen species was detectable in the yeast form of C. albicans cells after treatment with LL13–37 but not in the untreated cells. The results suggest that the increased membrane permeability caused by LL13–37 might not be the sole cause of cell death. It might lead to the uptake of the peptide, which might have some intracellular targets.     

Antifungal constituents of Northern prickly ash, Zanthoxylum americanum Mill.

Leaf, fruit, stem, bark and root of Zanthoxylum americanum were investigated for antifungal activity with 11 strains of fungi representing diverse opportunistic and systemic pathogens, including Candida albicans, Cryptococcus neoformans and Aspergillus fumigatus. All extracts demonstrated a broad spectrum of antifungal activity and inhibited at least eight fungal species in a disk diffusion assay (600 microg/disk). Antifungal activity was light-dependent, with fruit and leaf extracts most active in general. The presence of light-mediated compounds, such as psoralen, 8-methoxypsoralen and imperatorin in extracts of different organs was confirmed by RP-HPLC. A high furanocoumarin content was detected in fruit and leaf and low furanocoumarin levels were found in bark and wood. A high positive correlation was observed between total furanocoumarin content and fungal inhibition zones (r2=0.902, p<0.001). The results provide a phytochemical basis for the very widespread use of Z. americanum in indigenous North American ethnomedical tradition for conditions that may be related to fungal infections.     

Antifungal activity of a novel chromene dimer

The activity on Aspergillus spp. growth and on ochratoxin A production of two novel chromene dimers (3) was evaluated. The results of the bioassays indicate that the chromene dimer 3a inhibited mycelia growth by approximately 50% (EC₅₀) at 140.1 μmol L⁻¹ for A. niger, 384.2 μmol L⁻¹ for A. carbonarius, 69.1 μmol L⁻¹ for A. alliaceus and 559.1 μmol L⁻¹ for A. ochraceus. When applied at concentrations of 2 mmol L⁻¹, 3a totally inhibited the growth of all Aspergillus spp. tested. Furthermore, ochratoxin A production by A. alliaceus was reduced by about 94% with a 200 μmol L⁻¹ solution of this compound. A moderate inhibitory effect was observed for the analogous structure 3b on ochratoxin A production but not in mycelia growth. No inhibition was registered for compounds 2a and 2b, used as synthetic precursors of the dimeric species 3.     

Comparative analysis and insights into the evolution of gene clusters for glycopeptide antibiotic biosynthesis

The bal, cep, dbv, sta and tcp gene clusters specify the biosynthesis of the glycopeptide antibiotics balhimycin, chloroeremomycin, A40926, A47934 and teicoplanin, respectively. These structurally related compounds share a similar mechanism of action in their inhibition of bacterial cell wall formation. Comparative sequence analysis was performed on the five gene clusters. Extensive conserved synteny was observed between the bal and cep clusters, which direct the synthesis of very similar compounds but originate from two different species of the genus Amycolatopsis. All other cluster pairs show a limited degree of conserved synteny, involving biosynthetically functional gene cassettes: these include those involved in the synthesis of the carbon backbone of two non-proteinogenic amino acids; in the linkage of amino acids 1–3 and 4–7 in the heptapeptide; and in the formation of the aromatic cross-links. Furthermore, these segments of conserved synteny are often preceded by conserved intergenic regions. Phylogenetic analysis of protein families shows several instances in which relatedness in the chemical structure of the glycopeptides is not reflected in the extent of the relationship of the corresponding polypeptides. Coherent branchings are observed for all polypeptides encoded by the syntenous gene cassettes. These results suggest that the acquisition of distinct, functional genetic elements has played a significant role in the evolution of glycopeptide gene clusters, giving them a mosaic structure. In addition, the synthesis of the structurally similar compounds A40926 and teicoplanin appears as the result of convergent evolution.     

Isolation and characterization of bacteria from the rhizosphere of wheat

In this study, we isolated bacteria from rhizosphere and endorhizophere of wheat crops of the central region of Argentina. The isolates were phenotypically characterized and the restriction patterns of 16S rDNA (ARDRA) using endonuclease AluI were analysed. Representative isolates were used to evaluate the effect of the inoculation on the growth of wheat under greenhouse conditions. The effects of plant growth-promoting bacteria on wheat plants were studied by evaluating shoot fresh and dry weights and root fresh and dry weights. One native strain increased the shoot and root dry biomass by 23% and 45% respectively. Other strains increased the shoot dry biomass. A 1.5 kb fragment of the 16S rRNA gene of one isolate was sequenced. This isolate showed high identity with different species of Pseudomonas.     

Effect of soil amendement with root extract ofhibiscus cannabinus L. on its rhizosphere mycoflora

Summary Rhizosphere mycoflora ofH. cannabinus was studied in potted condition after its root extract obtained from two month old plants. Isolations of fungi from the root regions were done at the interval of 15 days by dilution plate method. Estimation of fungi/g dry soil showed a negative rhizosphere effect. A higher number of fungal species was recorded in the treated non-rhizosphere as compared to their number in the rhizosphere. Qalitative analysis of the fungal flora was done and the variation was recorded. Root extract was analysed by paper chromatography. Altogether 7 amino acids and 3 sugars were detected.