A rapid and gentle method for isolation of genomic DNA from pathogenic Nocardia spp

Toxicity of diatom polyunsaturated aldehydes to marine bacterial isolates reveals their mode of action

Diatoms produce and release polyunsaturated aldehydes (PUAs) during senescence in culture and at the end of blooms in nature and these compounds play different ecological roles, as infochemicals, allelochemicals and pheromones In order to elucidate the toxic effects of PUAs, we isolated six bacterial strains from the Mediterranean Sea during a diatom bloom and tested their tolerance to PUA in terms of growth and cell membrane properties. Based upon 16S rRNA sequencing, these bacteria were assigned to the genera Pseudomonas, Sufflavibacter, Halomonas, Vibrio, Idiomarina, and Labrenzia. Growth of these strains was reduced by 50% (EC₅₀) at PUA concentrations ranging from 600 to 1700 μM of 2E,4E/Z-heptadienal (HEPTA), 400-800 μM of 2E, 4E/Z-octadienal (OCTA), and 70-400 μM of 2E, 4E/Z-decadienal (DECA). Two of these strains, Vibrio sp. and Halomonas, sp. were also investigated for membrane fatty acid composition in terms of adaptive modifications of their degree of saturation (ratio between saturated and unsaturated fatty acids) by GC-FID. A direct correlation between hydrophobicity and PUA toxicity was observed, and these bacteria were also found to react to PUAs by increasing the degree of saturation of their membranes fatty acids. Tested PUAs were 4-fold more toxic than the well-investigated n-alkanols, most probably due to their additional chemical aldehyde toxicity to disrupting proteins by the formation of Schiff's bases, and therefore, they act as very toxic and effective poison, probably accumulating in cytoplasmic membranes because of their high hydrophobicity.

A Bacillus sp. isolated from sediments of the Sarno River mouth, Gulf of Naples (Italy) produces a biofilm biosorbing Pb(II)

A Pb-resistant bacterial strain (named hereinafter Pb15) has been isolated from highly polluted marine sediments at the Sarno River mouth, Italy, using an enrichment culture to which Pb(II) 0.48mmoll(-1) were added. 16S rRNA gene sequencing (Sanger) allowed assignment of the isolate to the genus Bacillus, with Bacillus pumilus as the closest species. The isolate is resistant to Pb(II) with a minimum inhibitory concentration (MIC) of 4.8mmoll(-1) and is also resistant to Cd(II) and Mn(II) with MIC of 2.22mmoll(-1) and 18.20mmoll(-1), respectively. Inductively coupled plasma atomic emission spectrometry (ICP-AES) showed that Pb inoculated in the growth medium is absorbed by the bacterial cells at removal efficiencies of 31.02% and 28.21% in the presence of 0.48mmoll(-1) or 1.20mmoll(-1) Pb(II), respectively. Strain Pb15 forms a brown and compact biofilm when grown in presence of Pb(II). Scanning Electron Microscopy (SEM) coupled with Energy Dispersive X-ray Spectroscopy (SEM-EDS) confirm that the biofilm contains Pb, suggesting an active biosorption of this metal by the bacterial cells, sequestering 14% of inoculated Pb as evidenced by microscopic analyses. Altogether, these observations support evidence that strain Pb15 has potentials for being used in bioremediation of its native polluted sediments, with engineering solutions to be found in order to eliminate the adsorbed Pb before replacement of sediments in situ.

DNA extraction from nocardia species for special genes analysis using PCR

BACKGROUND

Nocardia species have a complex cell wall structure similar to that of mycobacteria, and the extraction of DNA from this bacterium is extremely difficult. Currently, to identify Nocardia species particularly, it is essential to utilize molecular techniques.

AIMS

In the present study, we investigated STET (sodium chloride-TRIS-EDTA-triton) buffer for the extraction of high-quality genomic DNA from 20 clinical and environmental isolates.

MATERIALS AND METHODS

The extracted DNA was evaluated for portion of the 16S rRNA, 65-kDa heat-shock protein and 16S rRNA genes via polymerase chain reaction.

RESULTS

The extracted DNA had high molecular mass, and its concentration and purity was suitable when tested in 1% agarose gel, and using UV spectrophotometry. Amplification of three different genes was successfully performed.

CONCLUSION

This paper reveals an inexpensive, reproducible and efficient method of DNA extraction from Nocardia species, which is appropriate for accurate identification of this bacterium via polymerase chain reaction and polymerase chain reaction-restriction fragment length polymorphism.

Periodontal bacterial DNA suppresses the immune response to mutans streptococcal glucosyltransferase

Certain CpG motifs found in bacterial DNA enhance immune responses through Toll-like receptor 9 (TLR-9) and may also demonstrate adjuvant properties. Our objective was to determine if DNA from bacteria associated with periodontal disease could affect the immune response to other bacterial antigens in the oral cavity. Streptococcus sobrinus glucosyltransferase (GTF), an enzyme involved in dental caries pathogenesis, was used as a test antigen. Rowett rats were injected with aluminum hydroxide (alum) with buffer, alum-GTF, or alum-GTF together with either Escherichia coli DNA, Fusobacterium nucleatum DNA, or Porphyromonas gingivalis DNA. Contrary to expectation, animals receiving alum-GTF plus bacterial DNA (P. gingivalis in particular) demonstrated significantly reduced serum immunoglobulin G (IgG) antibody, salivary IgA antibody, and T-cell proliferation to GTF compared to animals immunized with alum-GTF alone. A diminished antibody response was also observed after administration of alum-GTF with the P. gingivalis DNA either together or separately, indicating that physical complexing of antigen and DNA was not responsible for the reduction in antibody. Since TLR triggering by DNA induces synthesis of prospective suppressive factors (e.g., suppressor of cytokine signaling [SOCS]), the effects of P. gingivalis DNA and GTF exposure on rat splenocyte production of SOCS family molecules and inflammatory cytokines were investigated in vitro. P. gingivalis DNA significantly up-regulated SOCS1 and SOCS5 expression and down-regulated interleukin-10 expression by cultured splenocytes. These results suggested that DNA from periodontal disease-associated bacteria did not enhance, but in fact suppressed, the immune response to a protein antigen from cariogenic streptococci, potentially through suppressive SOCS components triggered by innate mechanisms.

Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge

Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98.1-98.3 % similarity), Nocardia brasiliensis (97.9-98.0 %) and Nocardia tenerifensis (97.8-97.9 %). However, the results of DNA-DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.

Characterization of Nocardia asteroides isolates from different ecological habitats on the basis of repetitive extragenic palindromic-PCR fingerprinting

Thirteen isolates of Nocardia asteroides from both soils and aquatic samples (lake and moat sediments, as well as scum from activated sludge), together with a type strain and two known clinical isolates of this species, were characterized by repetitive extragenic palindromic-PCR fingerprinting with the BOX-A1R primer. The resulting DNA fingerprint patterns proved to be strain specific, and cluster analysis distinguished the soil isolates, the aquatic isolates, and the known strains as being in separate groups.

Application of sucrose-gradient centrifugation for selective isolation of Nocardia spp. from soil

AIMS

To devise and evaluate a method for selective isolation of the less abundant actinomycetes, Nocardia spp. in soil.

METHODS AND RESULTS

This newly developed method is based on differentiating Nocardia from other actinomycete taxa by centrifugation. A water suspension of air-dried soil is centrifuged through a gradient consisting of 10, 20, 30, 40 and 50% sucrose at 240 x g for 30 min. The 20% sucrose layer, which is enriched with Nocardia spp., is then diluted and plated on humic acid-vitamin agar supplemented with antibacterial agents. The proposed method consistently achieved selective isolation of Nocardia spp. in all 14 soil samples tested, which accounted for 5-89% of the total microbial population recovered. Tentative taxonomic characterization based on a restriction fragment length polymorphism (RFLP) analysis of the 16S ribosomal DNA suggested that many of the soil isolates could belong to N. asteroides, N. salmonicida or N. uniformis.

CONCLUSIONS

Differential centrifugation can successfully and efficiently isolate soil Nocardia populations that are suppressed by conventional dilution plating approaches.

SIGNIFICANCE AND IMPACT OF THE STUDY

The development and application of new methodologies with which to isolate less-explored actinomycete taxa is important for improving our knowledge about their taxonomy, ecology and industrial applications.

Molecular and immunological characterization of Mycobacterium avium 65 kDa heat shock protein (Hsp65)

The heat shock protein Hsp65 has been characterized previously in several mycobacterial species. This is the first report of the complete sequence of the coding region of the Mycobacterium avium homologue. The sequence was highly homologous to the Hsp65 of other mycobacterial species, as well as being related closely to the murine and human homologues. Recombinant Hsp65 (rHsp65) was expressed in Escherichia coli to high levels and the recombinant protein tested for its immunogenicity in a murine model of M. avium infection. Although mice infected with M. avium produced antibodies that reacted with rHsp65, they showed low proliferative T-cell responses and no cytokine production in response to the same antigen. However, immunization with rHsp65 in the adjuvant dimethydioctadecylammonium bromide (DDA), induced T cells that responded to native Hsp65 with proliferation and IFN-gamma production, indicating that the recombinant and native forms of the protein were antigenically similar. Therefore, the findings indicate that Hsp65 is not a dominant T-cell antigen during M. avium infection.