Small colony variants of <Emphasis Type=Italic>Staphylococcus aureus</Emphasis> — <Emphasis Type=Italic>review</Emphasis>

Bacterial variants of Staphylococcus aureus called small colony variants (SCVs) originate by mutations in metabolic genes, resulting in emergence of auxotrophic bacterial subpopulations. These variants are not particularly virulent but are able to persist viable inside host cells. SCVs show their characteristic auxotrophic growth deficiency and depressed α-cytotoxin activity. Environmental pressure such as antibiotics, select for isogenic SCV cells that are frequently found coexisting with their parent wild-type strains in a mixed bacterial culture. SCV strains often grow on blood agar as non-pigmented or pinpoint pigmented colonies and their key biochemical tests are often non-reactive. Their altered metabolism or auxotrophism can result in long generation time and thus SCV phenotype, more often than not SCV can be overgrown by their wild-type counterparts and other competitive respiratory flora. This could affect laboratory detection. Thus, molecular methods, such as 16S rRNA partial sequencing or amplification of species-specific DNA targets (e.g. coagulase, nuclease) directly from clinical material or isolated bacterial colonies, become the method of choice. Patients at risk of infection by S. aureus SCVs include cystic fibrosis patients (CF), patients with skin and foreign-body related infections and osteomyelitis, as they suffer from chronic staphylococcal infections and are subject to long-term antibiotic therapy. Molecular evidence of SCV development has not been found except for some random mutations of the thymidylate synthase gene (thyA) described in SCV S. aureus strains of CF patients. These variants are able to bypass the antibiotic effect of folic acid antagonists such as sulfonamides and trimethoprim. Resistance to gentamicin and aminoglycosides in the hemin or menadione auxotrophic SCVs was hypothesized as being due to decreased influx of the drugs into cells as a result of decreased ATP production and decreased electrochemical gradient on cell membranes.     

Comparative genetics of yeasts: A novel β-fructosidase gene <Emphasis Type=Italic>SUC8</Emphasis> in <Emphasis Type=Italic>Saccharomyces cerevisiae</Emphasis>

Molecular and genetic analyses revealed that the distillers race XII, which is an ancestor of Saccharomyces cerevisiae Peterhof and Gatchina genetic lines, has three polymeric β-fructosidase genes: SUC2, SUC5, and SUC8. The latter gene located on the X chromosome was identitied in this work for the first time. The presence of the single SUC2 gene in yeasts used in the international project on sequencing of the S. cerevisiae genome is discussed.     

Isozymes of <Emphasis Type=Italic>α</Emphasis>-amylases from newly isolated <Emphasis Type=Italic>Bacillus thuringiensis</Emphasis> CKB19: Production from immobilized cells

The aim of this study was to produce two isozymes of α-amylase by immobilization of a newly isolated soil bacterium. The bacterium was identified as Bacillus thuringiensis CKB19 on the basis of its 16S rRNA profile. Enzyme production by free cells increased linearly with cell growth up to 34 h in starch containing enriched liquid media. The active bacterial cells were immobilized in Caalginate beads, and operational stability of the entrapped cell was optimized for amylase production. Enzyme production was optimal at an alginate concentration of 2 g% (w/v), calcium chloride concentration of 1 M, and with 300 beads (each bead contained 2 × 10⁷ cells)/250 mL flask. Amylase production by the immobilized cells was about 3 times higher than free cell fermentation after 34 h of incubation. It was observed that the immobilized bacterium secreted two different amylases (Am-I and Am-II) into the culture fluid. The molecular masses of Am-I and Am-II were 59.6 and 44.7 kd, respectively, and showed optimum activity at pH 5.0 and 9.0. Both amylases showed optimum activity at 40°C and were stable at the same temperature, with losses of only 10 and 20% (for Am I and Am II, respectively) of their original activities after 24 h of incubation. Further, both amylases were salt tolerant (up to 4 M NaCl) and hydrolyzed raw starchy foods into glucose. All these characteristics make this enzyme mixture suitable for use as a digestive aid and for the improvement of digestibility of animal feed ingredients.     

Effect of <Emphasis Type=Italic>Azotobacter chroococcum</Emphasis> on <Emphasis Type=Italic>in vitro</Emphasis> pineapple plants’ growth during acclimatization

Pineapple is one of the most important tropical fruits, but the availability of planting material is insufficient to agricultural demands. Therefore, several pineapple micropropagation protocols have been developed. However, acclimatization of in vitro plants continues to take a prolonged period. Biofertilizers have been found as safe alternatives to improve the agricultural performances of many crops. This study highlights some of the effects of the application of Azotobacter chroococcum (INIFAT5 strain) on in vitro pineapple plants during acclimatization. The bacteria were sprayed immediately after transplanting to the ex vitro environment; the plants were then sprayed every 4 wk. A control group of plants was established. Subsequently, after 5 mo, the evaluated variables included fresh and dry plant weight, plant height (cm), and root length (cm). The anatomy of middle-aged leaves and roots was also studied: transversal thickness and width of cuticle, epidermis, hypodermis, aquiferous parenchyma, and photosynthetic parenchyma. Thickness of root exoderm, external cortex, internal cortex, and stele were also evaluated. In general, the INIFAT5 strain improved the plant development. Results showed that the bacteria significantly provoked changes in the plant fresh weight, the thickness of the leaf abaxial and adaxial cuticles, and the root exoderm width. Contrastingly, A. chroococcum did not affect the thickness of the leaf photosynthetic parenchyma.     

Characterization of a recombinant endo-1,5-α-<Emphasis Type=SmallCaps>l</Emphasis>-arabinanase from the isolated bacterium <Emphasis Type=Italic>Bacillus licheniformis</Emphasis>

The bacterium Bacillus licheniformis, which exhibits high hydrolytic activity toward arabinan, was isolated from soil, and its gene encoding endo-1,5-α-l-arabinanase was cloned and sequenced. The gene has an open reading frame that encodes 328 amino acids, including a signal peptide of 37 amino acids. Endo-1,5-α-l-arabinanase, a member of glycosyl hydrolase family 43, was expressed in Escherichia coli and purified as a 34-kD monomer with a specific activity of 27 U/mg. Optimal activity toward debranched arabinan (linear 1,5-α-l-arabinan) occurred at pH 6.0 and 35°C, with a k _cat of 160/sec and a K _m of 19 mg/mL.     

<Emphasis Type=Italic>Alcicornis haroldi</Emphasis> n. sp. (Digenea: Bucephalidae) from the yellowspotted trevally <Emphasis Type=Italic>Carangoides fulvoguttatus</Emphasis> (Forsskål) (Carangidae) from off New Caledonia

Alcicornis haroldi n. sp. is described from Carangoides fulvoguttatus from off New Caledonia, South Pacific. It differs from all other Alcicornis spp. in its large protuberant pharynx, and from the most similar species, A. baylisi Nagaty, 1937, in its broader rhynchus, indistinct withdrawn tentacles and vitelline distribution.     

Revision of “<Emphasis Type=Italic>Septonema ochraceum</Emphasis>” revealed three new species of <Emphasis Type=Italic>Venturiaceae</Emphasis> and <Emphasis Type=Italic>Herpotrichiellaceae</Emphasis>

Survey of seven strains determined as Septonema ochraceum (Dothideomycetes, inc. sed.) isolated from pine litter or obtained from public collections revealed three new species, Fusicladium cordae, F. sicilianum (Venturiaceae), Cladophialophora matsushimae (Herpotrichiellaceae) and a cryptic species morphologically identical to Devriesia americana (Teratosphaeriaceae), but phylogenetically distinct. Morphological survey and phylogenetic analysis using nucleotide sequence data from the nuclear ribosomal subunit genes indicate a close relationship within three species colonising pine litter needles, F. cordae, F. pini and F. ramoconidii. F. sicilianum is most related to F. rhodense. C. matsushimae represents a species belonging to one of the lineages of the polyphyletic genus Cladophialophora. None of the strains observed can be classified morphologically as S. ochraceum, of which the type material does not exist.     

<Emphasis Type="Italic">Acinetobacter kyonggiensis</Emphasis> sp. nov., a <Emphasis Type="Italic">β</Emphasis>-glucosidase-producing bacterium,isolated from sewage treatment plant

A Gram-negative, non-motile bacterium, designated KSL5401-037^T, was isolated from a sewage treatment plant in Gwangju in the Republic of Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain KSL5401-037^T belonged to the genus Acinetobacter in the family Moraxellaceae of the Gammaproteobacteria (Brisou and Prevot, 1954). According to a 16S rRNA gene sequence analysis, it was closely related to Acinetobacter johnsonii ATCC 17909^T (97.3%), A. bouvetii 4B02^T (97.2%), and A. beijerinckii 58a^T (96.8%). Chemotaxonomic data revealed that strain KSL5401-037^T possesses an ubiquinone system with Q-8 as the predominant compound and C_16:0 (19.2%), C_18:1 ω9c (19.5%), and summed feature 3 (C_16:1 ω6c / C_16:1 ω7c, 34.1%) as the predominant cellular fatty acids. The major polar lipids detected in strain KSL5401-037^T were diphosphatidylglycerol (DPG) and, phosphatidylethanolamine (PE), followed by phosphatidylglycerol (PG) and moderate amounts of phosphatidylcholine and phosphatidylserine. The G+C content of the genomic DNA was 41.2–42.1 mol%. Strain KSL5401-037^T exhibited relatively low levels of DNA-DNA relatedness with respect to A. johnsonii DSM 6963^T (17.7%) and A. bouvetii 4B02^T (9.3%). The DNA-DNA relatedness values, biochemical, and physiological characteristics of strain KSL5401-037^T strongly support its genotypic and phenotypic differentiation from other recognized type strains of the genus Acinetobacter. Based on these data, strain KSL5401-037^T (JCM 17071^T =KEMC 5401-037^T) should be classified in the genus Acinetobacter as a type strain of novel species, for which the name Acinetobacter kyonggiensis sp. nov. is proposed.     

<Emphasis Type="Italic">Paracoccus pueri</Emphasis> sp. nov., isolated from Pu’er tea

A Gram-stain negative, aerobic, short rod-shaped, motile by flagella bacterial strain (THG-N2.35^T), was isolated from Pu’er tea. Growth occurred at 10–40 °C (optimum 28 °C), at pH 4–7 (optimum 7) and at 0–5% NaCl (optimum 1%). Based on 16S rRNA gene sequence analysis, the near phylogenetic neighbours of strain THG-N2.35^T were identified as Paracoccus hibisci KACC 18632^T (99.0%), Paracoccus tibetensis CGMCC 1.8925^T (98.7%), Paracoccus beibuensis CGMCC 1.7295^T (98.2%), Paracoccus aestuarii KCTC 22049^T (98.2%), Paracoccus rhizosphaerae LMG 26205^T (98.1%), Paracoccus zeaxanthinifaciens ATCC 21588^T (97.1%), Paracoccus marcusii DSM 11574^T (97.0%). Levels of similarity between strain THG-N2.35^T and other Paracoccus species were lower than 97.0%. DNA-DNA hybridization values between strain THG-N2.35^T and P. hibisci KACC 18632^T, P. tibetensis CGMCC 1.8925^T, P. beibuensis CGMCC 1.7295^T, P. aestuarii KCTC 22049^T, P. rhizosphaerae LMG 26205^T, P. zeaxanthinifaciens ATCC 21588^T, P.marcusii DSM 11574^T were 47.5% (42.3%, reciprocal analysis), 36.1% (32.3%), 24.7% (22.1%), 19.2% (16.3%), 11.3% (8.8%), 11.1% (10.8%), 6.1% (5.8%), respectively. The DNA G+C content of strain THG-N2.35^T was 62.3 mol%. The polar lipids were diphosphatidylglycerol, phosphatidyl-N-methylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The quinone was ubiquinone-10 (Q-10). The major fatty acids were C_10:0 3OH, C_16:0, C_18:0 and C_18:1 ω7?. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain THG-N2.35^T represent a novel species of the genus Paracoccus, for which the name Paracoccus pueri sp. nov. is proposed. The type strain is THG-N2.35^T (= KACC 18934^T = CCTCC AB 2016177^T).     

<Emphasis Type="Italic">Nonomuraea aegyptia</Emphasis> sp. nov., a novel actinomycete isolated from a sand dune

The taxonomic position of an unknown actinomycete isolated from a sand dune soil sample collected at Borg El-Arab in Egypt was established using a combination of genotypic and phenotypic data. Isolate S136(T) had chemotaxonomic and morphological properties consistent with its classification in the genus Nonomuraea and formed a distinct phyletic line in the Nonomuraea 16S rRNA gene tree. It was most closely related to the type strains of Nonomuraea helvata, Nonomuraea kuesteri and Nonomuraea turkmeniaca, sharing 16S rRNA gene similarities with these species of 97.1, 97.2 and 97.3%, respectively. The organism was distinguished from representatives of validly described Nonomuraea species using a range of phenotypic properties. It is apparent that the isolate belongs to a novel Nonomuraea species. The name proposed for this taxon is Nonomuraea aegyptia sp. nov., the type strain is S136(T) (=CGMCC 4.2054(T) = DSM 45082(T)).     

An <Emphasis Type=Italic>R</Emphasis><Subscript>0</Subscript> theory for source–sink dynamics with application to <Emphasis Type=Italic>Dreissena</Emphasis> competition

Source–sink dynamics may be ubiquitous in ecology. We developed a theory for source–sink dynamics using spatial extensions of the net reproductive value, R ₀, which has been used elsewhere to define fitness, disease eradication, population growth, and invasion risk. R ₀ decomposes into biologically meaningful components—lifetime reproductive output, survival, and dispersal—that are widely adaptable and easily interpreted. The theory provides a general quantitative means for relating fundamental niche, biotic interactions, dispersal, and species distributions. We applied the methods to Dreissena and found a resolution to a paradox in invasion biology—competitive coexistence between quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels among lakes despite extensive niche overlap within lakes. Source–sink dynamics within lakes between deepwater and shallow habitats, which favor quagga and zebra mussels, respectively, yield a metacommunity distribution where quagga mussels dominate large lakes and zebra mussels dominate small lakes. The source–sink framework may also be useful in spatial competition theory, habitat conservation, marine protected areas, and ecological responses to climate change.     

<Emphasis Type=Italic>Pseudomonas seleniipraecipitatus</Emphasis> sp. nov.: A Selenite Reducing γ-<Emphasis Type=Italic>Proteobacteria</Emphasis> Isolated from Soil

Microbial fuel cells (MFCs) are a technology that provides electrical energy from the microbial oxidation of organic compounds. Most MFCs use oxygen as the oxidant in the cathode chamber. This study examined the formation in culture of an unidentified bacterial oxidant and investigated the performance of this oxidant in a two-chambered MFC with a proton exchange membrane and an uncoated carbon cathode. DNA, FAME profile and characterization studies identified the microorganism that produced the oxidant as Burkholderia cenocepacia. The oxidant was produced by log phase cells, oxidized the dye 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS), had a mass below 1 kD, was heat stable (121°C) and was soluble in ethanol. In a MFC with a 1000 Ω load and ABTS as a mediator, the oxidizer increased cell voltage 11 times higher than atmospheric oxygen and 2.9 times higher than that observed with ferricyanide in the cathode chamber. No increase in cell voltage was observed when no mediator was present. Organisms that produce and release oxidizers into the media may prove useful as bio-cathodes by improving the electrical output of MFCs.     

NaCl-induced photoinhibition and recovery of the photosynthetic activity of a <Emphasis Type=Italic>katG</Emphasis><Superscript>−</Superscript> mutant of cyanobacterium <Emphasis Type=Italic>Synechocystis</Emphasis> sp. PCC 6803

The joint effects of 0.5 M NaCl and light of different intensities on the activity of the photosynthetic apparatus and ATP content in cells of the katG ⁻ mutant of cyanobacterium Synechocystis sp. PCC 6803 have been studied. The mutant demonstrated a higher photoinhibition rate and a slower rate of recovery compared with the wild type, as shown by measurements of the CO₂-dependent O₂ production and delayed fluorescence of Chl a. The presence of 0.5 M NaCl in the incubation medium caused equal photoinhibition of the photosynthetic apparatus at I = 1200 μE m⁻² s⁻¹ in the mutant and wild-type cells. At I = 2400 μE m⁻² s⁻¹, we observed stronger inhibition and slower recovery of the photosynthetic apparatus in the katG ⁻ mutant than in wild-type cells. The data obtained evidence an important role of catalase-peroxidase in the system of reparation of the photosynthetic apparatus damaged by high-intensity light, especially at the background of NaCl stress.