Removal of Phenol by Rhodococcus opacus 1CP after Dormancy: Insight into Enzymes' Induction, Specificity, and Cells Viability.

Biodegradation of phenol is an effective method for removing this toxicant from contaminated sites. Phenol is a toxic compound for living cells, so many bacteria degrade phenol in relatively low concentrations, up to 0.75 g L-1. The Rhodococcus opacus strain 1CP is an effective destructor of a wide range of pollutants. In the absence of a carbon source in the medium, cells of the R. opacus 1CP strain easily form cyst-like resting cells (CLC). The purpose of this work was to evaluate the viability of cells during long-term storage and the efficiency of the process of phenol destruction by R. opacus 1CP cells germinating after dormancy. Resting cells were obtained by simple cultivation in a rich medium followed by storage under static conditions. This is a simple approach to obtain a large amount of biomass. Decomposition of phenol proceeded via catechol followed by ortho-cleavage of aromatic ring. The induction of three phenol hydroxylases was detected by RT-PCR in cells germinated in a mineral medium with phenol as the carbon source. The stability of the genome of cells germinating after dormancy is shown by box-PCR. Dormant R. opacus 1CP cells, both suspended and immobilized, can be directly used for the decomposition of phenol after 4-12 months storage. In addition to phenol, after 9 months of storage, immobilized germinating cells easily metabolized 4-chlorophenol and 2,4,6-trichlorophenol. The results demonstrate a potential and simple approach toward achieving long-term storage of cells for further use in bioremediation.

Caracterización molecular de bacterias con potencial probiótico aisladas de heces de neonatos humanos / Molecular characterization of bacteria with probiotic potential isolated from stool of human neonates

El objetivo de este estudio es caracterizar molecularmente bacterias con potencial probiótico aisladas de heces de neonatos humanos. Se evaluó 60 muestras de heces de neonatos (0-3 días) se enriquecieron en caldo Man Rogosa y Sharp (MRS) a 37°C/24h. Se seleccionó y se sometió a pruebas in vitro con sales biliares, resistencia a pH bajo y actividad antimicrobiana frente a Escherichia coli ATCC25922, E. coli ATCC35218, Salmonella enterica y Listeria inocua mediante el ensayo difusión en agar. La identificación molecular se realizó con amplificaciones PCR-BOX y el secuenciamiento del gen 16S rRNA. Se aislaron un total de 48 cepas y todas presentaron resistencia a pH 3 y 0.3% sales biliares; 3 cepas mostraron actividad antimicrobiana frente a E. coli ATCC25922, 1 cepa frente a E. coli ATCC35218, 5 cepas frente a L. inocua y todas frente a Salmonella entérica. De las 48 cepas se obtuvieron dos perfiles BOX-PCR pertenecientes a los géneros de Lactobacillus y Enterococcus. Nueve cepas (C5(2), C6(1), C7(1), C11(2), C16 2, C19(2), C20, C35, y C42) presentaron un 100% de similaridad a Lactobacillus plantarum ATCC 14917T [ACGZ01000098] y dos cepas (C15 y C40) un 99.93% y 99.80% de similaridad, respectivamente a Enterococcus faecium CGMCC 1.2136T [AJKH01000109]; estas cepas mostraron actividad en leche con diferencias significativas (p valor < 0.05) en la cinética de pH 3. En conclusión se encontró bacterias con potencial probiótico.

The aim of this study is to molecularly characterize bacteria with probiotic potential isolated from feces of human neonates. Sixty stool samples from neonates (0-3 days) were evaluated and enriched in Man Rogosa and Sharp (MRS) broth at 37 ° C / 24h. It was selected and subjected to in vitro tests with bile salts, resistance to low pH and antimicrobial activity against Escherichia coli ATCC25922, E. coli ATCC35218, Salmonella enterica and Listeria inocua by agar diffusion assay. The molecular identification was made with PCR-BOX amplifications and the sequencing of the 16S rRNA gene. A total of 48 strains were isolated and all showed resistance to pH 3 and 0.3% bile salts; 3 strains showed antimicrobial activity against E. coli ATCC25922, 1 strain against E. coli ATCC35218, 5 strains against L. innocuous and all against S. enterica. Of the 48 strains, two BOX-PCR profiles belonging to the genera of Lactobacillus and Enterococcus were obtained. Nine strains (C52, C61, C71, C112, C162, C192, C20, C35, and C42) presented 100% similarity to L. plantarum ATCC 14917T [ACGZ01000098] and two strains (C15 and C40) 99.93% and 99.80 % similarity, respectively to Enterococcus faecium CGMCC 1.2136T [AJKH01000109]; these strains showed activity in milk with significant differences (p value <0.05) in the kinetics of pH 3. In conclusion, bacteria with probiotic potential were found.

Hunting for cultivable Micromonospora strains in soils of the Atacama Desert.

Innovative procedures were used to selectively isolate small numbers of Micromonospora strains from extreme hyper-arid and high altitude Atacama Desert soils. Micromonosporae were recognised on isolation plates by their ability to produce filamentous microcolonies that were strongly attached to the agar. Most of the isolates formed characteristic orange colonies that lacked aerial hyphae and turned black on spore formation, whereas those from the high altitude soil were dry, blue-green and covered by white aerial hyphae. The isolates were assigned to seven multi- and eleven single-membered groups based on BOX-PCR profiles. Representatives of the groups were assigned to either multi-membered clades that also contained marker strains or formed distinct phyletic lines in the Micromonospora 16S rRNA gene tree; many of the isolates were considered to be putatively novel species of Micromonospora. Most of the isolates from the high altitude soils showed activity against wild type strains of Bacillus subtilis and Pseudomonas fluorescens while those from the rhizosphere of Parastrephia quadrangulares and from the Lomas Bayas hyper-arid soil showed resistance to UV radiation.

Isolation and identification by 16S rRNA sequence analysis of plant growth-promoting azospirilla from the rhizosphere of wheat

ABSTRACT The main objective of the present study was to isolate phytohormone-producing, phosphate-solubilizing strains of Azospirillum from wheat to be used as inoculants for plant growth promotion. Five Azospirillum strains were isolated from the rhizosphere of field-grown wheat (Triticum aestivum L.), and it was confirmed by BOX-polymerase chain reaction (PCR) that the isolates were different and not re-isolates of the same strain. Sequence analysis of the PCR-amplified 16S rRNA gene indicated that four isolates showed maximum similarity to Azospirillum brasilense and one isolate showed maximum similarity to Azospirillum zeae. This is the first report indicating the presence of an A. zeae like isolate in the wheat rhizosphere in Pakistan. The bacterial isolates were characterized for their plant growth-promoting traits, phosphate solubilization, and indole-3-acetic acid (IAA) production. None of the isolates showed phosphate solubilization activity in the commonly used Pikovskaya medium. However, all strains (except AzoK4) exhibited ability to solubilize tricalcium phosphate (TCP) in modified Pikovskaya medium in which sucrose was replaced by Na-malate, as well as in TCP-supplemented Luria-Bertani (LB) medium. Organic acids, such as acetic, citric, lactic, malic, and succinic acids, were detected in culture supernatants of the tested Azospirillum strains. All strains exhibited ability to produce IAA in the growth medium, except Azospirillum sp. AzoK1. Among the strains tested, the maximum IAA production (30.49 ± 1.04 mg L-1) and phosphate solubilization (105.50 ± 4.93 mg L-1) were shown by a pure culture of Azospirillum sp. AzoK2. In pot experiments, single-strain inocula of Azospirillum sp. AzoK1 and AzoK2 improved wheat plant growth.

Phenotypic and genotypic diversity of Pseudomonas aeruginosa strains isolated from hospitals in siedlce (Poland)

A total of 62 Pseudomonas aeruginosa strains isolated from two hospitals in Siedlce (Poland) were studied by repetitive element based PCR (rep-PCR) using BOX primer. BOX-PCR results revealed the presence of 7 numerous genotypes and 31 unique patterns among isolates. Generally, the strains of P. aeruginosa were characterized by resistance to many antibiotics tested and by differences in serogroups and types of growth on cetrimide agar medium. However, the P. aeruginosa strains isolated from faeces showed much lower phenotypic and genotypic variations in comparison with strains obtained from other clinical specimens. It was observed that genetic techniques supported by phenotypic tests have enabled to conduct a detailed characterization of P. aeruginosa strains isolated from a particular environment at a particular time.

Genetic diversity of indigenous common bean (Phaseolus vulgaris L) rhizobia from the state of Minas Gerais, Brazil

We characterized indigenous common bean rhizobia from five districts of the state of Minas Gerais, Brazil. The isolates were trapped by two common bean varieties, the Mineiro Precoce (Andean origin) and Ouro Negro (Mesoamerican origin). Analysis by BOX-PCR of selected isolates detected a high level of genetic diversity.

BOX-PCR-based identification of bacterial species belonging to Pseudomonas syringae: P. viridiflava group

The phenotypic characteristics and genetic fingerprints of a collection of 120 bacterial strains, belonging to Pseudomonas syringae sensu lato group, P. viridiflava and reference bacteria were evaluated, with the aim of species identification. The numerical analysis of 119 nutritional characteristics did not show patterns that would help with identification. Regarding the genetic fingerprinting, the results of the present study supported the observation that BOX-PCR seems to be able to identify bacterial strains at species level. After numerical analyses of the bar-codes, all pathovars belonging to each one of the nine described genomospecies were clustered together at a distance of 0.72, and could be separated at genomic species level. Two P. syringae strains of unknown pathovars (CFBP 3650 and CFBP 3662) and the three P. syringae pv. actinidiae strains were grouped in two extra clusters and might eventually constitute two new species. This genomic species clustering was particularly evident for genomospecies 4, which gathered P. syringae pvs. atropurpurea, coronafaciens, garçae, oryzae, porri, striafaciens, and zizaniae at a noticeably low distance.

Diversidad bacteriana en un biorreactor de lecho fluidificado durante el tratamiento de agua contaminada con nafta / Bacterial diversity in a fluidized bed bioreactor (FBR) treating gasoline-contaminated groundwater

El objetivo principal de esta investigación fue determinar la diversidad bacteriana del proceso de biorremediación de agua contaminada con nafta en un biorreactor de lecho fluidificado en el Recinto Universitario de Mayagüez, de la Universidad de Puerto Rico. El aislamiento y la caracterización de las colonias bacterianas del sistema de biorremediación fueron realizados en medio R2A. Las pruebas morfológicas incluyeron la determinación de la morfología celular y de las colonias, y la reacción frente a la coloración de Gram. Las propiedades fisiológicas se determinaron usando el sistema Biolog® y sobre la base de la habilidad para desarrollar en medio mínimo con nafta como única fuente de carbono. La caracterización molecular se llevó a cabo por BOX-PCR y por análisis de secuencia del ADNr 16S mediante la técnica de ARDRA (amplified ribosomal DNA restriction analysis). De los 162 morfotipos de colonias aislados, 75% fueron bacilos gram-negativos, 19% bacilos gram-positivos, 5% cocos gram-negativos y 1% cocos gram-positivos. Según el análisis ARDRA, estos morfotipos se distribuyeron en 90 grupos genéticos, de los cuales 53% incluyeron cepas con crecimiento en nafta. Las 86 cepas que crecieron en nafta presentaron 52 patrones de amplificación, los que a través de BOX-PCR se agruparon en 50 grupos metabólicamente no relacionados. El alto nivel de diversidad microbiana observado en el reactor permitió la remoción del contaminante y, al parecer, fue importante para la operación estable y eficiente del sistema.

The main objective of this research project was to determine the bacterial diversity during the process of bioremediation of water contaminated with gasoline in a fluidized bed reactor at Mayagüez, PR. Isolation and characterization of bacterial populations from the bioremediation system was performed on R2A medium. Morphological tests included cellular and colonial shape and reaction to Gram coloration. Physiological properties were determined by using carbon utilization profiles (Biolog®) and by the ability of axenic cultures to use gasoline as the sole carbon source. Molecular characterization was performed by BOX-PCR and 16S rDNA sequence analysis (ARDRA). From a total of 162 distinctive isolates, 75% were gram-negative bacilli, 19% gram-positive bacilli, 5% gram-negative cocci and 1% gram-positive cocci. The 162 axenic cultures corresponded to 90 different genetic groups; 53% of which included strains with growth in gasoline as sole carbon source. The 86 strains capable of growing in gasoline corresponded to 52 different amplification patterns in BOX-PCR; which were not metabolically related (Biolog® system). The high degree of microbial diversity in the FBR allowed efficient and stable hydrocarbon removal throughout the operation of the system.