Impact of phosphate solubilizing bacteria on wheat (Triticum aestivum ) in the presence of pesticides / Impacto das bactérias solubilizantes de fosfato no trigo (Triticum aestivum ) na presença de pesticidas

Abstract Three phosphate solubilizing bacteria were isolated and identified by 16S rRNA sequencing as Pseudomonas putida, Pseudomonas sp and Pseudomonas fulva . The strains were subjected to plant biochemical testing and all the PGPR attributes were checked in the presence of pesticides (chlorpyrifos and pyriproxyfen). The phosphate solubilizing index of strain Ros2 was highest in NBRIP medium i.e 2.23 mm. All the strains showed acidic pH (ranges from 2.5-5) on both medium i.e PVK and NBRIP. Strain Ros2 was highly positive for ammonia production as well as siderophore production while strain Rad2 was positive for HCN production. The results obtained by the strains Rad1, Rad2 and Ros2 for auxin production were 33.1, 30.67 and 15.38 µg ml-1, respectively. Strain Rad1 showed 16% increase in percentage germination in comparison to control in the presence of pesticide stress. Most promising results for chlorophyll content estimation were obtained in the presence of carotenoids upto 6 mgg-1 without stress by both strains Rad1 and Rad2. Study suggests that especially strain Ros2 can enhance plant growth parameters in the pesticide stress.

Resumo Três bactérias solubilizantes de fosfato foram isoladas e identificadas por seqüenciamento de rRNA 16S como Pseudomonas putida, Pseudomonas sp e Pseudomonas fulva. As estirpes foram submetidas a testes bioquímicos de plantas e todos os atributos PGPR foram verificados na presença de pesticidas (clorpirifos e piriproxifeno). O índice de solubilização de fosfato da estirpe Ros2 foi mais elevado no meio NBRIP, isto é, 2,23 mm. Todas as estirpes apresentaram um pH ácido (varia de 2,5-5) em ambos os meios, isto é PVK e NBRIP. A estirpe Ros2 foi altamente positiva para a produção de amoníaco, bem como a produção de sideróforos enquanto a estirpe Rad2 foi positiva para a produção de HCN. Os resultados obtidos pelas estirpes Rad1, Rad2 e Ros2 para a produção de auxina foram 33,1, 30,67 e 15,38 μg ml-1 , respectivamente. A deformação Rad1 mostrou aumento de 16% na germinação percentual em comparação com o controlo na presença de stress de pesticida. Os resultados mais promissores para a estimativa do teor de clorofila foram obtidos na presença de carotenóides até 6 mgg-1 sem estresse por ambas as cepas Rad1 e Rad2. Estudo sugere que especialmente a estirpe Ros2 pode melhorar parâmetros de crescimento de plantas no estresse de pesticidas.

Breastfeeding increases microbial community resilience / Aleitamento materno aumenta a resiliência da comunidade microbiana

Abstract Objective Since the present group had already described the composition of the intestinal microbiota of Brazilian infants under low social economic level, the aim of the present study was to analyze the microbial community structure changes in this group of infants during their early life due to external factors. Methods Fecal samples were collected from 11 infants monthly during the first year of life. The infants were followed regarding clinical and diet information and characterized according to breastfeeding practices. DNA was extracted from fecal samples of each child and subjected to Polymerase Chain Reaction - Denaturing Gradient Gel Electrophoresis. Results The results revealed a pattern of similarity between the time points for those who were on exclusive breastfeeding or predominant breastfeeding. Although there were changes in intensity and fluctuation of some bands, the Denaturing Gradient Gel Electrophoresis patterns in the one-year microbial analysis were stable for breastfeeding children. There was uninterrupted ecological succession despite the influence of external factors, such as complementary feeding and antibiotic administration, suggesting microbiota resilience. This was not observed for those children who had mixed feeding and introduction of solid food before the 5th month of life. Conclusion These results suggested an intestinal microbiota pattern resilient to external forces, due to the probiotic and prebiotic effects of exclusive breastfeeding, reinforcing the importance of exclusive breastfeeding until the 6th month of life.

Resumo Objetivo Como nosso grupo já havia descrito a composição da microbiota intestinal de neonatos brasileiros em baixo nível socioeconômico, o objetivo deste estudo foi analisar alterações estruturais da comunidade microbiana desse grupo de neonatos no início de sua vida devido a fatores externos. Métodos Amostras fecais foram coletadas mensalmente de 11 neonatos durante o primeiro ano de vida. Os neonatos foram acompanhados com relação a informações clínicas e nutricionais e caracterizados de acordo com práticas de amamentação. O DNA foi extraído das amostras fecais de cada criança e submetido a análise através da técnica de Reação em Cadeia da Polimerase - Eletroforese em Gel de Gradiente Desnaturante. Resultados Os resultados revelaram um padrão de similaridade entre seus próprios pontos temporais em indivíduos em aleitamento materno exclusivo ou predominante. Apesar de variações na intensidade e flutuação de algumas bandas, o padrão Eletroforese em Gel de Gradiente Desnaturante na análise microbiana de um ano foi estável em crianças em aleitamento materno. Houve sucessão ecológica ininterrupta apesar da influência de fatores externos, como alimentação complementar e administração de antibióticos, sugeriu resiliência da microbiota. Isso não foi observado nas crianças com alimentação heterogênea e introdução de alimentos sólidos antes do quinto mês de vida. Conclusão Nossos resultados sugerem um padrão de microbiota intestinal resiliente a forças externas, devido a efeitos probióticos e prebióticos do aleitamento materno exclusivo, reforçam a importância do aleitamento materno exclusivo até o sexto mês de vida.

Molecular detection of Anaplasmataceae agents in Dasyprocta azarae in northeastern Brazil / Detecção molecular de agentes Anaplasmataceae em Dasyprocta azarae no nordeste do Brasil

Abstract Recently, the importance of wild-living rodents for maintenance of pathogens of the family Anaplasmataceae in the environment was investigated. These mammals play a role as reservoirs for these pathogens and act as hosts for the immature stages of tick vectors. The aim of the present study was to investigate the prevalence of Ehrlichia sp. and Anaplasma sp. in 24 specimens of Azara's agouti (Dasyprocta azarae) that had been trapped in the Itapiracó Environmental Reserve, in São Luís, Maranhão, northeastern Brazil, using molecular methods. Four animals (16.7%) were positive for Ehrlichia spp. in nested PCR assays based on the 16S rRNA gene. In a phylogenetic analysis based on the 16S rRNA gene, using the maximum likelihood method and the GTRGAMMA+I evolutionary model, Ehrlichia sp. genotypes detected in Azara's agoutis were found to be closely related to E. canis and to genotypes relating to E. canis that had previously been detected in free-living animals in Brazil. The present work showed the first molecular detection of Ehrlichia sp. in Azara's agoutis in Brazil.

Resumo Recentemente, a importância de roedores selvagens na manutenção de agentes Anaplasmataceae no ambiente tem sido investigada, haja visto o papel que tais mamíferos podem desempenhar como reservatórios para os patógenos e como hospedeiros para estágios imaturos dos carrapatos vetores. O presente estudo objetivou investigar a ocorrência de Ehrlichia sp. e Anaplasma sp. em 24 cotias (Dasyprocta azarae) capturadas na Reserva Ambiental de Itapiracó, em São Luís, Maranhão, nordeste do Brazil, utilizando métodos moleculares. Quatro animais (16,7%) mostraram-se positivos nos ensaios de nested PCR para Ehrlichia spp. baseados no gene 16S rRNA gene. Na análise filogenética baseda no gene 16S rRNA e utilizando o método de Máxima Verossimilhança e modelo evolutivo GTRGAMMA+I, os genótipos de Ehrlichia sp. detectados em cotias mostraram-se filogeneticamente relacionados às sequências de E. canis e outros genótipos relacionados a E. canis detectados previamente em animais selvagens no Brasil. O presente trabalho mostrou a primeira detecção molecular de Ehrlichia sp. em cotias no Brasil.

Caracterización molecular de bacterias patógenas de las vías respiratorias de pacientes peruanos con fibrosis quística / Molecular characterization of pathogenic bacteria of the respiratory tract in peruvian patients with cystic fibrosis

RESUMEN Objetivos. Caracterizar a nivel molecular las bacterias patógenas de las vías respiratorias de pacientes peruanos con fibrosis quística (FQ). Materiales y métodos. Se caracterizaron las comunidades bacterianas cultivables a partir de muestras de esputo de pacientes pediátricos y adultos con FQ registrados en el Hospital Nacional Edgardo Rebagliati Martins y el Instituto Nacional de Salud del Niño (INSN). Para el cultivo bacteriano se utilizaron técnicas microbiológicas estándares, y para la caracterización molecular la secuenciación del gen ARNr 16S y espectrometría de masas de tipo desorción/ionización con láser asistido por matriz con tiempo de vuelo (MALDI TOF) y MALDI TOF/TOF. Resultados. Por secuenciación del ARNr 16S se identificaron 127 cepas, encontrando las bacterias patógenas Pseudomonas aeruginosa (31,5%), Staphylococcus aureus (12,6%), Pseudomonas spp. (11,8%), Klebsiella oxytoca (3,1%), otras especies mostraron baja prevalencia. El análisis por MALDI TOF permitió obtener una serie de espectros representativos de cada especie aislada, mientras que el análisis por MALDI TOF/TOF reveló péptidos y proteínas de las especies más comunes con informaciones complementarias que revelarían datos sobre su patogenicidad o sensibilidad a antibióticos. Conclusiones. Los principales microorganismos patógenos encontrados en las vías respiratorias son similares a los reportados en otros países. Estos son los primeros hallazgos en Perú que muestran la caracterización bacteriana por secuenciación del ARNr 16S, por MALDI TOF y MALDI TOF TOF. Los hallazgos permiten la identificación bacteriana de microorganismos nativos relacionados con la FQ basada en el análisis de su proteoma.

ABSTRACT Objectives. To molecularly characterize the pathogenic bacteria of the respiratory tract isolated from patients with cystic fibrosis (CF) in Peru. Materials and methods. Bacterial communities cultured from sputum samples of pediatric and adult patients with CF admitted to the Edgardo Rebagliati Martins National Hospital and the National Institute of Child Health were characterized. Standard microbiological techniques were used for bacterial culture, and gene sequencing of 16S rRNA and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and tandem MALDI-TOF mass spectrometry (MALDI TOF/TOF) were used for molecular characterization. Results. Seventeen bacterial strains were characterized by 16S rRNA sequencing, and the identified pathogenic bacteria were Pseudomonas aeruginosa (31.5%), Staphylococcus aureus (12.6%), Pseudomonas spp. (11.8%), and Klebsiella oxytoca (3.1%). MALDI-TOF analysis generated a series of spectra representative of each isolated bacterial species, whereas MALDI TOF/TOF analysis identified the peptides and proteins of the most common strains and provided data on pathogenicity and sensitivity to antibiotics. Conclusions. The primary pathogenic microorganisms found in the respiratory tract of patients with CF in Peru were the same as those found in other countries. This study is the first to perform 16S rRNA sequencing as well as MALDI-TOF and MALDI-TOF/TOF analysis of the bacterial pathogens circulating in Peru. The inclusion of proteomic analysis further allowed for the identification of native microorganisms involved in CF.

Bacterial diversity in the saliva of patients with different oral hygiene indexes

The objective of the present study was to evaluate the bacterial diversity in the saliva of patients with different oral hygiene indexes using of two 16S rRNA gene libraries. Each library was composed of samples from patients with different averages of the differentiated Silness-Löe biofilm index: the first library (A) with an index between 1.0 and 3.0 (considered a high index) and the second library (B) between 0 and 0.5 (considered a low index). Saliva DNA was extracted and the 16S rRNA gene was amplified and cloned. The obtained sequences were compared with those stored at NCBI and RDP GenBank. The saliva of patients with high index presented five known genera - Streptococcus, Granulicatella, Gemella, Veillonella and Peptostreptococcus - and 33.3% of nonculturable bacteria grouped into 23 operational taxonomic units (OTUs). The saliva of patients with low index differed significantly from the first library (p=0.000) and was composed of 42 OTUs distributed into 11 known genera - Streptococcus, Granulicatella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces - including 24.87% of nonculturable bacteria. It was possible to conclude that there is greater bacterial diversity in the saliva of patients with low dental plaque in relation to patients with high dental plaque.

O objetivo do presente estudo foi avaliar a diversidade bacteriana da saliva de pacientes com diferentes índices de higiene bucal através da construção de duas bibliotecas do gene 16S rRNA. Cada biblioteca foi composta por amostras de saliva de pacientes com índice de biofilme dental de Silness-Löe diferenciado, sendo a primeira (A) com índice de 1,0 a 3,0 (denominada de alto índice) e a segunda (B), entre 0 a 0,5 (denominada de baixo índice). O DNA da saliva foi extraído e o gene 16S rRNA foi amplificado, clonado e sequenciado. As sequências obtidas foram comparadas com aquelas armazenadas no GenBank do NCBI e RDP. A saliva de pacientes com alto índice de biofilme dental apresentou cinco gêneros conhecidos: Streptococcus, Granulicatella, Gemella, Veillonella e Peptostreptococcus e 33,3% de bactérias não-cultivadas, agrupados em 23 unidades taxonômicas operacionais (UTOs). A saliva de pacientes com baixo índice de biofilme dental, foi diferente significativamente da primeira (p=0,000) e foi composta de 42 UTOs, distribuídas em 11 gêneros conhecidos: Streptococcus, Granulicatella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces, além de 24,87% de bactérias não-cultivadas. Pode-se concluir que existe maior diversidade bacteriana na saliva de pacientes com baixo índice de biofilme dental em relação a pacientes com alto índice de biofilme dental.

Microbial colonization in orthodontic mini-implants

Peri-implant inflammation contributes for loss of secondary stability of orthodontic mini-implants. The investigation of microbial colonization in this area would benefit its control, and consequently favor the long-term success of mini-implants. Therefore, the aim of this study was to determine the establishment and the evolution of microbial colonization process in orthodontic mini-implants for 3 months, since the time of their installation. One-hundred and fifty samples collected from 15 mini-implants were investigated from baseline up to 3 months. The biological material was obtained from peri-implant area using paper points. Nonspecific, Streptococcus spp, Lactobacillus casei and Candida spp colonizations were analyzed by cell growth methods. Porphyromonas gingivalis colonization was observed by 16S rDNA-directed polymerase chain reaction. Data from cell growth were submitted to the Wilcoxon sign rank test and results from molecular analysis were presented in a descriptive way. There was no significant difference in the microbial colonization among the examined time intervals, except for Streptococcus spp, between baseline and 24 h, which characterized the initial colonization in this time interval. Lactobacillus casei and Candida spp colonizations were insignificant. No Porphyromonas gingivalis was detected among the analyzed samples. The microbial colonization of mini-implants did not significantly change during the study. However, it should be monitored by orthodontists, since it is an important factor for mini-implants success.

A inflamação peri-implantar contribui para a perda da estabilidade secundária dos mini-implantes ortodônticos. A investigação da colonização microbiana desta área beneficiaria o seu controle e, consequentemente, favoreceria o sucesso dos mini-implantes a longo prazo. Portanto, o objetivo dos autores foi determinar o estabelecimento e evolução do processo de colonização microbiana em mini-implantes ortodônticos por três meses desde a instalação. Cento e cinquenta amostras coletadas de 15 mini-implantes foram investigadas desde o tempo inicial até 3 meses. O material biológico foi obtido da área peri-implantar com auxílio de cones de papel absorvente. As colonizações inespecíficas de Streptococcus spp, Lactobacillus casei e Candida spp foram analisadas por métodos de crescimento celular. A colonização por Porphyromonas gingivalis foi observada por meio da reação em cadeia da polimerase 16S rDNA. Os dados do crescimento celular foram submetidos ao teste de Wilcoxon sign rank e os resultados da biologia molecular foram apresentados de modo descritivo. Não houve diferença estatisticamente significante da colonização microbiana entre os intervalos de tempo avaliados, exceto para Streptococcus spp entre os tempos inicial e 24 h, o que caracterizou o início da colonização neste intervalo de tempo. As colonizações por Lactobacillus casei e Candida spp foram insignificantes. Não foi detectada a presença de Porphyromonas gingivalis nas amostras analisadas. A colonização microbiana nos mini-implantes não se alterou significativamente durante o estudo. No entanto, deve ser monitorada por ortodontistas, uma vez que é um fator importante para o sucesso dos mini-implantes.

Partial characterization of cold active amylases and proteases of Streptomyces sp. from Antarctica

The aim of this study was to isolate novel enzyme-producing bacteria from vegetation samples from East Antarctica and also to characterize them genetically and biochemically in order to establish their phylogeny. The ability to grow at low temperature and to produce amylases and proteases cold-active was also tested. The results of the 16S rRNA gene sequence analysis showed that the 4 Alga rRNA was 100 percent identical to the sequences of Streptomyces sp. rRNA from Norway and from the Solomon Islands. The Streptomyces grew well in submerged system at 20ºC, cells multiplication up to stationary phase being drastically increased after 120 h of submerged cultivation. The beta-amylase production reached a maximum peak after seven days, while alpha-amylase and proteases were performing biosynthesis after nine days of submerged cultivation at 20ºC. Newly Streptomyces were able to produce amylase and proteases in a cold environment. The ability to adapt to low temperature of these enzymes could make them valuable ingredients for detergents, the food industry and bioremediation processes which require low temperatures.

Three Cases of Moraxella osloensis Meningitis: A Difficult Experience in Species Identification and Determination of Clinical Significance

We had three cases of Moraxella osloensis meningitis. The species identification was impossible by conventional and commercial phenotypic tests. However, we could identify the species using the 16S rRNA gene sequencing. Determination of clinical significance was difficult in one patient. All three patients recovered by appropriate antimicrobial therapy.

Detection of Porphyromonas gingivalis and Streptococcus intermedius in chronic periodontitis patients by multiplex PCR

Se muestra la utilización del ensayo de polimerasa en cadena (PCR) múltiplex para la detección de Porphyromonas gingivalis y Streptococcus intermedius en pacientes con periodontitis crónica. Se analizaron un total de 180 muestrasde 65 adultos con periodontitis no tratada y 17 voluntarios sanos, las células se procesaron inicialmente colocándolas a baño María durante 10 min. El lisado celular fue usado comofuente de ADN para los ensayos del PCR múltiplex. Los primers fueron diseñados a partir de secuencias génicas defracciones 16 rRNA obtenidas de la base de datos GenBank-EMBL y que mostraron especificidad para los patógenos mencionados. El sistema PCR múltiplex fue diseñado para identificar 8.2 células de P. gingivalis y S. intermedius. De los pacientes con periodontitis, sólo el 78.5 por ciento fueron positivos para una o ambas bacterias. En el 37 por ciento se identificó únicamente P. gingivalis, en el 17 por ciento S. intermedius y en un 24.5 por ciento ambos. P. gingivalis fue detectada en el 23.5 por ciento de los voluntarios sanos, mientras que, S. intermedius no se detectó en esegrupo de pacientes. La distribución de la identificación de estas bacterias está relacionada con la profundidad de las bolsas periodontales. Mientras que el 95.23 por ciento de los pacientes con bolsas de 6 a 7 mm fueron positivas para ambas bacterias, mientras que sólo el 70.45 por ciento de ellos fue positivo cuando las bolsas tenían de 4 a 5 mm de profundidad

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.

Rapid and easy detection of Helicobacter pylori by in situ hybridization

Various in situ hybridization (ISH) methods have been used to identify Helicobacter pylori, a causative organism responsible for chronic gastritis and peptic ulcer disease, but they were hard to perform and time consuming. To detect H. pylori in a rapid and easily reproducible way, we developed synthetic biotinylated oligonucleotide probes which complement rRNA of H. pylori. Formalin-fixed and paraffin-embedded tissues from 50 gastric biopsy specimens were examined. Using a serologic test and histochemical stain (Warthin-Starry silver stain and/or Giemsa stain) as a standard, 40 of them were confirmed to be H. pylori-positive. Our ISH was quickly carried out within one hr and results were compared with those obtained from immunohistochemical stain. The ISH produced a positive reaction in 38 of 40 cases (95%). All H. pylori-negative cases failed to demonstrate a positive signal. The ISH has a sensitivity comparable to those of conventional histochemical and immunohistochemical stain, and has high specificity. In conclusion, ISH with a biotinylated oligonucleotide probe provides a useful diagnostic method for detecting H. pylori effectively in routinely processed tissue sections.

Differentiation of Salmonella typhi strains by ribosomal RNA gene restriction patterns.

Owing to the limited value of phage typing to determine the epidemiological association of Salmonella typhi (S. typhi) strains isolated from the source of typhoid fever, we analyzed ribosomal RNA (rRNA) gene restriction patterns to differentiate the independently isolated strains of identical phage type. The data showed that the restriction patterns of PstI was most polymorphic among four enzymes (BamHI, EcoRI, PstI, and SmaI) used, which revealed 13 types among 25 strains belonged to 4 phage types, 1 untypable and 2 not-determined strains. Total 25 strains of S. typhi were divided into 15 combination types by the rRNA restriction patterns with three enzymes (BamHI, PstI, and SmaI).