DGGE with genomic DNA: Suitable for detection of numerically important organisms but not for identification of the most abundant organisms

Identification of all important community members as well as of the numerically dominant members of a community are key aspects of microbial community analysis of bioreactor samples. A systematic study was conducted with artificial consortia to test whether denaturing gradient gel electrophoresis (DGCE) is a reliable technique to obtain such community data under conditions where results would not be affected by differences in DNA extraction efficiency from cells. A total of 27 consortia were established by mixing DNA extracted from Escherichia coli K12, Burkholderia cepacia and Stenotrophomonas maltophilia in different proportions. Concentrations of DNA of single organisms in the consortia were either 0.04, 0.4 or 4 ng/mu l. DGGE-PCR of genomic DNA with primer sets targeted at the V3 and V6-V8 regions of the 16S rDNA failed to detect the three community members in only 7% of consortia, but provided incorrect information about dominance or co-dominance for 85% and 89% of consortia with the primer sets for the V6-V8 and V3 regions, respectively. The high failure rate in detection of dominant B. cepacia with the primers for the V6-V8 region was attributable to a single nucleoticle primer mismatch in the target sequences of both, the forward and reverse primer. Amplification bias in PCR of E. coli and S. maltophilia for the V6-V8 region and for all three organisms for the V3 region occurred due to interference of genomic DNA in PCR-DGGE, since a nested PCR approach, where PCR-DGGE was started from mixtures of 16S rRNA genes of the organisms, provided correct information about the relative abundance of original DNA in the sample. Multiple bands were not observed in pure culture amplicons produced with the V6-V8 primer pair, but pure culture V3 DGGE profiles of E. coli, S. maltophilia and B. cepacia contained 5, 3 and 3 bands, respectively. These results demonstrate DGGE was suitable for identification of all important community members in the three-membered artificial consortium, but not for identification of the dominant organisms in this small community. Multiple DGGE bands obtained for single organisms with the V3 primer pair could greatly confound interpretation of DGGE profiles. (C) 2008 Elsevier Ltd. All rights reserved.

Chemical variability within the marine sponge Aplysina fulva

Dibromotyrosine-derived metabolites are of common occurrence within marine sponges belonging to the order Verongida. However, previous chemical analysis of crude extracts obtained from samples of the verongid sponge Aplysina fulva collected in Brazil did not provide any dibromotyrosine-derived compounds. In this investigation, five samples of A. fulva from five different locations along the Brazilian coastline and one sample from a temperate reef in the South Atlantic Bight (SAB) (Georgia, USA) were investigated for the presence of bromotyrosine-derived compounds. All six samples collected yielded dibromotyrosine-derived compounds, including a new derivative, named aplysinafulvin, which has been identified by. analysis of spectroscopic data. These results confirm previous assumptions that dibromotyrosine-derived metabolites can be considered as chemotaxonomic markers of verongid sponges. The isolation of aplysinafulvin provides additional support for a biogenetic pathway involving an arene oxide intermediate in the biosynthesis of Verongida metabolites. It cannot yet be established if the chemical variability observed among the six samples of A.fulva collected in Brazil and the SAB is the result of different environmental factors, distinct chemical extraction and isolation protocols, or a consequence of hidden genetic diversity within the postulated morphological plasticity of this species. (C) 2007 Elsevier Ltd. All rights reserved.

Efeito da solarização e do brometo de metila sobre a comunidade de fungos do solo

A microbiota do solo é de grande importância no desenvolvimento de culturas. Os métodos de controle, químico (brometo de metila) e físico (solarização), alteram essa microbiota. O presente trabalho objetivou estudar o comportamento da comunidade de fungos em solo solarizado e fumigado (brometo de metila). O delineamento experimental foi de blocos ao acaso, com três tratamentos (solarização, brometo de metila e testemunha) e sete repetições. A comunidade de fungos do solo foi avaliada de forma quantitativa e qualitativa, em três momentos (antes, durante e após a solarização) com amostras coletadas de três profundidades (0-5; 10-15 e 20-25 cm). Durante a solarização ocorreu uma redução na comunidade de fungos do solo, em termos quantitativos, em todas as camadas amostradas. No entanto, essa diminuição foi mais significativa na camada superficial (0-5cm). em termos qualitativos, a solarização reduziu também o número de diferentes espécies de fungos do solo, mas na camada de 20-25 cm, essa diminuição foi a zero aos 56 dias de avaliação. A recolonização da microbiota do solo, em termos quantitativos, foi maior no tratamento com brometo de metila do que nos demais. Entretanto, esse aumento não foi o mesmo em termos qualitativos. Nos tratamentos solarizado e testemunha, o aumento na comunidade de fungos do solo foi acompanhado pela diversificação de espécies fúngicas.

Diversidade de bactérias de solo sob vegetação natural e cultivo de hortaliças

The microorganisms are essential components in the maintenance of the biological and physicochemical balance of the soil. They exert important function including the degradation of residues of plants and animals and the release of nutrients in the alimentary chain. This work had as objective to compare the microbiota of a soil under bush covering (SMS) and other cropped with vegetables (SHC), suppressive or not it Rhizoctonia solani. Total microbial community DNA was extracted of soils, amplification for PCR of the genes 16S rDNA, inserted into pGEM (R)-T cloning vector and sequencing of the genes of the ribosomal RNA. The analysis of the results demonstrated that this methodology was efficient for evaluation of bacteria in ground. In the bush soil suppressive the microorganisms more found belonged to the phyla of the Acidobacterias, Verrucomicrobia and Actinobacterias and in the soil cultivated with vegetables the biggest frequency was of organisms pertaining to the phyla of the Proteobacterias, Firmicutes and Bacteroidetes.

Do Atopobium vaginae, Megasphaera sp. and Leptotrichia sp. change the local innate immune response and sialidase activity in bacterial vaginosis?

Objectives: To investigate if the participation of Atopobium vaginae, Megasphaera sp. and Leptotrichia sp. in the bacterial community of bacterial vaginosis (BV) is associated with distinct patterns of this condition. Methods: In this cross-sectional controlled study, 205 women with BV and 205 women with normal flora were included. Vaginal rinsing samples were obtained for measuring the levels of pro-inflammatory cytokines and bacterial sialidases. Real-time PCR was used to quantify the BV-associated bacteria and to estimate the total bacterial load using the 16S rRNA. Principal component analysis (PCA) using the measured parameters was performed to compare the BV samples with lower and higher loads of the species of interest. Results: Higher bacterial load (p<0.001), levels of interleukin 1-β (p<0.001) and sialidase activity (p<0.001) were associated with BV. Women with BV and higher relative loads of A vaginae, Megasphaera sp. and Leptotrichia sp. presented increased sialidase activity, but unchanged cytokine levels. PCA analysis did not indicate a different pattern of BV according to the loads of A vaginae, Megasphaera sp. and Leptotrichia sp. Conclusions: Greater participation of A vaginae, Megasphaera sp. and Leptotrichia sp. in vaginal bacterial community did not indicate a less severe form of BV; moreover, it was associated with increased sialidase activity.

Lactobacillus acidophilus CRL 1014 improved gut health in the SHIME® reactor

Background: How to maintain gut health is a goal for scientists throughout the world. Therefore, microbiota management models for testing probiotics, prebiotics, and synbiotics have been developed.Methods: The SHIME® model was used to study the effect of Lactobacillus acidophilus 1014 on the fermentation pattern of the colon microbiota. Initially, an inoculum prepared from human feces was introduced into the reactor vessels and stabilized over 2-wk using a culture medium. This stabilization period was followed by a 2-wk control period during which the microbiota was monitored. The microbiota was then subjected to a 4-wk treatment period by adding 5 mL of sterile peptone water with L. acidophilus CRL1014 at the concentration of 108 CFU/mL to vessel one (the stomach compartment). Plate counts, Denaturing Gradient Gel Electrophoresis (DGGE), short-chain fatty acid (SCFA) and ammonium analyses were carried out for monitoring of the microbial community from the colon compartments.Results: A significant increase (p < 0.01) in the Lactobacillus spp. and Bifidobacterium spp. populations was observed during the treatment period. The DGGE obtained showed changes in the lactobacilli community from the colon compartments of the SHIME® reactor. The (SCFA) concentration increased (p < 0.01) during the treatment period, due mainly to significant increased levels of acetic, butyric, and propionic acids. However, ammonium concentrations decreased during the same period (p < 0.01).Conclusions: This study showed the beneficial influence of L. acidophilus CRL 1014 on microbial metabolism and lactobacilli community composition for improving human health. © 2013 Sivieri et al.; licensee BioMed Central Ltd.

Photodynamic inactivation of biofilm: Taking a lightly colored approach to stubborn infection

Microbial biofilms are responsible for a variety of microbial infections in different parts of the body, such as urinary tract infections, catheter infections, middle-ear infections, gingivitis, caries, periodontitis, orthopedic implants, and so on. The microbial biofilm cells have properties and gene expression patterns distinct from planktonic cells, including phenotypic variations in enzymic activity, cell wall composition and surface structure, which increase the resistance to antibiotics and other antimicrobial treatments. There is consequently an urgent need for new approaches to attack biofilm-associated microorganisms, and antimicrobial photodynamic therapy (aPDT) may be a promising candidate. aPDT involves the combination of a nontoxic dye and low-intensity visible light which, in the presence of oxygen, produces cytotoxic reactive oxygen species. It has been demonstrated that many biofilms are susceptible to aPDT, particularly in dental disease. This review will focus on aspects of aPDT that are designed to increase efficiency against biofilms modalities to enhance penetration of photosensitizer into biofilm, and a combination of aPDT with biofilm-disrupting agents. © 2013 Informa UK Ltd.

Bifunctional silica nanoparticles for the exploration of biofilms of Pseudomonas aeruginosa

Luminescent silica nanoparticles are frequently employed for biotechnology applications mainly because of their easy functionalization, photo-stability, and biocompatibility. Bifunctional silica nanoparticles (BSNPs) are described here as new efficient tools for investigating complex biological systems such as biofilms. Photoluminescence is brought about by the incorporation of a silylated ruthenium(II) complex. The surface properties of the silica particles were designed by reaction with amino-organosilanes, quaternary ammonium-organosilanes, carboxylate-organosilanes and hexamethyldisilazane. BSNPs were characterized extensively by DRIFT, 13C and 29Si solid state NMR, XPS, and photoluminescence. Zeta potential and contact angle measurements exhibited various surface properties (hydrophilic/hydrophobic balance and electric charge) according to the functional groups. Confocal laser scanning microscopy (CLSM) measurements showed that the spatial distribution of these nanoparticles inside a biofilm of Pseudomonas aeruginosa PAO1 depends more on their hydrophilic/hydrophobic characteristics than on their size. CLSM observations using two nanosized particles (25 and 68 nm) suggest that narrow diffusion paths exist through the extracellular polymeric substances matrix. © 2013 Copyright Taylor and Francis Group, LLC.

Diversidade bacteriana em piscicultura neotropical

Pós-graduação em Microbiologia Agropecuária - FCAV

Estabilização de landfarming de refinaria de petróleo, mediante metabolismo microbiano, e aplicabilidade em solos pré-desertificados

Pós-graduação em Ciências Biológicas (Microbiologia Aplicada) - IBRC

Aspectos microbiológicos e químicos em solo submetido à solarização

Pós-graduação em Agronomia (Proteção de Plantas) - FCA

Diversidade funcional, genética e estrutural de micro-organismos do solo após 13 anos de aplicações anuais de lodo de esgoto sob cultura do milho

Pós-graduação em Agronomia (Ciência do Solo) - FCAV

Amenizantes em solo contaminado com bário

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Perfil metagenômico de solo sob cultivo de cana-de-açúcar com perspectiva na produção de bioenergia

Pós-graduação em Microbiologia Agropecuária - FCAV

O papel dos microfungos associados aos jardins das formigas Attini (Hymenoptera: Formicidae)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)