Ecogenômica de archaea e monitoramento de comunidades de procariotos redutores de sulfato: aplicações na indústria de petróleo e gás

The human activities responsible for the ambient degradation in the modern world are diverse. The industrial activities are preponderant in the question of the impact consequences for brazilian ecosystems. Amongst the human activities, the petroliferous industry in operation in Potiguar Petroliferous Basin (PPB) displays the constant risk of ambient impacts in the integrant cities, not only for the human populations and the environment, but also it reaches the native microorganisms of Caatinga ground and in the mangrove sediment. Not hindering, the elaboration of strategies of bioremediation for impacted areas pass through the knowledge of microbiota and its relations with the environment. Moreover, in the microorganism groups associated to oil, are emphasized the sulfate-reducing prokaryotes (SRP) that, in its anaerobic metabolism, these organisms participate of the sulfate reduction, discharging H2S, causing ambient risks and causing the corrosion of surfaces, as pipelines and tanks, resulting in damages for the industry. Some ancestries of PRS integrate the Archaea domain, group of microorganisms whose sequenced genomes present predominance of extremophilic adaptations, including surrounding with oil presence. This work has two correlated objectives: i) the detection and monitoring of the gene dsrB, gift in sulfate-reducing prokaryotes, through DGGE analysis in samples of mDNA of a mangrove sediment and semiarid soil, both in the BPP; ii) to relate genomic characteristics to the ecological aspects of Archaea through in silico studies, standing out the importance to the oil and gas industry. The results of the first work suggest that the petrodegraders communities of SRP persist after the contamination with oil in mangrove sediment and in semiarid soil. Comparing the populations of both sites, it reveals that there are variations in the size and composition during one year of experiments. In the second work, functional and structural factors are the probable cause to the pressure in maintenance of the conservation of the sequences in the multiple copies of the 16S rDNA gene. Is verified also the discrepancy established between total content GC and content GC of the same gene. Such results relating ribosomal genes and the ambient factors are important for metagenomic evaluations using PCR-DGGE. The knowledge of microbiota associated to the oil can contribute for a better destination of resources by the petroliferous industry and the development of bioremediation strategies. Likewise, search to lead to the best agreement of the performance of native microbiota in biogeochemical cycles in Potiguar Petroliferous Basin ecosystem

Biodegradação de hidrocarbonetos aromáticos policíclicos: prospecção metagenômica e modelagem computacional 3-D de proteínas

Knowledge of the native prokaryotes in hazardous locations favors the application of biotechnology for bioremediation. Independent strategies for cultivation and metagenomics contribute to further microbiological knowledge, enabling studies with non-cultivable about the "native microbiological status and its potential role in bioremediation, for example, of polycyclic aromatic hydrocarbons (HPA's). Considering the biome mangrove interface fragile and critical bordering the ocean, this study characterizes the native microbiota mangrove potential biodegradability of HPA's using a biomarker for molecular detection and assessment of bacterial diversity by PCR in areas under the influence of oil companies in the Basin Petroleum Geology Potiguar (BPP). We chose PcaF, a metabolic enzyme, to be the molecular biomarker in a PCR-DGGE detection of prokaryotes that degrade HPA s. The PCR-DGGE fingerprints obtained from Paracuru-CE, Fortim-CE and Areia Branca-RN samples revealed the occurrence of fluctuations of microbial communities according to the sampling periods and in response to the impact of oil. In the analysis of microbial communities interference of the oil industry, in Areia Branca-RN and Paracuru-CE was observed that oil is a determinant of microbial diversity. Fortim-CE probably has no direct influence with the oil activity. In order to obtain data for better understanding the transport and biodegradation of HPA's, there were conducted in silico studies with modeling and simulation from obtaining 3-D models of proteins involved in the degradation of phenanthrene in the transport of HPA's and also getting the 3-D model of the enzyme PcaF used as molecular marker in this study. Were realized docking studies with substrates and products to a better understanding about the transport mechanism and catalysis of HPA s

Molecular Identification and Characterization of Ileal and Cecal Fungus Communities in Broilers Given Probiotics, Specific Essential Oil Blends, and Under Mixed Eimeria Infection

Broiler digestive tract fungal communities have gained far less scrutiny than that given corresponding bacterial communities. Attention given poultry-associated fungi have focused primarily on feed-associated toxin-producers, yeast, and yeast products. The current project focused on the use of pyrosequencing and denaturing gradient gel electrophoresis (DGGE) to identify and monitor broiler digestive fungal communities. Eight different treatments were included. Four controls were an Uninfected-Unmedicated Control, an Unmedicated-Infected Control, the antibiotic bacitracin methylene disalicylate plus the ionophore monensin as Positive Control, and the ionophore monensin alone as a Negative Control. Four treatments were two probiotics (BC-30 and Calsporin) and two specific essential oil blends (Crina Poultry Plus and Crina Poultry AF). All chickens except the Unmedicated-Uninfected Control were given, at 15 days of age, a standard oral Eimeria inoculum of sporulated oocysts. Ileal and cecal digesta were collected at pre-Eimeria infection at 14 days of age and at 7 days post-Eimeria infection at 22 days of age. Extracted cecal DNA was analyzed by pyrosequencing to examine the impact of diet supplements and Eimeria infection on individual constituents in the fungal community, while DGGE was used to compare more qualitative changes in ileal and cecal communities. Pyrosequencing identified three phyla, seven classes, eight orders, 13 families, 17 genera, and 23 fungal species. Ileal and cecal DGGE patterns showed fungal communities were clustered mainly into pre- and post-infection patterns. Post-infection Unmedicated-Uninfected patterns were clustered with pre-infection groups demonstrating a strong effect of Eimeria infection on digestive fungal populations. These combined techniques offered added versatility towards unraveling the effects of enteropathogen infection and performance enhancing feed additives on broiler digestive microflora.

Estudos ecogenômicos e bioprospectivos de Shewanella ssp

Bacteria trom Shewanella and Geobacter ganera are the most studied iron-reducing microorganisms particularly due to their electron transport systems and contribution to some industrial and environmental problems, including steel corrosion, bioenergy and bioremediation of petroleum-impacted sites. The present study was focused in two ways: the first is an in silico comparative ecogenomic study of Shewanella spp. with sequenced genomes, and the second is an experimental metagenomic work to detect iron-reducing Shewanella through PCR-DGGE of a metabolic gene. The in silico study resulted in positive correIation between copy number of 16S rDNA and genome size in Shewanella spp., with clusters of rrn near lhe origin of replication. This way, the genus is inferred as opportunist. There are no compact genomes and their sequences length varied, ranging from 4306142 nt in S. amazonensis SB2B to 5935403 nt in S. woodyi ATCC 51908, without correIation to temperature range characteristic of each specie. Intragenomic 16S rDNA sequences possess little divergence, but reasonable to resuIt in different phyIogenetic trees, depending on the sequence that is chosen to compare. For moIecuIar detection of iron-reducing Shewanella, it is proposed the mtrB gene as new biomarker. because it codes to a fundamental protein at Fe (III)-reduction. The specific primers were designed and evaluated in silico and resulted in a fragment of 360 pb. In the second study, these primers were tested in a genomic sample from S. oneidensis MR-1, amplifying the expected region. After this successfuI resuIt, the primer set was used as a tool to assess the iron-reducing communities of ShewaneIla genus under an environmental stress, i.e. crude oil contamination in mangrove sediment in Rio Grande do Norte State (Brazil). The primers presented high specificity and the reactions performed resulted in one single band of ampIification in the metagenomic samples. The fingerprinting obtained at DGGE reveaIed temporal variation of Shewanella spp. in analyzed samples. The resuIts presented show the detection of a biotechnological important group of microorganisms, the iron-reducing Shewanella spp. using a metabolic gane as target. It is concluded there are eight or more 16S rDNA sequences in Shewanella genus, with little divergence among them that affects the phylogeny; the pair of primers designed to ampIify mtrB sequences is a viable alternative to detect iron-reducing ShewanelIa in metagenomic approaches; such bacteria are present in the mangrove sediment anaIyzed, with temporal variations in the samples. This is the first experimental study that screened the iron-reducing Shewanella genus in a metagenomic experiment of mangrove sediments subjected to oil contamination through a key metabolic gene

Estudos in silico da proteína AlkB e prospecção de bactérias alcanotróficas em solos da bacia petrolífera potiguar

Some microorganisms from virgin ecosystems are able to use petroleum it as source of carbon and energy. The knowledge of microbial biodiversity can help to reveal new metabolic systems for utilization alkanes with biotechnological importance. The aim of this study is: i) Accomplish an in silico study of the AlkB protein aimed to understand the probable mechanism involved on selectivity of alkanes in Gram positive and Gram negative bactéria. ii) prospect and analyze the response of the microbial alkanotrophics communities in soil and mangrove sediments of BPP RN and soil of Atlantic forest in the Horto Dois Irmãos Reserve area/PE using the molecular biomarker, gene alkB; with the PCR and PCR-DGGE approach

Análise molecular dos éxons 8 a 11 do gene da p53 em amostras de câncer de colo de útero no Rio Grande do Norte

Mutations on TP53 gene are common in human cancer but not in cervical cancer where they are rarely found and the inactivation and degradation of p53 protein are attributed to the action of E6 viral oncogene from high risk human papillomavirus (HPV). Analysis of cervical cancer cell lines suggests that HPV negative samples shows mutation on TP53, but clinical approaches didn t confirmed this hypothesis. However, in most TP53 mutations studies on cervical cancer, only the exons 5 to 8 were analyzed. Approximately 90% of mutations described are on this region. Recent studies on several cancer suggests that mutation frequency in the other exons must be considered. The aim of this work was to verify whether mutations on coding and non-coding regions occur in cancer tissue from cervical cancer in patients from Rio Grande do Norte using Denaturing Gradient Gel Electrophoresis (DGGE) as screening tool. Exons 8 to 11 were analyzed including some introns from 80 tumor samples and 8 peripheral blood samples from healthy women. DNA were submitted to PCR using primers with GC clamp on the end of one of them. The results were observed for each region after DGGE and silver staining. It was observed no amplified fragment with different migration profile from those obtained from DNA of peripheral blood. These results agree with those from literature where TP53 mutations in cervical cancer have been described in a very low frequency

Molecular and ultrastructural profiles of the symbionts in Cephalotes ants

The molecular and ultrastructural profiles of the symbionts found in the midgut and ileum of Cephalotes atratus, Cephalotes clypeatus, and Cephalotes pusillus were determined using the V3 region of the bacterial 16S rDNA gene and transmission electron microscopy (T.E.M.). Two samples of C atratus, three of C clypeatus, and six of C. pusillus were analyzed. The coefficients of similarity ranged from 80% to 94% for the samples of symbionts from C. clypeatus and C. atratus, despite being collected in geographically distant sites. The variability within symbionts found in the samples of C. pusillus varied from 29% to 55%, in samples geographically close as well as distant. PCR-DGGE was effective for the purpose of this study and can be considered a versatile tool to analyze gut microbiota. Details of the ultrastructural aspect of these bacteria are presented. (C) 2010 Elsevier Ltd. All rights reserved.

Use of Pyrosequencing and Denaturing Gradient Gel Electrophoresis to Examine the Effects of Probiotics and Essential Oil Blends on Digestive Microflora in Broilers Under Mixed Eimeria Infection

A protective digestive microflora helps prevent and reduce broiler infection and colonization by enteropathogens. In the current experiment, broilers fed diets supplemented with probiotics and essential oil (EO) blends were infected with a standard mixed Eimeria spp. to determine effects of performance enhancers on ileal and cecal microbial communities (MCs). Eight treatment groups included four controls (uninfected-unmedicated [UU], unmedicated-infected, the antibiotic BMD plus the ionophore Coban as positive control, and the ionophore as negative control), and four treatments (probiotics BC-30 and Calsporin; and EO, Crina Poultry Plus, and Crina PoultryAF). Day-old broilers were raised to 14 days in floor pens on used litter and then were moved to Petersime batteries and inoculated at 15 days with mixed Eimeria spp. Ileal and cecal samples were collected at 14 days and 7 days postinfection. Digesta DNA was subjected to pyrosequencing for sequencing of individual cecal bacteria and denaturing gradient gel electrophoresis (DGGE) for determination of changes in ileal and cecal MC according to percentage similarity coefficient (%SC). Pyrosequencing is very sensitive detecting shifts in individual bacterial sequences, whereas DGGE is able to detect gross shifts in entire MC. These combined techniques offer versatility toward identifying feed additive and mild Eimeria infection modulation of broiler MC. Pyrosequencing detected 147 bacterial species sequences. Additionally, pyrosequencing revealed the presence of relatively low levels of the potential human enteropathogens Campylobacter sp. and four Shigella spp. as well as the potential poultry pathogen Clostridiun perfringens. Pre- and postinfection changes in ileal (56%SC) and cecal (78.5%SC) DGGE profiles resulted from the coccidia infection and with increased broiler age. Probiotics and EO changed MC from those seen in UU ilea and ceca. Results potentially reflect the performance enhancement above expectations in comparison to broilers not given the probiotics or the specific EO blends as feed supplements.

Tratamento de esgoto sanitário utilizando reatores anaeróbios operados em bateladas sequenciais (escala piloto)

The performances of two anaerobic sequencing batch reactors (1.2 m 3) containing biomass immobilized in inert support and as granular sludge in the treatment of domestic sewage from the Campus of São Carlos-University of São Paulo were evaluated. The experimental phase lasted seventy days. During this period, the reactors presented quite similar performances in respect to COD and total suspended solids removal, achieving average efficiencies of approximately 60% and 75%, respectively. The analysis using molecular biology techniques on biomass samples taken at 35 th and 70 th showed differences in the bacterial community in the reactors indicating that the type of biomass immobilization selected the populations differently. A higher similarity was found for the Archaea domain probably because these microorganisms utilize specific substrates formed at the end of the anaerobic process.

Remoção de etanol e benzeno em reator anaeróbio horizontal de leito fixo na presença de sulfato

In this study it is reported the operation of a horizontalflow anaerobic immobilized biomass (HAlB) reactor under sulfate-reducing condition which was also exposed to different amounts of ethanol and benzene. The HAIB reactor comprised of an immobilized biomass on polyurethane foam and ferrous and sodium sulfate solutions were used (91 and 550 mg.l -1, respectively), to promote a sulfate-reducing environment. Benzene was added at an initial concentration of 2.0 mg.l -1 followed by an increased to 9 e 10 mg. l -1, respectively. Ethanol was added at an initial concentration of 170 mg.l -1 followed by an increased range of 960 mg.l -1. The reactor was operated at 30 (± 2) °C with hydraulic detention time of 12 h. Organic matter removal efficiency of 90% with a maximum benzene degradation rate of 0.07 mv, benzene.mg -1 vss.d -1 Thus, this work corroborate the data obtained for Cattony et al (2005) and also demonstrate that compact units of HAIB reactors, under sulfate reducing conditions, are a potential alternative for in situ aromatic compounds bioremediation.

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.

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

Simbiontes do trato digestivo de formigas (Hymenoptera : Formicidae)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Avaliação do ecossistema microbiano de ratos wistar submetidos à carcinogênese química de cólon após o consumo de lactobacillus acidophilus crl 1014 e extrato aquoso

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Beneficial effects of fermented vegetal beverages on human gastrointestinal microbial ecosystem in a simulator

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)