In this study the composition of the denitrifying bacterial community among constructed wetlands in agricultural areas was investigated. Thirty-two constructed wetlands located in Southern Sweden were surveyed, and biofilm samples from each were analyzed by applying denaturing gradient gel electrophoresis, to investigate the community composition of the three denitrifying bacterial enzyme genes nirK, nirS and nosZ. The DNA sequences of the enzyme genes were compared to known DNA sequences in GeneBank using BLAST. The results of the denitrifying bacterial enzyme genes indicated that these habitats may harbour a heterogeneous denitrifying bacterial community. Individual analysis of the enzyme genes revealed that nirS was more heterogeneous than both nirK and nosZ. Most sequences from the present study clustered with known sequences from species belonging to the group of α-Proteobacteria, and to a lesser extent with β- Proteobacteria and γ-Proteobacteria, and only nirS clustered with a member of gram-positive bacteria. / <p>Included in doctoral thesis: Milenkovski, Susann. Structure and Function of Microbial Communities in Constructed Wetlands - Influence of environmental parameters and pesticides on denitrifying bacteria. Lund University 2009.</p>

In this study we used the phytoremediation techniques to treatment diesel contaminated wetland soil. At first, we compared the four common wetland plants, Typha orientalis Presl, Cyperus malaccensis, Bolbos choenus planieulmis and Phragmites communis, on the treatment efficiency of the diesel contaminated wetland soils. From the results, we find out that the Typha orientalis Presl has highest growth rate and activity on rhizosphere among the four species. The Typha orientalis Presl was planted on artifical diesel contaminated wetland soil and incubated inside a greenhouse, while a control system without vegetation is compared. After 240 days, the result shows that soil planted with Typha orientalis Presl can enhance the microbial and dehydrogenase activity. And adding with nutrients can help plants to prevent the diesel stress. Finally, we utilized the PCR/DGGE methods to analyze soil microbial diversity. According to the DGGE profiles, presence of Typha orientalis Presl can augment microbial diversity . So far as degradation of TPH-d to be concerned, because of the period was too short, it doesn¡¦t have significant difference between treatments. However, presence of Typha orientalis Presl and addition of nutrients, the TPH-D degradation rate was measured to be approximately 80 % and concentration of TPH-D could degrade from 16000 mg kg-1 to 3500 mg kg-1 after 240 days.

In this study we attempt to use phytoremediation techniques to treat the contaminated soil of cadmium. The experiment is divided into two stages. In the first stage, we selected three different species of plants which could tolerate heavy-metals: vetiver (Vetiveria zizanioides), Pteris ensiformis cv. 'Victoriae' according to the past records, and Alternanthera philoxeroides (Mart.) Griseb, which were sampled from the metal contaminated site in Hunei, Kaohsiung county. These three species were planted in three pots with 10, 20 and 30 mg Cd kg-1 in soil respectively. After 9 weeks of the growth, the vetiver was found accumulating the highest Cd and grew better than the other two species. Therefore, we selected the species of vetiver in the second stage of experiment. First, the species of vetiver was planted in the pots with concentrations of 30 and 50 mg Cd kg-1 in soil respectively. Then the pots were put in the greenhouse for incubation. After the test was run for 210 days, we found that the species of vetiver was helpful in the increasing the number of species and amounts of each species of microbe ( total bacteria, fungi and actinomycete ), as well as dehydrogenase activity. Meanwhile, it was effective to decrease the bioavailability of cadmium. In addition, the infection rate of mycorrhizal fungi was increased , which showed that the species of vetiver could resist the cadmium stress in soils and stimulate the soil fertility. Finally, we use molecular biotechniques of PCR-DGGE to observe the microbial diversity in the contaminated soil. We found that the pots with 30 mg Cd kg-1 in soil had more number of bands than the pots with different Cd concentrations in soil, while the pots without vegetation was found more fruitful than vegetated pots. These experimental results indicated that the pots planted with the species of vetiver under this situation would help some special microorganisms to grow, and thus that the microbial diversity was reduced. The results also showed that the pots planted with vetiver with initial cadmium concentrations of 30 and 50 mg Cd kg-1 respectively, in soil exhibited the degradation rate of about 30 percent for both. It was not satisfied to this result in this study. However, the phytoextraction rates of cadmium were measured equal to 7.8 and 8.9 percent, respectively. According to these results, we suggested that the plant, which could hyperaccumulate heavy metals, might be used to increase the removable ability of cadmium in the future.

In this study, the phytoremediation techniques are used to treat the soil contaminated by pentachlorophenol(PCP).First, four plants species were selected,including Allium tuberosum, Vigna radiata (L.) Wilczek, Pennisetum alopecuroides, and Medicago sativa to compare their treatment efficiencies for PCP in soil.The experimental results showed that the species of Allium tuberosum presented the highest degradation rate 76% after 35-day test run with the initial concentration of 20mg/kg in soil. In the second stage,the species of Allium tuberosum was thus selected to run the tests of feasibility of using phytoremediayion to treat the soils contaminated byPCP.During the e xperiment,the pot tests inside a greenhouse were run for 330 days.The result indicated that the species of Allium tuberosum contributed to the increase of microorganism and dehydrogenase activity in the soil. Bisides,we also found that adding with nutrients could help Allium tuberosum to depress the PCP stress.The test with vegetation of Allium tuberosum and addition of nutrients showed that the PCP degradation rate was measured equal to 98.4% with the concentration of PCP degraded from 42mgkg-1 to 0.68mgkg-1 after 330days. Finally, molecule biotechnology of PCR-DGGE was applied to the test of observing the microbiota in the soils.According to the test results,we found that the diversity of microorganisms could be raised through planting the species of Allium tuberosum. The microbiota in the soils with PCP pollutant have more varieties than the microbiota in soils without vegetation, which was infered that the addition of PCP might stimulate the vitality of microbes in the soils. Moreover, comparing the microbiota on rhizosphere of the plant species and in the bulk soils, it was found that the actitivies of root exudates might be able to increase the varieties of rhizospheric microorganisms.

No description available.

Les échanges commerciaux s'intensifient et s'étendent à l'ensemble de la planète. Le consommateur est exigeant et sensible à la qualité et à l'origine des produits alimentaires qu'il achète. Devant la difficulté de mettre en place des systèmes documentaires dans les pays d'Afrique sub-saharienne, des nouvelles stratégies de traçabilité émergent. Parmi les nouveaux moyens de tracer les produits d'origine végétale, l'idée de créer un « code barre biologique » basé sur l'analyse des ADN de microorganismes présents sur les fruits est une piste intéressante. Cette thèse est l'objet d'étude d'un WP dirigé par D. Montet obtenu dans le cadre du projet Inco Innovkar géré par JM Bouvet de l'UR 39. Cette méthode repose sur l'hypothèse que la microflore commensale du fruit de karité est spécifique entre autre d'une zone géographique de production. L'écologie des bactéries, levures et moisissures seront étudiées par le thésard sur le karité et le Physalis, une plante à fruit de la même zone géographique à fort potentiel commercial. L'analyse biochimique des fruits ainsi que l'activité antimicrobienne de certaines molécules sera étudiée (physaline). / Trade intensified and spread to the entire planet. The consumer is demanding and sensitive to the quality and origin of food products they buy. Given the difficulty of setting up documentation systems in countries in sub-Saharan Africa, new strategies are emerging traceability. Among the new means of tracing products of plant origin, the idea of creating a "biological bar code" based on the analysis of DNA of microorganisms on fruit is an interesting idea. This thesis is the subject of a study conducted by D. Montet WP obtained under the Inco project managed by JM Bouvet Innovkar of UR 39. This method assumes that the commensally microflora of the fruit of Shea is among other a specific geographical area of production. The ecology of bacteria, yeasts and molds will be reviewed by the PhD student on Shea butter and Physalis, a plant with fruit of the same geographical area with high commercial potential. Biochemical analysis of fruit and antimic robial activity of certain molecules will be studied (physaline).

As cianobactérias atuam no tratamento de águas residuárias em lagoas de estabilização. Seu estudo torna-se importante tanto pela atuação no referido tratamento como na possível produção de toxinas e seus efeitos nos sistemas aquáticos e saúde da população. Protocolos moleculares para culturas axênicas ou naturais foram testados e adaptados para as amostras analisadas. Este trabalho teve como objetivo avaliar o método molecular de eletroforese em gel de gradiente desnaturante nas espécies de Microcystis (cianobactérias) em um sistema de lagoas de estabilização. Foram utilizadas as técnicas de Reação de Polimerização em Cadeia (PCR) e Eletroforese em Gel de Gradiente Desnaturante (DGGE) do gene RNAr 16S como marcador molecular na análise de cianobactérias no sistema de lagoas de estabilização de São Lourenço da Serra - SP. Este sistema é composto por tratamento primário (caixa de areia), fossa séptica seguida de um sistema australiano (lagoa anaeróbia seguida por uma lagoa facultativa) e na saída do sistema de lagoas um tanque de cloração. Na amostra ambiental realizada na lagoa facultativa obteve-se, através de exame microscópico, o predomínio das espécies Microcystis aeruginosa e Microcystis flos-aquae. Através da técnica molecular de DGGE foi obtido um padrão de aproximadamente 18 bandas com a amostra ambiental. / Cyanobacteria are active in wastewater treatment in stabilization ponds. The study of these microrganisms is of a great importance considering their role in the referred wastewater treatments as well as their potential to produce toxins and their effects in aquatic systems and public health. Molecular protocols for pure or natural cultures were tested and adapted for the collected environmental samples. This work had as objective to evaluate the molecular method of denatuirng gradient gel electrophoresis in the Microcystis species (cyanobacteria) in a system of stabilization ponds. The techniques Polimerase Chain Reaction (PCR) and Denaturing Gradient Gel Electrophoresis (DGGE) of the gene 16S rRNA as molecular marker were used in the cyanobacteria analysis in the system of stabilization ponds of São Lourenço da Serra - SP. This system is composed by primary treatment (box of sand), septic tank followed by an Australian system (anaerobic pond proceeded by an facultative pond) and in the exit of the system a clorine tank. In environmental sample accomplished in the facultative pond it was obtained, as microscopic result, the prevalence of the species Microcystis aeruginosa and Microcystis flos-aquae. Through molecular techniques a pattern of approximately 18 bands with these environmental sample was obtained.

A metilamina ('CH IND.3'NH IND.2') é um composto orgânico usado na produção de inseticidas, herbicidas, fungicidas, surfactantes, combustíveis fósseis, explosivos, produtos farmacêuticos, químicos fotográficos, tintas, tecidos, solventes, borrachas e anti-corrosivos. Estudos sobre tratamento de águas residuárias contendo metilamina são escassos e se restringem aos trabalhos envolvendo pesticidas carbamatados. Visando contribuir com os estudos acerca da degradação anaeróbia da metilamina, esta pesquisa estudou a comunidade microbiana e a atividade metanogênica específica em reatores anaeróbios em batelada, inoculados com lodo granular oriundo de reator UASB usado no tratamento de água residuária de abatedouro de aves, sob diferentes condições nutricionais: controle – sem metilamina, 5 mM, 10 mM, 20 mM, 30 mM, 50 mM, 75 mM e 90 mM de metilamina. Os reatores foram incubados sob temperatura de 30°C e agitação de 150 rpm. Desses reatores foram obtidas amostras para a determinação da atividade metanogênica específica (AME), sólidos suspensos voláteis (SVT), nitrogênio amoniacal e exames microscópicos. Ao final do experimento, foram realizados exames da biomassa por meio da técnica do número mais provável (NMP) e análise da diversidade microbiana por PCR/DGGE e seqüenciamento. O aumento da AME foi proporcional ao aumento das concentrações de metilamina, com inibição de produção de metano apenas nos reatores alimentados com 90 mM de metilamina. Os reatores alimentados com 50 mM e 75 mM de metilamina apresentaram os melhores resultados, com valores médios de AME de 0,0804 mmol 'CH IND.4'/g SVT.h e 0,0825 mmol 'CH IND.4'/g SVT.h respectivamente. Nos exames microscópicos foi verificado semelhança de morfologias microbianas em todas as concentrações de metilamina estudadas. Os organismos presentes nos reatores foram Methanosarcina sp., Methanosaeta sp., bacilos, coco-bacilos, filamentos e cocos. Em relação à análise de DGGE, não houve variação significativa nos padrões de bandas, tanto para o domínio Archaea quanto para o domínio Bacteria. Com os resultados da técnica de número mais provável (NMP) observou-se a predominância de arquéias metanogênicas dentre as bactérias anaeróbias totais. / The methylamine ('CH IND.3'NH IND.2') is an organic compound used in the production of insecticides, herbicides, fungicides, surfactants, fossil fuels, explosives, pharmaceuticals, photographic chemicals, paints, textiles, dyes, rubber and anticorrosive chemicals. Some studies about the treatment of wastewater containing methylamine are scarce and limited to works involving carbamate pesticides. This research aimed to study the anaerobic degradation of methylamine, the microbial community and the specific methanogenic activity in anaerobic battled reactors. The reactors were inoculated with granular sludge from a UASB reactor treating poultry wastes. Different nutritional conditions were adopted in the operation of the reactors: control (without methylamine), 5 mM, 10 mM, 20 mM, 30 mM, 50 mM, 75 mM and 90 mM of methylamine. The reactors were incubated under standard conditions: 30ºC and 150 rpm. Samples had been removed from the reactors to determine the specific methanogenic activity, the concentration of volatile suspended solids and ammoniacal nitrogen and the microscopic analysis. At the end of the experiment, the biomass was studied by the most probable number (MPN) technique and by the microbial diversity analysis with PCR and DGGE techniques. The increase of the specific methanogenic activity was proportional to the increase of methylamine concentration. The methane production was inhibited only in the reactor that was fed with 90 mM of methylamine. The reactors that were fed with 50 mM and 75 mM of methylamine showed the best results, with medium values of specific methanogenic activity equal to 0,0804 mmol 'CH IND.4'/g SVT.h and 0,0825 mmol 'CH IND.4'/g SVT.h, respectively. The microscopic analysis showed similarity between the microbial morphologies in all of the reactors. The observed microorganisms were Methanosarcina sp., Methanosaeta sp., rods, cocci and filaments. The DGGE analysis did not show significant variation in the standard profile of the Archaea and Bacteria domains. The results of the MPN technique revealed the predominance of the methanogenic archaea among the total anaerobic bacteria.

O manguezal é um ecossistema costeiro, localizado em regiões de interface entre os ambientes terrestre e marinho, de ocorrência exclusiva em zonas tropicais e subtropicais. Esta localização confere ao sedimento deste ambiente características únicas, como alta salinidade e baixa disponibilidade de oxigênio, associado a grande riqueza em matéria orgânica. O resultado destas condições é a ocorrência de uma restrita diversidade de plantas em tais ambientes, associada a uma grande diversidade de animais, que usam o manguezal para sua proteção e reprodução. O presente estudo mostrou como as comunidades de arquéias (amoA e 16S DNAr) e bactérias (nifH e 16S DNAr) estão estruturadas em sedimentos de manguezais sob distintos estados de preservação. Os perfis de DGGE indicaram alterações na composição das comunidades alvo, ligando sua estruturação com a contaminação do ambiente, enquanto que as quantificações de tais genes por meio de PCR quantitativo em tempo real (qPCR) indicaram alterações apenas na comunidade de arquéias oxidadoras de amônio. A filogenia destes grupos revelou a presença de grupos comumente encontrados em solos e água, alem de grupos particulares, possivelmente relacionado ao processo de especiação no ambiente de manguezal. De maneira geral, os resultados indicam que as comunidades de arquéias e bactérias são responsivas ao estado de contaminação dos manguezais, o que pode gerar um processamento diferencial do nitrogênio nestes sedimentos / The mangrove is a coastal ecosystem, located in the interface regions between the land and sea environments, with exclusive occurrence in tropical and subtropical areas. Such location confers to the mangrove sediments unique characteristics, like as high salinity and low availability of oxygen, associated with the high abundance of organic matter. The result of these conditions is the occurrence of a restrict plant diversity, associated with a great diversity of animals, who use the mangroves for its protection and reproduction. The present study has shown how the communities of archaea (16S DNAr and amoA) and bacteria (16S DNAr and nifH) are structured in mangrove soils under distinct states of preservation. The DGGE patterns indicate alterations in the composition of targeted communities, linking its structure with the environmental contamination, while the quantifications of targeted genes by real time PCR (qPCR) has indicated alterations only in the community of ammonium oxidizers archaea. The phylogeny of these groups revealed the presence of groups commonly found in soils and water samples, besides the occurrence of particular groups, possibly resulted from a speciation process in the mangrove environment. In general, results indicated that archaeal and bacterial communities are responsive to the mangroves contamination, and its alteration can also lead to differential nitrogen processing in these soils

Neste trabalho foi realizada a caracterização microbiana, por meio de técnicas de biologia molecular, do lodo granulado de reator anaeróbio de fluxo ascendente e manta de lodo (UASB - Upflow Anaerobic Sludge Blanket Reactor) operado sob condições mesofílicas (30 \'+ OU -\' 2ºC) e sulfetogênicas, com (TDH) de 12 h, na presença de 3,0 \'+ OU -\' 0,7 mg/L de oxigênio dissolvido. Essa caracterização foi realizada no lodo granulado proveniente da manta inferior (P1) e superior (P2) do UASB. O reator UASB de 10,5 L foi alimentado com meio basal Zinder acrescido de solução de vitaminas, metais traços e bicarbonato de sódio (10%). O meio foi preparado diariamente com água de abastecimento público, pH 7-8. Etanol e sulfato de sódio foram utilizados como fonte orgânica e de enxofre, respectivamente. Nestas condições, foram estudadas três diferentes relações de demanda química de oxigênio (DQO)/sulfato (3,0, 1,6 e 2,0). A análise de hibridação in situ fluorescente (FISH) demonstrou que houve predomínio de arquéias metanogênicas, detectadas com a sonda ARC915, em todas as condições operacionais, com médias iguais a 75,9, 77,1 e 85,4% em P1 e 78,6, 73,4 e 83,1% em P2, respectivamente. Methanosaeta sp. foi a arquéia metanogênica acetoclástica predominante confirmada também por seqüenciamento da banda recortada do gel de DGGE (eletroforese em gel de cadeia desnaturante), com similaridade de 96%. As bactérias (sonda EUB338) variaram de 9,6 a 36,2% e de 15,5 a 37,4% em P1 e P2, respectivamente. As bactérias redutoras de sulfato (BRS), detectadas com a sonda SRB385, variaram de 7,9 a 10,8% e de 8,7 a 19,8% em P1 e P2, respectivamente. Outros microrganismos identificados foram Shewanella sp. e Desulfitobacterium hafniense Y51, e a bactéria redutora de sulfato Desulfovibrio vulgaris subsp. vulgaris DP4. A distribuição do tamanho dos grânulos não sofreu mudança significativa no decorrer dos ensaios. Grânulos de 2 a 3 mm, que geralmente representam biomassa ativa no reator, contou com média de 76% do total quantificado; enquanto, grânulos de 1 a 2 mm, os quais sugerem que novos grânulos estavam sendo formados representaram 17% no reator UASB. As concentrações médias de metano e sulfeto no biogás foram iguais a 33 e 1,5 \'mü\'mol/ mL, respectivamente. Os resultados obtidos neste trabalho demonstraram que a presença de oxigênio, na concentração aplicada, não afetou severamente o metabolismo dos microrganismos comumente considerados estritamente anaeróbios. Esse fato foi evidenciado também pelo valor do potencial redox obtido que se manteve aproximadamente constante em -208 mV, mesmo na presença de oxigênio. As eficiências de remoção de matéria orgânica (DQO) e redução de sulfato também alcançaram resultados favoráveis, com médias superiores a 74%. / A microbial characterization of granular sludge from an upflow anaerobic sludge blanket reactor (UASB) was carried out by molecular biology techniques. The reactor with 1,5 L of volume was operated with HRT of 12 h under mesophilic (30 \'+ OR -\' 2ºC) and sulfidogenic conditions, in the presence of 3.0 \'+ OR -\' 0.7 mg \'O IND.2\'/L. The granular sludge samples were withdrawn from the bottom (P1) and upper (P2) parts of the reactor. The synthetic substrate used in the reactor feeding was composed by Zinder basal medium in addition with a solution of vitamins, trace metal and sodium bicarbonate (10%). The Zinder basal medium was prepared daily with tap water with pH value varying from 7 to 8. Concentrations of ethanol and sodium sulfate were applied as organic and sulfur sources, respectively. Three different COD/sulfate ratios (3,0, 1,6 and 2,0) were evaluated in these conditions. The fluorescent in situ hibridization (FISH) analysis demonstrated the predominance of methanogenic archaea, detected by ARC915 specific probe, in all the operational conditions, with mean values of 75.9%, 77.1% and 85.4% in P1 and 78.6%, 73.4% and 83.1% in P2. The sequencing of the excised band of DGGE (denaturing gradient gel electrophoresis) showed similarity of 96% with the acetoclastic archaea Methanosaeta sp. The bacterial community (EUB338 probe) varied from 9.6% to 36.2% in P1 and from 15.5% to 37.4% in P2. Sulfate-reducing bacteria (SRB), detected by SRB385 probe, varied from 7.9% to 10.8% and from 8.7% to 19.8% in P1 and P2, respectively. Other identified microorganisms were Shewanella sp. and Desulfitobacterium hafniense Y51 bacteria, and the sulfate-reducing Desulfovibrio vulgaris subsp. vulgaris DP4. Granule-size distribution did not significantly change during the assays. Granules of size varying from 2 mm to 3 mm, that generally represent the active biomass inside the reactor, accounted for 76% of the total quantified percentage; while, granules of size varying from 1 mm to 2 mm, that suggest the formation of new granules in the reactor, presented mean percentage of 17% of the total. The mean produced concentrations of methane and sulfide in the reactor were equal to 33 \'mü\'mol/mL and 1.5 \'mü\'mol/mL of biogas, respectively. The obtained results indicated that the applied oxygen concentration did not severely affect the metabolism of the strictly anaerobic microorganisms. This fact was evidenced by the obtained result of the oxidation-reduction potential that remained equal to -208 mV, even in the presence of oxygen. The mean removal efficiencies of organic matter (COD) and sulfate also achieved favourable results with values higher than 74%.