The aim of this study was to access the efficacy of an enhanced in situ bioremediation technology at a 1,2-dichloroethane (1,2-DCA) polluted site in southern Taiwan. A water-soluble substrate was injected into the groundwater to provide carbon sources for microbial growth. After substrate injection, increased total organic carbon (TOC) concentrations and microbial populations including Dehalococcoides spp. and Desulfitobacterium spp. were observed in the groundwater. Microbial diversity was analyzed using denaturing gradient gel electrophoresis (DGGE) and 16S rDNA sequencing to identify the bacterial strains. The results showed that after 4.5 months of substrate injection, the reduction-oxidation potential (ORP) changed from aerobic to anaerobic conditions. The less oxygen-tolerable 1,2-DCA degrading bacteria Dehalococcoides spp. started to accumulate in groundwater. However, the more oxygen-tolerable Desulfitobacterium spp. didn¡¦t show a prominent change, although the ORP was suitable for Desulfitobacterium spp. to carry out reductive dechlorination. The DGGE results indicate that with the injected carbon sources and mineral nutrients, both the groundwater microbial diversity and the amount of dominant bacteria were increased. The 16S rDNA sequencing demonstrated that the amount and diversity of 1,2-DCA degradation-related bacteria also increased with the injection of substrate. Six groups of 1,2-DCA degradation related reactions were found: dechlorination, chlorinated-compound degradation, denitrification, iron-reduction, sulfate-reduction and methane-utilizing. Four species that can directly degrade 1,2-DCA were found: Dehalobacter sp., Dehalococcoides sp., Nitrosospira sp. and Pseudomonas sp. Moreover, 11 methane-utilizing bacterial species were also discovered. The presence of these methane-utilizing bacteria not only might assist the process of denitrification and sulfate-reduction, but also could diminish the emission of the greenhouse gas. The results of this study confirmed that the addition of substrates could affect the groundwater oxidation-reduction state and enhance the bioremediation at the 1,2-DCA-contaminated site. Thus, enhanced in situ bioremediation is a feasible technology for site remediation.

The century poison ¡§dioxins¡¨ are hydrophobic compounds that can combine with many organic matters and persist in the environment as well as to accumulate in living organisms. Dioxins caused great risk to the health of living organisms and to the entire ecological environment. We had isolated previously one bacterial species, Pseudomonas mendocina NSYSU, which can use pentachlorophenol (PCP) as its sole carbon source and degrade dioxin compounds. In order to study the feasibility of using this bacterial strain to bioremediate an PCDD/Fs polluted site, four microcosm experiment groups were designed to test the degradation efficiency of this strain: sterile soil group, non-sterile soil group, soya lecithin group and non-sterile soil with soya lecithin group. In addition, we also analyzed the shift of community structure of each microcosm by PCR-DGGE. The results show that the soya lecithin group has the highest efficiency to degrade OCDD/OCDF. After fifty days of reaction, the degradation rates of OCDD/OCDF were 62% and 47% respectively. The microbial diversity analysis indicated that the soya lecithin group presented less abundant from the initial stage, but increasing gradually over time. This might related to the formation of micelles in water phase which contained higher concentration of PCDD/Fs dissolved from the soil particles. Therefore, soya lecithin not only can reduce the toxicity of PCDD/Fs, but also can enhance the bioavailability of the organic pollutants to the microorganisms. In conclusion, monitoring the transition of P. mendocina NSYSU as well as the microbial diversity can provide valuable information during the bioremediation process by applying soya lecithin.

Groupers are an important mariculture fish in Taiwan and Southeast Asian countries. The rapidly growing orange spotted grouper (Epinephelus coioides) has experienced relatively severe bacterial disease problems. The proliferation of pathogens in fish can be suppressed by commensal microbiota. In this context, probiotic seem to offer an attractive alternative. Bacillus subtilisis a probiotic bacteriumthat is administered in diet to suppress proliferation of pathogens. In the present study, E.coioideswere fed for 6 months with diets containing B.subtilis at 0 (control), 0.1 % and 1 %. Percent weight gain and feed efficiency of the 0.1 and 1 % groups were significantlybetter than the control group. The innate cellular response, respiratory burst of the fish fed the 1 % and 0.1 % diet was significantly higher compared to the control group on 10 or 20 days after feeding, and even moresignificanton 30 days.ProbioticBacillus subtilis increased the fish¡¦s intestinal microbial diversity as measured by visible band number and Shannon diversity indexin DGGE analysis. Probiotic Bacillus subtilis also stimulated the population of bacterial species likePaenibacillussp,Lactobacillus oenistrain 59 b, and Methilacidophiluminfernorumstrain V4 that beneficial for Epinephelus coioides. The best dose of probiotic Bacillus subtilis based on growth performances, innate cellular responses and profile of microbiota in fish intestines is 0.1 %, which showed equal efficacy as the 1% diet.

I havet finns det flertalet olika bakteriearter, alltså en hög diversitet vilket teoretiskt sett borde betyda en hög funktionalitet. I denna studie har vi undersökt hur bakteriers funktionalitet och diversitet påverkas av förändrad salthalt. Två marina bakteriesamhällen har studerats och jämförts, dels ett Skagerraksamhälle samt ett Östersjösamhälle. Dessa två samhällen utsattes gradvis för hög respektive låg salthalt och efter avslutat experiment hade Skagerraksamhället en låg salthalt dvs Östersjöbetingelse och Östersjösamhället övergått till hög salthalt (Skagerrakbetingelse). Resultatet av detta blev att både funktionalitet och diversitet påverkades, vilket analyserades med Eco-plattor och DGGE (Denaturing Gradient Gel Electrophoresis). Bakterieantalet ökade respektive sänktes i Skagerrak- respektive Östersjö-samhället. Då Östersjösamhället fick en högre salthalt ledde detta till att funktionaliteten sänktes och en tidigare icke dominant art blev dominant. För Skagerraksamhället som fick en sänkt salthalt bedömdes funktionaliteten ha ökat i och med att en ny kolkälla nyttjades. Dock såg diversiteten ut att vara lägre, möjligtvis p.g.a. en förändring av dominanta och icke dominanta bakterier i samhället. Det är däremot inte möjligt att utifrån denna studie dra slutsatsen att en hög diversitet automatiskt ger en hög funktionalitet. / In the sea there is a high diversity of different microorganisms, especially bacteria. In other studies it has been shown that salinity is an important factor forming the bacterial communities. In this study we have investigated how diversity and functionality is affected by changing salinity. Bacterial communities from Skagerrak and the Baltic Sea were used in the study. In the Skagerrak community the bacteria live in an environment with high salinity and low DOC (dissolved organic carbon) concentration and the Baltic communitiy has a low salinity and a high DOC concentration. We made a salinity change between these communities to see how that would affect the communities. The diversity, genotype variation, and functionality of the bacteria were studied using DGGE-analysis and Eco-plates respectively. The results showed that the two communities were affected by the salinity change. The bacterial counts decreased and increased, in the Baltic and Skagerrak communities respectively, in relation to the salinity change and a diversity change was seen in the DGGE-analysis (Denaturing Gradient Gel Electrophoresis). The original Baltic and Skagerrak communities showed different functionality traits. Over time, along the experiment, the functionality changed and the communities showed different functionality at the end of the experiment. But we can’t definitely say that high diversity always gives high functionality.

In vitro gut models provide several advantages over in vivo models for the study of the human gut microbiota. However, because communities developed in these models are simplified simulations of the in vivo environment it is necessary to characterize the reproducibility, repeatability and stability of cultured communities. We also need to broadly define the differences between in vitro consortia and the communities from which they are derived. In this study we characterized and validated a twin-vessel (independent, identical) single-stage chemostat model of the human distal gut. Samples were analyzed using a molecular fingerprinting technique (Denaturing Gradient Gel Electrophoresis) to compare and monitor changes in the overall structure of the communities while a phylogenetic microarray (Human Intestinal Tract Chip) was used to obtain phylogenetic information. We found that twin-vessels inoculated with feces developed and maintained diverse communities that reached stable compositions by at most 36 days post-inoculation. Communities were enriched in Bacteroidetes but not Clostridium cluster XIVa, Bacilli or other Firmicutes relative to the fecal inocula. Vessels were very reproducible when inoculated with identical fecal inocula, less similar when inoculated with consecutive fecal donations from the same donor, and maintained donor-specific identities when inoculated with feces from different donors. Norepinephrine exposure (undefined perturbation) did not appear to have a substantial effect on the structure of chemostat communities, while clindamycin treatment (defined perturbation) caused large changes in the structure of chemostat communities. Packed-column biofilm reactors incorporated a simulated mucosal environment into our chemostat system, allowing us to simultaneously culture biologically relevant planktonic and biofilm communities that were complex, reproducible, and distinct. Defined communities were comparable to fecal communities at the phylum/class-level but established stable compositions more rapidly. While it was difficult to assess the persistence of synthetic stool in a healthy fecal chemostat community (+/- antibiotic perturbation), mixing communities from two donors resulted in a mixed community that more closely resembled one donor over the other. Although future experimentation is required, the results presented here show our twin-vessel single-stage chemostat model represents a valid simulation of the human distal gut environment and can support complex, representative microbial communities ideal for experimental manipulation. / Canadian Institutes of Health Research; Ontario Ministry of Agriculture, Food and Rural Affairs; Ontario Ministry of Research and Innovation; Canada Foundation for Innovation; Ontario Ministry of Training, Colleges and Universities

No description available.

Ziel der vorliegenden Arbeit war es, einen Beitrag zur Aufklärung der Ätiologie der Graskrankheit mit Hilfe der DGGE, besonders im Hinblick auf in vitro unkultivierbare Bakterien der Darmflora zu leisten. Es sollte ebenfalls geprüft werden, ob die DGGE die Diagnose der Graskrankheit erleichtern kann. Weiterhin sollte der Einfluß von C. botulinum auf die Erkrankung durch den Nachweis von Toxin, Bakterien und Antikörpern untersucht werden. Es standen zur Untersuchung Proben des Colons, Caecums und Kotes von erkrankten Pferden und Kontrolltieren, Kotproben von klinisch gesunden Pferden, die aus denselben Beständen wie die erkrankten Tiere stammen sowie Serum aller drei Gruppen zur Verfügung. Wegen der hohen individuellen Variabilität der Darmflora war kein eindeutiges Merkmal der Graskrankheit im Profil der mikrobiellen Gemeinschaft des Darmes oder Kotes nachweisbar. Allerdings ließ sich anhand der Clusteranalyse ein Abgrenzung der Flora des Caecums und besonders des Colons der erkrankten und gesunden Tiere erkennen. Für eine Diagnose der Graskrankheit am lebenden Tier anhand der Kotflora ist die DGGE jedoch wegen ihrer geringen Aussagekraft und methodischen Probleme nicht geeignet. Der Verdacht, dass C. botulinum an der Ätiologie der Graskrankheit beteiligt ist, konnte durch die Ergebnisse im Tierversuch und ELISA weiter untermauert werden.

Made available in DSpace on 2016-06-02T19:29:54Z (GMT). No. of bitstreams: 1 4871.pdf: 5072482 bytes, checksum: 1d8762ce5f321414db355400f4e7a38e (MD5) Previous issue date: 2012-02-17 / Reservoirs of Brazilian semiarid regions are essential to guarantee water supply to the people who live around them, and the multiple uses change the water quality and the communities of these ecosystems. This study aimed to evaluate the effects of dry and rainy periods during three consecutive years on the density and diversity of the prokaryotic community of the water column in the Armando Ribeiro Gonçalves dam, besides to analyze the fluctuations on some limnological variables. Dissolved oxygen, water temperature and pH were measured with a multiparametric probe (YSI). Sub-samples to the analysis of total phosphorus, phytoplankton density, bacterial and archaeal density determination, and DNA extraction were taken to the Laboratório de Microbiologia Aquática of the Universidade Federal do Rio Grande do Norte. Denaturing gradient gel electrophoresis (DGGE) was used to elucidate temporal shifts on planktonic prokaryotic community of the reservoir influenced by rainy and dry seasons. Bacterial and archaeal abundance and the DGGE band richness were influenced by pluviosity, water temperature, and total phosphorus (TP). Principal components analysis (PCA) showed strong correlations among these variables. Canonical correspondence analysis (CCA) showed temporal shifts on Bacterial and archaeal community composition, associated with the pluviosity, reservoir volume, water temperature, and prokaryotic density. This suggests the predominance of factors associated to precipitation events on community structure determination, that is probably composed by persistent and transitory populations. Considering the set of environmental variables, the results indicated two stability moments in reservoir: one moment when the reservoir volume is smaller; and another when the reservoir volume is greater. These stabilities were broken by the rain and by the water loss, respectively. / Reservatórios da região semiárida brasileira têm papel fundamental na manutenção do abastecimento para as populações do seu entorno, e os usos múltiplos desses ecossistemas alteram a qualidade das suas águas e consequentemente as comunidades aquáticas. O presente trabalho teve como objetivo avaliar os efeitos dos períodos secos e chuvosos durante três anos consecutivos sobre a densidade e diversidade da comunidade procariótica da coluna de água na Barragem Armando Ribeiro Gonçalves, bem como analisar as flutuações de algumas variáveis limnológicas medidas. Oxigênio dissolvido, temperatura da água e pH foram medidos in situ usando-se uma sonda multiparamétrica YSI. Para as análises laboratoriais de fósforo total, estimativa de densidade de fitoplâncton, bacterioplâncton e arqueoplâncton, e extração de DNA, alíquotas das amostras foram processadas no Laboratório de Microbiologia Aquática da Universidade Federal do Rio Grande do Norte. Eletroforese em gel com gradiente de desnaturação (DGGE) foi usada para analisar variações sazonais na composição das comunidades procarióticas planctônicas de em reservatório eutrófico de região tropical semiárida, influenciadas por períodos alternados de chuva e estiagem. A abundância do bacterioplâncton e arqueoplâncton e a riqueza das bandas da DGGE foram mais influenciadas pela pluviosidade, temperatura da água e concentração de fósforo total (TP). A análise de componentes principais (PCA) mostrou fortes correlações entre estes fatores. A análise de correspondência canônica (CCA) revelou diferenças temporais na composição das comunidades de Bacteria e Archaea relacionadas à pluviosidade, ao volume do reservatório, à temperatura e à densidade do bacterioplâncton e arqueoplâncton, indicando a predominância dos fatores ligados aos eventos de precipitação na determinação da estrutura dessas comunidades, possivelmente compostas por populações permanentes e populações transitórias. Isto sugere dois momentos de estabilidade no conjunto de variáveis ambientais: um quando o volume de água armazenada é menor; e outro quando o volume é maior, sendo as estabilidades quebradas pelos eventos de chuva e pela perda de água, respectivamente.

Submitted by Bruna Rodrigues (bruna92rodrigues@yahoo.com.br) on 2016-09-23T13:08:05Z No. of bitstreams: 1 TeseZADP.pdf: 1197588 bytes, checksum: 4e1f7602ee6da5dec0dbca0315893fa4 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-10-04T18:01:33Z (GMT) No. of bitstreams: 1 TeseZADP.pdf: 1197588 bytes, checksum: 4e1f7602ee6da5dec0dbca0315893fa4 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-10-04T18:01:40Z (GMT) No. of bitstreams: 1 TeseZADP.pdf: 1197588 bytes, checksum: 4e1f7602ee6da5dec0dbca0315893fa4 (MD5) / Made available in DSpace on 2016-10-04T18:01:48Z (GMT). No. of bitstreams: 1 TeseZADP.pdf: 1197588 bytes, checksum: 4e1f7602ee6da5dec0dbca0315893fa4 (MD5) Previous issue date: 2015-06-15 / The actual agricultural production system requires the use of chemicals such as pesticides and antimicrobials. These compounds, when reach aquatic environments, can cause serious environmental problems and affect target and non-target organisms such as microorganisms, that play key ecological functions to the ecosystem functioning. So, the objectives of this study were: (i) to evaluate the bactericidal action of oxytetracycline (OTC) and fungicide imazalil (IMZ) on bacterial ecological function of pesticide fipronil degradation; (II) evaluate the effect of oxytetracycline on density and aquatic bacterial diversity; (III) to monitor changes in bacterial dynamics in the presence of fipronil. Water was sampled in Beija-Flor Reservoir for mounting the experiments. Microcosms were prepared in triplicates for six different treatments: water; water and OTC; water and IMZ; water and fipronil; water, fipronil and OTC; water, fipronil and IMZ. The microcosms were kept in the dark at 21oC. Samples were collected at 1, 5, 10, 20, 45 and 70 days of incubation. It was determined the water pH, the dissolved organic carbon (DOC), total nitrogen (TN), OTC and fipronil concentrations. Water samples from the microcosms were also used for bacterial density analysis by epifluorescence microscopy and diversity by DGGE band profiles analysis. The presence of OTC alone and especially mixed with IMZ affects bacterial diversity, but does not cause significant effect on fipronil degradation, suggesting the existence of functional redundancy among the individuals that formed the bacterial community. The oxytetracycline, at certain concentrations, promotes a bacterial density decrease and diversity increase, probably by mediating the coexistence of species as a result of the growth control of the best competitive bacteria. Fipronil may cause bacterial density increase but, concerning its diversity, initially in the experiment, it was reduced, comparing with the control samples. However, after 70 days, the diversity was similar, suggesting that the community was reestablished, leading us to consider that the community was resilient to the impact caused by fipronil. / O atual sistema de produção agropecuário exige a utilização de produtos químicos como os antimicrobianos e agrotóxicos. Estes compostos, ao alcançarem os ambientes aquáticos, podem trazer sérios problemas ambientais e afetar vários organismos, como os microrganismos, que desempenham funções ecológicas fundamentais ao funcionamento ecossistêmico. Desta maneira, os objetivos deste trabalho foram: (I) avaliar a ação do bactericida oxitetraciclina (OTC) e fungicida imazalil (IMZ) na função ecológica bacteriana de degradação do agrotóxico fipronil; (II) avaliar o efeito da oxitetraciclina na densidade e diversidade bacteriana aquática; (III) acompanhar alterações na dinâmica bacteriana na presença do fipronil. Foi coletada água da Represa do Beija-Flor para a montagem dos experimentos. Foram preparados microcosmos em tréplica para seis tratamentos distintos: água; água e OTC; água e IMZ; água e fipronil; água, fipronil e OTC; água, fipronil e IMZ. Os microcosmos foram mantidos a 21 oC, no escuro. Foram feitas amostragens nos tempos 1, 5 10, 20, 45 e 70 dias de incubação. Foram determinados o pH da água, carbono orgânico dissolvido (COD), nitrogênio total (NT) e as concentrações de OTC e fipronil. Amostras de água provenientes dos microcosmos foram utilizadas para análise bacteriana de densidade por microscopia de epifluorescência e análise de diversidade por meio dos perfis de bandas do DGGE. A presença da OTC sozinha e principalmente em mistura com IMZ, afeta a diversidade bacteriana, porém não causa efeito significativo na degradação do fipronil, sugerindo existência de redundância funcional entre os indivíduos que constituíram a comunidade bacteriana. A oxitetraciclina, em determinadas concentrações, causa a diminuição na densidade bacteriana e pode promover o aumento da diversidade, provavelmente por mediar à coexistência de espécies em consequência do controle do crescimento de bactérias mais competitivas. O fipronil pode causar o aumento da densidade bacteriana mas quanto à diversidade, no início do experimento, ela foi menor que nas amostras controle. Porém, após 70 dias, as diversidades ficam semelhantes, sugerindo que a comunidade se reestabeleceu, podendo esta ser considerada resiliente a perturbação causada pelo fipronil.

Submitted by Daniella Sodre (daniella.sodre@ufpe.br) on 2015-03-17T13:29:19Z No. of bitstreams: 2 Dissertaçao VERA LÚCIA PEREIRA.pdf: 654781 bytes, checksum: 58208be95d7e3eb0df2a87d8e1323112 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-03-17T13:29:19Z (GMT). No. of bitstreams: 2 Dissertaçao VERA LÚCIA PEREIRA.pdf: 654781 bytes, checksum: 58208be95d7e3eb0df2a87d8e1323112 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2013-02-27 / CNPq e FACEPE / A região semiárida do nordeste brasileiro é ocupada por uma vegetação de fisionomia variada, adaptada às condições de aridez, denominada caatinga. A Caatinga vem sendo gradativamente impactada pelo desmatamento e uso inadequado dos recursos naturais. Ainda são práticas comuns no preparo da terra para a agropecuária, o desmatamento e as queimadas, que contribuem para desequilibrar o clima, piorar a qualidade do solo e prejudicar a manutenção de populações presentes. Embora grande volume de trabalhos sobre monitoramento da qualidade do solo, envolvendo variados cenários ambientais e de manejo sejam relatados, pouca ênfase é dada à degradação dos solos em regiões secas. Considerando que a atuação dos micro-organismos do solo pode contribuir para a qualidade edáfica, objetivou-se comparar a atividade microbiana em solos sob caatinga nativa e após o desmatamento. Coletas de solo foram realizadas em área sob caatinga nativa (T0), e com 60 (T1), 106 (T2) e 160 (T3) dias de desmatamento, no município de Petrolina, Pernambuco. Avaliaram-se: atividade enzimática, carbono da biomassa microbiana, respiração microbiana, quociente metabólico, ergosterol no solo e estrutura da comunidade microbiana por DGGE. O carbono da biomassa microbiana (CBM) teve maiores valores em T3 e a fosfatase ácida foi significativamente maior em T0. Com o resultado da análise multivariada foram formados três grupos envolvendo os períodos amostrais. O primeiro foi formado pela caatinga nativa (T0), o segundo por T1 e T2, e o último por T3. A maioria da variabilidade dos dados entre os tempos amostrais foi correlacionada positivamente com o carbono da biomassa microbiana e com a atividade da fosfatase ácida, correlação positiva também foi observada para respiração edáfica basal, o teor de ergosterol e atividade da β-glicosidase. As variáveis físicas e químicas do solo, temperatura, CTC, umidade, Na, Al, K e Mg, contribuíram para a separação dos tempos amostrais. A umidade foi determinante para a separação de T3. A temperatura do solo, CTC, os nutrientes K e Mg edáfico influenciaram na formação do grupo composto por T1 e T2. As duas amostragens realizadas após o desmatamento da caatinga apresentaram semelhança formando apenas um grupo, no entanto, após 160 dias de desmatamento, a área mostrou-se diferente de todos os tempos amostrados, fato atribuído às melhores condições proporcionadas pela umidade no solo em decorrência da chuva. Conclui-se que a umidade do solo é mais determinante para a atividade microbiana edáfica do que o desmatamento da caatinga.