Dissertations / Theses: 'Microbial consortium'

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Mashaphu, Nthabiseng. "The microbial composition of a natural methanogenic consortium." Thesis, University of the Western Cape, 2005. http://etd.uwc.ac.za/index.php?module=etd&amp.

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Wetlands account for approximately 20% of annual global methane emissions. Many wetlands receive inputs of organic matter, nutrients, metals and various toxic compounds from adjacent agricultural and industrial areas. The present study aimed to investigate the microbial composition of a natural methanogenic consortium. A consortium-based molecular approach to study diversity of methanogenic microbial communities in a natural wetland at the primary inflow was used. Key microorganisms of a nethane producing consortium were identified. Extracted high molecular mss DNA ws analysed by PCR combined with denaturing gradient gel electrophoresis and subsequent sequencing of 16S rDNA. This study was also aimed to identify syntrophic microorganisms in the wetland system. The data obtained suggest a well established syntrophic relationship within the wetland.

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Anieto, Ugochukwu Obiakornobi. "Engineered Microbial Consortium for the Efficient Conversion of Biomass to Biofuels." Thesis, University of North Texas, 2014. https://digital.library.unt.edu/ark:/67531/metadc699973/.

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Current energy and environmental challenges are driving the use of cellulosic materials for biofuel production. A major obstacle in this pursuit is poor ethanol tolerance among cellulolytic Clostridium species. The first objective of this work was to establish a potential upper boundary of ethanol tolerance for the cellulosome itself. The hydrolytic function of crude cellulosome extracts from C. cellulolyticum on carboxymethyl cellulose (CMC) with 0, 5, 10, 15, 20 and 25% (v/v) ethanol was determined. Results indicated that the endoglucanase activity of the cellulosome incubated in 5% and 10% ethanol was significantly different from a control without ethanol addition. Furthermore a significant difference was observed in endoglucanase activity for cellulosome incubated in 5%, 10%, 15%, 20% and 25% ethanol in a standalone experiment. Endoglucanase activity continued to be observed for up to 25% ethanol, indicating that cellulosome function in ethanol will not be an impediment to future efforts towards engineering increasing production titers to levels at least as high as the current physiological limits of the most tolerant ethanologenic microbes. The second objective of this work was to study bioethanol production by a microbial co-culture involving Clostridium cellulolyticum and a recombinant Zymomonas mobilis engineered for the utilization of oligodextrans. The recombinant Z. mobilis ZM4 pAA1 and wild type ZM4 were first tested on RM medium (ATCC 1341) containing 2% cellobiose as the carbon source. Ethanol production from the recombinant Z. mobilis was three times that observed from the wild type Z. mobilis. Concomitant with ethanol production was the reduction in OD from 2.00 to 1.580, indicating the consumption of cellobiose. No such change in OD was observed from the wild type. The recombinant ZM4 was then co-cultured with C. cellulolyticum using cellobiose and microcrystalline cellulose respectively as carbon sources. Results indicate that the recombinant ZM4 acted synergistically with C. cellulolyticum to utilize 2.0 g L-1 cellobiose, producing as much as 0.40 mM concentration of ethanol whereas only 0.20 mM ethanol was detected for the wild type ZM4 co-cultured with C. cellulolyticum under the same conditions. A co-culture of the recombinant ZM4 and C. cellulolyticum using 7.5 g L-1 microcrystalline cellulose gave lower ethanol yield than when using cellobiose. In the latter case, the recombinant began producing ethanol in 5 days whereas the wild type required 10 days to produce detectable ethanol. Future efforts will concentrate on identifying the correct concentration of cellulosic substrate at which synergy will be observed using the recombinant ZM4 and other cellulose degrading microorganisms, as well as optimizing medium formulations to better support both organisms.

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Alzahrany, Hashim. "Hydrocarbon remediation by microbial consortium : validation with molecular and biotechnological tools." Thesis, University of Aberdeen, 2012. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=185862.

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There is a need for sustainable approaches in the remediation of hydrocarbon (HC)-impacted environments. Bioremediation has gained prominence but to be effective this requires consideration of the physical, chemical and biological processes in an environmental matrix. In the first part of this study, physical constraints to effective bioremediation of drill cutting (DC) were quantified using slurry-phase treatments. The DC:water ratio and aeration of the DC slurries were optimised. Results indicated that physical parameters, unless effectively managed, could greatly influence the performance of bioremediation campaign, both in terms of end-point and duration. Once physical aspects have been addressed, it is important to understand both chemical and biological processes. There has been a great deal of work considering the significance of chemical processes such as bioavailability, pH performance range and nutrient optimisation. These were not investigated in this programme of research. Bioaugmentation (microbial seeding of contaminated soils) has been proposed as a significant method for bioremediating HC-contaminated matrices. However, the value of bioaugmentation has been the subject of considerable controversy. The performance of bioaugmentation was studied in this project both directly and indirectly. Compounds capable of encouraging the activity of HC degraders were added to media. This "conditioning" process was investigated and quantified in three major experiments. Firstly, the conditioning of a HC-degrading bacterial consortium using selective enrichment substrates was studied. Here, INT reduction was monitored over time using 96-well microplates containing mineral media supplemented with diesel, toluene, hexadecane and phenanthrene. The colour development resulting from conditioning on different substrates varied significantly (P≤ 0.05). Secondly, the performance of HC degraders (Pseudomonas putida F1 and it's bioluminescent derivative, P. putida TVA8) after conditioning on a range of catabolic inducer substrates was studied. The development of an optimised experimental procedure to study carbon transformation of toluene as a consequence of conditioning was reported. Cultures conditioned on toluene had significantly (P≤ 0.05) higher activity, biomass and toluene degradation rates than the other treatments. Finally, the effect of conditioning three HC-degrading bacteria (Pseudomonas putida NCIMB 9816, Pseudomonas sp. and Klebsiella sp.), individually and in combination, on degradative performance and relative species abundance was assessed. DGGE profiles indicated significant (P≤ 0.05) changes in relative species abundance but, generally, there were no significant differences in HC degradation or cumulative respiration. The results reported in this thesis, at the genotypic, phenotypic and functional levels reveal the complexity of HC remediation and the need to combine detailed analytical chemistry with focussed microbial measurements.

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Paixão, Douglas Antonio Alvaredo [UNESP]. "Prospecção gênica e diversidade bacteriana de um consórcio degradador de óleo diesel." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/94906.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
A estratégia de clonagem e sequenciamento do gene 16S rRNA é uma das técnicas moleculares que permite estimar e comparar a diversidade microbiana de diferentes amostras ambientais. O objetivo deste trabalho foi estimar a diversidade de microrganismos pertencentes ao Domínio Bactéria em um consórcio degradador de óleo diesel, por meio do sequenciamento parcial do gene 16S rRNA, assim como desenvolver uma nova metodologia de rastreamento em bibliotecas metagenômicas. O consórcio bacteriano foi obtido através de solo enriquecido com óleo diesel. O DNA metagenômico foi extraído com o auxílio do kit Fast DNA spin Kit for soil (Bio101- Quantum Biotechnologies) e amplificado por uma reação de PCR (Reação em Cadeia da Polimerase) com os oligonucleotídeos iniciadores FD1 e RD1 específicos para a o gene 16S rRNA. Os produtos de PCR foram clonados em vetor pGEM T Easy (Promega) e transformados em células competentes de Escherichia Coli DH5 . O sequenciamento parcial dos clones foi feito com oligonucleotideos universais do vetor. Para a prospecção gênica foi utilizado membranas de nylon com “pools” de DNA de todas as placas. A biblioteca obtida gerou 431 clones. Os clones obtidos apresentaram similaridade com o filo Proteobacteria, com representantes das classes Gammaproteobacteria, Alphaproteobacteira e Betaproteobacteria. O gênero Pseudomonas apresentou-se com maior frequência de clones na biblioteca. O “software” DOTUR foi usado para determinar o número de unidades taxonômicas operacionais (OTUs). A curva de extinção indicou que os 431 clones sequenciado foram suficientes para estimar a diversidade bacteriana do consórcio. A metodologia testada baseado em “pools” de DNA foi eficiente na detecção e isolamento do gene Alkb na bilbioteca metagenomica.
Cloning and sequencing of 16S rRNA gene it is one of the molecular techniques that permits estimate and compare the microbial diversity of different environmental samples. The aim of this work was estimate the diversity of microorganisms that belong to Bacteria domain in a consortium specialized in diesel oil degradation, through partial sequencing of 16S rRNA gene, as well as develop a new methodology for screening libraries in metagenomics. This consortium was obtained through enrichments achieved using diesel oil in soil samples. The metagenomic DNA was obtained using Fast DNA spin Kit for soil (Bio 101-Quantum Biotechnologies) and amplified by PCR (Polymerase chain reaction) with FD1 and RD1 oligonucleotides, which are specific for 16S rRNA gene. The PCR products were cloned into pGEM-TEasy vector (Promega) and Escherichia coli DH5 was used as the host cell for recombinant DNAs. The partial clones sequencing was obtained using universal primers of the vector. For the exploration of gene were used nylon membranes with Pools of DNA from all plates. The library generated from 431 clones. All clones sequenced showed similarity with the phylum Proteobacteria, distributed in Gammaproteobacteria, Alphaproteobacteira and Betaproteobacteria classes. The Pseudomonas genus was the most abundant genus found in the metagenomic library. The DOTUR software was used to assigns sequences to operational taxonomic units (OTUs). Using the OTUs composition data, rarefaction curves were made to show that 431 sequences were enough to obtain a satisfactory coverage of diversity of the microbial consortium. The test methodology based on Pools of DNA isolation was effective in detecting the gene Alkb Library metagenomics.

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Araújo, Solange Pires de. "Produção de inóculo microbiano, obtido de macrófitas aquáticas na Amazônia, com potencial de degradação de hidrocarbonetos de petróleo." Universidade Federal do Amazonas, 2014. http://tede.ufam.edu.br/handle/tede/4307.

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CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico
The Amazon, which owns the largest fauna and flora in the world presents unparalleled wealth of biological diversity, however, keep intact this megadiversity requires scientific and technological knowledge. In this context, there is an important biotechnological tool that is the bioremediation of impacted environments with petroleum hydrocarbons and derivatives. In the present study samples of microbial communities of fungi and bacteria associated with aquatic macrophytes Eichhornia crassipes (Mart.) Solms, Ichnanthus calvescens Döll and Cyperus ligularis L., were researched. These host plants common at Rio Negro were collected in contaminated environments by oil and oil products at Waterway Station from Manaus. From the species selected, 155 bacterial strains were isolated, being 97 epiphytic and 58 endophytic, and 54 fungi strains, being 30 epiphytic and 24 endophytic. Selective media were used for isolation of microorganisms such as BH liquid medium (Bushhnell Haas) plus oil. The oil and diesel used are from the Base Oil Urucu, Amazonas. The biodegradability tests were performed on selective medium (BH), with the addition of oil as the carbon source known as Medium I This test was repeated with the addition to the medium I the redox indicator 2,6-dichlorophenol indophenol (DCPIP), called medium II. After the evaluationof microbial isolates were selected 6 bacteria and 7 fungi. Molecular identification of bacteria was performed by the 16S ribosomal DNA region and revealed the presence of Bacillus pumilus (endophytic / epiphytic), Lysinibacillus fusiform (epiphytic), Pseudomonas aeruginosa (epiphytic) and Acinetobacter junii (epiphytic/epiphytic). For molecular identification of fungi was performed by the ITS1 and ITS2 region and revealed the presence of Curvularia trifolii (epiphytic), Curvularia clavata (endophytic / epiphytic), Gibberella intermedia (epiphytic/endophytic), Phoma herbarum (epiphytic) and Dothideomycetes sp (epiphytic). These microorganisms were selected for composition of microbial consortium that were used for hydrocarbon biodegradation tests. The measurement of biodegradation of oil and diesel activities was estimated by chromatography and mass spectrometry. In tests we used water of Rio Negro with the aim of approaching research the environment that are being studied. Degradation of hydrocarbons by consortia of fungi and bacteria had significant average values (98.7 to 100%), but did not show any statistical difference between the degradation of the control containing water of the Rio Negro (97.3%). In the experiment with the mixed consortium (FB), there were significant differences, because although the control containing water of the Rio Negro has promoted degradation of diesel by wild microbiota (81.7%), this degradation was lower and statistically different from the mixed consortium (97,5%). Analysis were carried out for degradation of the compounds naphthalene and phenanthrene of diesel by consortia . It was observed that phenanthrene was the best that has been degraded by the mixed consortium (F / B), however the naphthalene was better degraded by the control containing only water from the Rio Negro, highlighting the potential of wild microorganisms that deserve attention in future research, the isolation of these ones in waters from Rio Negro. In the experimental design with the consortia, the results showed that mixed consortia (FB) have potential for use in future bioremediation.
A Amazônia, detentora da maior fauna e flora do mundo apresenta riqueza inigualável de diversidade biológica, entretanto, manter intacta essa megadiversidade requer conhecimentos científicos e tecnológicos. Nesse contexto, situa-se uma importante ferramenta biotecnológica que é a biorremediação de ambientes impactados por hidrocarbonetos de petróleo e derivados. No presente trabalho realizou-se estudo de amostras das comunidades microbianas de fungos e bactérias associadas às macrófitas aquáticas Eichornia crassipes (Mart.) Solms, Ichnanthus calvescens Döll e Cyperus ligularis L. Essas plantas hospedeiras comuns nas águas do rio Negro foram coletadas em ambientes contaminados por petróleo e derivados na Estação Hidroviária de Manaus. Das espécies vegetais selecionadas foram isoladas 155 linhagens de bactérias, sendo 97 epifíticas e 58 endofíticas e 54 cepas de fungos, sendo 30 epifíticos e 24 endofíticos. Foram empregados meio seletivo para isolamento dos microrganismos tal como meio liquido BH (Bushhnell Haas) acrescido de petróleo. O petróleo e o diesel utilizados foram provenientes da Base Petrolífera de Urucu, Amazonas. Os ensaios de biodegradabilidade foram realizados em meio seletivo (BH), com a adição de petróleo como fonte de carbono denominado Meio I. Este ensaio foi repetido com a adição ao meio I do indicador redox 2,6-diclorofenol indofenol (DCPIP), denominado meio II. Após a avaliação dos isolados microbianos foram selecionados 6 bactérias e 7 fungos. A identificação molecular das bactérias foi realizada por meio da região do DNA ribossomal 16S e revelou a presença de Bacillus pumilus (Endofítica/epifítica), Lysinibacillus fusiformes (Epifítica), Pseudomonas aeruginosa (Epifítica) e Acinetobacter junii (Epifítica/epifítica). A identificação molecular dos fungos foi realizada por meio da região TS1 e ITS2 e revelou a presença das seguintes espécies: Curvularia trifolii (epifítica), Curvularia clavata (endofítica/epifítica), Gibberella intermedia (epifítica/endofitica), Phoma herbarum (epifítica) e Dothideomycetes sp (epifítica). Estes microrganismos foram selecionados para composição do consórcio microbianos que foram utilizados em ensaios de biodegradação de hidrocarbonetos. A mensuração das atividades de biodegradação de petróleo e diesel foi estimada por cromatografia e espectrometria de massa. Nos ensaios utilizou-se água do rio Negro com o objetivo de aproximar a pesquisa ao ambiente de estudo. A degradação dos hidrocarbonetos pelos consócios de fungos e bactérias apresentaram médias significativas (98,7-100%), mas não apresentaram diferenças estatísticas entre a degradação do controle contendo água do rio Negro (97,3%). No experimento com o consórcio misto (F/B), houve diferenças significativas, pois embora o controle contendo água do rio Negro tenha promovido degradação do diesel pela microbiota selvagem (81,7%), esta degradação foi inferior e diferente estatisticamente do consórcio misto (97,5%). Foram realizadas análises de degradação dos compostos naftaleno e fenantreno do óleo diesel pelos consórcios Observou-se que o composto fenantreno foi o que melhor foi degradado pelo consórcio misto (F/B). Entretanto, o naftaleno foi melhor degradado pelo controle contendo somente água do rio Negro, destacando o potencial dos microrganismos selvagens que merecem atenção nas futuras pesquisas, no isolamento destes em águas do rio Negro. O índice de toxicidade dos extratos microbianos foram avaliados como toxicidade moderada para o consórcio misto (F/B), já para o consórcio de fungos e consórcios de bactérias não apresentou toxicidade. No planejamento experimental com os consórcios, os resultados obtidos demonstraram que consórcios mistos (F/B) apresentaramm potencial para uso em futuros processos de biorremediação.

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Schoeman, Tersia. "Characterisation and identification of the active microbial consortium present in Kepi grains." Thesis, Stellenbosch : Stellenbosch University, 2001. http://hdl.handle.net/10019.1/52158.

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Thesis (MSc)--University of Stellenbosch, 2001.
ENGLISH ABSTRACT: Kepi is an acidic, self-carbonated milk beverage that is produced by fermenting milk with grain-like structures that contain naturally occurring microbes, including lactic acid bacteria (LAB) and yeasts. The specific microbes present in the Kepi grains are responsible for an acidic-alcoholic fermentation of the milk and also contributes to the various health properties exhibited by Kepi. The combination of microbes in the Kepi grains can vary considerably depending on which type of milk is fermented, the method by which Kepi is produced, the origin of the grains and how the grains are stored. In this study, the impact of various environmental conditions including the different stages during Kepi production, grain origin, Iyophilisation and packaging in three different packaging materials, on the microbial community of Kepi grains were studied using selective growth media, morphology and biochemical characteristics. It was found that there was a general decrease in the microbial counts from laboratory produced Kepi grains, the longer Kepi was produced on a continuous basis. This decrease in microbial counts was also observed during the different stages of Kepi production. The average LAB counts obtained from laboratory produced grains decreased from 1.1 x 108 cfu.q" after 3 d of activation to 6.3 x 107 cfu.q' after 10 d of mass production to 9.7 x 106 cfu.q' after a further 30 d of normal Kepi production. The average yeast counts increased from no detectable yeasts after 3 d of activation to 5.7 x 107 cfu.q' after 10 d of mass production and then decreased again to 7.2 x 106 cfu.q' after 30 d of normal Kepi production. The combination of the isolates varied according to the method by which the Kepi grains were produced and the stress conditions that were applied. Laboratory produced Kepi grains contained the following LAB: Lactobacillus fermentum, Lb. brevis 3, Lb. p/antarum, Lb. de/brueckii subsp. de/brueckii, Lactococcus /actis subsp. /actis and Leuconostoc mesenteroides subsp. cremoris. The identified yeasts and mycelial fungi were a Zygosaccharomyces strain, Cryptococcus humico/us, Candida /ambica, C. krusei, C. kefyr and Geotrichum candidum. The influence of grain origin on the microbial content of Kepi grains was also investigated using samples of Kepi grains from eight different Southern African sources. The microbial counts of the various Kepi grain samples were found to vary from 6.0 x 105 cfu.q" to 1.7 x 108 cfu.q". Five Lactobacillus, two Leuconostoc, four Candida, one Saccharomyces and a Zygosaccharomyces strain were isolated from these grains, with each grain type having its own unique microbial combination. The microbial content of the Kepi grains that were Iyophilised, packaged in three different packaging materials and stored at room temperature for two months, was very similar. Lactobacillus delbrueckii subsp. delbrueckii was isolated from the Kepi grains packaged in "low density polyethylene film" (LOPE). The grains packaged in "oriented polyester film" (OPET) contained Lb. delbrueckii subsp. delbrueckii and Lb. brevis, while Lb. delbrueckii subsp. delbrueckii and Lb. curvatus was present in the grains packaged in "methallised oriented polyester film" (MOPET). The average microbial counts obtained from the Kepi grains packaged in OPET (2.7 x 106 cfu.q') were only slightly higher than that of the grains packaged in LOPE (1.2 x 106 cfu.q') and OPET (1.4 x 106 cfu.q'). It was concluded that packaging materials for Kepi grains should rather be evaluated on the quality of Kepi produced with the packaged grains than by the specific characteristics of the packaging materials. The enrichment of Kepi grains with propionibacteria was also evaluated. A polymerase chain reaction (PCR) based method, specifically designed for the rapid identification of propionibacteria, was developed and tested successfully. Using this technique it was concluded that propionibacteria were not a natural part of the Kepi beverage and grains as used in this study. However, during the enrichment of the grains with propionibacteria it was determined that a propionibacteria concentration of 1 x 108 cfu.rnt' was needed for successful PCR amplification results. The data obtained in this study clearly showed that the method by which Kepi is produced, the origin of Kepi grains and the method of Kepi grain preservation changes the relationship between the microbes constituting the grains to such an extent that a different microbial community is assembled. It was also concluded that traditional methods should be used together with newer methods in determining this microbial community.
AFRIKAANSE OPSOMMING: Kepi is 'n self-gekarboneerde, effens suur melkdrankie wat geproduseer word deur melk te fermenteer met korrels waarin mikrobes (melksuurbakterieë en giste) natuurlik voorkom. Die mikrobes in die Kepi korrels is verantwoordelik vir 'n suuralkoholiese fermentasie en dra verder by tot die verskeie gesondheidseienskappe wat Kepi besit. Die kombinasie van mikrobes in die Kepi korrels wissel afhangende van die tipe melk wat gebruik word, die metode waarvolgens Kepi gemaak word, die oorsprong van die korrels en hoe die korrels geberg word. In hierdie studie is die impak van verskeie omgewingskondisies insluitende die verskillende stadiums tydens Kepi produksie, korreloorsprong, vriesdroging en verpakking in drie verskillende verpakkingsmateriale, op die mikrobiese samestelling van Kepi korrels bepaal m.b.v. selektiewe groei media en morfologiese en biochemiese eienskappe. Dit is gevind dat daar 'n afname was in die mikrobiese tellings van laboratorium geproduseerde Kepi korrels hoe langer Kepi op 'n aaneenlopende basis geproduseer is. Die afname in mikrobiese tellings is ook waargeneem tydens die verskillende stadiums van Kepi produksie. Die gemiddelde melksuurbakterieë tellings van laboratorium geproduseerde korrels het afgeneem vanaf 1.1 x 108 kve.q' na 3 d van aktivering tot 6.3 x 107 kve.q" na 10 d van massakweking tot 9.7 x 106 kve.q" na 'n verdere 30 d van normale Kepi produksie. Die gemiddelde gis tellings het gestyg vanaf geen giste na 3 d van aktivering tot 5.7 x 107 kve.q" na 10 d van massakweking en het toe weer gedaal tot 7.2 x 106 kve.q' na 30 d van normale Kepi produksie. Die kombinasie van die isolate het gewissel na gelang van die metode waarop die Kepi korrels geproduseer is en die stres kondisies wat toegepas is. Laboratorium geproduseerde Kepi korrels het bestaan uit Lactobacillus fermentum, Lb. brevis 3, Lb. p/antarum, Lb. de/brueckii subsp. de/brueckii, Lactococcus /actis subsp. /actis 1en Leuconostoc mesenteroides subsp. cremoris. Die giste en misiliëre fungi wat geïs~leer is was 'n Zygosaccharomyces stam, Cryptococcus humico/us, Candida lambica, C. krusei, C. kefyr en Geotrichum candidum. Die invloed wat die oorsprong van Kepi korrels op die mikrobiese samestelling daarvan het, is bepaal m.b.v. Kepi korrels afkomstig van agt verskillende dele in Suidelike Afrika. Die mikrobiese tellings van die verskeie tipes Kepi korrels het gewissel vanaf 6.0 x 105 kve.q' tot 1.7 x 108 kve.q", Vyf Lactobacillus, twee Leuconostoc, vier Candida, een Saccharomyces en 'n Zygosaccharomyces is geïsoleer vanuit die korrels, waarvan elke tipe korrel sy eie unieke mikrobiese samestelling gehad het. Die mikrobiese samestelling van korrels wat gevriesdroog, verpak is in drie verskillende verpakkingsmateriale en by kamertemperatuur gestoor is vir twee maande, was baie eenders. Vanuit die Kepi korrels wat verpak is in "lae digtheid polietileen film" (LOPE) is Lb. delbrueckii subsp. teetis geïsoleer. Die korrels wat verpak is in "georienteerde poltester film" (OPET) het Lb. delbrueckii subsp. leetis en Lb. brevis besit, terwyl Lb. delbrueckii subsp. leetis en Lb. curvatus teenwoordig was in die korrels wat in "gemetileerde georienteerde poltester film" (MOPET) verpak is. Die gemiddelde mikrobiese tellings van die korrels wat verpak is in OPET (2.6 x 106 kve.q') was effens hoër as dié van die korrels wat verpak is in LOPE (1.2 x 106 kve.q") en MOPET (1.3 x 106 kve.q"). Dit is bepaal dat verpakkingsmateriale vir Kepi korrels eerder geevalueer moet word op die kwaliteit van die Kepi wat met die verpakte korrels geproduseer word, as op die spesifieke eienskappe van die verpakkingsmateriale. Die mikrobiese verryking van Kepi korrels met propionibakterieë is ook ondersoek. 'n Polimerase ketting reaksie (PKR) gebaseerde metode, spesifiek ontwerp vir die vinnige identifikasie van propionibakterieë, is ontwikkel en suksesvol getoets. Met hierdie tegniek is bepaal dat propionibakterieë nie 'n natuurlike deel is van die Kepi drankie en korrels soos gebruik in hierdie studie. Gedurende die verryking van Kepi korrels met propionibakterieë is dit egter ook bepaal dat 'n propionibakterieë konsentrasie van 1 x 108 kve.rnl' nodig is vir suksesvolle PKR amplifikasie resultate. Die data verkry in hierdie studie het duidelik gewys dat die metode van Kepi produksie, die oorsprong van Kepi korrels en die metode waarop Kepi korrels gepreserveer word, verander die verhouding tussen die mikrobes in die korrels tot so 'n mate dat 'n nuwe mikrobiese gemeenskap saamgestel word. Die gevolgtrekking is ook gemaak dat tradisionele metodes saam met nuwer metodes gebruik moet word in die bepaling van hierdie mikrobiese gemeenskap.

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Camilo, Sofia Fernandes. "Origem e disseminação dos microrganismos do vinho." Master's thesis, ISA/UL, 2014. http://hdl.handle.net/10400.5/8298.

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Mestrado em Engenharia Alimentar - Qualidade e Segurança Alimentar - Instituto Superior de Agronomia
During the production of wine, various microorganisms may be involved such as yeasts, lactic acid bacteria and acetic acid bacteria. However, although there is a vast amount of information on the microorganisms that belong to the wine microbial consortium, its origin and persistence in environment close to the vineyard, through the year, has not be unraveled, yet. The aim of this study was to evaluate the microbial diversity associated with vineyard’s environments, through the year, to understand consortium microorganisms’ spread and prevalence. Soils, bark trees, insects, grapevine leaves, grapes, must and cellar equipment were analyzed. The isolated microorganisms were submitted to phenotypic tests and according to the results were selected to molecular identification. Therefore, it was noted that, in these environments, the consortium microorganisms’ prevalence was very low. Consequently, these microorganisms were only found on trees, insects, soils and damaged grapes. Nonetheless, in must and cellar equipment most of the isolated microorganisms belonged to wine microbial consortium. Thus, it remains to find which are the reservoirs preferred by wine consortium microorganisms

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Golela, Mhlangabezi Tolbert. "Effect of microbial consortium on the biokinetic test for assessing acid rock drainage potential." Thesis, Cape Peninsula University of Technology, 2018. http://hdl.handle.net/20.500.11838/2754.

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Thesis (Master of Engineering in Chemical Engineering)--Cape Peninsula University of Technology, 2018.
Acid rock drainage (ARD) is one of the most severe environmental challenges currently faced by the mining industry worldwide. ARD is formed from the oxidation of sulphide-bearing minerals, particularly pyrite, in the presence of water and oxygen. ARD generation is accelerated by the presence of naturally occurring iron and sulphur-oxidizing micro-organisms, which regenerate leaching agents that facilitate sulphide mineral oxidation. ARD pollution is characterized by a high concentration of metals and sulphates in solution, low pH and a high salt content (salinity) in the environment, contaminating soil and groundwater. In South Africa, ARD is a major challenge in the gold and coal mining industries, where millions of tons of sulphide waste rock and overburden are generated and discarded. Characterization of these waste materials is required to develop an appropriate disposal strategy to minimise the risk of pollution and the generation of ARD. Potential ARD generation prediction from waste rock depends on the precise characterization of ARD potential using Biokinetic tests. Commonly used ARD prediction methods are static and long-term kinetic tests. Static tests provide data for a worst-case scenario focussing on strong acid chemical leaching potential to give an overall acid forming potential of a sample. Such kinetic tests provide data illustrating the rate of the net acid generation capacity of mine waste. However, these tests are capital intensive and time-consuming and fail to provide adequate information on the effect of micro-organisms on the overall net acid generation capacity of mine waste. The Biokinetic test reported herein and developed at the University of Cape Town, focusses on addressing a worst case scenario provided by static tests in a cost-effective manner and reduced time frames provided for by conventional kinetic tests. This test primarily provides relative rates of ARD generation in the presence of micro-organisms within 90 days. However, the Biokinetic test is at the developmental stage and thus far, has not been consistently used for different waste ores to determine a standardised approach. Therefore, the aim of this study was to investigate the effects of microbial consortia and to develop a standardisation approach for the test for ARD formation potential using gold-bearing and copper-bearing waste rock. Additionally, to refine the Semi-continuous Biokinetic test simulation, a flow-through system where there is minimal seepage in the waste deposit, was also developed. The sulphur content of the gold and copper-bearing samples used in this study was between 2.3 and 3.15%, respectively. These waste rock samples were found to be potentially acid- forming. In the Biokinetic test, finely milled waste rock samples were slurrified, inoculated with consortia and cultured under standard bioleaching conditions. Leaching and acidification rates were monitored.

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Rehfuss, Marc Y. "Characterization and phylogenetic analysis of a phenol and halogenated aromatic compound degrading microbial consortium /." Search for this dissertation online, 2004. http://wwwlib.umi.com/cr/ksu/main.

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Schutte, Lionie Marie. "Isolation and identification of the microbial consortium present in fermented milks from Sub-Saharan Africa." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/80020.

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Thesis (MSc Food Sc)--Stellenbosch University, 2013.
ENGLISH ABSTRACT: A wide variety of traditionally and commercially fermented milks are commonly consumed in various countries of Sub-Saharan Africa. Commercially fermented milk is produced on an industrial scale according to well-managed, standardised production processes and starters are used to initiate fermentation. Traditionally fermented milk is prepared domestically and fermentation occurs spontaneously at ambient temperatures. Lactic acid bacteria (LAB) are responsible for milk fermentation during which they convert the milk carbohydrates to lactic acid, carbon dioxide, alcohol and other organic metabolites. Acetic acid bacteria (AAB), yeasts and mycelial fungi have also been isolated from fermented milks. In this study the microbial consortium present in three traditionally fermented milks, namely omashikwa from Namibia, masse from Mozambique and chekapmkaika from Uganda and two commercially fermented milks, namely chambiko from Malawi and omaere from Namibia, were isolated and enumerated on six different selective media that included MSR + C (specific for lactobacilli), KCA + TTC (specific for lactococci), KCA + V (specific for leuconostocs), MRS + E (specific for AAB), MEA (specific for mycelial fungi) and YPD (specific for yeasts). No significant differences were found between the enumeration values obtained for the three chambiko samples, as well as for enumeration values obtained for the two omaere samples on each of the selective media, indicating low sample variance. Significant differences between enumeration values obtained for the three omashikwa samples were found on all six selective media. Significant differences between enumeration values of the three masse samples and both the chekapmkaika samples were also observed on the selective media. In addition to this, significant differences were observed between average enumeration values obtained for each media between the masse and chekapmkaika, the chambiko and omaere, as well as when the traditional and commercial milks were compared. According to the average enumeration values obtained on each media selective for LAB, the highest bacterial counts were detected on KCA + TTC medium for omaere (2.3 x 106 cfu.ml-1), KCA + V for chambiko (1.8 x 105 cfu.ml-1), KCA + TTC for omashikwa and MRS + C for masse and chekapmkaika (6.2 x 106 and 2.0 x 103 cfu.ml-1, respectively). After isolation and enumeration of the microbes present in each milk, bacterial isolates on the media selective for LAB and AAB were obtained according to the Harrison Disk method. These isolates were identified by amplifying a 1.5 kilobase (kb) part of the 16S ribosomal RNA (rRNA) gene using the polymerase chain reaction (PCR), followed by DNA sequencing. The isolates were identified by comparing the sequences obtained to sequences listed in the NCBI database using the BLAST algorithm and searching for the closest relative. The main LAB group present in the omaere was lactococci (94%), in chambiko and chekapmkaika it was lactobacilli (30% and 45%, respectively), in omashikwa it was enterococci (43%) and in masse it was leuconostocs (68%). The same microbial species were present on a number of the selective media used in this study. Lactococcus spp., Enterococcus spp. and Lactobacillus spp. were isolated from MRS + C, KCA + TTC, KCA + V and MRS + E and Leuconostoc spp. were isolated from MRS + C, MRS + E and KCA + V. Hygienic standards during traditional milk fermentation is often poor and, therefore, microbial contaminants were isolated from the traditional milk and these included Acinetobacter johnsonii and Klebsiella pneumoniae from KCA + V, Mesorhizobium loti, Acinetobacter radioresistens, Escherichia coli, Staphylococcus spp., Kluyvera georgiana, Enterobacter spp. and Klebsiella oxytoca from KCA + TTC, Staphylococcus spp. from MRS + C and Bacillus spp. from MRS + E. Since the media used for the isolation of the LAB and AAB in this study were not selective further identification of the enumerated microbes is of importance for the identification of the microbial groups present in each fermented milk. The data obtained in this study clearly shows that fermented milks from Sub-Saharan Africa vary significantly from each other in terms of microbial numbers, microbial diversity and the dominant microbial groups present. The microbial diversity of the traditionally fermented milks was more diverse than the microbial diversity of the commercially fermented milks. LAB strains isolated from these traditionally fermented milks can be used to develop novel starters and as a result new commercially fermented dairy products with unique aromas, tastes and characteristics can be produced.
AFRIKAANSE OPSOMMING: 'n Wye verskeidenheid tradisioneel en kommersieel gefermenteerde melk produkte word algeneem verbruik in verskeie lande van Sub-Sahara Afrika. Kommersieel gefermenteerde melk word geproduseer op groot skaal, deur deeglik bestuurde gestandardiseerde produksieprosesse en 'n beginkultuur word gebruik om fermentasie te inisieer. Tradisioneel gefermenteerde melk word tuis gemaak en fermentasie gebeur spontaan by kamertemperatuur. Melksuurbakterieë (MSB) is verantwoordelik vir melkfermentasie waartydens die bakterieë koolhidrate omskakel na melksuur, koolstofdioksied, alkohol en ander organiese sure. Asetaatsuurbakterieë (ASB), giste en miseliale fungi is ook al van gefermenteerde melk geïsoleer. In hierdie studie is die mikrobiese konsortium teenwoordig in drie soorte tradisioneel gefermenteerde melk, naamlik omashikwa van Namibië, masse van Mosambiek en chekapmkaika van Uganda en twee soorte kommersieel gefermenteerde melk, naamlik chambiko van Malawi en omaere van Namibië, geïsoleer en getel op ses verskillende selektiewe groeimedia insluitend MRS + C (spesifiek vir lactobacilli), KCA + TTC (spesifiek vir lactococci), KCA + V (spesifiek vir leuconostocs), MRS + E (spesifiek vir ASB), MEA (spesifiek vir miseliale fungi) en YPD (spesifiek vir giste). Geen betekenisvolle verskille is gevind tussen die mikrobiese tellings verkry vir die drie chambiko monsters nie, sowel as tussen die mikrobiese tellings verkry vir die twee omaere monsters, op elk van die selektiewe groeimedia, wat dui op lae monster variansie. Betekenisvolle verskille is gevind tussen die mikrobiese tellings verkry vir die drie omashikwa monsters op al ses selektiewe groeimedia. Betekenisvolle verskille is ook waargeneem tussen die mikrobiese tellings van die drie masse monsters en beide die chekapmkaika monsters op die selektiewe groeimedia. Daarbenewens is betekenisvolle verskille waargeneem tussen gemiddelde mikrobiese tellings verkry vir elke groeimedium tussen die masse en chekapmkaika, die chambiko en omaere asook toe die tradisionele en kommersiële melk produkte met mekaar vergelyk is. Volgens die gemiddelde mikrobiese tellings verkry op elk van die groeimedia selektief vir MSB, is die hoogste mikrobiese telling waargeneem op KCA + TTC medium vir omaere (2.3 x 106 kve.ml-1), KCA + V vir chambiko (1.8 x 105 kve.ml-1), KCA + TTC vir omashikwa en MRS + C vir masse en chekapmkaika (6.2 x 106 en 2.0 x 103 kve.ml-1, respektiewelik). Na die isolasie en tel van die mikrobes teenwoordig in elke melk is bakteriese isolate op die media selektief vir MSB en ASB verkry volgends die Harrison Disk metode. Hierdie isolate is geïdentifiseer deur amplifikasie van „n 1.5 kilobasis (kb) gedeelte van die 16S ribosomale RNS (rRNS) geen deur gebruik te maak van die polimerase kettingreaksie gevolg deur DNS klonering. Die isolate is geïdentifiseer deur die gekloneerde insetsels se volgordes te vergelyk met volgordes beskikbaar op die NCBI webwerf deur van die BLAST algoritme gebruik te maak en die naas verwante insetsel op te spoor. Die hoof MSB groep teenwoordig in die omaere was lactococci (94%), in chambiko en chekapmkaika was dit lactobacilli (30% en 45%, respektiewelik), in die omashikwa was dit enterococci (43%) en in die masse was dit leuconostocs (68%). Dieselfde mikrobiese spesies was teenwoordig op verskeie van die selektiewe groeimedia gebruik in hierdie studie. Lactococcus spp., Enterococcus spp. en Lactobacillus spp. is geïsoleer van MRS + C, KCA + TTC, KCA + V en MRS + E en Leuconostoc spp. is geïsoleer van MRS + C, MRS + E en KCA + V. Higiëniese standaarde tydens tradisionele melkfermentasie is dikwels swak en dus is mikrobiese kontaminante geïsoleer van die tradisionele melk produkte insluitend Acinetobacter johnsonii en Klebsiella pneumoniae van KCA + V, Mesorhizobium loti, Acinetobacter radioresistens, Escherichia coli, Staphylococcus spp., Kluyvera georgiana, Enterobacter spp. en Klebsiella oxytoca van KCA + TTC, Staphylococcus spp. van MRS + C en Bacillus spp. van MRS + E. Aangesien die media wat gebruik is vir die isolasie van die MSB en ASB in hierdie studie nie selektief was nie, is verdere identifikasie van die getelde mikrobes belangrik vir die identifikasie van die mikrobiese groepe teenwoordig in elke melk. Die data verkry in hierdie studie dui aan dat gefermenteerde melk produkte van Sub-Sahara Afrika betekenisvol van mekaar verskil in terme van mikrobiese getalle, mikrobiese diversiteit en die dominante mikrobiese groepe teenwoordig. Die mikrobiese diversiteit van die tradisioneel gefermenteerde melk produkte was meer divers as die mikrobiese diversiteit van die kommersieel gefermenteerde melk produkte. MSB spesies geïsoleer van hierdie tradisioneel gefermenteerde melk produkte kan gebruik word om nuwe beginkulture te ontwikkel en gevolglik kan nuwe kommersieel gefermenteerde suiwelprodukte met unieke aromas, smake en eienskappe geproduseer word.

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Pereira, Arthur Prudêncio de Araujo. "Influência da profundidade do solo e do manejo de Eucalyptus grandis e Acacia mangium na estrutura das comunidades microbianas do solo." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-09042015-112037/.

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Pesquisas atuais demonstram respostas positivas em plantios de Eucalipto consorciados com Acacia mangium. O objetivo principal desse trabalho foi avaliar a influência dos sistemas puros e mistos de Eucalyptus grandis e A. mangium na estrutura das comunidades de bactérias e fungos do solo. Avaliou-se a estrutura dessas comunidades num gradiente de profundidade do solo. Foram abertas trincheiras profundas em plantios puros de Acácia (100A), Eucalipto (100E) e em sistemas mistos entre as duas espécies (A+E). No plantio misto fizeram-se coletas de solo e raízes na base da Acácia A(A+E) e na base do Eucalipto E(E+A). Cerca de 10 camadas do solo foram avaliadas ao longo do perfil das trincheiras, sendo coletados pontos de 0 a 800 cm, com 4 repetições cada. As comunidades microbianas foram monitoradas por PCR-DGGE, onde foi observado um forte efeito da profundidade do solo nas comunidades microbianas. Agrupamentos específicos foram formados em cada profundidade amostrada. Plantios puros de Eucalipto selecionaram grupos de bactérias diferentes dos que foram encontrados em 100A, A(A+E) e E(E+A). A comunidade de fungos totais não sofreu diferenciação de grupos nos plantios estudados, ao passo que os perfis de fungos micorrízicos arbusculares (FMA) do solo no tratamento A(A+E), foram significativamente diferentes dos grupos encontrados nos demais tratamentos. Numa análise de correlação, realizada por RDA, ficou indicado que a comunidade de FMA do tratamento A(A+E) correlacionou-se positivamente com os valores de P no solo. Outra variável quantificada foi a abundância de bactérias e fungos, indicadas pelo número de cópias do gene ribossomal 16S DNAr e ITS, respectivamente. Quando comparadas as camadas superficiais do solo (0-20 cm), não foi possível encontrar diferenças na abundância de cópias dos genes 16S e ITS em todos os tratamentos. Ocorreu uma queda exponencial no número de cópias desses genes com o aumento da profundidade do solo. Porém, o tratamento 100E apresentou maior número de cópias em profundidade (de 300-800 cm) dos genes 16S e ITS do que qualquer outro tratamento. Em relação a presença específica de FMA, houve baixa colonização e baixa abundância de esporos de FMA em todos os tratamentos, sendo o tratamento 100E mais colonizado que os demais. Ao todo foram encontradas 16 espécies de FMA, sendo a maior parte pertencente ao gênero Acaulospora. Ao contrário dos FMA, os plantios apresentaram colonização radicular pronunciada por ECM. Conclui-se que nestes sistemas florestais uma espécie de planta parece ser mais importante que a outra na estruturação da comunidade microbiana e que alguns fatores do solo podem ser preponderantes nessa separação. O conhecimento dessas comunidades é de suma importância em plantios florestais, principalmente por estarem envolvidos diretamente nos ciclos biogeoquímicos e, sobretudo, por se tratar de uma forma de plantio florestal nova, promissora e que aborda parâmetros de sustentabilidade.
Recently discoveries have shown positive responses in Eucalyptus plantations intercropped with Acacia mangium. The aim of this study was to evaluate the influence of pure and mixed systems (Eucalyptus grandis and A. mangium) on the microbial communities\' structure in soil. We evaluated the structure of these communities in a gradient of soil depth. In this context, deep trenches were digged in pure stands of Acacia (100A), Eucalyptus (100E) and mixed systems (A+E). In mixed forest plantations, soil and roots were sampled at the base of Acacia (A+E) and the base of Eucalyptus (E+A). Soil over 10 layers along the profile from 0 to 800cm were sampled, with 4 replicates each. The microbial communities were monitored by PCRDGGE, where we observed a strong effect of soil depth on microbial communities. As a result, specific clusters were formed in each soil layer. The community composition of Eucalyptus grandis stands was different from the community structure found in the 100A, A (A+E) and E (E+A) systems. The total fungal community did not show any group differentiation due to the plantation system, while the profiles of mycorrhizal fungi (AMF) of these three groups were significantly different from that of the treatment A (A+E). A correlation analysis performed by RDA indicated that the FMA community of the treatment (A+E) was correlated positively with P values in the soil. Another variable quantified was the community of bacteria and fungi, indicated by the number of copies of ribosomal 16S rDNA and ITS, respectively. Comparing the upper soil layers (0-20 cm), we couldn\'t find differences in the abundance of copies of 16S rRNA and ITS region genes in all treatments, but we observed an exponential decrease in 16S rRNA copy numbers with increasing soil depth. Regarding the presence of AMF, we found low root colonization and low abundance of AMF spores in all treatments, although 100E presented higher colonization rates than the others. Altogether, 16 AMF species were found, most of them belonging to the genus Acaulospora. We conclude that these forest systems a plant species seems to be more important than the other in the structuring of the microbial community and that some soil factors may be preponderant in this separation. The processes involving the dynamics of the microbial community structure is a crucial point in understanding the development of forest plantations, mainly by involving the biogeochemical cycles, when seeking for new promising approaches and sustainability parameters.

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Paixão, Douglas Antonio Alvaredo. "Prospecção gênica e diversidade bacteriana de um consórcio degradador de óleo diesel /." Jaboticabal : [s.n.], 2009. http://hdl.handle.net/11449/94906.

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Orientador: Eliana Gertrudes Macedo Lemos
Banca: Alessandro Minillo
Banca: Janete Apparecida Desidério Sena
Resumo: A estratégia de clonagem e sequenciamento do gene 16S rRNA é uma das técnicas moleculares que permite estimar e comparar a diversidade microbiana de diferentes amostras ambientais. O objetivo deste trabalho foi estimar a diversidade de microrganismos pertencentes ao Domínio Bactéria em um consórcio degradador de óleo diesel, por meio do sequenciamento parcial do gene 16S rRNA, assim como desenvolver uma nova metodologia de rastreamento em bibliotecas metagenômicas. O consórcio bacteriano foi obtido através de solo enriquecido com óleo diesel. O DNA metagenômico foi extraído com o auxílio do kit Fast DNA spin Kit for soil (Bio101- Quantum Biotechnologies) e amplificado por uma reação de PCR (Reação em Cadeia da Polimerase) com os oligonucleotídeos iniciadores FD1 e RD1 específicos para a o gene 16S rRNA. Os produtos de PCR foram clonados em vetor pGEM T Easy (Promega) e transformados em células competentes de Escherichia Coli DH5 . O sequenciamento parcial dos clones foi feito com oligonucleotideos universais do vetor. Para a prospecção gênica foi utilizado membranas de nylon com "pools" de DNA de todas as placas. A biblioteca obtida gerou 431 clones. Os clones obtidos apresentaram similaridade com o filo Proteobacteria, com representantes das classes Gammaproteobacteria, Alphaproteobacteira e Betaproteobacteria. O gênero Pseudomonas apresentou-se com maior frequência de clones na biblioteca. O "software" DOTUR foi usado para determinar o número de unidades taxonômicas operacionais (OTUs). A curva de extinção indicou que os 431 clones sequenciado foram suficientes para estimar a diversidade bacteriana do consórcio. A metodologia testada baseado em "pools" de DNA foi eficiente na detecção e isolamento do gene Alkb na bilbioteca metagenomica.
Abstract: Cloning and sequencing of 16S rRNA gene it is one of the molecular techniques that permits estimate and compare the microbial diversity of different environmental samples. The aim of this work was estimate the diversity of microorganisms that belong to Bacteria domain in a consortium specialized in diesel oil degradation, through partial sequencing of 16S rRNA gene, as well as develop a new methodology for screening libraries in metagenomics. This consortium was obtained through enrichments achieved using diesel oil in soil samples. The metagenomic DNA was obtained using Fast DNA spin Kit for soil (Bio 101-Quantum Biotechnologies) and amplified by PCR (Polymerase chain reaction) with FD1 and RD1 oligonucleotides, which are specific for 16S rRNA gene. The PCR products were cloned into pGEM-TEasy vector (Promega) and Escherichia coli DH5 was used as the host cell for recombinant DNAs. The partial clones sequencing was obtained using universal primers of the vector. For the exploration of gene were used nylon membranes with Pools of DNA from all plates. The library generated from 431 clones. All clones sequenced showed similarity with the phylum Proteobacteria, distributed in Gammaproteobacteria, Alphaproteobacteira and Betaproteobacteria classes. The Pseudomonas genus was the most abundant genus found in the metagenomic library. The DOTUR software was used to assigns sequences to operational taxonomic units (OTUs). Using the OTUs composition data, rarefaction curves were made to show that 431 sequences were enough to obtain a satisfactory coverage of diversity of the microbial consortium. The test methodology based on Pools of DNA isolation was effective in detecting the gene Alkb Library metagenomics.
Mestre

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DACCÒ, CHIARA. "Selection of new fungal strains and development of a microbial consortium for the bioremediation of complex hydrocarbon mixtures." Doctoral thesis, Università degli studi di Pavia, 2021. http://hdl.handle.net/11571/1431714.

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The release of hydrocarbons and their derivatives into the environment can have harmful effects on ecosystems and the organisms that populate them. Recently a further problem has arisen concerning the treatment of hydrocarbons in the oil industry, where large tanks are used to store raw materials and intermediate or finished products. Sludge and heavy oil deposits accumulated in tanks have to be cleaned periodically, usually by manual means. The procedure is dangerous, time-consuming, labour-intensive and expensive. Also, substances resulting from cleaning must be disposed of specifically as they are rich in hazardous substances. An alternative method to these methods is bioremediation, which involves using microorganisms to degrade toxic components in a substrate. This technique exploits algae, fungi, and bacteria's normal metabolic activities to modify harmful organic compounds into less complex metabolites, inorganic minerals, H2O and CO2. The biodegradation of hydrocarbons is a complex process that depends on the nature and quantity of the hydrocarbons present; moreover, one of the critical factors limiting the biodegradation of oil pollutants in the environment is their limited bioavailability to microorganisms, in particular, the compounds of oil hydrocarbons that bind to soil components. Many studies have reported how bacteria, yeasts and fungi can degrade hydrocarbons in different environments. In particular, fungi are excellent hydrocarbon degradation agents because they produce extracellular enzymes with low substrate specificity and are active even under micro-aerobic or anaerobic conditions and with low water activity. Many papers have been published on fungal degradation of polycyclic aromatic hydrocarbons (PAHs), among the most toxic components of oil, but few regarding the degradation of hydrocarbon mixtures, mainly resulting from gas or oil production processes. This PhD project aimed to assemble a fungi-bacteria consortium, selecting microorganisms directly from contaminated substrates to be treated to achieve the highest possible degradation rate, reducing the use of chemicals, costs and time required for remediation. From the contaminated substrates from a gas plant (Eni S.p.A.) in Pakistan, 29 fungal strains and 50 bacterial strains have been isolated and identified. The fungal strains were then selected based on their ability to grow using hydrocarbons as the only source of carbon, and from these first tests, 8 strains potentially useful for the project were selected. These fungi were tested in their degradative capacity, by analysing the composition of hydrocarbon substrates before and after treatment with the fungal strains. Qualitative enzymatic tests were also carried out to estimate the enzymatic production of the selected strains and tests to verify the ability to produce biosurfactants, substances useful in increasing the bioavailability of pollutants. Once the results of the various tests had been analysed, the fungi-bacteria consortium was set up, but the fungal strains were first subjected to antibiosis tests to select further only those capable of establishing positive relationships with the others. Therefore, 6 fungal strains contributed to the consortium formation, while the bacterial strains were 28. The consortium was also subjected to tests to verify its degradative capacity, demonstrating an excellent potential, degrading, within a week under laboratory conditions, all the hydrocarbon fractions that could be analysed. The project's last step was to set up an ecotoxicological test to demonstrate the consortium's bioremediation capacity. The results obtained in this work are encouraging and open the door to many applications. Consortia composed of different microorganisms, from the tests carried out, seems to be an effective bioremediation technique with high potential. Unquestionably further investigation is needed to understand how to optimise the consortium's performance.

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Barrett, E., and Phillip R. Scheuerman. "Effect of Inoculum level of a Freeze-Dried Consortium and Substrate Concentration on p-cresol Degradation." Digital Commons @ East Tennessee State University, 1998. https://dc.etsu.edu/etsu-works/2915.

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Silva, Wender Messiatto da. "Utilização de microrganismos na biorremediação de solo contaminado por derivados de petróleo." Ilha Solteira, 2018. http://hdl.handle.net/11449/154212.

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Orientador: William Deodato Isique
Resumo: Os impactos ambientais decorrentes de vazamentos em postos de combustíveis têm sido preocupantes para órgãos ambientais ao redor do mundo, sobretudo por deteriorarem a qualidade das águas subterrâneas utilizadas como fonte de abastecimento, sendo os compostos benzeno, tolueno e xilenos (BTX) os de maior preocupação à saúde pública. A biorremediação é uma técnica viável do ponto de vista econômico e ecológico quando se utiliza consórcio microbiano de bactérias e fungos aliado a solução de nutrientes. Este trabalho verificou os efeitos da biorremediação sobre microambientes formados em erlenmenyers contendo solo arenoso fino de textura arenosa fina, bastante comum no noroeste paulista, contaminado por soluções sintéticas de BTX por intermédio de consórcio de microrganismos (bactérias ácido láticas, leveduras, bactérias fototróficas e actinomicetes). O desempenho de um consórcio de microrganismos foi verificado por meio de alterações de pH, teor de umidade, teor de carbono e pela de remoção de BTX do microambiente constituído de solo arenoso fino contaminado por solução sintética de BTX mediante a bioestimulação comparando-se os efeitos do ácido esteárico como surfactante. O uso de ácido esteárico como surfactante prejudicou o processo de biorremediação nos microambientes, com isso a remoção de BTX foi menor do que nos microambientes que não possuíam ácido esteárico. De acordo com resultados deste trabalho, um valor adequado para a aplicação da solução de microrganismos em campo... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The environmental impacts resulting to leaks at fuel stations has been worrying for environmental agencies around the world mainly for deteriorating the quality of the groundwater used as a water supply whereby the BTX compounds (benzene, toluene and xylene) the most worrisome public health. Bioremediation is a viable technique because the use of bacterial, fungal and yeast microbial consortia is economic and ecological associated with nutrient solutions. The effects of bioremediation verified through a consortium of microrganisms (lactic acid bacteria, yeasts, phototrophic bacteria and actinomycetes) on microenvironment in enlermeyers containing fine sandy texture lateritic soil, very common in São Paulo northwest region, contaminated by synthetic solutions of BTX. The performance of a consortium of microorganisms verified by pH changes, moisture content and organic carbon content of the microenvironments and the rate of BTX removal in fine sandy soil contaminated with BTX synthetics solutions by bioestimulation, comparing the effects of stearic acid as surfactant. The use of stearic acid as a surfactant impaired the bioremediation process in the microenvironments, thus the removal of BTX was lower than in microenvironments that did not possess stearic acid. According to the results of this work, a value of microorganisms per cm³ of microorganisms solution to the soil is 0.02 mL of microorganisms solution 300 cm³ of fine sandy soil in the period of 7, 30 and 58 days of exper... (Complete abstract click electronic access below)
Mestre

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Silva, Antonio Marcos Miranda. "Aumento da produtividade e mudanças na microbiota do solo em cultivo de cana-de-açúcar com aplicação de composto e inoculação de bactérias solubilizadoras de fosfato." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-04102018-153553/.

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O fósforo (P) é limitante tanto na produtividade da cana-de-açúcar (Saccharum officinarum L.) quanto na atividade da microbiota do solo. Em solos de regiões tropicais, devido à elevada saturação por óxidos de ferro e alumínio, o P se encontra normalmente indisponível às plantas. Portanto, o manejo da adubação de P, baseado no uso de microrganismos capazes de promover uma melhor ciclagem do P, se faz necessário. Assim, o objetivo do estudo foi avaliar as mudanças na microbiota do solo e na produtividade da cana-de-açúcar, em condições de campo, em resposta ao manejo orgânico associado à inoculação de bactérias solubilizadoras de fosfato (BSF). Para tanto, foi utilizado um composto, obtido previamente por meio da compostagem de subprodutos da indústria sucroenergética (torta de filtro e cinzas), enriquecido com fosfatos de rocha (fosfato de Araxá-FA ou fosfato de Bayóvar-FB). No campo foram estabelecidos sete tratamentos, sendo um destes o tratamento controle, adubado com superfosfato triplo. Seis tratamentos compreendiam áreas adubadas com composto, sendo duas com composto que continha FA, duas com FB e duas somente com composto sem enriquecimento com P (C). A metade dessas áreas recebeu também inoculação com BSF, contendo os tratamentos FA+I, FB+I e C+I. A inoculação foi feita com Bacillus simplex BACBR04, Bacillus sp. BACBR06 e Rhizobium sp. RIZBR0. As avaliações foram realizadas durante o primeiro ano de cultivo (cana planta) em dois períodos (aos seis e 12 meses). As mudanças na microbiota foram acessadas por meio da atividade das enzimas fosfatases (ácida e alcalina), fitases e β-glucosidase. Mudanças na estrutura da comunidade bacteriana e fúngica foram acessadas por meio do T-RFLP. A abundância dos genes 16S RNAr, phoD (relacionado à solubilização de P) e ITS foram avaliadas por meio de PCR quantitativo. A atividade das fosfatases e β-glucosidase aumentaram com a inoculação na cana adubada com composto enriquecido com fosfato de Araxá (FA+I) e também no solo adubado com composto sem enriquecimento (C+I). Nos tratamentos FA+I e C+I houve incremento do fósforo disponível e aumento de 10% na produtividade, em relação ao tratamento controle (M). As comunidades bacteriana e fúngica do tratamento C+I se estruturaram de forma distinta em relação ao tratamento controle (M). Nos solos inoculados houve menor abundância do gene ITS aos seis meses, enquanto que, para o gene 16S RNAr, os solos inoculados apresentaram menor abundância no período de 12 meses. Verificou-se que o consórcio bacteriano inoculado, associado com a aplicação de composto, superou, no primeiro ano de cultivo, o manejo rotineiramente utilizado em cana-de-açúcar (adubação com superfosfato triplo). É possível que haja efeito residual no decorrer dos ciclos da cana-de-açúcar, o que ainda reforçaria a importância do manejo orgânico associado à inoculação com BSF.
Phosphorus (P) is limiting both the yield of sugarcane (Saccharum officinarum L.) and the activity of the soil microbiota. In tropical soils, due to the high saturation of iron and aluminum oxides, P is normally unavailable to plants. Therefore, the management of P fertilization, based on the use of microorganisms that promote better P cycling is necessary. Thus, the objective of this study was to evaluate changes in the soil microbiota and in sugarcane yield under field conditions, in response to the organic management associated with the inoculation of phosphate solubilizing bacteria (PSB). In our field experiment, our fertilizer was an organic compost, previously obtained by the composting process of by-products of the sugarcane industry (filter cake and ashes), enriched with rock phosphates (Araxá phosphate-AP or Bayóvar phosphate-BP). Seven treatments were established in the field, one of which was the control treatment, fertilized with triple superphosphate. Six treatments comprised compost fertilized areas, two with compost containing AP, two with BP, and two only with compost, and without any enrichment with P (C). Half of these areas were also inoculated with PSB, containing the treatments AP+I, BP+I and C+I. Field inoculation was done with Bacillus simplex BACBR04, Bacillus sp. BACBR06 and Rhizobium sp. RIZBR0. We performed evaluations during the first year of cultivation at two periods (at six and twelve months after planting). We accessed the changes in the microbiota through the activity of acid and alkaline phosphatases, phytases and β-glucosidase. Changes in bacterial and fungal community structure were accessed through T-RFLP. We evaluated the abundance of the 16S RNAr, phoD (related to P solubilization) and ITS genes by quantitative PCR. The phosphatases and β-glucosidase activity increased with the inoculation in sugarcane fertilized with compost and enriched with Araxá phosphate (AP+I) and in the soil fertilized with compost, but without any enrichment (C+I). In these treatments (AP+I and C+I), we found an increase in available phosphorus and a 10% increase in productivity, in relation to the control treatment (M). The bacterial and fungal communities of the treatments C+I presented a different structure in relation to the control treatment (M). In the soils that received bacterial inoculations, there was a lower abundance of the ITS gene at six months, whereas for the 16S RNAr gene the inoculated soils presented lower abundance at 12 months. We verified that the inoculated bacterial consortium, associated with the application of compost, overcame the conventional management in sugarcane (triple superphosphate fertilizer) in the first year of cultivation. In addition, it is possible residual effect during the sugarcane cycles, which would further reinforce the importance of organic management associated with BSF inoculation.

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Keyser, Maricel. "PCR detection, denaturing gradient gel electrophoresis (DGGE) fingerprinting and identification of the microbial consortium in different types of UASB granules." Thesis, Link to online version, 2006. http://hdl.handle.net/10019/558.

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Rafrafi, Yan. "Impact des facteurs biotiques sur le réseau métabolique des écosystèmes producteurs d’hydrogène par voie fermentaire en culture mixte." Thesis, Montpellier 2, 2012. http://www.theses.fr/2012MON20249/document.

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De nos jours, les cultures mixtes sont considérées comme une sérieuse alternative aux cultures pures pour les procédés de biotechnologie. En effet, les cultures mixtes peuvent fonctionner en réacteur continu, dans des conditions non-stériles et traiter une grande variété de substrats organiques. La principale restriction de l'utilisation de ces bioprocédés en cultures mixtes réside dans leur instabilité liée à la présence de voies métaboliques non désirées résultant d'interactions microbiennes complexes. Notamment, le rôle des bactéries de faible abondance reste à être élucidé. Ce travail a donc consisté, dans un premier temps à déterminer le rôle des bactéries minoritaires dans la production d'hydrogène par voie fermentaire en utilisant un chémostat alimenté en continu avec un milieu à base de glucose. Sept inocula ont été cultivés dans les mêmes conditions opératoires. De façon remarquable, Clostridium pasteurianum a été retrouvé comme espèce dominante de l'écosystème six fois sur sept. Seules la nature et la diversité des espèces minoritaires variaient d'un écosystème à l'autre. Ainsi, il a été montré que la structure des communautés microbiennes a une influence significative sur la production de bio-hydrogène. Au sein de ces communautés, les bactéries en proportion minoritaires jouent un rôle clé en orientant le métabolisme globale de l'écosystème. La deuxième étape de ce travail a consisté à utiliser certaines de ces espèces minoritaires comme Ingénieurs Ecologiques des Ecosystèmes microbiens (IEEM). Pour cela, la structure d'une communauté microbienne productrice d'hydrogène a été modifiée artificiellement en introduisant des souches bactériennes exogènes aux fonctions redondantes et/ou complémentaires des souches indigènes. Les résultats en réacteur batch ont montré que les performances de production d'hydrogène pouvaient être améliorées jusqu'à un facteur 3,5 par l'ajout de certaines souches. Dans l'ensemble, les résultats obtenus ne peuvent être expliqués par de simples interactions trophiques et suggèrent la présence de mécanismes d'interactions de coopération entre microorganismes. De plus, sous des conditions opératoires plus favorables (inoculum, milieu), l'insertion de certaines espèces minoritaires a permis plutôt de stabiliser le métabolisme de l'écosystème microbien sans pour autant en affecter favorablement la production d'hydrogène. Dans tous les cas, les interactions compétitives n'ont pas été favorables à la production d'hydrogène. Enfin, des essais en réacteur continu ont montré que le mode d'implantation des souches peut être un facteur primordial pour l'utilisation d'IEEM. En conclusion, ce travail a montré la potentialité d'utiliser des bactéries exogènes, en proportions minoritaires, comme facteurs biotiques pour stabiliser et/ou orienter les métabolismes microbiens vers des fonctions d'intérêt au sein des cultures mixtes microbiennes
Nowadays mixed cultures are considered as a serious alternative to pure cultures in biotechnological processes. Mixed cultures can be operated continuously, under unsterile conditions and from various organic substrates. One of the most constraints remains the chronic instability of the mixed culture processes due to the presence of unwanted metabolic pathways resulting from complex microbial interactions. More particularly the role of bacteria in low abundance remains to be elucidated. Therefore this work consisted initially to determine the contribution of sub-dominant bacteria to fermentative hydrogen production using a chemostat continuously fed with a glucose-based medium. Seven inocula were grown under the same operating conditions. Interestingly, Clostridium pasteurianum was found as dominant in six assays on seven at steady state. Only the minority bacterial population differed with regards to their identity and diversity. Acting as true keystone species, these minority bacteria impacted substantially the metabolic network of the overall ecosystem despite their low abundance. In a second step, this work consisted in using some of these minority species as Ecological Engineers of Microbial Ecosystem (EEME). In order to study this aspect, the structure of a hydrogen-producing microbial community has been artificially modified by adding exogenous bacterial strains with redundant functions and/or complementary native strains. Results in batch reactors have shown that the hydrogen production performances could be improved to a 3.5 factor by the addition of certain strains. Results obtained can not be explained by simple trophic interactions and suggest the presence of interaction mechanism of cooperation among microorganisms. Moreover, under more favourable operating conditions (inoculum, culture medium), the addition of certain species in low abundance could stabilize the metabolism of microbial ecosystem without necessarily favourably affect the hydrogen production. In all cases, competitive interactions were not favourable for hydrogen production. Trials were then realised in continuous reactors. These trials have shown that the method used to implant strains in reactors could be a key factor for using the EEME.As a conclusion, this study has shown the potential to use exogenous bacteria, in minority proportions, as biotic factors to stabilised and/or guides microbial metabolisms to functions of interest within microbial mixed cultures

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Walls, A., and Phillip R. Scheuerman. "The Effects of Substrate Concentration and Cell Density on the Rate of Degradation of o-cresol Using a Freeze-Dried Consortium." Digital Commons @ East Tennessee State University, 1998. https://dc.etsu.edu/etsu-works/2917.

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Waszak, Dafne Quintas. "Biorremediação por consórcio microbiano (Pseudonomas aeruginosa, Candida albicans, Aspergillus flavus e Fusarium sp.) em solo contaminado por benzo[a]pireno (B[a]P) quantificado via GC-MS." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2013. http://hdl.handle.net/10183/96498.

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O benzo[a]pireno é um contaminante da classe dos HPAs (Hidrocarbonetos Policíclicos Aromáticos) oriundo do processo pirolítico a partir da combustão incompleta da matéria orgânica. Possui potencial carcinogênico, mutagênico e baixa degradação no meio ambiente, gerando preocupações ambientais. O presente estudo visa desenvolver uma metodologia de biorremediação eficiente para o contaminante benzo[a]pireno em solo inerte, previamente contaminado com uma concentração conhecida. Para a biorremediação foi avaliado o potencial da utilização de um consórcio microbiano com a bactéria Pseudomonas aeruginosa, e os fungos Candida albicans, Aspergillus flavus e Fusarium sp. Para comprovação da redução do contaminante foi realizada uma quantificação inicial e final das amostras via cromatografia gasosa acoplada à espectrometria de massas (GC-MS). As análises foram realizadas a partir da correlação das áreas dos picos de padrões com as áreas obtidas das amostras extraídas. O tempo de incubação dos microrganismos foi de cinquenta dias, com monitoramento do crescimento microbiano a cada sete dias. As amostras foram divididas em três grupos, caracterizando a triplicata de todas as análises. Para cada grupo foi monitorado o crescimento dos microrganismos na presença e na ausência do contaminante. Para cada via foi pesado 55 g de solo, adicionado a solução contendo 6,2 mg L-1 do contaminante benzo[a]pireno (menos a via do branco) e adicionado 800μL do consórcio microbiano. As amostras ficaram em estufa na temperatura de 35°C durante o período de incubação. A quantificação inicial anterior ao processo de incubação dos microrganismos, foi obtida uma média de 3,74 mg kg-1, representando a adsorção do contaminante no solo. Para o monitoramento microbiano, foram observadas pelas curvas do crescimento dos microrganismos representativas diferenças, nas amostras do branco, que não continham B[a]P obtiveram um leve crescimento, tempo de vida curto, em torno de sete a quatorze dias, e um decrescimento brusco e repentino, enquanto as amostras com o contaminante B[a]P mostraram um número maior de Unidades Formadoras de Colônias (UFC) por grama de amostra, tempo de vida maior e um decrescimento normal. Esta diferença no comportamento dos microrganismos indicou a utilização o carbono orgânico do contaminante como fonte de energia, demonstrando a possibilidade da efetivação do processo de biorremediação. Após esta etapa, realizou-se a quantificação final do solo, foi obtida uma média de 1,29 mg kg-1. Avaliando ambas concentrações, antes e após o processo, constatou-se uma degradação do contaminante em 65,51%±0,95. Com estes resultados, comprovou-se a eficiência da metodologia proposta neste trabalho para a biorremediação do benzo[a]pireno.
Benzo[a]pyrene is a contaminant class of PAHs (Polycyclic Aromatic Hydrocarbons) arising from the pyrolytic process of incomplete combustion of organic matter. Are carcinogenic potential , mutagenic and low degradation in the environment, causing environmental concerns. This study aims to develop a methodology for efficient bioremediation of contaminant benzo[a]pyrene in soil inert previously contaminated with a known concentration. For bioremediation potential was evaluated using a microbial consortium with Pseudomonas aeruginosa bacteria and Candida albicans , Aspergillus flavus and Fusarium sp fungi. To prove the reduction of contaminant was performed to quantify the initial and final samples via gas chromatography- mass spectrometry (GC - MS). The analyzes were performed from the correlation of peak areas of standards with the areas obtained from extracted samples. The incubation of microorganisms was fifty days with monitoring of microbial growth every seven days. The samples were divided into three groups, featuring all of triplicate analyzes. For each group was monitored growth of micro-organisms in the presence and absence of the contaminant. For each route was weighed 55 g of soil added to a solution containing 6,2 mg L-1 of the contaminant benzo[a] pyrene ( the path of least white) and added to 800μL of a microbial consortium, which consists of a mixture of each species. The samples were left in an oven at 35°C. The quantification process prior to initial incubation of microorganisms was obtained an average of 3,74 mg kg-1, representing the adsorption of contaminants in the soil. For monitoring microbial curve was observed for the growth of microorganisms that the samples of the blank, containing no B[a]P had a slight growth short lifetime , about seven to fourteen days and decrease rate, while samples with contaminant B[a]P showed greater formation of Colony Forming Units (CFU) per gram of sample, lifetime , and a greater decrease normally. This difference in behavior indicated microorganisms using organic carbon as a dopant source of power, demonstrating the possibility of the realization of the bioremediation process . After this step, the measurement was carried out final soil was obtained an average of 1.29 mg kg-1. Evaluating concentrations both before and after the process , it was found a degradation of contaminant in 65.51 ± 0.95 % . With these results proved the efficiency of the methodology proposed in this work for the bioremediation of benzo[a]pyrene.

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Fettig, James Drew. "A Study of the Patterns, Stoichiometry, and Kinetics of Microbial BTX Degradation Under Denitrifying Conditions by an Activated Sludge Consortium Receiving a Mixed Waste." Thesis, Virginia Tech, 1998. http://hdl.handle.net/10919/45148.

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The patterns, stoichiometry, and kinetics of microbial benzene, toluene, p-xylene, m-xylene, and o-xylene degradation by a denitrifying activated sludge consortium was investigated in a sequencing batch reactor (SBR) receiving a mixed waste. After six months of acclimation, toluene and m-xylene were routinely degraded to below detection. Both toluene and m-xylene could serve as sole carbon and energy sources. The removal of o-xylene was also possible; however, its transformation was dependent upon gratuitous metabolism during toluene degradation. Benzene and p-xylene were recalcitrant throughout the study. The first order decay coefficient (b) of the denitrifying biomass was determined to be 0.016 Â± 0.006 h-1 on a theoretical oxygen demand (thOD) basis. The true growth yields (Y) for the biogenic and toluene/m-xylene components of the mixed waste were determined to be 0.41 Â± 0.02 and 0.35 Â± 0.04 mg thOD biomass per mg thOD substrate, respectively. The Monod parameters, qmax and KS, for toluene ranged from 0.059 to 0.14 mg toluene/mg protein/h and 0.84 to 6.9 mg/L, respectively. For m-xylene, the qmax and KS parameters ranged from 0.034 to 0.041 mg m-xylene/mg protein/h and 0.28 to 3.7 mg/L, respectively. Some of the variation observed between kinetic experiments was attributed to the different accumulation levels of the denitrification intermediate nitrite (NO2-) and the inhibitory effects of its conjugate acid, nitrous acid (HNO2). Other evidence suggested that part of the variation was also due to a continuous acclimation and refinement towards higher affinity toluene- and m-xylene-degrading enzyme systems within the biomass.
Master of Science

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Julien-Laferriere, Alice. "Models and algorithms applied to metabolism : from revealing the responses to perturbations towards the design of microbial consortia." Thesis, Lyon, 2016. http://www.theses.fr/2016LYSE1260/document.

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Lors de cette thèse, je me suis intéressée à la modélisation du métabolisme des micro-organismes. Nous nous sommes focalisé sur le métabolisme des petites molécules qui ne prend pas en compte les réactions associées aux macromolécules, telle que la synthèse des protéines.Nous avons ainsi utilisé différents formalismes de modélisation.Tout d'abord, nous avons développé TOTORO où les réseaux métaboliques sont représentés par des hypergraphes dirigés et qui permet d'identifier les réactions ayant participé à une transition métabolique. TOTORO a été utilisé sur un jeu de données sur la levure en présence de cadmium. Nous avons pu montrer que nous retrouvons les mécanismes connus de désintoxication.Ensuite, en utilisant une méthode de modélisation par contraintes, nous discutons d'un développement en cours, KOTOURA, qui propose d'utiliser les connaissances actuelles de concentrations de métabolites entre différentes conditions pour inférer de manière quantitative les possibles asynchronies des réactions lors du passage d'un état stable à un autre. Nous avons testé son implémentation sur des données simulées.Enfin, nous proposons MULTIPUS, une méthode d'extraction d'(hyper)-arbres de Steiner dirigés qui permet de sélectionner les voies métaboliques pour la production de composés au sein d'une communauté bactérienne. Les réseaux métaboliques sont modélisés en utilisant des hypergraphes dirigés et pondérés. Nous proposons un algorithme de programmation dynamique paramétré ainsi qu'une formulation utilisant la programmation par ensemble réponse. Ces deux propositions sont ensuite comparées dans deux cas d'applications
In this PhD work, we proposed to model metabolism. Our focus was to develop generic models, that are not specific to one organism or condition, but are instead based on general assumptions that we tried to validate using data from the literature.We first present TOTORO that uses a qualitative measurement of concentrations in two steady-states to infer the reaction changes that lead to differences in metabolite pools in both conditions.TOTORO enumerates all sub-(hyper)graphs that represent a sufficient explanation for the observed differences in concentrations. We exploit a dataset of Yeast (Saccharomyces cerevisiae) exposed to cadmium and show that we manage to retrieve the known pathways used by the organisms. We then address the same issue, but using a constraint-based programming framework, called KOTOURA, that allows to infer more quantitatively the reaction changes during the perturbed state. We use in this case exact concentration measurements and the stoichiometric matrix, and show on simulated datasets that the overall variations of reaction fluxes can be captured by our formulation.Finally, we propose MULTIPUS, a method to infer microbial communities and metabolic roads to produce specific target compounds from a set of defined substrates. We use in this case a weighted directed hypergraph. We apply MULTIPUS to the production of antibiotics using a consortium composed of an archae and an actinobacteria and show hat their metabolic capacities are complementary. We then infer for another community the excretion of an inhibitory product (acetate) by a 1,3-propanediol (PDO) producer and its consumption by a methanogene archae

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La, Angéla. "Process development for symbiotic culture of Saccharomyces cerevisiae and Chlorella vulgaris for in situ CO2 mitigation." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLC031/document.

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La levure et la microalgue sont des microorganismes très étudiés pour la production de composés à haute valeur ajoutée pour des secteurs tels que l’agroalimentaire et l’énergie. Ce travail de thèse propose un procédé de culture mixte entre la levure Saccharomyces cerevisiae et la microalgue Chlorella vulgaris pour la croissance des deux espèces tout en limitant le rejet en CO2. Le procédé repose sur la symbiose mutuelle entre les deux organismes autour des échanges de gaz, qui est rendu possible en imposant une co-dominance en termes de population. Les populations doivent être équilibrées pour que les microalgues puissent gérer la production de CO2. Le procédé est réalisé en photo-bioréacteur de 5 litres non-aéré et fermé, afin d’éviter les échanges gazeux avec l’environnement externe. Dans cette configuration, le CO2 est produit sous forme dissoute et directement accessible aux microalgues, évitant les phénomènes de dégazage et de dissolution. Les populations de levures et de microalgues atteignent une concentration égale (20 millions de cellules par ml) au bout de 24 heures de culture, restent stables jusqu’à la fin de la culture (168 heures) et les microalgues recyclent 12% du CO2 produit par les levures. Un modèle cinétique de la levure et de la microalgue en culture mixte est développé en combinant les modèles individuels de la levure et de la microalgue. Le modèle prédictif de la levure prend en compte les possibles voies métaboliques impliquées dans la fermentation et la respiration de ces voies est prédite en y intégrant des facteurs de limitation. Le modèle de la microalgue est basé sur l’activité photosynthétique. Les résultats de ce travail montrent la faisabilité du procédé de culture mixte entre hétérotrophe et autotrophe et pourrait apporter les bases pour le développement d’un procédé écologique à faible impact environnemental
Yeast and microalgae are microorganisms widely studied for the production of high-value compounds used in food and energy area. This work proposes a process of mixed culture of Saccharomyces cerevisiae and Chlorella vulgaris for both growth and CO2 mitigation. The process relies on mutual symbiosis between the two organisms through gas exchange, which is possible by engineering the co-dominance of populations. The two populations must be balanced in such a way so that microalgae can cope with the rate of CO2 production by the yeast activity. The process is performed in non-aerated 5l-photo-bioreactor fitted with a fermentation lock to prevent gas exchange with the outside atmosphere. With this set-up, the CO2 is produced in dissolved form and is available to the microalgae avoiding degassing and dissolution phenomena. The two organism populations are balanced at approximately 20 millions cells per ml, 12% CO2 produced by yeast was reutilized by microalgae within 168 hours of culture. A yeast and microalgae growth model in mixed culture is developed by combining each individual growth model. The predictive yeast model considers the possible metabolic pathways involved in fermentation and respiration and imposes limitation factors on these pathways, in this manner, the model can predict the partition of these pathways. The microalgae individual model is based on the photosynthetic activity. The results of this work show the feasibility of such process and could provide a basis for the development of a green process of low environmental impact

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Buchli, Fernanda 1989. "Análise metaproteogenômica de comunidades bacterianas enriquecidas visando a bioprospecção de enzimas de interesse biotecnológico = Prospection of biotechnological enzymes through metaproteogenomic analysis of a microbial consortium." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314205.

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Orientador: Fabio Marcio Squina
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A Biomassa vegetal tem sido reconhecida como uma potencial fonte de açúcares fermentescíveis para a produção de biocombustível, principalmente pelo crescente incentivo do uso de fontes renováveis de combustíveis e sustentabilidade. Atualmente, no Brasil, o etanol é quase exclusivamente produzido pela fermentação da sacarose, um açúcar que pode ser facilmente extraído da cana-de-açúcar, esse etanol produzido a partir da sacarose é chamado de etanol de primeira geração. O processo de extração dos açúcares da biomassa da cana, através da hidrólise enzimática para a produção do chamado etanol de segunda geração, ainda apresenta um baixo rendimento e elevado custo de produção. O objetivo deste trabalho foi à busca por enzimas capazes de promover uma degradação mais eficiente, contribuindo para a viabilidade da produção do bioetanol de segunda geração. Para este estudo foi utilizada uma abordagem de metagenômica e metaproteômica. A análise metagenômica baseou-se em uma amostra de solo de canavial a qual teve seu DNA extraído e sequenciado. Em paralelo utilizou-se este solo para o estabelecimento de dois consórcios microbianos utilizando o bagaço de cana-de-açúcar como única fonte de carbono, estes consórcios também foram sequenciados. As sequências foram anotadas e analisadas na plataforma MG-Rast. Para a abordagem metaproteômica foram utilizadas proteínas extraídas diretamente do solo e o secretoma de ambos os consórcios. A análise do sequenciamento revelou a predominância de bactérias, que representaram 94,86% do metagenoma de solo de canavial, sendo o filo Proteobacteria o grupo mais abundante em todos os metagenomas avaliados. Durante as análises foi possível observar mudanças populacionais entre os metagenomas, a exemplo, as classes Bacteroidia, Alphaproteobacteria e Gammaproteobacteria se mostraram mais abundantes nos metagenomas dos consórcios do que do solo. Analisando as proteínas identificadas nas análises de metaproteômica pertencentes à família das glicosil hidrolases nota-se uma predominância das hemicelulases seguida das celulases entre as enzimas mais abundantes identificadas para as três comunidades analisadas. Dentre as celulases identificadas as mais abundantes foram a GH1, GH3 e GH9, entres as hemicelulases as mais abundantes foram GH2, GH43 e GH51. As análises de metagenômica e metaproteômica sugerem que os consórcios apresentam um enriquecimento das enzimas de interesse e revelam o potencial destas comunidades para prospecção de novas enzimas envolvidas na degradação da biomassa lignocelulósica
Abstract: Plant Biomass has been recognized as a potential source of fermentable sugars for biofuel production, mainly by the growing concern with renewable fuels and sustainability. Ethanol is currently almost exclusively produced by fermentation of sucrose, a sugar that can be easily extracted from sugar cane and thus, this process is called first generation ethanol. The process of extracting the sugars from sugarcane biomass, through enzymatic hydrolysis to produce the so-called second-generation ethanol, still has a low yield and high cost process. The objective of this study was to search for enzymes capable of promoting a more efficient degradation, making possible the production of second generation bioethanol. We used the metagenomic and metaproteomic approaches. The metagenomic analysis was based on a soil sample of sugar cane which had its DNA extracted and sequenced. In parallel the soil was used to establish two microbial consortia using sugarcane bagasse as a sole carbon source, these consortia were also sequenced. The sequences were annotated and analyzed in MG-Rast platform. Proteins extracted directly from soil and the secretome of both consortia were used for metaproteomic approach. The sequencing analysis revealed the predominance of bacteria, representing 94.86 % of the soil metagenome, phylum Proteobacteria is the most abundant group in all metagenomas reviews. During the analysis it was observed population changes between the metagenomes, we notice some groups that seem to be more abundant in consortia¿s metagenomes than in soil. Between these enriched classes of microorganisms we have the Bacteroidia, Alphaproteobacteria and Gammaproteobacteria classes. Among the proteins identified in the metaproteomic 61% of the soil¿s proteins represent glycosyl hydrolases and 25% glycosyl transferases, the consortia presented a similar profile. Analyzing the enzymes belonging to the family of glycoside hydrolases we can notice a predominance of hemicellulases then cellulases among the most abundant enzymes identified for the three communities. Among the most abundant cellulases identified were the GH1, GH3 and GH9, among hemicellulases the most abundant were GH2, GH43 and GH51. The metagenomic and metaproteomic analyzes suggest that consortia have an enrichment of the enzymes of interest and reveal the potential of these communities to search for new enzymes involved in the degradation of lignocellulosic biomass
Mestrado
Bioquimica
Mestra em Biologia Funcional e Molecular

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França, Hiléia Camargo Ribeiro. "Produção de ácido cítrico a partir do cultivo de Aspergillus niger e Trichoderma reesei em bagaço de cana-de-açúcar e fermentação etanólica do extrato fúngico." Universidade Federal de São Carlos, 2016. https://repositorio.ufscar.br/handle/ufscar/7976.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Solid-state cultivation (SSC) are characterized by microbial growth on solid supports, often agroindustrial by-products, in conditions of absence of free water. Citric acid and ethanol are important commercial bioproducts used in various industrial sectors, which could be obtained by SSC of fungi from bagasse sugarcane and vinasse, with subsequent fermentation, minimizing the cost of production with the use two industrial byproducts. Fungi consortium has advantages over the isolated cultures, highlighting the best use of substrates due to enzyme supplementation, especially in terms of hydrolases. In this sense, the aim of this research was to evaluate the SSC of Aspergillus niger and Trichoderma reesei alone for the production of citric acid from sugarcane bagasse impregnated with different solutions (sucrose and vinasse) and the consortium of these fungi followed by ethanol fermentation of fungal yeast extract. The experimental steps set up the cultivation of A. niger for production of citric acid from submerged particles of sugarcane bagasse; SSC of A. niger and T. reesei alone and mixed using as impregnating with and without sucrose solution and vinasse pretreated with acid hydrolysis; ethanol fermentation of fungal extract by Saccharomyces cerevisiae. Results indicate the feasibility of Aspergillus niger´growth on submerged particles of sugarcane bagasse for citric acid production in medium with addition of sucrose. SSC of this fungus from sugarcane bagasse resulted in 103 mg L-1 of citric acid content in 4 days without addition of sucrose to the solid medium. Similarly, SSC of Trichoderma reesei in sugarcane bagasse leads citric acid production around 67 mg L-1 with raw vinasse in the first growth day. Specific production of 2.51 mg g-1 h-1 in terms of citric acid was obtained from the fungal consortium higher than that obtained using the two fungi alone. Ethanol fermentation tests by Saccharomyces cerevisiae from the fungal extract obtained by the SSC indicated that it is feasible to obtain a second bioproduct, especially high yield of glucose into ethanol to extract condition obtained from T. reesei without sucrose in 5 days. Results suggests the viability in the use of two important by-products of the sugarcane industry via microbial consortium by SSC, leading an interesting research field with various scientific and regional aspects.
O cultivo em estado sólido (CES) caracteriza-se pelo crescimento microbiano em suportes sólidos, muitas vezes subprodutos agroindustriais, em condições próximas da ausência de água livre. Ácido cítrico e etanol são importantes bioprodutos comerciais utilizados em vários setores industriais, os quais poderiam ser obtidos agregando o CES de fungos a partir de bagaço de cana-de-açúcar e vinhaça, com posterior fermentação, minimizando o custo de sua produção com o aproveitamento de dois subprodutos industriais. O consórcio de fungos apresenta vantagens sobre as culturas isoladas, destacando-se no melhor aproveitamento dos substratos devido à complementação enzimática, principalmente em termos de hidrolases. Nesse sentido, o objetivo do trabalho foi avaliar o CES de Aspergillus niger e Trichoderma reesei isoladamente para a produção de ácido cítrico a partir de bagaço de cana-de-açúcar impregnado com soluções distintas (sacarose e vinhaça), assim como o consórcio destes fungos, seguido de fermentação etanólica do extrato fúngico por leveduras. As etapas experimentais desta dissertação compreendem o cultivo de A. niger para produção de ácido cítrico a partir de partículas de bagaço de cana-de-açúcar submersas; CES de A. niger e T. reesei isoladamente e consorciados utilizando como soluções impregnantes água deionizada com e sem sacarose e vinhaça bruta e pré-tratada com hidrólise ácida; fermentação etanólica do extrato fúngico por Saccharomyces cerevisiae. Os resultados indicam a viabilidade do cultivo de Aspergillus niger em partículas de bagaço de canade- açúcar submersas com produção de ácido cítrico em meio com adição de sacarose. O CES deste fungo a partir de bagaço de cana-de-açúcar levou a uma produção máxima de 103 mg L-1 de ácido cítrico em 4 dias sem adição de sacarose ao meio sólido. Da mesma forma, Trichoderma reesei apresentou crescimento em bagaço de cana-deaçúcar, com destaque para a produção de ácido cítrico em torno de 67 mg L-1 com vinhaça bruta em 1 dia. A produção específica de 2,51 mg g-1h-1 em termos de ácido cítrico foi obtida com o consórcio fúngico, superior ao obtido empregando os dois fungos isoladamente. Os ensaios de fermentação etanólica por Saccharomyces cerevisiae a partir do extrato fúngico obtido pelo CES indicaram que é viável a obtenção de um segundo bioproduto, com destaque para o elevado rendimento de glicose em etanol para a condição de extrato obtido a partir de T. reesei sem sacarose em 5 dias. Os resultados da pesquisa indicaram a viabilidade no aproveitamento de dois subprodutos importantes do setor sucroenergético via consórcios microbianos por CES, possibilitando um campo de pesquisas interessante devido aos seus diversos aspectos científicos e regionais.

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Gaulin, Jean-Philippe. "Selective caffeine removal by microbial consortia." Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=80272.

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Coffee processing presents a considerable waste disposal problem, mainly because of the large volumes generated and the chemical composition of the by-products, particularly the caffeine levels. The use of Pseudomonas putida IF-3, a caffeine-degrading microorganism, in a microbial consortium for bioremediation of caffeine found in coffee wastes was investigated. Caffeine degradation was observed in fed-batch reactor experiments with caffeine as sole source of carbon and nitrogen. Metabolic regulation and caffeine removal potential by Pseudomonas putida IF-3 were investigated by supplementing with other nutrient sources. Diauxic growth was not observed. Nitrogen release from caffeine breakdown was found to be rate-limiting.
Effects of caffeine on microbial consortia were studied using denaturing gradient gel electrophoresis (DGGE), providing a community-scale view of changes in microbial consortia upon caffeine addition. Surprisingly, caffeine removal was achieved indigenously by the microbial consortium. Principal component analysis was used to analyze differences in DGGE banding patterns between control and caffeine-exposed mixed cultures.

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Jiranuntipon, Suhuttaya. "Décoloration d’effluents de distillerie par un consortium microbien." Thesis, Toulouse, INPT, 2009. http://www.theses.fr/2009INPT009G/document.

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Les effluents de distillerie de mélasse de canne à sucre génèrent une pollution environnementale due à, d’une part de grands volumes et d’autres part à la présence de composés de couleur brune foncée, connus sous le nom de mélanoïdines. Dans cette étude, un consortium bactérien CONS8 isolé dans des sédiments de chute d'eau a été choisi comme consortium apte à la décoloration de la mélasse. On a montré que le consortium CONS8 pouvait décolorer, trois eaux usées synthétiques différentes, élaborées respectivement à base de Viandox (13,48% v/v), d’eau usée de mélasse de betterave (41,5% v/v) ou d’eau usée de mélasse de canne à sucre (20% v/v). Les décolorations obtenues en 2 jours seulement, en fioles d’Erlenmeyer sont respectivement de 9,5, à 8,02 et à 17,5%. Quatre bactéries prédominantes ont été identifiées dans le consortium CONS8 par l'analyse de l'rADN 16S. Sur la base de cette identification, et afin de réaliser la décoloration la plus élevée, un consortium bactérien artificiel MMP1 a été reconstruit avec Klebsiella oxytoca, Serratia mercescens (T2) et la bactérie inconnue DQ817737 (T4). Dans des conditions optimisées (aération, pH) le consortium bactérien MMP1 a permis de décolorer l'eau usée synthétique contenant de la mélanoidine à 18,3% en 2 jours. La comparaison de la décoloration par le consortium MMP1 avec un milieu abiotique a démontré que la décoloration était principalement due à l'activité biotique des cellules bactériennes, sans aucun phénomène d'adsorption. Un complément en minéraux et vitamines B n'a pas amélioré la décoloration de mélanoïdines avec le consortium bactérien MMP1. Enfin, les performances d'un bioréacteur à membrane pour traiter les eaux résiduaires synthétiques contenant de la mélanoïdine ont été évaluées à l’échelle du laboratoire. L'ensemencement du réacteur a été réalisé avec un inoculum sur la base du consortium MMP1. Le réacteur a fonctionné sous plusieurs conditions de temps de séjour hydrauliques (HRT) de 15, 20, et 40 heures. Les performances ont été analysées en termes de DCO (demande chimique en oxygène), décoloration et croissance de biomasse. Les résultats ont indiqué qu’une efficacité accrue d’élimination de la DCO et de la couleur ont été obtenues avec le HRT le plus long
Distillery effluent from sugarcane molasses leads to an environmental pollution due to its large volume and the presence of dark brown colored compounds, known as melanoidins. In this study, a bacterial consortium CONS8 isolated from waterfall sediments in Maehongsorn province was selected as a molasses-decolorizing consortium. Consortium CONS8 was able to decolorize, only within 2 days, in Erlenmeyer flasks, three different synthetic wastewaters containing either Viandox sauce (13.5% v/v), beet molasses wastewater (41.5% v/v) or sugarcane molasses wastewater (20% v/v) at 9.5, 8.0 and 17.5%, respectively. Four predominant bacteria present in the consortium CONS8 were identified by the 16S rDNA analysis. To achieve the highest decolorization, the artificial bacterial consortium MMP1 comprising Klebsiella oxytoca, Serratia mercescens (T2) and unknown bacterium DQ817737 (T4), was constructed. Under optimized conditions (aeration, pH), the bacterial consortium MMP1 was able to decolorize the synthetic melanoidins-containing wastewater at 18.3% within 2 days. The comparison of decolorization by the consortium MMP1 with abiotic control proved that the color removal for synthetic melanoidins-containing wastewater medium was mainly due to biotic activity of bacterial cells, without any adsorption phenomena. Supplement of nutrients and vitamin B did not promote melanoidins decolorization by bacterial consortium MMP1. Finally, the performance of a membrane bioreactor (MBR) for synthetic melanoidins-containing wastewater treatment was investigated at laboratory scale, with a mineral membrane. The reactor seeding was made with the MMP1 bacterial consortium inoculum. The reactor was performed with several hydraulic retention times (HRT) of 15, 20, and 40 hours. The performances were analyzed in terms of COD, color removal and biomass in the reactor. The results indicated that the higher COD and color removal efficiency were achieved with the longer HRT

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Amouric, Agnès. "Biodiversité d'un consortium microbien et études génétiques de SP2B, un actinomycète isolé du consortium, capable de dégrader l'hexane." Aix-Marseille 1, 2006. http://www.theses.fr/2006AIX11007.

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Un consortium microbien capable de dégrader l'essence a été réadapté en culture liquide sur essence sans plomb/ méthyl tert-butyl éther. Les cinétiques de dégradation de l'hexane par ce consortium ont été étudiées en microcosme liquide et dans un biofiltre de paillasse. Sur les 28 derniers jours en biofiltre, le taux de production de CO2 et la capacité d'élimination du consortium se sont stabilisés. Un échantillon a été prélevé pour caractériser la biodiversité, et la comparer à celles du consortium initial réadapté sur essence, et de ce même consortium adapté sur l'hexane en microcosme liquide. Des différences significatives entre les populations ont été observées, indiquant une adaptation probable en fonction des conditions de cultures. Trois souches bactériennes dont deux Actinomycètes ont été isolées à partir du consortium "hexane liquide". L'une d'entre elle, SP2B, dégrade l'hexane et d'autres alcanes à courte chaîne contrairement à la souche type phylogénétiquement la plus proche (Rhodococcus ruber DSM 43338T). Le profil d'acides gras cellulaires sur différents alcanes et la croissance sur les intermédiaires du métabolisme de l'hexane similaires pour les deux souches n'ont pas permis d'expliquer la différence de phénotype. De plus, un gène identique alkB a été identifié dans les deux souches. Il code pour une alcane monooxygénase qui pourrait être impliquée dans la dégradation des alcanes à longues chaînes. La spécificité de dégradation de SP2B pourrait être liée à la présence d'une autre copie de alkB identifiée. Des études pour caractériser ce nouveau gène ainsi que la régulation de tous ceux impliqués dans la dégradation de l'hexane, sont en cours
A gasoline-degrading consortium was readapted in liquid using gasoline/methyl tert-butyl ether and was tested for its hexane-degradation kinetics in liquid microcosm and in a bench-scale biofilter. On the 28 last days, Elimination Capacity and CO2 production rate in the biofilter remained constant. A sample was collected to characterize the biodiversity and compare it with that of the initial gasoline consortium and the same consortium adapted on hexane in liquid microcosm. Significant differences between the populations were observed, indicating a probable adaptation to the culture conditions. Three strains including two Actinomycetes were isolated from the consortium. One of them, SP2B, degrade hexane and other short-alkane compared with the type strain phylogenetically related (Rhodococcus ruber DSM 43338T). Cellular fatty-acid profiles on various alkanes, as well as the growth in the presence of hexane-metabolism intermediaries identical for both strains didn't allow to understand the phenotypic differences. Moreover, an identical gene, alkB, was found in both strains. It codes for an alkane monooxygenase, which product is probably involved in long-chain-alkane degradation. Another alkB gene, identified in SP2B, could therefore be involved in the degradation specificity of the strain. Studies are in progress in order to precisely characterize this new gene and to understand the regulations on the expression of all the elements involved in hexane degradation

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Darwin. "Product accumulation and its control during microbial carbohydrate Fermentations by Rumen- and other mixed microbial consortia." Thesis, Darwin, (2017) Product accumulation and its control during microbial carbohydrate Fermentations by Rumen- and other mixed microbial consortia. PhD thesis, Murdoch University, 2017. https://researchrepository.murdoch.edu.au/id/eprint/40959/.

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This abstract compiles the abstracts of the individual thesis chapters. Anaerobic acid stage fermentation of carbohydrates can generate a variety of desired or undesired end-products. Besides physical parameters such as pH and temperature, the types of carbohydrate being fermented influences the fermentation end-products. The results of the current study indicate that under uncontrolled pH, microbial mixed cultures from activated sludge and anaerobic digester sludge anaerobically produced ethanol from glucose while producing lactic acid from starch conversion. This trend was confirmed by batch and chemostat trials. After shifting from glucose to starch feed or vice versa the chemostat enrichment culture responded by shifting from ethanol to lactic acid or the reverse. Results also showed that only 25% of starch was converted to the lactic acid. The low conversion yield could be explained by the low pH in the broth that is known to become inhibitory already at a pH of below 5. As maltose is an intermediate sugar derived from the digestion of starch, it was tested as a fermentation substrate and compared to glucose fermentation. Results showed that independent of the inoculum source maltose supported lactic fermentation while glucose led to ethanolic fermentation. The trend was confirmed in batch as well as chemostat culture. Under uncontrolled pH, fermentation of maltose ceased with the production of small amounts of lactic acid and acetate as the main metabolites, while fermentation of glucose continued and produced ethanol as the main end-product. Further investigation with other disaccharides (lactose and sucrose) showed that lactose was fermented to lactic acid and acetate as the main metabolites while sucrose formed ethanol as the major fermentation end-product. Comparative experiments showed that mixed microbial consortia and chemostat enrichments reproducibly produced lactate from maltose fermentation and ethanol from glucose fermentation. However, when using rumen bacteria as the inoculum, lactic acid was the key fermentation end-product, suggesting that rumen microflora comprises larger populations of lactic acid producing bacteria. Lactic acid accumulation in the rumen is a well-known problem known as rumen acidosis and was investigated further in this study. Acute ruminal acidosis can occur when pH in the rumen drops below 5.0. This condition can completely disrupt rumen microbiota leading to the mortality of ruminants. The results of the current study showed that acidosis could occur within 6 hours of incubation in the rumen culture fermenting sugars or starch. Along with the formation of lactic acid, acetic acid alone or in mixture with ethanol was found to be the reason for high acid build-up in the rumen. Acidosis resulted even with only 20% of a normal daily feed load for all soluble and non-soluble carbohydrates. DNA-based microbial analysis revealed that Prevotella was the dominant species present in the rumen fluid, which is considered as the main lactic acid producing bacteria. The phenomenon of acidosis comprises at least two components, a dramatic drop in pH and the over-production of lactic acid. Two approaches can be used to ameliorate the effects, the addition of pH buffering or neutralizing species, or the addition of active microbial cultures that can degrade lactate at a rate that reduces lactate accumulation. The former can be harmful to the animal when the buffering is locally too concentrated due to a lack of uniform distribution; the latter can be costly, if produced as a pure strain. The results of the current study showed that from rumen cultures, mixed microbial lactic acid utilizing bacteria (LUB) could be enriched and subsequently used as a controlling agent against in vitro acidosis. The addition of liquid cultures of LUB enrichments to a rumen culture that was producing lactic acid from fermentation of starch resulted in a reduction of lactic acid, and produced VFA with acetate and propionate as the main metabolites. Breeding lactate utilizing bacteria (LUB) from rumen fluid that can be used as probiotics is potentially useful for the cattle industry. This is because probiotics can be used as a supplement to prevent lactic acidosis when ruminants are fed with readily fermentable carbohydrates. The results of the current study showed that the addition of concentrated cell suspensions of LUB as probiotics to rumen cultures fermenting corn starch successfully prevented lactic acid accumulation, and could also be used as a therapy by converting lactic acid accumulated in rumen cultures into volatile fatty acids (VFA) with acetate and propionate as the main end-products. The combination of concentrated cell suspensions of LUB with buffer could prevent lactic acid accumulation, and rapidly degrade lactic acid without the use of excessive amounts of LUB probiotics. Metagenomic sequencing analysis showed the key LUB that was enriched to include Bacteroides, Acinetobacter, Oscillospira, Clostridium, Dysgonomonas and Pseudomonas.

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Yunita, Dewi. "The role of non-starter bacterial consortia in mould-ripened cheese." Thesis, University of Nottingham, 2016. http://eprints.nottingham.ac.uk/33010/.

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Stichelton is a blue-veined raw milk cheese which is made following the Stilton cheese making process. In a previous study, a preliminary examination of its microflora during production was examined by traditional culture methods and initial PCR DGGE profiling. The aim of this study was to complete the profiling of Stichelton cheese and examine the contribution of its microbiota components to product characteristics. Stored samples of cheese production isolates were sequenced and in addition whole population DNA was extracted directly from a fully ripened Stichelton cheese (12 weeks) and from bulk cell suspensions collected on various media. The V3, V4V5 and V6V8 regions of 16S rDNA were amplified by PCR and separated by DGGE using 20 – 80 % urea formamide denaturing gradient. While Lactobacillus casei/paracasei, Staphylococcus equorum, Bacillus sp., Brevibacterium sp., Halomonas sp., Acinetobacter sp., Alkalibacterium sp. and Corynebacterium casei were only found by the molecular method, traditional culture detected a large number of potentially raw milk microbiota. Lactococcus lactis was detected in the raw milk sample and along the process by both methods. The L. lactis subsp. lactis which was detected in the core of matured Stichelton was shown by PFGE to be from the raw milk and not the starter culture used in Stichelton production. S. equorum was found in the crust of cheese pre-piercing and in all parts of the cheese post-piercing by the molecular approach only. This suggested this organism was introduced originally via handling. Five S. equorum isolated from Stilton, Danish Blue and Reblochon could grow up to 10% salt but did not tolerate low pH levels suggesting S. equorum in Stichelton must have been introduced by handling before or during ripening as if it was present in the early fermentation then it would die as fermentation progressed due to pH sensitivity. A model cheese system made with commercial UHT milk was used to examine the interaction between mixed Lc. lactis, P. roqueforti and S. equorum B2 isolated from the Stilton crust. S. equorum was either added 1.5 h after the addition of L. lactis or it was smeared on the surface of the cheese immediately after un-moulding. The viable counts and pH were analysed throughout the process, while texture, water activity and flavour volatiles using GCMS SPME were determined for one month ripened cheeses only. The results showed S. equorum survived in the cheese following either method of introduction and that in cheeses without P. roqueforti addition, the presence of incorporated and surface-spread S. equorum could inhibit the surface growth of a contaminant Penicillium. It also slowed the growth of starter P. roqueforti in cheeses made with this mould. A paler coloured crust, firmer textured cheese and a low amount of alcohols were shown in the model cheeses made with surface-smear S. equorum. Conversely, addition of S. equorum in the initial process made the cheese core softer and produced low amounts of acids. Ethanol, 3-methyl-1-butanol and 2-pentanone were the main flavour compounds in the model cheeses examined. The antifungal activity of the isolate was confirmed in laboratory media. Its ability to prevent Penicillium surface growth could be beneficial for white cheeses where this is an undesirable flaw. The results showed that the sporulation inhibitory effect on P. roqueforti was because of an antifungal agent produced by S. equorum, but it was not acid, bacteriocin or H2O2. Further study is needed to detect the antifungal agent. Overall, the study has expanded the understanding of the role non-starter bacteria may have in contributing to cheese ripening.

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Ranava, David. "Etude d'un consortium microbien producteur d'hydrogène : de l'interaction inter-bactérienne au bioréacteur." Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM4700.

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Dans la nature, les microorganismes s’organisent en communauté où la concertation de leur métabolisme leur permet de coloniser des endroits peu propices. La biodégradation de la matière organique nécessite un couplage métabolique entre les différents microorganismes impliqués et constitue un modèle de choix pour l'étude des interactions où leurs relations restent mal définies et nécessitent d’être mieux caractérisées. Le décryptage du mécanisme mis en jeu permettrait d'optimiser la production de composés bioénergétiques comme l'hydrogène. Nous avons étudié un consortium composé de Desulfovibris vulgaris Hildenborough, une bactérie sulfato-réductrice et de Clostridium acetobutylicum, une bactérie fermentaire. Ces deux bactéries sont retrouvées dans des consortia naturels impliqués dans la dégradation de la biomasse. Des approches de microbiologie, de métabolisme et de microscopie ont permis de démontrer l’existence d’une interaction physique et d'un échange de molécules cytoplasmiques entre les deux bactéries. Ceci s'associe à une réorientation du flux de carbone dans la bactérie C. acetobutylicum qui se traduit par une production d’hydrogène accrue. Ce comportement est lié aux conditions de stress nutritionnel pour la bactérie D. vulgaris. De plus, des molécules signal de type AI-2 jouent un rôle important dans la mise place de l'interaction physique. Un inhibiteur de cette interaction, produit par D. vulgaris dans certaines conditions, a été découvert. Ce travail a permis d'acquérir de nouvelles connaissances sur les relations métaboliques et les interactions physiques entre les bactéries impliquées dans la biodégradation de la biomasse dans un consortium
In nature microorganisms live in communities, in which the complementarity of their metabolism allows them to colonize less favourable ecological niches. Biodegradation of organic matter requires tight metabolic coupling between the different microorganisms involved, and constitutes an ideal model for studying the interactions between them, which are still not well established and require further characterization. Furthermore, deciphering the metabolic couplings established between the partners would allow optimization of this process for production of compounds of biotechnological interest, such as hydrogen. During the course of this work we have studied an artificial consortium constituted by Desulfovibris vulgaris Hildenborough sulphate-reducing bacterium, and Clostridium acetobutylicum a fermentative bacterium; both of them are found in natural consortia involved in biomass degradation. Microbiological, metabolic and microscopic approaches allowed us to show the existence of a physical interaction, with exchange of cytoplasmic molecules, between the two bacteria. This is associated with reorientation of the carbon flux in Clostridium acetobutylicum, resulting in increased hydrogen production. This behaviour is linked with the nutritional stress of D. vulgaris. Moreover, AI-2 type signal molecules produced in these conditions are crucial for the physical interaction between the two bacterial partners. An inhibitor produced by D. vulgaris in certain conditions has been discovered. This work has allowed us to acquire new knowledge about metabolic relations and physical interactions between bacteria involved in biomass degradation in a consortium

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32

Ortiz, Onofre. "Degradation studies of 2, 4, 6, trinitrotoluene by a microbial consortia." DigitalCommons@Robert W. Woodruff Library, Atlanta University Center, 1997. http://digitalcommons.auctr.edu/dissertations/3269.

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Microbial mats are natural heterotrophic and autotrophic communities dominated by cyanobacteria (blue-green algae). These constructed mats are durable, tolerant to a variety of toxins and resilient under changing environmental conditions. This research demonstrates that microbial mats provide an effective remediation treatment for 2,4,6 Trinitrotoluene (TNT) in water and soil. It showed that TNT is removed to undetectable limits after 5 days of treatment under any of the following conditions: light/dark; total light; total dark. This work also shows that in the presence of an inorganic material (lead), mats were able to remove both contaminants efficiently, thus making the microbial mat a good choice for mixed waste remediation. Kinetic studies performed during the first five hours of microbial treatment showed a pseudo first order reaction indicating that TNT removal is initially proportional to the concentration of TNT. The major metabolites detected after 24 hour of treatment were 4-amino-2,6- dinitrotoluene, 2-amino-4,6-dinitrotoluene, and 2,4-diamine-6-nitrotoluene. These metabolites have a toxicity level similar to TNT. However, mat extracts and growth medium concentrates taken after 24 hours treatment of TNT showed little or no toxicity. The lack of toxicity demonstrated by treated mat extracts and media concentrates suggest that these metabolites are not the final metabolic products. The chemical nature of these metabolites suggests that the chemical mechanism of biotransformation involves reduction of the nitro groups at the ortho and para position of the TNT structure. Results obtained from light and dark experiment suggest that photooxidation or photodegradation is not an important mechanism for degradation of TNT by mats. Results show that live mats likely degrade TNT via a biotransformation process. In comparison, heat killed mats show a much slower removal of TNT than live mats. TNT was the only species found in the water column and extracts of heat killed mats, which indicates that TNT is removed by a passive absorption process, but no evidence of biodegradation was observed.

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33

Lambert, Stefan. "Seasonality and dynamics of microbial consortia in the Bay of Banyuls." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS231.

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Dans les océans tempérés, les transitions printanières annuelles sont accompagnées de blooms phytoplanctoniques. Le phytoplancton joue un rôle essentiel dans les cycles biogéochimiques et produit la moitié de la production primaire globale. Une série temporelle établie en 2007 à SOLA, un site côtier dans le Nord-Ouest méditerranéen, surveille les paramètres environnementaux et biologiques. Dans le premier chapitre, plusieurs « amplicon sequence variants » (ASVs) microbiens avaient des motifs annuels récurrents, malgré les perturbations environnementales caractéristiques des zones côtières. L’analyse de réseaux, décrite dans le deuxième chapitre, a révélé que la salinité et la température impactaient la structure des communautés microbiennes. Des sous-réseaux ont montré que des ASVs persistant changeaient de partenaires en fonction des perturbations environnementales. Ces observations suggèrent l’existence de redondance fonctionnelle dans les communautés microbiennes marines. Dans le troisième chapitre, des expériences microcosmes ont confirmé que des variations de température affectaient la structure des communautés microbiennes naturelles. À basse température, les picophytoplanctons étaient dominants, tandis que les diatomées prévalaient aux températures plus fortes. Ces résultats permettent d’expliquer le maximum d’abondance de Bathycoccus prasinos tous les ans au minimum de température à SOLA. Ce manuscrit, intégrant à la fois les résultats d’une série temporelle, de cultures cellulaires et de microcosmes, a permis d’éclaircir l’impact anthropologique sur les communautés microbiennes marines
In temperate oceans, yearly transitions from winter to spring are accompanied by a phytoplanktonic bloom. Phytoplankton, at the basis of the food chain in the oceans, plays an essential role in biogeochemical cycles as it generates 50\% of the global primary production. A time series established in 2007 at SOLA, a coastal site in the North Western Mediterranean Sea, monitors environmental and biological parameters. In the first chapter, we demonstrated that several microbial amplicon sequence variants (ASVs) displayed yearly rhythmicity, despite stochastic environmental perturbations, inherent to coastal ecosystems. Network analyses, described in the second chapter, revealed that salinity and temperature deeply impacted the microbial community structure. Subnetworks highlighted that persistent ASVs switched their first neighbors depending on environmental perturbations. These observations suggest the existence of functional redundancy in marine microbial communities. In the third chapter, microcosms confirmed that temperature fluctuations strongly affected natural microbial community structure. Picophytoplankton dominated the incubated communities at low temperature, whereas diatoms prevailed at higher temperatures. These results help explain Bathycoccus prasinos peak of abundance every year at the temperature minimum at SOLA. By integrating results from a time series, cell culture and microcosms experiments, this manuscript helps unravel the impact of anthropologically driven climate change on marine microbial communities

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34

Jeanbille, Mathilde. "Réponse des consortia microbiens benthiques à une contamination chronique aux hydrocarbures." Thesis, Pau, 2015. http://www.theses.fr/2015PAUU3043/document.

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Les communautés microbiennes procèdent au recyclage des nutriments et à la degradation de la matière organique, et sont ainsi essentielles aux cycles biogéochimiques dans le sédiment et plus largement dans les océans. La contamination chronique aux hydrocarbures représente près de 80% des déversements totaux dans les océans. Toutefois, en comparaison des marées noires, son impact sur les communautés microbiennes est encore mal compris. Dans cette étude, nous avons d’abord utilisé une approche de type méta-analyse pour élucider l’effet global de la contamination aux hydrocarbures dans différents habitats. La réponse des communautés bactériennes à la contamination s’est révélée être dépendante du type d’habitat, les sols étant plus impactés que d’autres habitats, comme par exemple les sédiments marins. Nous nous sommes ensuite intéressés aux communautés microbiennes des trois domaines du vivant de sédiments côtiers provenant des côtes méditerranéennes et atlantiques. La contamination chronique n’influençait que marginallement les communautés benthiques, et la diversité alpha n’était pas réduite dans les sédiments contaminés. Cedendant, la comparaison des réseaux de co-occurrence des échantillons contaminés et non-contaminés a montré que le réseau des communautés contaminées présentait une topologie différente, indiquant une vulnérabilité plus importante à d’éventuelles perturbations environnementales. Des indicateurs potentiels de la contamination identifiés avec la méta-analyse ont été ciblés pour étudier l’impact de la contamination chronique aux hydrocarbures sur les services écologiques qu’ils assurent (i.e. la dégradation de la matière organique et des hydrocarbures) en utillisant la technique de Micro-FISH
Within the sediment, microbial communities play a pivotal role by driving essential processes such as nutrient cycling and organic matter degradation. Chronic hydrocarbons contamination represents almost 80% of the total input in the oceans. However, as compared to oil spills, its impact on microbial communities remains poorly understood. In this study, we first used a meta-analysis approach to decipher the global effect of hydrocarbons contamination in different habitats. Bacterial community response to the contamination was found to be dependant of the habitat studied, with soils being more impacted than other habitats, like marine sediments. Because bacteria are in interactions with other important members of microbial communities such as Archaea and Eukaryotes, we focused on microbial communities from the three domains of life in coastal marine sediments from the Mediterrranean and the French Atlantic coasts. Independently of the domains of life, chronic hydrocarbons contamination appeared to be a poor driver of communities structuration, and alpha diversity was not reduced in contaminated sediments. However, the comparison of co-occurences networks of contaminated and non-contaminated samples showed that the network from the contaminated samples exhibited a different topology, which suggests a higher vulnerability to eventual environmental perturbations. Potential indicators species identified using the meta-analysis approach were targeted to study the impact of chronic contamination on the ecological services they provide (i.e. organic matter and hydrocarbons degradation) using the Micro-FISH method

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35

Iguchi, Hiroyuki. "Functional analysis of interaction mechanism in C1-microbial consortia stimulating methane oxidation." Kyoto University, 2012. http://hdl.handle.net/2433/157680.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第16889号
農博第1905号
新制||農||996(附属図書館)
学位論文||H24||N4650(農学部図書室)
29564
京都大学大学院農学研究科応用生命科学専攻
(主査)教授阪井康能, 教授矢﨑一史, 教授小川順
学位規則第4条第1項該当

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36

Bradácová, Klára [Verfasser], and Günter [Akademischer Betreuer] Neumann. "Microbial consortia as inoculants for improvedcrop performance / Klára Bradácová ; Betreuer: Günter Neumann." Hohenheim : Kommunikations-, Informations- und Medienzentrum der Universität Hohenheim, 2020. http://d-nb.info/1214709761/34.

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Wong, Ting Mabel, and 黃婷. "A metagenomic investigation of microbial consortia underpinning anaerobic digestion for renewable biogas production." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/198831.

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Anaerobic digestion (AD), as one of the oldest human biotechnology, has attracted revived research focus on the underpinning biological principle in recent years due to its potential in renewable green energy. With the assistance of the latest 454 deep sequencing technology, two independent studies were conducted with a shared goal to understand the operational influences on the AD microbiology from the unprecedented depth and breadth of genetic information. The first study aimed to decipher the contribution of a newly-devised waste sludge pretreatment method, which promised significant improvement in downstream biogas production. The first application of whole genome metagenomic approach on this topic revealed extensive shifts in both microbial and functional consortia towards higher biodegradation after pretreatment; meanwhile dominant acetoclastic and hydrogenotrophic methanogenesis pathways were identified concurrently with an alternative enzymology in Methanosaeta. The second study focused on the temporal dynamics of bacteria residing in production-scale biogas bioreactor coupled with multiple-sampling strategy for a realistic description of the actual microbial structure. Both bacterial fingerprint marked by feedstock and evolutionary drive towards biodegradation were revealed by 16S rDNA amplicon multiplex pyrosequencing, where clustering analyses further delineated the taxonomic plasticity and functional resilience of the bacterial communities over time. Phylogeny coverage of the highly diverse population was also improved by the adopted strategy, providing insights for sampling and sequencing standards. Altogether, the combined results garnered knowledge enrichment to the relationship between AD microbiology and operational parameters, which will assist the design of more efficient bioenergy platform in future.
published_or_final_version
Biological Sciences
Master
Master of Philosophy

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38

Batista, Ieda Hortêncio. "Biorremediação de ambientes aquáticos contaminados por resíduos de petróleo: um estudo com bactérias isoladas de eichornia crassipes na Amazônia." Universidade Federal do Amazonas, 2009. http://tede.ufam.edu.br/handle/tede/3116.

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Made available in DSpace on 2015-04-20T12:31:44Z (GMT). No. of bitstreams: 1 Tese Ieda.pdf: 2549784 bytes, checksum: a9a4b9fb883e1aa2757719de2c81ea18 (MD5) Previous issue date: 2009-06-24
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Biodiversity is a fundamental element for biotechnology development, especially in Amazon because its incontestable potential. One aspect of high interest is the search for management mechanisms that can promote environmental quality, ensuring the maintenance of natural features of ecosystems. In this context is located an important biotechnology tool that is the bioremediation of environments contaminated with toxic and recalcitrant compounds. Thus the exploration of microrganisms for use in these processes has been a challenge. This work presents a study about sample of bacterial community associated with the aquatic macrophyte Eichornia crassipes, assessing their potential for biodegradation of petroleum hydrocarbons. Selective isolations and preliminary identification of some of the isolates by region of 16S ribosomal DNA sequences to compare with the Gen Bank were done. The potential to produce biossurfactantes was evaluated by the activity of bacteria in emulsification. The growth of strains was assessed by mineral medium with hydrocarbons mixing and mineral medium with crude oil. The rate of toxicity was evaluated in mixture of hydrocarbon extracts with the five strains that showed the best growth. Considering the results of these first tests, it was produced a consortium with bacteria more efficient. It was evaluated the degradation of aliphatic and aromatic hydrocarbons in experiment containing Amazon river water, using the techniques of bioaugmentation and biostimulation. There were isolated 71 bacteria, 42 epiphytic and 29 endophytic. The preliminary identification revealed the predominance of the genera Acinetobacter, Pseudomonas, Bacillus and Stenotrophomonas. There was more bacterial growth in medium with crude oil, especially the strain Stenotrophomonas sp,. reaching around 13.4 x106 UFCs / mL. The methods used in bacterial growth indicated the degradation of petroleum hydrocarbons, whereas they were the sole source of carbon. Highlighted in the production of biossurfactantes the strains Methylobacterium sp and Stenotrophomonas radiotolerans, with better results in the medium with oil. The indices of toxicity showed better results in extracts of bacterial growth compared to control extracts. The strains that showed better results were used for consortium production: Stenotrophomonas sp., Uncultured Klebsiella sp., Enterobacter sp., Methylobacterium radiotolerans and Acinetobacter baumannii. In the experimental design with the consortium, the results showed that the main effect of all parameters studied influenced the degradation of the hydrocarbons studied, however the addition of the consortium was the most important factor in this decline, demonstrating the potential of these strains for use in future processes of bioremediation.
A biodiversidade é elemento fundamental para o desenvolvimento da Biotecnologia, em especial na Amazônia devido sua inconteste potencialidade. Um dos aspectos de elevado interesse é a busca por mecanismos de gestão que possam promover a qualidade ambiental, garantindo a manutenção das características naturais dos ecossistemas. Neste contexto situa-se uma importante ferramenta biotecnológica que é a biorremediação de ambientes contaminados por compostos tóxicos e recalcitrantes. Assim, a prospecção de microrganismos para uso nesses processos tem sido um desafio permanente. No presente trabalho realizou-se estudo de amostra da comunidade bacteriana associada à macrófita aquática Eichornia crassipes, avaliando seu potencial de biodegradação de hidrocarbonetos de petróleo. Foi feito isolamento seletivo e identificação preliminar de parte dos isolados por meio da região do DNA ribossomal 16S com comparação com sequências do Gen Bank. Verificou-se o potencial para a produção de biossurfactantes por meio da avaliação da atividade de emulsificação em cepas bacterianas. O crescimento de cepas foi avaliado em meio mineral com mistura de hidrocarbonetos e em meio mineral com petróleo bruto. O índice de toxicidade foi avaliado nos extratos dos meios com mistura de hidrocarbonetos das cinco cepas que apresentaram melhor crescimento. Considerando os resultados destes primeiros testes, foi produzido um consórcio com as cepas bacterianas mais eficientes. Este consórcio foi avaliado quanto à degradação de hidrocarbonetos alifáticos e aromáticos em experimento contendo água de rio da Amazônia, sendo utilizadas as técnicas de bioaumentação e bioestimulação. Obteve-se no isolamento 71 bactérias, sendo 42 epifíticas e 29 endofíticas. A identificação preliminar revelou a predominância dos gêneros Acinetobacter, Pseudomonas, Bacillus e Stenotrophomonas. Verificou-se melhor crescimento bacteriano no meio com petróleo bruto, destacando-se a cepa Stenotrophomonas sp. que atingiu cerca de 13,4x106 UFCs/mL. O crescimento bacteriano nos meios utilizados indicou a degradação dos hidrocarbonetos de petróleo, considerando que estes eram a única fonte de carbono. Destacaram-se na produção de biossurfactantes as cepas Stenotrophomonas sp e Methylobacterium radiotolerans, com melhores resultados no meio com petróleo. Os índices de toxicidade mostraram melhores resultados nos extratos do crescimento bacteriano em comparação aos extratos controles. As cepas que demonstraram melhores resultados e que foram utilizadas para a produção do consórcio foram Stenotrophomonas sp., Uncultured Klebsiella sp., Enterobacter sp., Methylobacterium radiotolerans e Acinetobacter baumannii. No planejamento experimental com o consórcio, os resultados obtidos demonstraram que o efeito principal de todos os parâmetros analisados influenciaram na degradação dos hidrocarbonetos avaliados, entretanto a adição do consórcio foi o fator mais importante nesta degradação, demonstrando o potencial destas linhagens para uso em futuros processos de biorremediação.

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39

Nancucheo, Ivan. "Acidophillic consortia and microbial interactions involved in securing mineral wastes and remediating mine waters." Thesis, Bangor University, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.540414.

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40

Chan, On-chim, and 陳安潛. "Characterization of microbial consortia in anaerobic granular sludge: a ribosomal RNA-based molecular approach." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2000. http://hub.hku.hk/bib/B31239924.

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41

Pietrzyk, Julian Darius. "Use of microbial consortia for conversion of biomass pyrolysis liquids into value-added products." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31562.

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Lignocellulosic biomasses are considered promising feedstocks for the next generation of biofuels and chemicals; however, the recalcitrance of lignocellulose remains a barrier to its utilisation over conventional sources. Pyrolysis is the heating of biomass to several hundred degrees Celsius in the absence of oxygen, which can thermally depolymerise lignocellulose. Products of pyrolysis are a solid biochar, liquid bio-oil and syngas. Biochar has roles in both carbon sequestration and soil amendment however bio-oil has no defined use, despite a high concentration of fermentable sugars. Bio-oil is a complex organic microemulsion with a host of biocatalyst inhibitors that makes its microbial degradation a challenge. In this work, the use of aerobic cultures using microbial communities isolated from natural environments saw limited potential; however, the use of anaerobic digestion (AD) successfully generated a higher volume of biogas from reactors with bio-oil than controls. Biogas yield test reactors were set up with anaerobic digestate from a wastewater treatment plant as the substrate for degradation and conversion of bio-oils. Next-generation 16S rRNA gene sequencing was utilised to characterise the communities in the reactors while the ultrahigh resolution mass spectrometry technique of Fourier transform ion cyclotron resonance (FT-ICR) was used for characterisation of the chemical changes occurring during AD. Both sets of high-resolution data were additionally combined for multivariate analysis and modelling of the microbial genera that correlated best with the changes in digestate chemistry. This represents a novel analysis method for the microbial degradation of complex organic products. Bio-oil from common lignocellulosic feedstock was the most easily degradable by the AD communities, with significant inhibition observed when bio-oils from anaerobic digestate and macroalgae were used. Additionally it was found that the inclusion of biochars that were pre-incubated in anaerobic digestate prior to use in AD were capable of significantly reducing the lag time observed for biogas production in bio-oil-supplemented reactors. The addition of biochars that were not pre-incubated had no effect on biogas production. Specific inhibition of methanogenesis was also capable of causing the digestates to accumulate volatile fatty acids (VFAs) as a product of greater value than biogas. Scale-up experiments will be required to confirm the precise practicalities of the addition of bio-oil to AD as well as to establish the potential for isolation and purification of VFAs.

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42

Sakuntala, Saijai. "Analysis and application of microbial consortia involved in ammonification and nitrification for organic hydroponics." Kyoto University, 2016. http://hdl.handle.net/2433/217184.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第20009号
農博第2193号
新制||農||1045(附属図書館)
学位論文||H28||N5018(農学部図書室)
33105
京都大学大学院農学研究科応用生命科学専攻
(主査)教授小川順, 教授阪井康能, 教授栗原達夫
学位規則第4条第1項該当

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43

Xia, Yu, and 夏雨. "Exploring microbial structure and carbohydrate metabolism of thermophilic anaerobic cellulose-degrading consortia by metagenomics based on next generation sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/195961.

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The pressing need for clean renewable energy sources has aroused worldwide research interest on the exploration of biofuels produced from lignocellulosic feedstock (e.g. forestry or agricultural residues and municipal wastes). The general absence of cost-effective method to overcome the recalcitrant nature of cellulosic biomass is the major challenge for the industrialization of this so-called second-generation biofuel. With the purpose to enhance our understanding of the fundamental mechanism of thermophilic microbial cellulose conversion process, we used culture-independent metagenomic analysis based on Next Generation Sequencing to explore the physiological ecology of thermophilic cellulolytic microbial community and more importantly to discover metabolic potentials. During the enrichment of thermophilic cellulolytic consortium, noticeable effects of co-substrate and pH was observed and subsequently investigated. Based on the community structure revealed by 16S rRNA gene sequencing at various pH values, we concluded that keeping pH higher than 6.0 was crucial to maintain effective cellulose conversion because the growth of Thermoanaerobacterium over other more efficient cellulolytic populations could be practically avoided. Given in mind that uncharacterized microbial populations may possess critical enzymatic components that are essential for the breakdown of cellulosic feedstock, gene-centric metagenomic pipeline was developed to discover genes that are functionally beneficial for thermophilic cellulose hydrolysis. Aside from that, metagenomic gene mining based on functional prediction using HMM (Hidden Markov Model) showed higher positive ratio in identifying novel carbohydrate-active genes than that of functional screening. Without cultivation, near complete genomes of the major thermophilic cellulose degraders were recovered from the metagenome by a gene binning pipeline combining tetranucleotide frequency based primary k-means clustering and subsequent scaffolding with paired-end relationship between two reads (sequences). Furthermore, by quantifying the transcriptional activities of various carbohydrate-active genes in the metatranscriptome of the enriched thermophilic cellulose-degrading consortium, we disclosed significance of enzymes of GH09 and GH48 which had been underestimated by previous metagenomic studies. Eventually, metagenomic survey of various sludge samples collected at specific operational conditions helped to confirm the metabolism potential of thermophilic sludge in cellulose up taking by possessing more enzymes of GH05 and GH04 families.
published_or_final_version
Civil Engineering
Doctoral
Doctor of Philosophy

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44

Pereira, Mariana Rangel. "Caracterização funcional e estrutural de enzimas lipolíticas de um consórcio microbiano degradador de óleo diesel." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-04012016-073001/.

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O comércio mundial de enzimas industriais estava estimado em 2.3 bilhões de dólares entre detergentes (U$ 789 milhões), aplicações alimentícias (U$ 634 milhões), agricultura (U$ 237 milhões), entre outros. Neste contexto, as enzimas lipolíticas estão atraindo enorme atenção devido ao seu potencial biotecnológico, visto que estas podem catalisar múltiplas reações (hidrólise, acidólise, interesterificação e glicerólise). Enzimas lipolíticas de origem microbiana são economicamente atrativas por serem biodegradáveis, atuarem normalmente em condições brandas, e serem quimio-seletivas propiciando à indústria farmacêutica a obtenção de drogas com efeito colateral reduzido. Neste projeto, quatro genes potenciais codificadores de esterases/lipases, advindos de uma biblioteca metagenômica de um consórcio microbiano degradador de óleo diesel, foram clonados em vetores de expressão e expressos em Escherichia coli BL21 (DE3), e as proteínas correspondentes foram submetidas a ensaios funcionais e estruturais.
The global trade of industrial enzymes is estimated at 2.3 billion U.S. dollars, divided mainly between detergents (US$ 789 million), food applications (US$ 634 million), and agriculture (US$ 237 million). Within this trade, lipolytic enzymes have attracted enormous attention because of their biotechnological potential as catalysts of multiple reaction types (including hydrolysis, acidolysis, interesterification and glycerolysis). Lipolytic enzymes of microbial origin are economically attractive because they are easily biodegradable, usually act in mild conditions, and are chemo-selective, providing the pharmaceutical industry a method for obtaining drugs with reduced side effects. In this project, four individual genes encoding putative esterases/lipases identified in a metagenomic library obtained from a microbe consortium isolated from diesel oil-contaminated soil were cloned into expression vectors and expressed in Escherichia coli BL21 (DE3), and their corresponding recombinant proteins were used for functional and structural studies.

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45

Patel, Jignasa. "Meta-Transcriptome Profiles of the Marine Sponge, Axinella corrugata and its Microbial Consortia: A Pyrosequencing Approach." NSUWorks, 2012. http://nsuworks.nova.edu/occ_stuetd/174.

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Marine micro-organisms are important components of various biogeochemical cycles, complex food webs and ecological niches. Metagenomic sequencing can provide rapid profile of metabolic activities within the sponge and resident microbes. However, the study of metatranscriptomes from sponges using high throughput sequencing technology has only recently begun. Through this study we isolated, characterized and compared metatranscriptome profiles of Axinella corrugata host and sponge-specific microbial communities using 454 pyrosequencing technology. Four cDNA libraries (two eukaryotic and two prokaryotic) were generated from Axinella corrugata sponge samples collected in December 2009 and May 2010, and were characterized to a) reveal which metabolic genes were actively expressed and b) reveal possible interactions between the sponge and its microbial symbionts. The techniques used for isolation of mRNA and cDNA normalization also helped in optimization of whole-transcriptome amplification. More than 130,000 ESTs were generated for the two seasonal sponge samples and the metagenomic data sets were analyzed using bioinformatics tool, MG-RAST. Several stress-related transcripts were found which can increase our understanding of sensitivity of the sponge to changes in physical parameters in nature. The involvement of the sponge and its microbial consortia is depicted through actively expressed nitrogen and sulfur metabolism genes. Novel genes involved in several functional pathways may be discovered upon further studying hypothetical genes found across all four metagenomic data sets. Metatranscriptomic data sheds light on the functional role of microbes within the sponges and the extent of their involvement in sponge metabolism. 16S rRNA analysis was also carried out using genomic DNA of the same samples, to better elucidate the bacterial taxa abundance in the sponge. This study provides a profile of active mRNA trancripts in Axinella corrugata which include eukaryotic as well as prokaryotic sequences. The data analysis of this research provides new information at the cross-disciplinary interface between molecular biology and computational science.

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Bécaert, Valérie. "Production et caractérisation d'un consortium microbien pour le traitement de sol contaminé aux produits de préservation du bois." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape8/PQDD_0021/MQ57392.pdf.

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Lazuka, Adele. "Production de synthons par des consortia microbiens à partir de paille de blé : approches macrocinétique, enzymatique et métaprotéomique." Thesis, Toulouse, INSA, 2018. http://www.theses.fr/2018ISAT0049.

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Alors que la biomasse lignocellulosique constitue le plus grand réservoir de carbone renouvelable sur Terre, sa valorisation reste encore limitée par sa récalcitrance à la dégradation. Bien que sa bioconversion ait été largement étudiée dans le cadre de la production de bio-combustibles, d’autres approches comme la plateforme des carboxylates permettent de produire des intermédiaires et composés chimiques d’intérêt industriel. De plus dans la Nature, la lignocellulose est prise en charge par des écosystèmes microbiens qui déploient une large diversité enzymatique. Ainsi, nous avons étudié l’enrichissement de communautés microbiennes naturelles issues d’écosystèmes digestifs animaux sur paille de blé et en conditions d’anaérobiose en bioréacteur contrôlé, en vue de produire des carboxylates. Via une procédure de culture en bioréacteur batch séquentiel, deux communautés stables ont été obtenues à partir de rumen bovin (nommée RWS) et de microbiote intestinal de termite de l’espèce Nasutitermes ephratae (nommée TWS). RWS et TWS dégradaient 55% et 45% du substrat non prétraité, en produisant 6,5 g-AGV.L-1 et 5,8 g-AGV.L-1 en 15 jours, respectivement. En combinant des approches de suivi dynamique des paramètres macroscopiques, des activités enzymatiques impliquées dans la dégradation du substrat, ainsi que par une étude métaprotéomique dynamique, nous avons pu révéler des particularités intéressantes entre ces deux communautés microbiennes. De plus, la communauté RWS a été soumise à des prétraitements du substrat permettant d’augmenter sa vitesse de production de carboxylates
Lignocellulose (LC) is the most abundant terrestrial reservoir of renewable carbon on Earth but its valorization is still limited due to its recalcitrance. In the field of bioconversion, the production of biofuels has been widely studied, whereas others valorization routes – as the carboxylate platform- enable the production of intermediate building blocks or industrial componuds. However in Nature, the recycling of LC is performed by microbial consortia which deploy complex arsenals of enzymes to deconstruct LC. In this PhD thesis we studied the anaerobic enrichment of natural microbial communities from animal digestive systems, aiming to production of carboxylates from wheat straw as substrate. Thanks to a sequencial batch reactor procedure, we obtained two stable communities from bovine rumen (named RWS) and intestinal microbiote from the termite species Nasutitermes ephratae (named TWS). RWS and TWS transformed 55% and 45% VS unpretreated wheat straw into 230 mCmol-AGV.L-1 (6.5 g-AGV.L-1) and 180 mCmol-AGV.L-1 (5.8 g-AGV.L-1) within 15 days, respectively. Combing the dynamic measurment of macroscopic parameters (i.e. degradation and production) to the quantification of enzymatic activities involved in LC degradation, as well as to a dynamic metaproteomic approach we revealed some interesting features between these two consortia. Moreover, RWS was used to study the impact of pretreatments on its acidogenic biological potential

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VOLPATO, SILVIA. "Controllo qualità dei microrganismi." Doctoral thesis, Università degli studi di Modena e Reggio Emilia, 2020. http://hdl.handle.net/11380/1201052.

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L'agricoltura simbiotica è un nuovo processo di coltivazione che prevede l’utilizzo di microrganismi benefici, come funghi, batteri e lieviti che rendono la rizosfera (lo spazio da 1 a 3 millimetri che avvolge le radici delle piante), estremamente ricca di micro-organismi cosiddetti “buoni” o funzionali. Tali microorganismi costituiscono il biota microbico che oltre a fungere da supporto per il benessere delle piante che li ospitano può contribuire all’azione antagonista nei confronti di microrganismi potenzialmente patogeni. Numerosi prodotti a base microbica sono disponibili sul mercato: essi sono commercializzati come biofertilizzanti, biostimolanti, biopesticidi, promotori della crescita, induttori di resistenza, ecc… Pertanto, l’obiettivo della ricerca è quello di stabilire delle regole, delle procedure e dei protocolli da usarsi durante la produzione industriale di tali bioformulati, in modo da ottenere una formulazione microbica la cui qualità sia controllata durante il processo produttivo. Solamente operando un controllo di qualità oggettivo e preciso è possibile ottenere inoculi microbici efficienti, efficaci e sostenibili, tali che possano essere una valida alternativa ai pesticidi chimici. Partendo da un prodotto biostimolante commerciale molto noto, Micosat F UNO, costituito da un consorzio microbiologico, la ricerca è stata orientata allo sviluppato un "protocollo di qualità" considerando sia i singoli microrganismi presenti sia il consorzio nel suo insieme. I singoli componenti sono stati selezionali, accuratamente identificati, studiati e caratterizzati considerando le interazioni microrganismo-microrganismo e pianta-microrganismo. Di un microrganismo, in particolare, è stato sequenziato l’intero genoma e studiate le possibili vie biosintetiche al fine di dare supporto scientifico al suo ruolo di microrganismo benefico o funzionale e facilitarne il suo brevetto e inquadramento normativo come sostanza attiva. Infine è stato analizzato il processo produttivo ed identificati i punti di controllo al fine di ottenere un prodotto commerciale qualitativamente valido.
Symbiotic agriculture is a new cultivation process that involves the use of microbial inoculants, such as fungi, bacteria and yeasts that make the rhizosphere (the space from 1 to 3 millimeters that envelops the roots of plants), extremely rich in beneficial microorganisms. These microorganisms constitute the microbial biota which, in addition to acting as a support for the well-being of the plants that host them, can contribute to the antagonistic action against potentially pathogenic microorganisms. Several products based on microorganisms are available on the market: they are advertised as biofertilisers, biostimulants, biopesticides, growth enancers, resistance inducers, etc... Therefore, the aim of the research is to set up rules, procedures and protocols to be used during the industrial production of microbials, in order to obtain an efficient, effective and sustainable microbial formulation, whose quality is checked along the production chain. Only by performing quality control checks, microbials can be a valid alternative to chemical pesticides. Research started from a well known, commercial biosimulant, namedMicosat F UNO, consisting of a microbiological consortium. Research was oriented towards the development of a "quality protocol" considering both the individual microorganisms present in the product and the consortium as a whole. The individual components were selected, thoroughly identified, studied and characterized considering their microbe-microbe and plant-microbe interactions. Full genome sequence and biochemical pathways were done and characterised for one particular benficial organism, in order to scietifically support its role as beneficial organisms and as possible, patentable active substance. Additionally, the production process was analyzed and control points were identified in order to obtain a qualitatively valid commercial product.

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Goerges, Stefanie. "Microbial consortia from smear-ripened cheese biodiversity, incidence of commercial starter microorganisms and anti-listerial activity of yeasts /." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=978998758.

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Almeida, Ana Carolina Maganha de [UNESP]. "Estudo da biodegradação de corantes azóicos por inóculo proveniente de biodigestor anaeróbio de alimentos." Universidade Estadual Paulista (UNESP), 2008. http://hdl.handle.net/11449/94980.

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Made available in DSpace on 2014-06-11T19:27:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-04-17Bitstream added on 2014-06-13T20:35:52Z : No. of bitstreams: 1 almeida_acm_me_rcla.pdf: 908754 bytes, checksum: c67dc89a044d50c60fbdc87558d820a3 (MD5)
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
O uso de biodigestores anaeróbios é uma versátil alternativa para produção de biomassa microbiana a partir de resíduos orgânicos. O reaproveitamento das sobras alimentares, produzidas pelo Restaurante Universitário da Unesp Campus Rio Claro, foi o responsável pela produção de um Inóculo Líquido Residual (I.L.R.) utilizado como agente biodegradador e biossorvente para os corantes azóicos “Acid Yellow 25” e “Direct Violet 51” de importante destaque industrial. O projeto dividiu-se em duas etapas, a primeira contemplando a produção do inóculo em grande escala (biodigestor de fluxo contínuo) e a segunda em escala de laboratorial (biodigestor em batelada). Os resultados da análise microbiológica revelaram a presença predominante de bactérias acidogênicas e de leveduras em menor escala. Estes microrganismos foram aplicados como inóculo nas soluções dos dois corantes em condições variadas de pH (2,50; 4,50 e 6,50). A análise dos produtos formados a partir da interação com o I.L.R demonstraram as potencialidades biodegradativas e biossorventes do consórcio microbiano e sua ação diferenciada de acordo com a mudança de pH.As aminas aromáticas e sulfonadas, formadas após a redução da ligação azóica, foram estudada a partir do sobrenadante dos tratamentos dos corantes através do uso dos métodos difundidos do UV-Vis e do HPLC aliados às analises vanguardistas do FTIR.
The use of anaerobic bioreactor is a versatile alternative for the production of microbial biomass from organic waste. The reuse of the leftovers from the University Restaurant of Unesp Rio Claro Campus, was responsible for producing a Residual Liquid Inoculum (R.L.I.) used as a biodegradator and biosorptive agent for two azo dyes Acid Yellow 25 and Direct Violet 51 with a major role in the industrial scenery. The project was divided in two steps, the first covering the production of the inoculum in large scale (continuous flow bioreactor) and the second in bench-scale (in-batch bioreactor) The results of the microbiological analysis revealed a predominant presence of acidogenic bacteria and a few yeasts. These microorganisms were used as inoculum in both dye solutions at different pH conditions (2.50, 4.50 and 6.50) The analysis of the resultant by-products demonstrated the biodegradation and biosorptive potential of the consortium and its differentiated pH-regulated action. The aromatic sulfonated amines, formed after the reduction of the azoic bounds, were studied through the spreaded analytic methods of UV-Vis and HPLC in conjunct with the vanguard of FTIR device.

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