Nessa pesquisa foram testados separadamente dois inóculos solo/compostagem e lodo termofílico de reator anaeróbio de manta de lodo e fluxo ascendente (UASB) do tratamento de vinhaça em relação ao potencial de produção de compostos de valor agregado a partir do bagaço de cana-de-açúcar (BCA) em reatores em batelada em condição mesofílica e termofílica, respectivamente. Pré-tratamentos térmico, ácido e diluição seriada foram aplicados ao inóculo termofílico, como tentativa de inibir as arqueias metanogênicas. A diluição seriada foi o pré-tratamento aplicado em ambos os inóculos, mesofílico e termofílico, para obtenção de consórcio de bactérias fermentadoras. Cinco meios de culturas foram testados como fonte de nutrientes para o crescimento de bactérias celulolíticas e fermentadoras. Dentre esses foi selecionado para os ensaios mesofílicos e termofílicos, o meio de cultura mais complexo suplementado com extrato de levedura. O BCA foi submetido à pré-tratamento biológico, térmico, explosão a vapor, deslignificação alcalina e hidrotérmico sendo o último utilizado nos ensaios do planejamento fatorial. O efeito das variáveis independentes de concentração de extrato de levedura e temperatura foi avaliado na produção de hidrogênio, metano e ácidos orgânicos a partir do inóculo termofílico. O efeito da concentração de extrato de levedura e substrato (BCA) foi avaliado na produção de bioprodutos a partir do inóculo mesofílico (37ºC). A maior produção de hidrogênio foi de 17,30 mmol/L à 60ºC e 3,42 g/L de extrato de levedura para a condição termofílica. Em relação aos ensaios mesofílicos observou-se 1,53 mmol/L com 3,42 e 5,00 g/L de extrato de levedura e BCA, respectivamente. Caracterização taxonômica e funcional dos microrganismos dos reatores de melhor desempenho de produção de hidrogênio dos planejamentos fatoriais termofílico e mesofílico foi realizada por análise Metagenômica (Illumina HiSeq). Nestas condições foram identificados microrganismos dos domínios Archaea, Bacteria, Eukarya, além de vírus. Para o domínio Bacteria foram identificados microrganismos celulolíticos e fermentadores como Coprothermobacter e Clostridium, enquanto para o domínio Archaea, foram identificadas metanogênicas hidrogenotróficas e acetoclásticas, como Methanothermobacter e Methanosarcina. Foram ainda identificados genes codificantes de enzimas catalisadoras da degradação de celulose, hemicelulose e lignina, constituintes principais da biomassa lignocelulósica utilizada como substrato, tais como celulase, carboxylesterase e 2-ácido hidroxi oxidase, respectivamente. Microrganismos aderidos no BCA in natura foram observados por microscopia eletrônica de varredura (MEV) e identificados por sequenciamento do RNAr 16S, e semelhantes a Streptomyces, Paenibacillus, Stenotrophomonas, Sphingomonas. Os microrganismos do lodo termofílico, solo e compostagem foram caracterizados por sequenciamento do RNAr 16S, e foram semelhantes a Clostridium, Thermoanaerobacter, Caloramator, Anaerobaculum, Tatlockia, Coprothermobacter, Dysgonomonas, Coprococcus, Sporomusa, Methanobacterium, Methanothermobacter, Methanosaeta, dentre outros. / In the present study, two inoculum (soil/compost and thermophilic sludge from upflow anaerobic sludge blanket from vinasse treatment) were separately evaluated as potential to production of value-added products from sugarcane bagasse in mesophilic and thermophilic conditions, respectively. Thermal, acid and serial dilution pretreatments were performed in the thermophilic inoculum to inhibition of methanogenic archaea. Serial dilution was applied into the mesophilic inoculm. Five culture medium were evaluated as nutritional source to enrichment of cellulolytic and fermenters bacteria; between then, the most complex one, supplemented with yeast extract was selected for the mesophilic and thermophilic bioassays. The sugarcane bagasse (SCB) was submitted to biological, thermal, stem explosion alkaline delignification and hydrothermal pretreatments, and the last one was used as substrate for the factorial designs. The effect of independent variables, such as yeast extract and temperature were evaluated on the hydrogen, methane and organic acids production from the thermophilic inoculum. The effect of yeast extract and substrate (SCB) concentrations were evaluated on the bioproducts generation from the mesophilic inoculum. The highest hydrogen production of 17.3 mmol/L was obtained at 60ºC and 3.42 g/L of yeast extract, on the thermophilic factorial design. In relation to the mesophilic factorial design, obtained 1.53 mmol/L of hydrogen with 3.42 and 5.00 g/L of yeast extract and SCB, respectively. Taxonomical and functional characterizations from the microorganisms were performed in the reactors with highest hydrogen production on the factorial designs using Metagenomics analysis (Illumina HiSeq). In both condition, mesophilic and thermophilic were found microorganisms from Archaea, Bacteria, Eukarya domin, besides Viruses. Concerning the Bacteria domain were found cellulolytic and fermenters microorganisms similar to Coprothermobacter and Clostridium, whiles for Archaea domain were identified hydrogenotrophic and acetoclastic methanogenic similar to Methanothermobacter and Methanosarcina. There were obtained genes coding to enzymes related to the cellulose, hemicellulose and lignin degradation such as carboxylesterase e 2-acid-hydroxioxidase, respectively. Microorganisms adhered into the in natura SCB fiber were observed by scanning electronic microscopy (SEM) and identified by 16 S rRNA sequencing, mainly as similar to Streptomyces, Paenibacillus, Stenotrophomonas, Sphingomonas. The microorganisms from the thermophilic sludge, soil and composting were also characterized by 16S RNAr sequencing and were similar to Clostridium, Thermoanaerobacter, Caloramator, Anaerobaculum, Tatlockia, Coprothermobacter, Dysgonomonas, Coprococcus, Sporomusa, Methanobacterium, Methanothermobacter, Methanosaeta, among others.

Nessa pesquisa foram testados separadamente dois inóculos solo/compostagem e lodo termofílico de reator anaeróbio de manta de lodo e fluxo ascendente (UASB) do tratamento de vinhaça em relação ao potencial de produção de compostos de valor agregado a partir do bagaço de cana-de-açúcar (BCA) em reatores em batelada em condição mesofílica e termofílica, respectivamente. Pré-tratamentos térmico, ácido e diluição seriada foram aplicados ao inóculo termofílico, como tentativa de inibir as arqueias metanogênicas. A diluição seriada foi o pré-tratamento aplicado em ambos os inóculos, mesofílico e termofílico, para obtenção de consórcio de bactérias fermentadoras. Cinco meios de culturas foram testados como fonte de nutrientes para o crescimento de bactérias celulolíticas e fermentadoras. Dentre esses foi selecionado para os ensaios mesofílicos e termofílicos, o meio de cultura mais complexo suplementado com extrato de levedura. O BCA foi submetido à pré-tratamento biológico, térmico, explosão a vapor, deslignificação alcalina e hidrotérmico sendo o último utilizado nos ensaios do planejamento fatorial. O efeito das variáveis independentes de concentração de extrato de levedura e temperatura foi avaliado na produção de hidrogênio, metano e ácidos orgânicos a partir do inóculo termofílico. O efeito da concentração de extrato de levedura e substrato (BCA) foi avaliado na produção de bioprodutos a partir do inóculo mesofílico (37ºC). A maior produção de hidrogênio foi de 17,30 mmol/L à 60ºC e 3,42 g/L de extrato de levedura para a condição termofílica. Em relação aos ensaios mesofílicos observou-se 1,53 mmol/L com 3,42 e 5,00 g/L de extrato de levedura e BCA, respectivamente. Caracterização taxonômica e funcional dos microrganismos dos reatores de melhor desempenho de produção de hidrogênio dos planejamentos fatoriais termofílico e mesofílico foi realizada por análise Metagenômica (Illumina HiSeq). Nestas condições foram identificados microrganismos dos domínios Archaea, Bacteria, Eukarya, além de vírus. Para o domínio Bacteria foram identificados microrganismos celulolíticos e fermentadores como Coprothermobacter e Clostridium, enquanto para o domínio Archaea, foram identificadas metanogênicas hidrogenotróficas e acetoclásticas, como Methanothermobacter e Methanosarcina. Foram ainda identificados genes codificantes de enzimas catalisadoras da degradação de celulose, hemicelulose e lignina, constituintes principais da biomassa lignocelulósica utilizada como substrato, tais como celulase, carboxylesterase e 2-ácido hidroxi oxidase, respectivamente. Microrganismos aderidos no BCA in natura foram observados por microscopia eletrônica de varredura (MEV) e identificados por sequenciamento do RNAr 16S, e semelhantes a Streptomyces, Paenibacillus, Stenotrophomonas, Sphingomonas. Os microrganismos do lodo termofílico, solo e compostagem foram caracterizados por sequenciamento do RNAr 16S, e foram semelhantes a Clostridium, Thermoanaerobacter, Caloramator, Anaerobaculum, Tatlockia, Coprothermobacter, Dysgonomonas, Coprococcus, Sporomusa, Methanobacterium, Methanothermobacter, Methanosaeta, dentre outros. / In the present study, two inoculum (soil/compost and thermophilic sludge from upflow anaerobic sludge blanket from vinasse treatment) were separately evaluated as potential to production of value-added products from sugarcane bagasse in mesophilic and thermophilic conditions, respectively. Thermal, acid and serial dilution pretreatments were performed in the thermophilic inoculum to inhibition of methanogenic archaea. Serial dilution was applied into the mesophilic inoculm. Five culture medium were evaluated as nutritional source to enrichment of cellulolytic and fermenters bacteria; between then, the most complex one, supplemented with yeast extract was selected for the mesophilic and thermophilic bioassays. The sugarcane bagasse (SCB) was submitted to biological, thermal, stem explosion alkaline delignification and hydrothermal pretreatments, and the last one was used as substrate for the factorial designs. The effect of independent variables, such as yeast extract and temperature were evaluated on the hydrogen, methane and organic acids production from the thermophilic inoculum. The effect of yeast extract and substrate (SCB) concentrations were evaluated on the bioproducts generation from the mesophilic inoculum. The highest hydrogen production of 17.3 mmol/L was obtained at 60ºC and 3.42 g/L of yeast extract, on the thermophilic factorial design. In relation to the mesophilic factorial design, obtained 1.53 mmol/L of hydrogen with 3.42 and 5.00 g/L of yeast extract and SCB, respectively. Taxonomical and functional characterizations from the microorganisms were performed in the reactors with highest hydrogen production on the factorial designs using Metagenomics analysis (Illumina HiSeq). In both condition, mesophilic and thermophilic were found microorganisms from Archaea, Bacteria, Eukarya domin, besides Viruses. Concerning the Bacteria domain were found cellulolytic and fermenters microorganisms similar to Coprothermobacter and Clostridium, whiles for Archaea domain were identified hydrogenotrophic and acetoclastic methanogenic similar to Methanothermobacter and Methanosarcina. There were obtained genes coding to enzymes related to the cellulose, hemicellulose and lignin degradation such as carboxylesterase e 2-acid-hydroxioxidase, respectively. Microorganisms adhered into the in natura SCB fiber were observed by scanning electronic microscopy (SEM) and identified by 16 S rRNA sequencing, mainly as similar to Streptomyces, Paenibacillus, Stenotrophomonas, Sphingomonas. The microorganisms from the thermophilic sludge, soil and composting were also characterized by 16S RNAr sequencing and were similar to Clostridium, Thermoanaerobacter, Caloramator, Anaerobaculum, Tatlockia, Coprothermobacter, Dysgonomonas, Coprococcus, Sporomusa, Methanobacterium, Methanothermobacter, Methanosaeta, among others.

Submitted by Mario BC (mario@bc.ufrpe.br) on 2016-11-28T14:07:58Z No. of bitstreams: 1 Michelle Barros Pantoja.pdf: 1641953 bytes, checksum: 3ccb5972f0e3ceb3779eebd3c7ee502f (MD5) / Made available in DSpace on 2016-11-28T14:07:58Z (GMT). No. of bitstreams: 1 Michelle Barros Pantoja.pdf: 1641953 bytes, checksum: 3ccb5972f0e3ceb3779eebd3c7ee502f (MD5) Previous issue date: 2015-02-26 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The peanut (Arachis hypogaea) is an oleaginous plant belonging to the Fabaceae family, native to South America. Its kernels are widely used as a food source and the production of oil. The main producing countries are China, India and the United States, which occupy the 1st, 2nd and 3rd places, respectively, in the ranking of world production. Brazil occupies the 17th position, in which the State of São Paulo stands out with 95% of total production of the country. The peanut is infected by several virus species, which limit the development of the crop in different parts of the world. The objective of this study was to detect the presence of virus in peanut plants in 10 counties of the State of São Paulo. Thirty-five samples (s) from 18 fields (f) were analyzed from Santa Adélia (3f/6s), Lusitânia (1f/1s), Jaboticabal (3f/6s), Itápolis e Pindorama (1f/2s, each), Tupã (4f/8s), Rancharia e Marília (1f/2s, each), Guaimbê (2f/4s) and Guarantã (1f/2s). The maintenance of the virus isolates was done in peanut plants graft inoculated. The isolates were submitted to biological, serological e molecular analyses. For host range study, Lactuca sativa, Capisicum annuum, C. annuum var. 679, C. annuum var. Ikeda, Chenopodium amaranticolor, C. quinoa, Datura stramonium, Gomphrena globosa, Nicotiniana tabacum, N. benthamiana, N. rustica, N. glutinosa, Physalis floridana and Solanum sculentum were mechanically inoculated and the symptoms analyzed. Based on Dot-ELISA results, the presence of the tospoviruses Groundnut ringspot virus (GRSV) (16s), Tomato chlorotic spot virus (TCSV) (6s) and do Tomato spotted wilt virus (TSWV) (3s) was detected. The comparison of the sequence obtained in the RT-PCR test with those deposited in the GenBank, revealed the occurrence of the GRSV. Furthermore, the metagenomic analysis showed the presence of the GRSV, as well as, the potyvirus Peanut motlle virus (PeMoV), both with complete genome. / O amendoim (Arachis hypogaeae L.) é uma oleaginosa pertencente à família Fabaceae, originária da América do Sul. Seus grãos são muito utilizados como fonte de alimento e na produção de óleo. Os principais países produtores são China, Índia e Estados Unidos, que ocupam o 1°, 2° e 3º lugar, respectivamente. O Brasil situa-se na 17ª posição, tendo o Estado de São Paulo contribuído com 95% da produção total do país. O amendoim é hospedeiro de um grande número de espécies de vírus, que limitam o desenvolvimento da cultura em diferentes partes do mundo. O objetivo deste trabalho foi detectar a presença de vírus em plantas de amendoim oriundas de 10 municípios paulistas, sendo analisadas amostras (am) de campos (cam) de Santa Adélia (3cam/6am), Lusitânia (1cam/1am), Jaboticabal (3cam/6am), Itápolis e Pindorama (1cam/2am, cada), Tupã (4cam/8am), Rancharia e Marília (1cam/2am, cada), Guaimbê (2cam/4am) e Guarantã (1cam/2am). Plantas de amendoim foram usadas para manutenção dos isolados virais, empregando-se transmissão sucessivas por meio de enxertias. Os isolados foram submetidos a análises biológicas em gama de hospedeiros, sorológicas pelo método Dot-ELISA e moleculares por RT-PCR e metagenômica. Os hospedeiros indicadores testado foram: Lactuca sativa, Capisicum annuum, C. annuum var. 679, C. annuum var. Ikeda, Chenopodium amaranticolor, C. quinoa, Datura stramonium, Gomphrena globosa, Nicotiniana tabacum, N. benthamiana, N. rustica, N. glutinosa, Physalis floridana e Solanum sculentum. Com base nos resultados do teste Dot-ELISA foi detectada a presença dos tospovírus Groundnut ringspot virus (GRSV) (16am), Tomato chlorotic spot virus (TCSV) (6am) e do Tomato spotted wilt virus (TSWV) (3am). Ao ser comparado os resultados obtidos no sequenciamento (Macrogen) do fragmento obtido no teste RT-PCR, com as sequências disponíveis no GenBank, ficou comprovada ocorrência do GRSV. Por outro lado, a análise metagenômica confirmou a presença do GRSV e detectou o potyvírus Peanut motlle virus PeMoV), ambos com genoma completo.

O Alquilbenzeno Linear Sulfonado (LAS) é um surfactante aniônico de degradação complexa. Via ensaio cinético em batelada ajustou-se modelo de inibição por excesso de substrato na remoção de LAS e matéria orgânica de água residuária de lavanderia comercial (ARLC) em co-digestão com esgoto doméstico (ED). A adição de 50 mg L-1 de etanol (EOH) resultou em maiores valores para velocidade específica de utilização do substrato (robs) e concentração mais elevada de LAS que fornece o maior robs (18,98 mg LAS L-1 e 2,39 mg LAS L-1 na presença e ausência de etanol, respectivamente). Areia com 1,0 mm de diâmetro foi escolhida como material suporte). Objetivou-se otimizar a remoção do surfactante de ARLC + ED (1:3 volume; &#8764; 20 mg LAS L -1) em RLF em escala aumentada (19,8L) através de: (i) adição de etanol em diferentes dosagens; (ii) variação da velocidade ascensional (vasc) aplicada ao leito; e (iii) aumento do tempo de detenção hidráulica (TDH). Desta forma, para TDH de 18 h foram realizadas as seguintes fases operacionais: (I) ARLC + ED + 1,3 velocidade mínima de fluidificação (vmf); (II) ARLC + ED + 50 mg EOH L -1 + 1,3 vmf; (III) ARLC + ED+200 mg EOH L-1 + 1,3 vmf; (IV) ARLC + ED +200 mg L-1 + 1,0 vmf; (V) ARLC + ED + 200 mg L-1 + 0,7 vmf; (VI) ARLC + ED + 100 mg L-1 + 1,0 vmf; e para TDH de 30 h: (VII) ARLC + ED + 1,0 vmf. Não se observou diferença significativa na eficiência de remoção de DQO e LAS (&#8764; 50%; p < 0,5) nas fases I à IV. O decréscimo da vasc (0,7 vmf) resultou em 29% de eficiência de remoção de LAS (V) e o aumento do TDH em 86% de eficiência de remoção de LAS (VII). Nas fases VI e VII observou-se maior remoção de DQO (&#8805; 70%). As menores vasc e 200 mg EOH L-1 favoreceram acúmulo de ácidos no sistema (IV e V). No efluente do RLF foram identificados 17 compostos recalcitrantes. Para vasc = 0,7 vmf, foi observada maior diversidade de compostos recalcitrantes, em sua maioria, ftalatos. Caracterização taxonômica e funcional dos microrganismos para as fases III, IV e V (variação da vasc) e VII (maior eficiência de remoção de LAS e DQO) foi realizada por metagenômica. Foram identificados microrganismos dos domínios Archaea e Bacteria, sendo que a diminuição da vasc resultou em maior abundância relativa de arqueias metanogênicas, como Methanosarcina e genes relacionados a F420 reducing hydrogenase que é transportadora central de elétrons na metanogênese. Diversidade de gêneros foram identificados do domínio Bacteria (Geobacter, Thauera, Pseudomonas, Chryseobacterium, Sulfuricurvum e Sulfurospirillum, etc.) e genes codificadores de enzimas que atuam nas diferentes etapas de degradação do LAS: (a) adição de fumarato (fumarate redutase); (b) beta-oxidação (3-hidroxiacil-CoA desidrogenase); (c) clivagem do anel benzênico (benzoyl-CoA reductase); (d) dessulfonação (Adenylyl-sulfate reductase). Na amostra da fase VII, foram identificados genes relacionados à etapa de dessulfonação com maior abundância relativa, se comparada às demais fases. Para maior vasc observou-se maior abundância relativa de genes relacionados à fosforilação oxidativa com Chryseobacterium como principal representante. / The linear alkylbenzene sulfonate (LAS) is in the laundry detergent composition and it presents complex degradation. Through kinetics assays in batch tests, an inhibition kinetic model by subtrate excess was adjusted to the data in the removal of LAS and organic matter from laundry wastewater (LW) in co-digestion with domestic sewage (DS). The addition of 50 mg L-1 of ethanol (EOH) to the influent resulted in higher values for the specific substrate rate (robs) as well as higher LAS concentration that provided the maximum LAS utilization rate by the biomass (Sbm) (18.98 mg LAS L-1 and 2. 39 mg LAS L-1 in the presence and absence of ethanol, respectively). Sand with 1.0 mm of diameter was chosen as supporting material for the fluidized bed reactor (FBR). The purpose of the present study was to optimize the removal of surfactant in LW + DS (1: 3 volume; &#8764; 20 mg LAS L-1) by using an upscale FBR (19.8 L) through: (i) adding ethanol in different dosages; (ii) varying the upflow velocity (vup) applied to bed; and (iii) increasing the hydraulic retention time (HRT). Thus, for 18h of HRT, the following stages were performed: (I) LW + DS + 1,3 fluidization minimum velocity (vfm); (II) LW + DS + 50 mg EOH L-1 + 1.3 vfm; (III) LW + DS + 200 mg EOH L-1 + 1.3 vfm; (IV) LW + DS + 200 mg L-1 + 1.0 vfm; (V) LW + DS + 200 mg L-1 + 0.7 vfm; (VI) LW + DW + 100 mg L-1 + 1.0 vfm; and for 30 h of HRT: (VII) LW + DS + 1.0 vfm. There was no significant difference in the efficiency of COD and LAS removal (&#8764; 50%, p < 0.5) in stages I to IV. The vup decrease (0.7 vfm) resulted in LAS removal efficiency of 29% (V) and the HRT increase resulted in LAS removal efficiency of 86% (VII). In stages VI and VII, COD removal &#8805; 70% was observed. Lower vup as well as ethanol dosage of 200 mg L-1 favored system acidification (IV and V). In the FBR effluent, 17 recalcitrant compounds were identified. For vup = 0.7 vfm, large diversity of recalcitrant compounds, mostly phthalates, was observed. A taxonomic and functional characterization of the microorganisms was performed by metagenomics analysis in stages III, IV and V (vup variation) and VII (higher efficiency of LAS and COD removal). Microorganisms of Archaea and Bacteria domains were identified, and the decrease of vup resulted in a higher relative abundance of methanogenic archaea, mainly Methanosarcina. Genes related to F420, which are the central electron carrier in the methanogenesis, were identified. Genera diversity was classified in Bacteria domain (Geobacter, Thauera, Pseudomonas, Pseudomonas, Chryseobacterium, Sulfuricurvum and Sulfurospirillum, etc.). Enzyme-encoding genes that act on different stages of LAS degradation were found: (a) addition of fumarate (fumarate reductase); (b) beta-oxidation (3-hydroxyacyl-CoA dehydrogenase); (c) benzene ring cleavage (benzoyl-CoA reductase) and (d) desulfonation (Adenylyl-sulfate reductase). In stage VII sample, genes related to the desulfonation step were identified with higher relative abundance, when compared to the other stages. For a higher vup, a higher relative abundance of genes related to oxidative phosphorylationwas observed and the genus main representative in that category was Chryseobacterium.

L'objectif de cette thèse est d'évaluer les modifications du métabolisme secondaire des plantes contaminées aux éléments trace métalliques (ETM) et leurs conséquences sur les communautés bactériennes rhizosphériques associées incluant des bactéries présentant des phénotypes de MultiDrug Résistance (MDR). Nous nous sommes focalisés sur deux contextes de sols exposés aux métaux : la phytoremédiation de sites miniers au Vietnam et la reconversion de sols agricoles contaminés par la re-déposition atmosphérique d'activités métallurgiques en France. Nos résultats ont mis en évidence que la contamination par différents types de métaux (dont Cu et Pb principalement) a conduit à une altération de la production des métabolites secondaires des racines, tiges et feuilles de la plante hyperaccumulatrice Pteris vittata et que concernant les racines des tendances similaires dans les changements métaboliques ont pu être observés dans un autre type de contexte de pollution (Zn et Pb plus particulièrement). De même, les profils métaboliques des parties souterraines (racines et rhizomes) de Miscanthus x giganteus ont été modifiés par les concentrations en Pb, Cd et Zn des sols agricoles. Pour les deux plantes examinées des dérivés de l'acide chlorogénique ont été retrouvés en proportions augmentées dans les racines malgré des contextes de nature des sols et de pollutions métalliques très contrastés. Cependant, les dérivés de tanin catéchiques sont spécifiquement trouvés en proportions plus élevées dans les racines de P. vittata sous pression métallique. Ces polyphénols sont connus pour leur capacité à piéger les radicaux libres et leur pouvoir antioxydant et pourraient donc être impliqués dans l'adaptation de ces plantes au stress métallique en contribuant à limiter le stress oxydatif généré par les ETM. Au niveau des parties aériennes, nous n'avons étudié que le changement pour P. vittata et avons mis en évidence une proportion plus élevée de dérivés flavonoïdiques pour les plantes contaminées. Nos résultats de métagénomique nous permettent de conclure également sur un effet des ETM sur la diversité et la richesse spécifique des communautés bactériennes des sols étudiés : une forte contamination en Cu (10 fois la limite autorisée) a diminué la diversité et la richesse bactérienne, alors que pour des niveaux en ETM plus modérés incluant Cu, Pb et Zn, la diversité des communautés bactériennes rhizosphériques semble plus influencée par la plante ou la saison plutôt que par l'effet des ETM. Cet effet sur la composition bactérienne de la rhizosphère de P. vittata se traduit par un enrichissement de certains genres connus comme pathogènes opportunistes de l'homme, notamment Ralstonia, Acinetobacter, Burkholderia et Mycobacterium. En outre, le genre Cupriavidus, connu comme très résistant aux ETM est le seul genre spécifiquement associé à P. vittata qui ait été augmenté au sein de la communauté rhizosphérique pour les deux sites miniers étudiés par rapport aux sols rhizosphériques non pollués. Ce genre pourrait donc être impliqué dans le processus d'adaptation de cette plante au stress métallique. Quant aux communautés rhizosphériques de Miscanthus x giganteus, la sélection de Stenotrophomonas et Pseudomonas dans les sols agricoles contaminés a été observée. Dans le cadre de cette thèse nous avons également mis au point une méthode rapide pour tester l'impact de métabolites végétaux sur des souches pathogènes d'origine clinique et environnementale et également évaluer leur activité inhibitrice de pompes à efflux (IPE) de la famille des RND. Nos données ont ainsi permis de mettre en évidence des activités intéressantes et comparables à celle de l'inhibiteur de pompe à efflux PAßN pour des composés testés qui étaient extraits des racines de Fallopia x bohemica ou des dérivés de ces derniers. / The objective of this thesis is to evaluate the modification of plant secondary metabolism production contaminated with metallic trace elements (MTE) and its consequences on the associated rhizospheric bacterial communities including bacteria presenting MultiDrug Resistant (MDR) phenotypes. We have focused on two contexts of metals exposure: the phytoremediation of mining sites in Vietnam and the reconversion of agricultural soils contaminated by the atmospheric re-deposition of metallurgical activities in France. Our results highlighted that contamination by different types of metals (mainly Cu and Pb) has led to an alteration in the production of secondary metabolites in the roots, stems and leaves of the hyper-accumulating Pteris vittata and for roots, a similar trend in the metabolic changes could be observed in another type of pollution context (Zn and Pb more particularly). Similarly, the metabolic profiles of the underground parts (roots and rhizomes) of Miscanthus x giganteus were modified by the concentrations of Pb, Cd and Zn in agricultural soils. For the two plants examined chlorogenic acid derivatives have been found in increased proportions in the roots despite soil type and pollution context were highly contrasted. However, catechic tannin derivatives are specifically found in higher proportions in the roots of P. vittata under metal pressure. These polyphenols are known for their ability to scavenge free radicals and their antioxidant properties and thus could be involved in the adaptation of these plants to metallic stress by helping to limit the oxidative stress generated by MTE. At the level of the aerial parts, we studied only the change for P. vittata and evidenced higher proportions of flavonoid derivatives for contaminated plants. Our metagenomic results allow us to conclude also on the effect of MTE on the diversity and the specific richness of the bacterial communities of the studied soils: a high contamination of Cu (10 times the allowed limit) decreased dramatically bacterial richness and diversity, while for more moderate MTE levels including Cu Pb and Zn, the diversity of rhizosphere bacterial communities was more explained by plant or season effect rather than an effect of MTE. This effect on P.vittata rhizosphere bacterial composition is reflected by an enrichment in genera known as opportunistic human pathogens, including Ralstonia, Acinetobacter, Burkholderia and Mycobacterium. In addition, Cupriavidus, known as a highly resistant genus, is the only P. vittata specifically associated genus found in increased proportions at both mining sites compared to non-contaminated rhizosphere soils. This genus could then be involved in the adaptation process of this plant with metal stress. As for the rhizospheric communities of Miscanthus x giganteus, the selection of Stenotrophomonas and Pseudomonas in agricultural soils contaminated with MTE was observed. As a part of this thesis, we have also developed a rapid method for testing the impact of plant metabolites on pathogenic strains of clinical and environmental origin and their efflux pump inhibition (EPI) activity of RND family. Our data thus showed interesting and notable EPI activities comparable to that of the efflux pump inhibitor PAßN for tested compounds issued from Fallopia x bohemica roots or for their derivatives.

Water reuse has become a promising alternative to alleviate stress on conventional freshwater resources in the face of population growth, sea level rise, source water depletion, eutrophication of water bodies, and climate change. Potable water reuse intentionally looks to purify wastewater effluent to drinking water quality or better through the development and implementation of advanced treatment trains. While membrane-based treatment has become a widely-adopted treatment step to meet this purpose, there is growing interest in implementing treatment trains that harness microorganisms as a more sustainable and less energy-intensive means of removing contaminants of emerging concern (CECs), through biological degradation or transformation. In this dissertation, various aspects of the operation of a microbially-active carbon-based advanced treatment train producing water intended for potable reuse are examined, including fate of dissolved organic carbon, underlying microbial populations, and functional genes are explored. Further, dynamics associated with antibiotic resistance genes (ARGs), identified as a microbially-relevant CECs, are also assessed. Overall, this dissertation advances understanding associated with the interplay between and within treatment processes as they relate to removal of various organic carbon fractions, microbially community dynamics, functional genes, and ARGs. Further, when relevant, these insights are contextualized to operational conditions, process upsets, water quality parameters, and other intended water uses within the water industry with the goal of broadening the application of advanced molecular tools beyond the scope of academic research. Specifically, this dissertation illuminates relationships among organic carbon fractions and molecular markers within an advanced treatment train employing flocculation, coagulation, and sedimentation (FlocSed), ozonation, biologically active carbon (BAC) filtration, granular active carbon (GAC) contacting, and UV disinfection. Biodegradable dissolved organic carbon (BDOC) analysis was adapted specifically as an assay relevant to assessing dissolved organic carbon biodegradability by BAC/GAC-biofilms and applied to profile biodegradable/non-biodegradable organic carbon as wastewater effluent passed through each of these treatment stages. Of particular interest was the role of ozonation in producing bioavailable organic carbon that can be effectively removed by BAC filtration. In addition to understanding the removal of fractionalized organic carbon, next generation DNA sequencing technologies (NGS) were utilized to better understand the microbial dynamics characteristic of complex microbial communities during disinfection and biological treatment. Specifically, this analysis was focused on succession and colonization of taxa, genes related to a wide range of functional interests (e.g. metabolic processes, horizontal gene transfer, DNA repair, and nitrogen cycling), and microbial CECs. Finally, NGS technologies were employed to assess the differences between a wide range of water use categories, including conventional drinking water, potable reuse, and non-potable reuse effluent's microbiomes to identify core and discriminatory taxa associated with intended water usage. The outcomes of this dissertation provide valuable information for optimizing carbon-based treatment trains as an alternative to membrane-based treatment for sustainable water reuse and also advance the application of NGS as a diagnostic tool for assessing the efficacy of various water treatment technologies for achieving treatment goals. / Doctor of Philosophy / Several factors have led to increased stress on conventional drinking water sources and widespread global water scarcity. Projections indicate that continued population growth, increased water demand, and degradation of current freshwater resources will negatively contribute to water needs and underscore the need to secure new potable (i.e. fit for human consumption) sources. Water reuse is a promising alternative to offset the growing demands on traditional potable sources and ameliorate negative consequences associated with water scarcity. Discharge of treated wastewater to marine environments is especially a lost opportunity, as the water will no longer be of value to freshwater habitats or as a drinking water source. Water reuse challenges the conventional wastewater treatment paradigm by providing advanced treatment of wastewater effluent to produce a valuable resource that can be safely used directly for either non-potable (e.g., irrigation, firefighting) or potable (i.e., drinking water) applications. The means of achieving advanced treatment of wastewater effluents can take many forms, commonly relying on the utilization of membrane filtration. However, membrane filtration is an intensive process and suffers from high initial costs, high operational costs, membrane fouling with time, and the production of a salty and difficult to dispose of waste stream. These drawbacks have motivated the water reuse industry to explore more sustainable approaches to achieving high quality effluents. One such alternative relies on the utilization of microorganisms to provide biological degradation and transformation of contaminants through a process known as biologically active filtration (BAF). Comparatively to membrane systems, BAF is more cost effective and produces significantly fewer byproducts while still producing high quality treated water for reuse. However, the range in quality of the resulting treated water has not yet been fully established, in part due to the lack of understanding of the complex microbial communities responsible for biological treatment. As water and wastewater treatment technologies have evolved over the past century, many biological treatments have remained largely 'black box' due to the lack of effective tools to identify the tens of thousands of species of microbes that inhabit a typical system and to track their dynamics with time. Instead, analysis has largely focused on basic water quality indicators. This dissertation takes important steps in advancing the implementation of the study of DNA and biodegradable organic carbon (BDOC) analysis to improve understanding of the mechanisms that drive different water reuse treatment technologies and to identify potential vulnerabilities. Insights gained through application of these tools are contextualized to observed operational conditions, process upsets, and water quality measurements. This helped to advance the use of DNA-based tools to better inform water treatment engineering practice. Specifically, this dissertation dives into the relationships between organic carbon and DNA-based markers within an advanced treatment train employing flocculation, coagulation, and sedimentation (FlocSed), ozonation, biologically active carbon (BAC) filtration, granular active carbon (GAC) contacting, and UV disinfection. Development and application of the BDOC test revealed that the bulk of organic carbon entering the treatment train is dissolved. Further, BDOC analysis served to characterize the impact of specific treatment processes and changes in operational conditions on both biodegradable and non-biodegradable organic carbon fractions. Such information can help to inform continued process optimization. Utilization of DNA-based technologies shed light on the functional capacity of microbial communities present within each stage of treatment and the fate of antibiotic resistance genes (ARGs). ARGs are of concern because, when present in human pathogens, they can result in the failure of antibiotics to cure deadly infections. Other functional genes of interest were also examined using the DNA-based analysis, including genes driving metabolic processes and nitrogen cycling that are critical to water purification during BAF treatment. Also, the DNA-based analyses made it possible to better understand the effects of disinfectants on microbes. Interestingly, some ARG types increased in relative abundance (a measure analogous to percent composition) response to treatments, such as disinfection, and others decreased. Characterization of the microbial communities and their dynamic response to changing operation conditions were also observed. For example, it was possible to characterize how the profiles of microbes changed with time, an ecological process called succession, during BAC filtration and GAC contacting. Generally, this analysis, coupled with the functional analysis, shed light on the important, divergent roles of bacterial communities on organic degradation during both BAC and GAC treatment. Finally, a study was conducted that compared the microbiome (i.e. entire microbial community) between a wide range of conventional drinking water, potable reuse water, and non-potable reuse waters. Here it was found that significant differences existed between the microbial communities of water intended for potable or non-potable usage. This work also looked to expand the application of NGS technologies beyond strictly academic research by developing the application of more advanced DNA-based tools for treatment train assessment and monitoring.