O 4-Nonilfenol (4-NF) é o principal produto formado a partir da degradação do Nonilfenol etoxilado, surfactante não iônico amplamente utilizado em formulações de uso doméstico e industrial. Objetivou-se neste estudo desenvolver método de quantificação de 4-NF em HPLC; avaliar a remoção de 4-NF em reatores em batelada com co-substratos (etanol, metanol e fumarato) e avaliar a remoção e degradação de 4-NF em Reator Anaeróbio de Leito Fluidificado (RALF) em escala aumentada (20L), bem como caracterizar a comunidade microbiana estabelecida no material suporte por meio das técnicas de PCR/DGGE do gene RNAr 16S e sequenciamento massivo via plataforma Illumina-Miseq®. O RALF foi preenchido com areia como material suporte, operado com Tempo de Detenção Hidráulico (TDH) de 18,2±1,1 horas e alimentado com meio de cultura acrescido de 4-NF PESTANAL® (Sigma-Aldrich®). Análises de monitoramento da concentração de 4-NF e matéria orgânica, bem como, dos parâmetros físico-químicos foram realizadas para avaliar a estabilidade do reator quanto a remoção e degradação do composto de interesse. A operação do reator foi dividida em distintas etapas, contando com inoculação do RALF em circuito fechado, adaptação ao meio de cultura e subsequentes fases com adição de 4-NF. Para reatores em batelada a adição de 4-NF (de 288,97±96,49 a 469,98±182,42 µg L-1) favoreceu a produção média de metano acumulada (de 2.292,3 para 2.744,7 mol, respectivamente) para todos os co-susbtratos testados, todavia, retardou o tempo médio de início da produção (de 15,9 h para 107,9 h), bem como reduziu a velocidade de produção (de 24,4 para 10,9 µmol d-1). Para ensaio com adição de 4-NF e Fumarato foram verificados os maiores valores de produção acumulada de metano (3.163,68±169,17 µmol) e de remoção de DQO (75,52±0,34% para DQO inicial de 1.242,00±27,48 mg L-1), em relação aos demais ensaios com adição de 4-NF. Para a remoção de 4-NF em reatores em batelada os valores não diferiram significativamente. Para o RALF, foram verificadas eficiências médias de remoção de DQO de 90,34±6,1% (Fase I), 94,0±1,2% (Fase II), 97,0±1,3% (Fase III) e 95±1,5% (Fase IV) e 4-NF de 73,2±11,1% (Fase II), 67,3±7,3% (Fase III) e 77,88±8,9% (Fase IV). As diferentes concentrações de 4-NF aplicadas ao RALF não afetaram a eficiência de remoção de DQO e promoveram a seleção dos microrganismos que compuseram a biomassa do leito. Os gêneros mais abundantes identificados no reator sem adição de 4-NF foram Prolixibacter, Geothrix, Klebsiella, Lactobacillus e Geobacter. Os gêneros com maior abundância relativa identificados após adição de 4-NF foram os seguintes: Geothrix, Holophaga, Elusimicrobium, Paludibacter, Lactobacillus, Aeromonas, Pelobacter, Aquaspirillum, Pseudomonas, Delftia, Acinetobacter, Arcobacter, Ignavibacterium, Treponema, Lysinibacillus e Enterococcus. / 4-Nonylphenol (4-NP) is the main product formed in the Nonylphenol ethoxylate degradation, nonionic surfactant used in formulations of domestic and industrial use. The objective of this study was to develop a method to determine 4-NP in HPLC; to evaluate the 4-NP removal in batch reactors with co-substrates (ethanol, methanol and fumarate) and removal and degradation of 4-NP in anaerobic Fluidized Bed Reactor (AFBR) on an enlarged scale (20L), as well as characterize the microbial community established in the support material by PCR / DGGE techniques of the 16S RNAr gene and massive sequencing by the Illumina-Miseq® platform. The AFBR was filled with sand as carrier material, operated with Hydraulic Retention Time (HRT) of 18.2±1.1 hours and fed with synthetic sewage plus 4-NP PESTANAL® (Sigma-Aldrich®). Monitoring of the 4-NP concentration and organic matter, as well as physical-chemical parameters were performed to evaluate the stability of the reactor for the removal and degradation of the compound of interest. Reactor operation was divided into different stages, with inoculation of the RALF in closed circuit, adaptation to the culture medium and subsequent phases with 4-NF addition. The addition of 4-NP (from 288.97±96.49 to 469.98±182.42 µg L-1) in batch reactors favored the average accumulated methane production (from 2,292.3 to 2,744.7 µmol, respectively) for all tested co-susbtrates, however, delayed the mean time to start production (from 15.9 h to 107.9 h), as well as reduced production rate (from 24.4 to 10.9 µmol d-1). The highest accumulated values of methane production (3,163.68 ± 169.17 µmol) and COD removal (75.52±0.34% for the initial COD of 1,242±27.48 mg L-1) were verified for the addition of 4-NP and Fumarate, compared to the other tests with addition of 4-NP. For the 4-NP removal in batch reactors the values did not differ significantly. Mean values of COD removal for the AFBR were 90.34±6.1% (Phase I), 94.0±1.2% (Phase II), 94.0±1.2% (Phase III) and 97.0±1.3% (Phase IV) and 4-NF of 73.2±11.1% (Phase II), 67.3±7.3% (Phase III) and 77.88±8.9% (Phase IV). Different concentrations of 4-NP applied to the AFBR did not affect the COD removal efficiency and promoted the selection of the microorganisms that composed the bed biomass. The most abundant genera identified in the reactor without addition of 4-NP were Prolixibacter, Geothrix, Klebsiella, Lactobacillus and Geobacter. The genotypes with the highest relative abundance identified after addition of 4-NP were as follows: Geothrix, Holophaga, Elusimicrobium, Paludibacter, Lactobacillus, Aeromonas, Pelobacter, Aquaspirillum, Pseudomonas, Delftia, Acinetobacter, Arcobacter, Ignavibacterium, Treponema, Lysinibacillus and Enterococcus.

Yes / Bacillus sp. is a Gram-positive bacterium that is commonly found in seawater. In this study, the genome of marine Bacillus sp. strain G3(2015) was sequenced using MiSeq. The fosfomycin resistant gene fosB was identified upon bacterial genome annotation. / University of Malaya through HIR grants (UM-MOHE HIR grant UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027; UM-MOHE HIR grant UM C/625/1/HIR/MOHE/CHAN/01, A000001- 50001); Postgraduate Research grant PG083-2015B

Os Espodossolos são os solos de maior ocorrência na planície costeira do litoral do Estado de São Paulo e são caracterizados pela presença de um horizonte espódico (Bh ou Bhm). Poucas são as informações relacionadas à gênese destes solos em regiões tropicais, assim como da composição química da matéria orgânica (MO) nos mesmos e da influência dos micro-organismos em sua formação. É possível que micro-organismos envolvidos na degradação seletiva da MO sejam importantes para a gênese de Espodossolos, como observado anteriormente em Espodossolos de Bertioga e Ilha Comprida. O primeiro estudo teve como objetivo avaliar a variação espacial da estrutura das comunidades e a abundância de bactérias e fungos em três perfis de Espodossolos sob drenagem intermediária, nos diferentes horizontes e nas manchas brancas através de PCR-DGGE e quantificação por qPCR dos genes rRNA 16S de bactérias e ITS de fungos. O segundo estudo teve como objetivo avaliar a variabilidade espacial das comunidades de bactérias nos horizontes e nas manchas brancas de Espodossolos sob três regimes de drenagem, e determinar se a diversidade genética e estrutura das comunidades de bactérias estão associadas à composição molecular da MO nessas regiões, através do sequenciamento massivo da região V4 do gene do rRNA 16S de bactéria e análise de compostos orgânicos por pirólise-GC/MS. As estruturas das comunidades bacterianas, determinada por PCR-DGGE, nos diferentes horizontes de cada perfil foram mais similares entre si do que nos mesmos horizontes em diferentes perfis de Espodossolos. A estrutura das comunidades fungos não apresentou diferenças significativas, independente da localidade do perfil e profundidade dos horizontes. A abundância de cópias do gene rRNA 16S e região ITS, determinada por qPCR, foi maior no horizonte A do que no horizonte Bh, para os três perfis de Espodossolos estudados. Apesar de não haver diferenças significativas na estrutura das comunidades, grupos específicos de bactérias e fungos podem estar envolvidos na degradação seletiva da matéria orgânica nos diferentes horizontes, bem como nas manchas brancas e suas adjacências. A estrutura das comunidades de bactérias, determinada por sequenciamento massivo do gene rRNA 16S, nos horizontes mais superficiais (A e AE) foi distinta daquela observada nos horizontes mais profundos (EB, BE e Bh). Porém, as comunidades bacterianas nas manchas brancas e suas regiões adjacentes foram mais similares entre si, do que em relação as comunidades bacterianas nos horizontes, em todos os perfis analisados, independente do regime de drenagem. Acidobacteria, Proteobacteria e Actinobacteria foram os filos mais abundantes nos solos estudados. Actinobacteria e Alphaproteobacteria mostraram associação positiva com moléculas orgânicas derivadas da pirólise da lignina, as quais foram mais abundantes nos horizontes superficiais (A e AE), enquanto Acidobacteria mostrou associação positiva com compostos mais recalcitrantes encontrados em horizontes mais profundos (Bh), sugerindo um papel específico e diferenciado de cada grupo bacteriano na degradação de compostos orgânicos específicos. Os resultados desses estudos sugerem que grupos bacterianos específicos podem estar envolvidos na gênese de Espodossolos através da degradação de compostos orgânicos específicos em diferentes horizontes. / Podzols are highly frequent soils in the coastal plains of the São Paulo State, and are characterized by the presence of a spodic horizon (Bh or Bhm). Studies on the pedogenetic processes in Podzols of tropical regions are scarce, as well as studies on the molecular characterization of their organic matter (OM) and on the microorganisms involved in their genesis. It is possible that microorganisms involved in the selective degradation of the soil OM are important for the genesis of Podzols, as previously observed in Podzols of Bertioga and Ilha Comprida. The aim of the first study was to evaluate the spatial variation of the community structure and abundance of bacterial and fungi in the different horizons, bleached mottles and their immediate vicinity of three Podzol profiles under intermediary drainage regime, using PCR-DGGE and qPCR of the bacterial rRNA 16S gene and fungal ITS region. The aim of the second study was to determine the spatial variability of the bacterial communities in the horizons and bleached mottles of Podzols under three drainage regimes, and whether the bacterial genetic diversity and community structure were associated to the molecular OM composition, using high-throughput sequencing of the V4 region of the bacterial 16S rRNA gene and analyses of organic compounds by pyrolysis GC/MS. The structure of bacterial communities, determined by PCRDGGE, in the different horizons of each soil profile were more similar to each other than in the same horizons of different soil profiles. The fungal community structures did not show significant differences, independent of the soil profile location and horizons depth. Abundance of copies of the bacterial 16S rRNA gene and fungal ITS region, determined by qPCR, was higher in the A horizon than in the Bh horizon, for the three Podzol profiles studied. Even though there were no significant differences in community structures, specific groups of bacteria and fungi may be involved in the selective degradation of organic matter in different horizons, bleached mottles and their immediate vicinity. The bacterial community structures, determined by highthroughput sequencing of the 16S rRNA gene, in the surface horizons (A and AE) were distinct of that in the deeper horizons (EB, BE and Bh). However, the bacterial community structures in the bleached mottles and their immediate vicinity were more similar to each other than to the community structures in the horizons, in all profiles studied, regardless of the drainage regime. Acidobacteria, Proteobacteria and Actinobacteria were the most abundant phyla in the soils studied. Actinobacteria and Alphaproteobacteria showed a positive relationship organic compounds derived from lignin degradation, which were more abundant in the surface horizons (A and AE), whereas Acidobacteria showed a positive relationship with more recalcitrant compounds detected in deeper horizons (Bh), suggesting a specific and distinct roles of each bacterial group in the degradation of specific organic compounds. The results of these studies suggest that specific bacterial groups may be involved in the genesis of Podzols by degrading specific organic compounds in different horizons.

Os Espodossolos são os solos de maior ocorrência na planície costeira do litoral do Estado de São Paulo e são caracterizados pela presença de um horizonte espódico (Bh ou Bhm). Poucas são as informações relacionadas à gênese destes solos em regiões tropicais, assim como da composição química da matéria orgânica (MO) nos mesmos e da influência dos micro-organismos em sua formação. É possível que micro-organismos envolvidos na degradação seletiva da MO sejam importantes para a gênese de Espodossolos, como observado anteriormente em Espodossolos de Bertioga e Ilha Comprida. O primeiro estudo teve como objetivo avaliar a variação espacial da estrutura das comunidades e a abundância de bactérias e fungos em três perfis de Espodossolos sob drenagem intermediária, nos diferentes horizontes e nas manchas brancas através de PCR-DGGE e quantificação por qPCR dos genes rRNA 16S de bactérias e ITS de fungos. O segundo estudo teve como objetivo avaliar a variabilidade espacial das comunidades de bactérias nos horizontes e nas manchas brancas de Espodossolos sob três regimes de drenagem, e determinar se a diversidade genética e estrutura das comunidades de bactérias estão associadas à composição molecular da MO nessas regiões, através do sequenciamento massivo da região V4 do gene do rRNA 16S de bactéria e análise de compostos orgânicos por pirólise-GC/MS. As estruturas das comunidades bacterianas, determinada por PCR-DGGE, nos diferentes horizontes de cada perfil foram mais similares entre si do que nos mesmos horizontes em diferentes perfis de Espodossolos. A estrutura das comunidades fungos não apresentou diferenças significativas, independente da localidade do perfil e profundidade dos horizontes. A abundância de cópias do gene rRNA 16S e região ITS, determinada por qPCR, foi maior no horizonte A do que no horizonte Bh, para os três perfis de Espodossolos estudados. Apesar de não haver diferenças significativas na estrutura das comunidades, grupos específicos de bactérias e fungos podem estar envolvidos na degradação seletiva da matéria orgânica nos diferentes horizontes, bem como nas manchas brancas e suas adjacências. A estrutura das comunidades de bactérias, determinada por sequenciamento massivo do gene rRNA 16S, nos horizontes mais superficiais (A e AE) foi distinta daquela observada nos horizontes mais profundos (EB, BE e Bh). Porém, as comunidades bacterianas nas manchas brancas e suas regiões adjacentes foram mais similares entre si, do que em relação as comunidades bacterianas nos horizontes, em todos os perfis analisados, independente do regime de drenagem. Acidobacteria, Proteobacteria e Actinobacteria foram os filos mais abundantes nos solos estudados. Actinobacteria e Alphaproteobacteria mostraram associação positiva com moléculas orgânicas derivadas da pirólise da lignina, as quais foram mais abundantes nos horizontes superficiais (A e AE), enquanto Acidobacteria mostrou associação positiva com compostos mais recalcitrantes encontrados em horizontes mais profundos (Bh), sugerindo um papel específico e diferenciado de cada grupo bacteriano na degradação de compostos orgânicos específicos. Os resultados desses estudos sugerem que grupos bacterianos específicos podem estar envolvidos na gênese de Espodossolos através da degradação de compostos orgânicos específicos em diferentes horizontes. / Podzols are highly frequent soils in the coastal plains of the São Paulo State, and are characterized by the presence of a spodic horizon (Bh or Bhm). Studies on the pedogenetic processes in Podzols of tropical regions are scarce, as well as studies on the molecular characterization of their organic matter (OM) and on the microorganisms involved in their genesis. It is possible that microorganisms involved in the selective degradation of the soil OM are important for the genesis of Podzols, as previously observed in Podzols of Bertioga and Ilha Comprida. The aim of the first study was to evaluate the spatial variation of the community structure and abundance of bacterial and fungi in the different horizons, bleached mottles and their immediate vicinity of three Podzol profiles under intermediary drainage regime, using PCR-DGGE and qPCR of the bacterial rRNA 16S gene and fungal ITS region. The aim of the second study was to determine the spatial variability of the bacterial communities in the horizons and bleached mottles of Podzols under three drainage regimes, and whether the bacterial genetic diversity and community structure were associated to the molecular OM composition, using high-throughput sequencing of the V4 region of the bacterial 16S rRNA gene and analyses of organic compounds by pyrolysis GC/MS. The structure of bacterial communities, determined by PCRDGGE, in the different horizons of each soil profile were more similar to each other than in the same horizons of different soil profiles. The fungal community structures did not show significant differences, independent of the soil profile location and horizons depth. Abundance of copies of the bacterial 16S rRNA gene and fungal ITS region, determined by qPCR, was higher in the A horizon than in the Bh horizon, for the three Podzol profiles studied. Even though there were no significant differences in community structures, specific groups of bacteria and fungi may be involved in the selective degradation of organic matter in different horizons, bleached mottles and their immediate vicinity. The bacterial community structures, determined by highthroughput sequencing of the 16S rRNA gene, in the surface horizons (A and AE) were distinct of that in the deeper horizons (EB, BE and Bh). However, the bacterial community structures in the bleached mottles and their immediate vicinity were more similar to each other than to the community structures in the horizons, in all profiles studied, regardless of the drainage regime. Acidobacteria, Proteobacteria and Actinobacteria were the most abundant phyla in the soils studied. Actinobacteria and Alphaproteobacteria showed a positive relationship organic compounds derived from lignin degradation, which were more abundant in the surface horizons (A and AE), whereas Acidobacteria showed a positive relationship with more recalcitrant compounds detected in deeper horizons (Bh), suggesting a specific and distinct roles of each bacterial group in the degradation of specific organic compounds. The results of these studies suggest that specific bacterial groups may be involved in the genesis of Podzols by degrading specific organic compounds in different horizons.

Célèbres depuis l'accident de Seveso en 1976, les dioxines/furanes (PCCD/F) restent, malgré une forte baisse de leurs émissions, un sujet de préoccupation permanent en France et dans le monde. Le rémanence de ces composés organochlorés dans le sol et le risque toxique qu'ils représentent pour l'homme et l'environnement font que la gestion et la remédiation des sols contaminés par les PCDD/F sont devenues une priorité des industriels, législateurs et scientifiques. La phytoremédiation compte parmi les méthodes émergentes de dépollution des sols contaminés en raison de son adéquation avec le développement durable. Elle combine les capacités naturelles des plantes et de leur microbiote rhizosphérique à biodégrader les polluants organiques. Cependant, l'efficacité de cette phytotechnologie est encore souvent limitée, en particulier lorsqu'il s'agit de composés chlorés, à cause de leur récalcitrance, de leur phytotoxicité et leur faible biodisponibilité dans le sol. Ainsi, l'objectif de ce travail de thèse a consisté à étudier les performances de la phytoremédition assistée, en particulier par les champignons mycorhiziens arbusculaires, d'un sol agricole historiquement pollué par les PCDD/F prélevé sur une parcelle expérimentale située à proximité d'un ancien incinérateur. L'ensemble des résultats obtenus mettent en évidence, en particulier, le potentiel de deux espèces végétales, la luzerne et la fétuque, dans la rhizodégradation des PCCDD/F. La végétalisation du sol permet de moduler les communautés microbiennes du sol (bactéries, Archées et champignons) et notamment celles qui semblent impliquées dans la dissipation des PCCDD/F. En revanche, bien que la mycorhization agisse sur les communautés microbiennes du sol, celle-ci n'a pas eu d'impact, dans nos conditions expérimentales, sur la dissipation des PCCDD/F quelles que soit l'origine de l'inoculum utilisé et les espèces mycorhiziennes qui le compose. La dégradation de ces composés organochlorés est plus marquée dans un sol préalablement stérilisé, puis recolonisé par certaines communautés microbiennes spécifiques, impliquées dans la dissipation des PCCDD/F. L'utilisation combinée d'un mélange de rhamnolipides avec l'introduction dans le sol d'une bactérie Sphingomonas wittichii RWI, décrite pour ses capacités de dégradation des PCCDD/F, permet d'accroitre l'efficience de la rhizodégradation des PCDD/F qui se traduit par une baisse significative de la cytotoxicité du sol après phytoremédiation. / Famous since the Seveso accident in 1976, dioxins/furans (PCCD/F) remain, despite a sharp decline in emissions, a subject of permanent concern in France and in the world. The remanence of these organochlored compounds in soil and the toxic risk they represent for humans and the environment mean that the management and remediation of PCDD/F contaminated soil has become a priority for industrialists, legislators and scientists. Phytoremediation is one of the emerging depollution methods of contaminated soils due to Its suitability for sustainable development. It combines the natural capacities of plants and their rhizospheric microbiota to biodegrade organic pollutants. However, the effectiveness of this phytotechnology is still often limited, especially in the case of chlorinated compounds, due to their recalcitrance, phytotoxicity and low bioavailability in the soil. Thus, the thesis aims to study the performance of assisted phytoremission, in particular by mycorrhizal fungi, of an agricultural PCDD / F based-polluted soil from an experimental plot near an old incinerator. The results obtained show the potential of two plant species, alfalfa and tall fescue, in the rhizodegradation of PCCDD/F. Soil vegetation shows to modulate soil microbial communities (bacteria, archaea and fungi) includind those that appear to involved in the dissipation of the PCCDD/F. On the other hand, although mycorrhization affects soil microbial communities, it has not had any impact on the dissipation of PCCDD/F in our experimental conditions, whatever the inoculums origin and the mycorrhizal species which compose it. The degradation of these organochlorined compounds is more significant in a previously sterilized soil and then recolonized by specific microbial communities involved in the PCCDD/Fdissipation. The combined use of rhamnolipids mixture and Sphingomonas wittichii RWI bactrerium described for its degradation capabilities of PCCDD/F makes it possible to increase the efficiency of PCDD/F rhizodegradation which results in a significant decrease in soil cytotoxicity after phytoremediation.

A otimização e padronização de métodos moleculares são fundamentais para evitar distorções nos resultados causadas por processamento de ácidos nucleicos da abundância relativa de micro-organismos de uma amostra. Nos estudos sobre identificação microbiana, a etapa de validação é, na maioria dos casos, negligenciada. As principais etapas em que podem ocorrer vieses capazes de alterar a informação sobre a composição da comunidade microbiana são a extração e a RT-PCR. O rRNA é a molécula ideal para identificar os micro-organismos metabolicamente ativos por estar em maior quantidade dentro da célula. A inexistência de um protocolo de extração de RNA gold standard e de kits comerciais específicos para cada tipo de amostra ambiental pode comprometer as etapas posteriores à extração. O protocolo de extração de RNA adaptado neste trabalho mostrou alta eficácia na lise celular e na remoção de contaminantes co-extraidos, garantindo a integridade e a qualidade do rRNA extraído de amostras contendo altas concentrações de contaminantes. Devido as diferentes características químicas das amostras ambientais, o uso deste protocolo adaptado pode preservar a informação sobre os indivíduos metabolicamente ativos de uma comunidade microbiana. Foram utilizados consórcios artificiais na validação da etapa de PCR. O efeito sinérgico do uso de aditivos, da Taq polimerase de alto rendimento, do programa de sub-ciclagem e da limitação do programa de amplificação em 10 ciclos, mantiveram a proporção dos moldes dos consórcios analisados próximo ao esperado. Após a padronização da técnica de ARDRA, foi definido que há necessidade de entre 500 e 550 UFC para uma cobertura completa da diversidade de lodo ativado. O uso de enzimas combinadas MspI/HaeIII e HhaI/RsaI em uma mesma reação double digest proporcionou a separação dos clones de lodo ativado utilizando menos etapas de ARDRA. E o critério de corte em 3% do total agrupamentos, possibilitou selecionar os perfis mais representativos sem a perda de grupos importantes para a análise das bibliotecas. Foi concluído que, o uso de um protocolo inadequado de extração de RNA de amostras complexas pode gerar extratos contendo contaminantes co-extraidos que interferem na atividade da Taq polimerase e nas enzimas de restrição. Após o sequenciamento de nova geração, foi observado que o uso de diferentes iniciadores de PCR e do pré-processamento manual para os dados obtidos, foram essenciais para ampliar a cobertura observada para a amostra de lodo e melhorar a resolução dos resultados e a profundidade de identificação taxonômica, respectivamente. / The optimization and standardization of molecular methods are fundamental to avoid distortions in the results caused by nucleic acid processing of the relative abundance of microorganisms in a sample. In the studies on microbial identification, the validation step is, in most cases, neglected. The main steps in which biases capable of altering the composition of the microbial community can occur are extraction and RT-PCR. The rRNA is the ideal molecule to identify metabolically active microorganisms because they are in the greatest amount within the cell. The lack of a gold standard RNA extraction protocol and specific commercial kits for each type of environmental sample may compromise the post-extraction steps. The RNA extraction protocol adapted in this work showed high efficacy in cell lysis and in the removal of co-extracted contaminants, guaranteeing the integrity and quality of the rRNA extracted from samples containing high concentrations of contaminants. Due to the different chemical characteristics of the environmental samples, the use of this adapted protocol can preserve the information about the metabolically active individuals of a microbial community. Artificial consortia were used to validate the PCR step. The synergistic effect of the use of additives, the high yield Taq polymerase, the sub-cycling program and the limitation of the amplification program in 10 cycles, kept the proportion of the molds of the consortia analyzed close to the expected. After standardization of the ARDRA technique, it was defined that there is a need for between 500 and 550 CFU for a complete coverage of the diversity of activated sludge. The use of MspI / HaeIII and HhaI / RsaI combined enzymes in the same double digest reaction provided the separation of activated sludge clones using fewer ARDRA steps. And the criterion of cut in 3% of the total groupings, allowed to select the most representative profiles without the loss of important groups for the analysis of the libraries. It was concluded that the use of an inadequate RNA extraction protocol from complex samples can generate extracts containing co-extracted contaminants that interfere with Taq polymerase activity and restriction enzymes. After the sequencing of the new generation, it was observed that the use of different PCR primers and manual preprocessing for the obtained data were essential to increase the coverage observed for the sludge sample and to improve the resolution of the results and the depth of taxonomic identification, respectively.

Y-chromosome testing has become more prevalent in recent years as a means of identifying forensic samples using STRs or identifying biomarkers for disease or determining geographic origins of populations. Additionally, Y-chromosome analysis is especially useful in paternity testing as the Y chromosome is inherited paternally and the male-specific region of the Y chromosome does not undergo any recombination events, allowing the genotypic data of both the father and son to be identical. Though in most cases a father-son pair will have the same Y-allelic data, random mutations like allele insertions and deletions can occur, which can interfere and result in incorrect conclusions in regards to paternity testing, forensic analysis, or genealogy. Though the exact mechanism of Y loci mutability is unknown, postulations of factors that can cause mutations have been studied, as well as attempts to determine mutation rate specific to each locus. A multi-generational pedigree consisting of 9 males was analyzed using two different methodologies: capillary electrophoresis and next-generation sequencing. The samples were amplified using either a ForenSeq™ Signature DNA Prep Kit (Verogen, San Diego, CA) or a YFiler™ Plus PCR Amplification Kit (Thermo Fisher Scientific, Waltham, MA). Between the two methods, five Y-STR loci were identified as being discordant between a father-son pair. Next-generation sequencing identified an allele insertion at DYS385a/b, resulting in a potential tri-allelic locus, but was disproved after comparison with the capillary electrophoresis data of the sample. The capillary electrophoresis data identified four discordances between father-son pairs, one of which was an allele mutation with a gain of a repeat at DYS458. At DYS 389II, an allele insertion was identified, but was contradicted after comparison with the next-generation sequencing data. There was a potential null allele at DYS518 and either an OL variant allele or a 2 base pair deletion at DYS481. Following peak height ratio, stutter, and comparative analysis between the genotypic data of the two analysis methods, two of these discordances were proven to be errors, one was a definitive mutational event, and the other two could neither be confirmed nor denied due to differences in loci tested in each kit.

The following is a comparison study of the Globalfiler™ PCR Amplification Kit analyzed on an ABI 3130 Genetic Analyzer Capillary Electrophoresis (CE) versus the ForenSeq™ DNA Signature Prep Kit analyzed on the MiSeq FGx™ System. The MiSeq FGx™ System measures results by Allele Read Count (ARC), while the CE measures results as Relative Fluorescent Units (RFU). Mixture samples were prepared in ratios of 1:1, 1:4, and 1:10 in replicates of four using a female major contributor and a male minor contributor, intended to represent some commonly seen mixture samples ratios in forensic cases [48]. Both systems performed equally well for the 1:1 mixture while the MiSeq FGx™ System had improved accuracy and precision for the 1:4 mixture compared to CE (4.033 + 1.506 ARC and 4.678 + 2.093 RFU, respectively). The MiSeq FGx™ System showed increased variation in the 1:10 mixture compared to CE (10.347 + 5.184 ARC and 9.311 + 3.363 RFU, respectively). Over the four replicates, the MiSeq FGx™ System had a total of 15 out of 528 possible alleles (2.84%) dropout compared to a total of 13 out of 384 possible alleles (3.39%) dropout on CE. The additional loci analyzed by the MiSeq FGx™ System results in a lower percentage of alleles lost due to dropout compared to CE. Isoalleles in sequence data may reveal the presence of minor contributor alleles that would otherwise be masked by the major contributor in length-based STR analysis. The presence of isoalleles are most helpful in mixture ratios greater than 1:1, where it is easier to assign alleles to a specific contributor. In certain cases, deconvolution of loci with shared alleles may not be improved by sequencing if intra-contributor isoalleles are present. Unless using known reference profiles, it is difficult to accurately assign alleles to contributors when intra-contributor isoalleles are present. Additionally, the sequencing data from the MiSeq FGx™ System provided information to aid the separation of stutter from true alleles. Previous studies report a significant increase in the amount of alleles present at some loci due to differences by nucleotide sequence, which may improve the discriminating power of those loci [31,52,53,54]. With all its potential, there is still much room for sequencing technology to improve before it becomes a standard analysis method in forensic laboratories.

Yes / We report the draft genome sequence of Pandoraea sp. strain E26 isolated from a former landfill site, sequenced by the Illumina MiSeq platform. This genome sequence will be useful to further understand the quorum-sensing system of this isolate. / University of Malaya High-Impact Research (HIR) grants (UM C/625/1/HIR/MOHE/CHAN/01, grant A-000001- 50001 and UM-MOHE HIR UM C/625/1/HIR/MOHE/CHAN/14/1, grant H-50001-A000027)

A digestão anaeróbia tem se apresentado como um processo de grande interesse sob a ótica da potencial produção de energia renovável (H2 e CH4), considerando-se a ampla variedade de compostos orgânicos que podem ser utilizados. Neste estudo desejou-se avançar na compreensão do sistema de reatores anaeróbios de duas fases (acidogênico seguido de metanogênico) operados em condições termofílicas (55°C), alimentados com melaço da cana-de-açúcar, subproduto da indústria sucroalcooleira. Os experimentos foram conduzidos em reatores anaeróbios de leito fixo estruturado com fluxo ascendente e o melaço foi diluído com água de abastecimento, para adequação da concentração aos processos de tratamento de águas residuárias. Na 1ª Etapa dois reatores acidogênicos foram operados em paralelo para avaliar diferentes formas de inoculação e meios suportes, a fim de manter a produção continua e estável de hidrogênio. Para isso foram aplicadas diferentes cargas orgânicas (2,5, 5 e 10 gDQO.L-1) que resultam em COV de 30, 60 e 120 g.DQO.Lreator1.dia-1, com TDH fixo de 2 horas. A expressão do gene hidrogenase foi detectado em ambos os reatores, mas em maior proporção no reator inoculado com lodo de reator UASB e usando como material suporte a espuma de poliuretano. Sequencialmente a este reator, foi acoplado um reator metanogênico, alimentado com efluente do reator acidogênico, estabilizado nas condições apresentadas, e operado com COV crescentes de 1, 2, 5, 7, 14, 17 e 26,5 gDQO.Lreator-1.dia-1 e consequente diminuição do TDH de 240, 96, 48, 32, 24, 16 e 12 horas. O reator acidogênico na 2ª etapa foi operado por 417 dias consecutivos e COV de 120 g.DQO.Lreator1.dia-1, produzindo hidrogênio continuamente, alcançado valores de produção bruta de H2 de 7,60 LH2.dia-1. O reator metanogênico foi operado por 251 dias consecutivos, produzindo metano e alcançado valores de produção bruta de CH4 de 5,90 LCH4.dia-1. A eficiência de remoção de DQO do sistema de reatores foi de aproximadamente 90%, com contribuição aproximadamente de 10% para o reator acidogênico e contribuição aproximadamente de 80% para o reator metanogênico. O reator acidogênico alcançou rendimento de produção de hidrogênio por kg de melaço aplicado de 392 LH2.kgmelaço-1 e o reator metanogênico de 387 LCH4.kgmelaço-1. Para finalidade de comparações e aplicabilidade, o ganho energético global do sistema de reatores de duas fases foi de aproximadamente 5,7 kWh.kgmelaço-1 (1,4 kWh.kgmelaço-1 para o reator acidogênico e 4,3 kWh.kgmelaço-1 para o reator metanogênico). A produção continua de H2 obtida neste estudo está relacionada à associação das vias dos ácidos produtores de hidrogênio já consolidados pela literatura pertinente (acético e butírico) e pela produção de hidrogênio pela rota do ácido lático, devido a associação entre as comunidades de microrganismos estabelecidas no reator. O sequenciamento massivo MiSeq mostrou a seleção de diversos gêneros de microrganismos com redundância funcional e pertencentes principalmente aos Filos Firmicutes, Proteobacteria e Thermotogae, tais como Clostridium sensu stricto, Thermohydrogenium, Thermoanaerobacterium e Cellulosibacter (Firmicutes); Pseudomonas, Enterobacter, Shewanella e Petrobacter (Proteobacteria) e Fervidobacterium (Thermotogae). Microrganismos produtores de ácido lático também foram selecionados tais como: Lactobacillus, Leuconostoc, Sporolactobacillus e Trichococcus. Dos pontos de vista científico e tecnológico este estudo deu mais um passo para a compreensão dos bioprocessos envolvidos nos sistemas anaeróbios em dois estágios produzindo H2 e CH4 continuamente por longo período de tempo. / Anaerobic digestion has shown as an interesting process for renewable energy production (H2 and CH4), for a wide variety of organic compounds (carbon source). This study aimed to advance the understanding of a two-stage process anaerobic system (acidogenic bioreactor followed by methanogenic bioreactor) under thermophilic condition (55°C) fed with molasses, a sugarcane industry by-product. The experiments were conducted at up-flow structured bed reactors and sugarcane molasses was diluted with tap water, to adjust the concentration to the wastewater treatment. At first stage two acidogenic reactors were operated in parallel to evaluate different source of inocula and support bed, to obtain continuous and stable hydrogen production. It was applied 2.5, 5 and 10 gCOD.L-1 resulting in OLR of 30, 60 and 120 g.COD.Lreactor-1.day-1, with HRT fixed at 2 hours of hydrogenase gene was detected in both reactors but with higher number of copies of the gene in the reactor that showed higher hydrogen production: the reactor sed with sludge of UASB reactor and using polyurethane foam as support material. To this reactor was coupled a methanogenic reactor fed with effluent from acidogenic reactor and operated with increasing OLR (1, 2, 5, 7, 14, 17 e 26,5 gCOD.Lreactor-1.day-1) decreasing the HRT (240, 96, 48, 32, 24, 16 and 12 hours). The acidogenic reactor was operated during 471 days with OLR of 120 g.COD.Lreactor-1.day-1, with HRT fixed at 2 hours, with continuous hydrogen production with a gross production of 7.60 LH2.day-1. The methanogenic reactor was operated for 251 days, with continuous methane production of up to 5.90LCH4.day-1. The COD removal efficiency using the two-stage system was approximately 90% , with 10% contribution by the acidogenic reactor and 80% contribution by the methanogenic reactor. The acidogenic reactor achieved hydrogen yield per kg of applied molasses equal to 392 LH2.kgmolases-1. The methanogenic reactor achieved methane yield per kg of applied molasses equal to 387 LCH4.kgmolasses-1. For comparison and applicability purposes, the overall energy yield using the two stage reactor system was approximately 5.7 kWh.kgmolasses-1 (Acidogenic reactor 1.4 kWh.kgmolasses-1 and Methanogenic reactor 4.3 kWh.kgmolasses-1). The continuous production of H2 obtained in this study is related to the association of the hydrogen producer acids pathway established by the relevant literature (acetic and butyric) and the hydrogen production by the lactic acid pathway due to the microorganisms association established in the reactor. Metagenomic analysis by MiSeq Plataform revealed that hydrogen production was due the selection of microorganisms with functional redundancy mainly of Phyla Firmicutes, Proteobacteria and Thermotogae, such as Clostridium sensu stricto, Thermohydrogenium, Thermoanaerobacterium, Cellulosibacter (Firmicutes); Pseudomonas, Enterobacter, Shewanella and Petrobacter (Proteobacteria) and Fervidobacterium (Thermotogae). Genera of acid latic producers, such as Lactobacillus, Leuconostoc, Sporolactobacillus and Trichococcus, were also selected. From the scientific and technological point of view this study has taken another step towards the understanding of bioprocesses involving two stage anaerobic systems for a long term continuous production of H2 and CH4.