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Stream microbes that occur in the Mediterranean Basin have been shown to possess heightened sensitivity to intensified water stress attributed to climate change. Here, we investigate the effects of long-term drought (150 days), storms and rewetting (7 days) on the diversity and composition of archaea, bacteria and fungi inhabiting intermittent streambed sediment (surface and hyporheic) and buried leaves. Hydrological alterations modified the archaeal community composition more than the bacterial community composition, whereas fungi were the least affected. Throughout the experiment, archaeal communities colonizing sediments showed greater phylogenetic distances compared to those of bacteria and fungi, suggesting considerable adaptation to severe hydrological disturbances. The increase in the class abundances, such as those of Thermoplasmata within archaea and of Actinobacteria and Bacilli within bacteria, revealed signs of transitioning to a drought-favoured and soil-like community composition. Strikingly, we found that in comparison to the drying phase, water return (as sporadic storms and rewetting) led to larger shifts in the surface microbial community composition and diversity. In addition, microhabitat characteristics, such as the greater capacity of the hyporheic zone to maintain/conserve moisture, tended to modulate the ability of certain microbes (e.g., bacteria) to cope with severe hydrological disturbances Giulia Gionchetta was awarded a grant (UdG 2016) from the University of Girona. This study was supported by the Spanish Ministry of Economy and Competitiveness through the project FUNSTREAM (CGL2014-58760-C3-R); by the Economy and Knowledge Department of the Catalan Government, through Grant/Award Number: 2014 SGR 484; and through the Short-Term Scientific Mission (STSM) Grant awarded by the Science and Management of Intermittent Rivers and Ephemeral Streams (SMIRES) Cost-Action (Action number: 40271). This study was also partially supported by project BIGLY (ANR-16-CE32-0001) and the project DryHarshSal (RTI2018-097950-B-C21) of the Spanish Ministry of Science, Innovation and Universities

Background The understanding of the roles of gut bacteria in the fitness and vectorial capacity of mosquitoes that transmit malaria, is improving; however, the factors shaping the composition and structure of such bacterial communities remain elusive. In this study, a high-throughput 16S rRNA gene sequencing was conducted to understand the effect of developmental stage, feeding status, species, and geography on the composition of the gut bacterial microbiota of two main Colombian malaria vectors, Anopheles nuneztovari and Anopheles darlingi. Results The results revealed that mosquito developmental stage, followed by geographical location, are more important determinants of the gut bacterial composition than mosquito species or adult feeding status. Further, they showed that mosquito gut is a major filter for environmental bacteria colonization. Conclusions The sampling design and analytical approach of this study allowed to untangle the influence of factors that are simultaneously shaping the microbiota composition of two Latin-American malaria vectors, essential aspect for the design of vector biocontrol strategies. Electronic supplementary material The online version of this article (10.1186/s40168-018-0528-y) contains supplementary material, which is available to authorized users.

The aim of this research was to analyze the relationship between soil microorganisms and the major diseases affecting promising clones of cocoa (Theobroma cacao L.) in the Ecuadorian Amazon. The EET-95, EET-96, EET-103 and CCN-51 clones were evaluated, respectively, the latter used as a control, for this, the amount of bacteria, fungi and total actinomycetes, expressed in colony forming units (CFU) per soil gram, was determined, present in the soil rhizosphere of the three cocoa clones, as well as the appearance of the major plant diseases which attacks the cocoa crop. Data were statistically analyzed by one-way ANOVA and Tukey HSD test p≤0.05. The bacteria were the microorganisms with the greatest association to the evaluated cocoa clones in this study, followed by actinomycetes and fungi. Clone CCN-51 had achieved the highest number of bacteria, clones EET-96 and EET-103, had achieved a higher incidence of actinomycetes and clone EET-103, the greater presence of parasitic fungi. The witch broom disease, whose causative agent is Cripinellis perniciosa Sthael Singer., affected to a lesser extent the EET-103 and CCN-51 clones, while frosty pod rot caused by the parasitic fungus Moniliophthora roreri (Cif and Par) Evans et al., showed the EET-103 clone with the highest incidence of this disease and conversely to the CCN-51 clone with the lowest incidence of this pathogen. El objetivo de la presente investigación fue analizar la relación de los microorganismos del suelo y las principales enfermedades que afectan los clones promisorios de cacao (Theobroma cacao L.) en la Amazonía Ecuatoriana. Se evaluaron los clones EET-95, EET-96, EET-103 y CCN-51, respectivamente, éste último utilizado como control, para ello, se determinó la cantidad de bacterias, hongos y actinomicetos totales, expresados en unidades formadoras de colonias (UFC) por gramo de suelo, presentes en la rizósfera de los tres clones de cacao, así como la aparición de las principales enfermedades que atacan al cultivo del cacao. Los datos fueron analizados estadísticamente mediante ANOVA de un factor y prueba HSD de Tukey p≤0,05. Las bacterias fueron los microorganismos de mayor asociación a los clones en este estudio, seguido de actinomicetos y hongos. El clon CCN-51 presentó la mayor cantidad de bacterias, los clones EET-96 y EET-103, presentaron mayor incidencia de actinomicetos y el clon EET-103, la mayor presencia de hongos. La enfermedad escoba de bruja, cuyo agente causal es Cripinellis perniciosa Sthael Singer., afectó en menor medida a los clones EET-103 y CCN-51, mientras que la moniliasis causada por el hongo Moniliophthora roreri (Cif and Par) Evans et al., puso en evidencia al clon EET-103 con la mayor incidencia de esta enfermedad y conversivamente al clon CCN-51 con la menor incidencia del patógeno.

Introduction.Moniliophthoraspp. species are endemic from South America and infect America’s cocoa crops.Objective.The objective of the study was to analyze the potential distribution and the fundamental niche ofMoniliophthora roreri (Mr)andM. perniciosa (Mp)in America and Africa.Materials and methods.The occurrence records were obtained from a bibliographic review. Bioclimatic variables were used as predictors in the maximum entropy niche model (MaxEnt) and for its visualization in Niche Analyst 3.0.Results.The areas whereMrwas most likely to occur were Esmeraldas and Los Ríos, Ecuador, coastal zones of Costa Rica, Santander and Antioquia of Colombia, and forMpthe States of Bahia and Acré of Brazil. The variables that most influenced the distribution ofMrare those associated with precipitation. Temperature-related conditions were more important in theMpmodel. The risk ofMrinvasion was identified in the Acre and Pará regions, Brazil. The transfer of the models evidenced the potential ofMrandMpinvasion in cocoa crops in Africa. The fundamental niche of pathogens and cocoa showed average similarity values, while the niche of fungal species showed a low similarity. Low pathogen niche similarity and differences in bioclimatic variables affecting pathogens distribution were related to a process of niche partitioning.Conclusion.Geographical regions with a greater potential distribution of pathogens and bioclimatic characteristics that would favor their probability of presence in America’s cocoa crops were identified. It is necessary to regulate the transport of contaminated plant material and equipment between regions to avoid the introduction of pathogens in healthy cocoa crops. Introducción.Las especies deMoniliophthoraspp. son endémicas de Sudamérica e infectan los cultivos de cacao de América.Objetivo.El objetivo del estudio fue analizar la distribución potencial y el nicho fundamental deMoniliophthora roreri (Mr)yM. perniciosa (Mp)en América y África.Materiales y métodos.Los registros de ocurrencia fueron obtenidos de una revisión bibliográfica. Se utilizaron variables bioclimáticas como predictores en el modelo de nicho de máxima entropía (MaxEnt) y para su visualización en Niche Analyst 3.0.Resultados.Las zonas donde se registró mayor probabilidad de ocurrencia deMrfueron Esmeraldas y Los Ríos, Ecuador, zonas costeras de Costa Rica, Santander y Antioquia de Colombia, y paraMplos Estados de Bahía y Acré de Brasil. Las variables que más influyeron en la distribución deMrestán asociadas a las precipitaciones. Las condiciones relacionadas con la temperatura fueron más importantes en el modelo deMp. Se identificó el riesgo de invasión deMren las regiones de Acré y Pará, Brasil. La transferencia de los modelos evidenció el potencial de invasión deMryMpen los cultivos de cacao en África. El nicho fundamental de los patógenos y el cacao presentó valores de similitud medios, mientras que, el nicho de las especies de hongos mostró una baja similitud. La baja similitud de los nichos de los patógenos y las diferencias en las variables bioclimáticas que afectan su distribución se podrían relacionar a un proceso de partición del nicho.Conclusión.Se identificaron las regiones geográficas con una mayor distribución potencial de los patógenos y las características bioclimáticas que favorecerían su probabilidad de presencia en los cultivos de cacao de América. Es necesario regular el transporte de material vegetal y equipo contaminado entre regiones para evitar la introducción de los patógenos en cultivos de cacao sanos.

Submitted by Maria Fernanda Zaneli Campanari (fernanda.campanari@unesp.br) on 2019-09-25T13:37:01Z No. of bitstreams: 1 dissertation.pdf: 14133454 bytes, checksum: d637a3cca6d630e7614a99fbe72b1757 (MD5) Rejected by Adriana Helena Vitta Zoratti (adriana.zoratti@unesp.br), reason: Solicitamos que realize correções na submissão seguindo as orientações abaixo: 1- Conforme orientado no tutorial, na submissão online é obrigatório adicionar também o resumo em inglês (abstract) e palavras chaves em inglês. 2- Inserir o Certificado de Aprovação (item obrigatório). 3- A ficha catalográfica e o certificado de aprovação devem ser inseridos no mesmo arquivo de sua tese, seguindo a ordem (segundo as "Normas para elaboração de dissertação e tese dos programas de pós-graduação", disponível na página da Pós-graduação): -Primeira página -Página de rosto -Ficha catalográfica -Certificado de aprovação 4- Retirar todas as folhas em branco. 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No. of bitstreams: 1 campanari_mfz_me_jabo.pdf: 16345208 bytes, checksum: 090191932b8c8772b5c38743eb1c4a7c (MD5) Previous issue date: 2019-08-26 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) O cultivo intensivo agrícola, apesar de altamente produtivo, possui diversos pontos questionáveis, como suplementação acentuada de insumos sintéticos, além da aplicação de defensivos para o controle de pragas que muitas vezes são danosos ao meio ambiente. Como alternativa, a agricultura orgânica propõe uma forma de manejo menos agressiva, que promove o uso sustentável dos recursos naturais renováveis, como o aproveitamento de resíduos orgânicos, além de possuir um maior valor agregado no produto final. No presente estudo, investigamos por meio de uma abordagem metagenômica os efeitos do manejo (orgânico ou convencional) na microbiota da rizosfera de cana-de-açúcar, região da planta que notoriamente causa um grande impacto no seu desenvolvimento e produtividade. Identificamos a abundância maior na rizosfera com manejo orgânico de porções genômicas que codificam enzimas associadas ao metabolismo do nitrogênio e enxofre, sendo que estes são nutrientes fundamentais para o sucesso da planta e assim, seu desenvolvimento e produtividade em campo. Contraditoriamente, encontramos também que os genomas da microbiota orgânica possuem conteúdo ligado a um potencial mais acentuado para a degradação de compostos xenobióticos, que são ativamente aplicados no manejo convencional. De acordo com nossa predição, os microrganismos dessa microbiota poderiam realizar sua completa mineralização, o que é muito favorável na remoção desses resíduos no ambiente. Esses achados indicam que há um potencial único para exploração do cultivo orgânico, além da capacidade de fornecer alimentos livres de agroquímicos por meio de um manejo que propende causar um menor impacto ao ambiente agroecológico. Consideramos, com base nos resultados, que esse ambiente pode ser uma fonte de bioprospecção de microrganismos associados aos ciclos de nutrientes, como N e S, além de potenciais degradadores de xenobióticos para biorremediação. Modern industrialized agriculture although highly productive, has several sustainability problems such as the for intense supplementation of synthetic inputs, beyond the application of pesticides for pest control. Which are often harmful to environment. As an alternative to this system, organic agriculture is considered more environmentally progressive, having several characteristics favorable to the crop producer, promotes sustainable use of renewable natural resources, such as the use of organic waste, besides that a higher aggregated value in the final product. This study investigates the changes that an organic system brings when compared to conventional management for the sugarcane rhizosphere microbiome, a plant region known to be determinant of plant development and associated with net productivity, using a metagenomic approach. We identified a higher abundance of genomic portions which encode enzymes associated with nitrogen and sulphur metabolism, which are fundamental nutrients for plant success and subsequently, crop productivity. Conversely, we also found that genomes of the organic microbiome contain higher portions linked to xenobiotic degradation, compounds that are actively applied in conventional management. Microorganisms from this sequenced microbiome could perform complete mineralization of these damaging compounds, which is desirable in their removal from the environment. These findings indicate that there is a unique potential for exploitation of organic farming, in addition to the ability to provide agrochemical-free through management that tends to have a lower impact on the agroecological environment. Based on the results, the organic system environment may be a source of microorganisms associated with nutrient cycles - nitrogen and sulphur, as well as microbes associated with bioremediation through xenobiotics degradation. FAPESP: 20179008-5 CAPES: 132200/2018-0

The secretion of metabolites with antimicrobial activity is one of the strategies employed by bacteria in response to negative stimuli promoted during interspecies competition. In its stationary phase Pseudomonas aeruginosa and Escherichia coli can synthesize diffusible exometabolites whose action is to mutually inhibit the exposed cells, ensuring the balance of both populations in a given place. The former may have an advantage due to the production of pyocyanine. However, the excretion of indol and acetate by E. coli can balance this advantage. This study aimed to detect the influence of indol and acetate on the synthesis of pyocyanin and adhesion of P. aeruginosa, as well as the action of pyocyanin on viable E. coli cells, as well as its adhesion. For this purpose, in vitro tests were conducted to determine the Minimum Inhibitory Concentration (MIC), extraction and quantification of pyocyanin and adhesion by the violet crystal method. The synthesis of piocyanin by Pseudomonas aeruginosa was reduced by up to 50% in the presence of indol. On the other hand, no change in pigment production was observed in the presence of acetate, alone or associated with concentrations lower than 0.5 mM, reflecting an increase of more than 20% in piocyanine production. Indol was also effective in reducing the adhesion of Pseudomonas aeruginosa cells compared to control. For the E. coli strains, the MIC of pyocyanin was 37.5 µg/mL, also reducing cell adhesion. It was observed that despite the inhibition having occurred, no exometabolite promoted biocidal effect in the evaluated strains. The results contribute to the understanding of the ecological mechanisms that occur during the competition between these two bacterial species in aqueous medium. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES A secreção de metabólitos com atividade antimicrobiana é uma das estratégias empregadas por bactérias como resposta aos estímulos negativos promovidos durante a competição interespécies. Em sua fase estacionária Pseudomonas aeruginosa e Escherichia coli podem sintetizar exometabólitos difusíveis cuja ação é inibir mutualmente as células expostas, garantindo o equilíbrio de ambas as populações num determinado sítio. A primeira pode levar vantagem em razão da produção de piocianina. Entretanto, a excreção de indol e acetato pela E. coli pode equilibrar esta vantagem. Este trabalho teve o objetivo de detectar a influência do indol e acetato sobre a síntese de piocianina e adesão da P. aeruginosa, bem como a ação da piocianina sobre as células viáveis de E. coli, bem como de sua adesão. Para isso, foram conduzidos ensaios in vitro de determinação da Concentração Inibitória Mínima (CIM), de extração e quantificação de piocianina e da adesão, pelo método do cristal violeta. A síntese de piocianina por Pseudomonas aeruginosa foi reduzida em até 50% na presença do indol. Por outro lado, não foi observada alteração na produção do pigmento na presença de acetato, isoladamente ou associado com concentrações menores que 0,5 mM, refletindo um aumento de mais de 20% da produção de piocianina. O indol também se mostrou eficaz na redução da adesão de células de Pseudomonas aeruginosa, comparadas ao controle. Para as linhagens de E. coli, a CIM de piocianina foi 37,5 µg/mL, reduzindo também a adesão celular. Observouse que apesar da inibição ter ocorrido, nenhum exometabólito promoveu efeito biocida nas linhagens avaliadas. Os resultados contribuem para a auxiliar a compreensão dos mecanismos ecológicos que ocorrem durante a competição entre estas duas espécies bacterianas em meio aquoso.

Se realizó un estudio sobre la influencia de la contaminación orgánica por vertidos de alpechín. En las poblaciones microbianas de dos sistemas acuáticos y los impactos producidos en la dinámica de dichos sistemas como resultado de los procesos de depuración, Universidad de Granada, Facultad de Ciencias. Leída el 25-04-1981

1. Microbial heterotrophic activity is a major driver of nutrient and organic matter processing in the hyporheic zone of headwater streams. Additionally, the hypor‐ heic zone might provide refuge for microbes when surface flow ceases during drought events. 2. We investigated chemical (organic and inorganic nutrients) and microbiological parameters (bacterial cell concentration, live–dead ratios, and extracellular en‐ zyme activities) of surface and interstitial pore water in a period of progressive surface-hyporheic disconnection due to summer drying. The special situation of the chosen study reach, where groundwater mixing is impeded by the bedrock forming a natural channel filled with sediment, allowed as to study the transfor‐ mation of these parameters along hyporheic flow paths. 3. The chemical composition of the hyporheic pore water reflected the connectivity with the surface water, as expressed in the availability of nitrate and oxygen. Conversely, microbiological parameters in all hyporheic locations were different from the surface waters, suggesting that the microbial activity in the water changes rapidly once the water enters the hyporheic zone. This feature was prin‐ cipally manifested in higher live–dead ratios and lower leucine aminopeptidase (an activity related to nitrogen acquisition) in the hyporheic pore waters. 4. Overall, bacterial cell concentration and extracellular enzyme activities increased along hyporheic flow paths, with a congruent decrease in inorganic nutrients and dissolved organic matter quantity and apparent molecular size. 5. Our findings show two important functions of the hyporheic zone during drought: (1) deeper (−50 cm) water-saturated layers can act as a refuge for microbial activity; and (2) the hyporheic zone shows high rates of carbon and nitrogen turnover when water residence times are longer during drought. These rates might be even enhanced by an increase in living microbes in the remaining moist locations of the hyporheic zone FP7 People: Marie-Curie Actions, Grant/ Award Number: 607150; FP7 Environment, Grant/Award Number: 603629-ENV-6.2.1

Memoria de tesis doctoral presentada por Guillem Salazar Guiral para obtener el título de Doctor en Ciencias del Mar por la Universitat Politècnica de Catalunya (UPC), realizada bajo la dirección del Dr. Josep M. Gasol y la Dra. Silvia G. Acinas del Institut de Ciències del Mar (ICM-CSIC).-- 233 pages, [EN] The dark ocean contains about 70% of the ocean’s microbial cells and 60% of its heterotrophic activity, which is mainly fueled by the flux of organic particles produced in the surface ocean and exported to the bathypelagic ocean (1,000 – 4,000 m depth). The bathypelagic ocean represents a nonhomogeneous environment and contains a variety of particles that are considered as the main supply of organic carbon to this environment. The microorganisms inhabiting this realm play a pivotal regulatory role in the biogeochemical cycles at a planetary scale. Accordingly, the study of these microorganisms is an essential step to decipher the ecological functioning of the deep ocean. Chapters 1 to 3 in this Thesis are dedicated to the description of the prokaryotic community composition in the bathypelagic ocean at a global scale through the sequencing of ribosomal DNA and RNA fragments using data collected during the Malaspina 2010 expedition. [...], [ES ] El océano profundo contiene el 70% de las células microbianas del océano las cuales suponen el 60% de la actividad heterotrófica. Dicha actividad biológica está mantenida por un flujo de partículas orgánicas producidas en el océano superficial y exportadas al océano batipelágico (1,000 - 4,000 m de profundidad). Éste no es, por tanto, un ambiente homogéneo, sino que contiene una variedad de partículas consideradas el aporte dominantede carbono orgánico. Los microorganismos de este ambiente tienen, por tanto, unpapel regulatorio central en los ciclos biogeoquímicos planetarios. Consecuentemente, el estudio de estos microorganismos supone un paso esencial para descifrar el funcionamiento ecológico del océano profundo. [...], [CAT] L’oceà profund conté el al voltant d’un 70% de las cèl·lules microbianes de l’oceà, les quals suposen el 60% de la activitat heterotròfica. Aquesta activitat biològica està mantinguda por un flux de partícules orgàniques produïdes a oceà superficial y exportades al batipelàgic (1,000 - 4,000 m de profunditat). L’ecosistema batipelàgic no és un ambient homogeni, sinó que conté una varietat de partícules considerades la font dominant de carboni orgànic. Els microorganismes d’aquest ambient tenen, doncs, un paper regulador central als cicles biogeoquímics planetaris. Conseqüentment, l’estudi d’aquests microorganismes suposa un pas essencial per desxifrar el funcionament ecològic de l’oceà profund. [...]

Orientador: Prof. Dr. Higo Forlan Amaral Coorientador: Prof.ª Dr.ª Neucimara Rodrigues Ribeiro Dissertação (mestrado em Agroecologia)--Universidade Estadual de Maringá, Centro de Ciências Agrárias, Departamento de Agronomia, 2019 Resumo: Existe relevante perspectiva que ao adotar as técnicas conservacionistas de plantas de cobertura, enriquecimento da matéria orgânica e controle biológico os solos tornem-se mais supressivos que controle a população de M. incognita em soja. O objetivo deste trabalho foi avaliar o nível de controle populacional de M. incognita em milheto, urochloa, soja em solos tratados com matéria orgânica ativada e controle biológico (Paecilomyces) em curto e médio prazo. Utilizou-se Delineamento Inteiramente Casualizado (DIC) em esquema fatorial (3 x 2 x 2), sendo o primeiro fator duas plantas de cobertura (urochloa e milheto), segundo fator com e sem matéria orgânica ativada, o terceiro fator com e sem controle biológico somando aos fatores um tratamento branco, com quatro repetições, totalizando 72 parcelas. Ocorreram três etapas experimentais: primeiro, preparo do inóculo e matéria orgânica inoculada com microrganismos, segundo inoculação de Paecilomyces nas sementes das plantas de cobertura e soja, e por último, novo plantio de soja nos mesmos solos dos tratamentos anteriores. Aferiu-se nos finais das etapas 2 e 3 as seguintes variáveis: nota, massa fresca de raiz, número final de nematoide que foi convertido para número de nematoide por grama de raiz, fator de reprodução e percentual de controle. Aplicou-se ANOVA e teste de Duncan 5%, foi utilizado transformação log(x*1) para os dados que não atingiram pressupôs para ANOVA. Aplicou-se também, análise multivariada de Cluster pelo algoritmo UPGMA e índice de similaridade Bray-Curtis. Em curto prazo, houve distinto efeito das plantas e suas interações com matéria orgânica ativada e controle biológico. Sob soja, independente de matéria orgânica ativada e controle biológico, não se observou diminuição de M. incognita. Já milheto*matéria orgânica ativada*controle biológico e urocloa*matéria orgânica ativada*controle biológico, em curto prazo, apresentaram maior efeito de controle deste nematoide. Em médio prazo, para verificar o efeito residual dos tratamentos da etapa 2, também o efeito do tipo de planta foi mais expressivo. O efeito residual urocloa-soja demonstrou que o tratamento urocloa*matéria orgânica ativada*controle biológico resultou para a soja massa fresca de raiz, menor número de nematoide por grama de raiz e menor fator de reprodução e consequente maior percentual de controle. O cultivo de soja-soja demonstrou efeito de percentual de controle positivo quando em controle biológico, no entanto, a massa fresca de raiz ficou menor sendo limitante para potencial produtivo. O efeito de milheto-soja um percentual de controle positivo quando milheto*matéria orgânica ativada*controle biológico, porém, com altos valores de número de nematoide por grama de raiz e fator de reprodução. As técnicas de manejo integrado Meloidogyne são diversas e complexas, mas existe uma crescente perspectiva do uso de urocloa para melhorias da qualidade do solo, que pelos resultados somam-se o benefício para supressão desse nematoide, sendo potencializado com o uso de matéria orgânica inoculada com microrganismos Abstract: There is a relevant perspective that when adopting the techniques of conservation of cover crops, organic matter enrichment and biological control, the soils become more suppressive that control the M. incognita population in soybean. The objective of this work was to evaluate the level of population control of M. incognita in millet, urochloa, soybean in soils treated with activated organic matter and biological control (Paecilomyces) in the short and medium term. It was used a completely randomized design (DIC) in a factorial scheme (3 x 2 x 2), the first factor being two covering plants (urochloa and millet), second factor with and without activated organic matter, the third factor with and without control with a white treatment, with four replications, totaling 72 plots. There were three experimental stages: first, preparation of the inoculum and organic matter inoculated with microorganisms, according to inoculation of Paecilomyces in the seeds of cover crops and soybean, and finally, new soybean planting in the same soils of previous treatments. The following variables were checked at the end of steps 2 and 3: note, fresh root mass, final nematode number converted to nematode number per root gram, reproduction factor and control percentage. ANOVA and 5% Duncan test were used, log transformation (x * 1) was used for data that did not reach assumptions for ANOVA. It was also applied, Cluster multivariate analysis by the UPGMA algorithm and Bray-Curtis similarity index. In the short term, there was a distinct effect of the plants and their interactions with activated organic matter and biological control. Under soybean, independent of activated organic matter and biological control, no decrease of M. incognita was observed. On the other hand, millet * activated organic matter * biological control and urocloa * activated organic matter * biological control, in the short term, presented greater control effect of this nematode. In the medium term, to verify the residual effect of the treatments of step 2, also the effect of the type of plant was more expressive. The residual urocloa-soja effect showed that the urocloa * activated organic matter * biological control treatment resulted in fresh root mass, lower nematoid number per gram of root and lower reproductive factor and consequent higher percentage of control. Soya-soybean cultivation showed a positive control percentage effect when in biological control, however, the fresh root mass was lower, being limiting to productive potential. The effect of millet-soybean was a positive control percentage when millet * activated organic matter * biological control, however, with high numbers of nematode per grass root and reproduction factor. The integrated management techniques of Meloidogyne are diverse and complex, but there is a growing perspective on the use of urocloa for soil quality improvements, which add to the benefits of suppressing this nematode, being potentiated with the use of organic matter inoculated with microorganisms

Agradecimentos: This study was funded by Fundação de Amparo à Pesquisa do Estado de São Paulo (15/02395-8) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (141298/2017-0). The authors thank the Centroflora group for their assistance in the collection of passionflower leaves, as well as to Ph.D. Glyn Maria Figueira of the Agricultural, Biological and Chemical Research Center (University of Campinas) for the expertise on the biology of the plant Abstract: Plants and endophytic microorganisms have coevolved unique relationships over many generations. Plants show a specific physiological status in each developmental stage, which may determine the occurrence and dominance of specific endophytic populations with a predetermined ecological role. This study aimed to compare and determine the structure and composition of cultivable and uncultivable bacterial endophytic communities in vegetative and reproductive stages (RS) of Passiflora incarnata. To that end, the endophytic communities were assessed by plating and Illumina-based 16S rRNA gene amplicon sequencing. Two hundred and four cultivable bacterial strains were successfully isolated. From the plant’s RS, the isolated strains were identified mainly as belonging to the genera Sphingomonas, Curtobacterium, and Methylobacterium, whereas Bacillus was the dominant genus isolated from the vegetative stage (VS). From a total of 133,399 sequences obtained from Illumina-based sequencing, a subset of 25,092 was classified in operational taxonomy units (OTUs). Four hundred and sixteen OTUs were obtained from the VS and 66 from the RS. In the VS, the most abundant families were Pseudoalteromonadaceae and Alicyclobacillaceae, while in the RS, Enterobacteriaceae and Bacillaceae were the most abundant families. The exclusive abundance of specific bacterial populations for each developmental stage suggests that plants may modulate bacterial endophytic community structure in response to different physiological statuses occurring at the different plant developmental stages CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQ FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP Aberto

As áreas destinadas à revegetação na região explorada pela Petrobras para a extração de gás e petróleo na Amazônia é constituída de solos com baixa fertilidade e baixo potencial de inoculo de microrganismos benéficos para as plantas. Por isso, a colonização das raízes pelos fungos micorrízicos arbusculares podem acelerar o crescimento e as chances de sobrevivência das plântulas no campo. O objetivo deste trabalho foi avaliar a importância da associação micorrízica arbuscular em espécies nativas cultivadas em áreas de clareiras visando a revegetação e recuperação de solos degradados e sua relação com os teores de nutrientes foliares. Foram amostradas folhas, solos e raízes de plantas que atingiram índice de colonização por FMAs acima de 10% em 12 clareiras/jazidas da Província Petrolífera de Urucu no mês de julho de 2005. Os teores de nutrientes nas folhas variaram muito entre as espécies. A sequência de macronutrientes acumulados foi K > Ca > Mg > P para a goiaba de anta, palheteira e vermelhinho e micronutrientes Fe >> Zn > Mn para a goiaba de anta, jucá e visgueiro. Os solos se mostraram ácidos, com baixos teores de K, Zn e Mn, porém com altos níveis de P, Al e Fe. A colonização por FMAs variou entre 0 a 34,8%, com a presença apenas de vesículas, não sendo encontrados hifas e arbúsculos. A ausência de hifas sugere falta de contribuição efetiva da associação micorrízica na nutrição das plantas.

El objetivo de esta tesis fue dilucidar los mecanismos fisiológicos involucrados en el control de la dormición en aquenios de girasol (Helianthus annuus L.) y derivar tecnologías para su eliminación a escala industrial. Se utilizó una línea endocriada y un híbrido comercial y los resultados permitieron identificar que, en ambos genotipos, la dormición está impuesta por el pericarpio (uno de los tejidos que recubre al embrión) y su expresión ocurre sólo a altas temperaturas de incubación (i.e., 30°C). Sin embargo, no fue posible derivar un único patrón de comportamiento fisiológico para ambos genotipos. Estos patrones se encuentran gobernados por la temperatura a la que se hayan expuestos los aquenios durante la incubación (sólo se expresan a 30ºC), pero varían los componentes intervinientes en la respuesta a la dormición en cada genotipo. El pericarpio impuso limitación de oxígeno al embrión (hipoxia) y estos genotipos exhibieron diferencias en su sensibilidad embrionaria a la hipoxia a 30°C. En la línea endocriada, la principal limitación para la germinación del aquenio estuvo impuesta por la alta sensibilidad embrionaria a la hipoxia (mediada por una interferencia en la sensibilidad al ABA), que aumenta a 30ºC, la cual, en combinación con el aumento del consumo de oxígeno por la actividad (respiración) microbiana, resultó en expresión de la dormición. En aquenios del híbrido comercial, en cambio, la principal limitación para la germinación provino principalmente de la presencia del pericarpio que representa una severa restricción cuando la actividad microbiana en el pericarpio es aumentada por la alta temperatura de incubación. Esta tesis, además, permitió desarrollar una herramienta tecnológica aplicable a escala industrial, que fue la utilización del hipoclorito de sodio (agente oxidante), y, a su vez, planteó la posibilidad de aplicar un tratamiento de fungicidas y bactericidas durante el curado de las semillas en la industria semillera.

Hydrological drought is a process of natural desiccation mainly due to large shortage of rainfall events. Reduced precipitations and prolonged droughts are spreading worldwide and threaten the integrity of aquatic ecosystems. Most Mediterranean streams have an intermittent flow which may become more variable and with larger duration of their no-flow periods under climate change. The enlargement of the dry period can importantly influence the ecosystem functioning, altering the microbiota inhabiting the streambed sediment as well as the processes they carry out (e.g. nutrients cycling). Consequently, hydrological alterations can reduce, limit or change microbial community functions, structure and composition, and therefore compromise the overall aquatic ecosystem functioning. The main objectives of this thesis are to study the responses of bacteria archaea and fungi inhabiting sediment to prolonged dry phase events and to wet episodes, spacing from punctual rains to rewetting events La sequía hidrológica es un proceso de desecación natural debido principalmente a la gran escasez de eventos de lluvia. Las precipitaciones reducidas y las sequías prolongadas se están extendiendo por todo el mundo y amenazan la integridad de los ecosistemas acuáticos. La mayoría de las corrientes mediterráneas tienen un flujo intermitente que puede volverse más variable y con una mayor duración de sus períodos sin flujo bajo el cambio climático. La ampliación del período seco puede influir de manera importante en el funcionamiento del ecosistema, alterando la microbiota que habita en el sedimento fluvial, así como los procesos que llevan a cabo (por ejemplo, el ciclo de nutrientes). En consecuencia, las alteraciones hidrológicas pueden reducir, limitar o cambiar las funciones, la estructura y la composición de la comunidad microbiana y, por lo tanto, comprometer el funcionamiento general del ecosistema acuático. Los objetivos principales de esta tesis son estudiar las respuestas de bacterias, arqueas y hongos que habitan en sedimentos a eventos prolongados de fase seca y episodios húmedos, espaciando desde lluvias puntuales hasta eventos de rehumectación Programa de Doctorat en Ciència i Tecnologia de l'Aigua

The objective of the study was to evaluate the effect of a change in management on the soil microbial community and C sequestration. We conducted a 3-year field study in La Pampa (Argentina) with rotation of sorghum (Sorghum bicolor) in zero tillage alternating with rye (Secale cereale) and vetch (Vicia villosa ssp. dasycarpa). Soil was sampled once a year at two depths. Soil organic matter fractions, dissolved organic matter, microbial biomass (MBC) and community composition (DNA extraction, qPCR, and phospholipid FAME profiles) were determined. Litter, aerial- and root biomass were collected and all material was analyzed for C and N. Results showed a rapid response of microbial biomass to a bacterial dominance independent of residue quality. Vetch had the highest diversity index, while the fertilized treatment had the lowest one. Vetch–sorghum rotation with high N mineralization rates and diverse microbial community sequestered more C and N in stable soil organic matter fractions than no-till sorghum alone or with rye, which had lower N turnover rates. These results reaffirm the importance of enhanced soil biodiversity for maintaining soil ecosystem functioning and services. The supply of high amounts of N-rich residues as provided by grass–legume cover crops could fulfill this objective. EEA Anguil Fil: Frasier, Ileana. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Pampa. Facultad de Agronomía; Argentina Fil: Noellemeyer, Elke. Universidad Nacional de La Pampa. Facultad de Agronomía; Argentina Fil: Figuerola, Eva Lucia Margarita. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular; Argentina Fil: Erijman, Leonardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular; Argentina Fil: Permingeat, Hugo. Universidad Nacional de Rosario. Facultad de Ciencias Agrarias; Argentina Fil: Quiroga, Alberto Raul. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil; Argentina. Universidad Nacional de La Pampa. Facultad de Agronomía; Argentina

Tesis Univ. Granada. Departamento de Microbiología. Tesis leída el 19 de diciembre de 2005

Los objetivos del presente trabajo han sido: Evaluar la eficacia antimicrobiana de NaClO al 2.5%, CHX al 2%, ALX al 2% y CTR al 0,2%, frente a biopelículas polimicrobianas de origen endodóntico, formadas en dentina, mediante tinción de fluorescencia y microscopía de barrido láser confocal. Comparar entre sí la efectividad antimicrobiana de las distintas soluciones ensayadas sobre biopelículas polimicrobianas maduras. Determinar si la adicción de cetrimida al 0,2% mejora la actividad antimicrobiana de soluciones de CLX y ALX., Tesis Univ. Granada. Programa Oficial de Doctorado en Medicina Clínica y Salud Pública

This Doctoral Thesis has been focused on the role of the Rsm family of global post-transcriptional regulators on bacterial biofilm formation and c-di-GMP signaling, using as a model system Pseudomonas putida KT2440, a bacterium of agronomic interest for its properties as PGPR. Earlier work in the research group had established that the two-component regulatory system GacS/GacA controls expression of adhesins required for biofilm formation in this bacterium. Given that in other microorganisms this two-component system is part of a regulatory cascade mediated by Rsm family proteins, the objectives of this Thesis have included the characterization of these proteins in P. putida KT2440, analyzing their involvement in biofilm formation and c-di-GMP signaling, and to begin studying their role as global regulators. Chapter 1, “Self-Regulation and Interplay of Rsm Family Proteins Modulate the Lifestyle of Pseudomonas putida”, describes the role of the three proteins of the CsrA/RsmA family of post-transcriptional regulators present in P. putida KT2440 (RsmA, RsmE and RsmI) in the lifestyle of this bacterium. For that purpose, single, double and a triple mutant were constructed and characterized, and the three genes overexpressed under the control of a constitutive promoter. The triple mutant showed reduced swimming and swarming motility, and altered dynamics of biofilm formation. The biomass attached to abiotic surfaces is higher than in the wild type, but the biofilm disperses earlier, although the phenotype varies on different surfaces. On the other hand, overexpression of RsmE or RsmI causes reduced biofilm formation. Expression analysis of the different adhesins and exopolysaccharides revealed that these alterations could be due to changes in the extracellular matrix and in the timing of synthesis of its elements (Huertas-Rosales et al., 2016) In chapter 2, “The Pseudomonas putida CsrA/RsmA homologues negatively affect c-di-GMP pools and biofilm formation through the GGDEF/EAL response regulator CfcR”, we expanded the study of the regulation of cfcR expression. This gene encodes the unique response regulator with GGDEF/EAL domains in P. putida KT2440. Expression of cfcR is regulated at the transcriptional level by RpoS, ANR and FleQ, and its diguanylate cyclase activity requires the multisensor hybrid histidine kinase CfcA. In this chapter, an additional level of regulation is described, operating at the post-transcriptional level through RsmA, RsmE and RsmI. Direct binding of these proteins to a specific motif overlapping the initiation codon of cfcR (5´-CAUGGAUG-3´) is demonstrated. The lack of Rsm proteins causes de-repression of cfcR. We also show that in stationary phase the c-di-GMP pool in KT2440 is mostly dependent on the activity of CfcR, and that in a triple rsm mutant the levels of second messenger are not only higher but increase earlier during growth. Results from this chapter allow us to establish that the Gac/Rsm/c-di-GMP signaling cascade operates in P. putida through CfcR. In the third charper “Global analysis of the Rsm regulon in Pseudomonas putida KT2440”, a RIP-seq study was performed to elucidate all possible genes that are directly regulated by Rsm proteins in P. putida. Over 400 genes, intergenic regions and potential sRNA are targets for these proteins, some being specific for each of them and others being shared by two (95) or the three (38) Rsm proteins. We have confirmed that cfcR and elements involved in its regulation are among the identified targets, as expected from the results in chapter 2. Other biofilm related genes have also been found in this study. Although the analysis of targets is still preliminary, thanks to this work we have a long list of genes and new sRNA that will allow us to complete the regulatory map associated to Rsm proteins in P. putida KT2440., Tesis Univ. Granada. Programa Oficial de Doctorado en: Biología Fundamental y de Sistemas, Proyectos del Ministerio de Economía y Competitividad y EFDR BFU2010-17946, BFU-2013-43469-P y BFU2016-80122-P y la beca de doctorado FPI EEBB-BES-2011-017539).

"Gran parte de la producción de los alimentos en México se basa en el uso de insumos industriales, entre los cuales se encuentran una gran diversidad de agroquímicos, los cuales causan diversos efectos al ambiente y a la salud pública. Es por esto que se recomienda optar por una producción más cercana a la Agroecología y biorremediar los suelos contaminados con estas sustancias. El objetivo del presente trabajo fue evaluar los procesos metabólicos en aislamientos bacterianos ambientales con aplicación en prácticas agroecológicas. Se realizaron muestreos de suelo en zonas con diferente manejo agrícola, las zonas de estudio son pertenecientes a Vicente Guerrero localizado en Tlaxcala, Los Mochis, Sinaloa y Chachapa, Puebla. De cada una de las muestras se realizó la identificación bacteriana mediante un medio cromogénico, las bacterias se colocaron en diferentes medios para conocer su actividad metabólica, se determinó su capacidad de formación de biopelícula, la inhibición bacteriana en presencia de 2,4-D, Malation y Carbofuran. Y se evaluó la degradación de los plaguicidas por medio de un consorcio bacteriano conformado de los aislamientos que presentaron mayor viabilidad en presencia de los plaguicidas."

The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS) in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition – isolated from sediments of the Eden Estuary (Scotland, UK) – on non-cohesive glass beads (

Uncertainties exist regarding the magnitude of in situ dissolved organic matter (DOM) processing in lotic systems. In addition, little is known about the effects of extreme hydrological events on in-stream DOM retention or release during downriver transport. This study quantified the net in-stream retention/release efficiencies (η) of dissolved organic carbon (DOC) and its humic and protein-like fluorescent fractions along a Mediterranean river during drought, baseflow and flood conditions. High performance size exclusion chromatography was used to describe the apparent size distributions of the humic and protein-like DOM moieties. A snapshot mass balance allowed estimating the η values of DOC and humic and protein-like fractions. Significant DOM net retention (η < 0) was detected during the drought condition and the protein-like fraction was more retained than the humic-like fraction and bulk DOC. In addition, small substances were more efficiently retained than larger substances. DOC retention decreased under baseflow conditions, but it remained significant. The humic and protein-like net efficiencies exhibited high variability, but the net retention were not significant. From a longitudinal perspective, the entire fluvial corridor contributed net retention of DOC and humic and protein-like moieties net retention during drought condition. In contrast, net retention/release efficiencies exhibited spatial variability during baseflow condition. The flood preferentially mobilized large size DOM molecules and the fluvial corridor behaved as a homogeneous passive DOM (η = 0) conduit. This research highlights the relevance of hydrological extreme events on the magnitude of DOM retention/release mass balance and emphasizes the need to perform measurements during these conditions to quantify the impact of fluvial corridors on DOM fate and transport This research is funded by the Spanish Ministry of Education and Science (MEC) (CGL2011-30151-C02 and CGL2014-5876-C3-R) and European Community 7th Framework Programme (No. 603629- ENV-2013-6.2.1-Globaqua)

Tese de Doutoramento, Ciências do Mar, especialidade de Biologia Marinha, 20 de abril de 2018, Universidade dos Açores. Os oceanos são o maior habitat da Terra e cobrem aproximadamente dois terços da superfície do planeta. Desde as águas superficiais até às fossas abissais, os ambientes marinhos podem atingir 11 km de profundidade e pressões superiores a 1000 bar, variar entre temperaturas de 0 ºC nas regiões polares e mais de 300 ºC nas fontes hidrotermais. Em todos estes ecossistemas marinhos proliferam microorganismos que, independentemente das condições, conseguem colonizar até mesmo as regiões mais inóspitas do mar profundo e do subsolo oceânico. As fontes hidrotermais de profundidade são ambientes marinhos reconhecidos como pontos de ligação entre a litosfera e os oceanos, sendo mesmo consideradas “janelas” para a biosfera do subsolo. Nestes locais, por entre fissuras da crosta oceânica, há emissões de fluidos hidrotermais, uma combinação de gases e metais vinda do interior da Terra que é projectada para o oceano a elevadas temperaturas. Estes fluidos transportam espécies químicas reduzidas, geradas pelo contacto entre gases e minerais existentes na crosta oceânica, que servem de alimento a microorganismos quimioautotróficos dos domínios Bacteria e Archaea. Estes microorganismos desenvolveram estratégias fisiológicas únicas para conseguirem prosperar em tais condições, como a produção de enzimas e compostos activos alternativos, despertando o interesse dos cientistas para o potencial biotecnológico dos seus recursos genéticos. Bactérias e arqueas quimioautotróficas são os únicos organismos capazes de produzir matéria orgânica a partir de energia química. Estes microorganismos asseguram a produção primária nestes ambientes e a transferência de energia para a cadeia trófica, sustentando assim a vida no mar profundo. Dado o património genético, metabolismos próprios e capacidade de estabelecer relações de simbiose com outros organismos, estas bactérias e arqueas são potencialmente representativas dos organismos primordiais da Terra, e o seu estudo pertinente na explicação da origem e evolução da vida. Por desempenharem também um papel importante no ciclo biogeoquímico entre a crosta e o oceano, existe um interesse acrescido da comunidade científica na actividade, diversidade e distribuição destes microorganismos no subsolo e fundos oceânicos. Até à data desta dissertação, inúmeros estudos foram realizados no sentido de caracterizar a fauna hidrotermal e sua distribuição, incidindo sobretudo nas comunidades de invertebrados marinhos, mas apesar disso ainda muito se desconhece sobre a ecologia microbiana local, nomeadamente a associada a sedimentos hidrotermais de profundidade. Em particular, a informação sobre a diversidade microbiana associada a sedimentos do Menez Gwen, Lucky Strike e Rainbow, três campos hidrotermais de profundidade dos mares dos Açores, é ainda escassa. Apenas três estudos foram efectuados em sedimentos do Rainbow com recurso a métodos tradicionais de construção de bibliotecas genómicas de RNA ribossomal. O principal objectivo deste trabalho foi, por isso, caracterizar o microbiota associado a sedimentos dos três campos hidrotermais de profundidade mais conhecidos dos Açores, e elucidar o potencial metabólico dos microorganismos. Desta forma, obtemos informação relevante sobre formas de vida pouco ou nada conhecidas, sustentadas por mecanismos moleculares únicos e enzimas promissoras para potenciais aplicações biotecnológicas. Visto que a maioria dos microorganismos associados ao mar profundo não são cultiváveis em laboratório, os estudos de diversidade desenvolveram-se com recurso a ferramentas de sequenciação de DNA. Assim, os perfis taxonómicos de bactérias, arqueas e micro-eucariotas foram obtidos por pirosequenciação de um segmento do gene de RNA ribossomal. As comunidades microbianas associadas a sedimentos hidrotermais distintos foram comparadas e as suas funções metabólicas identificadas, por sequenciação metagenómica do DNA obtido directamente das amostras ambientais. Pela primeira vez, os microbiotas associados a sedimentos do Menez Gwen foram caracterizados. Verificou-se que as comunidades encontradas em sedimentos influenciados pelo hidrotermalismo diferiam significativamente daquelas encontradas em sedimentos não influenciados pelo hidrotermalismo. Em sedimentos amostrados perto de uma chaminé hidrotermal foram detectados microorganismos mesofílicos, termofílicos e hipertermofílicos pertencentes aos domínios Archaea (e.g., Archaeoglobus, ANME-1) e Bacteria (e.g., Caldithrix, Thermodesulfobacteria). Por outro lado, associados a sedimentos amostrados numa planície batial, abundavam representantes de filogrupos ubíquos no mar profundo (e.g., Thaumarchaeota MGI, Gamma- e Alphaproteobacteria). Da mesma forma, foram comparados os microbiomas associados a sedimentos recolhidos em três campos hidrotermais de profundidade dos Açores, Menez Gwen, Lucky Strike e Rainbow. Dadas as diferenças geológicas e geoquímicas registadas nos três campos, os seus sedimentos albergam comunidades microbianas distintas. Associados ao campo hidrotermal Menez Gwen foram identificados maioritariamente membros da classe Epsilonproteobacteria assim como alguns microorganismos metanogénicos anaeróbios pertencentes ao domínio Archaea. Em contrapartida, as comunidades do Lucky Strike e Rainbow revelaram ser dominadas por representantes da classe Gammaproteobacteria (e.g. Nitrosococcus, Acidiferrobacter e Marine Benthic Group JTB255). Para além disso, entre todos os sedimentos estudados, as comunidades associadas à fonte hidrotermal Rainbow foram as que apresentaram maior diversidade de representantes do domínio Archaea. A composição química dos sedimentos e a influência hidrotermal foram vistos como possíveis factores que explicam as diferenças encontradas nos microbiomas associados aos sedimentos de cada campo: Menez Gwen, Lucky Strike e Rainbow. Os resultados deste trabalho permitiram caracterizar a diversidade e distribuição dos microorganismos hidrotermais e permitiram seleccionar as amostras mais interessantes a serem investigadas num estudo metagenómico posterior. Neste contexto, as comunidades microbianas dos sedimentos hidrotermais dos campos Menez Gwen e Rainbow foram investigadas quanto à presença de genes intervenientes na fixação de carbon e metabolismos do enxofre, azoto e metano. A análise metagenómica destes dois microbiotas revelou quais os genes-chave envolvidos nos fluxos de carbono e energia em ambos ecossistemas hidrotermais. Para além de confirmar a variabilidade microbiana e geoquímica observada na composição dos diferentes sedimentos hidrotermais, os resultados revelaram o carácter amplamente autotrófico das comunidades microbianas aí residentes. A análise metagenómica aponta para a oxidação do enxofre como via metabólica dominante dos processos quimioautotróficos, que ocorre principalmente pela via metabólica das SOX nos sedimentos do Menez Gwen ou pela via reversa da redução do sulfato nos sedimentos do Rainbow. Foram igualmente detectados outros processos de obtenção de energia – como a oxidação do metano, do nitrito e do amoníaco – no entanto, parecem contribuir em menor escala para a quimioautotrofia nestes locais. Este trabalho de investigação contribui para o conhecimento global da ecologia microbiana de sedimentos hidrotermais de profundidade, e constitui um importante repositório de sequências de novos genes com potencial interesse biotecnológico. The world’s oceans cover two-thirds of the planet’s surface being by far the largest habitat on Earth. The marine habitats range from sunlight surface waters to ocean trenches 11,000 m deep with pressures exceeding 1000 bar. Water temperatures range from sea ice, in the polar regions, to over 300 ºC, at deep-sea hydrothermal vents. Microorganisms are able to survive and grow throughout these environments, including the subsurface and the deep-sea. Deep- sea hydrothermal systems represent an important interface between the lithosphere and the oceans, and are considered to be “windows” into the subsurface biosphere. At these locations, thermally charged hydrothermal fluids, enriched with metal compounds and dissolved gases, are ejected into the ocean, providing conditions for supporting chemosynthesis and microbial growth. Extremophile organisms have adapted to the high pressures and temperature shifts, developed novel physiological strategies to thrive in such conditions resorting to unique enzymes and proteins with interesting activities and potential biotechnological applications. Chemoautotrophic Bacteria and Archaea are the primary source of nutrition for the overall organisms dwelling around the vents. They are primary producers of organic carbon, able to establish intricate chemosynthetic symbioses with micro- and macroorganisms, and to transfer the energy up to the food web, sustaining life in the deep-sea. Because of their unique features, they are considered plausible analogues to the early microorganisms of Earth. Therefore, the study of such putative early microbes may help us understanding the origin and evolution of life, and the adaptation mechanisms to these extreme environmental conditions. Moreover, these microorganisms are potentially playing important roles in global geochemical cycling between crusts and oceans, what makes their distribution and activities in deep-sea floors interesting subjects for contemporary microbial ecologists. So far, the diversity and distribution patterns of invertebrate vent communities have been reasonably investigated, however few studies reported on the microbial ecology of free-living Archaea and Bacteria in deep-sea hydrothermal sediments, even though their remarkable activity at these ecosystems. Prior to this work, sediment-associated microbial diversity in the Menez Gwen, Lucky Strike and Rainbow hydrothermal vent fields, southwest of the Azores, was still largely unexplored. Only three microbiological surveys based on 16S clone libraries were conducted in sediments from Rainbow field. The overall goal of this thesis was therefore to characterize the microbiota associated with hydrothermal sediments from the three most visited deep-sea vent fields of the Azores region, and the elucidation of the microorganisms’ metabolic potential. The outcome of this work gives useful insights into yet undiscovered organisms with unique living conditions, molecular mechanisms, and promising enzymes for biotechnological applications. As most of the vent-associated microorganisms remain uncultured, diversity studies are usually based in culture-independent sequencing technologies. Here, the bacterial, archaeal and micro-eukaryotic taxonomic profiles were addressed by barcoded pyrosequencing of a segment of the ribosomal RNA gene. The taxonomic profiles obtained were used to compare communities associated with different hydrothermal sediments retrieved from different sites. Metagenomic approaches were then used to characterize the metabolic potential of the communities. The microbial community associated with sediments from the Menez Gwen vent system was surveyed for the first time. The microbiota of hydrothermally influenced sediments was compared with the one in non-hydrothermally influenced sediments. Microbial communities were shown to be significantly different in the two geographical areas. Specific mesophilic, thermophilic and hyperthermophilic archaeal (e.g., Archaeoglobus, ANME-1) and bacterial (e.g., Caldithrix, Thermodesulfobacteria) taxa were detected in sediments near an active vent chimney, and contrasted with members affiliating with ubiquitous deep-ocean phylogroups (e.g., Thaumarchaeota MGI, Gamma- and Alphaproteobacteria) found in the sediments from a permanently cold bathyal plain. Similarly, the sediment-associated microbiota from three neighbouring vent fields, the Menez Gwen, Lucky Strike and Rainbow systems, was also compared. The distinct geological and ecological features allow these fields to support a diversity of vent microbial communities, which were shown to be distinct between the three separated sites. Taxonomic analyses identified anaerobic methanogens and microaerobic Epsilonproteobacteria, dominating the Menez Gwen community, which contrasted with the Gammaproteobacteria Nitrosococcus, Acidiferrobacter and marine benthic group JTB255 members found to dominate both Lucky Strike and Rainbow microbial communities. Besides, the Rainbow field presented the highest archaeal diversity among all the studied sediments. Trace metal contents and distance from an active vent were suggested to influence the sediment-associated microbiota from the three vent sites. Results from this study provided a better understanding of the distribution of microorganisms in deep-sea hydrothermal sediments and allowed for specifically choosing the most interesting samples to be explored in a a posteriori metagenomic approach. Accordingly, the microbial communities from the Menez Gwen and Rainbow hydrothermal sediments were investigated for the presence and diversity of genes responsible for carbon fixation and sulfur, nitrogen and methane metabolisms. A metagenomic study of the microbiotas elucidated the gene sequences responsible for carbon and energy flux in both hydrothermal ecosystems. The metagenomic analyses confirmed the microbial and geochemical variability and revealed the largely autotrophic communities thriving in both sites. Chemolithotrophy appeared to be primarily driven by sulfur oxidation, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments, and represents a n important repository of novel genes with potential biotechnological interest. This research was funded by the Fundo Regional para a Ciência e Tecnologia (Teresa doctoral grant M3.1.2/F/052/2011) and conducted with the support of the projects SEAZYME (M2.1.2/F/024/2011 ), FCT/PEst project (PEst-OE/EEI/LA0009/2011-2014), and MARE (UID/MAR/04292/2013). All the work was conducted at DOP-University of the Azores: NorStruct- University of Tromsø and CNC - Biocant.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Studies in microbial ecology have had rapid advances in the last decades, in part due to the influence of technological innovations that allowed us to perceive a much greater microbial diversity than was previously found. There are increasing evidences that ecological patterns previously attributed only to macro-organisms can also be observed in microorganisms, a fact that brings the study of microorganisms closer to the application of theories and models already consecrated in classical ecology. Still, the contribution of microorganisms to theoretical ecology is still in its infancy. The present dissertation aims to study the patterns of spatial distribution in prokaryotic organisms of dozens of small lakes inserted in a tropical region in a perimeter of more than 3000 km. This thesis is divided in four chapters, first focusing on the historical context of ecological studies related to spatial attributes of species distribution, which was the basis for the creation of new paradigms such as metapopulations and metacommunities, and discussed the advances of microbiological studies in convergence with these new paradigms and how molecular technologies have contributed to bring microbial ecology closer to general ecology. The second chapter aims to present in a more detailed view on the methods used, problems faced and their solutions, in order to facilitate future studies where the same techniques of extraction, sequencing and data processing (bioinformatics) need to be applied. In the third chapter two well-known extraction methods were tested to evaluate their influence in indices commonly used in ecological studies. The last chapter demonstrates the presence of a bimodal distribution of occupancy-frequency distribution through the analysis of 60 shallow lakes near springs distributed in a large-scale matrix covering the entire state of São Paulo, a pattern already widely demonstrated for macro-organisms, but not yet tested in freshwater bacteria. In addition, the most abundant bacterial groups among the 'core' organisms and the most diverse among the 'satellite' and their potential relevance for the communities in which they were inserted were evaluated. This study is a contribution of microbial ecology to general ecology, aiming at a full understanding of the processes that drive the composition of microbial communities in a given environment. Estudos em ecologia microbiana vêm avançando rapidamente nas últimas décadas, em parte por influencia de avanços tecnológicos que nos permitiram perceber uma diversidade microbiana muito maior que se esperava. É cada vez mais evidente que padrões ecológicos inicialmente descritos para macro-organismos também podem ser observados em micro-organismos, fato que aproxima o estudo destes últimos à aplicação de teorias e modelos já consagrados pela ecologia clássica. Mesmo assim, a contribuição de microrganismos para o avanço de teorias ecológicas está ainda na sua infância. A presente dissertação tem como objetivo estudar os padrões de distribuição espacial de organismos procariotos de dezenas de pequenos lagos inseridos em uma região tropical com um perímetro superior a 3000 km. Esta dissertação está dividida em quatro capítulos. Primeiro foco no contexto histórico dos estudos ecológicos relacionados a atributos espaciais de distribuição de espécies e servindo de base para a criação de novos paradigmas como o das metapopulações e das metacomunidades. Além disso, discuti os avanços dos estudos microbiológicos em convergência com estes novos paradigmas e como tecnologias moleculares contribuíram para aproximar a ecologia microbiana da ecologia geral. O segundo capítulo visa apresentar de forma mais detalhada os métodos utilizados, além de problemas enfrentados e suas soluções, com o objetivo de facilitar futuros estudos onde se necessite aplicar as mesmas técnicas de extração, sequenciamento e processamento de dados (bioinformática). No terceiro capítulo foram aplicadas duas técnicas de extração bastante conhecidas para que pudéssemos avaliar sua influência em índices comumente utilizados em estudos ecológicos. O ultimo capítulo demonstra a presença de uma distribuição bimodal de distribuição de frequências de ocupação através da análise de 60 lagoas próximas a nascentes distribuídas por uma macrorregião, abarcando todo o Estado de São Paulo, padrão já largamente demonstrado para macro-organismos, mas que ainda não havia sido testado em bactérias de água doce. Além disso, foram avaliados os grupos bacterianos mais abundantes dentre os organismos ‘core’ e os mais diversos dentre os ‘satellite’ e sua potencial relevância nas comunidades em que estão inseridas. Este estudo constitui uma contribuição da ecologia microbiana para a ecologia geral, visando uma plena compreensão dos processos que dirigem a composição das comunidades microbianas de determinado ambiente. FAPESP: 2014/14139-3 FAPESP: 2011/50054-4

La ecología microbiana de los alimentos, comprende la interacción entre los atributos químicos, físicos y estructurales del alimento, los factores tecnológicos y la biota que constituye la población microbiana de los mismos. En el caso que nos ocupa la carne y los productos cárnicos. El estudio del efecto de las condiciones medioambientales sobre los microorganismos es el fundamento de la ecología microbiana. La relación entre la matriz alimentaria, los factores medioambientales y la biota respectiva, son los ejes principales de la ecología microbiana de los alimentos. El artículo considera aspectos relacionados con la ecología microbiana en alimentos de origen animal, los principales factores que condicionan la respuesta de los microorganismos, la biota alterante en carnes frescas y refrigeradas, la vida útil de los productos, los ensayos de desafío y el desarrollo y diseño de productos. Instituto de Economía Fil: Rodriguez, Héctor Ricardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Economía; Argentina Fil: Aparicio, María Laura. Universidad Nacional de San Martín. Instituto de la Calidad Industrial; Argentina

El Primer Taller Internacional de Biorremediación 2013 (PRITIBIO) fue realizado entre la Facultad de Agronomía de la Universidad de Buenos Aires (FAUBA), la Agencia Nacional de Promoción Científica y Tecnológica del Ministerio de Ciencia, Tecnología e Innovación Productiva (MINCYT) y el Instituto de Suelos del Instituto Nacional de Tecnología Agropecuaria (INTA) de Castelar. A partir de la realización de este taller surgió la idea de publicar parte de la información presentada agregándole distintos aportes de otros investigadores que no participaron de este. Esta publicación une trabajos realizados en el país y en el extranjero, referidos a la biorremediación de los recursos naturales. Cada investigador que aquí participa tiene en su desarrollo profesional varias publicaciones del tema por haberlo trabajado durante años. Es del sentir de estos autores el saberse útil a los principios de la sustentabilidad ambiental y de la producción, atendiendo a los requisitos propios de cada recurso permitiendo el uso de este sin perturbar el ambiente. Instituto de Suelos Fil: Brutti, Lucrecia Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Cátedra de Edafología; Argentina Fil: Beltran, Marcelo Javier. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; Argentina Fil: García de Salamone, Inés. Universidad de Buenos Aires. Departamento de Biología Aplicada y Alimentos. Cátedra de Microbiología Agrícola; Argentina

A utilização de produtos naturais e fitoterápicos para cura de doenças é milenar. O interesse no desenvolvimento desses produtos é muito significativo e isso não seria diferente na odontologia. Quando se avalia a etiologia das principais doenças da cavidade bucal, cárie e doença periodontal, pode-se fazer uma analogia de uma “batalha” frente a um microbioma complexo e, por vezes, muito agressivo. Como são doenças de origem infecciosa a utilização de mecanismos que impeçam ou estabilizem o processo patológico é de suma importância. A presente tese teve como objetivo principal, avaliar a utilização do óleo de copaíba frente ao microbioma bucal. Nese sentido a tese se divide em 3 capítulos científicos, sendo uma revisão de literatura, uma revisão sistemática e um ensaio clínico randomizado. O primeiro capítulo de revisão de literatura procurou demostrar o potencial do óleo de copaíba e suas aplicações na odontologia. O segundo capítulo, de revisão sistemática da literatura, elucidou a lacuna existente da ação do óleo de copaíba frente a patógenos orais. Esta revisão sistemática constatou que nenhum estudo clínico havia sido realizado utilizando óleo de copaíba frente às bactérias orais propostas no estudo. Assim, resultados promissores mostraram que o mesmo poderia ser utilizado na cavidade bucal, como forma de prevenção e tratamento da cárie e doença periodontal. No terceiro capítulorealizou-se umestudo clínico randomizado, avaliando o efeito imediato de enxaguatório contendo óleo decopaíba a 5% e 10%. Foram realizadas análises microbiológicas paracaracterização das comunidades microbianas presentes em saliva e AnáliseIntergênicade Espaçadores Ribossomais(RISA) além da análise da percepção gustativa (Escala Hedônica egustativa). Os resultados mostraram que não houveuma diminuição significativa nacontagem total debactérias após autilização dosenxaguatórios. Os resultados da análise de percepção gustativa mostraram que sensação dosabor doce foi o resultado predominante.A partir dos resultados obtidos nos artigos constituintes da presente tese e frente considerações realizadas, pode-se concluir que a utilização do óleo de copaíba frente a bactérias orais é comprovada nos estudos in vitro, mas recomenda-se estudos clínicos capazes de confirmar sua efetividade in vivo. The use of natural and herbal products for diseases cure is millenarian. The interest in the development of this products is very significant and this would not be different in dentistry. When evaluating the etiology of the main diseases of the oral cavity, caries and periodontal disease, we can make an analogy of a "battle" against a complex and sometimes very virulent microbiome. As diseases of infectious origin are the use of mechanisms that prevent or stabilize the disease process is of paramount importance. The main objective of this thesis was to evaluate the use of copaiba oil against the oral microbiome.In this sense were produced 3 scientific articles, being a literature review, a systematic review and a randomized clinical trial. The first chapter of literature review sought to demonstrate the potential of copaiba oil and its applications in dentistry. The second chapter, a systematic review of the literature, elucidated the existing gap in the action of copaiba oil against oral pathogens. The systematic review found that no clinical study had been conducted using copaiba oil against the bacteria proposed in the study. Even so, promising results showed that could be used in the oral cavity as a form of prevention and treatment of caries and periodontal disease. In the third chapter, a randomized clinical study was executed, evaluating the immediate effect of 5% and 10% copaiba oil. Microbiological analyzes were performed to characterize the microbial communities present in saliva and Intergenic Ribosomal Spacer Analysis (RISA) in addition to the analysis of gustatory perception (Hedonic and gustatory scale). The results showed that there was no significant decrease in total bacterial counts after the use of mouthwashes. The results of the gustatory perception analysis showed that sweet taste sensation was the predominant result. From the results obtained in the articles of this thesis and the considerations made, it can be concluded that the use of copaiba oil against oral bacteria is proven in vitro studies, but clinical studies are recommended to confirm its effectiveness in vivo.

Orientador : Prof. Dr. Leonardo Magalhães Cruz Coorientador : Prof. Dr. Luciano Fernandes Huergo Dissertação (mestrado) - Universidade Federal do Paraná, Setor de Educação Profissional e Tecnológica, Programa de Pós-Graduação em Bioinformática. Defesa : Curitiba, 05/02/2018 Inclui referências Resumo: Metagenômica é o estudo das comunidades microbiológicas encontradas em um ambiente, combinando técnicas de extração de material genético, genômica e bioinformática. Através deste estudo, podemos acessar um microbioma que não pode ser encontrado e analisado normalmente através de técnicas tradicionais de cultivo, devido à impossibilidade de cultivar muitos microrganismos em condições de laboratório. O acesso mais amplo à biodiversidade que esta tecnologia pode fornecer, nos permite identificar novos microrganismos, sua quantidade e seu papel no ecossistema, através da classificação taxonômica e predição funcional. O solo é considerado um dos ecossistemas biológicos mais complexos. Eles são responsáveis pelos ciclos biogeoquímicos mais fundamentais na Terra, mantendo relações vitais entre si e com organismos superiores. Os seus papéis principais estão relacionados com a decomposição da matéria orgânica, fornecimento de nutrientes para as plantas e degradação de substâncias químicas. A inoculação de microrganismos que podem realizar uma relação simbiótica benéfica com plantas, pode ajudar no crescimento vegetal e aumentar a produção agrícola. Vários microrganismos já foram identificados como bactérias promotoras de crescimento vegetal, como por exemplo o Azopirillum brasilense, uma bactéria fixadora de nitrogênio, que é usada como bio-fertilizante na agricultura em vários compostos comerciais. Este microrganismo não é aplicado apenas para promover o crescimento das plantas, mas também para moldar a região da rizosfera com outros microrganismos benéficos, que também podem atuar diretamente como bactérias promotoras de crescimento vegetal ou indiretamente na solubilização de minerais, controle biológico patógenos ou contribuindo para a estrutura e agregação de solo. Palavras-chave: Bioinformática, Fixação Biológica de Nitrogênio, Bactérias Promotoras de Crescimento Vegetal Abstract: Metagenomics is the study of the microbiological communities recovered from a environment by combining techniques of genetic material extraction, genomics and bioinformatics. Through this study we are able to access a microbiome that can't be found normally with traditional techniques of cultivation and analysis due to the impossibility to cultivate many microorganisms in laboratory conditions. The broader access to biodiversity that this technology can provides allows us to identify new microorganisms, their abundance and their roles in the ecosystems through taxonomic classification and functional predictions. The soil is considered one of the most complex biological ecosystems. They are responsible to the most fundamentals biogeochemical cycles in earth, maintaining vital relationships between each other and with higher organisms. Their main roles are related with the decomposition of the organic matter, nutrients privation to the plants and the degradation of chemical substances. The inoculation of microorganisms that can performed a beneficial symbiotic relationship with plants, can help in the plant growth and increase the agricultural production. Several microorganisms were already identified as plant growth promoting bacterias such as Azopirillum brasilense, a nitrogen-fixation bacteria, that has been used as bio-fertilizer in agriculture in several commercial compounds. This microorganism is not only applied to promote plant growth, but also to shape the rhizosphere region with other beneficial microorganisms that can also acts directly as plant promoting bacterias or indirectly in the solubilization of minerals, biological control of plant pathogens or contributing to the structure and aggregation of soil. Keywords: Bioinformatics, Biological Nitrogen Fixation, Plant Growth Promoting Bacterias

Orientador: Anderson de Souza Sant'Ana Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos Resumo: No Brasil, a legislação vigente para a fabricação de queijos artesanais é a Instrução Normativa n° 30, de 07 de agosto de 2013, do Ministério da Agricultura, Pecuária e Abastecimento. A produção artesanal de queijos no Brasil constitui uma atividade pouco documentada, porém a prática queijeira se difundiu nas fazendas e pequenas propriedades rurais por todo o território nacional, gerando produtos variados e apreciados pelos consumidores. Apesar de sua importância na cultura e alimentação brasileira, inexistem estudos para elucidar a ecologia microbiana dos queijos artesanais brasileiros através de ferramentas avançadas como a metagenômica. O conhecimento da microbiota e suas interações nos queijos artesanais brasileiros precisam ser elucidados, visando o fortalecimento dos padrões de qualidade e segurança característicos destes produtos. Sendo assim, o principal objetivo deste trabalho foi caracterizar a diversidade microbiana de diferentes tipos de queijos artesanais produzidos no Brasil, envolvendo 578 amostras. A microbiota de 11 tipos de queijos provenientes de cinco regiões geográficas foi investigada pelo sequenciamento do gene 16S rRNA. Além disso, foram coletadas amostras do ambiente de processamento de queijos artesanais (matérias-primas, produto final e esponjas superficiais) em três fazendas da região da Serra da Canastra, Brasil, totalizando 24 amostras, para a investigação da ecologia microbiana e analisadas pelo método independente de cultivo, através do sequenciamento do amplicon. Os resultados mostraram que as bactérias ácido lácticas foram prevalentes em todos os tipos de queijos, embora Enterobacteriaceae e Staphylococcus tenham ocorrido em queijos das regiões Norte, Nordeste e Central do Brasil. Os gêneros Streptococcus, Leuconostoc, Lactococcus e Lactobacillus foram encontrados, combinados diferentemente em termos de abundância relativa de acordo com o tipo de produto e a região produtora. Em cultura starter natural e em amostras de queijo curado, houve o predomínio de bactérias lácticas (Lactobacillus, Streptococcus, Lactococcus e Leuconostoc), importantes para conferir as características desejadas ao produto final. Por outro lado, possíveis contaminantes como Pseudomonas, Staphylococcus, Pasteurella, Enterobacter, Klebsiella e Acinetobacter, foram encontrados em amostras de leite cru, piso e pano de dessoragem. Esses resultados são importantes porque fornecem um mapeamento microbiológico dos queijos brasileiros, destacando o impacto da origem geográfica e o modo de produção na diversidade microbiana. Além disso, a caracterização destes queijos contribui para o estabelecimento de ações que garantam a qualidade e segurança microbiológica destes produtos Abstract: The Normative Instruction n° 30 of August 7th, 2013 from Ministry of Agriculture, Livestock and Food Supply (MAPA) is the legislation for artisanal cheese production in Brazil. The production of artisanal cheese constitutes a seldom documented activity in Brazil. Despite this, the practice of producing cheeses has been spread throughout the years in farms and small rural properties in Brazilian territory leading to the development of a variety of products that are highly appreciated by consumers. Despite its importance in Brazilian food and culture, there are no studies to elucidate the microbial ecology of Brazilian artisanal cheeses through advanced tools such as metagenomics. The knowledge of the microbiota and its interactions in Brazilian artisanal cheeses needs to be elucidated in order to strengthen the quality and safety standards characteristic of these products. Thus, the main objective of this work was to characterize the microbial diversity of different types of artisanal cheeses produced in Brazil, involving 578 samples. The microbiota of 11 types of cheeses from five geographic regions was investigated by sequencing the 16S rRNA gene. In addition, samples from the processing environment of artisanal cheeses (raw materials, final product and surface sponges) were collected from three farms in Serra da Canastra region, Brazil, totalizing 24 samples for investigation of the microbial ecology and analyzed by culture independent method, through the amplicon sequencing. The results showed that lactic acid bacteria were dominant in all types of cheeses, although Enterobacteriaceae and Staphylococcus occurred in cheeses from North, Northeast and Central of Brazil. The genera Streptococcus, Leuconostoc, Lactococcus and Lactobacillus were found, combined differently in terms of relative abundance according to the type of product and the producing region. In natural starter culture and ripened cheese samples there were the dominance of lactic acid bacteria (Lactobacillus, Streptococcus, Lactococcus and Leuconostoc), important to confer the desired characteristics on the final product. On the other hand, possible contaminants as Pseudomonas, Staphylococcus, Pasteurella, Enterobacter, Klebsiella and Acinetobacter, were found in raw milk, floor and cheesecloth samples. These results are important because they provide a microbiological mapping of Brazilian cheeses, highlighting the impact of geographical origin and the mode of production on microbial diversity. In addition, the characterization of these cheeses contributes to the establishment of actions that ensure the quality and microbiological safety of these products Doutorado Ciência de Alimentos Doutora em Ciência de Alimentos FAPESP 2013/20456-9 ; 2016/12406-0 CAPES CNPQ 403865/2013-1

Background: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to ?spillover effects? on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures. Results: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical?chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes. Conclusions: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and ?spillover effects? of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology. Made available in DSpace on 2018-11-22T00:48:49Z (GMT). No. of bitstreams: 1 2018JosiMicrobiomeDirect.pdf: 1270795 bytes, checksum: aa05ddeb2cf5aa8b11561434538baf79 (MD5) Previous issue date: 2018-11-19

El sistema de barros activados es uno de los modelos más estudiados en ecología microbiana. En las últimas décadas se han realizado grandes avances en el conocimiento de la composición de las complejas poblaciones microbianas participantes en dicho proceso. Si bien se ha visto que las variables ambientales y operativas son factores críticos en la estructuración de las comunidades bacterianas, aún son escasos los estudios sobre los diferentes niveles tróficos presentes en el sistema. El objetivo de este trabajo es comprender la influencia de factores bióticos y abióticos en la estructura y dinámica de los diferentes niveles tróficos de comunidades microbianas de un sistema de tratamiento de efluentes cloacales. Para ello, se estudiaron los tres niveles tróficos principales de los barros activados: bacterias, eucariotas y bacteriófagos, en una planta de tratamiento de efluentes domiciliarios de Buenos Aires. El período evaluado comprendió tres años en los que la planta operó bajo un gradiente creciente de tiempo de residencia de sólidos (TRS) y atravesó una etapa de fluctuaciones operacionales. Los microorganismos eucariotas se analizaron por microscopía mientras que la composición bacteriana se estudió por secuenciación de amplicones de la región hipervariable V3-V4 del gen ARNr 16S y secuenciación al azar sobre el ADN metagenómico. La presencia y abundancia de bacteriófagos se siguió por secuenciación al azar del ADN presente en el sobrenadante (metaviroma). Luego del co-ensamblado de los 60 metagenomas, de la serie temporal, se utilizó una metodología de binning basada principalmente en cobertura diferencial con la que se reconstruyeron 257 genomas. Los perfiles de co-ocurrencia de especies bacterianas resultaron altamente dependientes del régimen operativo, donde el período de fluctuaciones y de bajo TRS, fue dominado por filos mayormente compuestos por estrategas-r (copiótrofos); contrastando con el período de alto TRS, en el que predominaron los estrategas-K (oligótrofos). La partición de poblaciones bacterianas en base a diferencias en las estrategias de crecimiento fue confirmada por la determinación del número de operones ARN ribosomales (rrn) estimados a partir de los genomas ensamblados. Por su parte, el índice biótico de barros (SBI), basado en la abundancia y diversidad de protozoos, correlacionó positivamente con la abundancia total de bacterias oligotróficas, apoyando el uso del SBI como indicador para el control de calidad del tratamiento y reflejando la modulación por depredadores eucariotas. Finalmente, los cambios en la composición de fagos reflejaron un patrón similar al revelado por las poblaciones bacterianas. La reducción en la abundancia relativa de virus de la familia Podoviridae y el correspondiente aumento en Siphoviridae que acompañan el aumento en TRS es consistente con el hecho de que los Podoviridae infectan principalmente Proteobacteria, mientras que sifovirus pueden ser lisogénicos por varias generaciones, un comportamiento que ha sido asimilado a estrategas K. Las interacciones entre los fagos y las poblaciones bacterianas, detectadas a través de la búsqueda de elementos CRISPR y por similitud de secuencias, permitieron la identificación de mecanismos de interacción tipo Lotka-Volterra depredador-presa, así como de modelos alternativos de interacciones múltiples, en los que un fago infecta a más de un hospedero y/o un hospedero es infectado por más de un tipo de fago. Se concluye que los parámetros de proceso determinan la composición de poblaciones bacterianas en base a sus estrategias de crecimiento, mientras que sobre esta estructuración, determinada por factores abióticos, se superpone una modulación fina mediada por depredadores. Activated sludge system is one of the most studied models in microbial ecology. In the last decades, large progress has been made in the knowledge of the composition of these complex microbial populations. Although it has been seen that environmental and operative variables are critical factors on the bacterial community structuring, there are still few studies regarding to different trophic levels in this system. The aim of this work is to understand the influence of biotic and abiotic factors on the structure and dynamics of different trophic levels of microbial communities of a sewage treatment system. For this, the three main trophic levels in activated sludge: bacteria, eukaryotes and phages, were studied in a wastewater treatment plant of Buenos Aires. The evaluated period comprise three years in which the plant operates under an increasing gradient of sludge retention time (SRT) and went through a stage of operational fluctuations. Eukaryotic organisms were analyzed by microscopy while bacterial composition was studied by amplicon sequencing of the 16S rRNA gene V3-V4 hypervariable region and metagenomic DNA shotgun sequencing. Phages presence and abundance were followed by shotgun sequencing of DNA present in the supernatant (metavirome). After co-assembling the 60 metagenomes, from the time series, we applied a binning methodology, based mainly on the differential coverage, from which 257 genomes were reconstructed. The co-ocurrence profiles of bacterial species resulted highly dependent on the operational regime, where the disturbed period with low SRT was dominated for phyla mostly composed of r-strategist (copiotrophs); contrasting with the high SRT period, where K-strategist (oligotrophs) predominated. The separation of bacterial populations based on differences in their growth strategies was confirmed by determining the ribosomal RNA (rrn) operon number, estimated from the assembled genomes. Meanwhile, the sludge biotic index (SBI), based on protozoa abundance and diversity, correlated positively with total abundance of oligotroph bacteria, supporting the use of the SBI as an indicator of treatment quality control and displaying a modulation by Eukaryotic predators. Finally, changes in phage composition showed a similar pattern than observed in bacterial populations. Reduction of the relative abundance of Podoviridae family viruses and the corresponding increase on Siphoviridae along with the increase on SRT is consistent with the fact that Podoviridae mainly infect Proteobacteria, while siphoviruses could be lysogenic for several generations, a feature assimilated to K-strategists. Phage-bacteria interactions, detected by searching for CRISPR elements and sequence homologies, allowed to identify prey-predator interactions mechanisms type Lotka-Volterra, as well as multiple interactions alternative models, in which a phage infects more than one host and/or a host is infected by more than one type of phage. We conclude that bacterial population composition based on their growth strategies is determined by process parameters, while this structuring, determined by abiotic factors, is superposed by a fine modulation mediated by predators. Fil: Pérez, María Victoria. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.

Para transmitir conceptos científicos complejos en un entorno escolar, la utilización de experimentos llamativos representa una herramienta muy útil. En este artículo se presenta la columna bioelectrogénica, un sistema experimental que une la columna de Winogradsky clásica con las más recientes investigaciones en el campo de la microbiología aplicada. A través de su implementación es posible visualizar procesos físicos, químicos y biológicos que forman parte de la enseñanza científica en institutos de secundaria. Además, la columna bioelectrogénica ha sido ideada para demostrar la existencia de bacterias capaces de producir energía eléctrica, un fenómeno que induce curiosidad y estupor, elementos claves para estimular la participación de los estudiantes. Este sistema ha sido presentado en varias actividades de divulgación para estudiantes de secundaria y siempre ha despertado un elevado grado de interés., The use of inspiring experimental demonstrations is a fundamental tool for teaching complex scientific concepts in secondary schools. In this article we present the bioelectrogenic column, an experimental system that joins the classic Winogradsky column to the most recent findings in the field of applied microbiology. With this system we can visualise physical, chemical and biological processes that are at the heart of a sound scientific education. Furthermore, the bioelectrogenic column had been designed to demonstrate the existence of bacteria capable of producing electric energy, an astonishing phenomenon that leaves students highly inquisitives, a key for stimulating their participation. This system has been presented in various scientific outreaching activities for secondary school, always awakening a strong interest in the audience.

River sediment microorganisms have the capacity to metabolize, uptake and decompose flowing water organic materials, which strongly depend on their metabolic capabilities. The changes of microbial functional diversity in river sediments were analysed at five sites along the River Llobregat (NE Spain), using the Biolog EcoPlates incubation method. In parallel, we tested the potential application of the EcoPlates with preserved frozen samples (-80 °C). Although functional diversity (Shannon index) did not show significant differences, the specific carbon substrates that were used differed between sampling sites. The microbial community from the upstream site was the most active as shown by the highest respiratory activity and abundance of living bacteria, being able to metabolize more labile substrates. Downstream sediment communities showed a decrease in bacterial viability, respiration activity and EPS content, suggesting a less structured biofilm. The functional fingerprint analyses clearly distinguish the sediment microbial communities from the downstream most polluted sites, which showed a potential capacity to use more complex carbon substrates such as polymers. Freezing sediment samples is not recommended, since a significant reduction in the functional diversity and changes in the fingerprint patterns were observed together with a reduction of the number of substrates utilisation especially at two downstream sites. The Biolog EcoPlates appear to be useful for detecting changes in the microbial functional fingerprint in fresh sediments along a river pollution gradient This study was funded by the Spanish Ministry of Economy and Competitiveness projects FLUMED-HOTSPOTS (CGL2011-30151-C02-01) and SCARCE (Consolider-Ingenio CSD2009-00065)