Psoroptes ovis mites are the causative parasites of sheep scab disease. It is a contagious disease which causes intense pruritus, wool loss and the development of lesions. These lesions are exacerbated by secondary bacterial infections. Bacteria appear to play an integrated role in the pathogenicity of this disease and are found in the internal cavities of P. ovis. The aim of this study was to investigate these bacterial associations, with the aim of identifying a microbial target for sheep scab control. The microbial communities associated with sheep scab were investigated using both molecular and bacteriological techniques. Several environmental niches were targeted: scab-infected fleece, internal mite cavity and excreted faecal trails. Microbial communities were very complex, with a variety of species and bacterial groups identified. Some bacteria were common to all environments, whereas others were isolated from one sample. Both natural and in vivo cultured mites were investigated in an attempt to identify universal and potentially beneficial bacteria. In addition, P. ovis mites were screened using PCR to detect potential endosymbiotic bacteria. Positive identification was made of Comamonas sp. in both natural and in vivo cultured mites; this species has been identified as an endosymbiont in other arthropods and its role in P. ovis requires further investigation. In vitro feeding experiments were carried out with P. ovis mites in the laboratory. Initially mite chambers were constructed and optimised to encourage maintenance of P. ovis off-host. A number of diets were tested and antibiotics were compared for their effect on bacteria within P. ovis. In vitro experiments revealed that P. ovis survival was significantly reduced with the administration of antibiotics and there was also evidence that they altered internal bacterial densities. The potential of bacteriophage therapy for the microbial control of bacteria associated with P. ovis was investigated. Bacteria isolated from P. ovis faecal trails were used to isolate bacteriophage from environmental samples. Sixteen bacteriophage were successfully isolated, which were infective against three mite faecal bacteria. Isolated bacteriophage were characterised by a number of methods including their response to chemicals, enzyme and infection dynamics in both solid and liquid phases. In vitro experiments with bacteriophage were also investigated, resulting in a significantly reduced mite lifespan seen with some bacteriophage lysates. The potential for using bacteriophage for the control of P. ovis mites is discussed.

>Magister Scientiae - MSc / Marine macroalgae are known to carry diverse bacterial communities which interact with their hosts in both harmful and beneficial ways. Algae hosts provide the bacteria with a rich source of carbon in the form of carbohydrate polysaccharides such as fucoidan, agar and alginate, which the bacteria enzymatically degrade. Splachnidium rugosum is a brown alga (Phylum: Phaeophyta) that grows exclusively in the Southern Hemisphere along the temperate shores of South Africa, New Zealand and Australia. While several studies have investigated S. rugosum distribution and fucoidan production, the microbiome of S. rugosum remains largely uncharacterized. Thus, the major objective of the present study was to isolate, identify and characterize epiphytic bacterial communities associated with S. rugosum. Algae were sourced from Rooi Els (Western Cape, South Africa) during winter 2012. Culture based methods relied on a range of selective marine media including marine agar, nutrient sea water agar, nutrient agar and thiosulfate-citrate-bile-salts-sucrose agar to determine the composition and uniqueness of bacterial communities associated with S. rugosum. Epiphytic isolates were identified to species level by 16S rRNA gene sequence analysis and encompassed 39 Gram-negative and 2 Grampositive bacterial taxa. Isolates were classified into four phylogenetic groups, Gamma - Proteobacteria, Alpha-Proteobacteria, Firmicutes and Bacteriodetes. Bacteria belonging to the phylum Gamma-Proteobacteria were the most abundant, with Vibrio and Pseudoalteromonas being the dominant genera. Three isolates with low sequence identity (˂97%) to their closest relatives could possibly represent novel species. These isolates were grouped into the genera Shewanella, Sphingomonas and Sulfitobacter. All bacterial isolates (41) were screened for antimicrobial activity against the following test strains: Escherichia coli, Bacillus cereus, Staphylococcus epidermidis, Mycobacterium smegmatis Micrococcus luteus and Pseudomonas putida. Fifteen isolates (36%) displayed antimicrobial activity against one or more of the test strains, while one isolate (Pseudomonas species) showed broad spectrum antimicrobial activity against all the test strains except for E. coli. This study provides the first account of the diversity and composition of bacterial populations on the surface of S. rugosum, and demonstrates the ability of these bacteria to produce antimicrobial compounds. Despite recent advances in metagenomics, this study highlights the fact that traditional culturing technologies remain a valuable tool for the discovery of novel bioactive compounds of bacterial origin.

No description available.

Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2017-08-23T18:13:31Z No. of bitstreams: 1 2015 - Jakson Leite.pdf: 1055808 bytes, checksum: fa105f74410a81a1f30e45ae5e911c9d (MD5) / Made available in DSpace on 2017-08-23T18:13:31Z (GMT). No. of bitstreams: 1 2015 - Jakson Leite.pdf: 1055808 bytes, checksum: fa105f74410a81a1f30e45ae5e911c9d (MD5) Previous issue date: 2015-02-27 / CAPES / Cowpea [Vigna unguiculata (L.) Walp] is an important crop in northeastern Brazil with strategic advantages for production in semi-arid region, such its drought tolerance and good performance in low fertility soils. In addition, the nitrogen (N) fixed in symbiosis with rhizobia eliminates the demand for N fertilizers, with economic, social and environmental benefits. Little is known about the genetic diversity of bacteria associated to cowpea nodules in Brazilian semi-arid. The aim of the study was to characterize the bacterial diversity of Brazilian semi-arid soils associated with nodules of different cowpea cultivars by dependent and independent bacterial cultivation strategy. Initially a collection of 86 bacteria cowpea nodules isolated from semiarid soils was genetically characterized by partial 16S rRNA gene sequencing and symbiotic genes nifH and nodC. The sequences were compared with the NCBI database to identify isolates and phylogenetic relationships were built. In another study, we applied the independent cultivation method to evaluate bacterial communities associated with the nodules of two cowpea cultivars (BRS and BRS Acau? Pujante), in Ultisol with no history of cowpea cultivation. Nodules (N) were collected 35 days after germination, and soil samples (BS) from 0-20 cm deeper. DNA was extracted for analysis of bacterial communities with 454 pyrosequencing of the 16S ribosomal gene rRNA. The analysis of the diversity of the bacterial collection of the nodules 54 of the 86 isolates were Bradyrhizobium. Other (32) belong to Rhizobium (13) and Microvirga (1), Alfaproteobact?ria class; Burkholderia (8), and Ralstonia (1), Betaproteobacteria class; Acinetobacter (1), Cronobacter (3), Enterobacter (1), and Pantoea (1), Gamaproteobact?ria; and Leifsonia (3), phylum Actinobacteria. As Bradyrhizobium predominated, analyzes were performed with the almost full 16S rRNA, nifH and nodC and isolates were distributed in 5 lines: 16S rRNA type I (44 isolates), type II (6), Type III (1), Type IV ( 2) and type IV (1). Phylogenetic analysis of the 16S rRNA gene grouped the Type I strain in the large group Bradyrhizobium japonicum and close to the type strain of Bradyrhizobium yuanmingense. The analyses of the nifH and nodC gene separated the isolates in 5 symbiotic lines (I, II, III, IV and IV) and were congruent among them, which supports the theory of monophyletic in origin symbiotic gene Bradyhrizobium. The symbiotic lineages I and II are nearby and correspond to all isolates with 16S rRNA type I, being the dominant group associated with nodules. The partial 16S rRNA gene sequencing of bacterial communities showed high diversity in the three environments (BS, RS and N). The communities associated with the nodes were significantly different (p> 0.01) from the surrounding nodules (LS and RS). Phyla Actinobacteria, Bacteriodetes, Proteobacteria were plentiful for BS and RS. In nodes, the Proteobacteria and Bacteriodetes phyla predominated, Gammaproteobacteria being (58.8%) and Alphaproteobacteria (37.4%) in the phylum Proteobacteria and dominant Flavobacteriia (84.8%) and Sphingobacteriia (10.9%) in the phylum Bacteriodetes. For gender, Chryseobacterium, Entreobacter and Bradyrhizobium dominate in all nodes samples where Chryseobacterium prevailed in BRS Acau? and Enterobacter in BRS Pujante. / O feij?o-caupi [Vigna unguiculata (L.) Walp] ? uma das principais culturas no Nordeste do Brasil com vantagens estrat?gicas para produ??o no semi?rido, como toler?ncia a seca e bom desempenho em solos de baixa fertilidade. Al?m disso, fixa N em simbiose com riz?bios eliminando a demanda de fertilizantes nitrogenados, com benef?cios econ?micos, sociais e ambientais. Pouco se sabe sobre a diversidade gen?tica de bact?rias associadas aos n?dulos de feij?o-caupi no semi?rido. O objetivo do estudo foi caracterizar a diversidade de bact?rias de solos do semi?rido brasileiro associadas aos n?dulos de diferentes cultivares de feij?o-caupi com arbordagem que depende e independe de cultivo das bact?rias. Inicialmente uma cole??o de 86 bact?rias de n?dulos de feij?o-caupi isoladas de solos do semi?rido foi caracterizada geneticamente pelo sequenciamento parcial do gene 16S rRNA e dos genes simbi?ticos nifH e nodC. As sequ?ncias foram comparadas com as do banco de dados do NCBI para identificar os isolados e as rela??es filogen?ticas dos mesmos com as de esp?cies conhecidas. Em outro estudo, aplicou-se o m?todo independente de cultivo para avaliar comunidades de bact?rias associadas aos n?dulos de dois cultivares de feij?o-caupi (BRS Pujante e BRS Acau?), em Argissolo Amarelo sem hist?rico de uso com a lavoura. Os n?dulos (N) foram coletados 35 dias ap?s a germina??o e a amostragem do solo (BS) de 0-20 cm. O DNA das amostras foi extra?do para an?lises das comunidades bacterianas com 454 pirosequenciamento do gene ribossomal 16S rRNA. Na an?lise da diversidade da cole??o de n?dulos 54 dos 86 dos isolados foram de Bradyrhizobium. Os demais (32) pertencem aos g?neros Rhizobium (13) e Microvirga (1), classe Alfaproteobact?ria; Burkholderia (8) e Ralstonia (1), classe Betaproteobact?ria; Acinetobacter (1), Cronobacter (3), Enterobacter (1) e Pantoea (1), Gamaproteobact?ria; e Leifsonia (3), filo Actinobact?ria. Como Bradyrhizobium predominou, foram feitas an?lises com os genes 16S rRNA, nifH e nodC e os isolados distribu?ram-se em 5 linhagens: 16S rRNA tipo I (44 isolados), tipo II (6), tipo III (1), tipo IV (2) e tipo IV (1). A an?lise filogen?tica do gene 16S rRNA agrupou a linhagem tipo I no grande grupo Bradyrhizobium japonicum e pr?ximo da estirpe tipo de Bradyrhizobium yuanmingense. A an?lise dos genes nifH e nodC separou os isolados em 5 linhagens simbi?ticas (I, II, III, IV e IV) e as ?rvores foram congruentes, o que suporta a teoria da origem monofil?tica de genes simbi?ticos em Bradyhrizobium. As linhagens simbi?ticas I e II s?o pr?ximas e correspondem a todos os isolados com 16S rRNA tipo I, sendo o grupo dominante associado aos nodulos. O sequenciamento parcial do gene 16S rRNA das comunidades bacterianas mostrou alta diversidade nos tr?s ambientes (BS, RS e N). As comunidades associadas aos n?dulos foram significativamente diferentes (p> 0,01) das que cercam os n?dulos (LS e RS). Os filos Actinobacteria, Bacteriodetes, Proteobacteria foram abundantes para BS e RS. Em n?dulos, os filos Proteobacteria e Bacteriodetes predominaram, sendo Gammaproteobacteria (58,8%) e Alphaproteobacteria (37,4%) dominantes no filo Proteobacteria e Flavobacteriia (84,8%) e Sphingobacteriia (10,9%) no filo Bacteriodetes. Para g?nero, Chryseobacterium, Entreobacter e Bradyrhizobium dominam em todas as amostras de n?dulos, onde Chryseobacterium predominou em BRS Acau? e Enterobacter em BRS Pujante.

16S rRNA gene analysis has shown that bacterial diversity in the GAB bores studied was limited to the genera Hydrogenobacter in the phylum Aquificae, Thermus in the phylum Deinococcus-Thermus, Desulfotomaculum in the phylum Firmicutes, the alpha-, beta- and gamma-classes of the phylum Proteobacteria and the phylum Nitrospirae. There was no clone closely related to members of the delta-proteobacteria and epsilon-proteobacteria classes detected. The number of bacterial strains directly isolated from the Fairlea and the Cooinda bores were far less than the numbers of distinctive phylotypes detected by the 16S rRNA gene characterisation. In addition none of the bacterial strains directly isolated from the water samples were represented in the 16S rRNA gene clone libraries. Similar discrepancies between the bacterial populations obtained from the 16S rRNA gene analysis and those obtained from direct isolation have been reported in the literature (Dunbar et al., 1999; Kampfer et al., 1996; Suzuki et al., 1997; Ward et al., 1998; Ward et al., 1997). However, in general, the phyla with which the isolates were affiliated were the same as those phyla to which the clones belonged. The environmental changes introduced (by bringing the artesian water up to the surface and exposing it to four types of metal coupons made of carbon steels identified by codes ASTM-A53B, ASTM-A53, AS-1074 and AS-1396 and commonly used in bore casings) led to changes in the bacterial community structures. In general, the species which proliferated in the communities before and after the changes were different. The diversity of the bacterial species in the community decreased following the environmental changes. Clones dominating the clone libraries constructed from newly established bacterial communities also differed from the clones dominating the libraries constructed from the bacterial communities which had existed naturally in the bores. These trends toward change in the bacterial communities were observed at both the Fairlea and the Cooinda bore sites. All four metal types incubated in the Fairlea bore water lost between 3.4 and 4.7% of their original weight. In contrast none of the metals incubated in Cooinda bore water lost weight. Clone library A1 showed that the natural population of the Fairlea bore was dominated by clone A1-3, which represented a novel species related to the isolate boom-7m-04. But after metal incubation (and recording of the metal weight loss), the bacterial community was dominated by clone PKA34B, which has a 95% similarity in its 16S rRNA gene sequence with Desulfotomaculum putei. Desulfotomaculum species are known to cause metal corrosion due to their byproduct H2S. But the low level of phylogenetic relatedness found does not provide enough information to speculate on whether the species represented by clone PKA34B is a member of the genus Desulfotomaculum or not. However, the fact that clone PKA34B dominated the PKA clone library by 50% makes the species it represents a suspected candidate likely to be involved with the metal weight loss at the Fairlea bore. In contrast, clone library 4381 showed that the natural population of the Cooinda bore was dominated by clone 4381-15 representing a species distantly related to a hydrogen oxidiser Hydrogenophaga flava (95% similarity). The dominating clone of the new community formed after metal incubation was clone COO25, which has 99% similarity with Thermus species that have not been reported to be involved with metal corrosion to my knowledge. In this project detection, identification and comparative quantification by 16S rRNA gene-targeted PCR probing with probes 23B and 34B were successfully developed for a Leptothrix-like species and for a Desulfotomaculum-like species represented by clones PKA23B and PKA34B respectively. This method of probing permits a fast, sensitive and reproducible detection, identification and at least a comparative quantification of the bacteria in the environment without the need for culturing. Therefore it is extremely suitable for use in bacterial population monitoring. PCR probing with the 34B probe has a potential commercial use as a means of screening for bores with a potential high risk of corrosion due to this Desulfotomaculum-like species. Direct isolation of bacteria from the GAB water has resulted in the isolation of seven strains from the Fairlea bore and eight from the Cooinda bore. Among these isolates, three novel strains were studied in detail. Reports on the characterisation of strain FaiI4T (T=Type strain) from the Fairlea bore (Kanso & Patel, 2003) and strain CooI3BT from the Cooinda bore have been published (Kanso et al., 2002). The data generated during this project add to our current information and extend our knowledge about the bacterial communities of the GAB's sub-surface environment. This information will provide a basis for further ecological studies of the GAB. Studies on involvement of certain groups of bacteria with the corrosion of metals used in bore casings could provide a foundation for further studies to develop maintenance and managing strategies for the GAB bores.

Orientador: Laura Maria Mariscal Ottoboni / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-24T16:24:46Z (GMT). No. of bitstreams: 1 Carlos_Camila_D.pdf: 3834562 bytes, checksum: ae067ac8bf3731e5d1ab6af674e63c67 (MD5) Previous issue date: 2014 / Resumo: Os recifes de corais são ecossistemas sensíveis que estão ameaçados pelas mudanças climáticas. Estudos têm demonstrado a importância da microbiota associada aos corais na resistência às doenças e aos estresses. Neste trabalho, a caracterização taxonômica e funcional da microbiota associada a corais encontrados no litoral de São Paulo permitiu a identificação de associações espécie-específicas entre corais e bactérias e a identificação de funções bacterianas responsáveis pelo estabelecimento de associações coral-bactéria. A composição taxonômica associada a ambientes coralíneos (muco, água e sedimento do entorno) de quatro espécies de corais encontradas no litoral de São Paulo foi avaliada por pirosequenciamento do gene de rRNA 16S. Os resultados indicam que a comunidade microbiana do muco não é apenas distinta do ambiente do entorno, todavia é, também, mais estável ao longo das estações do ano. A composição taxonômica da microbiota do coral mole Palythoa caribaeorum foi bastante distinta das demais espécies, pertencentes estas à ordem Scleractinia, indicando a influência das relações filogenéticas na moldagem das comunidades microbianas associadas aos corais. O metagenoma de Madracis decactis e da espécie brasileira endêmica Mussismilia hispida foi sequenciado por pirosequenciamento. A maior parte das sequências obtidas não pôde ser anotada, o que pode indicar a abundância de micro-organismos, especialmente vírus, ainda não estudados. Entre as sequências anotadas, foi observada uma grande abundância de sequências de origem viral em ambas as bibliotecas. Os metagenomas de M. hispida e M. decactis foram comparados a outros metagenomas disponíveis no banco de dados do MG-RAST e foi possível identificar genes ou funções mais abundantes nessas bibliotecas, como genes de resistência a antibióticos da classe dos aminoglicosídeos, que podem estar sujeitos à transferência horizontal nesse ambiente. Por último, foi sequenciado o genoma de uma bactéria isolada de muco de M. hispida, Paracoccus sp. SM22M-07. A análise comparativa desse genoma com outros genomas do gênero Paracoccus revelou funções únicas do isolado de muco de coral, por exemplo, genes do sistema de secreção do tipo IV podem exercer a função de contribuir com o estabelecimento de interações bactéria-coral. Todos os resultados aqui apresentados e analisados apontam para uma grande diversidade tanto taxonômica quanto funcional da comunidade bacteriana associada aos corais brasileiros. A estabilidade sazonal dessas comunidades é uma propriedade importante que contribui para a prevenção da colonização de bactérias patogênicas. Os resultados aqui apresentados representam um extenso inventário da diversidade microbiana em um ecossistema ameaçado pelas mudanças climáticas globais e permitirão futuros estudos comparativos e a criação de modelos e estimativas das taxas de redução da diversidade microbiana em ambientes marinhos / Abstract: Coral reefs are one of the ecosystems most threatened by global climate changes. Studies have shown the importance of the coral microbiota in stress and disease resistance. In this work, the taxonomic and functional characterization of the bacterial communities associated with corals from the coast of São Paulo State, Brazil, allowed the identification of species-specific interactions between corals and bacteria and the identification of the bacterial functions responsible for the establishment of these interactions. The taxonomic composition of mucus, water and surrounding sediment of four coral species found in the coast of Sao Paulo State was assessed by 16S rDNA pyrosequencing of metagenomic DNA. The microbial communities found in samples of mucus, water, and sediment differed according to the taxonomic composition, and the coral mucus community seemed to be more stable to seasonal changes. The taxonomic composition of the microbiota of the soft coral Palythoa caribaeorum was distinct from the other species belonging to the order Scleractinia, indicating the influence of phylogenetic relationships in shaping the microbial communities associated with the coral. The metagenome of Madracis decactis and the Brazilian endemic species Mussismilia hispida was sequenced by pyrosequencing. Most of the sequences obtained could not be annotated, which might indicate an abundance of unknown microorganisms, especially viruses. Among the annotated sequences, an abundance of viral sequences in both libraries was observed. The metagenomas M. decactis and M. hispida were compared with metagenomes datasets available in the MG-RAST database and through these comparisons, the most abundant genes or functions of the corals¿ metagenomes were identified, for example, genes for resistance to antibiotics of the aminoglycoside class. Finally, the genome of an isolate of mucus of M. hispida, Paracoccus sp . SM22M - 07 was sequenced. The comparative analysis of this genome with other genomes of the genus Paracoccus revealed unique functions of the bacteria isolated from coral mucus, such as genes of the type IV secretion system, which may contribute to the establishment of coral-bacteria interactions. All results presented and analyzed in this work show a great diversity, both taxonomic and functional, of the bacterial community associated with Brazilian corals. The seasonal stability of these communities is an important property that contributes to preventing the colonization by pathogenic bacteria. The results presented here represent an extensive inventory of microbial diversity in an ecosystem threatened by global climate change and will allow future comparisons, modeling and estimates of the rates of reduction of microbial diversity in marine environments / Doutorado / Genetica de Microorganismos / Doutora em Genética e Biologia Molecular

Surgical preparation reduces commensal bacterial load. Currently, no standardized preoperative ocular preparation method in the dog has been reported. Previous studies use culture-based methods to determine commensal bacterial populations. Recent reports suggest that high-throughput sequencing may be superior to culture techniques to determine bacterial communities in the eye and other tissues. The goal of this study was to describe the conjunctival commensal ocular microbiome and bacterial community using DNA sequencing and aerobic cultures of six normal, healthy dogs and investigate the short and long-term effects of an antiseptic protocol on the ocular microbiome. Samples were obtained prior to, immediately following, 24 hours following, and 4 weeks following ocular preparation. The Mississippi State University microbiology laboratory evaluated aerobic cultures, and the Gastrointestinal Laboratory of Texas A&M University performed DNA sequencing. This is the first study to show short and long-term effects of standard ocular surgical preparation on the ocular surface microbiome.

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Manguezais são ambientes costeiros que proveem diversos recursos para ecossistemas adjacentes devido à alta produtividade decorrente da decomposição de matéria orgânica e principalmente da constante ciclagem de carbono, realizada pelas comunidades microbianas presentes nos sedimentos. Desde a década de 70, com o aumento da liberação de gases pela queima de combustíveis fósseis, diversas anormalidades, como o aumento da temperatura e acidificação dos oceanos, têm sido observadas. Com base na hipótese de que as mudanças climáticas provocam alterações na diversidade microbiana associada à decomposição da matéria orgânica em sedimentos de manguezais, estimulando a liberação de Gases do Efeito Estufa (GEE), o presente estudo teve como objetivo avaliar a dinâmica da diversidade microbiana sob alteração das condições climáticas durante o processo de decomposição, correlacionando-a com a emissão de GEE. Microcosmos destrutivos contendo material orgânico proveniente das principais espécies vegetais encontradas nos manguezais do Estado de São Paulo (Rhizophora mangle, Laguncularia racemosa e Avicennia schaueriana) foram incubados em condições simulando as mudanças climáticas (aumento de temperatura e pH). Amostragens do material em decomposição (para sequenciamento da região 16S rRNA e quantificação do gene mcrA) e de gases foram coletadas durante 45 dias. As variações no tempo resultaram em impactos significativos no aumento da α diversidade e na composição da comunidade, inicialmente com maior abundância de Gammaproteobacteria para todas as espécies vegetais independente das variações nas condições climáticas. Análises do tipo PCoA evidenciaram o processo de sucessão em decorrência do tempo na β diversidade, indicando o aumento da incidência de Deltaproteobacteria ao final do processo. As emissões de GEE variaram em função da fonte de material orgânico e observou-se relação entre a emissão de metano (CH4) e a presença do gene mcrA em duas das espécies vegetais estudadas, admitindo-se que o aumento na população de Deltaproteobacteria tenha controlado sua emissão. Apesar da quantidade de estudos relacionados à decomposição de matéria orgânica, à diversidade microbiana e à emissão de gases em manguezais, poucos apresentam uma abordagem como a proposta pelo presente trabalho, que busca compreender melhor a relação entre os três processos, relacionando-os a um quarto evento, as alterações climáticas, que são um problema imanente da atualidade. / Mangrove are coastal environments that provide resources for adjacent ecosystems due to its high productivity that comes from decay of organic matter and carbon cycling, made by microbial communities in sediments. Since the increase of gas release due to fossil fuel burning in the 1970\', many abnormalities have been observed such as temperature and acidification increase. Base on the hypothesis that climate change modifies microbial diversity associate to decay of organic matter in mangrove sediments, changing the emission of Greenhouse Gases (GHG) rate, the goal of this research is to evaluate the dynamics of microbial diversity under the climate change conditions during de decay process, correlating with the emission of GHG. Destructive microcosms containing organic matter from the main plant species found in mangroves throughout the State of São Paulo, Brazil (Rhizophora mangle, Laguncularia racemosa e Avicennia schaueriana) were incubate simulating climate changes (increase in temperature and pH). Sampling of decaying material (for sequencing of 16S rRNA region and quantification of the mcrA gene) and of gasses were collected for 45 days. The variation in time resulted in important increases of α diversity impacts and in the community composition, initially with greater abundancy of Gammaproteobacteria for all plant species despite of the climate conditions variations. The PCoA analysis bespeak the chronological sequence in β diversity, indicating the increase of Deltaproteobacteria at the end of the process. The GHG emission varied in function of the organic matter source and the relation between methane (CH4) release and the presence of the mcrA gene in two of the plant species studied, if the increase in the Deltaproteobacteria population controlled its emission. Despite the great number of studies about the decay of organic matter and emission of gases in mangroves, few present an approach like this work, which aims to understand the relation between these three processes and the climate changes, a pressing problem nowadays.

Made available in DSpace on 2017-07-10T19:25:13Z (GMT). No. of bitstreams: 1 isamara.pdf: 1125655 bytes, checksum: 8f7b2f7606310b4ddb2713e9e4043ec0 (MD5) Previous issue date: 2012-02-13 / Chemical contamination removal in soil and water depends on microbiological community that is able to degrade these compounds. There is a great evolutionary interest on studying microorganisms that metabolize the xenobiotic ones, since they have relatively been seen as new in the last five decades. Little is known about structure variation of microbiological community of soil due do the absence and presence of s-triazine herbicides.Unlike crop dependent methods that require time to detect bacteria, molecular techniques have been developed to identify individual species in mixed populations under natural enviromments. Fluorescence in situ Hibiridization (FISH) technique overcomes some difficulties that are found out in other molecular techniques, as it does not need DNA isolation and amplification steps and allows the identification of specific genes in intact cells. Thus, this study aimed at comparing the absence/presence of atrazine effect on bacteriological community structure in soil according to the phylogenetic aspect. Target probes were used on subdivisions of alpha, beta and gamma Proteobacteria, gram-positive bacteria with high G+C content, ammonia oxidizing bacteria, nitrite oxidizing bacteria and Planctomycetes. It was also used an AtzB1 specific probe to check the atzB gene presence, which makes part of s-triazine degradation. Bacteriological amount was determined by direct counting on epifluorescence microscopy, while the corresponding values to each probe were expressed in percentages of the total count with DAPI for each sample. According to this study, positive cells were found out for all probes used in both soils, but the abundance of all groups was lower in soil contaminated with atrazine herbicide, thereby demonstrating its negative influence. Planctomycetes was the most affected group with 57% lower abundance in contaminated soil. The nitrite oxidizing bacteria was the second most affected group followed by β-Proteobacteria. It was also detected the gene atzB presence, so, it can be inferred that there are potentially degrading s-triazine bacteria in both soils. / A remoção da contaminação química no solo e água é dependente principalmente da presença de uma comunidade microbiana capaz de degradar tais compostos. A existência de microorganismos capazes de metabolizar xenobióticos é de um considerável interesse evolucionário, uma vez que estes compostos são relativamente novos no planeta nas últimas cinco décadas. Pouco se sabe sobre a variação da estrutura da comunidade microbiana do solo em função da ausência e presença dos herbicidas s-triazínicos. Diferentemente dos métodos dependentes de cultivo, que requerem tempo para a detecção de bactérias, técnicas moleculares vem sendo desenvolvidas para o reconhecimento de espécies individuais em populações mistas em ambientes naturais. A técnica de Hibridização Fluorescente in situ (FISH) supera algumas dificuldades encontradas com outras técnicas moleculares, pois dispensa as etapas de isolamento e amplificação de DNA e permite a identificação de genes específicos em células intactas. Em virtude disso, o presente trabalho teve como objetivo comparar o efeito da ausência/presença de atrazina na estrutura da comunidade bacteriana do solo no aspecto filogenético. Foram utilizadas sondas alvo para as subdivisões de Proteobactéria alfa, beta e gama, bactérias Gram-positivas com alto teor de G + C e Betaproteobactérias oxidantes de amônia, Bactérias oxidantes de Nitrito e Planctomicetos. Também foi utilizada uma sonda específica AtzB1 para verificar a presença do gene atzB que está envolvido na degradação das s-triazínas. A abundância bacteriana foi determinada através de contagem direta em microscopia de epifluorescência, e os valores correspondentes a cada sonda foram expressos em porcentagem da contagem total com DAPI para cada amostra. No presente estudo células positivas para todas as sondas utilizadas foram encontradas em ambos os solos, porém a abundância de todos os grupos foi menor no solo contaminado com o herbicida atrazina, demonstrando dessa forma a influência negativa do mesmo, sendo o grupo mais afetado o dos Planctomicetos com uma abundância 57% menor em solo contaminado. O segundo grupo mais afetado foi o das bactérias oxidantes de nitrito seguido pelo grupo das β-Proteobactérias. Foi também detectado no presente estudo a presença do gene atzB demonstrando que em ambos os solos existem bactérias potencialmente degradadoras de s-triazinas.