Thesis (M.S.)--University of Toledo, 2009. / Typescript. "Submitted as partial fulfillment of the requirements for The Master of Science Degree in Biology (Ecology-track)." "A thesis entitled"--at head of title. Bibliography: leaves 28-32.

Thesis (M.S.)--Worcester Polytechnic Institute. / Keywords: AFM, Bacterial Adhesion. Includes bibliographical references (p.130-143).

Thesis (M.S.)--Oregon State University, 2008. / Printout. Includes bibliographical references (leaves 159-167). Also available on the World Wide Web.

No description available.

Thesis (PhD) - Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, 2008. / Submitted for the degree of Doctor of Philosophy, Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, 2008. Typescript. Includes bibliographical references (p. 215-247)

Proposed thesis is focused on the role of soil microbial crusts in the extreme environmental conditions of high-elevation cold desert of W Himalaya. Despite the importance of microbial soil crusts in arid soils, the biodiversity of their microbial communities, their role and function are still unclear. Our knowledge about functioning of these outlying ecosystems in this part of the world is still very insufficient in general. The area of Ladakh is perfect place for studying the microbial soil crust arid climate and extreme elevation aroud 6000 m a.s.l. represents unique condition for well-developed soil crusts communities. The whole region is unaffected by human activities or plant invasions, so we can study soil crusts in pristine natural condition. Our investigations is focused on soil microbial community of BSCc in Ladakh region. It combines range of aspects connected with BSCs such as taxonomical composition, changes of diversity and activity in relation to environmental condition. The thesis is the first compilation of studies concerned on microbial communities in area of Ladakh and one of the first work investigating the ecophysiology of BCSs in cold desert.

Orientador: Sueli dos Santos Freitas / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-05T22:05:12Z (GMT). No. of bitstreams: 1 Donzeli_VanessaPolon_D.pdf: 754794 bytes, checksum: 0d25f60426155f9e9b87dd4c334befa8 (MD5) Previous issue date: 2006 / Resumo: A solarização do solo vem se destacando como um método promissor para o controle de fitopatógenos; no entanto, as mudanças nas populações e atividades microbianas após o processo de solarização são ainda pouco estudadas. O presente trabalho teve como objetivos: estudar parte da comunidade e atividades microbianas em solo solarizado em comparação a solo não solarizado; selecionar isolados de rizobactérias promotoras de crescimento em alface em substrato comercial, visando à produção de mudas, e verificar os possíveis benefícios da solarização do solo à promoção de crescimento de plantas de alface por esses isolados microbianos. Para a avaliação do efeito da solarização sobre a microbiota do solo, os tratamentos foram: solarização em coletor solar (substrato solarizado e não solarizado) e amostragens no tempo (0, 30, 60, 90 e 120 dias após a solarização). As parcelas foram vasos com 2L de substrato (mistura de solo e substrato orgânico cama-de-frango), mantidos com plantas da variedade de alface crespa Verônica. Os parâmetros avaliados foram: carbono, nitrogênio e relação entre C e N da biomassa microbiana; liberação de CO2; quociente metabólico; microrganismos amonificadores, nitrificadores, celulolíticos, amilolíticos e proteolíticos; Pseudomonas spp. fluorescentes e bactérias não fluorescentes no substrato e na rizosfera de plantas de alface; número de folhas, matéria seca da parte aérea e raízes de alface e emergência de plantas invasoras. Para avaliar a promoção de crescimento de mudas de alface utilizaram-se um substrato comercial para hortaliças, com metade da adubação recomendada, solarizado e não solarizado e 50 isolados de Pseudomonas spp. da coleção do IAC. Os isolados foram escolhidos de acordo com um pré-teste e resultados de Freitas et al.(2003) e Sotero (2003) . O delineamento experimental foi o inteiramente casualizado, com 10 repetições, totalizando 1000 vasos. Vinte e cinco dias após a semeadura, as mudas de alface foram coletadas e realizou-se a contagem do número de folhas e avaliação da massa de matéria seca da parte aérea. A solarização do substrato causou uma redução da microbiota logo após ser realizada, refletida pela diminuição do carbono e nitrogênio da biomassa microbiana, microrganismos amonificadores, nitrificadores, celulolíticos, amilolíticos e bactérias não fluorescentes. O aumento da relação C/N da biomassa microbiana na primeira amostragem e a redução da liberação de CO2 pela respiração de microrganismos do solo e aumento do quociente metabólico aos 30 dias após a solarização também foram indicativos da alteração na microbiota. No entanto, com o tempo, a microbiota do substrato solarizado se restabeleceu, sendo que aos 30 dias após a solarização alguns grupos de microrganismos, como os amonificadores e amilolíticos, já haviam tido seu número igualado aos do substrato não solarizado e outros grupos como os nitrificadores e celulolíticos apresentaram-se em maior número no substrato solarizado nessa amostragem. Nem todos os grupos de microrganismos foram imediatamente afetados pela solarização, como os microrganismos proteolíticos, que tiveram o seu número diminuído apenas na amostragem feita aos 60 dias, as também se restabeleceram nas amostragens seguintes. As Pseudomonas spp. do grupo fluorescente foram positivamente influenciadas pela solarização, tendo seu número aumentado aos 60 dias no substrato e 120 dias na rizosfera. Assim, aos 90 dias, a maioria dos grupos microbianos funcionais já havia voltado ao equilíbrio, com exceção apenas dos nitrificadores e Pseudomonas spp. fluorescentes que se apresentaram em número maior no substrato solarizado na amostragem seguinte. As plantas de alface cultivadas em substrato solarizado tiveram maior crescimento na primeira amostragem após a solarização e nesse tratamento houve uma redução média de 92,3% na emergência de plantas invasoras. A solarização do substrato favoreceu o efeito benéfico de 17 isolados de Pseudomonas spp. fluorescentes na promoção de crescimento de mudas de alface e favoreceu também o efeito deletério de dois isolados. Dezoito isolados foram capazes de promover o crescimento de mudas de alface, independente da solarização, e a solarização também foi responsável pelo maior crescimento das plantas, independente da inoculação de rizobactérias / Abstract: Soil solarization has been reported as an efficient soil disinfestations method for controlling soil borne pathogens; however few studies about changes in microbial activity and populations after soil polarization have been published. The present work was carried out to study the microbial activity and part of the microbial community in solarized soil; selected plant growth promoting rhizobacteria strains in commercial substrate to seedling yield and verify the possible contribution of soil solarization to promotion of lettuce seedling growth by these microbial strains. To evaluate the effect of solarization on the soil microorganisms, the treatments were: solarization in solar collector (solarized and non solarized substrate) and time sampling (0, 30, 60, 90 and 120 days after solarization). The plots bowls (2L) were maintained with lettuce plants of cultivar Verônica. The following parameters were evaluated: carbon, nitrogen and C/N in the microbial biomass; basal respiration; metabolic quotient; number of ammonifying, nitrifying, cellulolytic, amylolytic, proteolytic microorganisms and fluorescent and non fluorescent bacteria grown in B King media, in bulk substrate and lettuce rhizosphere; number of leafs, shoot and root dry matter and weed emergence. To evaluate promotion of seedling lettuce growth a substrate for production of vegetable seedlings was used, with half-full fertilizer, solarized and non solarized, and fifty pseudomonads strains of the IAC collection. The experiment had a completely randomized design in 1000 plots. Twenty five days after sowing the number of leafs and the shoot dry matter lettuce were evaluated. The substrate solarization immediately reduced the microbial groups as showed by carbon and nitrogen in microbial biomass, ammonifying, nitrifying, cellulolytic, amylolytic microorganisms and fluorescent bacteria decrease. The increase of the C/N in microbial biomass ratio in the first sampling and decrease of the CO2 evolved rate and higher metabolic quotient rate at 30 days after substratesolarization indicated changes in microbial community. However, after some time, the functional microbial groups were reestablished. Thirty days after solarization the number of some groups of microorganisms ¿ as ammonifying and amylolytic microorganisms ¿ were similar in solarized and non solarized substrate, and others ¿ as nitrifying and cellulolytic microorganisms ¿ ad higher numbers in solarized substrate in this sampling. Proteolytic microorganisms were not affected immediately by solarization and decreased only in the samplings 60 days after solarization. In the samplings 90 and 120 days after solarization the number of proteolytic were similar in the treatments. Fluorescent pseudomonads were positively affected by solarization: the number of these bacteria was higher in the bulk solarized substrate in third sampling and in the rhizosphere in fifth sampling. Thus, at 90 days, most of functional microbial groups were reestablished, except nitrifying and fluorescent pseudomonads, that were in higher number in solarized substrate. The solarization contributed to increase the growth of lettuce plants in first sampling and provided effective weed control that were reduced 92,3% over the untreated control. Solarization propitiated the beneficial effect of 17 fluorescent Pseudomonas spp. strains, that promoted seedling lettuce growth, and deleterious effect of 2 strains on lettuce seedlings. Eighteen Pseudomonas spp. Strains promoted plant growth, independent of solarization, and solarization promoted plant growth, independent of bacteria inoculation / Doutorado / Microbiologia / Doutor em Genetica e Biologia Molecular

Este trabalho teve por objetivo avaliar a biodegradação do glifosato em amostras de solos, quantificando o grupo de microrganismos mais ativos durante este período, além de determinar um método de extração e análise para este herbicida. Foram utilizadas amostras de dois tipos de solos, um da Fazenda Experimental da ESALQ-USP, classificado como podzólico vermelho-amarelo (PV), e outro da Estação Experimental do IAPAR/PR, classificado como latossolo vermelho (LV), ambos com e sem histórico de aplicação de glifosato. O trabalho foi realizado no Laboratório de Ecotoxicologia do Centro de Energia Nuclear na Agricultura, da Universidade de São Paulo, utilizando o glifosato em sua fórmula técnica, na dosagem para condições de campo (2,16 mg i.a./kg de solo). A biodegradação do glifosato foi avaliada monitorando a evolução do CO2 pelos microrganismos durante um período de 32 dias. Foram também quantificados durante o período, os resíduos de glifosato e do seu metabólito ácido aminometil fosfônico (AMPA) através de extração seguida de análise por cromatografia liquida de alta eficiência (CLAE). Além disso, foi avaliada a atividade microbiana e o número de microrganismos presentes durante o período. Os resultados mostraram que o glifosato foi degradado pelos microrganismos do solo durante o período avaliado, com a formação do metabólito AMPA. O glifosato favoreceu um aumento na atividade microbiana das amostras dos solos que receberam aplicação do herbicida. Em relação ao número de microrganismos, os fungos e actinomicetos tiveram um aumento em população com a presença do glifosato, enquanto que as bactéria permaneceram em número constante durante o período de incubação. Os resíduos de glifosato e AMPA, extraídos com NH4OH e KH2PO4 e analisados por CLAE, foram detectados nas amostras avaliadas, mostrando que o método de extração utilizado foi eficiente, com recuperação acima de 70%, para estes dois compostos. / The aim of this work was to evaluate the biodegradation of glyphosate in soil samples, quantifying the group of more active microorganisms during this period, and also to establish an extraction and analysis methods for this herbicide. Two soils types were analysed, one from the ESALQ Experimental Station (USP), classified as typic hapludult (PV), and another from the IAPAR Experimental Station, classified as typic hapludox, with and without report of glyphosate application, in total of 4 samples. The work was carried out using the technical glyphosate in the doses for field conditions (2,16 mg a.i./kg of soil). The assessment of degradation was made using the CO2 evolution during a period of 32 days. The residues of glyphosate and metabolite aminomethyl phosphonic acid (AMPA) were quantified during the same period, through extraction and analysis by high-pressure liquid chromatography (HPLC). The soil microbial activity and the enumeration of microorganisms were evaluated during the same period. The results showed that glyphosate was degraded by the soil microorganisms, with the formation of the metabolite AMPA. The application of glyphosate provided an increase in the microbial activity of the soil samples. In relation to enumeration of fungi and actinomycetes had an increase in the population with the glyphosate application, while the number of bacteria remained constant through the whole experiment. The HPLC analyse of glyphosate and AMPA residues, extracted with NH4OH and KH2PO4, resulted in a recovery above 70% showing that the extraction method used was efficient for these two compounds.

The adenylate energy charge values of twenty bacteria isolated from soil and cultured in a medium consisting of soil and distilled water were determined by the luciferin-luciferase bioluminescense method. The purpose of this study was to examine the growth and energy charge values of these organisms in soil extract medium, and to determine what effect the addition of glucose has on their energy charge values. Three of the organisms employed in this study showed energy charge values similar to those reported for bacteria grown in enriched media. The remainder of the isolates demonstrated low energy charge values, and scant growth in the soil medium.

Burkholderia cepacia is a common soil bacterium of significance in agriculture and bioremediation. B. cepacia is also an opportunistic pathogen of humans causing highly communicable pulmonary infections in cystic fibrosis and immunocompromized patients. The pyrB gene encoding ATCase was cloned and ATCase was purified by the glutathione S-transferase gene fusion system. The ATCase in B. cepacia has been previously classified as a class A enzyme by Bethell and Jones. ATCase activity gels showed that B. cepacia contained a holoenzyme pyrBC complex of 550 kDa comprised of 47 kDa pyrB and 45 kDa pyrC subunits. In the course of purifying the enzyme, trimeric subunits of 140 kDa and 120 kDa were observed as well as a unique proteolysis of the enzyme. The 47 kDa ATCase subunits were cleaved to 40 kDa proteins, which still demonstrated high activity as trimers. The proteolysis site is between Ser74 and Val75 residues. To confirm this, we converted the Ser74 residue to an Ala and to an Arg by site-directed mutagenesis. After this primary sequence changed, the proteolysis of ATCase was not observed. To further investigate the characteristics of B. cepacia pyrB gene, a pyrB knock-out (pyrB-) was constructed by in vitro mutagenesis. In the assay, the 550 kDa holoenzyme and 140 kDa and 120 kDa trimers disappeared and were replaced with a previously unseen 480 kDa holoenzyme pyrB- strain. The results suggest that B. cepacia has two genes that encode ATCase. ATC1 is constitutive and ATC2 is expressed only in the absence of ATC1 activity. To check for the virulence of these two strains, a eukaryotic model virulence test was performed using Caenorhabditis elegans (C. elegans). The pyrB1+pyrB2+ (wild type) B cepacia killed the nematode but pyrB1-pyrB2+ B. cepacia had lost its virulence against C. elegans. This suggests that ATC1 (pyrB1) is involved in virulence in B.cepacia and ATC2 (pyrB2) is not.