Thesis (doctoral)--Swedish University of Agricultural Sciences, 2007. / Thesis documentation sheet inserted. Includes appendix of four papers and manuscripts, three co-authored with others. Includes bibliographical references. Also issued electronically via World Wide Web in PDF format; online version lacks appendix.

Thesis (Ph.D.) -- University of Western Sydney, 2008. / A thesis submitted to the University of Western Sydney, College of Health and Science, School of Natural Sciences, in fulfilment of the requirements for the degree of Doctor of Philosophy. Includes bibliographical references.

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Une meilleure compréhension du rôle des bactéries dans les écosystèmes aquatiques nécessite une meilleure connaissance de la dynamique, de la composition et des facteurs de contrôle des groupes qui constituent ces communautés. Toutefois, les études qui se sont intéressées à cet aspect de l'écologie microbienne aquatique ont, pour la plupart, concerné les groupes bactériens dominants. Parmi les phyla bactérien non dominants, les Planctomycetes restent peu connus tant en terme de dynamique que de rôle fonctionnel en milieu naturel, bien qu'étant reconnus ubiquistes. Le manque de connaissances sur ce groupe est encore plus marqué dans les écosystèmes lacustres. Pourtant, les quelques études consacrées à ce groupe bactérien dans les écosystèmes aquatiques indiquent qu'ils sont impliqués dans deux processus clés de leur fonctionnement à savoir l'oxydation de l'ammonium en conditions anaérobies (anammox) ainsi que la dégradation et le changement de qualité de la matière organique dissoute. L'objectif principal de cette thèse était donc de caractériser la diversité, la dynamique spatio-temporelle ainsi que les facteurs de contrôle des Planctomycetes dans les lacs, dans le but de mieux connaître la dynamique des bactéries non dominantes, qui constituent une très large part de la diversité bactérienne totale. L'absence d'outils moléculaires permettant de caractériser les communautés de Planctomycetes dans les lacs nous a tout d'abord conduit à faire une rigoureuse mise au point méthodologique. Cette dernière a abouti à la caractérisation d'un couple d'amorces (PLA352F/PLA920R) permettant de détecter et d'amplifier spécifiquement tous les genres de Planctomycetes dans ces écosystèmes, et pouvant être utilisé dans les approches d'empreintes moléculaires comme la DGGE. L'étude spatio-temporelle, réalisée dans deux lacs péri-alpins à partir de ce couple d'amorces, a ensuite permis de révéler que les Planctomycetes, malgré leur faible abondance relative dans la communauté bactérienne lacustre, présentent une richesse taxonomique élevée jusqu'ici insoupçonnée. Ils sont caractérisés par une structure taxonomique similaire aux bactéries dominantes puisqu'ils sont composés d'un nombre réduit d'OTUs dominantes et d'un très grand nombre d'OTUs faiblement représentées en nombre de séquences. Ce résultat soutient l'idée selon laquelle le concept de cores species (espèces dominantes) et de satellites species (espèces rares), récemment transposé aux groupes bactériens dominants, s'applique aussi aux groupes moins abondants ou rares. Nos résultats ont également mis en évidence que les communautés de Planctomycetes des lacs étaient très structurées dans l'espace et dans le temps. Les patterns de distribution de ce phylum bactérien étaient très similaires à ceux décrits pour les groupes bactériens plus abondants à savoir (i) une forte hétérogénéité verticale (certains genres étant présents essentiellement dans les couches profondes des lacs) ainsi qu' (ii) une dynamique saisonnière importante principalement mise en évidence dans la partie épilimnique des lacs. Cette structuration n'est pas le fruit d'une dispersion aléatoire liée à des processus stochastiques comme l'immigration mais est au contraire fortement dépendante des facteurs environnementaux. Nos résultats ont en effet montré que la richesse spécifique ainsi que la diversité des communautés de Planctomycetes sont fortement dépendantes de l'évolution du pH. De même, la température semble également être un facteur clé dans la dynamique et la composition globale des Planctomycetes. En revanche, l'effet des nutriments inorganiques semble moins influent dans le contexte de notre étude et la compétitivité des Planctomycetes vis-à-vis de ces ressources pourrait dépendre d'autres facteurs que nous n'avons pas analysés. / Understanding the role of microbes in the functioning of ecosystems is currently one of the major challenges in microbial ecology. One important step to this challenge is the assessment of the diversity of these microbial communities and their driving factors. With the recent methodological advances in molecular approaches, knowledge on the structural and functional diversity of bacterial communities in aquatic ecosystems has considerably increased during the last twenty years. However most of these studies concerned either the bacterial community or the most abundant bacterial groups, such as Actinobacteria and Proteobacteria. Only few data are available on the dynamics and diversity of less abundant but ubiquitous phyla such as Planctomycetes. This is particularly true for freshwater ecosystems, for which data on this phylum are much less abundant, compared to marine and soil ecosystems. Yet, members of this bacterial group are thought to play an important role in biogeochemical processes in aquatic systems, including nitrogen cycling and degradation of organic matter. Thus, the aims of this thesis were (1) to compare the structure and the composition of the Planctomycetes communities in two peri-alpine lakes with contrasting environmental conditions (2) to assess the vertical and temporal variations in the composition of these communities and (3) to characterize the different environmental factors that control these communities.

The master thesis lists the basic effects of nitrogen transformation in soil (nitrification), subsequent leaching of nitrates from soil to water and the effects of eutrophication of aquatic environment on the human health. The results of this experiment show that the interaction of all three factors (fertilization, soil moisture, vegetation) has a significant effect on the rate of nitrification. Generally, the nitrification rate increases with fertilization, decreases with presence of vegetation and decreases with soil moisture decrease. The health risk of nitrates in water consists in their consumption and the subsequent development of methemoglobinemia (especially in young infants) and the formation of N-nitroso compounds (e.g.nitrosamines), which have carcinogenic and teratogenic effects. Nitrate together with phosphates also promote the growth of cyanobacteria and algae. Cyanobacteria can produce cyanotoxins causing several groups of diseases.

Nitrogen in its molecular form (N2) is an available gas that makes up 78% of the atmospheric air and is characterized by being a stable and inert gas. The other nitrogen-based reactive species (Nr) are generated through innumerable natural and anthropogenic processes. When poorly applied, it is an agent harmful to agriculture and forests. The same Nr atom can cause multiple undesirable effects on the atmosphere, on terrestrial and aquatic ecosystems as well as on human health. These effects are known as effects of the nitrogen cascade. The present work aims to estimate the sources of Nr at the Ondina Campus of the Federal University of Bahia (UFBA) and the São Cristóvão Campus of the Federal University of Sergipe (UFS), as well as propose alternatives to mitigate and/or compensate, the generation of Nr on these campuses. To do so, this exploratory thesis made use of bibliographical review and field visits in both campuses to obtain the data of electric energy consumed, terrestrial and aerial trips made by the academic community, food, waste and effluent of the campus among others necessary estimate of such emissions. As main results, it was observed that in relation to Ondina Campus by UFBA, its sources were estimated, where the highest emission was related to the aerial trips of this campus carried out by the academic population that represents about 60% of all campus broadcasting. As for São Cristóvão Campus by UFS, the highest estimated emission was related to the transportation of buses that serve the academic community, which represented about 30% of the total emission of said campus. There were several negative environmental aspects in both institutions, such as the significant waste of food, unnecessary use of energy-consuming equipment, irrational use of fuel in official cars of the campus, use of many private cars with only one individual, drastic reduction of green areas for construction of buildings, among others. In view of the diagnoses made, several mitigating actions were suggested to minimize the generation of reactive nitrogen in these campuses, mainly focusing on the aspects identified with higher emission value, namely: reduction of air travel opting for the use of computer technology, when justified for the purpose of evaluating academic work; Reduction of the use of animal protein based diets; Encourage the use of collective transportation when possible as well as generate a carpool program in the case of private cars; Segregate, treat and store urine generated on campus, taking advantage of fertilizer for green areas etc. / O Nitrogênio em sua forma molecular (N2) é um gás disponível que compõe 78% do ar atmosférico e caracteriza-se por ser um gás estável e inerte. Já as demais espécies reativas de base nitrogenada (Nr) são geradas através de inúmeros processos, tanto de origem natural como de origem antrópica. Quando mal aplicado trata-se de um agente danoso à agricultura e florestas. O mesmo átomo de Nr pode causar múltiplos efeitos indesejáveis na atmosfera, nos ecossistemas terrestres e aquáticos bem como na saúde humana. Esses efeitos são conhecidos como efeitos da cascata de nitrogênio. O presente trabalho tem por objetivo estimar as fontes de Nr no Campus Ondina da Universidade Federal da Bahia (UFBA) e no Campus São Cristóvão da Universidade Federal de Sergipe (UFS), bem como propor alternativas para mitigar e/ou compensar, a geração de N nestes campus. Para tal, esta tese de caráter exploratório fez uso de revisão bibliográfica e de visitas de campo em ambos os campus para obtenção dos dados de energia elétrica consumida, viagens terrestres e aéreas realizadas pela comunidade acadêmica, alimentos, resíduos e efluentes dos campus dentre outros necessários à estimativa de cálculo das referidas emissões. Como resultados principais observou-se que no tocante ao Campus Ondina da UFBA, foram estimadas as suas fontes, onde a mais alta emissão foi referente às viagens aéreas desse campus realizadas pela população acadêmica que representa cerca de 60% de toda emissão do campus. Já para o Campus São Cristóvão da UFS, a mais alta emissão estimada foi referente ao transporte de ônibus que servem à comunidade acadêmica, que representou cerca de 30% da emissão total do referido campus. Constatou-se a existência de diversos aspectos ambientais negativos em ambas instituições, tais como o significativo desperdício de alimentos, uso desnecessário de equipamentos consumidores de energia, uso irracional de combustível em carros oficiais dos campus, uso de muitos carros particulares com apenas um indivíduo, redução drástica de áreas verdes para construção de edificações, dentre outros. Diante dos diagnósticos realizados, sugeriu-se diversas ações mitigadoras para minimização da geração do nitrogênio reativo nesses campus, principalmente com foco nos aspectos identificados com maior valor de emissão, a saber: redução das viagens aéreas optando pelo uso de tecnologia de informática, quando a viagem for justificada para fins de avaliação de trabalhos acadêmicos; Redução do uso de dietas a base de proteína animal; Incentivar o uso de transporte coletivo quando possível bem como gerar um programa de caronas no caso dos carros particulares; Segregar, tratar e armazenar a urina gerada no campus, aproveitando como fertilizante para as áreas verdes etc. / São Cristóvão, SE

A recuperação de funções e processos ecossistêmicos, entre outros atributos, é um dos indicadores mais importantes no processo de retorno de um ecossistema à sua trajetória histórica. A ciclagem de nutrientes é um atributo fundamental do ecossistema, e relaciona-se diretamente à regulação do funcionamento e do desenvolvimento dos ecossistemas e inclui, em um modelo geral, as entradas de nutrientes, as transferências internas entre plantas e solo e as saídas do sistema. A compreensão das mudanças nos processos biogeoquímicos durante a sucessão secundária em áreas em restauração ecológica ainda é incipiente, principalmente em áreas de florestas tropicais. Esse estudo tem por objetivo elucidar a dinâmica do nitrogênio ao longo do processo de restauração ecológica em áreas reflorestadas com espécies nativas da Mata Atlântica. A questão norteadora deste estudo é a seguinte: A restauração florestal com alta diversidade de espécies e predominância de espécies arbóreas nativas regionais restaura a dinâmica original do nitrogênio? Esse estudo visa investigar o funcionamento da ciclagem de nutrientes, com foco no nitrogênio, que é um elemento limitante à sucessão secundária, especialmente em florestas tropicais. Para tal, alguns indicadores da ciclagem do nitrogênio foram mensurados em uma cronosequência florestal formada por uma floresta natural preservada e florestas restauradas de diferentes idades (21 e 52 anos) reflorestadas com alta diversidade de espécies e predominância de nativas regionais. Os indicadores utilizados foram: 15N e teor de N da vegetação, serrapilheira e solo; razão N:P da vegetação e da serrapilheira; taxas líquidas de mineralização e nitrificação; teor de amônio, nitrato, N mineral e razão nitrato:amônio. As florestas foram amostradas entre agosto de 2008 e abril de 2009, nas seguintes estações: seca, transição entre seca e chuvosa, chuvosa, e transição entre chuvosa e seca. Foram encontrados padrões claros de mudanças na ciclagem do N ao longo da cronosequência estudada, incluindo diferenças nos valores de 15N foliar, teor de N, razão N:P, N mineral e taxas líquidas de mineralização e nitrificação, caracterizadas por um aumento de valores médios dessas variáveis ao longo da cronosequência. Os resultados encontrados sugerem que as florestas em processo de restauração, mesmo a de 52 anos, ainda não possuem uma ciclagem de N característica de uma floresta madura e, portanto, a recuperação da ciclagem de N ainda não foi completamente atingida. Entretanto, é possível afirmar que as florestas em processo de restauração estudadas estão seguindo uma trajetória de desenvolvimento caracterizada por uma ciclagem de N cada vez mais parecida com a de uma floresta natural madura, como a da floresta natural madura utilizada como referência. Através dos modelos de restauração utilizados para as florestas da cronosequência estudada, os processos da ciclagem do N são recuperados à medida que a floresta desenvolve-se, com uma clara tendência de mudança na economia de N para economia de P típica de florestas tropicais maduras. / The recuperation of ecosystem processes and functions, among other attributes, is one of the most important indicators in the process of return of an ecosystem to its historic trajectory. Nutrient cycling is a fundamental ecosystem attribute, and relates directly to regulation of functioning and development of ecosystems and includes, in a general model, nutrients entering, being transferred internally between plants and soil, end leaving the system. The comprehension of changes in biogeochemical processes during secondary succession in areas in ecological restoration is still incipient, mainly in tropical forests. This study aims to elucidate nitrogen dynamics along the process of ecological restoration in areas reforested with Atlantic Forest native species. The question driving this study is: Does ecological restoration with high diversity of species and predominance of regional native tree species restore nitrogen original dynamics? This research investigated nutrients cycling functioning, focusing on nitrogen, which is a limiting nutrient in secondary succession, particularly in tropical forests. In order to do so, some indicators of nutrient cycling were assessed in a forest chronosequence formed by a preserved natural forest and restored forests of different ages (21 and 52 years) reforested using high species diversity and predominance of regional native species. The indicators used were: 15N and N content in green foliage, litter and soil; N:P ratio of green foliage and litter; net mineralization and net nitrification rates; content of ammonium, nitrate, inorganic N, and nitrate:ammonium ratio. The forests were sampled between August 2008 and April 2009, in the following seasons: dry, dry-rainy transition, rainy, rainy-dry transition. Clear patterns of change in the N cycling along the studied chronosequence were found, including differences in green foliage 15N values, N content, N:P ratio, inorganic N and net mineralization and nitrification rates, characterized by an increase in the mean values of these variables along the chronosequence. The results found suggest that the forests in restoration process, even the 52 years old one, still do not present a N cycling characteristic of a mature forest and, therefore, the recuperation of the N cycling was not completely reached yet. However, it is possible to state that the forests in restoration process studied here are following a development trajectory characterized by a N cycling progressively more similar to what is common to a mature native forest, as the one used as the reference ecosystem in this study. Through the restoration models used for the forests studied, the N cycle processes are recovered as the forests develop, as they present a clear tendency of changing from N economy to P economy, typical to mature tropical forests.

Dans les vasières intertidales dominées par les diatomées, la production primaire est particulièrement forte à marée basse. Ce microphytobenthos peut être limité par les nutriments azotés en lien avec les communautés de procaryotes impliquées dans le cycle de l’azote. Ainsi, ce travail de thèse cherche, via une approche écologique, à décrire le rôle des communautés de procaryotes benthiques notamment liées au cycle de l’azote et ce, suivant différentes échelles temporelles liées aux cycles du microphytobenthos. Des échantillons de sédiment ont été prélevés dans la baie de Marennes-Oléron (Côte Atlantique, France) entre 0 et 10 cm de profondeur suivant 5 couches (0-0,5 cm, 0,5-1 cm, 1-2 cm, 2-5 cm, 5-10 cm). Différents facteurs biotiques et abiotiques ont été mesurés et mis en relation avec la production bactérienne, les activités enzymatiques et les gènes fonctionnels liés au cycle de l’azote (impliqués dans la nitrification, la dénitrification et l’anammox). De plus, la diversité bactérienne et archéenne a été évaluée par pyroséquençage 454 afin de caractériser les communautés et leurs dynamiques en lien avec les facteurs forçants biotiques et abiotiques. Dans le but d’évaluer l’influence des paramètres abiotiques et de la production du microphytobenthos, des mesures in situ ont été couplées avec des mesures en conditions semi-contrôlées. / In diatoms-dominated intertidal mudflats, at low tide the primary production is particularly high and microphytobenthos that can be limited by nitrogen-related nutrients is linked with N-related prokaryotic communities. Thus, this PhD thesis aim at describing by ecological approach, the role of benthic prokaryotic communities especially N-related ones, at various temporal scales linked to microphytobenthos life cycles. Sediment samples from Marennes-Oleron mudflat (Atlantic coast, France) were collected according to 5 layers : 0-0.5 cm, 0.5-1 cm, 1-2 cm, 2-5 cm and 5 to 10 cm below sediment surface (bsf). Various biotic (i.e. chlorophyll a) and abiotic parameters (i.e. nutrients, exopolymeric substances, water content, salinity, pH, temperature…) were recorded and linked with benthic bacterial production, enzymatic activities and N-related functional genes (i.e. implied in nitrification, denitrification, and anammox). Furthermore, the bacterial and archaeal diversity was assessed by 454 pyrosequencing in order to characterize the communities and shift in link with biotic and abiotic drivers. Aiming at evaluating the influence of abiotic parameters and microphytobenthic activities on the prokaryotic communities, in situ measurements were coupled to a semi-controlled approach.

Thesis (S.M.)--Joint Program in Chemical Oceanography (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Nitrogen and trace metal biogeochemical effects on phytoplankton productivity were compared through whole water bottle incubations and proteomic evaluation of in situ harvested particulate matter from two distinct oceanographic regions: the Equatorial Pacific Upwelling and the South Pacific Gyre. Phytoplankton growth in both regions was stimulated by nitrogen additions with equivalent response from nitrate and urea. In the gyre, trace metal additions did not yield a chlorophyll response, however nickel treatments showed evidence of nickel-limited nitrogen fixation. In contrast, cell growth at the upwelling site was primarily iron-limited and iron plus urea or nitrate additions further enhanced the chlorophyll response, indicative of secondary nitrogen limitation. Nitrogen stress proteins and urea transporters from cyanobacteria in these field sites showed similar trends, with both increasing in waters containing lower dissolved inorganic nitrogen. Together with bottle incubations, the abundant urea transporters and nitrogen stress proteins indicate the importance of urea in these field sites. Representative cyanobacteria cultures (Synechococcus strain WH8020, and Prochlorococcus strain MED4) were evaluated to constrain urea uptake rates and explore the potential for compound specific uptake rates. Together, results from this study indicate that urea may represent an under-recognized component of the marine microbial nitrogen cycle. / by Tyler Jay Goepfert. / S.M.

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