Alguns ecossistemas chamam atenção devido à particular combinação de condições ambientais únicas, que resultam na evolução de espécies capazes de colonizar estes ambientes. Os manguezais compõem um bioma composto por espécies de plantas, animais e microrganismos que interagem neste ambiente, que tem como principal característica a interface entre o continente e o oceano em regiões intertropicais. Nosso objetivo foi acessar via sequenciamento massivo de DNA e RNA (via Illumina HiSeq 2000) o perfil taxonômico e funcional da comunidade microbiana de quatro manguezais com distintos níveis de contaminação. As sequências foram analisadas na plataforma MG-RAST, para a análise taxonômica foi utilizado BlastN contra a base de dados RDP ou M5NR, enquanto que a análise funcional foi baseada na comparação por BlastX das sequências obtidas com as disponíveis no banco de dados M5RNA e M5Nr. Na análise funcional, as sequências classificadas foram ainda integradas na classificação hierárquica SEED (subsystems), KEGG (Kyoto Encyclopedia of Genes and Genomes) e COG (Clusters of Orthologous Group). No total, foram obtidas 682 milhões de sequências válidas ( 88,2, 303,1 e 290,9 milhões a partir das análises de DNA, RNA total e RNA purificado, respetivamente). Estas indicaram como grupos taxonômicos mais abundantes as classes Gammaproteobacteria e Deltaproteobacteria (dentro do domínio Bacteria), e Methanomicrobia e Methanobacteria (dentro do domínio Archaea). Além destas observações, alterações na representação de determinados grupos quando as análises de DNA e RNA são comparadas. Em relação a classificação funcional das sequências, foi possível observar uma similaridade no número de funções encontradas nos diferentes manguezais, mas uma maior quantidade de sequências anotadas foi observada, como esperado, na análise de DNA. De maneira mais detalhada, o estudo das funções relacionadas a transformação de nitrogênio e enxofre indicou que há uma correlação entre a abundância de sequências de um referido gene na análise metagenômica, e sua correspondente quantidade dentro dos grupos de dados de metatranscriptômica. Os grupos microbianos mais representados nestes ciclos foram Deltaproteobacteria e Gammaproteobacteria, atuantes principalmente nos processos de fixação de nitrogênio atmosférico (N2), desnitrificação e redução de sulfato, enquanto que para oxidação do enxofre as classes mais frequentes foram Gammaproteobacteria, Betaproteobacteria e Epsilonproteobacteria. De maneira geral, este estudo fornece indícios sobre a atividade microbiana nos manguezais, e indica que as frequentemente correlações observadas entre os resultados da análise metagenômica e metatranscriptômica, porém essas correlações se tornam menos evidentes quando analisamos em nível de ordem ou em níveis mais específicos. / Some ecosystems call particular attention due to unique combination of environmental conditions that result in evolution of species capable of colonizing these environments. Mangroves constitute a biome composed of species of plants, animals and micro-organisms that interact in this environment, whose main characteristic is the interface between the continent and the ocean in tropical areas. Our goal was to access via massive sequencing of DNA and RNA (via Illumina HiSeq 2000) the taxonomic and functional profile of the microbial community four mangroves with different levels of contamination. The sequences were analyzed on MG-RAST platform for taxonomic analysis was performed using BLASTN against the RDP database or M5NR, while the functional analysis was based on comparison of the sequences obtained by BlastX available on M5RNA with the database and M5Nr . In functional analysis, the sequences were classified yet integrated into the hierarchical classification SEED (subsystems), KEGG (Kyoto Encyclopedia of Genes and Genomes) and COG (Clusters of Orthologous Group). A total of 682 million valid sequences were obtained (88.2, 303.1 and 290.9 million from DNA analyzes, purified total RNA and RNA, respectively). These indicated as the most abundant taxa Gammaproteproteobacteria and Deltaproteobacteria classes (within the domain Bacteria), and Methanomicrobia and Methanobacteria (within the domain Archaea). In addition to these observations, changes in the representation of particular groups when analyzes of DNA and RNA are compared. Regarding the functional classification of the sequences was observed in the number of a similarity functions found in different mangrove, but a greater amount of annotated sequences was observed, as expected, the analysis of DNA. In more detail, the study of the functions related to transformation of nitrogen and sulfur indicated that there is a correlation between the abundance of sequences of said gene in metagenomic analysis, and its corresponding quantity within the metatranscriptômica data groups. The microbial groups were over-represented in these cycles and Deltaproteobacteria Gammaproteobacteria mainly active in nitrogênioatmosférico fixation processes (N2), the denitrification and sulfate reduction, while for sulfur oxidation were the most frequent class Gammaproteobacteria, and Betaproteobacteria Epsilonproteobacteria. Overall, this study provides evidence of microbial activity in the mangroves, and often indicates that the correlations observed between the results of metagenomics and metatranscriptômica analysis, but these correlations become less evident when we look at order level or other specific levels.

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Landscape position and depth in the soil column influence the movement of microbial substrate throughout a catchment, from upslope areas to downslope areas, thereby impacting nutrient cycling rates and capabilities of the microbial communities in those areas. Wildfire also shapes the biogeochemistry of the landscape, creating a mosaic with variations in substrate type and concentration that also influence microbial communities and biogeochemical cycling. Nitrogen (N) in particular is altered by wildfire, as it is easily volatilized and the removal of organic matter (OM) reduces N inputs. We aimed to understand how landscape position and soil depth, first and foremost, influence microbial communities and their N-cycling, but also how this may differ from wildfires and their relative impacts on the soil microbial communities. Landscape position proved to influence few soil and microbial characteristics, while movement from soil surface to deep in the column and the incidence of wildfire caused many variations in soil physical and biogeochemical cycling properties. The interaction of landscape position and soil depth also showed little variation in any measurements, while wildfire and soil depth interactions showed drastic changes that indicate high order controls over the soil microbial community. It can be surmised that while landscape position is important for many soil properties, it is soil depth and wildfire that truly control the soil microbial communities and their N-cycling capabilities.

Une savane est définie par la coexistence entre des arbres et des Poacées. Dans la savane de Lamto en Côte d’Ivoire, l’espèce dominante de Poacée est connue pour inhiber la nitrification et avant mon étude, l’impact des arbres sur la nitrification était très mal connu. L’étape de la nitrification est conduite par deux différentes communautés, les archées et les bactéries nitrifiantes ayant le gène amoA. Le but de cette étude est de comprendre l’impact de ces deux types de végétaux sur le cycle de l’azote, notamment sur les communautés nitrifiantes et également de comprendre l’impact de la saisonnalité et du passage du feu sur ces processus. Des échantillonnages ont été réalisés sous les Poacées et les arbres à Lamto durant les saisons humides et sèche et également avant et après le passage du feu. Cela a mis en évidence plusieurs effets : (i) les Poacées dominantes de la savane inhibent la nitrification, (ii) les arbres dominants stimulent la nitrification, (iii) les archées nitrifiantes son prédominantes dans cette savane et elles contribueraient majoritairement à la nitrification, (iv) la saisonnalité à un impact direct sur les abondances et l’activité des micro-organismes du sol (l’activité transcriptionelle des archées nitrifiantes diminuent en saison humide), (v) le feu a un effet indirect sur les communautés microbiennes du sol par son impact sur les caractéristiques physico-chimiques des sols, notamment il diminue l’activité des archées nitrifiantes. Enfin, la dénitrification est supérieure sous les arbres que sous les Poacées. Cette étude a permis de mieux comprendre les interactions entres les bactéries et archées nitrifiantes, la végétation et la saisonnalité. / A savanna is defined by the coexistence between trees and grasses. Savannas represent 12-13% of continental surfaces. In the Lamto savanna in Ivory Coast, the dominant grass species inhibits nitrification (the transformation of ammonium into nitrate) and the impact of trees on nitrification before this study was not known. Nitrification is conducted by two different communities. The archaea nitrifiers that have the amoA-AOA gene and bacteria nitrifiers that have the amoA-AOB gene. The aim of this study is to analyse the impacts of both plant types on nitrogen cycling, particularly on the nitrifier communities, and understand the impact of seasonality and fire on these processes. Sampling was conducted under grasses and trees in the Lamto savanna during the wet and dry seasons and also before and after the fire. This study has highlighted for the first time different effects including: (i) the dominant savanna grasses inhibit nitrification, (ii) dominant trees stimulate nitrification, (iii) the archaea nitrifiers are predominant in this savanna and they are mainly responsible for nitrification in this ecosystem, (iv) seasonality has a direct impact on the abundances and activities of soil microorganisms and the wet season reduced archaea nitrifier transcriptional activities, (v) fire has an indirect impact on soil microbial communities due to its impacts on soil physico-chemical characteristics: it decrees the abundance of archaea nitrifiers. In addition, denitrification is higher under trees than grasses. This study permitted to better understand the interactions between nitrifiers, vegetation and seasons.

<p>Variations in stable isotope abundances of nitrogen (δ¹⁵N) and oxygen (δ¹⁸O) of nitrate are a useful tool for determining sources of nitrate as well as understanding the transformations of nitrogen within soil (Chapter 2). Various sources of nitrate are known to display distinctive isotopic compositions, while nitrogen transformation processes fractionate both N and O isotopes and can reveal the reaction pathways of nitrogen compounds. However, to fully understand the δ¹⁵N and δ¹⁸O values of nitrate sources, we must understand the chemistry and the isotopic fractionations that occur during inorganic and biochemical reactions. Among all N cycle processes, nitrification and denitrification displayed some of the largest and most variable isotope enrichment factors, ranging from -35 to 0‰ for nitrification, and -40 to -5‰ for denitrification. In this dissertation, I will first characterize the isotopic enrichment factors of ¹⁵N during nitrification and denitrification in a Midwestern agricultural soil, two important microbial processes in the soil nitrogen cycle. Nitrification incubations found that a large enrichment factor of -25.5‰ occurs during nitrification NH₄⁺ è NO₃^-, which agrees well with previous studies (Chapter 3). Additionally, oxygen isotopic exchange that occurs between nitrite and water during nitrification was also quantified and found that 82% of oxygen in NO₃^- are derived from H₂O, much greater than the 66% predicted by the biochemical steps of nitrification. The isotopic enrichment that occurs during denitrification was assessed by measuring the change in δ¹⁵N as the reactant NO₃^- was reduced to N₂ gas (Chapter 4). The incubations and kinetic models showed that denitrification can causes large isotopic enrichment in the δ¹⁵N of remaining NO₃^-. The enrichment factor for NO₂^- è gaseous N was -9.1‰, while the enrichment factors for NO₃^- è NO₂^- were between -17 to -10‰, both of which were within the range of values report in literature. The results demonstrated that nitrification and denitrification caused large isotope fractionation and can alter the presumed δ¹⁵N and δ¹⁸O values of nitrate sources, potentially leading to incorrect apportionment of nitrate sources.</p> <p>The results of the denitrification incubation experiments were applied to a field study, where the measured enrichment factor was utilized to quantify loss of N by field-scale denitrification (Chapter 5). Field-based estimates of total denitrification have long been a challenge and only limited success has been found using N mass balance, N₂O gas flux, or isotope labeling techniques. Here, the flux of nitrate and chloride from tile drain discharge from a small field was determined by measuring both dissolved ions (ion chromatography) and monitoring water discharge. The δ¹⁵N and δ¹⁸O of tile nitrate was also measured at a high temporal resolution. Fluxes of all N inputs, which included N wet and dry deposition, fertilizer application, and soil mineralization were determined. The d¹⁵N and d¹⁸O values of these nitrate sources was also determined. Using this data, I first detected shifts in δ¹⁵N and δ¹⁸O values in the tile drain nitrate, which indicated variable amounts of denitrification. Next, a Rayleigh distillation model was used to determine the fraction of NO₃^- loss by field scale denitrification. This natural abundance isotope method was able to account for the spatial and temporal variability of denitrification by integrating it across the field scale. Overall, I found only 3.3% of applied N was denitrified. Furthermore, this study emphasized the importance of complementary information (e.g. soil moisture, soil temperature, precipitation, isotopic composition of H₂O, etc.), and the evidence it can provide to nitrogen inputs and processes within the soil.</p>

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Thesis: Sc. D., Massachusetts Institute of Technology, Department of Civil Engineering, 1975 / Vita. / Bibliography: leaves 266-271. / Sc. D. / Sc. D. Massachusetts Institute of Technology, Department of Civil Engineering

Eutrophication is one of the greatest threats for the Baltic Sea, and one of its more critical consequences is bottom water hypoxia. Nutrient enrichment and oxygen-depletion affect both the deep central basins and a number of coastal areas, even though strategies for nutrient reduction have lately been implemented. In order to better understand why those threats are expanding and formulate more effective remediation strategies two main achievements are needed: (1) new data on benthic nutrient dynamics should be available in order to develop updated budgets for sensitive Baltic areas; (2) the main transformation processes and their regulation mechanisms (i.e. oxygen availability, presence of macrofauna, different organic loading scenarios) should be better constrained. Paper I was able to demonstrate that re-oxygenation of previously anoxic sediment has a positive effect on the ecosystem because of better retention of nutrients and efficient conversion of fixed nitrogen to nitrogen gas. Sediment colonization by the invasive genus Marenzelleria counteracts some of the positive aspects provided by benthic oxygenation (in particular, nutrient retention, N2 loss). A possible explanation for this reversal can be that Marenzelleria does stimulate anaerobic more that aerobic metabolism. Results from Paper II suggest that at the outermost stations of Himmerfjärden denitrification follows a pronounced seasonal pattern, primarily regulated by bottom water temperatures. At the innermost and impacted site oxygen level in the bottom water varies considerably during the year and causes denitrification/DNRA predominance to be the main nitrate reduction pathway. On an annual scale, the net amount of lost N2 is comparable at the four sampling sites and accounts for 96% of the total DIN discharged from the sewage treatment plant, suggesting that denitrification in the estuarine sediment acts as a major nitrogen sink for external N inputs.