Microbial Community Responses to Environmental Perturbation

Microorganisms mediate many biogeochemical processes critical to the functioning of ecosystems, which places them as an intermediate between environmental change and the resulting ecosystem response. Yet, we have an incomplete understanding of these relationships, how to predict them, and when they are influential. Understanding these dynamics will inform ecological principles developed for macroorganisms and aid expectations for microbial responses to new gradients. To address this research goal, I used two studies of environmental gradients and a literature synthesis.

With the gradient studies, I assessed microbial community composition in stream biofilms across a gradient of alkaline mine drainage. I used multivariate approaches to examine changes in the non-eukaryote microbial community composition of taxa (chapter 2) and functional genes (chapter 3). I found that stream biofilms at sites receiving alkaline mine drainage had distinct community composition and also differed in the composition of functional gene groups compared with unmined reference sites. Compositional shifts were not dominated by groups that could benefit from mining associated increases of terminal electron acceptors; two-thirds of responsive taxa and functional gene groups were negatively associated with mining. The majority of subsidies and stressors (nitrate, sulfate, conductivity) had no consistent relationships with taxa or gene abundances. However, methane metabolism genes were less abundant at mined sites and there was a strong, positive correlation between selenate reductase gene abundance and mining-associated selenium. These results highlighted the potential for indirect factors to also play an important role in explaining compositional shifts.

In the fourth chapter, I synthesized studies that use environmental perturbations to explore microbial community structure and microbial process connections. I examined nine journals (2009–13) and found that many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant. No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure. Together, the findings suggested that few publications report statistically testing structure-process links; but when tested, links often occurred yet shared few commonalities in linked processes or structures and the techniques used for measuring them.

Although the research community has made progress, much work remains to ensure that the vast and growing wealth of microbial informatics data is translated into useful ecological information. In part, this challenge can be approached through using hypotheses to guide analyses, but also by being open to opportunities for hypothesis generation. The results from my dissertation work advise that it is important to carefully interpret shifts in community composition in relation to abiotic characteristics and recommend considering ecological, thermodynamic, and kinetic principles to understand the properties governing community responses to environmental perturbation.

Protected Areas' Impacts on Brazilian Amazon Deforestation: Examining Conservation-Development Interactions to Inform Planning.

Protected areas are the leading forest conservation policy for species and ecoservices goals and they may feature in climate policy if countries with tropical forest rely on familiar tools. For Brazil's Legal Amazon, we estimate the average impact of protection upon deforestation and show how protected areas' forest impacts vary significantly with development pressure. We use matching, i.e., comparisons that are apples-to-apples in observed land characteristics, to address the fact that protected areas (PAs) tend to be located on lands facing less pressure. Correcting for that location bias lowers our estimates of PAs' forest impacts by roughly half. Further, it reveals significant variation in PA impacts along development-related dimensions: for example, the PAs that are closer to roads and the PAs closer to cities have higher impact. Planners have multiple conservation and development goals, and are constrained by cost, yet still conservation planning should reflect what our results imply about future impacts of PAs.

Structural Time Series Modeling: an Application to Environmental Variables

A structural time series model is one which is set up in terms of components which have a direct interpretation. In this paper, the discussion focuses on the dynamic modeling procedure based on the state space approach (associated to the Kalman filter), in the context of surface water quality monitoring, in order to analyze and evaluate the temporal evolution of the environmental variables, and thus identify trends or possible changes in water quality (change point detection). The approach is applied to environmental time series: time series of surface water quality variables in a river basin. The statistical modeling procedure is applied to monthly values of physico- chemical variables measured in a network of 8 water monitoring sites over a 15-year period (1999-2014) in the River Ave hydrological basin located in the Northwest region of Portugal.

The Kinome of Pacific Oyster Crassostrea gigas, Its Expression during Development and in Response to Environmental Factors

Oysters play an important role in estuarine and coastal marine habitats, where the majority of humans live. In these ecosystems, environmental degradation is substantial, and oysters must cope with highly dynamic and stressful environmental constraints during their lives in the intertidal zone. The availability of the genome sequence of the Pacific oyster Crassostrea gigas represents a unique opportunity for a comprehensive assessment of the signal transduction pathways that the species has developed to deal with this unique habitat. We performed an in silico analysis to identify, annotate and classify protein kinases in C. gigas, according to their kinase domain taxonomy classification, and compared with kinome already described in other animal species. The C. gigas kinome consists of 371 protein kinases, making it closely related to the sea urchin kinome, which has 353 protein kinases. The absence of gene redundancy in some groups of the C. gigas kinome may simplify functional studies of protein kinases. Through data mining of transcriptomes in C. gigas, we identified part of the kinome which may be central during development and may play a role in response to various environmental factors. Overall, this work contributes to a better understanding of key sensing pathways that may be central for adaptation to a highly dynamic marine environment.

Fish Reproduction Is Disrupted upon Lifelong Exposure to Environmental PAHs Fractions Revealing Different Modes of Action

Polycyclic aromatic hydrocarbons (PAHs) constitute a large family of organic pollutants emitted in the environment as complex mixtures, the compositions of which depend on origin. Among a wide range of physiological defects, PAHs are suspected to be involved in disruption of reproduction. In an aquatic environment, the trophic route is an important source of chronic exposure to PAHs. Here, we performed trophic exposure of zebrafish to three fractions of different origin, one pyrolytic and two petrogenic. Produced diets contained PAHs at environmental concentrations. Reproductive traits were analyzed at individual, tissue and molecular levels. Reproductive success and cumulative eggs number were disrupted after exposure to all three fractions, albeit to various extents depending on the fraction and concentrations. Histological analyses revealed ovary maturation defects after exposure to all three fractions as well as degeneration after exposure to a pyrolytic fraction. In testis, hypoplasia was observed after exposure to petrogenic fractions. Genes expression analysis in gonads has allowed us to establish common pathways such as endocrine disruption or differentiation/maturation defects. Taken altogether, these results indicate that PAHs can indeed disrupt fish reproduction and that different fractions trigger different pathways resulting in different effects.

Behavioral Response to Environmental Taxation: Evidence from the Transportation Sector

This dissertation analyzes how individuals respond to the introduction of taxation aimed to reduce vehicle pollution, greenhouse gases and traffic. The first chapter analyzes a vehicle registration tax based on emissions of carbon dioxide (CO2), a major greenhouse gas, adopted in the UK in 2001 and subject to major changes in the following years. I identify the impact of the policy on new vehicle registrations and carbon emissions, compared to alternative measures. Results show that consumers respond to the tax by purchasing cleaner cars, but a carbon tax generating the same revenue would further reduce carbon emissions. The second chapter looks at a pollution charge (polluting vehicles pay to enter the city) and a congestion charge (all vehicles pay) adopted in 2008 and 2011 in Milan, Italy, and how they affected the concentration of nitrogen dioxides (NOx). I use data from pollution monitoring stations to measure the change between areas adopting the tax and other areas. Results show that in the first quarter of their introduction, both policies decreased NOx concentration in a range of -8% and -5%, but the effect declines over time, especially in the case of the pollution charge. The third chapter examines a trial conducted in 2005 in the Seattle, WA, area, in which vehicle trips by 276 volunteer households were recorded with a GPS device installed in their vehicles. Households received a monetary endowment which they used to pay a toll for each mile traveled: the toll varied with the time of the day, the day of the week and the type of road used. Using information on driving behavior, I show that in the first week a $0.10 toll per mile reduces the number of miles driven by around 7%, but the effect lasts only few weeks at most. The effect is mainly driven by a reduction in highway miles during trips from work to home, and it is strongly influenced by past driving behavior, income, the size of the initial endowment and the number of children in the household.

Seasonal differences in migration patterns of a soaring bird in relation to environmental conditions: a multi-scale approach

Many studies suggest that migratory birds are expected to travel more quickly during spring, when they are en route to the breeding grounds, in order to ensure a high-quality territory. Using data recorded by means of Global Positioning System satellite tags, we analysed at three temporal scales (hourly, daily and overall journey) seasonal differences in migratory performance of the booted eagle (Aquila pennata), a soaring raptor migrating between Europe and tropical Africa, taking into account environmental conditions such as wind, thermal uplift and day length. Unexpectedly, booted eagles showed higher travel rates (hourly speed, daily distance, overall migration speed and overall straightness) during autumn, even controlling for abiotic factors, probably thanks to higher hourly speeds, more straight routes and less non-travelling days during autumn. Tailwinds were the main environmental factor affecting daily distance. During spring, booted eagles migrated more quickly when flying over the Sahara desert. Our results raise new questions about which ecological and behavioural reasons promote such unexpected faster speeds in autumn and not during spring and how events occurring in very different regions can affect migratory performance, interacting with landscape characteristics, weather conditions and flight behaviour.

Greening the city: an ecosystem-based framework to support planning towards urban sustainability and resilience

Cities are small-scale complex socio-ecological systems, that host around 60% of world population. Ecosystem Services (ES) provided by urban ecosystems offer multiple benefits necessary to cope with present and future urban challenges. These ES include microclimate regulation, runoff control, as well as opportunities for mental and physical recreation, affecting citizen’s health and wellbeing. Creating a balance between urban development, land take containment, climate adaptation and availability of Urban Green Areas and their related benefits, can improve the quality of the lives of the inhabitants, the economic performance of the city and the social justice and cohesion aspects. This work starts analysing current literature around the topic of Ecosystem Services (ES), Green and Blue Infrastructure (GBI) and Nature-based Solutions (NBS) and their integration within current European and International sustainability policies. Then, the thesis focuses on the role of ES, GBI and NBS towards urban sustainability and resilience setting the basis to build the core methodological and conceptual approach of this work. The developed ES-based conceptual approach provides guidance on how to map and assess ES, to better inform policy making and to give the proper value to ES within urban context. The proposed interdisciplinary approach navigates the topic of mapping and assessing ES benefits in terms of regulatory services, with a focus on climate mitigation and adaptation, and cultural services, to enhance wellbeing and justice in urban areas. Last, this thesis proposes a trans-disciplinary and participatory approach to build resilience over time around all relevant urban ES. The two case studies that will be presented in this dissertation, the city of Bologna and the city of Barcelona, have been used to implement, tailor and test the proposed conceptual framework, raising valuable inputs for planning, policies and science.

Límites del ordenamiento ambiental del territorio al turismo: el caso del Aeropuerto Internacional en la Isla de Providencia

El presente trabajo comenzará por abordar los antecedentes históricos y la caracterización del grupo étnico raizal desde una perspectiva jurídica enfocada en el turismo, el medio ambiente y la especial protección nacional e internacional del grupo étnico para el caso de la isla de Providencia, Colombia. A continuación se realizará un análisis del fenómeno turístico, incluyendo aspectos relacionados con los estudios del turismo y el desarrollo sostenible de esta actividad. A partir de este análisis, se examinarán los antecedentes y las características del modelo actual de desarrollo turístico en el municipio de Providencia y Santa Catalina. En el marco de los resultados del análisis anterior, se realizará una exposición de los aspectos jurídicos relacionados con el ordenamiento ambiental del territorio en el caso de la ampliación y remodelación del Aeropuerto el Embrujo en zona amortiguadora del Parque Nacional Natural Old Providence and Mc Bean Lagoon. Por último se expondrán las conclusiones y algunas recomendaciones.

Comunidades tradicionais em áreas protegidas: convergências e lacunas da Política Urbana e Ambiental na Reserva de Desenvolvimento Sustentável Estadual Ponta do Tubarão/RN

This work presents a reflection on possibilities and boundaries of consolidation and expansion of human settlements characterized as traditional communities that are located within protected areas, using as study reference the State Sustainable Development Reserve Ponta do Tubarão, at Rio Grande do Norte state. The main topics highlight the conflict between the right to housing and the prevalence of fundamental rights of traditional populations, opposed to the diffuse right to environment, according to the regulatory framework of the Brazilian Urban and Environmental Policies. At the same time that these settlements, historically built, are substantiated by the principles of recognition of rights to traditional populations, they are in a condition of complexity to the resolution of conflicts in its urban dimension and lead to an impairment of natural sites. This work questions how the instruments of land use and occupation are defined and relate to environmental planning, especially considering that the settlements are located in Permanent Preservation Areas (APP). It aims to further the discussion of the urban dimension in settlements, characterizing its formation and growth process, to identify the gaps and convergences between the Urban and Environmental Policy, under the foundations of a socio-environmental approach. The results spotlights the conflicts between occupation and natural areas, inferring that the definition of Urban Policies instruments and its integration with Environmental Policies instruments account for essential and priority actions to the achievement to the rights to a sustainable city, as determined in the Cities Statute and environmental protection goals, defined for the Conservation Units

Dinâmica do uso e ocupação da terra em área de mineração de argila: o caso da bacia hidrográfica do Ribeirão Santa Gertrudes/SP

Pós-graduação em Geologia Regional - IGCE

Planejamento ambiental e gestão de recursos hídricos na Bacia Hidrográfica da Represa de Chapéu D‟Uvas – Zona da Mata e Campo das Vertentes/MG

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Caracterização ambiental da bacia hidrográfica do Córrego Rico, Jaboticabal - SP

Pós-graduação em Agronomia (Produção Vegetal) - FCAV