Increasing demand for freshwater and energy is pushing towards the development of alternative technologies that are sustainable. One of the realistic solutions to address this is utilization of the renewable resources like wastewater. Conventional wastewater treatment processes can be highly energy demanding and can fails to recover the full potential of useful resources such as energy in the wastewater. As a consequence, there is an urgent necessity for sustainable wastewater treatment technologies that could harness such resources present in wastewaters. Advanced treatment process based on microbial electrochemical technologies (METs) such as microbial fuel cells (MFCs) and microbial electrolysis cells (MECs) have a great potential for the resources recovery through a sustainable wastewater treatment process. METs rely on the abilities of microorganisms that are capable of transferring electrons extracellularly by oxidizing the organic matter in the wastewater and producing electrical current for electricity generation (MFC) or H2 and CH4 production (MEC). Propionate is an important volatile fatty acid (VFA) (24-70%) in some wastewaters and accumulation of this VFA can cause a process failure in a conventional anaerobic digestion (AD) system. To address this issue, MECs were explored as a novel, alternative wastewater treatment technology, with a focus on a better understanding of propionate oxidation in the anode of MECs. Having such knowledge could help in the development of more robust and efficient wastewater treatment systems to recover energy and produce high quality effluents. Several studies were conducted to: 1) determine the paths of electron flow in the anode of propionate fed MECs low (4.5 mM) and high (36 mM) propionate concentrations; 2) examine the effect of different set anode potentials on the electrochemical performance, propionate degradation, electron fluxes, and microbial community structure in MECs fed propionate; and 3) examine the temporal dynamics of microbial communities in MECs fed with low or high concentration of acetate or propionate relating to the reactor performance. Overall, the findings from these studies provides new knowledge on propionate oxidation in MECs. The discovery of such findings may shed light on the development of an energy positive wastewater treatment process capable of producing a high quality effluent.

The disposal of large amounts of waste still containing energetic value is a central challenge in the waste management of the Brazilian sugarcane industry. As a sustainable solution, the biogas process appears to be a suitable technology for treating sugarcane waste products and for providing valuable commodities such as energy-rich biogas and digestate with fertilizer properties. Additionally, the proper treatment of the four major waste types (straw, bagasse, filter cake and vinasse) would avoid greenhouse gas emissions, air pollution and environmental contamination of soil and water. In order to investigate the feasibility and reliability of biogas production from sugarcane wastes, the microbial community dynamics of laboratory-scale reactors were assessed under different start-up strategies. Despite the promising results of the methane potential for all the waste products, chemical and physical pre-treatments were applied successfully to increase the methane yield of straw, bagasse and filter cake. The microbial community dynamics observed during co-digestion of filter cake and bagasse showed, together with the process parameters, that cattle manure can be effectively used as an inoculum for the start-up of a biogas process in the remote-located sugarcane industry. Monitoring methanogenic community dynamics at high organic loading rate of filter cake and bagasse demonstrated that the genera Methanosarcina and Methanobacterium are the major methanogens that produce biogas, even under process imbalances. Moreover, the results obtained from the process parameters and methanogenic community analyses revealed that the stable isotope fingerprinting technique may be a potential monitoring tool for quickly identifying changes in the methanogenic pathway, which indicates process disturbances. In conclusion, these studies established techniques for the efficient substrate processing and start-up procedure of a biogas process designed for the anaerobic digestion of sugarcane wastes, and by these means provided a highly detailed profile of the microbial community in relation to process parameters.

Numerous studies have focused on the drivers of diversity and stability of communities, especially under global change. However, multi-dimensionality of ecosystems due to biotic components (e.g predation, competition and adaptive dynamics) and abiotic factors (e.g. disturbances, resource dynamics and their distinct attributes) cause context-dependent outcomes and challenge the predictions. There are still controversies around complex community dynamics under varying regimes, however, finding mechanistical explanations will illuminate the fate of multispecies assemblages. Using model microbial communities, consisting of bacterial prey and protist predator, combined with simulation modelling and advanced statistics, this thesis investigated the impact of imposed disturbances (i.e. increased dilution rates that simulate density-independent mortality as press or pulse disturbances) (i) on transient recovery dynamics of a simple microbial food web, and (ii) on bacterial abundance, diversity and community structure in the absence or presence of a protist predator. In addition, this thesis questioned the impacts of species interactions and rapid trait shifts, as a response to predation and competition, on the community dynamics and stability. Our results revealed that the predator suffered more from disturbances over longer time periods. Reduced predation pressure caused a transient phase of prey release during and even after disturbances. Recovery time depended on the strength and duration of disturbances, however, coupling to an alternative resource increased the chance of fast recovery and stabilized the communities. In multi-species prey communities, bacterial abundance, diversity, and community composition were more affected by predation than by the disturbances and resource dynamics. Predator abundance, on the other hand, was strongly affected by the type of disturbance imposed. Importantly, community attributes had differential sensitivities, as reflected by their different response and recovery dynamics. Prey community dynamics varied more temporally andwere less stable under predation stress, while prey diversity increased significantly. Predation rapidly induced anti-predation traits, which altered population dynamics of both prey and predator. More importantly, predator and the resistant prey, in turn, elevated the number of direct cause-effect relationships between the community members. Our findings are not limited to the studied system and can be used to understand the dynamic response and recovery potential of many natural predator-prey or host-pathogen systems. They can be used as a base for future studies to illuminate the debates on the future communities.:Summary Zusammenfassung 1 Scope and Outline 2 General Introduction 2.1 Context dependency of community dynamics 2.2 Ecological disturbances 2.2.1 Transient dynamics and stability 2.2.2 Catastrophic shifts 2.3 Species interactions and evolutionary dynamics under environmental change 2.3.1 Species interactions and coexistence 2.4 Eco-evolutionary dynamics 2.5 Community assembly mechanisms 2.6 Dealing with complexities 2.6.1 Microbial model systems as a tool in ecology 2.6.2 Correlation, causation and the future of predictions 2.7 Aims of this study 3 Community Dynamics under Disturbances 3.1 Transient recovery dynamics of a predator-prey system 4 Interactions of Community Drivers 4.1 Interactions between predation and disturbances shape prey communities 5 Species Interactions and Evolutionary Dynamics Shaping Communities 5.1 Summary 5.2 Introduction 5.2.1 Predator-Prey Dynamics and Community Stability 5.2.2 Causal inferences 5.3 Aim of the study 5.4 Methods 5.4.1 Organisms 5.4.2 Microcosm experiments and estimation of species abundances 5.4.3 Statistical analysis 5.5 Results 5.5.1 Community dynamics 5.5.2 Dynamics of prey diversity and community stability 5.5.3 Causal links between the species dynamics 5.6 Discussion 5.7 Synopsis 6 General Discussion 6.1 Communities under disturbances: Predator{ prey dynamics 6.2 Temporal species dynamics and community assembly Synthesis and Outlook 7.1 Increasing complexity of species interactions 7.2 Going further from causal links 7.3 Metacommunities References 8 Appendix 8.1 Declaration of the authorship 8.2 Author contributions of published articles 8.3 List of publications and conference contributions 8.4 Acknowledgments 8.5 Supplementary material for Chapter 3 8.6 Supplementary material for Chapter 4 8.7 Supplementary material for Chapter 5

Streams have been impacted by human activities in a variety of ways. Over time, these ecosystems become dominated by the most resilient species, with significant losses in the natural components that provide valuable ecosystem services to people. In impacted streams, the loss of ecosystem services often is not recognized until the stream has already been dramatically altered. In this study, I provide data on the natural distribution of freshwater decapods and the status of decapod communities in streams with different land use histories. I reviewed the decapod distribution for the Caribbean to provide an update of the species that inhabit the freshwater systems. I determined the presence of 18 species of decapods in Puerto Rico and concluded that these decapods follow the island-species relationship in the Caribbean. Also, I present data associated with decapod community dynamics in watersheds with different urban development. As, expected the highly urban watershed had lower diversity and density of decapods than the medium and low urban watersheds. The variations in decapod communities among watersheds correlated with the degradation of the physical-chemical environments and clearing of the riparian zones. I compare the food webs among streams with different human impacts. Specific influences of point/nonpoint sources of N could be distinguished in food web components. This shows to an effect of human activities on the stream and watershed. In addition, I determined the effect of abiotic and biotic factors on the growth of A.lanipes (0.27 mm) and X.elongata (0.1 mm) over the 10-year period of study. The results showed that these species transform a wide range of organic materials into their biomass. Finally, I developed a series of education projects which promote the understanding and knowledge of freshwater ecosystems; interactions and the organisms that inhabit these systems. The results showed an increasing interest about freshwater fauna and ecosystems. I concluded that: a) the distribution of freshwater decapods in the Caribbean islands follows the area-species relationship; b) urbanization represents one of the many distinct land uses that affect habitat structure, energy sources and biotic interactions; and c) it’s necessary to present the results of our research to the general public in ways that are easily understood.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24083号 / 理博第4850号 / 新制||理||1694(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 緒方 博之, 教授 高田 彰二, 教授 望月 敦史 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Tree growth influences forest community dynamics and responses to environmental variations, but currently is not well understood. Tree growth in highly diverse wet tropical forests have been well studied and characterised compared to the species-poor dry tropical forests. Thus, it is not clear if growth rates and community dynamics of dry forests are similar to those of wet forests, given the longer dry season, greater rainfall variability, more open canopy and lower number of species in dry forests. This thesis focuses on identifying important factors that influence tree diameter growth rates in the dry tropical forest at Mudumalai, southern India, and also compares growth patterns at this dry forest with those at moister forests. The thesis thus contributes towards closing the gap in understanding of tree growth patterns across the tropics. An initial analysis involving matrix-based population projections of four common canopy species at Mudumalai showed that variations in diameter growth have the potential to drastically modify population trajectories of dominant species. Thus the main focus of this thesis is aimed at identifying the important intrinsic and extrinsic factors affecting growth in this dry forest, as this information could be useful for future management of the forest. The second important aim of the thesis was to find out if growth rates are influenced by different sets of factors in tropical dry versus moist forests. A large permanent 50ha plot vegetation monitoring plot was set up in 1988-89 in the Mudumalai dry deciduous forest, and was subsequently monitored annually by staff of the Centre for Ecological Sciences. Data used in this thesis represent a 12-year interval between 1988 and 2000. Girth measurements were obtained from all woody tree stems ≥1cm in diameter every four years during this 12 year interval, which provided three census intervals of diameter increment data on >13,000 trees. For the comparison between dry and moist deciduous forests, data were obtained from a similar large plot maintained and monitored at the Barro Colorado Island (BCI) in Panama. Influences of the intrinsic factors, tree size, individual identity, species identity and growth form, were examined using t-tests, Wilcoxon signed ranks tests, linear regressions, analysis of variance (ANOVA), principal components analysis (PCA) and cluster analysis. Among the intrinsic factors tested, species identity explained approximately 20% of growth rates at the community level, while tree diameter explained less of growth variation, and growth form had a minor influence on growth. Growth rates also were examined for variations across the three census intervals, and for relationships with rainfall and survival from fire. Statistical tests included t-tests, Wilcoxon and other non-parametric sign tests, logistic regression and ANOVA. Most species and individuals showed significant reductions of growth in the second census interval (1992-1996), and growth rates of most trees were positively related to rainfall. Growth rate variations generally were not related to survival from fire, and few species were capable of escaping fire mortality by fast growth. Spatial environmental influences were tested in the commonest fifteen species, using five habitat categories, local elevation, slope, aspect, and the biotic neighbourhood variables of local conspecific and heterospecific density. Statistical tests included analysis of covariance, multiple linear regression and redundancy analysis. The tests were quadrat-based or individual-based, and species' growth responses were tested at different levels of distance and spatial scale. Topographic features and habitat categories had ephemeral effects on species growth. Only the most dominant species, Lagerstroemia microcarpa, showed consistent conspecific neighbour density effects. Redundancy analysis using a subset of common species and environmental factors did not reveal common growth responses to spatial environmental factors. Comparison of factors influencing growth at Mudumalai versus at BCI using multiple factor ANOVA and multiple linear regressions showed a similar influence of temporal variation at the two sites, but stronger and more widespread influence of tree size (diameter) at BCI. The greater influence of tree size at BCI may be related to greater light limitation in this dense moist forest. Spatial environmental factors had weak influences at both plots. Species were less differentiated from each other at the more diverse BCI plot compared to the relatively species-poor Mudumalai plot, suggesting that species' growth niches may be weakly related to diversity across tropical forests. Overall the results showed that among the factors tested species identity and census intervals were the most important influences on diameter growth at the Mudumalai dry deciduous forest. Tree diameter was less important and less consistent in affecting growth at the Mudumalai dry forest, contrary to expectations based on moist tropical forests where this relationship has been established previously. When comparing Mudumalai and BCI, the relative importance of different factors was different at the two sites, and the most important difference was a dominant influence of light limitation at the wetter forest in Panama. In terms of management applications, this study showed that fires at Mudumalai might be an inescapable source of mortality for many vulnerable species, and improved fire management is crucial for long term survival of species in this dry forest. At a larger scale, light and other environmental variables were found to influence growth differently at Mudumalai compared to BCI. This suggests that location-specific responses may be important for projections of tree biomass and carbon sequestration, especially under future climatic change scenarios.

Os elevados custos de plantio e de manutenção de espécies nativas limitam a restauração florestal no Brasil. Buscando reduzir custos e acelerar a recuperação de vegetação ripária em região de cerrado, testou-se a utilização de espécie exótica de rápido crescimento (Pinus elliottii var. elliottii) como facilitadora da regeneração natural de espécies nativas lenhosas, no município de Assis, Estado de São Paulo, Brasil. A exploração de madeira e resina de Pinus poderia gerar receitas aos proprietários rurais e estimular ações de restauração com a compensação dos custos de plantio. Três tratamentos com plantio de Pinus nos espaçamentos 3 x 3 m, 3 x 2 m e 2 x 2 m, mais um quarto tratamento com áreas sem plantio (controle), foram instalados. Cada tratamento teve quatro repetições, em blocos ao acaso. Foram alocadas 16 parcelas (18 x 12 m cada) paralelamente ao rio, distando 20 a 40 m da margem. A área experimental fora utilizada como pastagem por duas décadas. Na ocasião do plantio (1995), predominavam gramíneas africanas. Plantas lenhosas e estruturas subterrâneas existentes foram preservadas. Avaliou-se área basal, cobertura de copas e sobrevivência das árvores plantadas, assim como composição florística, estrutura e cobertura de copas das plantas lenhosas em regeneração (altura mínima de 50 cm) em 1996, 1998, 1999, 2001 e 2006. Desejava-se verificar se: 1) Pinus facilitaria a regeneração da comunidade nativa; 2) Pinus dificultaria a regeneração da comunidade nativa ou 3) Pinus não alteraria a regeneração da comunidade nativa. Até 2006, a densidade média de plantas lenhosas regenerantes foi de 4923 ind/ha sob Pinus (maior quanto maior a densidade de Pinus) e de 3472 ind/ha no controle. Foram registradas 68 espécies lenhosas nativas em regeneração na área experimental, pertencentes a 31 famílias. Houve correlação positiva entre densidade das plantas regenerantes e densidade e área basal de Pinus, e correlação negativa entre parâmetros estruturais de Pinus e cobertura do terreno por gramíneas. Conclui-se que Pinus eliminou as gramíneas pelo sombreamento, favorecendo indiretamente as plantas nativas. Até 2006, não se constatou competição entre plantas nativas e Pinus pelos recursos do ambiente. Houve maior proporção de plantas zoocóricas regenerantes no controle, e correlação negativa entre proporção de regenerantes zoocóricos e parâmetros estruturais de Pinus. Foram favorecidas por Pinus 40% das espécies regenerantes e, 25%, prejudicadas. A sucessão deverá conduzir as duas situações a comunidades distintas, especialmente em função da tolerância das espécies à sombra, predominantes sob Pinus. A análise econômica do uso de Pinus elliottii como facilitadora da regeneração natural demonstrou menores custos de plantio (cerca de um terço dos custos de plantios mistos com espécies nativas), compensados por um ano de exploração de resina. Porém, as técnicas usuais de exploração podem danificar as plantas regenerantes do sub-bosque. Assim, a restauração da comunidade nativa exige meios menos impactantes de exploração dos plantios de espécies exóticas. / Among the obstacles to the native forests restoration in Brazil we find the high costs of planting high diversity of native trees. Searching for reduction of costs and vegetation recovery acceleration, the use of a fast growing exotic species (Pinus elliottii var. elliottii) as pioneer was tested in a riparian area in the cerrado domain, at Assis municipality, São Paulo State, Brazil. As observed in forest plantations with exotic species in the same region, we expected the natural regeneration of native species to occur under the planted exotic trees. In addition, the later exploitation of the exotic species could bring some profit to the land owner, surpassing the restoration costs, and thus stimulating forest restoration initiatives. Pinus was planted in three different spacings (treatments): 3 x 3 m, 3 x 2 m and 2 x 2 m, and a fourth treatment consisted of not planted plots (control). Every treatment had four replications in randomized blocks, the 16 plots (18 x 12 m each) settled along the stream, from 20 to 40 m far from the margin. The experimental area had been used as pasture for at least two decades, mostly covered by african grasses. Some native species then existing were preserved when the Pinus trees were planted, in 1995, without revolving the soil. Basal area, crown cover and survival of planted trees, as well as floristic composition, density and crown cover of native species regenerating in every plot (minimum height 50 cm) were assessed in 1996, 1998, 1999, 2001 and 2006. The aim was to verify if: 1) Pinus trees facilitating the regeneration of the native species, 2) Pinus trees obstructing the evolution of the native community or 3) the exotic species not affecting the native community. In 2006, density of the native woody species regenerating was 4923 ind/ha under Pinus and 3472 ind/ha in the control, from a total of 68 woody species (31 families) in the experimental area. Density of the regenerating community was positively correlated to density and basal area of Pinus. Thus, we concluded that Pinus eliminating grasses by shading (ground cover by grasses was inversely correlated to Pinus structure), indirectly favored the native woody species and are still not competing with them. The proportion of zoochorous species was negatively correlated to the Pinus density, showing that the exotic species does not attract animal seed dispersers. In the open areas (control), the zoochory was relatively more frequent. Density of some species (40%) increasing under Pinus and others (25%) decreasing or disappearing, which means secondary succession should go toward different directions if under Pinus plantation or in open areas. Analyzing the economical aspects of using Pinus as pioneer, we found that planting costs corresponded to a third part of those of planting mixed stands with native species. In addition, planting costs can be compensated by a single year of resin exploitation. However, current techniques of resin extraction or timber exploitation could cause considerable damages to the understory. Alternative exploitation techniques of the exotic species must be encouraged if restoration of the native community in the understory is expected.

<p>The abundance of predators and their impact on ecosystem dynamics is a vividly discussed topic in current ecology. In my studies, incorporating field observations, field experiments and theoretical modeling, I explored the importance of predators and predation in a low arctic tundra ecosystem in northern Norway. This involved observing the abundance and spatial activity of predators (raptors and small mustelids); manipulating the abundance of predators (spiders and birds) in an arthropod community; and exploring the theoretical consequences of intraguild predation on the coexistence among predators.</p><p>The results show that predation is important both in the arthropod assemblage and, depending on the productivity of the community, in the vertebrate assemblage. In arthropod communities predators are at least as abundant as their prey, whereas in the vertebrate part of ecosystem, predators are substantially less abundant than their prey. Still, in both cases predators had strong impact on their prey, influencing the abundance of prey and the species composition of prey assemblages. The impact of predation cascaded to the plant community both in the reticulate and complex arthropod food web and in the linear food chain-like vertebrate community. In the vertebrate-based community we could even observe the long time scale effect on plant community composition.</p><p>Within the predator community, exploitation competition and intraguild predation were the structuring forces. As the arthropod communities consist of predators with different sizes, intraguild predation is an energetically important interaction for top predators. As a consequence, they reduce the abundance of intermediate predators and the impact of intermediate predators on other prey groups. Moreover, being supported by intermediate predators, top predators can have stronger impact themselves on other prey groups.</p><p>In vertebrate communities, intraguild predation seems to be unimportant as energetic link, instead it manifests as an extreme version of interference competition. Therefore intraguild predation reduces the likelihood of coexistence, as it is due limited prey diversity and intense exploitative competition already precarious in the low arctic tundra.</p><p>In conclusion, predators have strong impact on their prey, especially in the more productive parts of the low arctic tundra. This applies even to the food webs with complex and reticulate structure, and these effects carry through the community both in the short time scale of population growth and on the long time scale of population generations.</p>

The abundance of predators and their impact on ecosystem dynamics is a vividly discussed topic in current ecology. In my studies, incorporating field observations, field experiments and theoretical modeling, I explored the importance of predators and predation in a low arctic tundra ecosystem in northern Norway. This involved observing the abundance and spatial activity of predators (raptors and small mustelids); manipulating the abundance of predators (spiders and birds) in an arthropod community; and exploring the theoretical consequences of intraguild predation on the coexistence among predators. The results show that predation is important both in the arthropod assemblage and, depending on the productivity of the community, in the vertebrate assemblage. In arthropod communities predators are at least as abundant as their prey, whereas in the vertebrate part of ecosystem, predators are substantially less abundant than their prey. Still, in both cases predators had strong impact on their prey, influencing the abundance of prey and the species composition of prey assemblages. The impact of predation cascaded to the plant community both in the reticulate and complex arthropod food web and in the linear food chain-like vertebrate community. In the vertebrate-based community we could even observe the long time scale effect on plant community composition. Within the predator community, exploitation competition and intraguild predation were the structuring forces. As the arthropod communities consist of predators with different sizes, intraguild predation is an energetically important interaction for top predators. As a consequence, they reduce the abundance of intermediate predators and the impact of intermediate predators on other prey groups. Moreover, being supported by intermediate predators, top predators can have stronger impact themselves on other prey groups. In vertebrate communities, intraguild predation seems to be unimportant as energetic link, instead it manifests as an extreme version of interference competition. Therefore intraguild predation reduces the likelihood of coexistence, as it is due limited prey diversity and intense exploitative competition already precarious in the low arctic tundra. In conclusion, predators have strong impact on their prey, especially in the more productive parts of the low arctic tundra. This applies even to the food webs with complex and reticulate structure, and these effects carry through the community both in the short time scale of population growth and on the long time scale of population generations.

This thesis concerns Social Network Analysis as a mechanism for exploring Community Dynamics. To be able to use the Social Network methodologies, relationships existing between the modeling entities are required. In this thesis, we use two different kinds of relationships: e-mails exchanged and co-authorship of papers. The e-mails exchanged, as an indicator of information exchange in an organization, is used to facilitate the emergence of structure within the organization. In this thesis we demonstrate the effectiveness of using e-mail communication patterns for crisis detection in a hierarchically set organization. We compare the performance of a Social Network based Classifier with some of the traditional classifiers from the data mining framework for inferring this hierarchy. A generic framework for studying dynamic group transformations is presented and the co-authorship of papers, as an indicator of collaboration in an academic institution, is used to study the community behavioral patterns evolving over time. Enron e-mail corpus and the IISc Co-authorship Dataset are utilized for illustrative purposes.