abstract: Despite the breadth of studies investigating ecosystem development, an underlying theory guiding this process remains elusive. Several principles have been proposed to explain ecosystem development, though few have garnered broad support in the literature. I used boreal wetland soils as a study system to test a notable goal oriented principle: The Maximum Power Principle (MPP). The MPP posits that ecosystems, and in fact all energy systems, develop to maximize power production or the rate of energy production. I conducted theoretical and empirical investigations to test the MPP in northern wetlands. Permafrost degradation is leading to rapid wetland formation in northern peatland ecosystems, altering the role of these ecosystems in the global carbon cycle. I reviewed the literature on the history of the MPP theory, including tracing its origins to The Second Law of Thermodynamics. To empirically test the MPP, I collected soils along a gradient of ecosystem development and: 1) quantified the rate of adenosine triphosphate (ATP) production--literally cellular energy--to test the MPP; 2) quantified greenhouse gas production (CO2, CH4, and N2O) and microbial genes that produce enzymes catalyzing greenhouse gas production, and; 3) sequenced the 16s rRNA gene from soil microbes to investigate microbial community composition across the chronosequence of wetland development. My results suggested that the MPP and other related theoretical constructs have strong potential to further inform our understanding of ecosystem development. Soil system power (ATP) decreased temporarily as the ecosystem reorganized after disturbance to rates of power production that approached pre-disturbance levels. Rates of CH4 and N2O production were higher at the newly formed bog and microbial genes involved with greenhouse gas production were strongly related to the amount of greenhouse gas produced. DNA sequencing results showed that across the chronosequence of development, the two relatively mature ecosystems--the peatland forest ecosystem prior to permafrost degradation and the oldest bog--were more similar to one another than to the intermediate, less mature bog. Collectively, my results suggest that ecosystem age, rather than ecosystem state, was a more important driver for ecosystem structure and function. / Dissertation/Thesis / Doctoral Dissertation Biology 2015

Organism succession during ecosystem development has been well studied for aboveground plant communities while the associated pattern of change in microbial communities remains largely unknown. A study was conducted along developmental sand-dune chronosequences bordering Lake Michigan at Wilderness State Park and Altamaha river valley of southeast Georgia with the hypothesis that soil bacterial communities will follow a pattern of change that is associated with soil, plant, and ecosystem development. This study site included 5 replicate sites along 14 dunes ranging in age from 105 to 500,000 years since deposition. The microbial composition and diversity in the soil was studied using bacterial tag-encoded FLX amplicon pyrosequencing of the 16S rRNA gene. As hypothesized, Bray-Curtis ordination indicated that bacterial community assembly changed along the developmental gradient at both sites. However, there was no seasonal effect at Michigan sites despite likely differences in plant carbon inputs. At the Michigan site, soil Ca, Mg levels and pH showed a significant log-linear correlation with soil development (r = 0.83, 0.84 and 0.81, respectively). Bacterial diversity represented by Simpson’s reciprocal index (Simpson’s 1/D) showed a steady decline from the youngest to the oldest dunes with the largest decline (212 to 58) during the initial stages of soil development (105 to 450 years). The change in plant species abundance was higher in the youngest sites than the older sites. This change was significantly correlated with the change in microbial community distribution (p < 0.0001; r = 0.56). Similarly, at Georgia sites, soil development showed significant log-linear correlation with soil base cations (Ca and Mg) (r = 0.93and 0.95). However, diversity indices and PLFA failed to show any particular change in trend across the developing chronosequences. When the results from both sites were used to study bacterial spatial patterns, local geochemical features were found to be a dominant factor in driving bacterial community structure, while geographic distance as a single factor could contribute to some community variation at a scale (50 – 1700 km). The results suggest that soil nutrients and plant community could be a strong driving force in shaping microbial community assembly across a developing soil ecosystem.

Surface mining in the central Appalachian coalfield disturbs landscapes. Post-mining reforestation efforts now achieve successful reestablishment and growth; however, it is unclear whether reforestation efforts also restore the native forest ecosystem functions. We quantified rates of return of key ecosystem functions and structural attributes of the post-mining forested ecosystem. A chronosequence of four reforested mine sites and an unmined reference stand were studied in southwestern Virginia. Total soil nitrogen (N) and component (mineral soil, forest floor, root, and aboveground biomass) ecosystem carbon (C) pools were quantified. Throughout the growing season, soil gas fluxes [i.e., carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4)], soil inorganic-N [nitrate (NO3-) and ammonium (NH4+)], and total and active microbial biomass were measured. Soil organic C (SOC) and total ecosystem C are returning to the mined landscape. Ecosystem C was correlated with N (r= 0.80; p= 0.0003) and with total and active microbial biomass (r= 0.92; p=<.0001 and r= 0.86; p=<.0001). Available soil inorganic-N and CO2 and N2O fluxes showed no significant differences among study sites; however, the reforested mine soils showed a diminished capacity for CH4 uptake. Although some ecosystem components and functions rapidly returned to the mined landscape, others did not. Our results indicate that reforestation on surface mined lands is largely successful at restoring many ecosystem functions, yet certain functions are decoupled from the redeveloping ecosystem structure. Improved understanding of relationships between ecosystem functions and structural measures in this context can aid development of ecosystem restoration science and mine reclamation practice. / Master of Science

Numerous studies have looked at biotic succession at the aboveground level; however, there are no studies describing fungal community change associated with long-term ecosystem development. To understand ecosystem development, the organisms responsible for shaping and driving these systems and their relationships with the vegetation and soil factors, it is critical to provide insight into aboveground and belowground linkages to ultimately include this new information into ecosystem theory. I hypothesized that fungal communities would change with pedogenesis, that these changes would correlate with vegetation community change, and that they should show change of composition and diversity as the seasons change. Chapter 1 discusses the main topics related to this dissertation. Chapter 2 includes a publication draft that describes a study of sand-dune soil samples from northern Michigan that were analyzed to pinpoint the structural change in the fungal community during the development of the ecosystem. The samples were analyzed by pyrosequencing the soil DNA, targeting the internal transcribed spacer region. Chapter 3 contains a coauthored published paper that describes plant invasion of fields in Virginia to determine how they impact soil bacterial and fungal communities. The bacterial and fungal communities that were invaded by 3 different plant species exhibited similar changes, regardless of plant species, suggesting that some functional traits of invasives may have similar impacts on belowground communities. Chapter 4 remarks the conclusions of this research. / Master of Science / Ecosystems, including the soils underneath, are the environments that surround us perform a large number of critical human-relevant functions (playing roles in production of food, filtration of water for drinking, sequestration of carbon and nitrogen to build soil organic matter, and buffer against flooding). Yet, how these systems naturally develop over time are still in need of detailed study. One particular area of interest and need is the study of belowground fungal communities. It is not commonly known, but plants and ecosystems are highly dependent on the underground web of fungal hyphae that transform nutrients and provide water to plants. A first step in gaining this understanding utilized a natural ecosystem development gradient known as a chronosequence. It was expected that fungal communities would change as soil and ecosystem development progressed and that they would mimic changes in soil and vegetative properties. Discerning if these linkages occur is the first step to assessing how they work together to create ecosystems and their valuable environmental services. Chapter 1 provides a discussion of the main topics in this dissertation. Chapter 2 is at the heart of the dissertation via a study of fungal communities in a developmental soil ecosystem in northern Michigan in addition, in Chapter 3, I include a coauthored published paper that describes plant invasion of fields in Virginia. Chapter 4 remarks on the major conclusions of this Master thesis, supporting the role that vegetation and fungal community change in soil are associated with one another.

Im Rahmen der Untersuchung zur Entwicklung der pelagischen Gemeinschaft des ehemals sauren Tagebauseenkomplexes Goitsche (pH~3) während dessen Flutung und Neutralisierung wurden Wechselwirkungen zwischen der Zusammensetzung von Organismengemeinschaften und der Variabilität des abiotischen Umfeldes untersucht.Im Mittelpunkt standen zwei von ihrer Kausalität her unterschiedliche Aspekte: • Der erste Aspekt betraf die Reifung von Ökosystemen: War der Reifungsprozess von pelagischen Gemeinschaften anhand der von Odum (1969) formulierten Kriterien zur Energetik der Gemeinschaft, zu den Nährstoffkreisläufen sowie zu strukturellen Merkmalen auf Ökosystem- und Individuenebene zu erfassen? Führten der physiologische Stress durch den niedrigen pH und physikalische Störungen der Schichtung durch das einströmende Flutungswasser zu einer Umkehr des Reifungsprozesses? Auf welchen Organisationsebenen der Lebensgemeinschaften waren die Auswirkungen dieser Stressoren erkennbar? • Der zweite Aspekt behandelte die Entwicklung der Artenzahl, die Gleichverteilung der Dominanz von Arten (Eveness) und die Diversität von Planktongemeinschaften entlang des Produktivitätsgradienten. Speziell wurde untersucht, ob die Artenzahl und die Diversität eine monoton positive oder eine unimodale Funktion der Produktivität waren und ob die Eveness eine monoton abnehmende Funktion der Produktivität war. Zur besseren Vorhersagbarkeit der Entwicklung dieser Indizes wurden in einem nächsten Schritt zusätzliche biotische und abiotische Faktoren (z.B. Konsumenteneffekte, physikalische Störung, Immigration) berücksichtigt. Zuletzt wurde die Hypothese getestet, dass unter dem Einfluss von extremem physiologischem Stress keine Abhängigkeit zwischen den betrachteten Indizes und der Produktivität von Ökosystemen besteht. Die Untersuchungen der vorliegenden Arbeit führten zu folgenden Ergebnissen und Schlussfolgerungen: 1) Der Reifungsprozess der Planktongemeinschaft war unter neutralen Bedingungen nicht eindeutig an einzelnen Kriterien festzumachen. Vielmehr schienen idiosynkratische Effekte einzelner Arten auf die Zusammensetzung und Funktion der Organismengemeinschaft von Bedeutung. Coenobiumbildende Kieselalgen sowie größere Cladoceren und Copepoden dominierten sehr rasch die Planktongemeinschaft und vermittelten den Eindruck eines reifen Ökosystems fast unmittelbar nach der Neutralisierung des Tagebausees. 2) Der Einfluss von physiologischem Säurestress und physikalischer Störung der Schichtung durch das eintretende Flutungswasser war gegenüber einem neutralen, ungestörten Teilbecken des Tagebausees (Referenzzustand) eindeutig zu erkennen. Die isolierte Betrachtung der Wirkung der Stressoren lieferte hinsichtlich fast aller Kriterien Anzeichen einer Verjüngung des Systems sensu Odum (1969, 1985). 3) Im betrachteten Ökosystem existierte eine Hierarchie innerhalb der Stressoren. Der Einfluss des Säurestresses dominierte gegenüber dem Einfluss der physikalischen Störung, wahrscheinlich indem er die Reaktionsmöglichkeiten der Planktongemeinschaft einschränkte. 4) Für Primärproduzenten war die Artenzahl eine monoton positive Funktion der realisierten Biomasse (einem Surrogatparameter für die Produktivität des Systems). Die Eveness war eine monoton negative Funktion der Produktivität. Die beobachtete unimodale Beziehung zwischen der Diversität und der Produktivität der Primärproduzenten muss als eine Folge der mathematischen Formulierung dieser Indizes betrachtet werden. 5) Die Ergebnisse multivariater Modelle zur Vorhersage der Artenzahl und der Eveness der Primärproduzenten in Abhängigkeit zusätzlicher erfassbarer biotischer und abiotischer Faktoren ermöglichten eine differenziertere Betrachtung der Ergebnisse: • Im Tagebausee Goitsche war die Eveness hauptsächlich von dichteabhängigen Prozessen gesteuert (negative Abhängigkeit zum Quadrat der Biomassen und zu den Lichtverhältnissen). • Die Entwicklung der Artenzahl war neben dem primären Einfluss der zunehmenden Biomasse auch durch qualitative und quantitative Aspekte der Konsumentengemeinschaft (Diversität und Biomasse des Zooplanktons) beeinflusst. Der Einfluss einer erhöhten Immigration auf die Artenzahl wurde nur zu Beginn der Flutung des Tagebausees beobachtet. 6) Auf Ebene der Konsumenten war die einzige eindeutig feststellbare Abhängigkeit ein Anstieg der Artenzahl mit steigender Biomasse. Das Fehlen von weiteren Beziehungen zwischen Diversitätsindizes und dem Produktivitätsgradienten wird darauf zurückgeführt, dass auf den unteren trophischen Ebenen der Primärproduzenten Ressourceneffekte (Bottom-Up) stärker ausgeprägt sind, wohingegen auf höheren trophischen Ebenen Konsumenteneffekte (Top-Down) dominieren. 7) In durch physiologischen Stress beeinflussten Systemen bestand keine Abhängigkeit zwischen den Diversitätsindizes (Artenzahl, Eveness und Diversität) und der Produktivität. / The objective of this study was to investigate the development of the pelagic plankton community of the formerly acidic open mining lake Goitsche (pH~3) during its flooding and neutralization. The emphasis was on the interaction between the community composition of an ecosystem and the variability of the abiotic environment. The focus was on two aspects, differing in their causality: • The first aspect concerned the maturation process of the studied ecosystem: Was it possible to picture the development of the pelagic community, based on the criteria formulated by Odum (1969) about the energetics of communities, the nutrient cycling and the structural characteristics at the level of the whole system and of individuals? Do the physiological stress and the physical disturbances, caused by the acidic environment and the inflowing water, induce a reversal of the maturation process? And on which levels of organization can the effect of these stressors be detected? • The second aspect concerned the relationship between selected diversity indices of the community (Species richness, Eveness and Diversity) and the whole-system productivity gradient. I looked whether the Species richness and the Diversity were a monotonous increasing or a unimodale function of the productivity, and if the Eveness was a monotonous decreasing function of the productivity. In a next step, to assure a better predictability of these indices, I took additional biotic and abiotic variables (e.g. consumer effect, physical disturbance, and immigration) into consideration. Lastly, I tested the hypothesis that under the influence of extreme physiological stress there would be no relationship between the diversity indices and the productivity. Main results and conclusions are as follows: 1) The maturation process of the plankton community under neutral conditions could not clearly be depicted by single criteria alone. The structure and function of the community seemed much more driven by idiosyncratic effects of individual species. Coenobial diatoms as well as larger Cladocera and Copepoda, which rapidly dominated the plankton community, made the ecosystem look mature almost immediately after the neutralization of the mining lake. 2) The influence of the physiological stress and the physical disturbances on the maturation process was observed, when compared to an unimpaired reference basin of the open mining lake. When the effects of the two stressors were considered alone, nearly all criteria confirmed a reversal of the maturation process sensu Odum (1969, 1985). 3) In the ecosystem there existed a hierarchy within stressors. The influence of the acid stress dominated over the influence of the physical disturbance, probably by restraining the reaction potential of the plankton community. 4) For primary producers, the Species richness was a monotonous positive function of the realized biomass (a surrogate for the productivity of the ecosystem), and the Eveness a monotonous negative function of the productivity. The observed unimodale relationship between the Diversity and the productivity of primary producers must be seen as a consequence of the mathematical formulation of these indices. 5) The results of multivariate models regarding the forecast of both Species richness and Eveness of the primary producers in relation to the additionally considered biotic and abiotic factors revealed following dependences: • In the mining lake Goitsche the realized Eveness was mainly explained by density dependent processes (negative dependence to the square of the producer biomass and to the light level). • Besides the main influence of increasing biomasses, the Species richness was a function of qualitative and quantitative aspects of the consumer community (Diversity and biomass of the zooplankton). A significant impact of species immigration from the regional pool on the realized Species richness was observed only at the beginning of the flooding of the mining lake. 6) At the consumer level, the only significant relationship was an increase of the Species richness with increasing biomass. The absence of further dependencies between diversity indices and the productivity gradients is attributed to the fact that on lower trophic levels Bottom-Up effects play a major role in the regulation of the community structure, whereas on higher trophic levels Top-Down effects dominate. 7) In ecosystems affected by physiological stress no relationship existed between the diversity indices (Species richness, Eveness and Diversity) of the plankton community and the productivity.

Ce travail de thèse s'inscrit dans l'effort actuel de construction d'une écologie intégrative. J'y étudie les mécanismes d'interaction entre ressources abiotiques, réseaux trophiques et propriétés des écosystèmes, au moyen d'une expérience d'évolution, d'un modèle de méta-écosystème et d'un modèle bioénergétique d'assemblage d'écosystèmes. Les organismes modifient la disponibilité des ressources en les prélevant pour leur croissance. Inversement, la disponibilité des ressources influence la diversité et la composition en espèces du réseau trophique, en agissant comme force de sélection sur les traits d'acquisition des ressources (chap. 1, 5). Les propriétés de l'écosystème, telles que stabilité et productivité, dérivent des interactions entre la dynamique des ressources et celle du réseau trophique (chap. 2). Enfin, le fonctionnement de l'écosystème rétroagit sur les ressources abiotiques via le recyclage de la biomasse (chap. 2, 5). Ces processus interviennent lors de l'assemblage des réseaux trophiques et structurent le développement des écosystèmes (chap. 3-5). Dans cette thèse j'analyse ces mécanismes de rétroaction biotique-abiotique sur plusieurs échelles d'organisation, d'espace et de temps. Notamment, les modèles développés ici fournissent des outils novateurs pour étudier les mécanismes de construction des écosystèmes, en mettant en évidence les liens entre métabolisme des espèces, structure du réseau trophique et fonctionnement de l'écosystème, et leur variation au cours du temps. Ce travail ouvre de vastes perspectives de recherche en combinant les derniers progrès d'une écologie intégrative dans une conception mécaniste du développement des écosystèmes. / This thesis participates to the current effort towards the construction of an integrative ecology. I study the feedback mechanisms between abiotic resources, food webs and ecosystem properties, through an evolution experiment, a model of metaecosystem, and a bioenergetic ecosystem assembly model. Organisms modify resource availability by consuming them for their growth. Conversely, resource availability influences the species diversity and composition of the food web, by acting as a selection pressure on traits for resource acquisition (chap. 1, 5). Ecosystem properties, such as stability and productivity, derive from the interactions between resource and food web dynamics (chap. 2). Finally, ecosystem functioning feeds back on abiotic resources through the recycling of biomass (chap. 2 and 5). These processes occur during the food web assembly and drive the development of ecosystems (chap. 3-5). In this thesis I analyze these biotic-abiotic feedback mechanisms on several scales of organization, space and time. The models developed here provide innovative tools to study the mechanisms of ecosystem construction by pointing out the links between species metabolism, food web structure and ecosystem functioning, and their variation through time. This work opens wide research perspectives, as it combines the most recent progress of an integrative ecology into a mechanistic framework of ecosystem development.