The dhole (Cuon alpinus) is one of the least studied endangered top predators inhabiting the Asian jungle. Today, dholes population are estimated fewer than 2500 mature individuals remain in the wild and the declining population trend is expected to continue. These facts lead the IUCN to classify this species as an endangered species. In order to protect this species, the Indonesian government declared the dhole as a protected species through Act No. 5 in 1990 with respect to the law on the conservation of biodiversity and ecosystems as well as in the Government Regulation of the Republic of Indonesia No. 7 in 1999 with respect to the law on the conservation of flora and fauna. Nevertheless, the efforts to conserve this species are not as intensive as other large predator such as tiger (Panthera tigris) and leopard which are listed as high priority mammals to conserve in the Government Regulation of the Republic of Indonesia No. P.57/Menhut-II/2008 with respect to the strategic direction of the national species conservation 2008-2018. Not only conservation action is absent in the field, but basic data on the population status of this species are hard to find in many protected areas including the national parks of Sumatra and Java. These limitations are critical constraints for the conservation and management of dholes in Indonesia and if no significant immediate action is taken soon, this species will face extinction in a number of its natural range. In order to support the conservation and management of this species we established a first systematic research concerning dhole’s ecology in Baluran National Park (BNP), East Java, Indonesia. The research attempted to answer four basic questions concerning dhole’s ecology including the actual status of dhole’s population and prey, dhole’s respond against the gradients of environment conditions anthropogenic disturbance, activity and movement pattern during the denning season, and the feeding habit of this species. The dynamics of dhole populations and its prey populations are fundamental for the successful management and conservation of the dhole. Therefore, estimates of the dhole’s abundance as well as its prey are critical information for management. Distance sampling based on a 287.5 km line transect was applied to estimate the density of dholes and their prey. In addition, a camera trap survey was conducted to detect the presence of this cryptic species and its prey. The dhole population was recorded for two consecutive dry seasons in 2013 and 2014 respectively. We were able to identify at least 4 packs that were frequently sighted at different locations: Bama, Balanan, Merak and Watu Numpuk. However, only two packs were found breeding in 2013 / 2014. In total, 15 prey species were identified during the field survey, consisting of small mammals (6 species), medium-large mammals (5 species), birds (2 species), and primates (2 species). The occurrence of at least four dhole packs with evidence of two of the packs reproducing successfully and the availability of prey in various sizes and from a range of taxa are evidence that BNP provides essential habitat for the dhole and plays a major role in the conservation of dholes on Java in Indonesia. An understanding of the response of the species under various environmental conditions in its natural habitat is critical for its conservation and management. The negative influence of anthropogenic activities on dhole distribution has also been reported in India at the landscape level as well as at the reserve scale. Nevertheless, the evidence of the dhole’s response to anthropogenic activities and the extent of environmental factors beyond site-specific studies are needed to support the management and conservation of dholes at the local scale, which might be associated with different habitat types and environmental conditions. In this research, the impacts of human activities as well as environmental factors on the presence of dholes were studied on 755 plots, which were distributed systematically across the park and their relationships were analysed using a binomial generalized linear model. We found that the presence of dholes was negatively associated with anthropogenic activities and positively associated with the presence of prey. This suggests that reducing anthropogenic activities and ensuring the availability of natural prey are crucial factors for maintaining the long term survival of this species in their natural habitat. It is also important to have a good understanding of their ecology during the denning season (including information about denning ecology and home ranges) if one is to support the management and conservation of this species. Knowledge about den ecology is crucial for understanding the denning strategies of targeted species in given environments, ultimately leading to reproductive success, while knowledge about home ranges on the other hand is also crucial to understand how much space is required, which kind of habitat is necessary, and the effects of various factors (e.g. food resources and breeding requirements) on spacing behaviour and movements during the denning season. Camera traps and radio telemetry surveys were employed to observe dhole activity patterns and movement over the denning period. The dholes showed crepuscular and diurnal activity patterns with most activities intensifying at dawn and dusk, and becoming less intense in the middle of the day. The dhole’s home range comprised of hunting grounds, water resources, and a den in the centre. The home range size was estimated at 744.86 ha (using the 95% Minimum Convex Polygon/MCP method), at 1418.28 ha (using the 80% Kernel Utilization Distribution/KUD analysis), and at 479.59 ha (using 90% Local Convex Hull/LoCoH), whereas the core area was estimated to be 636.36 ha (50% KUD) and 67.37 ha (50% LoCoH), and the size of the most greatly used area at 231.57 ha (25% KUD) comprising of the den sites and the hunting grounds. The dhole’s den ecology strategy was to use other animal’s burrows on steep slopes with dense vegetation cover and located on the opposite side of the hill to where human activity occurred. Den switching occurred every 2 weeks. These results indicate that dholes selected a den site that fulfilled their needs for food, water, cover, and predator evasion. As carnivore, the dhole’s life history strategy depend upon various factors like food, spacing pattern, habitat selection, distribution, social structure and movement pattern. Among those factors, food is the most essential resources for carnivore, because the evolutionary fitness of any predator depends on the quality and quantity of its diet. Therefore, information concerning food habits is important consideration in formulating management strategies, both in species and ecosystem levels. In this research, we studied the dhole’s feeding habit using scat analysis. In total, 54 scats were collected across the park during the dry season 2013 and analyzed to identify the food habits of this species. At least 20 prey species were identified during the scat analysis. Ungulates are the most important prey which was estimated to contribute more than 95 % of the biomass consumed by dholes in BNP. This result implies that as the major preys, ungulates have essential role to the dholes foraging ecology and survival in BNP. Efforts to ensure ungulates availability and to secure habitat will be the key for the dhole’s conservation in Java. Understanding the biology and ecology of managed species is the key to achieve the management success. However, most of wildlife management decision were made based more on the emotion and political agenda than on scientific data. As the result, the impact of management process become far from the expectation and in some occasion raise the new problem. We found that lethal control is an approach which mostly used along the history of dhole’s management and resulting the dramatic dhole’s population decline and explosion of wild ungulates population. Although the dhole’s received protected status from the most countries of its natural ranges, the conservation actions focused in this species have never been reported. The lack of baseline data for dhole’s conservation is still the common phenomenon in the most of dhole’s range. In Java, from 6 national parks which are identified as dhole’s habitat, only 1 national park which have baseline data on dhole’s ecology. This fact has hampered the conservation this species and has placed the future of this species survival into uncertainty. Gathering scientific data related to the dhole’s conservation by multidisciplinary team become the first priority which must be conducted. These will benefit to the management in resolving the problem arises during the management process. The reliable information can also be used improve public understanding to the biology and ecology of dholes and to shape public attitude to be more tolerance to existing of this species.

The biosphere harbors a large quantity and diversity of microbial organisms that can thrive in all environments. Estimates of the total number of microbial species reach up to 1012, of which less than 15,000 have been characterized to date. It has been challenging to delineate phenotypically, evolutionary and ecologically meaningful lineages such as for example, species, subspecies and strains. Even within recognized species, gene content can vary considerably between sublineages (for example strains), a problem that can be addressed by analyzing pangenomes, defined as the non-redundant set of genes within a phylogenetic clade, as evolutionary units. Species considered to be ecologically and evolutionary coherent units, however to date it is still not fully understood what are primary habitats and ecological niches of many prokaryotic species and how environmental preferences drive their genomic diversity. Majority of comparative genomics studies focused on a single prokaryotic species in context of clinical relevance and ecology. With accumulation of sequencing data due to genomics and metagenomics, it is now possible to investigate trends across many species, which will facilitate understanding of pangenome evolution, species and subspecies delineation. The major aims of this thesis were 1) to annotate habitat preferences of prokaryotic species and strains; 2) investigate to what extent these environmental preferences drive genomic diversity of prokaryotes and to what extent phylogenetic constraints limit this diversification; 3) explore natural nucleotide identity thresholds to delineate species in bacteria in metagenomics gene catalogs; 4) explore species delineation for applications in subspecies and strain delineation in metagenomics. The first part of the thesis describes methods to infer environmental preferences of microbial species. This data is a prerequisite for the analyses performed in the second part of the thesis which explores how the structure of bacterial pangenomes is predetermined by past evolutionary history and how is it linked to environmental preferences of the species. The main finding in this subchapter that habitat preferences explained up to 49% of the variance for pangenome structure, compared to 18% by phylogenetic inertia. In general, this trend indicates that phylogenetic inertia does not limit evolution of pangenome size and diversity, but that convergent evolution may overcome phylogenetic constraints. In this project we show that core genome size is associated with higher environmental ubiquity of species. It is likely this is due to the fact that species need to have more versatile genomes and most necessary genes need to be present in majority of genomes of that species to be highly prevalent. Taken together these findings may be useful for future predictive analyses of ecological niches in newly discovered species. The third part of the thesis explores data-driven, operational species boundaries. I show that homologous genes from the same species from different genomes tend to share at least 95% of nucleotide identity, while different species within the same genus have lower nucleotide identity. This is in line with other studies showing that genome-wide natural species boundary might be in range of 90-95% of nucleotide identity. Finally, the fourth part of the thesis discusses how challenges in species delineation are relevant for the identification of meaningful within-species groups, followed by a discussion on how advancements in species delineation can be applied for classification of within-species genomic diversity in the age of metagenomics. / Die Biosphäre beherbergt eine große Zahl verschiedener Mikroorganismen, die fast alle bekannten Lebensräume besiedeln können. Die Gesamtzahl mikrobieller Spezies liegt Schätzungen zu Folge bei bis zu 1012, von denen jedoch bis heute erst 15.000 beschrieben worden sind. Die Beschreibung von phänotypisch, evolutionsbiologisch und ökologisch kohärenten Spezies, Sub-Spezies oder Stämmen stellt Forscher vor konzeptionelle Herausforderungen. Selbst innerhalb anerkannter Spezies kann die Kombination einzelner Gene oft stark variieren. Diese Beobachtung ist die Grundlage der Analyse von Pan-Genomen. also der Konstellation originärer Gene innerhalb einer Abstammunsglinie, als evolutionsbiologische Einheiten. Spezies entsprechen prinzipiell ökologisch und evolutionär kohärenten Einheiten, jedoch sind die primären Habitate und ökologischen Nischen vieler prokaryotischer Spezies bis heute nur unzureichend beschrieben, insbesondere mit Blick auf den Einfluss ökologischer Präferenzen auf die Evolution von Genomen. Die Mehrheit vergleichender genomischer Studien untersucht einzelne prokaryotische Spezies mit Bezug auf deren klinische oder ökologische Relevanz. Aufgrund der wachsenden Verfügbarkeit genomischer Daten ist es nun jedoch möglich, vergleichende Studien über Speziesgrenzen hinweg durchzuführen, um allgemeine Prinzipien der Evolution von Pan-Genomen, Spezies und Sub-Spezies zu untersuchen. Die wesentlichen Ziele der vorliegenden Arbeit waren 1) die Annotation von Habitatpräferenzen prokaryotischer Spezies und Stämme; 2) die Quantifizierung des Einflusses von Umwelt und Evolutionsgeschichte (Phylogenie) auf die genomische Diversität von Prokaryoten; 3) die Bestimmung natürlicher Schwellenwerte der Genomsequenzähnlichkeit zwischen Spezies, auch anhand von Genkatalogen; 4) die Untersuchung der Abgrenzung zwischen Spezies, Sub-Spezies und Stämmen mithilfe metagenomischer Daten. Im ersten Teil der Arbeit werden Methoden zur Bestimmung ökologischer Präferenzen mikrobieller Spezies beschrieben. Die so gewonnenen Daten dienen in der Folge als Grundlage für die Quantifizierung von Umwelt- und evolutionsgeschichtlichen Einflüssen auf die Struktur und Evolution bakterieller Pan-Genome im zweiten Teil der Arbeit. Ein zentrales Ergebnis dieser Untersuchung war, dass bis zu 49% der strukturellen Varianz in Pan-Genomen durch Habitatpräferenzen erklärt werden kann, im Gegensatz zu lediglich 18% durch phylogenetische Trägheitseffekte. Dies zeigt, dass die Größe und Diversität von Pan-Genomen nicht phylogenetisch limitiert ist, insbesondere in Fällen von konvergenter Evolution. Große Kern-Genome sind ferner mit einer weiten ökologischen Verbreitung von Spezies assoziiert; eine mögliche Erklärung ist, dass weit verbreitete Spezies vielseitigere Genome mit mehr notwendigen Genen besitzen, die ein Überleben in vielfältigen Umgebungen ermöglichen. Die vorgelegte Arbeit kann weiterhin einen Beitrag zur Vorhersage ökologischer Profile neu beschriebener Spezies leisten. Im dritten Teil der Arbeit werden datenbezogene, operationelle Definition von Spezies-Grenzen untersucht. Es konnte gezeigt werden, dass Gene verschiedener Genome innerhalb derselben Spezies normalerweise mindestens 95% Ähnlichkeit der Nukleotidsequenz aufweisen, während die Ähnlichkeit zwischen Spezies desselben Genus geringer ausfällt. Dieser Wert liegt im Rahmen früherer Schätzungen. Der vierte Teil der Arbeit beschreibt abschließend die Herausforderungen bei der Bestimmung von evolutionären Linien innerhalb von Spezies und diskutiert anschließend, wie konzeptionelle Entwicklungen in dieser Frage für die Klassifizierung und Quantifizierung von Diversität anhand metagenomischer Daten genutzt werden kann.

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Aquatische Gemeinschaften sind stark körpergrößenstrukturiert mit einer exponentiellen Abnahme der Häufigkeit der Individuen mit zunehmender Körpergröße, die als Größenspektrum (SS) bezeichnet wird. Körpergrößenbasierte Ansätze bieten eine einfache und kostengünstige Methode zur Beantwortung komplexer ökologischer Fragestellungen in aquatischer Forschung. Widersprüchliche Ergebnisse zu den wichtigsten Faktoren, die Größenspektren beeinflussen unterstreichen jedoch die Notwendigkeit weiterer Studien. Um einige dieser widersprüchlichen Schlussfolgerungen anzugehen, habe ich eine Reihe von Fragen in den Bereichen Limnologie und Korallenriffökologie untersucht. In dieser Dissertation wurden größenbasierte Ansätze wie SS verwendet, um zu untersuchen, (i) was die Größenverteilung von Zooplankton beeinflusst und ob Zooplankton-fressende Fische (topdown) oder Ressourcenverfügbarkeit und Umweltbedingungen (bottom-up) die SS der Zooplanktongemeinschaft bestimmen, (ii) ob traditionelle Schleppnetze oder moderne hydroakustische Methoden Fisch-SS zuverlässiger darstellen, und (iii) ob SS von Korallenriff- Fischgemeinschaften und die strukturelle Komplexität der Korallen bzw. deren Beziehung zueinander sich unter verschiedenen anthropogenen Stressoren verändert. Zuallererst konnte ich zeigen, dass weder Top-down- noch Bottom-up-Kräfte stark die Größenverteilung der Zooplanktongemeinschaft beeinflussten. Zooplankton SS scheinen robust gegenüber Prädationseffekten zu sein, aber ein empfindlicher Indikator für die Energieverfügbarkeit und Transfereffizienz im Nahrungsnetz des untersuchten Sees. Des Weiteren konnten meine Studien bestätigen, dass hydroakustische Methoden die SS von pelagischen Fischgemeinschaften zuverlässig darstellen, was sie zu einer kostengünstigen und minimalinvasiven Alternative zu traditionellen Fischentnahmemethoden macht. Ich konnte jedoch kein allgemeingültiges Muster hinsichtlich der Größenverteilung von Korallenrifffischen und der strukturellen Komplexität der Korallen in Beziehung zu unterschiedlichen anthropogenen Stressoren finden. Insgesamt zeigt die Dissertation das weite Anwendungsspektrum von SS, um Strukturen und Prozesse in aquatischen Gemeinschaften und Fischfangmethoden zu untersuchen. Die hohe Variabilität von Größenspektren und der Einfluss von Umweltbedingungen unterstreicht weiter die Wichtigkeit, Daten über einen langen Zeitraum einzubeziehen. Darüber hinaus unterstreichen die Ergebnisse dieser Arbeit auch die Grenzen der Anwendung von SS, da für die Beantwortung mancher ökologischer Fragestellungen artenspezifische Informationen, wie Lebensraum- und Nahrungspräferenzen benötigt werden. / Aquatic communities are highly body-size structured with an exponential decline of abundance with increasing body size, which is referred to as the size spectrum (SS). The importance of body size as a principal and simplifying framework within aquatic communities, has led to a high number of theoretical and empirical studies on energy fluxes in food webs and predatorprey interactions using Size Spectra. These size-based approaches offer a rather simple and inexpensive method to answer complex ecological questions. However, conflicting findings on the key drivers of SS highlight the need for further studies. To address some of these conflicting conclusions, I investigated a range of questions within the fields of limnology and coral reef ecology. In this thesis size-based approaches such as SS were employed to explore (i) what drives zooplankton size distribution and whether zooplanktivorous fish (top-down) or resource availability and environmental condition (bottom-up) determine zooplankton community SS, (ii) whether traditional midwater trawling or modern hydroacoustic methods more reliably represent fish SS, and (iii) coral reef fish community SS and habitat structural complexity and their relationship across site-specific anthropogenic stressors. By analysing long term data, I first found that neither top-down or bottom-up forces drove the zooplankton community size distribution. Zooplankton SS seem robust against predation effects but a sensitive indicator for lake-wide energy availability and transfer efficiency in the food web. Then I found that hydroacoustic methods reliably represent pelagic fish community SS, making it a great alternative to traditional and more invasive fish removal sampling methods. Finally, I discovered that coral reef fish SS slope and structural complexity of the reef exhibited a significant negative relationship on two of the examined reef sites which are least exposed to anthropogenic disturbances. A consistent pattern of fish SS and reef complexity was missing, indicating that other environmental factors may also impact the assessed parameters. Overall, my studies show the range of applications of SS to effectively answer universal questions from trophic interactions and the importance of habitat characteristics in a community to a methodological comparison of fish sampling methods. The high variability of SS behaviour and the influence of environmental conditions further underlines the importance to include data on a large temporal scale. Community information, such as taxonomic identity and consideration of species-specific feeding and habitats preferences, for example, are still beneficial in some cases to answer ecologically questions extensively.

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Kleine, flache Gewässer gelten als sogenannte „hotspots“ der Primärproduktion und Kohlenstoffbindung. Diese Doktorarbeit zielt darauf ab, die Primärproduktion verschiedener kleiner Gewässer zu quantifizieren sowie die Mechanismen, die den Kohlenstoffkreislauf dieser Systeme beeinflussen, zu analysieren. Der Fokus liegt dabei auf dem Einfluss globaler Veränderungen, die diese Mechanismen verändern können Im ersten Abschnitt wurde die Primärproduktion (PP) in kleinen, temporären Söllen untersucht, die sehr anfällig für Störungen sind. Ich konnte zeigen, dass die PP der Sölle im Sommer außergewöhnlich hoch ist, was hauptsächlich auf eine hohe Makrophytenproduktion zurückzuführen ist Im zweiten Teil analysiere ich die Ergebnisse eines Experiments zum Einfluss erhöhter Temperaturen auf die benthische PP kleiner Gewässer im Frühjahr. Acht Mesokosmen wurden bei normalen und um 4°C erhöhten Wassertemperaturen gemäßigter Breiten betrieben. In der ersten Hälfte des Experiments konnte ich eine erhöhte benthische PP in den erwärmten Mesokosmen feststellen, die auf direkte Temperatureffekte und indirekte Auswirkungen einer höheren Nährstoffverfügbarkeit zurückzuführen war. Anfang Juni stieg jedoch der Einfluss der Makroinvertebraten auf das Periphyton in den erwärmten Mesokosmen, so dass keine Unterschiede in der PP mehr auftraten. Schließlich, untersuche ich die Resilienz eines Sees gegenüber einem plötzlichen Eintrag gelösten organischen Kohlenstoffs (DOC) aus dem terrestrischen Umland, der zu einer starken Braunfärbung des Wassers führte. Der Fokus liegt dabei auf Veränderungen der Wasserqualität und der aquatischen PP des Sees, nachdem sich die DOC-Konzentration verfünffacht hatte. Drei Jahren nach Erreichen der maximalen DOC- und Gesamt-Phosphor im See sanken diese signifikant, lagen jedoch noch immer 1,5- bzw. 2-fach oberhalb der Ausgangskonzentrationen vor dem DOC-Eintrag. Die benthische PP zeigte eine teilweise Erholung, erreichte jedoch ebenfalls nicht die Ausgangswerte. / Small, shallow freshwater ecosystems are now considered hotspots of primary production & carbon sequestration. Yet till recently they’ve been mostly neglected. This thesis aims at explaining the underlying mechanisms affecting carbon cycling in these systems, particularly focusing on how contemporary global changes alter ecological equilibria. In the first section, using a compartmental approach, I study primary production in small, temporary ponds (kettle holes) within agricultural fields that are highly susceptible to environmental & anthropogenic disturbances. I show that summertime gross primary production (GPP) in kettle holes is exceptionally high, mostly driven by a strong macrophyte production. In winter, periphyton contributes to the majority of the systems’ GPP. High summertime deposition, correlated to GPP, and low sediment mineralization rates, signified a high potential for carbon burial. In the second experiment, I test the impact of increased temperatures on periphyton production during spring. I use eight mesocosms running at normal & +4°C temperatures. Initially, I recorded elevated periphyton GPP in the warmed treatment driven by direct temperature effects & indirect effects of higher nutrient availability. By late spring, the trend is reversed due to increased grazing pressure in the warm treatment. In the third study, I investigate a lake’s resilience to a sudden brownification event: A 5-fold increase in dissolved organic carbon (DOC) concentrations. Within three years after peak brownification, the lake DOC & total phosphorous concentrations dropped significantly but seem to have plateaued at 1.5 & 2-fold their pre-brownification levels, respectively. Consequently, benthic GPP, which had collapsed due to light limitation at peak brownification, marked only a partial recovery, while phytoplankton (& whole-lake) GPP remained higher than pre-brownification levels. Phytoplankton & periphyton exhibited an inverse response to DOC & TP concentrations.

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