I april-juli år 2010 undersöktes tre studieområden i mellersta Sverige avseende hur fördelningen av vildsvinsbök såg ut i dessa områden. Resultaten visade att vildsvinsbök främst återfanns i miljöer dominerade av tall-och granskog där åldern på träden låg runt 45-90 år, samt med fältskikt bestående av bärris, mossa eller gräs. På två utav de tre lokalerna påverkades inte arealen på bök av faktorer såsom trädartsammansättning, trädålder eller fältskikt men det fanns däremot korrelationer mellan dessa faktorer på en utav lokalerna. Vidare påverkades arealen på bök inte av populationstäthet eller hur lång tid vildsvin förekommit i området. / In April-July in 2010, three forest dominated areas in central Sweden were studied to investigate wild boar rooting habits. The results showed that rooting mainly occurred in pine-and spruce dominated habitats where tree-ages varied between 45-90 years old and with ground surface vegetation consisting of shrubs (blueberry/lingonberry), mosses and grass. In two of the three study areas the size of rooted areas was not affected by factors such as tree species composition, forest age or vegetation ground cover, but correlations between these factors were found in one of the areas. The size of rooted areas was not affected by the population density or the time with wild boar present in the area.

Our understanding of microbial evolution is largely dependent on available genomic data of diverse organisms. Yet, genome-sequencing efforts have mostly ignored the diverse uncultivable majority in favor of cultivable and sociologically relevant organisms. In this thesis, I have applied and developed cultivation independent methods to explore microbial diversity and obtain genomic data in an unbiased manner. The obtained genomes were then used to study the evolution of mitochondria, Rickettsiales and Haloarchaea. Metagenomic binning of oceanic samples recovered draft genomes for thirteen novel Alphaproteobacteria-related lineages. Phylogenomics analyses utilizing the improved taxon sample suggested that mitochondria are not related to Rickettsiales but rather evolved from a proteobacterial lineage closely related to all sampled alphaproteobacteria. Single-cell genomics and metagenomics of lake and oceanic samples, respectively, identified previously unobserved Rickettsiales-related lineages. They branched early relative to characterized Rickettsiales and encoded flagellar genes, a feature once thought absent in this order. Flagella are most likely an ancestral feature, and were independently lost during Rickettsiales diversification. In addition, preliminary analyses suggest that ATP/ADP translocase, the marker for energy parasitism, was acquired after the acquisition of type IV secretion systems during the emergence of the Rickettsiales. Further exploration of the oceanic samples yielded the first draft genomes of Marine Group IV archaea, the closest known relatives of the Haloarchaea. The halophilic and generally aerobic Haloarchaea are thought to have evolved from an anaerobic methanogenic ancestor. The MG-IV genomes allowed us to study this enigmatic evolutionary transition. Preliminary ancestral reconstruction analyses suggest a gradual loss of methanogenesis and adaptation to an aerobic lifestyle, respectively. The thesis further presents a new amplicon sequencing method that captures near full-length 16S and 23S rRNA genes of environmental prokaryotes. The method exploits PacBio's long read technology and the frequent proximity of these genes in prokaryotic genomes. Compared to traditional partial 16S amplicon sequencing, our method classifies environmental lineages that are distantly related to reference taxa more confidently. In conclusion, this thesis provides new insights into the origins of mitochondria, Rickettsiales and Haloarchaea and illustrates the power of cultivation independent methods with respect to the study of microbial evolution.

Ziel des Forschungsprojektes war der Gewinn umfassender verjüngungsökologischer Kenntnisse zu den Pionierbaumarten Sandbirke (Betula pendula Roth), Salweide (Salix caprea L.) und Eberesche (Sorbus aucuparia L.) im Hinblick auf eine natürliche, eingriffsfreie Wiederbewaldung von Schadflächen (z.B. nach Sturmwurf). Die Abschätzung des Besiedlungserfolges von Schadflächen durch Pionierbaumarten ist aufgrund unzureichender verjüngungsökologischer Kenntnisse gegenwärtig noch mit großen Unsicherheiten verbunden. Die Untersuchungen fanden auf fünf 4-12 ha großen Kyrill-Sturmwurfflächen in den Hoch- und Kammlagen (750-900 m ü. NN) des Thüringer Waldes statt. Alle potenziellen Samenbäume der Pionierbaumarten wurden in den angrenzenden, geschlossenen Fichtenbeständen lokalisiert. Als Versuchsdesign wurde in Abhängigkeit der vorgefundenen Samenbaumdichten und -verteilungen ein Kreuz- bzw. Sterntransekt auf den Sturmwurfflächen etabliert. Entlang der Transektlinien wurden alle 20 m Samenfallen installiert. Als Samenfallen kamen für die Sandbirke Netztrichterfallen (0,2 m²), für die Salweide Klebfallen (0,043 m²) und für die endozoochore Ausbreitung durch frugivore Vogelar-ten Kotfallen (0,25 m²) zum Einsatz. Für die Modellierung der Samenausbreitung von Sandbirke und Salweide wurden inverse Modelle bzw. geostatistische Modelle erstellt. Zudem wurden auf einer der Sturmwurfflächen genetische Nachkommenschaftsanalysen bei Sal-weide mittels Kern-DNA-Primer durchgeführt. Die Bodensamenbankuntersuchungen fanden in jeweils drei geschlossenen Birkenbeständen, Fichten-Birken-Beständen, Fichtenbeständen mit einer einzeln eingemischten Birke und reinen Fichtenbeständen im Tharandter Wald und Thüringer Wald statt. Mittels eines 10,2 cm breiten Stechzylinders wurden 10 cm tiefe Bodenproben gewonnen. Die Lagerung der Proben fand im Kaltgewächshaus statt, wo alle 14 d die gekeimten Samen erfasst wurden. Weiterhin wurde ein Eingrabungsexperiment installiert. Dafür wurden Sandbirkensamen, Ebereschensamen und Ebereschenfrüchte in 2 cm, 5 cm und 10 cm tiefen Mineralboden vergraben und in sechsmonatigen Intervallen jeweils eine Keimprobe zum Test der verbliebenen Keimfähigkeit entnommen. Die Auswertung der Bodensamenbankuntersuchungen erfolgte mittels GLM und GLMM. Während der zweijährigen Untersuchung zur zeitlichen und räumlichen Samenausbreitung von Salix caprea auf fünf Sturmwurfflächen konnten ein schwächeres und ein stärkeres Samenjahr nachgewiesen werden. Des Weiteren erstreckte sich der Samenflugzeitraum im Frühjahr in Abhängigkeit von den klimatischen Bedingungen über 12 Wochen in 2015 und 6 Wochen in 2016. Die höchsten Samenmengen von 23-156 Samen je Falle wurden jeweils unter den Kronen von Salweiden-Samenbäumen nachgewiesen. Ab einer Entfernung von 350 m zum Samenbaum bis zur untersuchten Distanz von 870 m wurden, unabhängig von der Distanz, der Hangneigung, der Anzahl der Samen-bäume und der Windrichtung (Anisotropie), im Durchschnitt 0,6-2,1 Samen je Falle er-fasst. Die genetischen Analysen zur Nachkommenschaft ergaben, dass 29 % der untersuch-ten Verjüngungspflanzen von einem der 20 lokalisierten Elternbäume in der bewaldeten, 500 m breiten Suchzone abstammten. Die Ausbreitungsdistanzen der nachweislich am erfolgreichsten verjüngten Samenbäume betrugen dabei 550-800 m. Insgesamt zeigte die Salweidenverjüngung eine höhere Allel-Variation, als die 20 Elternbäume, was auf einen externen Genfluss und lange Samen- und Pollenausbreitungsdistanzen hinweist. Im Zuge des zweijährigen Untersuchungszeitraums zur Samenausbreitung von Betula pendula auf zwei Kyrill-Sturmwurfflächen konnten ein Mastjahr und ein Zwischenjahr nachgewiesen werden. Die Ergebnisse der inversen Modellierung mittels isotroper Mo-delle ergaben dabei flächenunabhängig Produktionsmengen für einen Samenbaum von 20 cm im Bhd von 300.000-366.000 Samen je Baum im Zwi-schenjahr 2015 und 1.430.000-1.530.000 Samen je Baum im Mastjahr 2016. Mittels räumlicher Modellierung der Samenausbreitung konnte keine Anisotropie belegt werden. Unabhängig von den beprobten Flächen und Un-tersuchungsjahren, belegen die Modellschätzungen allesamt eine isotrope Ausbreitung der Samen. Die mittleren Ausbreitungsdistanzen (MDD) beliefen sich dabei hangaufwärts auf 86-97 m und hangabwärts auf 367-380 m. Maximal ab-gelagerte Samendichten von 2.015 n m-² im Zwischenjahr und 9.557 n m-² im Mastjahr fanden sich bis 40-50 m Entfernung zum Samenbaum. Die Untersuchungen der endozoochoren Samenausbreitung auf fünf Sturmwurfflächen weisen auf eine bevorzuge Nutzung der Vogelarten von Rast- und Sitzgelegenheiten (Strukturelemente) auf Freiflächen zum Absetzen von Kot hin (2,7 Kothaufen je m²). Unter Freiflächenbedingungen - ohne Strukturelemente - ergaben sich im Mittel 0,4 Kothaufen je m². Die höchsten mittleren Kotdichten wurden unter aufra-genden Totästen (20 n m-²), umgeklappten Wurzeltellern (4,6 n m-²) und Hochstubben (3,9 n m-²) nachgewiesen. Schwach dimensionierte Verjüngungspflanzen der Sandbirke, Eberesche und Fichte, und Strukturelemente unter einem Meter Höhe wurden dagegen weitgehend für das Absetzen von Kot gemieden. Das Vermögen zum Aufbau einer Bodensamenbank durch Betula pendula und Sorbus aucuparia unterschied sich deutlich. 56-100 % der eingegrabenen Sandbirkensamen wa-ren auch nach 2,5 Jahren keimfähig, wohingegen lediglich 3-16 % der eingegrabenen Ebereschensamen ohne Fruchthülle und 0-19 % der eingegrabenen Ebereschensamen mit Fruchthülle vital waren. Die Auswertung mittels GLM prognostizierte einen kom-pletten Verlust der Keimfähigkeit nach 12 Jahren, 4,5 Jahren und 3 Jahren der Sandbirkensamen, sowie der Ebereschensamen mit und ohne Fruchthülle. Ein Einfluss der Lagerungstiefe war nur für Sandbirke nachweisbar. Die Untersuchungen der Bodensamenbank von Birke in Fichtenbeständen mit unter-schiedlichen Birkensamenbaumanteilen ergab einen straffen Zusammenhang zwischen der Anzahl von Samenquellen und den nachgewiesenen Samendichten im Boden. In den Birkenbeständen fanden sich stets die höchsten Dichten von 489-1.142 Birkensamen je m². Die Analyse unterschiedlicher Bodenschichten zeigte zudem signifikant abneh-mende Birkensamendichten mit zunehmender Bodentiefe. Die Ergebnisse der Untersuchungen zeigen, dass die Fruktifikation von Betula pendula, Salix caprea und Sorbus aucuparia durch klimatische Verhältnisse beeinflusst wird, weshalb die drei Pionierbaumarten nicht alljährlich hohe Samenmengen produzieren (Mastjahre und Zwischenjahre). Zum Ausgleich von Produktionsdefiziten in den Zwischenjahren unter-scheiden sich die Pionierbaumarten in ihrer Strategie. Dies gilt es bei der Umsetzung des Konzeptes einer natürlichen, eingriffsfreien Wiederbewaldung von Schadflächen nach Sturmwurf durch die Naturverjüngung von Pionierbaumarten zu beachten. Die einzige der drei Pionierbaumarten, die dem allgemeinen Bild einer Pionierbaumart ent-spricht, ist die Salweide. Ihr Besiedlungserfolg ist allein von den aktuellen, alljährlich variierenden, aber dennoch stets hohen Samenproduktionsmengen und den enorm weiten Aus-breitungsdistanzen (>800 m) abhängig. Hinsichtlich der Samenausbreitung haben die Him-melsrichtung, die Position der Samenbäume und die Anzahl vorhandener Samenquellen ab einer Distanz von 50 m zur Schadfläche keinen bedeutenden Einfluss auf die abgelagerten Samenmengen mehr. Die auf 86-380 m limitierte Samenausbreitung von Sandbirke wurde dagegen stark vom Geländerelief (Hangneigung), der Position der Samenbäume (Tal, Kuppe, Hanglage) und der Distanz der Samenbäume zur Sturmwurffläche beeinflusst. Zum Ausgleich der limitierten Samenausbreitung und deutlich reduzierten Samenmengen im Zwischenjahr ist Sandbirke jedoch zum Aufbau einer short-term persistenten Bodensamenbank befähigt. Den gesamten Verjüngungszyklus betrachtend entspricht die Eberesche eher einer Schluss-waldbaumart. Unter ungünstigen klimatischen Bedingungen kommt es häufig zum kompletten Ausfall der Samenproduktion. Ihr enormes Wiederbewaldungspotential von Sturmwurfflächen speist sich hauptsächlich aus dem Aufbau einer Sämlingsbank und weni-ger durch den aktuellen Samenregen oder der short-term persistenten Bodensamenbank. Die limitierte Samenausbreitung von Sandbirke und Eberesche macht eine „räumliche Optimierung“ der Samenbaumpositionen durch die Forstwirtschaft erforderlich. Aufgrund der allgegenwärtigen Omnipräsenz von Weidensamen ist dies für Salweide nicht zwingend not-wendig. Das detailreiche Wissen zur Verjüngungsökologie der untersuchten Pionierbaumar-ten ermöglicht eine gezielte waldbauliche Steuerung im Sinne des Vorhalts und der Pflege von Pionierbaumarten im Wirtschaftswald. Dies ist gegenwärtig und zukünftig vor allem von besonderer Bedeutung, da aufgrund der zu erwartenden Zunahme von Schadereignissen und deren Unvorhersehbarkeit die Fähigkeit der Wälder zur natürlichen Wiederbewaldung von Schadflächen durch Pionierbaumarten zunehmend an Interesse gewinnen wird.:Table of abbreviations III Summary IV Zusammenfassung VIII Chapter 1 – General introduction 1 1.1 Introduction 2 1.1.1 Importance and relevance of the study 2 1.1.2 Research interest - regeneration ecology 5 1.3 Aims, scope and hypotheses 9 1.4 Study outline 12 1.5 References 13 Chapter 2 – Seed dispersal capacity of Salix caprea L. assessed by seed trapping and parentage analysis 25 2.1 Abstract 26 2.2 Introduction 26 2.3 Materials and methods 29 2.3.1 Study area 29 2.3.2 Experimental design 31 2.3.3 Genetic analysis 32 2.3.4 Seed trap data analysis 33 2.3.5 Geostatistical models 34 2.4 Results 36 2.4.1 Temporal patterns of seed dispersal 37 2.4.2 Dispersal distance and spatial patterns of seed dispersal 37 2.4.3 Genetic parentage analysis 40 2.5 Discussion 42 2.5.1 Seed production and temporal patterns of seed dispersal 42 2.5.2 Dispersal distance and spatial patterns of seed dispersal 43 2.5.3 Genetic parentage analysis 45 2.6 Conclusions for silvicultural practice 46 2.7 References 48 Chapter 3 – Restrictions on natural regeneration of storm-felled spruce sites by silver birch (Betula pendula Roth) through limita-tions in fructification and seed dispersal 57 3.1 Abstract 58 3.2 Introduction 58 3.3 Materials and methods 60 3.3.1 Study area 60 3.3.2 Experimental design 63 3.3.3 Data analysis 64 3.3.4 Seed dispersal model 64 3.3.5 Simulations for practical management decisions 66 3.4 Results 66 3.4.1 Seed production 66 3.4.2 Seed dispersal and spatial patterns 68 3.5 Discussion 71 3.5.1 Seed production 71 3.5.2 Directionality 72 3.5.3 Spatial patterns and seed dispersal distances 72 3.6 Seed dispersal scenarios for silvicultural management decisions 74 3.6.1 Seed dispersal scenarios 74 3.6.2 Conclusions for silvicultural management decisions 76 3.7 References 78 Chapter 4 – The impact of structural elements on storm-felled sites on endozoochorous seed dispersal by birds – a case study 85 4.1 Abstract 86 4.2 Introduction 86 4.3 Materials and methods 88 4.3.1 Study area 88 4.3.2 Experimental design 90 4.3.3 Data analysis 91 4.4 Results 92 4.5 Discussion 95 4.6 Conclusions for silvicultural practice 97 4.7 References 98 Chapter 5 – Soil seed banks of pioneer tree species in European tempe-rate forests: a review 104 5.1 Abstract 105 5.2 Introduction 105 5.3 Methods of literature search 107 5.4 Species-specific reproductive ecology determining the potential of soil seed banks 110 5.5 Characterization and classification of soil seed banks 112 5.5.1 Soil seed bank of Betula spp. 114 5.5.2 Soil seed bank of Alnus glutinosa (L.) GAERTN. 116 5.5.3 Soil seed banks of Salix spp. and Populus tremula L. 117 5.5.4 Soil seed bank of Sorbus aucuparia L. 118 5.6 Conclusions 119 5.7 References 120 Chapter 6 – Do birch and rowan establish soil seed banks sufficient to compensate for a lack of seed rain after forest disturbance? 134 6.1 Abstract 135 6.2 Introduction 135 6.3 Materials and methods 137 6.3.1 Study areas 137 6.3.2 Data collection 139 6.3.3. Statistical analysis 140 6.4 Results 141 6.4.1 Study A - Artificial seed burial experiment 141 6.4.2 Study B - Soil core sampling in the forest 145 6.5 Discussion 147 6.5.1 Study A - Artificial seed burial experiment 147 6.5.2 Study B - Soil core sampling in the forest 149 6.6 Conclusions 151 6.7 References 152 Chapter 7 – General discussion 160 7.1 Discussion of important aspects of regeneration ability 161 7.1.1 Fructification and seed production in Salix caprea, Betula pendula and Sorbus aucuparia 165 7.1.2 Ecological processes within the regeneration cycle of Salix caprea 167 7.1.3 Ecological processes within the regeneration cycle of Betula pendula 168 7.1.4 Ecological processes within the regeneration cycle of Sorbus aucuparia 169 7.2. Conclusions for silviculture and management recommendations 172 7.3 References 175 Table of appendix i / The aim of the study was to obtain comprehensive knowledge of the regeneration ecology of the pioneer tree species silver birch (Betula pendula Roth), goat willow (Salix caprea L.) and rowan (Sorbus aucuparia L.). The findings should contribute to better management of the natural regeneration of disturbed sites (e.g., windthrown sites) by pioneer tree species. Insufficient knowledge of the regeneration ecology of pioneer tree species renders forest managers’ abilities to assess the success of regeneration of windthrown sites uncertain. The study took place in the years 2015 and 2016. The study sites were located on the slopes and mountain tops (plateaus) of the Thuringian Forest (715-900 m a.s.l.), on five windthrown open areas (4-13 ha) created by the storm ‘Kyrill’ in January 2007. All seed trees of pioneer tree species were mapped within the forested search zone around each site. This zone extended 200 m for silver birch and rowan and 500 m for goat willow. Following the mapping of these seed trees and an analysis of their spatial distribution, seed traps were placed along two or four crossing line transects, with intervals of 20 m between traps. The traps were funnel shaped net seed traps for silver birch (0.2 m²), seed traps with a sticky, non-drying glue for goat willow (0.043 m²) and dropping traps for seeds dispersed endozoochorously by frugivorous birds (0.25 m²). A phenomenological model and model-based geostatistics were used to investigate silver birch and goat willow seed dispersal. For goat willow a parentage analysis was performed at one of the study sites using nuclear-DNA-primers. The soil seed bank study was carried out in three birch stands, spruce stands with admixed birch, spruce stands with one isolated birch tree and pure spruce stands in the Tharandter Forest and in the Thuringian Forest. Soil core samples with a diameter of 10.2 cm were taken from the litter layer and the mineral soil to a depth of 10 cm. The soil samples were placed in a greenhouse and seed germination was checked every 14 days. An artificial seed burial experiment was also carried out. Silver birch seeds, rowan seeds and rowan fruits were buried in mineral soil at depths of 2 cm, 5 cm and 10 cm. At intervals of 6 months sample sets were removed from the soil and the germination capacity checked. The analysis of the soil seed banks was based on generalized linear mixed models (GLMM) and generalized linear models (GLM). The 2-year study of the temporal and spatial dispersal of seeds of Salix caprea on five Kyrill-felled areas involved one year with lower seed production and one with more bountiful seed production. The duration of the spring seed rain was about 12 weeks in 2015, and only 6 weeks in 2016 because of contrasting weather conditions. The highest seed numbers of 23-156 n per trap occurred close to the base of the seed trees. Beyond 350 m from the seed trees, up to the maximum distance in the study of 870 m, the average numbers of seeds per trap (0.6-2.1 seeds) were independent of the dispersal distance, inclination, the number of seed sources and the dispersal direction (anisotropy). Parentage analyses showed that 29% of the saplings stemmed from one of the 20 parent trees within the 500 m search zone extending from the edge of the open area. The seed dispersal distances of the most successful seed parents were between 550-800 m. The saplings revealed a higher allelic variation than the 20 parent trees, indicating external gene flow and long seed and pollen dispersal distances. During the 2-year study of Betula pendula seed dispersal on two Kyrill-felled areas there was a mast year and a non-mast year. Independent of the site, the seed production rate of a silver birch seed tree with a mean diameter at breast height (dbh) of 20 cm predicted by isotropic inverse models was approximately 300,000-366,000 seeds in 2015 and 1,430,000-1,530,000 seeds per tree in the mast year 2016. Directionality (anisotropic inverse modelling) of seed dispersal around an individual seed tree could not be confirmed. The model results revealed the isotropic model (no directionality) to be an appropriate approach for all sites and years. The mean dispersal distances (MDD) were 86 m and 97 m (uphill) and 367 m and 380 m (downhill). The maximum seed numbers occurred within 40-50 m of a seed tree, amounting to 2,015 n m-² in the non-mast year and 9,557 n m-² in the mast year. The study of endozoochorous seed dispersal on the five sites felled by the storm Kyrill showed a preference of frugivorous birds for perches and resting places (structural elements) from which to defecate onto open areas (2.7 droppings per m²). On completely open areas – with no structural elements – an average of 0.4 droppings per m² was recorded. The highest mean bird dropping density was observed under towering dead branches (20 n m-²), upturned root plates (4.6 n m-²) and high stumps (3.9 n m-²). Young, small diameter silver birch, rowan and spruce trees, and structural elements less than 1 m in height generally, were avoided by frugivorous birds as a place from which to defecate. The abilities of Betula pendula and Sorbus aucuparia to form a soil seed bank differed. Between 56-100 % of the buried silver birch seeds were still viable after 2.5 years, whereas only 3-16 % of the rowan seeds buried without pulp and 0-19 % of the rowan seeds within pulp were viable. The maximum durations of storage in the soil predicted for silver birch seeds and rowan seeds with and without pulp by GLM were 12 years, 4.5 years and 3 years. An influence of the storage depth was found for silver birch seeds only. The investigation of the soil seed banks of birch in three birch stands and nine spruce forests with different numbers of admixed birch seed trees showed a strong correlation between the number of seed sources and the seed density in the soil. The birch stands contained the highest mean densities of viable birch seeds in soil, between 489-1,142 n m-². The analysis of the different soil layers showed significantly declining birch seed densities with increasing soil depth across all sites. The results of the study showed that the fructification of Betula pendula, Salix caprea and Sorbus aucuparia is influenced by weather conditions, with the three pioneer tree species failing to produce high numbers of seeds every year (mast and non-mast years). The three species differed in their strategies to compensate for low seed production in non-mast years. This must be considered when implementing a concept for the reforestation of disturbed sites based on natural regeneration by pioneer tree species. Goat willow was the only one of the three specie studied with characteristics corresponding to the general assumptions made about pioneer tree species. The regeneration success of goat willow is dependent upon the variable but generally high annual seed production and long seed dispersal distances (> 800 m). The azimuth direction, position and number of seed trees have no meaningful influence on seed numbers at a distance of more than 50 m from the seed source. The limited mean seed dispersal distances of 86-380 m determined for silver birch were influenced by site inclination, the seed tree location (valley, slope or plateau) and the distance between the seed tree and the windthrown site. Silver birch seed shadow is also influenced by the number of seed sources. To compensate for the limited dispersal distances and the significantly lower seed production in non-mast years, silver birch is able to build up a short-term persistent soil seed bank. The regeneration cycle of rowan is more reminiscent of that of a shade-tolerant tree species. Unfavorable weather conditions often result in a complete failure to produce seeds. The enormous regeneration potential of rowan on disturbed sites stems primarily from a seedling bank, which is built up over years. The seed rain in any given year and its short-term persistent soil seed bank are of secondary importance. Forest management targeting a ‘spatial optimization’ of silver birch and rowan seed trees is necessary to ensure successful natural regeneration given the limited seed dispersal. The omnipresence of goat willow seeds renders specific spatial management measures for its establishment unnecessary. Detailed knowledge of the regeneration ecology of the studied pioneer tree species makes possible an approach to silviculture that is targeted to the conservation and revitalization of pioneer tree species in managed forests. The expected increase in the frequency of disturbances, and their unpredictability, means that the ability of forests to naturally regenerate using pioneer tree species is likely to grow in importance.:Table of abbreviations III Summary IV Zusammenfassung VIII Chapter 1 – General introduction 1 1.1 Introduction 2 1.1.1 Importance and relevance of the study 2 1.1.2 Research interest - regeneration ecology 5 1.3 Aims, scope and hypotheses 9 1.4 Study outline 12 1.5 References 13 Chapter 2 – Seed dispersal capacity of Salix caprea L. assessed by seed trapping and parentage analysis 25 2.1 Abstract 26 2.2 Introduction 26 2.3 Materials and methods 29 2.3.1 Study area 29 2.3.2 Experimental design 31 2.3.3 Genetic analysis 32 2.3.4 Seed trap data analysis 33 2.3.5 Geostatistical models 34 2.4 Results 36 2.4.1 Temporal patterns of seed dispersal 37 2.4.2 Dispersal distance and spatial patterns of seed dispersal 37 2.4.3 Genetic parentage analysis 40 2.5 Discussion 42 2.5.1 Seed production and temporal patterns of seed dispersal 42 2.5.2 Dispersal distance and spatial patterns of seed dispersal 43 2.5.3 Genetic parentage analysis 45 2.6 Conclusions for silvicultural practice 46 2.7 References 48 Chapter 3 – Restrictions on natural regeneration of storm-felled spruce sites by silver birch (Betula pendula Roth) through limita-tions in fructification and seed dispersal 57 3.1 Abstract 58 3.2 Introduction 58 3.3 Materials and methods 60 3.3.1 Study area 60 3.3.2 Experimental design 63 3.3.3 Data analysis 64 3.3.4 Seed dispersal model 64 3.3.5 Simulations for practical management decisions 66 3.4 Results 66 3.4.1 Seed production 66 3.4.2 Seed dispersal and spatial patterns 68 3.5 Discussion 71 3.5.1 Seed production 71 3.5.2 Directionality 72 3.5.3 Spatial patterns and seed dispersal distances 72 3.6 Seed dispersal scenarios for silvicultural management decisions 74 3.6.1 Seed dispersal scenarios 74 3.6.2 Conclusions for silvicultural management decisions 76 3.7 References 78 Chapter 4 – The impact of structural elements on storm-felled sites on endozoochorous seed dispersal by birds – a case study 85 4.1 Abstract 86 4.2 Introduction 86 4.3 Materials and methods 88 4.3.1 Study area 88 4.3.2 Experimental design 90 4.3.3 Data analysis 91 4.4 Results 92 4.5 Discussion 95 4.6 Conclusions for silvicultural practice 97 4.7 References 98 Chapter 5 – Soil seed banks of pioneer tree species in European tempe-rate forests: a review 104 5.1 Abstract 105 5.2 Introduction 105 5.3 Methods of literature search 107 5.4 Species-specific reproductive ecology determining the potential of soil seed banks 110 5.5 Characterization and classification of soil seed banks 112 5.5.1 Soil seed bank of Betula spp. 114 5.5.2 Soil seed bank of Alnus glutinosa (L.) GAERTN. 116 5.5.3 Soil seed banks of Salix spp. and Populus tremula L. 117 5.5.4 Soil seed bank of Sorbus aucuparia L. 118 5.6 Conclusions 119 5.7 References 120 Chapter 6 – Do birch and rowan establish soil seed banks sufficient to compensate for a lack of seed rain after forest disturbance? 134 6.1 Abstract 135 6.2 Introduction 135 6.3 Materials and methods 137 6.3.1 Study areas 137 6.3.2 Data collection 139 6.3.3. Statistical analysis 140 6.4 Results 141 6.4.1 Study A - Artificial seed burial experiment 141 6.4.2 Study B - Soil core sampling in the forest 145 6.5 Discussion 147 6.5.1 Study A - Artificial seed burial experiment 147 6.5.2 Study B - Soil core sampling in the forest 149 6.6 Conclusions 151 6.7 References 152 Chapter 7 – General discussion 160 7.1 Discussion of important aspects of regeneration ability 161 7.1.1 Fructification and seed production in Salix caprea, Betula pendula and Sorbus aucuparia 165 7.1.2 Ecological processes within the regeneration cycle of Salix caprea 167 7.1.3 Ecological processes within the regeneration cycle of Betula pendula 168 7.1.4 Ecological processes within the regeneration cycle of Sorbus aucuparia 169 7.2. Conclusions for silviculture and management recommendations 172 7.3 References 175 Table of appendix i

Firewood is a dominant household fuel type used in many developing countries. Even in countries where there is improved access to electricity, most households still rely on firewood for their energy needs. Harvesting of some wood is illegal, however the high poverty rate, absence of alternative fuels and lack of law enforcement means even the protected wood species will continue to be used, with consequent pressure on the forests. Furthermore, the combustion of firewood for domestic use takes place in poorly ventilated homes emitting hazardous pollutants, which causes indoor air pollution and affect human health. The use of firewood as a household fuel can be superimposed nearly perfectly on that of socioeconomic development. Additionally, the use of household firewood is invariably associated with poverty in countries, in communities within a country and in households within a community. Indoor air pollution studies on human health should then consider socio-economic factors which seem to be one of the determinants of both firewood use and ill health, a determinant which is often neglected in most indoor air pollution studies. Domestic inhalation of firewood smoke is one of the mechanisms linking socio-economic (poverty) to disease. The current study sought to determine a baseline of wood usage and health risks caused by volatile organic compounds in Senwabarwana villages. This study integrated observations, ethnobotanical meta-analysis and experimental into one comprehensive integrated environmental health risk assessment framework to assess the risks associated with exposure to volatile organic compounds from firewood combustion. Basic information about firewood usage, socio-economic dynamics and perceived health problems related to volatile organic compounds was collected using a structured questionnaire. The Vac-U-Chamber was used to sample the air. The results show that firewood is extensively used in poorly ventilated kitchens for cooking and home heating in Senwabarwana villages. Ten priority firewood plant species are frequently used in the study area, namely Mohweleri (Combretum apiculatum), Moretshe (Dichrostachys cinera), Motswiri (Combretum imberbe), Mokgwa (Acacia burkei), Mushu (Acacia tortilis), Motshe (Cussonia paniculate), Mokata (Combretum hereroense), Mphata (Lonchocarpus capassa), Mokgalo (Ziziphus mucronate) and Mogwana (Grewia monticola), in their order of preference. The results also indicated thirteen common reasons or factors that influence the hoice of firewood plant species by households, the main four being: (i) the embers formed during combustion, (ii) heat value, (iii) low ash content and (iv) availability of the firewood plant species. Further analysis revealed several uses and ranking thereof, including reviewing the national status and legal profile of each identified plant species. The study found that most of the firewood species used in Senwabarwana Village were indigenous. Major drivers of firewood use are household income, educational status of breadwinners, family sizes, and place of residence, fuel affordability and accessibility, among others. Concentrations of benzene, toluene, ethylbenzene and xylene per plant species were studied to assess the risk exposed to the Senwabarwana community. Literature indicates that these pollutants have several health effects associated with acute exposure such as eye, nose and throat irritation, headaches, dizziness, nausea and vomiting. Both hazard quotient and hazard index were found to be less than one indicating no risk exists with the use of plant species used for firewood in Senwabarwana even to sensitive individuals. The risk of developing health effects due to the presence of the studied volatile organic compounds can be assessed as negligible. Since firewood is a more convenient source of energy, it is recommended that the size of the windows be extended for ventilation. Agroforesty should also be implemented as a conservation method. The wood that emits less concentration of pollutants be used for firemaking. / Environmental Sciences

Methane (CH4) is guaranteed to affect climate change and is essential in rising temperatures. Scientists have known for over two decades that wetlands emit CH4 to such an extent that it affects our climate. Tropical trees that grow in wetlands tend to emit or act as a conduit of CH4, to the extent that it has a negative environmental impact. However, until this study, no one has examined whether wetland species growing in another environment have the same effects. Hence, this thesis aimed to collect data from wetland-adapted tropical trees in a non-wetland environment, namely the Botanical Garden in Rio de Janeiro. The results showed a difference in the sampling height of the stem, namely that a decrease in emission is seen with an increased height. All the species except one (Pseudobombax munguba) showed both assimilation and emission from the day-to-day measurements of CH4, which speaks for the trees acting both as a sink and a source of CH4. This suggests that the species are more robust than the environmental stressors in a non-wetland environment. Previous studies have found that increased CH4 emissions can be seen with different meteorological parameters. The results presented in this thesis show the opposite, that some species tend to emit less or assimilate more CH4 during days with increased rainfall, humidity, and temperature.

La télédétection des forêts est devenue de plus en plus accessible grâce à l'utilisation de véhicules aériens inoccupés (UAV) et à l'apprentissage profond, ce qui permet d'obtenir des images répétées à haute résolution et d’observer les changements phénologiques à des échelles spatiales et temporelles plus importantes. Dans les forêts tempérées, à l'automne, la sénescence des feuilles se produit lorsque les feuilles changent de couleur et tombent. Cependant, l'influence de la sénescence foliaire sur la segmentation des espèces d'arbres à l'aide d'un réseau neuronal convolutif (CNN) n'a pas encore été évaluée. Nous avons acquis de l’imagerie haute résolution par UAV au-dessus d’une forêt tempérée au Québec à sept reprises entre mai et octobre 2021. Nous avons segmenté et identifié 23 000 couronnes d'arbres de 14 classes différentes pour entraîner et valider un CNN pour chaque acquisition d'imagerie. La meilleure segmentation (F1-score le plus élevé) était au début de la coloration des feuilles (début septembre) et le F1-score le plus bas au pic de la coloration automnale (début octobre). La chronologie de la sénescence varie considérablement d’une espèce à l’autre et au sein d’une même espèce, ce qui entraîne une grande variabilité du signal télédétecté. Les espèces d'arbres à feuilles caduques et à feuilles persistantes qui présentaient des traits distinctifs et moins variables dans le temps entre les individus ont été mieux classées. Bien que la segmentation des arbres dans une forêt hétérogène demeure un défi, l'imagerie UAV et l'apprentissage profond démontrent un grand potentiel pour la cartographie des espèces d'arbres. Les résultats obtenus dans une forêt tempérée où la couleur des feuilles change fortement pendant la sénescence automnale montrent que la meilleure performance pour la segmentation des espèces d'arbres se produit au début de ce changement de couleur. / Remote sensing of forests has become increasingly accessible with the use of unoccupied aerial vehicles (UAV), along with deep learning, allowing for repeated high-resolution imagery and the capturing of phenological changes at larger spatial and temporal scales. In temperate forests during autumn, leaf senescence occurs when leaves change colour and drop. However, the influence of leaf senescence in temperate forests on tree species segmentation using a Convolutional Neural Network (CNN) has not yet been evaluated. Here, we acquired high-resolution UAV imagery over a temperate forest in Quebec, Canada on seven occasions between May and October 2021. We segmented and labelled 23,000 tree crowns from 14 different classes to train and validate a CNN for each imagery acquisition. The CNN-based segmentation showed the highest F1-score (0.72) at the start of leaf colouring in early September and the lowest F1-score (0.61) at peak fall colouring in early October. The timing of the events occurring during senescence, such as leaf colouring and leaf fall, varied substantially between and within species and according to environmental conditions, leading to higher variability in the remotely sensed signal. Deciduous and evergreen tree species that presented distinctive and less temporally-variable traits between individuals were better classified. While tree segmentation in a heterogenous forest remains challenging, UAV imagery and deep learning show high potential in mapping tree species. Our results from a temperate forest with strong leaf colour changes during autumn senescence show that the best performance for tree species segmentation occurs at the onset of this colour change.

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A major argument for incorporating deciduous tree species in coniferous forest stands is their role in the amelioration and stabilisation of biogeochemical cycles. Current forest management strategies in central Europe aim to increase the area of mixed stands. In order to formulate statements about the ecological effects of mixtures, studies at the stand level are necessary. In a mixed stand of Norway spruce (Picea abies (L.) Karst.) and silver birch (Betula pendula Roth) in the Ore Mountains (Saxony, Germany), the effects of these two tree species on chemical and microbial parameters in the topsoil were studied at one site in the form of a case study. Samples were taken from the O layer and A horizon in areas of the stand influenced by either birch, spruce or a mixture of birch and spruce. The microbial biomass, basal respiration, metabolic quotient, pH-value and the C and N contents and stocks were analysed in the horizons Of, Oh and A. Significantly higher contents of microbial N were observed in the Of and Oh horizons in the birch and in the spruce-birch strata than in the stratum containing only spruce. The same was found with respect to pH-values in the Of horizon and basal respiration in the Oh horizon. Compared to the spruce stratum, in the birch and spruce-birch strata, significantly lower values were found for the contents of organic C and total N in the A horizon. The findings of the case study indicated that single birch trees have significant effects on the chemical and microbial topsoil properties in spruce-dominated stands. Therefore, the admixture of birch in spruce stands may distinctly affect nutrient cycling and may also be relevant for soil carbon sequestration. Further studies of these functional aspects are recommended.