Cells exposed to heat stress experience an increase in the amount of misfolded and aggregated proteins. Cells respond to this threat through coordinated and finely tuned ad- justments in gene expression. When the ambient temperature increases, cells activate the heat stress response (HSR), a process in which the transcription of mRNAs encoding heat shock proteins (Hsps) is upregulated. During severe heat stress, cells also downregulate the synthesis of misfolding-prone housekeeping proteins while the synthesis of Hsps takes precedence. Consequently, the amount of misfolded and aggregated proteins is reduced by Hsps. While the transcriptional HSR has been studied in depth over the last 50 years, our understanding of protein translation regulation during heat stress remains limited. Biomolecular condensates have been proposed as a new way to regulate cellular functions. In budding yeast exposed to severe heat stress, the repression in the synthesis of housekeep- ing proteins coincides with the formation of condensates called heat stress granules (HSGs). HSGs are enriched for translation factors and translationally-repressed mRNAs and they have been implicated in translation regulation. However, if and how HSGs regulate translation during severe heat stress has remained elusive. Using in vitro reconstitution assays, I demonstrate that the heat-induced condensation of translation factors together with mRNA is an adaptive mechanism to regulate protein synthesis during severe heat stress. My thesis work focused on the translation initiation factor complex eIF4F from Saccharomyces cerevisiae. eIF4F was previously shown to promote global translation of capped mRNAs. One subunit of eIF4F is eIF4G, an RNA-binding and scaffold protein that interacts with numerous translation initiation factors. Two other subunits of eIF4F are the RNA helicase eIF4A and the mRNA cap-binding protein eIF4E. eIF4G also interacts with the poly(A) binding protein (Pab1p) and the RNA helicase Ded1p, which like eIF4F, are crucial in translation initiation. Importantly, eIF4G, eIF4E, Pab1p and Ded1p condense into HSGs in yeast upon severe heat stress, while eIF4A remains soluble in the cytosol. To investigate the function of these translation factors in regulating translation, I purified eIF4F, Pab1p and Ded1p. Using purified eIF4F, nanoluciferase-encoding reporter mRNAsand an in vitro translation assay, I showed that eIF4F enhances general protein synthesis. Together with Pab1p and Ded1p, eIF4F enhances the translation of reporter mRNAs with 5’ UTRs of housekeeping transcripts to a greater extent than reporter mRNAs with 5’ UTRs of Hsp-encoding genes. These findings suggest important differences in translation regulation at physiological temperatures and that efficient translation of housekeeping mRNAs requires synergy between eIF4F, Pab1p and Ded1p. Next, I reconstituted eIF4G condensates in vitro using biochemical approaches. I found that eIF4G forms condensates with mRNA. The condensation of eIF4G-mRNA is promoted by heat-induced structural rearrangements and interaction valences between eIF4G RNAbinding domains (RBDs). eIF4G has three RBDs, where the removal of either RBDs did not affect the RNA binding affinity but repressed condensation. Thus, eIF4G-mRNA condensation requires cooperativity between the three RBDs. Critically, I found that the mechanism of heat-induced condensation is conserved and adapted in eIF4G orthologues from yeast species that thrive in colder or warmer temperatures. Using multi-component in vitro assays, I found that heated eIF4G-mRNA condensates recruit eIF4E and Pab1p. In agreement with the fact that eIF4A does not assemble into HSGs in cells, eIF4A did not partition into eIF4G-mRNA condensates, which is likely due to a heat-induced weakening of interactions with eIF4G. I next characterized eIF4G variants with targeted mutations in the eIF4E- and Pab1-binding sites of eIF4G. This allowed me to demonstrate that the recruitment of eIF4E into eIF4G-mRNA condensates is driven by protein-mediated interactions. Furthermore, I found that heterotypic interactions between eIF4G, Pab1 and the poly(A) tail of mRNA promote the solidification of heated condensates. This is consistent with previous observations reporting solid-like properties of HSGs. Finally, I investigated the translation activity of heated translation factor condensates in yeast cell-free extracts. Solid-like eIF4F-mRNA condensates with Pab1p or Ded1p resulted in a pronounced repression of translation. This coincided with the recruitment of reporter mRNAs into condensates. Based on these findings, I thus propose that the repression in translation of housekeeping mRNAs during severe heat stress in yeast is a consequence of the formation of solid-like translation factor and mRNA condensates. Further analyses revealed that mRNA outside of condensates are translated in an eIF4A-dependent manner. This is because eIF4A is not recruited to the condensates and remains active upon heating. In summary, I propose that heat stress promotes the condensation of mRNA with eIF4G, eIF4E, Pab1p and Ded1p into solid-like condensates. In vitro assays suggest that translation factors inside of condensates are inactive while the mRNA is translationally repressed. This model highlights a mechanism for the downregulation in the synthesis of housekeeping proteins during severe heat stress in yeast. My findings also suggest that the preferential translation of mRNAs encoding Hsps occurs independently of the condensate-forming translation factors and may be mediated by eIF4A, which does not localise into HSGs. I thus conclude that translation regulation during severe heat stress is achieved by specific translation initiation factors that form inactive and solid-like condensates with mRNA.

Editorial on the Research Topic. Nature’s Contributions to People: On the Relation Between Valuations and Actions.

Background: Autosomal polycystic kidney disease is distinguished into dominant (ADPKD) and recessive (ARPKD) inheritance usually caused by either monoallelic (PKD1/PKD2) or biallelic (PKHD1) germline variation. Clinical presentations are genotype-dependent ranging from fetal demise to mild chronic kidney disease (CKD) in adults. Additionally, exemptions from dominant and recessive inheritance have been reported in both disorders resulting in respective phenocopies. Here, we comparatively report three young adults with microcystic-hyperechogenic kidney morphology based on unexpected genetic alterations beyond typical inheritance. Methods: Next-generation sequencing (NGS)-based gene panel analysis and multiplex ligation-dependent probe amplification (MLPA) of PKD-associated genes, familial segregation analysis, and reverse phenotyping. Results: Three unrelated individuals presented in late adolescence for differential diagnosis of incidental microcystic-hyperechogenic kidneys with preserved kidney and liver function. Upon genetic analysis, we identified a homozygous hypomorphic PKHD1 missense variant causing pseudodominant inheritance in a family, a large monoallelic PKDH1-deletion with atypical transmission, and biallelic PKD1 missense hypomorphs with recessive inheritance. Conclusion: By this report, we illustrate clinical presentations associated with atypical PKD-gene alterations beyond traditional modes of inheritance. Large monoallelic PKHD1-alterations as well as biallelic hypomorphs of both PKD1 and PKHD1 may lead to mild CKD in the absence of prominent macrocyst formation and functional liver impairment. The long-term renal prognosis throughout life, however, remains undetermined. Increased detection of atypical inheritance challenges our current thinking of disease ontology not only in PKD but also in Mendelian disorders in general.

The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.

Editorial on the Research Topic. Biomechanical Properties of Cells and Tissues and Their Impact on Cellular Adhesion andMotility.

Background: The mechanisms through which immunosuppressed patients bear increased risk and worse survival in oral squamous cell carcinoma (OSCC) are unclear. Here, we used deep learning to investigate the genetic mechanisms underlying immunosuppression in the survival of OSCC patients, especially from the aspect of various survival-related subtypes. Materials and methods: OSCC samples data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and OSCCrelated genetic datasets with survival data in the National Center for Biotechnology Information (NCBI). Immunosuppression genes (ISGs) were obtained from the HisgAtlas and DisGeNET databases. Survival analyses were performed to identify the ISGs with significant prognostic values in OSCC. A deep learning (DL)-based model was established for robustly differentiating the survival subpopulations of OSCC samples. In order to understand the characteristics of the different survival-risk subtypes of OSCC samples, differential expression analysis and functional enrichment analysis were performed. Results: A total of 317 OSCC samples were divided into one inferring cohort (TCGA) and four confirmation cohorts (ICGC set, GSE41613, GSE42743, and GSE75538). Eleven ISGs (i.e., BGLAP, CALCA, CTLA4, CXCL8, FGFR3, HPRT1, IL22, ORMDL3, TLR3, SPHK1, and INHBB) showed prognostic value in OSCC. The DL-based model provided two optimal subgroups of TCGA-OSCC samples with significant differences (p = 4.91E-22) and good model fitness [concordance index (C-index) = 0.77]. The DL model was validated by using four external confirmation cohorts: ICGC cohort (n = 40, C-index = 0.39), GSE41613 dataset (n = 97, C-index = 0.86), GSE42743 dataset (n = 71, C-index = 0.87), and GSE75538 dataset (n = 14, C-index = 0.48). Importantly, subtype Sub1 demonstrated a lower probability of survival and thus a more aggressive nature compared with subtype Sub2. ISGs in subtype Sub1 were enriched in the tumorinfiltrating immune cells-related pathways and cancer progression-related pathways, while those in subtype Sub2 were enriched in the metabolism-related pathways. Conclusion: The two survival subtypes of OSCC identified by deep learning can benefit clinical practitioners to divide immunocompromised patients with oral cancer into two subpopulations and give them target drugs and thus might be helpful for improving the survival of these patients and providing novel therapeutic strategies in the precision medicine area.

Modern humans, archaic humans and great apes are genetically closely related and share many behavioral and anatomical similarities. However, modern humans differ from the others by a fast development of complex culture and technologies, that rely on complex cognitive abilities. Cognition is directly linked to brain structure and neuronal function. In this thesis, I study neuronal differences between humans and chimpanzees and bonobos as well as morphological differences of “ancestralized” and “modernized” human neurons, that could possibly contribute to cognitive differences among the different hominid species. The comparison of human and ape induced pluripotent stem cell-derived neurons (iNeurons) revealed that the human neurons mature transcriptionally, morphologically and functionally slower than their ape counterparts. By injecting the mRNA of 16 genes that are relevant for neuronal function and carry amino acid substitutions on the modern human lineage, I could show that the 16 proteins are able to increase the total neurite length and suggest a potential slower development of neurons injected with the modern human variants. In a single gene approach, I investigated the effect of modern and ancestral human SSH2 variants on neurite outgrowth and found differences in neurite length and branching pattern, making SSH2 a promising candidate for being involved in human neuron-specific morphology. I showed that iNeurons can serve as a model system for evolutionary neurobiology. I gained insights into features of neurons that are unique to modern humans in comparison to their closest relatives, the great apes and archaic humans.:BIBLIOGRAPHISCHE DARSTELLUNG 2 TABLE OF CONTENTS 3 1. THESIS SUMMARY 6 COMPARISON OF HUMAN AND APE INDUCED NEURONS 7 MICROINJECTION AS A TOOL TO STUDY RECENT HUMAN HISTORY 8 MODELING THE EFFECT OF A SINGLE GENE BY USING TRANSFECTION OF PRIMARY NEURONS 9 CONCLUSION 10 2. ZUSAMMENFASSUNG 11 VERGLEICH VON NERVENZELLEN VON MENSCHEN UND MENSCHENAFFEN 12 MIKROINJEKTION ZUR UNTERSUCHUNG DER JÜNGSTEN MENSCHLICHEN VERGANGENHEIT 14 MODELLIERUNG DES EFFEKTS EINES EINZELNEN GENS AUF DAS NEURITEN WACHSTUM VON PRIMÄREN NEURONEN 15 FAZIT 16 3. INTRODUCTION 17 3.1 THE HOMINID FAMILY 17 3.2 THE HOMINID BRAIN 19 3.3 THE INEURON MODEL SYSTEM 23 3.4 MICROINJECTION OF INS: A TOOL TO STUDY ANCIENT AND MODERN HUMAN NEURONS 24 4. MATERIAL AND METHODS 27 4.1 METHODS 27 4.1.1 GENERATION OF RTTA/NGN2-POSITIVE PLURIPOTENT STEM CELL LINES 27 4.1.2 CULTURING OF PLURIPOTENT STEM CELL LINES 27 4.1.3 CRYOPRESERVATION OF PLURIPOTENT STEM CELLS 28 4.1.4 DIFFERENTIATION OF RTTA/NGN2-POSITIVE PLURIPOTENT STEM CELLS TO INEURONS 28 4.1.5 SINGLE CELL TRANSCRIPTOMIC ANALYSIS 29 4.1.5.1 SINGLE CELL RNA-SEQ DATA GENERATION 29 4.1.5.2 DATA PROCESSING 30 4.1.5.3 IDENTIFICATION OF NEURONAL CELLS AND DIFFERENTIALLY EXPRESSED GENES 30 4.1.5.4 GENE ONTOLOGY ENRICHMENT ANALYSIS 31 4.1.6 ELECTROPHYSIOLOGY 32 4.1.6.1 RECORDINGS 33 4.1.6.2 ANALYSIS 33 4.1.7 LIPOFECTION OF INEURONS 34 4.1.8 IMMUNOSTAINING OF INEURONS 34 4.1.8.1 PREPARATION OF PARAFORMALDEHYDE FIXATIVE 34 4.1.8.2 FIXATION OF GFP-LABELLED INEURONS 34 4.1.8.3 QUENCHING AND IMMUNOSTAINING OF GFP-LABELLED INEURONS 35 4.1.9 IMAGE ACQUISITION 35 4.1.10 IMAGE QUANTIFICATION 35 4.1.10.1 QUANTIFICATION OF NEURONAL MORPHOLOGY. 35 4.1.10.2 QUANTIFICATION OF TUJI SIGNAL. 36 4.1.11 ASSIGNMENT OF CELL IDENTITY. 36 4.1.12 MICROINJECTION 36 4.13 TRANSFECTION OF PRIMARY NEURONS WITH SSH2 PLASMIDS 40 4.1.3.1 CELL CULTURE 40 4.1.3.2 TRASFECTION 40 4.2 MATERIALS 41 5. RESULTS 48 5.1 COMPARISON OF INDUCED NEURONS REVEALS A SLOWER STRUCTURAL AND FUNCTIONAL MATURATION IN HUMANS THAN IN APES 48 5.1.1 ABSTRACT 49 5.1.2 INTRODUCTION 49 5.1.3 RESULTS 51 5.1.3.1 MATURATION OF HUMAN AND APE INDUCED NEURONS IN VITRO 51 5.1.3.2 MORPHOLOGICAL HETEROGENEITY IN IN POPULATIONS 53 5.1.3.3 MORPHOLOGICAL MATURATION OF APE AND HUMAN INS 55 5.1.3.4 SCRNASEQ REVEALED THAT NGN2 INDUCES CORTICAL AND SENSORY NEURON FATES 56 5.1.3.5 NGN2 ALSO INDUCES CORTICAL SENSORY NEURON FATE 59 5.1.3.6 TRANSCRIPTIONAL MATURATION OF HUMAN AND CHIMPANZEE INS 60 5.1.3.7 INTRINSIC PASSIVE ELECTROPHYSIOLOGICAL PROPERTIES OF HUMAN AND APE INS 62 5.1.3.8 ACTIVE ELECTROPHYSIOLOGICAL PROPERTIES OF APE AND HUMAN INS 63 5.1.4 DISCUSSION 65 5.1.4.1 NGN2 INDUCES HETEROGENEOUS NEURONAL FATES 65 5.1.4.2 EVOLUTIONARY ASPECTS OF NEURONAL MATURATION 65 5.5. SUPPLEMENTARY INFORMATION 68 5.5.1 SUPPLEMENTARY FIGURES 68 5.5.2 SUPPLEMENTARY TABLES 81 5.2 MRNA MICROINJECTION AS A TOOL TO STUDY RECENT HUMAN BRAIN EVOLUTION 88 5.2.1 ABSTRACT 89 5.2.2 INTRODUCTION 89 5.2.3 RESULTS 91 5.2.3.1 NEURONAL GENES CARRYING AMINO ACID SUBSTITUTIONS BETWEEN MODERN AND ARCHAIC HUMANS 91 5.2.3.2 SCREEN OF DISTINCT TRANSCRIPTOME DATASETS FOR EXPRESSION ANALYSES OF THE 16 NEURONAL GENES 94 5.2.3.3 TRANSCRIPTIONAL ANALYSES OF THE 16 NEURONAL GENES IN INEURONS 97 5.2.3.4 MICROINJECTION OF THE 16 NEURONAL GENES INTO INEURONS 99 5.2.3.5 EFFECT OF SSH2 GENE VARIANTS ON HUMAN PRIMARY NEURONS 101 5.2.4. DISCUSSION 103 6. DISCUSSION 108 6.1 COMPARISON OF HUMAN AND APE INDUCED NEURONS 108 6.2 EXPERIMENTAL SYSTEMS TO MODEL RECENT HUMAN HISTORY 109 6.3 MRNA MICROINJECTION TO MODEL MULTIGENIC HUMAN TRAITS 110 6.4 MODELING THE EFFECT OF A SINGLE GENE BY USING TRANSFECTION OF PRIMARY NEURONS 111 6.5 CONCLUDING REMARKS 111 INDEX OF FIGURES 113 SUPPLEMENTARY FIGURES 113 INDEX OF TABLES 114 SUPPLEMENTARY TABLES 114 REFERENCES 115 SOFTWARE AND SCRIPTS 128 ACKNOWLEDGEMENTS 129 CURRICULUM VITAE 130 PUBLICATIONS 133 SELECTED TALKS 134 POSTER PRESENTATIONS 134 SELBSTÄNDIGKEITSERKLÄRUNG 135

Soils harbor a huge diversity of microorganisms, which are dominated by bacteria and fungi. These soil microorganisms, collectively termed as the soil microbiome, are major contributors to soil biodiversity and play essential roles in soil functions (e.g. soil fertility and plant nutrition, organic matter degradation and nutrient cycling, and soil formation). Therefore, many studies in recent decades have explored soil microbial diversity in order to unravel driving forces of its variations. Hence, this thesis reports on spatial and temporal variations of the soil microbiome in response to site specificities, i.e. local climate as well as soil physico-chemistry, and host tree parameters. To avoid effects of intraspecific genetic variations, the pedunculate oak clone DF159 (Quercus robur L.) generated by the project TrophinOak-PhytOakmeter of the Soil Ecology Department at the Helmholtz Centre for Environmental Research (UFZ) was used as phytometer system. In the PhytOakmeter project of which this thesis is a part, saplings regenerated from microcuttings of DF159 were out-planted in grassland, forest and urban field sites in Central Germany and along a European North-South transect. The overall goal of the project is to analyze how the clone adapts to and performs under different regional climatic contexts and changing environment conditions. Pedunculate oak was chosen as a model tree species because it is engaged in highly complex and diverse multitrophic interactions, including soil microorganisms. Q. robur displays an endogenous rhythmic growth with alternating growing flushes in shoot and root, which can be repeated two to four times along a vegetation period. These alternating flushes have been shown to impact on variations of biological activities in soil zones close to the tree roots. Based on the above-described background, the current PhD study investigated changes in the soil microbial communities associated to the pedunculate oak phytometer outplanted in grassland sites at two different spatial scales: (1) the local scale by comparing the soil microbiomes associated to the phytometer in sites located within a close geographic space of Central Germany with similar climatic conditions; and (2) continental scale by making a similar comparison among sites along a European North-South transect, which encompasses a wide range of climatic and soil physico-chemical conditions. Moreover, temporal scale was considered, whereby the variability of the microbiomes intra-annually along a vegetation period was analyzed. Soil samples were taken not only in the tree root zone (RZ), i.e. soil zone containing living roots of the tree, but also in the tree root-free zone (RFZ), i.e. soil zone out of reach of any tree roots, but within the same field plot, to access also the local microbial pools. The analyses used a PCR-based Illumina MiSeq amplicon sequencing approach targeting bacteria and fungi, to assess their diversity, community structure and functionality after assignment of their OTUs to functional groups. In addition to Chapter 1, which introduces the whole work of this PhD research, the findings are presented within Chapters 2-4, of which two studies were already published in international peer-reviewed journals, while another study was published as a conference paper. The thesis is closed by the synopsis Chapter 5 that integrates discussion of all the publication chapters together with an outlook section. Chapter 2 “Tree root zone microbiome: exploring the magnitude of environmental conditions and host tree impact” published in Frontiers in Microbiology investigates the relative contribution of abiotic environmental and host tree parameters among four sites characterized by homogeneous climatic conditions in Central Germany, two years after the tree out-plant. We first compared at each field site the composition of the bacterial and fungal communities between the RZ of the oak clone, called PhytOakmeter in this chapter, and the tree RFZ. The chapter further evaluates the diversity and structure of the microbial communities within the tree RZ among the sites. The results revealed different microbial compositions between the tree RZ and RFZ, whereby the tree RZ-associated microbiome included numerous ectomycorrhizal fungi of the genera Hebeloma, Exophiala, Scleroderma, Tomentella, Trichophaea, and Tuber. This quick recruitment of specific beneficial microbial taxa from the local microbial pool seems to be among the tree strategies to acclimate to local site conditions. However, the overall tree contribution to shape soil microbial communities was lower than the impact of abiotic environmental parameters. The results revealed also a similar level of microbial diversity within the tree RZ among the sites for both the bacteria and fungi, an outcome attributed to the homogeneous climatic conditions within the sites and the common genetic identity of the host trees. In contrast, structure of the microbial communities was site-specific. Chapter 3 “Balance between geographic, soil, and host tree parameters to shape soil microbiomes associated to clonal oak varies across soil zones along a European North-South transect” published in Environmental Microbiology, also examines the relative impact of geographic, soil physico-chemical, and pedunculate oak clone parameters on the variability of the soil microbiome, but at a larger spatial scale from Lapinjärvi (Finland) to Bordeaux (Southwestern France), which is characterized by a broad range of geographic and soil physico-chemical conditions. In addition to the tree RFZ total microbiome and the tree RZ total microbiome, this chapter introduces a new sub-microbiome called tree RZ affine microbiome. The latter was defined as a subset of the RZ bacteria and fungi, significantly enriched in this zone compared to the tree RFZ. The results demonstrated an interplay among abiotic environmental and host tree parameters in shaping bacterial and fungal communities of the tree RZ along the European transect. These parameters showed a descending order of magnitude of their impact on the tree RZ total microbiome: geographic > soil physico-chemical > host tree parameters. However, for the variability of the RZ affine microbiome alone, the impact of the abiotic environmental parameters decreased, while the tree influence was strongly increased, particularly for fungi. Another important result was the highest proportion of the tree RZ affine microbial OTUs shared among all four sites, which was here designated as the tree “core” microbiome. These bacteria and fungi with significant affinity to the host tree, and shared by all the sites because of their ability to cope with diverging environmental conditions across the transect, may be playing a crucial role in supporting the wide distribution of Q. robur across Europe. Interestingly, we found no members of the RZ affine microbiome to be exclusive of only one particular site. Chapter 4 “Temporal changes and alternating host tree root and shoot growth affect soil microbiomes” published in Proceedings as conference paper after “The 1st International Electronic Conference on Microbiology”, considers a temporal scale, and here the variability of the tree RZ and RFZ total microbiomes was analyzed along a vegetation period in two sites of Central Germany. The soil was sampled at different time points coinciding with the tree alternating root and shoot growth, and the fall senescence that concludes the vegetation period. The results show a directional change over time along a vegetation period for the bacterial communities. However, the fungal communities did not show such temporal changes; they rather displayed a fine spatial scale partitioning closely linked to host plant individuals. In addition to the effect of temporal succession, deeper analyses of the generated data set will enable us to specify the impact of the alternating root and shoot growth characteristic of the tree endogenous rhythmic growth in the near future. These further analyses will include for example zooming in the tree RZ affine microbiome and in individual microbial functional groups. The results presented in this thesis evidence the quick impact of pedunculate oak tree clone on the soil microbiome within a two-year time span after the tree out-plant. Also, to different extents, geographic, soil physico-chemical, and host tree concurrently shape the soil bacterial and fungal communities. This thesis shows different spatial and temporal responses to the abiotic environmental and tree parameters between the soil bacterial and fungal communities. The use of tree clonal phytometer to study the tree-related parameters on soil microbiomes was proved to be a promising tool, to unravel the hierarchy of different abiotic and biotic factors in shaping the soil microbiome associated to long live trees. Finally, this work represents a first step toward establishing a long term monitoring of the dynamics of soil microbiomes associated to trees, as a strategy to unravel how these microorganisms participate to the long term acclimation of these long live plants to diverse and changing environments.

Systematik ist das grundlegende Fachgebiet der Biologie, dessen Ziel es ist, die Vielfalt des Lebens zu beschreiben und zu verstehen. Ihre Bedeutung kann nicht außer Acht gelassen werden, da uns die Systematik Werkzeuge lieferte, um auf Verwandtschaftsbeziehungen zwischen lebenden Organismen zu schließen, und wir diese Informationen genutzt haben, um unsere Lebensqualität zu verbessern, die Umwelt zu schützen, die Vergangenheit zu verstehen und die Vielfalt der natürlichen Welt wertzuschätzen. Systematik unterteilt sich in drei Fachrichtungen, nämlich Taxonomie, Phylogenie und Biogeographie. In dieser Dissertation habe ich die Systematik der philippinischen Angehörigen der größten Gattung der Familie Gesneriaceae, Cyrtandra, untersucht. Cyrtandra ist eine Gattung mit fast 800 Arten von krautigen Pflanzen, Sträuchern, kletternden Pflanzen und kleinen Bäumen und hat das größte Verbreitungsgebiet innerhalb der Familie der Gesneriaceae, dass sich vom Indo-Australischen Archipel bis zum Pazifik erstreckt. Ihr Vorkommen in Biodiversitätshotspots und ihre hohe Artenzahl machen sie zu einer ausgezeichneten Modellgruppe für die Untersuchung von Biogeografie, Artbildung, Diversifizierung und Prioritätensetzung bei der Erhaltung. Ihr Nutzen als Modellgruppe wird jedoch dadurch behindert, dass nur wenige Systematiker/innen aktiv an der Gattung arbeiten. Jüngste Arbeiten haben glücklicherweise dazu beigetragen, dass die Vielfalt und die Biologie dieser Gattung nun endlich besser verstanden werden. Mit dieser Dissertation, in der ich taxonomische, phylogenetische und biogeografische Untersuchungen an philippinischen Taxa durchführte, möchte ich zu diesem langsam wachsenden Wissen beitragen. Die Dissertation ist in fünf Kapitel unterteilt, wobei das erste und das letzte Kapitel eine allgemeine Einleitung bzw. eine Schlussfolgerung enthalten. In Kapitel 2 berichte ich über taxonomische Neuheiten bei den philippinischen Cyrtandra. Zunächst habe ich neue Namen für zwei Homonyme in der philippinischen Flora vorgeschlagen, C. coriaceifolia für C. humilis in Anlehnung an ihre lederartigen Blätter und C. bacanii für C. umbellata zu Ehren des Sammlers des Typusexemplars, E.S. Bacani. Cyrtandra argentii wird als eine neue endemische Art beschrieben und nach G. Argent benannt. Es handelt sich um eine eigenständige endemische Art, die an ihren hängenden, zusammengesetzten, zymösen Blütenständen mit 10-15 Blüten zu erkennen ist. Schließlich wird C. villosissima var. flavovirens als neue Farbvarietät von C. villosissima beschrieben, benannt nach ihren blassgelben bis gelbgrünen Blütenkronen. Für die neuen Taxa werden Diagnosen, Beschreibungen, Bilder, Strichzeichnungen, Schlüssel und vorgeschlagene IUCN-Kategorien bereitgestellt. ZUSAMMENFASSUNG In Kapitel 3 stelle ich eine taxonomische Synopse der philippinischen Cyrtandra (Gesneriaceae) vor. Dies ist nach 100 Jahren die erste Aktualisierung von Merrills Aufzeichnungen der Blütenpflanzen aus dem Jahr 1923. Ich erkenne 98 Cyrtandra-Arten für die philippinische Flora an. Ich bestätige einen Artnamen, der zuvor ohne lateinische Diagnose beschrieben wurde (C. peninsula), synonymisiere drei Namen (C. quisumbingii und C. quisumbingii var. minor werden unter C. hypochrysoides synonymisiert, während C. florulenta unter C. incisa synonymisiert wird), und schlage zwei neue Namen vor (C. edanoi für C. pallida und C. siporensis für C. chiritoides). Taxonomische Anmerkungen folgen jeder Art und jeder korrekten Typisierung, um die Stabilität der Namen zu gewährleisten und die Identifizierung der Arten zu erleichtern. Eine Tabelle erleichtert das Nachschlagen der derzeit akzeptierten Namen der philippinischen Cyrtandra. In Kapitel 4 führe ich phylogenetische und biogeografische Analysen über das gesamte Verbreitungsgebiet von Cyrtandra durch, wobei ich die philippinischen Taxa stärker in die Stichproben einbeziehe, um die bisherigen Sammel-Lücken zu schließen. In der phylogenetischen Analyse zeige ich, dass es bei den südostasiatischen Vertretern wenig geografische Strukturierung gibt, was darauf hindeutet, dass die biogeografischen Linien für Pflanzentaxa sehr durchlässig sind, wie dies auch von anderen gezeigt wurde. In der biogeografischen Analyse prüfte ich, ob die Muster und die Diversifizierungsdynamik von Cyrtandra mit der allgemeinen dynamischen Theorie der ozeanischen Inselbiogeografie (general dynamic theory of oceanic island biogeography, GDT) vereinbar sind. Um dies zu prüfen, führte ich eine datierte phylogenetische Analyse durch, gefolgt von einer BioGeoBeaRS- und einer BAMM-Analyse. Ich zeige, dass ozeanische Inseln, insbesondere Wallacea, wichtige Quellen für die Ausbreitung von Cyrtandra-Linien sind. Die GDT betrachtet ozeanische Inseln hauptsächlich als Senken für sich ausbreitende Linien. Der relativ hohe Beitrag von Wallacea lässt sich auf seine zentrale Lage im Verbreitungsgebiet von Cyrtandra und seine komplexe geologische Geschichte zurückführen, die für eine erhöhte Ausbreitungsfähigkeit sorgt. Ich untersuche weiterhin, ob die Diversifizierungsdynamik von Cyrtandra den Vorhersagen der adaptiven Radiation folgt, die auf ozeanischen Inseln von der GDT als dominanter Prozess vorhergesagt wird. Die Diversifizierungsdynamik von Cyrtandra im südostasiatischen Grade zeigt frühe Schübe in den Diversifizierungsraten, gefolgt von einem Plateau, was mit adaptiver Radiation vereinbar ist. Es werden keine Anzeichen für eine diversitätsabhängige Diversifizierung festgestellt, was darauf zurückzuführen ist, dass die südostasiatischen Cyrtandra-Arten verschiedene Nischen besetzen, was durch ihre große morphologische Bandbreite, insbesondere in Bezug auf Habitus und Blütenmerkmale, deutlich wird. Die Gruppe mit den meisten pazifischen Mitgliedern, die in den frühen Stadien der Ontogenese der pazifischen Inseln auftraten, zeigt eine Diversifizierungsdynamik, die durch das Island Immaturity Speciation Pulse (IISP)-Modell vorhergesagt wurde, und ihr morphologisches Spektrum wird durch den Least-Action-Effekt kontrolliert, der Verholzung und fleischige Früchte begünstigt. In dieser Dissertation gebe ich neue Einblicke in die Systematik von Cyrtandra, indem ich den Schwerpunkt auf die philippinischen Mitglieder lege. Außerdem stelle ich neue Informationen zur Verfügung, die zur Standardisierung eines prädiktiven Klassifizierungssystems für die Gattung beitragen sollen. Darüber hinaus ist dies ein erster Schritt in Richtung eines Rahmens für die Untersuchung der Diversifizierungsdynamik, wie sie von der GDT für sehr erfolgreiche insulare Taxa vorhergesagt wird. / Systematics is the foundational field of biology wherein it aims to describe and understand the diversity of life. Its importance cannot be disregarded since systematics provides us tools to infer relationships among living organisms and we utilize this information to improve our quality of living, protect the environment, understand the past, and simply appreciate the variation and diversity of the natural world. Systematics is composed of three branches, namely taxonomy, phylogenetics, and biogeography. In this dissertation, I explore the systematics of the Philippine members of the largest genus in the family Gesneriaceae, Cyrtandra. Cyrtandra is a genus of almost 800 species of herbs, shrubs, vines, and small trees and it has the widest distributional range in the family Gesneriaceae starting from the Indo-Australian Archipelago extending farther eastwards to the Pacific. Its presence in biodiversity hotspots and its high species number make it an excellent model group for studying biogeography, speciation, diversification, and conservation prioritization. Its utility as a model group, however, is hampered because of the few systematists actively working on the genus. Recent works have fortunately acted as stimuli to finally pick up the pace in understanding the diversity and biology of this genus. I aim to contribute to this slowly increasing knowledge with this dissertation wherein I conduct taxonomic, phylogenetic, and biogeographic research on Philippine members. This dissertation is divided into five chapters and the first and last chapters provide a general introduction and conclusion, respectively. In Chapter 2, I report taxonomic novelties in Philippine Cyrtandra. First, I propose new names to two homonyms in the Philippine flora, C. coriaceifolia for C. humilis in reference to its coriaceous leaves and C. bacanii for C. umbellata to honor the collector of the type specimen, E.S. Bacani. I describe Cyrtandra argentii as a new endemic species and named after G. Argent. This is a distinct endemic recognized by its pendulous compound cymose inflorescences with 10–15 flowers. Lastly, I describe C. villosissima var. flavovirens as a new color variety of C. villosissima named for its pale yellow to yellow-green corollas. I provide diagnoses, descriptions, images, line drawings, keys, and IUCN categories for the novel taxa. In Chapter 3, I present a taxonomic synopsis of Philippine Cyrtandra (Gesneriaceae). This is the first update, after 100 years, of Merrill’s 1923 enumeration of flowering plants. I recognize 98 species of Cyrtandra for the Philippine flora. I validate a species name that was previously described without a Latin diagnosis (C. peninsula), synonymize three names (C. quisumbingii and C. quisumbingii var. minor are in synonymy under C. hypochrysoides while C. florulenta is in synonymy under C. incisa), and propose two new names (C. edanoi for C. pallida, and C. siporensis for C. chiritoides). Taxonomic notes follow every species and correct typification to ensure stability of the names and aid in the identification of species. I also provide a look-up table to facilitate referencing of currently accepted names in Philippine Cyrtandra. In Chapter 4, I perform phylogenetic and biogeographic analyses across the entire distributional range of Cyrtandra with increased sampling of Philippine members to fill-in sampling gaps. In the phylogenetic analysis, I show that there is little geographic structuring in Southeast Asian members indicating that biogeographic lines are highly permeable for plant taxa, as has been shown in others. In the biogeographic analysis, I test whether patterns and diversification dynamics in Cyrtandra are consistent with the general dynamic theory of oceanic island biogeography (GDT) by performing a dated-tree analysis, followed ancestral range estimation via BioGeoBeaRS, and then diversification rate analysis using BAMM. I show that oceanic islands, specifically Wallacea, are important sources of dispersing lineages for Cyrtandra. GDT views oceanic islands mainly as sinks for dispersing lineages. The relatively high contribution of Wallacea is attributed to its central location along the distributional range of Cyrtandra and its complex geological history selecting for increased dispersibility. I show that diversification dynamics in Cyrtandra follow predictions of adaptive radiation, which is the dominant process on oceanic islands as predicted by the GDT. Diversification dynamics of Cyrtandra in the Southeast Asian grade show early bursts in diversification rates followed by a plateau which is consistent with adaptive radiation. No signals of diversity-dependent diversification are detected, and this is attributed to Southeast Asian cyrtandras occupying various niche spaces as evident by its wide morphological range, particularly in habit and floral characters. The clade containing mostly Pacific members, which arrived at the early stages of the ontogeny of the Pacific islands, show diversification dynamics predicted by the Island Immaturity Speciation Pulse (IISP) model and their morphological range is controlled by the least action effect favouring woodiness and fleshy fruits. In this dissertation, I provide novel insights into the systematics of Cyrtandra by putting focus on Philippine members. Also, I provide new information that aims to contribute to the standardization of a predictive classification system for the genus. Additionally, this provides a first step towards a framework for investigating diversification dynamics as predicted by the GDT in highly successful insular taxa.

In a network, the components of a given system are represented as nodes, the interactions are abstracted as links between the nodes. Boolean networks refer to a class of dynamics on networks, in fact it is the simplest possible dynamics where each node has a value 0 or 1. This allows to investigate extensively the dynamics both analytically and by numerical experiments. The present article focuses on the theoretical concept of relevant components and their immediate application in plant biology. References for more in-depth treatment of the mathematical details are also given.