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The main goal of this work is to contribute to the existing knowledge of soil micro-fungi in Panama and Germany. Studies about soil degradation and its influents in the soil fungi diversity have not been investigated as extensively in these countries. This is an extensive and challenging topic to examine since there is an immense phenotypic and genetic diversity in the soil fungal community and relating this community together with factors of soil degradation is an extensive task. For this reason, the present thesis studies the species identified in the study areas, in other words, the soil fungal diversity in relation to environmental factors in the Taunus Mountain range in Frankfurt, Germany, and in the Majagua valley in Chiriquí, Panama. Two complementary objectives were achieved, the first was the development of a theoretical irrigation model for degraded soils. The second was the development of a mobile application to facilitate laboratory work in the cultivation of soil micro-fungi.
The design of the methodology was based on identifying the species and relating the diversity found to soil factors. Soil samples were taken in both countries: the Taunus Mountain range was sampled eight times from January to November 2012 and the Majagua valley was sampled on three occasions between February and July 2012. In both studies, the areas included three different vegetation types (forest, grassland, and bare soil). Samples were separated for two purposes: the assessment of fungal diversity by molecular and morphological methods and soil characterization.
Soil samples used in the methodology of pyrosequencing were related to global climatic factors. Morphological identification was achieved with identification keys. Micro-fungi were cultivated in different media until obtaining pure cultures. Molecular identification was performed by getting the DNA sequences using the ITS1 and ITS4 primers and comparing the sequences with other reference sequences from GenBank. This was done considering the BLAST algorithm, which considered sequences that matched 98 % or more of maximum identity as reliable identifications.
Soil characterization was carried out to measure the soil's Physico-chemical properties; those abiotic factors were compaction, temperature, pH, moisture, and soil composition.
Species richness was calculated in each study area with the estimators Chao, Jackknife, and Bootstrap. Furthermore, the species accumulation curves were performed to observe the species discovery rate and estimate sample completeness. Estimate linear regression models correlated the influence between the soil factors (temperature, moisture, pH, soil compaction, and soil composition) and the species richness. In the same way, an analysis of ecological distance was undertaken based on the similarity in the species composition, compared across samples, and correlated with soil factors, using non-metric multidimensional scaling (NMDs).
Study of abundance showed differences between the bare soil abundances and the forest abundances in Germany and Panama; the grasslands in both countries work as transitional areas in the fungi abundance. The key stone species in Germany were Penicillium daleae, and Pochonia bulbillosa, whereas in Panama were Purpureocillium lilacinum and Trichoderma harzianum. Based on Pareto analysis, a theoretical irrigation model was developed to counteract the degradation effects on the abundance of micro-fungi in the soil.
Applications for mobile devices dealing with the cultivation of soil micro fungi were sought. Due to the small number of existing applications, a new App called Soil-Fungi-Cultures (SFC) was developed to facilitate data collection of cultivated soil micro fungi. App Inventor was the program used to design, program, test, and publish the application developed. The developed application was compared with other applications used in identifying bacteria cultures. The results showed that the new application needed more time to capture the records because it saves more information, the navigation flow was acceptable, the number of clicks was high, but it is due to the usefulness in data capture, and finally, the users rated it as a good application with an eight out of ten rating.
Pyrosequencing resulted in 204 Operational Taxonomic Units (OTUs) considering the two study areas (the Taunus Mountain range and the Majagua valley). The Pyrosequencing database was used to contribute to the most important study of fungal diversity globally based on OTUs, which surpasses any study of molecular and taxonomic diversity previously conducted. The principal result in this study was that the climatic factor is the best predictor of fungal richness and community composition on a global scale. However, the part of the research that focused on the local scale, that is to say, on the correlation patterns between the distribution of fungal species and abiotic factors, showed that the soil properties and degradation levels were not associated with fungal richness, diversity or soil composition in the study areas in Germany or Panama. The above confirms that there are exceptions to the way relationships between soil factors with fungal diversity are established at the local level.
In the case of soil samples used for morphological identification, 71 fungal species were obtained, 47 from Germany, and 32 from Panama.
Hyperparasitic fungi on black mildews (Meliolales, Ascomycota) : hidden diversity in the tropics
(2023)
Meliolales (Sordariomycetes, Ascomycota) is a group of obligate plant parasitic microfungi mainly distributed in the tropics and subtropics. Meliolalean fungi are commonly known as “black mildews”, as they form black, superficial hyphae on the surface of vegetative and reproductive organs of vascular plants. They are considered biotrophic parasites, and the infections caused by black mildews can lead to a decrease in the photosynthetic activity of plants, as well as to an increase in the temperature and respiration rate of their leaves.
Meliolales are frequently parasitized by hyperparasitic fungi, i.e., parasitic fungi that have parasitic hosts. These hyperparasites are all Ascomycota and belong mainly to the Dothideomycetes and Sordariomycetes. Although hyperparasites represent a megadiverse group, species were only described by morphology until 1980, and the systematic position of more than 60 % of known species is still unclear. In addition, there are no DNA reference sequences available in public databases for any of the species of hyperparasites of Meliolales, and no ecological studies have been done up to now.
Before this study, no exact number of hyperparasitic fungi growing on colonies of black mildews existed. Here, we present a checklist including 189 species of fungi known to be hyperparasitic on Meliolales, but the number of existing species is likely to be even higher. The elaboration of this species checklist laid the foundations for this investigation, as it helped to understand the present state of knowledge of hyperparasitic fungi on Meliolales worldwide.
For the present study, fresh specimens of leaves infected with colonies of Meliolales and hyperparasites were opportunistically collected at 32 collection sites in Western Panama and Benin, West Africa, in 2020 and 2022, respectively. In total, 100 samples of plant specimens infected with black mildews were collected, of which 58 samples were parasitized by hyperparasitic fungi. 31 species and morphospecies of hyperparasitic fungi were identified. In addition, 35 historical specimens, including 12 type specimens, were examined for the present work.
DNA of hyperparasitic fungi was isolated directly from conidia, synnemata, apothecia, perithecia or pseudothecia of fresh and dried specimens. The main challenges faced by scientists in doing molecular studies of hyperparasitic fungi are related to the fact that the hyperparasitic fungi are intermingled with tissues of the meliolalean hosts and other organisms present in a given sample. This makes the isolation of DNA exclusively from the hyperparasite difficult. Moreover, hyperparasitic fungi on Meliolales are biotrophs and cannot be grown axenically. The hosts themselves are also biotrophic, further complicating DNA isolation from either partner. These factors have contributed to a lack of reference sequences in public databases. After more than 100 attempts, DNA of 20 specimens of hyperparasitic fungi, representing seven species, has been isolated in the context of the present investigation. Three partial nuclear gene regions were amplified and sequenced: nrLSU, nrSSU and nrITS. The datasets were assembled for phylogenetic analyses applying Maximum Likelihood (ML) and Bayesian inference (BI) methods. DNA sequences of hyperparasitic fungi on Meliolales were generated for the first time in the context of the present investigation.
Hyperparasitic fungi on Meliolales do not represent a single systematic group, but a polyphyletic ecological guild of fungi. Because of this huge diversity, only the systematics of species of perithecioid hyperparasites, as well as of the species of the genera Atractilina and Spiropes known to be hyperparasitic on black mildews was discussed in this thesis, as they represented the most common groups of fungi found in Benin and Panama. The results indicated, for example, the systematic position of Dimerosporiella cephalosporii and Paranectriella minuta in the Sordariomycetes and Dothideomycetes, respectively. In addition, the first record of a hyperparasitic fungus of black mildews in the Lecanoromycetes, namely Calloriopsis herpotricha, is reported here. The systematics of Atractilina parasitica and of some species of Spiropes is also discussed here.
In the context of the present investigation, four species new to science were described. They are presented with detailed descriptions, photos and scientific illustrations. Taxonomic studies of this thesis also generated seven new synonyms, nine new records for Benin, seven for Panama, one for Africa and two for mainland America, as well as the confirmation of one anamorph-teleomorph connection by molecular sequence data.
The ecology of hyperparasitic fungi on Meliolales is complex and far from being completely understood. The hypothesis of host specificity between hyperparasitic fungi, their meliolalean hosts and their plant hosts was tested for the first time, through a tritrophic network analysis. Results indicate that hyperparasites of Meliolales are generalists concerning genera of Meliolales, but apparently specialists at the level of order. In addition, hyperparasitic fungi tend to be found alongside their meliolalean hosts, suggesting a pantropical distribution.
Anthropogenic interventions have altered all ecosystems around the world. One of those ecosystems are forests, the main resource for timber. They have been strongly transformed in their structure with large consequences on forest biodiversity. Especially the decrease in dead-wood volume due to the timber extraction and alternation of natural forest structures with even-aged stands of less diverse tree species composition has put especially saproxylic, i.e., dead-wood dependent species, under threat, which comprise about 20% of all forest species. Beetles, fungi and bacteria are three functional important groups for decomposition processes but we still lack much information about their sampling and the drivers of their diversity, thus it is difficult to comprehensively protect their diversity. Saproxylic fungi are a highly diverse species group and the main drivers of dead-wood decomposition; hence they play a major role in the global carbon cycle. Due to their cryptic lifestyle, many species are still unknown, but the recent advances in environmental DNA barcoding methods (metabarcoding) shed light on the formerly underestimated diversity. Yet, this method's accuracy and suitability in detecting specific species have not been assessed so far, limiting its current usefulness for species conservation. On the other hand, these methods are a convenient tool to study highly diverse areas with high numbers of unknown species, enabling the study of global diversity and its drivers, which are unknown for saproxylic fungi, but important to assess to predict the future impacts of global change. Since nature conservation concepts are usually not applied on a global scale, the drivers of diversity must also be assessed on smaller scales. Besides understanding the drivers of diversity, to identify focus scales to create comprehensive, evidence-based conservation concepts must utilize multi-taxonomic studies since saproxylic species are differently sensitive towards environmental variables and closely interact with each other. Filling these knowledge gaps is utterly needed to protect the high saproxylic diversity and ensure the functional continuity of decomposition processes, especially regarding the global change.
To address the usefulness of metabarcoding for fungal species conservation, I compared the traditional method of fruit body sampling with metabarcoding and their efficiency in detecting threatened fungal species in the first chapter of this thesis. Both methods have advantages and disadvantages. Their ability to detect threatened saproxylic fungal species and their dependencies on detecting specific fungal groups have not been compared, albeit they are important to inform species conservation like Red Lists properly. I found metabarcoding to generally detect more threatened fungal species than fruit body sampling with a higher frequency than fruit body sampling. Moreover, fruit body sampling detected a unique set of species, while fruit body sampling missed large parts of fungal diversity due to species-specific fruiting characteristics. Metabarcoding with high sampling intensity is thus a viable method to assess threatened saproxylic fungal diversity and inform nature conservation like Red Lists about distribution and abundances. Nevertheless, a complementary approach with fruit body sampling is indispensable for assessing all threatened fungal species.
In order to analyse the global diversity of saproxylic fungi and its drivers, I examined whether fungal species richness increases from the poles towards the equator and thus follows the latitudinal diversity gradient already found in many other species groups. I further investigated whether such an increase is caused by increasing ecological specialisation, i.e., niche partitioning, or local tree diversity, i.e., niche space. Gamma diversity per biome increased from the boreal, over the temperate to the tropics and thus confirmed the latitudinal diversity for saproxylic fungi. Contrastingly, alpha diversity at the log level did not significantly increase towards the tropics, suggesting a grain size dependency of the observed pattern and an equal niche space within dead-wood across latitudes. Ecological specialisation on the plot level was globally on a high level but did not increase significantly towards the equator. Additionally, I found local tree species richness to drive plot-based fungal diversity. Further analysis of gamma diversity against the total number of sampled tree species strengthened the assumption that tree species diversity and not increased ecological specialisation was the main driver of the latitudinal diversity gradient, as there was no significant difference between the gamma diversity of the temperate and tropical biome. Nonetheless, as the gamma diversity of the boreal biome was still significantly smaller, my results do not allow a complete neglection of the ecological specialisation hypothesis. The overall results indicate a strong dependency of saproxylic fungi diversity with host tree species diversity and that the global loss of tree species threatens saproxylic fungi with an unpredictable impact on carbon and nutrient cycling.
To support saproxylic conservation, I conducted two analyses. First, I compared the beta diversity of the three main decomposer groups (beetles, fungal fruit bodies, mycelial fungi (metabarcoding), and bacteria (metabarcoding)) across different scales to assess the impact of different environmental variables on their overall diversity. I used an experimental design to disentangle two different spatial scales, influenced by differences in macroclimate, forest microclimate and spatial distance, and two host scales, driven by differences between tree lineages and tree species. I set these beta diversities in relation to the gamma diversity of the three main decomposer groups to identify whether a unified conservation concept could be applied to one scale to optimally protect the diversity of all three species groups. Second, I identified whether diversity and community composition of fungi and bacteria differed among climate and land use gradients. Further I explored whether specialisation and niche packing could explain the expected pattern. To do so I used an experimental design disentangling climate and land use across a large gradient in Germany. The results differed among the species groups, denying a unified conservation concept focusing on one scale. Saproxylic beetle and fruit body beta diversity was equally high on each scale, as they are more sensitive towards environmental factors like macro- and microclimate. On the other hand, mycelial fungi and bacteria beta diversity was highest on the host scale, especially the host tree scale, indicating a high host specificity of the two groups. The second study also identified tree species as the main driver of diversity and community composition of these two study groups. Specialisation of fungi was not influenced by land use or climate. Bacterial specialisation and diversity were under a strong influence of mean precipitation. Comprehensive conservation of multi-taxonomic diversity across regions thus requires the integration of several scales. Within different macroclimatic regions, forests of varying microclimates, i.e., forest management, must be implemented. In these forests, dead-wood of different tree lineages, i.e., angio- and gymnosperms and tree species, must be provided.
Taken together, I could demonstrate that metabarcoding is an efficient method to sample threatened fungal species and identify differing drivers of fungal diversity present as fruit bodies or mycelium. Its usefulness will further increase due to the ongoing improvement of sequencing databases and thus better inform conservation concepts. Using metabarcoding, I could demonstrate that high host specialisation of saproxylic fungi is not a European but a global phenomenon and identify tree species loss under global change as one major concern for saproxylic diversity. My dissertation further highlighted the importance of multi-taxonomic studies for evidence-based nature conservation, as different species groups require varying concepts. These results were especially important for saproxylic bacteria as the drivers of their diversity are still largely unknown. Howbeit, large research gaps still exist regarding the impacts of global change on species and processes. Moreover, the spatial coverage of studies is needed to confirm or neglect the generality of current research especially concerning the highly diverse tropical areas. An increased focus on the drivers of diversity in these areas is crucial to ensure a globally comprehensive saproxylic conservation and the various ecosystem functions they control.
Der Verzehr von radioaktiv belasteten Pilzfruchtkörpern stellt ein Gesundheitsrisiko für den Menschen dar und auch fast 35 Jahre nach der Reaktorkatastrophe von Tschernobyl im Jahr 1986 sind Pilze aus Waldökosystemen zum Teil noch stark durch das ausgetretene radioaktive 137Cs belastet. Die Einschätzung der Belastung und somit des Gesundheitsrisikos ist aufgrund einer Vielzahl von Einflussfaktoren, wie z. B. der Pilzart, der Tiefe des Myzels, der Bodenkontamination und der Feuchtigkeit des Bodens, schwierig. Ziel dieser Arbeit war es die Variabilität, den Einfluss verschiedener Faktoren sowie die effektive Halbwertszeit der 137Cs-Aktivität in Pilzfruchtkörpern zu ermitteln. Des Weiteren wurde überprüft, ob die Bodenkontamination für eine Abschätzung der 137Cs-Aktivität von Pilzfruchtkörpern herangezogen werden kann. Für die Untersuchungen wurden über mehrere Jahre Proben von Maronenröhrlingen (Imleria badia) und Steinpilzen (Boletus edulis) aus vier Waldgebieten in Mittel- und Süddeutschland mit unterschiedlichem Aktivitätseintrag nach der Reaktorkatastrophe von Tschernobyl im Jahr 1986 analysiert. Die Gebiete waren Eichenzell, Wülfersreuth, Oberschönenfeld und der Nationalpark Bayerischer Wald. Als Ergänzung dienten zugesendete Proben derselben Pilzarten von Mitgliedern aus Pilzvereinen aus ganz Deutschland. Zusätzlich zu den Pilzproben wurden Bodenproben gemessen, um zum einen die aktuelle Bodenkontamination zu bestimmen und zum anderen zu überprüfen, ob der Großteil des 137Cs weiterhin im Bereich des Pilzmyzels zu finden ist.
Für die Untersuchung der örtlichen Variabilität der 137Cs-Aktivität wurden Maronenröhrlinge (Imleria badia) aus dem Waldgebiet Eichenzell in den Jahren 2017 bis 2019 analysiert. Innerhalb eines Sammeltages variierten die Messwerte verschiedener Proben innerhalb des Waldgebietes teilweise um den Faktor sechs. Dabei ist die Variabilität innerhalb eines Teilgebietes größer als zwischen beiden Teilgebieten des Waldgebietes Eichenzell. Für ein repräsentatives Ergebnis eines Gebietes ist es aufgrund der Variabilität erforderlich, eine ausreichende Menge an Fruchtkörpern zu analysieren.
Um die effektive Halbwertszeit der 137Cs-Aktivität in Maronenröhrlingen (Imleria badia) zu ermitteln, wurden Proben aus drei Waldgebieten über fünf bis neun Jahre analysiert. Die Wahl der drei Waldgebiete erfolgte anhand des 137Cs-Aktivitätseintrags nach der Reaktorkatastrophe von Tschernobyl im Jahr 1986. Die Bodenkontaminationswerte variieren von 3.000 Bq/m² in Eichenzell über 12.500 Bq/m² in Wülfersreuth bis 35.000 Bq/m² in Oberschönenfeld. Die effektiven Halbwerts-zeiten liegen in einem engen Bereich von 5,2 bis 5,8 Jahre mit einem Mittelwert von 5,4 ± 0,3 Jahren. Damit reduziert sich die radioaktive Belastung der Pilzfruchtkörper in etwa fünfmal schneller als durch die rein physikalische Halbwertszeit des 137Cs von 30,08 Jahren. Durch die Hinzunahme von bereits im Jahr 1990 veröffentlichten Daten ergab sich eine längere effektive Halbwertszeit von 7,7 ± 0,6 Jahren.
Für die Untersuchung der zwei Einflussfaktoren Exposition des Sammelgebiets (Hangausrichtung nach Ost oder West) und Höhenlage wurden sowohl Maronenröhrlinge (Imleria badia) als auch Steinpilze (Boletus edulis) hinsichtlich der 137Cs-Aktivität gemessen, um die Auswirkung auf Pilzarten mit unterschiedlichem Akkumulationsvermögen zu analysieren. Als Untersuchungsgebiet diente der Nationalpark Bayerischer Wald, da dieser ein großes Gebiet umfasst und verschiedene Ausprägungen der beiden Faktoren abbildet. Zudem wurde das Gebiet in Folge der Reaktorkatastrophe von Tschernobyl stark kontaminiert und der Park ist ein beliebtes Pilzsammelgebiet. Anhand der 137Cs-Aktivität von Bodenproben konnte das Gebiet in zwei Regionen (Cluster) eingeteilt werden: eine Region mit hohem und eine mit niedrigem Aktivitätseintrag. Im Vergleich wiesen Maronenröhrlinge (Imleria badia) durchschnittlich eine um den Faktor fünf höhere 137Cs-Aktivität als Steinpilze (Boletus edulis) auf. Der Faktor Höhenlage zeigte im Gegensatz zur Exposition einen Einfluss auf die Kontamination der Pilzfruchtkörper. In Bezug auf die Höhenlage war der Einfluss nur im Falle eines hohen Aktivitätseintrags signifikant, wobei die Pilzproben aus der niedrigsten Höhenlage am höchsten belastet waren.
Zur Ermittlung der vertikalen Verteilung des 137Cs im Boden wurden in den Waldgebieten Eichenzell und Nationalpark Bayerischer Wald Proben bis zu einer Tiefe von 24 cm entnommen und anschließend in 2 cm Schichten analysiert. Alle Verteilungen konnten mit einem Gauß-Fit oder einem multiplen Gauß-Fit mit 2 bis 3 Maxima abgebildet werden. Das erste Maximum lag in allen Fällen in den organischen Horizonten oder im Übergangsbereich zum Ah-Horizont. Folglich befindet sich der Großteil des 137Cs fast 35 Jahre nach der Reaktorkatastrophe von Tschernobyl immer noch im Bereich des Pilzmyzels und kann somit von den Pilzen aufgenommen und in den Fruchtkörpern angereichert werden.
Der Vergleich der 137Cs-Aktivität der Pilz- und Bodenproben aus dem Nationalpark Bayerischer Wald ergab sowohl für Maronenröhrlinge (Imleria badia) als auch für Steinpilze (Boletus edulis) eine positive Korrelation. Nach Unterteilung der Proben anhand der Höhenlage zeigte sich eine noch stärkere Korrelation. Dies zeigt, dass neben der Bodenkontamination auch die Höhenlage einen Einfluss auf die 137Cs-Aktivität der Fruchtkörper hat.
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The division Ascomycota(Fungi) contains a large number of taxa known to reproduce only asexually by the formation of conidia or other non-motile propagules produced by mitotic cellular devisions. They are called anamorphic, mitosporic, asexual or conidial fungi and ecologically, they are often found associated with plant debris in different stages of decay. In general, saprobic anamorphs of ascomycetous affinities are poorly studied and their outstanding diversity is currently underexplored. Phylogenetic relationships are unknown for many of them and they are still largely underrepresented in the current phylogenetic classification system of Fungi, with many morphologically defined anamorphic taxa still awaiting taxonomic reassessment in the light of molecular approaches. The increasing usage of molecular markers combined with robust statistical methods has allowed their phylogenetic affinities to be revealed and to gradually incorporate many of them into the different taxonomic groups of the division Ascomycota. However, the phylogenetic placement and taxonomic status of a large number of saprobic taxa remain unresolved due to the lack of DNA sequence data.
The present dissertation aims to explore the rich but understudied diversity of those anamorphic fungi traditionally known as hyphomycetes that inhabit dead plant debris. It consists of five publications in which a polyphasic approach integrating morphological, developmental, cultural and molecular data was used to incorporate novel or incertae sedis taxa within Ascomycota and to make more sound decisions regarding their taxonomic status. Specific objectives include: 1. the collection, isolation and morphological characterization of selected anamorphic fungi representing putative new or interesting taxa of uncertain phylogenetic placement; 2. the generation of novel DNA sequence data to infer their phylogenetic relationships and to resolve their taxonomic affinities within Ascomycota; 3. the testing of any previously available morphologically based hypotheses on their putative position, generic placement or relationships with teleomorphic, pleomorphic or other anamorphic taxa; and 4. the determination of their generic validity, monophyly and taxonomic boundaries using molecular data and phylogenetic analyses methods.
Materials studied in these five projects consisted of specimens collected during field work carried out by the author or collaborators in different countries including USA, the Czech Republic and Panama between the years 2014 and 2017. The target substrates were dead leaves of different palm trees, dead wood and bark of pines and twigs or stems of unknown shrubs and woody vines that are all known to harbor a rich saprobic mycobiota. Putative novelties or anamorphic taxa with unknown or poorly studied phylogenetic affinities were selected for further morphological and molecular investigation. Micromorphological studies were based on fungal structures observed on natural substrate, herbarium specimens and in culture. DNA was extracted from cultures and PCR amplification followed by Sanger sequencing was carried out using relevant molecular markers employed in fungal phylogenetic studies. Newly obtained DNA sequence data were analyzed following a standard phylogenetic analysis pipeline and phylogenetic relationships were reconstructed using character-based methods such as Maximum Likelihood and Bayesian inference.
Conclusion is that anamorphic Ascomycota inhabiting dead plant debris represents a largely untapped source of biodiversity and information still in need of further exploration. A new capnodiaceous genus Castanedospora, seven new species named Taeniolella sabalicola, Hermatomyces bifurcatus, H. constrictus, H. megasporus, H. sphaericoides, H. verrucosus and Septonema lohmanii, and two new combinations, Castanedospora pachyanthicola and H. reticulatus, are proposed based on morphological and DNA sequence data. Molecular phylogenetics was confirmed as the tool of choice for the inference of relationships in novel or incertae sedis anamorphic fungi that are otherwise difficult to assess in the absence of a teleomorphic state. They were first resolved or revisited for several saprobic species such as Ernakulamia cochinensis, H. sphaericus, H. tucumanensis or Septonema fasciculare in a suitable framework for phylogenetic hypothesis testing. Molecular data allowed to fully incorporate all these taxa in Ascomycota, particularly within the classes Dothideomycetes and Sordariomycetes, and to provide a foundation for better taxonomic decisions on their classification. Large and polyphyletic genera such as Taeniolella, Sporidesmium and Septonema, partially treated in this work and containing mostly saprobic species of obscure affinities, remained in need of further investigation.
Antagonistic and mutualistic species interactions provide important ecosystem functions affecting plant population dynamics and distribution. Many of these functions are important for the regeneration of plants, either by limiting or facilitating successful transition between life stages. Interactions can occur across the whole geographical range of a species and thereby encompass different environmental gradients, such as changes in temperature or water availability. Understanding the joint effects of species interactions and environmental factors on the regeneration of plants is key for understanding plant population dynamics under global change and could provide important recommendations for managing and conservation efforts.
My thesis aimed at advancing the knowledge of how species interactions depend on environmental conditions and jointly affect plant recruitment along the elevational distribution of plants. This thesis includes three chapters in which I studied the effects of animal seed deposition, seed predation, mycorrhizal and pathogenic fungi occurrences as well as abiotic and biotic environmental factors on the recruitment of Swiss stone pine (Pinus cembra). I conducted fieldwork in the Swiss Alps across the entire elevational distribution of the pine (1850 – 2250 m a.s.l). Over a period of three years, I recorded animal seed deposition by spotted nutcrackers (Nucifraga caryocatactes) and conducted seed translocation experiments. Further, I assessed fungal communities using DNA metabarcoding. I measured abiotic environmental factors such as temperature, water and light availability, pH, as well as biotic environmental factors such as distance to conspecific adults and ground vegetation cover. In my thesis, I used a broad range of community ecology approaches, from seed dispersal ecology to experimental plant ecology and microbial ecology.
First, I investigated the effects of environmental factors on four recruitment processes (i.e. seed deposition, seed predation, seed germination, seedling survival) of Swiss stone pine. Further, I aimed at identifying the most important recruitment processes potentially limiting pine regeneration across its elevational range. To investigate pine recruitment, I firstly tested how seed deposition, seed predation, seed germination and seedling survival were affected by the microhabitat characteristics ultimately determining where a seed arrives in the environment (i.e. canopy cover & ground vegetation cover). Secondly, I applied a sensitivity analysis to investigate which of the four recruitment processes poses limitation to the pines’ regeneration across its range. My results reveal that the importance of particular recruitment processes varies along the pines’ elevational range. I found that at the lower range margin and the distribution centre seed germination and seedling survival were the main limiting factors, whereas animal-mediated seed dispersal became especially important at the upper range margin. My study contributes to the field with a new approach for disentangling the relative importance of recruitment processes across environmental gradients and thereby could help to project how plant recruitment might respond to future changes in environmental conditions.
The second aim of my study was to investigate how abiotic and biotic environmental factors affect the occurrence of Swiss stone pine-associated pathogenic and mutualistic fungi by combining field measurements of environmental factors with a DNA metabarcoding approach. I identified potentially important fungal interaction partners of the pine and determined drivers shaping their occurrences. My results reveal that generalist fungi were not affected by abiotic and biotic environmental factors. However, specialist pathogens showed patterns according to the Janzen-Connell framework (i.e. accumulation of pathogen close to adult plants). Interestingly, I found evidence for an “inverse” Janzen-Connell effect, i.e. high abundance of a specialist mutualist close to adult plants, potentially mitigating effects of soil pathogens close to parent trees. Further, I found that pine-associated fungi are distributed widely within and beyond the range of their host plant, adding knowledge on how mutualisms and antagonisms might be affected when plants move their distributional range upwards.
Finally, I investigated how known and unknown plant-associated fungi affect the regeneration of Swiss stone pine in an environmental context. My results suggest that seedling establishment was most strongly affected by abiotic environmental factors, such as light availability and maximum summer temperature. Further, the results indicate that seedling survival was affected by biotic environmental factors, i.e. fungal agents, with high abundances of a known fungal pathogen co-occurring with low seedling survival rates. My results also reveal that known mycorrhizal partners as well as a large number of unknown fungal operational taxonomic units (OTUs) were associated with the survival of seedlings. My findings highlight the importance of plant-fungal interactions for plant recruitment and offer a feasible approach for the identification of hidden plant-fungal associations in highly complex DNA metabarcoding datasets. This approach offers a valuable tool for investigating plant-microbe interactions, ultimately helping to understand plant population dynamics.
My dissertation adds to a deeper understanding on the linkage between plant regeneration and species interactions, especially on how plant-animal and plant-fungal interactions in concert with environmental factors shape plant recruitment. My study reveals the importance of animal-mediated seed dispersal and fungal pathogens in plant recruitment with consequences for potential range shifts of plant species. My thesis has important implications for conservation and management efforts by informing on key species interactions under environmental change.
The fungal interaction with plants is a 400 million years old phenomenon, which presumably assisted in the plants’ establishment on land. In a natural ecosystem, all plant-ranging from large trees to sea-grasses-are colonized by fungal endophytes, which can be detected inter- and intracellularly within the tissues of apparently healthy plants, without causing obvious negative effects on their host. These ubiquitous and diverse microorganisms are likely playing important roles in plant fitness and development. However, the knowledge on the ecological functions of fungal root endophytes is scarce. Among possible functions of endophytes, they are implicated in mutualisms with plants, which may increase plant resistance to biotic stressors like herbivores and pathogens, and/or to abiotic factors like soil salinity and drought. Also, endophytes are fascinating microorganisms in regard to their high potential to produce a great spectrum of secondary metabolites with expected ecological functions. However, evidences suggest that the interactions between host plants and endophytes are not static and endophytes express different symbiotic lifestyles ranging from mutualism to parasitism, which makes difficult to predict the ecological roles of these cryptic microorganisms. To reveal the ecological function of fungal root endophytes, this doctoral thesis aims at assessing fungal root endophytes interactions with different plants and their effects on plant fitness, based on their phylogeny, traits, and competition potential in settings encompassing different abiotic contexts. To understand the cryptic implication of nonmycorrhizal endophytes in ecosystem processes, we isolated a diverse spectrum of fungal endophytes from roots of several plant species growing in different natural contexts and tested their effects on different model plants under axenic laboratory conditions. Additionally,we aimed at investigating the effect of abiotic and biotic variables on the outcome of interactions between fungal root endophytes and plants.
In summary, the morphological and physiological traits of 128 fungal endophyte strains within ten fungal orders were studied and artificial experimental systems were used to reproduce their interactions with three plant species under laboratory conditions. Under defined axenic conditions, most endophytes behaved as weak parasites, but their performance varied across plant species and fungal taxa. The variation in the interactions was partly explained by convergent fungal traits that separate groups of endophytes with potentially different niche preferences. According to my findings, I predict that the functional complementarity of strains is essential in structuring natural root endophytic communities. Additionally, the responses of plant-endophyte interactions to different abiotic factors, namely nutrient availability, light intensity, and substrate’s pH, indicate that the outcome of plant-fungus relationships may be robust to changes in the abiotic environment. The assessment of the responses of plant endophyte interactions to biotic context, as combinations of selected dominant root fungal endophytes with different degrees of trait similarity and shared evolutionary history, indicates that frequently coexisting root-colonizing fungi may avoid competition in inter-specific interactions by occupying specific niches, and that their interactions likely define the structure of root-associated fungal communities and influence the microbiome impacts on plant fitness.
In conclusion, my findings suggest that dominant fungal lineages display different ecological preferences and complementary sets of functional traits, with different niche preferences within root tissues to avoid competition. Also, their diverse effects on plant fitness is likely host-isolate dependent and robust to changes in the abiotic environment when these encompass the tolerance range of either symbiont.
Gallery forests (GFs) are floristically and functionally distinct forests along rivers and watercourses. The GFs of the West African savannas form thin stripes with a particular, species-rich flora differing significantly from the surrounding vegetation. Due to their relative isolation in the savannas and their dependence on rivers, GFs are particularly endangered by the expected global climate changes in the 21st century. Despite their high diversity, little is known about the ecology and biogeography of GFs in West Africa. Especially, their response to climate changes and their vegetation dynamics remain largely unknown. This thesis combines floristic, phylo-geographic and ecological data to investigate the biodiversity, historical and recent biogeography and conservation status of GF species in Burkina Faso (BFA) as a model for West Africa.
Ein Ziel dieser Arbeit war die Entwicklung und biologische Evaluierung einer Sensorik zur Verbesserung der Prognose des Apfelschorfs. Als Grundlage für die Schorfprognose dient nach dem Modell von Mills die Länge der Blattnässedauer in Abhängigkeit von der Lufttemperatur. Es wurden mehrjährige Vergleiche verschiedener käuflicher Blattnässesensoren durchgeführt und in Zusammenarbeit mit der Firma THIES Clima ein Sensor für Wasserbenetzung entwickelt. Der Vergleich der käuflichen Sensoren zeigte deutliche Unterschiede in der Anzeige der Nässedauer zwischen den verschiedenen getesteten Sensoren. Die Eignung dieser Sensoren für die Prognose war sehr verschieden. Der im Rahmen des Verbundprojektes entwickelte Sensor ist zuverlässig, wetterfest, korrosionsbeständig und wartungsarm. Die einzelnen Prototypen wurden nach der Evaluierung in der Klimakammer im Freiland getestet und die Einstellungen anhand von Bioassays auf ihre Eignung zur Prognose überprüft. Der marktreife Prototyp kann ohne weitere Modellierung zur Erfassung der Blattnässe von Apfelblättern in die Prognose eingebunden werden.
Ein weiteres Ziel der vorliegenden Arbeit war es, die Zusammenhänge der diurnalen Rhythmik der Sporenausschleuderung von Venturia inaequalis zu untersuchen. Im Freiland wurden die Ascosporenflüge unter natürlichen Bedingungen und mit Störlicht registriert. Im Labor wurde der Sporenausstoß unter dem Einfluss der Beleuchtungsstärke und Wellenlängen-Zusammensetzung untersucht. Sowohl im Freiland als auch im Labor konnte eine Aufhebung der Dunkelhemmung des Sporenausstoßes erreicht werden. Der sichtbare Anteil des Lichts konnte auch bei Helligkeiten von über 10000 Lux als Auslöser des Sporenausstoßes ausgeschlossen werden. Durch die Bestrahlung der Pseudothecien tragenden Blätter mit nicht sichtbaren infraroten Lichtanteilen wurde eine Freisetzung der Ascosporen auch im Dunkeln erreicht und die diurnale Rhythmik der Sporenausschleuderung im Freiland wurde aufgelöst.
Fungi are an important component of every ecosystem but hardly considered in biodiversity monitoring projects. This thesis aims at characterizing fungal diversity, with an emphasis on epigeous fungi, encompassing different biogeographic zones and points in time. A main sampling area was established in the Taunus mountain range in Germany, which was sampled monthly over three years.
For testing species richness on spatial scale, the Taunus transect was compared with four other areas, which were assessed with lower sampling effort. One of these areas was Bulau in Germany, in which four excursions were made. Furthermore, two sampling events were performed in Somiedo in Spain and one sampling event in Kleinwalsertal in Austria. Already existing data of a two-year monitoring project in Panama next to the river Majagua were additionally used for comparison.
All these areas were investigated with a standardized sampling protocol focusing on macroscopically evident fungi and vascular plants using a time-restricted transect design. The transects consisted of strips, which were 500 m long and about 20 m broad, and were sampled for 2 hours at each single sampling event....