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Stoffflüsse in Makrophytensystemen: Ein Vergleich zwischen Küstenlagunen der südlichen Ostsee
(2017)
In früheren Jahrzehnten verschlechterte sich der ökologischen Zustand von zahlreichen inneren Küstengewässern der Ostsee durch die Eutrophierung, was z. B. zu intensiven Algenblüten führte. Submerse Makrophyten können den ökologischen Zustand von Süßgewässern verbessern, denn sie unterstützen z. B. die Sedimentation von suspendiertem Material und verringern die Resuspension. Zudem reduzieren sie indirekt das Phytoplankton, weil sie Zooplankton einen Prädationsschutz bieten und somit die Beweidung des Phytoplanktons durch das Zooplankton fördern. Es ist möglich, dass diese Rückkopplungsmechanismen in Brackgewässern weniger effektiv sind. Das Zooplankton ist anders zusammengesetzt und beweidet dadurch weniger effektiv das Phytoplankton. Außerdem wird es selbst, innerhalb der Makrophyten, durch bestimmte Fische und Invertebraten gefressen. In der vorliegenden Arbeit, wurden die Interaktionen zwischen submersen Makrophyten und ihrer abiotischen und biotischen Umgebung in zwei verschiedenen Küstengewässern der südlichen Ostsee untersucht: Vitter Bodden (mesotroph, Makrophyten-dominiert) und Darß-Zingster Boddenkette (DZBK, eutroph bis stark eutroph, Phytoplankton-dominiert). Die folgenden Parameter wurden von Juni bis September 2013 (Vitter Bodden) und von März bis November 2014 (DZBK) gemessen: Lichtattenuation, Konzentration von Gesamt-suspendiertem Material (TSM), von Chlorophyll a (Chl a), von Gesamt-Phosphor (TP) und von Gesamt-Stickstoff (TN). Zudem wurden die Verhältnisse TP zu TN und Chl a zu TP bestimmt. Der Beweidungsdruck des Zooplanktons auf das Phytoplankton wurde sowohl für den Tag als auch für die Nacht berechnet, in dem das jeweilige Zooplankton ausgezählt, die Biomasse und die Beweidungsrate berechnet wurde. Im Vitter Bodden wurde die Zusammensetzung der Makrophyten bestimmt, sowie ihr Bedeckungsgrad und ihr Anteil an der Wassersäule (PVI) in einer Wassertiefe <1 m geschätzt. In der DZBK wurde die Biomasse der Makrophyten bis in eine Wassertiefe von 1,9 m bestimmt. Die Tiefenverbreitung der Makrophyten war im Vitter Bodden nicht Licht-limitiert, aber in der DZBK, da sich dort der Hauptanteil der Makrophytenbiomasse nur bis in eine Wassertiefe von 1 m befand. In der DZBK hatte das Phytoplankton einen großen Anteil an der Lichtattenuation und limitierte dadurch vermutlich die Lichtverfügbarkeit nicht nur für die Makrophyten sondern auch für sich selbst. Aufgrund der TN zu TP Verhältnisse war das Phytoplankton in der DZBK P-limitiert, während es im Vitter Bodden durch beide Nährstoffe gleichzeitig limitiert war. Die Beweidung durch das Zooplankton konnte zeitweise vermutlich das Phytoplankton im Vitter Bodden reduzieren, aber nicht in der DZBK. Der Bedeckungsgrad der Makrophyten war hoch, aber sie hatten eine flache Wachstumsform und daher nur einen geringen PVI. Zusammenfassend kann gesagt werden, dass der vermutlich hohe Wasseraustausch mit der Ostsee und der fehlende Eintrag aus Fließgewässern verantwortlich für die hohe Lichtverfügbarkeit im Vitter Bodden sind. Ein möglicher Einfluss der Makrophyten auf Wassertrübung, Nährstoffe, Phytoplankton und Zooplankton wurde vermutlich durch diesen Wasseraustausch maskiert. Im Gegensatz dazu gab es keine Effekte der Makrophyten auf Nährstoffe in der Wassersäule, sowie auf Phytoplankton und Zooplankton in der DZBK, da die Makrophyten nur auf die Randbereiche der Bodden beschränkt sind. Da Sedimentation und Resuspension hauptsächlich die Wassertrübung beeinflussen, wurde in einem weiteren Teil der vorliegenden Arbeit ermittelt, in wie weit Wind-induzierte Wellen die Sedimentationsraten beeinflussen, wenn sie unmittelbar sedimentiertes Material wieder resuspendieren. Zu diesem Zweck wurden zwei verschiedene Sedimentationsfallen verwendet: Zylinderfallen (ZF) und Tellerfallen (TF). Die TF wurden in dieser Studie das erste Mal an einem Wellen-exponiertem Standort verwendet. Sie erlaubten, dass unmittelbar sedimentiertes Material wieder resuspendiert werden konnte, was die ZF nicht konnten. Sedimentationsraten wurden mit beiden Fallentypen in einer Wassertiefe zwischen 0,9 m und 1,6 m bestimmt. Die Wellenexposition wurde berechnet, indem die halbe Oberflächenwellenlänge (λ/2) durch die Wassersäule oberhalb der Fallen (dF) dividiert wurde. Eine hohe Wellenexposition war definiert als (λ/2) / dF >1. Die Sedimentationsraten in beiden Fallentypen waren von der Wellenexposition beeinflusst. Jedoch in gegensätzlicher Weise. Bei hoher Wellenexposition sedimentierte ein geringerer Anteil des TSM pro Stunde auf den TF als bei geringer Wellenexposition, während in den ZF ein größerer Anteil sedimentierte. Daher wurde die Sedimentationsrate bei hoher Wellenexposition mit den ZF überbestimmt. Die verwendeten TF sind ein viel versprechendes Mittel um Sedimentationsraten in flachen, Wellen-exponierten Orten abzuschätzen, denn sie reflektieren den unmittelbaren Einfluss von Wellenbewegungen auf die Sedimentation von suspendiertem Material.
Leaf-inhabiting fungi are a hyperdiverse group of microbiota found in all terrestrial habitats. Comparative studies targeting the drivers of endophytic fungal biodiversity are rare and identified multiple effectors, such as plant chemistry, climate and seasonal attributes. Our project aimed to study the pattern of the leaf-associated mycobiome of European beech (Fagus sylvatica) at altitudinally distinct sites to reveal diversity, composition and seasonal dynamics of fungal endophytes by a combination of metabarcoding, cultivation and subsequent ecological analyses. This thesis also intended to study the fungal relationship with biotic and abiotic factors: elevation, local site conditions, leaf biochemistry and leaf status. Metabarcoding and cultivation were applied for same leaf samples to trace both environmental drivers and method-dependent signals of the detected fungi. An experimental field site consisting of 100 (2-years old beech) trees was established called ‘beech phytometer’ system at two altitudes (517 and 975 m a.s.l.) in a German mountain forest. Beech trees were randomly selected from both sites as well as from neighboring beech trees. Ten trees from each site were chosen and 10 leaves per tree were sampled. Climatic and leaf biochemistry (Chlorophyll, flavonoid and nitrogen) data were seasonally (Autumn, Spring and Summer) investigated for two continuous years (Oct 2013 to Oct 2015) at these two elevations. In the first year (autumn, 2013) of the project (chapter 3.1), the leaf-inhabiting fungi of natural beech trees were investigated by using high-throughput sequencing (metabarcoding) at three altitudinally distinct sites (with timberline at 1381 m a.s.l.) in the German Alps. This paper focuses on a detailed description and evaluation of metabarcoding amplicon library preparation and a subsequent analytical workflow. Fungal diversity and community composition were compared as a function of different elevated sites and leaf status (i.e., vital or senescent). However, three investigation sites resulted in 969 OTUs (operational taxonomic units) from 820441 sequences. Taxonomic compositions (order) of beech fungi differed strongly among the three sites but were less distinct between the vital and the senescence leaves. Fungal community composition at valley site clearly differed from those of mountain and timberline where differences between mountain and timberline were less prominent. Vital and senescence leaf differed in fungal community structures indicating a strong dynamics of leaf fungi in autumn. Elevation and leaf status were found to be the main explaining factors, which affected the fungal richness and compositions. Another survey (Chapter 3.2) was conducted just after the establishment of the ‘beech phytometer’ trees in the same period (autumn 2013) where leaf mycobiome of the phytometer trees (trees originally came from Northern Germany and grown in nursery) were compared with the fungi of surrounding natural beech habitat at valley (517 m a.s.l.) and mountain site (975 m a.s.l.) in the same location “Untersberg”. Fungal diversity was lowest in the managed habitat in the nursery and was highest in natural habitat. Fungal diversity and compositions significantly associated the origin of the trees. Under natural conditions, the fungi were more diverse at lower altitudes than at higher altitudes. Additionally, leaf chlorophyll and flavonoid contents showed negative correlations with fungal richness in natural stands. In the second year (autumn 2014), another survey (chapter 3.3) was conducted on leaf endophytes of phytometer trees with metabarcoding and cultivation approaches to trace the environmental drivers and method-dependent indications. Metabarcoding resulted in 597 OTUs from 170480 curated ITS1 reads and cultivation revealed 70 OTUs from 438 culture-based Sanger sequences. Both approaches resulted in non-overlapping community compositions and pronounced differences in taxonomic classification and trophic stages. However, both methods revealed similar correlations of the fungal communities with local environmental conditions. Our results indicate undisputable advantages of metabarcoding over cultivation in terms of representation of the major functional guilds, rare taxa and diversity signals of leaf-inhabiting fungi. This stressed out the importance of cultivation for complementing sequence databases with good quality reference data and encouraged the use of both approaches in future microbial biodiversity assessment studies. Phytometer and natural trees were intensively investigated in this study (chapter 3.4) to assess the influence of site characteristics (altitudes, local microclimate), seasonality, leaf biochemistry and leaf age on fungal diversity and composition. In total, our analytical Illumina workflow resulted in 15703599 demultiplexed and ITS1 reads from 165 samples. Clustering at 97% similarity resulted in 1199 OTUs. Climatic parameters were significantly differed between valley and mountain on daily basis but were insignificantly differed on monthly basis. The compositional difference between phytometer and natural mycobiome was significant for combined data as well as for the seasonal data (Oct 2013-Oct 2014). We observed a strong seasonal turnover in phyllosphere fungi in both habitats over the two years of investigation, suggesting that the plant-fungal system not only responds to cyclic climatic conditions but depends as well on various parameters, e.g., geographic position, substrates age and surrounding vegetation. A side (chapter 3.5) study was done to see the connection between the foliar endophytes and foliar phenolic compounds of European aspen (Populus tremula) in the presence and absence of specialist beetles (Chrysomela tremula). A distinct pattern of the leaf endophytes was found to be associated with aspen genotype and chemotype, but this specificity disappeared in the presence of herbivorous beetles. This suggested that leaf endophytes responded to the herbivory in aspen. In general, the altitudinal difference is the most important explaining factor for fungal community differences, which shapes many dependent abiotic and biotic habitat factors. Regarding cost and time per sequence, metabarcoding is superior to cultivation approaches and offers surprisingly profound insights by yielding much more data, allowing to test at once multiple hypotheses in fungal ecology.
Forests are and have been of major importance to cover a variety of societal needs. Today the demands on forests are ever increasing with sequestering carbon and balancing the climate, to name only a few. To cover those requirements forests need vital, productive, and sustainable. A difficult concept as such as the understanding of a healthy forest varies greatly. Nevertheless, forests still have to produce a sufficient amount of yield while threatened by changing climate conditions. These are predicted to bring extended and more intense drought periods as well as a higher frequency of storms and the promotion of secondary disturbances like insects calamities to also rise. In this complex situation of high and versatile demand the focus is on the allocation of the “right” forest. Forest management is requested to balance the needs of humans against those of wildlife against those of the trees themselves. To gain the respective knowledge on species responses and provenance growth, now and in the future research gaps need to be closed. All factors influencing tree growth and therefore ultimately yield need to be understood and special focus needs to be on the interactions within the forest ecosystem. One of the parameters in understanding aggregated tree growth is the dynamic of growth. This can be visualised by dendroecological methods, providing a picture of growth within the individual years. Growth dynamics are dependent on multiple factors, some, like soil being preconditioning and other like climate causing short-term responses. In this thesis I focus on the influence of climate on annual tree growth using a new approach of daily climate data to calculate climate-growth correlations. This method has the advantage of representing tree processes better than the former approach of using monthly means. Furthermore the program enables the user to feed climate scenarios and therefore estimate future growth. To gather information on species as well as provenance differences to provide advice to foresters I used different trials in Britain and Germany. On the British site different oak species were planted while the German sites are stocked with various spruce provenances. For the latter we additionally used stable carbon isotope analysis to calculate intrinsic water use efficiency. The climate-growth correlations revealed differences between the oak species with a generally higher linkage to precipitation than temperature. While the differences are clear, the question of thresholds and the role of extreme events became apparent in this work. VII Abstract Assessing the impact of extreme events using dendrometer data revealed little differences in the response to short term events of the three investigated species, oak, beech, and pine. We were able to pick up stimulus-response-relationships and as a novel result no species-specific responses were found when focusing on such a small time frame. The provenance trials offered the opportunity to investigate the potential of the use of daily climate data more closely. The two contrasting sites planted with six spruce provenances each gave an insight on the adaptive potential of provenances as well as an indication on the response times. Depending on the proceeding environmental and the local climate conditions decisions have to be made on the species or provenance selection. This thesis provides a method as well as insight on the behaviour of the important European species beech, oak, pine, and spruce. It, however, highlights the limitations such methods have for large scale estimates. While general trends on the response to specific soil factors can be used, the climatic responses, be it thresholds or climate-growth correlations can only be seen within the ecological context of their sampling region.
Whether mice are an appropriate model for S. aureus infection and vaccination studies is a matter of debate, because they are not considered as natural hosts of S. aureus. We previously identified a mouse-adapted S. aureus strain, which caused infections in laboratory mice. This raised the question whether laboratory mice are commonly colonized with S. aureus and whether this might impact on infection experiments. Publicly available health reports from commercial vendors revealed that S. aureus colonization is rather frequent, with rates as high as 21% among specific-pathogen-free mice. In animal facilities, S. aureus was readily transmitted from parents to offspring, which became persistently colonized. Among 99 murine S. aureus isolates from Charles River Laboratories half belonged to the lineage CC88 (54.5%), followed by CC15, CC5, CC188, and CC8. A comparison of human and murine S. aureus isolates revealed features of host adaptation. In detail, murine strains lacked hlb-converting phages and superantigen-encoding mobile genetic elements, and were frequently ampicillin-sensitive. Moreover, murine CC88 isolates coagulated mouse plasma faster than human CC88 isolates. Importantly, S. aureus colonization clearly primed the murine immune system, inducing a systemic IgG response specific for numerous S. aureus proteins, including several vaccine candidates. Phospholipase C emerged as a promising test antigen for monitoring S. aureus colonization in laboratory mice. In conclusion, laboratory mice are natural hosts of S. aureus and therefore, could provide better infection models than previously assumed. Pre-exposure to the bacteria is a possible confounder in S. aureus infection and vaccination studies and should be monitored.
Water Consumption of Agriculture and Natural Ecosystems along the Ili River in China and Kazakhstan
(2017)
Zusammenfassung
Der Iran besitzt zwölf UNESCO-Biosphärenreservate, die reich an einmaligen Natur- und Kulturschätzen und hohem menschlichen Potenzial aus verschiedenen ethnischen Gruppen sind. Die ersten neun Biosphärenreservate wurden frühzeitig mit den ersten Biosphärenreser-vaten der Welt im Jahr 1976 gegründet, die auch gleichzeitig andere Kategorien der Schutz-gebiete im Iran wie Nationalparks, geschützte Lebensräume für Wildtiere und Naturschutzge-biete beinhalten und bis heute unter ihrem alten Status verwaltet werden. Damit entsprechen sie nicht den aktuellen internationalen Anforderungen an Biosphärenreservate und besteht die Gefahr, dass diese Gebiete in baldiger Zukunft ihre natürlichen und kulturellen Werte verlie-ren und irreversibel beschädigt werden.
Diese Studie untersucht und bewertet die zwei exemplarisch ausgewählten iranischen Bio-sphärenreservate Golestan und Dena unter Berücksichtigung der UNESCO-Kriterien, unter anderem die Ziele und Grundlagen der Sevilla-Strategie und der Internationalen Leitlinien für das Weltnetz der Biosphärenreservate (1995). Das Biosphärenreservat Golestan wurde im Jahr 1976 gegründet und ist somit eines der ältesten Biosphärenreservate des Irans. Bei dem im Jahre 2010 gegründeten Biosphärenreservat Dena, handelt es sich um das jüngste Biosphä-renreservat im Iran zu Beginn der Studie.
Beide Schutzgebiete sind gebirgig und beinhalten die wichtigsten Waldökosysteme mit einer großen Biodiversität. Das Biosphärenreservat Golestan befindet sich im Nordosten des Irans im östlichsten Teil des Elburs-Gebirge und Dena liegt im zentralen Zagros-Gebirge im Westiran.
Für den methodischen Ansatz dieser Studie wurde ein Methodenmix aus qualitativen Elemen-ten: Oral History, Interviews, offenen Fragen und Teilnehmender Beobachtung und quantita-tiven Elementen: SWOT-Analyse (engl. Akronym für Strengths (Stärken), Weaknesses (Schwächen), Opportunities (Chancen) und Threats (Bedrohungen) und Auswertung der Fra-gebögen mit Hilfe des statistischen Programms SPSS20 angewendet.
Die untersuchten Gruppen bestanden gemäß der jeweiligen Analyse aus Experten des De-partments für Umwelt (DoE) in Teheran, den Provinz-Umweltschutzbehörden von Golestan und Kohgiluye und Boyer Ahmad, Akademikern, der Nationale Commission for UNESCO in Teheran, Zeitzeugen, lokaler Bevölkerung, Rangern, Umwelt-NGOs (engl. Non-Governmental Organization), dem Tourismus-Sektor und den Umwelt-Medien.
Die Ergebnisse in dieser Studie zeigen, dass die Entwicklung der iranischen Biosphärenreser-vate seit ihrer Gründung 1976 bis heute von den Veränderungen der wirtschaftlichen, politi-schen und gesellschaftlichen Situation des Irans und demzufolge von den Veränderungen in der Organisationsstruktur des Departemants für Umwelt (DoE) und der Prioritätensetzung in Bezug auf die Gesetze zu Umwelt- und Naturschutz beeinflusst wurden.
Überdies stellen die Ergebnisse dar, dass in den beiden untersuchten Biosphärenreservaten Golestan und Dena hinsichtlich der internationalen UNESCO-Kriterien und Richtlinien ver-gleichsweise ähnliche Defizite und Mängel bestehen:
• fehlende nationale Rechtsstruktur für die Biosphärenreservate im Iran,
• fehlender Managementplan für Biosphärenreservate und somit auch schwaches Mana-gementsystem der Biosphärenreservate,
• Mangel an Kenntnissen über Biosphärenreservate,
• beschränkte Beteiligung an den Angelegenheiten der Biosphärenreservate seitens aller untersuchten Gruppen – von der lokalen Bevölkerung bis hin zu den staatlichen Ent-scheidungsträgern und
• ungenügende Zusammenarbeit zwischen Staat und Interessengruppen in diesen Gebie-ten.
Ebenso wurde in dieser Studie versucht, konkrete Lösungsansätze zur Verwirklichung der Ziele der Biosphärenreservate bzw. der Verbesserung ihrer aktuellen Situation zu empfehlen.
In diesem Zusammenhang ist es erforderlich, dass Gesetze für die Biosphärenreservate auf nationaler Ebene definiert und die vorhandenen Biosphärenreservate im Iran gründlich nach internationalen Kriterien untersucht und mit einem systematischen Managementplan auf wis-senschaftlicher Grundlage verwaltet werden. Des Weiteren benötigen diese Gebiete für ihre Funktionalität eine Erhöhung und Verbesserung der Kenntnisse über die Biosphärenreservate der aktiven Personen, sowie der Kooperation und Kommunikation zwischen allen zuständigen Behörden und Interessengruppen. Hiermit soll allen sozialen, kulturellen, geistigen und wirt-schaftlichen Anliegen der Interessengruppen, vor allem aber der lokalen Bevölkerung, Rech-nung getragen werden, entsprechend dem weltweiten Ansatz der UNESCO-Biosphärenreservate.
The rapid anthropogenic climate change that is projected for the 21st century is predicted to have severe impacts on ecosystems and on the provision of ecosystem services. With respect to the longevity of trees, forestry in particular has to adapt now to future climate change. This requires profound multidisciplinary knowledge on the direct and indirect climate sensitivity of forest ecosystems on various spatial scales. Predictions on growth declines due to increasing drought exposition during climate change are widely recognized for European beech (Fagus sylvatica L.), which is the major forest tree in European temperate deciduous forests. However, research from other continents or other biomes has shown that winter climate change may also affect forest growth dynamics due to declining snow cover and increased soil cooling. So far, this winter cold sensitivity is largely unexplored in Europe. Thus, particularly focussing on forest growth dynamics and winter cold sensitivity, the goal of this PhD-project was to explore how climate sensitivity of forest ecosystems differs regionally. By doing so, the project aimed to deliver insights about possibilities and limits of upscaling regional knowledge to a global understanding of climate sensitivity. To achieve these goals, this PhD-project integrated five studies (Manuscripts 1–5) that investigated the climate sensitivity of biogeochemical cycles, plant species composition in forests, and forest growth dynamics across spatial scales. In particular, a large-scale gradient-design field experiment simulated the influence of winter climate change on forest ecosystems by snow cover and soil temperature manipulations (Manuscript 1). This study indicated that soil cooling and decreased root nutrient uptake may indirectly reduce growth of adult forest trees. Moreover, this study indicated uniform ecological sensitivity to soil temperature changes across sites along a large winter temperature gradient (ΔT = 4 K across 500 km), irrespective of the site-specific history of snow cover conditions, which motivates upscaling from local winter climate change studies to the regional scale. Although regional climate drives growth of adult forest trees, local factors, such as site-specific edaphic conditions, might control plants in the forest understory. This assumption was tested by mapping the forest understory composition along the same winter temperature gradient as introduced above (Manuscript 2). Across sites, this study found that edaphic conditions explained the spatial turnover in the forest understory composition more than climate, which might moderate direct climate change impacts on the forest understory composition. However, edaphic conditions, forest structure, and climate are linked by triangular interactions. Thus, climate change might still indirectly affect the forest vegetation dynamics. Moreover, a dendroecological study focussed on the same winter temperature gradient from central to cold-marginal beech populations as above in order to identify gradual changes in summer drought and winter cold sensitivity in tree growth (Manuscript 3). Towards the cold distribution margin, the influence of drought on tree growth gradually decreased, while growth reductions were increasingly related to winter cold due to harsher winter climate. By a large-scale dendroecological network study assessed the relationship of growth dynamics to climate and reproductive effort in beech forests across Europe (Manuscript 4). Indeed, this study found the general pattern across the distribution range of beech that high temperature controlled growth indirectly via resource allocation to reproduction. However, the strong, direct drought signal that could be generally detected from dry-marginal to central populations vanished towards the cold-marginal populations, where the more focussed study of Manuscript 3 identified a stronger relationship of tree growth to winter cold. Further extending the scope of this PhD-thesis to global scales, litter decomposition rates were assessed across biomes (Manuscript 5). This study found a robust relationship between climate and decomposition rates, but it also demonstrated large within-biome variability on a local scale. These local scale differences might depend on habitat conditions that, in turn, could be modulated by climate change, which calls for a better exploration of indirect climate sensitivity. In conclusion, this PhD-thesis highlighted that multidisciplinary research can advance the understanding of ecological interactions in forest ecosystems under changing climate scenarios. In this PhD-project, a winter climate change experiment, where site-representative target trees were selected by means of dendroecology, contributed to a mechanistic understanding of winter cold sensitivity in forest growth dynamics. Dendroecological investigations then put the findings in a broader temporal and spatial context by describing local climate sensitivity of tree growth on different spatial scales. This thesis further shows that global generalizations about the relationship of climate and ecological processes in ecosystem models have to be critically reviewed for the need of local and regional adjustment because these processes might experience considerable regional- or local-scale variation. However, this thesis reports uniform sensitivity of ecological processes to altered winter soil temperature regimes across a large winter temperature gradient. Thus, upscaling from insights of previous winter climate change experiments to regional scales is encouraged.
Myxomycetes are protists belonging to the super-group Amoebozoa. The traditional taxonomic system, which is now largely outdated by molecular studies, recognizes five orders: Liceales, Trichiales, Physarales, Stemonitales and Echinosteliales. Molecular phylogenies revealed two basal clades: Physarales and Stemonitales (the so-called dark-spored myxomycetes) are the first; the other above-mentioned orders form the second (the bright-spored myxomycetes). However, except for Echinosteliales none of the traditional orders appears to be monophyletic in the traditionally used delimitation. The dark-spored myxomycetes encompass the majority of the described morphospecies. Due to the high genetic divergence in DNA sequences between the bright- and dark-spored myxomycetes, only the latter are considered in this dissertation. Historically myxomycetes have been described as fungi, due to their macroscopically visible fructifications which, though considerably smaller, resemble those of fungi. These fruit bodies provide enough morphological traits to support a morphological species concept with currently ca. 1000 species described. Therefore diversity studies of myxomycetes have been conducted for over 200 years and a substantial body of data on ecology and distribution of these fructifications exist. From these studies myxomycetes are known to form often distinct communities across terrestrial ecosystems with highly specific habitat requirements, such as snowbanks (nivicolous), herbivore dung (coprophilous) or decaying wood (xylophilous). However knowledge on the myxamoebae – the trophic life stage of the myxomycetes – is very scarce. Only recent advances in molecular techniques such as direct species identification based on DNA sequences from environmental samples (ePCR), have made studies of myxamoebae (and other microbes) possible. From these first molecular based studies myxomycetes are currently estimated to account for between 5 to almost 50% of all soil amoebae, and have been shown to be present in a wide variety of soils. To fully take advantage of these new methods, a molecular DNA marker needs to be established as well as a reference sequence database. The usability of a DNA marker gene depends on its ability to separate species by a distinction between intra- and interspecific divergence between sequences of the same and related species, the so-called ‘barcoding gap’.
The first part of this thesis (article I and II) deals with the subject of establishing such a DNA marker and database, and in doing so touches upon the subject of ‘what is a myxomycetes species?’
A total of 1 200 specimens were compiled into a reference database (the largest database to date of dark-spored myxomycetes). The genetic distance from sequence-to-sequence was used to assess genetic clade structures within morphospecies and putative biospecies (sexually isolated linages) were identified. The result was an estimate of hidden diversity, exceeding that of described morphospecies by 99%. The optimum sequence similarity threshold for OTU-picking (genetic species differentiation, denoted Operational Taxonomic Unit) with the used SSU marker was identified as 99.1% similarity.
The second part of this thesis (article III and IV) presents ecological studies conducted with NGS (ePCR) in which the established threshold and database are applied and are demonstrated to provide reliable and novel insights into the soil myxamoebae community. It is investigated whether the occurrence of fruit bodies reflects the distribution of soil myxamoebae, and the research questions ‘do myxomycetes show broader realized niches as soil amoebae than as fructifications?’ and ‘are myxamoebae distributions correlated to potential prey organisms (fungi and bacteria)?’ are investigated.
In the ecological study presented in article III parallel metabarcoding of bacteria, fungi and dark-spored myxomycete was used for the first time in a joint approach to analyze the communities from an elevational transect in the northern limestone German Alps (48 soil samples). Illumina sequencing of the soil samples revealed 1.68 Mio sequences of a section of the rRNA gene, which were assigned to 578 operational taxonomic units (OTU) from myxomycetes. These show a high similarity (>98%) to 42 different morphospecies (the respective figures for bacteria and fungi were 2.16/5710/215 and 3.68/6133/260, respectively). Multivariate analyses were carried out to disentangle microbial interplay and to identify the main environmental parameters determining the distribution of myxamoebae and thus setting the boundaries for their ecological niches. Potential interactions between the three target organisms were analysed by integrating community composition and phylogenetic diversity with environmental parameters. We identified niche differentiation for all three communities (bacteria, fungi and myxamoebae) which was strongly driven by the vegetation. Bacteria and fungi displayed similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae showed a more patchy distribution, though still clearly stratified among genera, which seemed to be a response to both structural properties of the habitat and specific bacterial taxa. In addition we find an altitudinal species turn-over for all three communities, most likely explained by adaptation to harsh environmental conditions. Finally a high number of myxomycetes OTUs (associated with the genus Lamproderma) not currently represented in our reference database were found, representing potentially novel species. This study is the first to report niche differentiation between the guild of nivicolous (“snowbank”) myxomycetes and thus fine-scale niche differentiation among a predatory soil protist; identifying both potential food preferences and antagonistic interactions with specific bacterial taxa.
Finally, the second ecological study (article IV) focuses on comparing the distribution of myxamoebae revealed by ePCR of soil samples with fructifications collected from the same area (714 specimens determined to 30 morphospecies, which form 70 unique ribotypes that can be assigned to 45 ribotype clusters using a 99.1% similarity threshold). The study found a strong coherency between the two inventories, though with species specific relative differences in abundance, which can in part be attributed to the visibility of the fructifications. In addition, a year to year comparison of fructification records gives support to the hypothesis that the abundance of fructifications depends strongly on the onset of snowfall in the previous autumn and the soil temperature regime throughout the winter.
Because Moringa is rich in secondary metabolites and phenolics, we faced a challenge in extracting a pure DNA required for AFLP (the first proposed genotyping method). Later, different DNA isolation methods were tested to overcome the obstacles caused by phenolics and sugars, an AFLP protocol that worked well with the cultivated seedlings at the botanical garden in Greifswald. The markers for the Internal Transcribed Spacer (ITS) were as well tested that showed a monomorphic structure between all samples. Finally, SSR (microsatellite) markers were established. To optimize DNA extraction, the method of Doyle and Doyle was modified and optimized. This is an ideal method for obtaining a non-fragmented DNA that could be used for AFLP. In addition, two other DNA extraction methods; (KingFisher Flex robot using Omega M1130 extraction Kits, and spin columns and 96-plates using Stratec kits). Although we achieved similar results for both Robot kits (Omega) and Stratec kits, the amplification for most of the samples extracted with Robot did not work, therefore the Stratec kit was the method of choice as it has also a lower cost, combined with a high quality of DNA. For ITS, no polymorphism was found for 28 samples of M. peregrina from Sinai (sequences submitted to GenBank). However, since microsatellite markers of M. peregrina were not known, it was a challenge to try a cross amplification from other species with well-known microsatellite primers. Cross-amplification of 16 primers known from the related species M. oleifera was tested, and three multiplex PCR reactions were established after testing different annealing temperatures and different primers concentrations. This included 13 primers out of the 16 investigated markers which gave a reliable band. All methods used for genetic assessments for the different Moringa species are compiled in a comparative review to look for connections between the different Moringa species. For Moringaceae, M. oleifera and M. peregrina are closely related to each other. Both species have slender trunks, with thick, tough bark and tough roots and bilaterally symmetrical flowers with a short hypanthium. All but one SSR markers used in this study are highly informative However, the degree of polymorphy varied considerably within the 13 markers used. The Probability of Identity (PI) for all loci was 2.6 x 10-9 with high resolution. The percentage of polymorphic loci for all populations was 88.5±2.2; figures for single populations were 92.3%, 84.6%, 84.6%, and 92.3% for the wadis WM, WA, WF, and WZ, respectively. The genotype accumulation curve as well demonstrated that 7–8 markers were necessary to discriminate between 100% of the multilocus genotypes. Significant departures from HWE were detected for eight loci (P < 0.001), probably due a high degree of inbreeding within population. The observed (HO) and expected (HE) heterozygosities ranged from 0 to 0.86 and from 0 to 0.81, respectively. However, for the pooled population, excluding the monomorphic locus MO41, HO and HE ranged from 0.069 to 0.742 and from 0.126 to 0.73 with averages of 0.423 and 0.469, respectively. The mean of FST was 0.133, indicating that, due to the long generation time of M. peregrina, there is still relatively little differentiation between the four remaining populations. An analysis of molecular variance (AMOVA) revealed that the old populations of M. peregrina are still genetically diverse where 75% of variance was recorded within individuals and 83% within populations. An analysis with STRUCTURE, varying the parameter K between 1 and 7, revealed the most pronounced genetic structure for K=3, thus uniting the populations from two neighboured wadis (W. Agala and W. Feiran). The three groups seem to be now genetically isolated. (They may be remainders of a formerly contiguous population, especially when considering the change towards a drier climate in Northern Africa within the last 6000 years). Six clones of each two individuals collected from the same wadi were found, pointing to vegetative dispersal via broken twigs, which may have rooted after flash floods. It may be an alternative mode of reproduction under harsh conditions. Our data reveal a low gene flow between three of the four wadis, suggesting that the trees are relictual populations. In general, conservation of populations from the three genetically most diverse wadis and cross-breeding of trees within a reforestation program is recommended as an effective strategy to ensure the survival of M. peregrina at Sinai, Egypt.