The ecological niche of the vagina contains a large number of different microbes that are constantly interacting with each other and the host. Culture methods have not been sufficient in order to resolve the complexity of the normal vaginal flora. Further, the methods for delineating normal flora from not normal flora are not easily handled and are traditionally not based on culture but on microscopy of elements of the vaginal fluid. In the work presented in this thesis, an international collaboration was established that pin-pointed some of the difficulties in classifying vaginal floras, including staining, sampling, and discordance when lactobacilli are few in number, and that emphasized the importance of the size of the vision field in microscopes. As lactobacilli are prominent members of the normal vaginal flora they need to be carefully classified if further work towards more robust scoring tools is to be achieved. Phenotypic methods have not been able to separate the closely related Lactobacillus species of the vagina. Progress in molecular biology has provided possibilities to characterize these lactobacilli, which are mainly from the Lactobacillus acidophilus group. In this work a large number of strains collected by true random sampling were subjected to RAPD-PCR, TTGE and multiplex PCR for species identification. The major species found were L. crispatus, L. gasseri and L. jensenii and the recently described L. iners. The presence of L. iners has not been detected in previous studies due to its special nutrient requirements. Development of pyrosequencing technology also made it possible to match signatures of the two variable regions V1 and V3 of the 16S rRNA gene of the vaginal lactobacilli and identify them to the species level in a high throughput manner. The study confirmed that the dominating flora in women with normal vaginal flora comprises the four species mentioned previously. Repetitive sampling during IVF-treatment with highly varying oestrogen levels demonstrates changes that possibly occur during changes in the natural life cycle. Furthermore, L. iners was found to be the first species to be established after spontaneously resolved or treated Bacterial Vaginosis. These findings can be of help in developing new strategies for regaining and retaining the normal vaginal flora.

Gastrointestinal (GI) health is an important contributor to one’s overall well-being. In the past decade, the focus of this aspect of health has been on the organisms that inhabit the intestines: gut microbes. A concept central to understanding bacterial behavior for health or disease promotion is biological film (biofilm) formation. The predominant form of growth for bacteria is biofilm formation, an as yet poorly described phenomenon for gut microbes. In order to better understand bacterial behavior in response to nutrients that pass through the GI system, a high throughput system to assess biofilm formation was developed. Gastrointestinal-associated microbes, Escherichia coli and Enterococcus faecalis, were assayed for biofilm formation in 96-well plates after 24 hours of incubation. Nutrients, inter-and intrakingdom signaling molecules such as monosaccharides, calcium, insulin, endocannabinoids, and AI-1, AI-2 like signaling compounds, respectively, were added to cultures in order to test their effects on biofilm formation. Biofilm was quantified spectrophotometrically by the measurement of optical density of each well measured at 580nm following crystal violet staining of adherent biofilm. Values were expressed as means ± standard error of the mean (SEM); differences between means were assessed using t-testing and ANOVA using GraphPad Prism, with mean differences considered significant at P < 0.05. Results showed that biofilm formation by E. coli was enhanced by glucose, galactose, lactose, AI-1 like signaling compound and insulin at 50 and 100µU/ml, while AI-2 like compound and calcium inhibited biofilm formation. Biofilm formation by E. faecalis was also enhanced by AI-1 like compound and insulin at 50µU/ml in RPMI medium and inhibited in cultures grown in BHI medium or with added calcium. We conclude that gastrointestinal-associated microbes are influenced by nutrients as well as various factors, including the culture medium, signaling compounds, as well as host-signaling compounds such as insulin and calcium. This study provides a platform required for future studies involving nutrient effect on biofilm formation.

The weathering of shales is a globally important process affecting both natural and built environments. Shales form roughly 70 % of worldwide sedimentary rock deposits and therefore the weathering of these rocks has substantial effects on the geochemical cycling of elements such as carbon, iron and sulfur. Microbes have been shown to play a key role in weathering shales, primarily through the oxidation of the iron and sulfur of embedded pyrite and the resultant production of sulfuric acid. Despite significant interest in the microbial weathering of shales within industrial sectors such as biohydrometallurgy and civil engineering, comparatively few studies have investigated microbial shale weathering in natural environments. Furthermore, the role of microbes in natural shale weathering processes beyond iron oxidation has largely remained unexplored. In this thesis, the weathering capabilities of microbial communities from natural weathered shale was investigated. The North Yorkshire coastline was used as a study location, due to the abundance and diversity of natural cliffs and historic, disused industrial sites. Cliff erosion and recession on the North Yorkshire coastline is a major concern for local authorities and is the focus of current research. The aim of this work has been to evaluate microbial shale weathering processes within these environments, and hypothesise the possible contribution they may have to erosive processes. Phenotypic plate assays inoculated with weathered shale material were used to obtain rock weathering bacterial isolates that tested positive for a specific weathering phenotype, such as iron oxidation or siderophore production. Subsequent 16S rRNA sequencing enabled genera level identification, revealing 15 genera with rock weathering capabilities with several being associated with multiple weathering phenotypes including Aeromonas sp., Pseudomonas sp. and Streptomyces sp. Shale enrichment liquid cultures were incubated with shale rock chips to simulate natural biological weathering conditions, and the concentration of rock-leached elements in the fluid measured. No evidence of microbially-enhanced leaching was found consistently for any element, however the significant reduction in leachate iron concentration under biological conditions indicates that iron precipitation occurred via microbial iron oxidation. Enrichment cultures inoculated with weathered shale and containing organic matter (OM) rich rocks in water or M9 medium, both liquids lacking an organic carbon source, were grown over several months. The cultures yielded microbial isolates that could utilise rock bound OM sources and one bacterial isolate, Variovorax paradoxus, was taken forward for ecophysiological study. The shale rock that the organism was isolated from, along with other OM rich rocks (mudstones and coals), elicited complex responses from V. paradoxus including enhanced growth and motility. Finally, mineral microcosms in vitro and mesocosms in situ investigated microbial colonization and weathering of shale-comprising minerals (albite, calcite, muscovite, pyrite and quartz). Microcosms were established using iron oxidizing enrichment cultures, as based on the results of the simulated rock weathering experiments, while the in situ mesocosms were buried within weathered shale scree within a disused mine level. Levels of colonization significantly varied between minerals within the microcosms (pyrite > albite, muscovite > quartz > calcite). Although differences in mineral colonization were seen in the mesocosms, they did not match those in the microcosms and were not statistically significant. Pyrite incubated in the microcosms became significantly weathered, with extensive pit formation across the mineral surface that is consistent with microbial iron oxidation. In the mesocosms, pit formation was not identified on pyrite surfaces but dark etchings into the pyrite surface were found underneath fungi hyphal growth. The results of this thesis highlights that a range of microbial rock weathering mechanisms are abundant across weathered shale environments. Microbial iron oxidizing activity was a dominant biogeochemical process that altered rock-fluid geochemistry and weathered pyrite surfaces. However, the impact on rock or mineral weathering of other microbial mechanisms was not elucidated by this work. Given the known capabilities of these mechanisms, the conditions under which they are active may not have been met within the experimental setup used. Microbial iron oxidation in shale and shale-derived materials has previously been demonstrated to weaken rock structure through acid production and secondary mineral formation. From the results of this thesis, it is clear that microbial iron oxidation is an active process within some of the weathered shale environments studied, including cliff surfaces. Therefore, it can be hypothesised that microbial activity could play a role in structurally weakening shale rock within cliffs and accelerate their erosion. Future work should attempt to quantify the rate and extent of microbial iron oxidizing activity within shale cliff environments and investigate its contribution to erosive processes.

The maintenance of cooperation and altruism in the face of manipulation by exploitative cheaters that reap the benefits of cooperative acts without paying the associated costs is a conundrum in evolutionary biology. Cheaters should spread through a population causing it to crash, yet cooperation is common. There are many models and theories that attempt to explain this apparent contradiction. The social amoeba Dictyostelium discoideum, like many microbial species has been used as a model organism to test these theories and to begin to understand the genetic mechanisms behind social behaviours. The aim of this PhD project is to quantify the interactions that occur between naturally-occurring genotypes during social competition in order to identify the types of cheating behaviours and to understand the evolutionary consequences of such behaviours. I first demonstrate that there is a social hierarchy of genotypes and that cheaters can increase their own fitness by increasing their own spore allocation or decreasing their partner's allocation the precise nature of which is dependent upon unique interactions between each competing pair. I also show that the outcome of social competition is dependent upon the physical environment where it can be significantly reduced, or even avoided by segregation of genotypes during development. Finally, it is demonstrated in a collaborative project that much of the observed social behaviour can be explained in terms of the production of and response to developmental signals.

Diploma thesis The influence of nutritional measures on the course of ulcerative colitis deals with the influence of dietary habits on the course of ulcerative colitis (especially probiotic foods), namely impact on relapses of the disease. The theoretical part is divided into two parts. The first part describes ulcerative colitis, from definition to treatment. The second part deals with the intestinal microbiome and the factors that affect it, with an emphasis on the influence of food. The semi-structured interview method based on the questionnaire was used to elaborate the practical part. The research group consisted of respondents with ulcerative colitis who were in remission and relapse. A questionnaire was filled with respondents, which consisted of questions about the course of the disease and a frequency questionnaire targeting different groups of foods. The established eating habits were compared to each other among the respondents, given the frequency of relapse of their illnesses. Research has shown that only fermented dairy products are related to relapse rate and retention of remission. For foods that contain fiber that also modulates the intestinal microbe, the relationship between food consumption and relapse has not been proven. Also, the relationship between consumption of fatty...

Phages are the most abundant components of the marine environments and can control host abundances. The severity of viral infections may depend on whether phages are lytic, lysogenic, or chronic, which can be influenced by host activity and by environmental conditions. Lysogeny remains the least understood process. Knowledge of virioplankton dynamics and their life strategies in the Red Sea remain unexplored. In this Ph.D. research we aimed to quantify virioplankton abundance, the variability on viral and bacterial dynamics, and to investigate the occurrence of lytic and lysogenic phages in the Red Sea. Accordingly, we used the flow cytometric technique to enumerate viral and bacterial abundances in the coastal pelagic area during two years of sampling and in the coastal lagoon waters for one year, together with water column distribution in open Red Sea waters. We conducted incubations of natural microbial communities in the laboratory to induce lysogenic bacteria by using the chemical mutagenic mitomycin C. We also explored the influence of host abundance, temperature, and ultraviolet radiation on viral dynamics and lysogeny. Our results showed that abundances of virses in the Red Sea ranged from 106 to 107 virus-like particles per mL, and bacteria ranged from 104 to 105 cells per mL. We observed a large variability i the values of virus-to-bacterium ratios, and lower values of viral production to those for temperate coastal waters and relatively close to values reported in other oligotrophic areas. Although the lytic phase was prevalent, lysogeny was detected when bacterial abundances decreased. We determined inducible lysogenic bacteria from undetectable to ~56% in the coastal Red Sea, although we found a lower maximum of 29.1% at a eutrophic coastal lagoon. The decay rates of viruses were influenced by UVB exposure, suggesting their susceptibility to solar radiation. Exposure to UVB radiation-induced prophage varied between 4 and 34%. Our findings identified the significant role of viral infections in controlling bacterial abundance and the importance of both lytic and lysogenic phases in the Red Sea waters. This study contributes to the understanding of lysogeny in marine phages.

One of the major challenges for agricultural research in the 21st century is to increase crop productivity to meet the growing demand for food and feed. Biotic (e.g. plant pathogens) and abiotic stresses (e.g. soil salinity) have detrimental effects on agricultural productivity, with yield losses being as high as 60% for major crops such as barley, corn, potatoes, sorghum, soybean and wheat, especially in semi-arid regions such as Saudi Arabia. Plant growth promoting bacteria isolated from pioneer desert plants could serve as an eco-friendly, sustainable solution for improving plant growth, stress tolerance and health. In this dissertation, culture-independent amplicon sequencing of bacterial communities revealed how native desert plants influence their surrounding bacterial communities in a phylogeny-dependent manner. By culture-dependent isolation of the plant endosphere compartments and a number of bioassays, more than a hundred bacterial isolates with various biochemical properties, such as nutrient acquisition, hormone production and growth under stress conditions were obtained. From this collection, five phylogenetically diverse bacterial strains were able to promote the growth of the model plant Arabidopsis thaliana under salinity stress conditions in a common mechanism of inducing transcriptional changes of tissue-specific ion transporters and lowering Na+/K+ ratios in the shoots. By combining a number of in vitro bioassays, plant phenotyping and volatile-mediated inhibition assays with next-generation sequencing technology, gas chromatography–mass spectrometry and bioinformatics tools, a candidate strain was presented as a multi-stress tolerance promoting bacterium with potential use in agriculture. Since recent research showed the importance of microbial partners for enhancing the growth and health of plants, a review of the different factors influencing plant-associated microbial communities is presented and a framework for the successful application of microbial inoculants in agriculture is proposed. The presented work demonstrates a holistic approach for tackling agricultural challenges using microbial inoculants from desert plants by combining culturomics, phenomics, genomics and transcriptomics. Microbial inoculants are promising tools for studying abiotic stress tolerance mechanisms in plants, and they provide an eco-friendly solution for increasing crop yield in arid and semi-arid regions, especially in light of a dramatically growing human population and detrimental effects of global warming and climate change.

Investigating forest soil biodiversity is essential to increase our understanding of ecosystem functions, assess potential consequences of global change, and thus optimize future decision-making processes. This cumulative PhD thesis contributes to this field by elucidating responses of bacterial and fungal forest soil communities, and their associated functions, in relation to tree diversity using a trait-based ecological approach with a focus on microbial living strategies. The three main chapters investigated microbial communities, using PCR-amplicon molecular methods, bioinformatics and novel statistics in the frame of the SoilForEUROPE project funded through the 2015–2016 BiodivERsA COFUND call for research proposals. Links between above-belowground biodiversity are crucial to understand forest functionality. For instance, studies on relationships of tree diversity and tree identity with microbial diversity reveal shifts in litter decomposition, nutrient cycling, primary production and the regulation of greenhouse gas emissions. These kinds of studies commonly compare microbial populations of different tree taxonomical groups. However, the effects of different tree taxa on microorganisms are mediated by tree morphology, physiology, phenology and genetics. Therefore, the use of specific plant traits to study biodiversity has become more frequent, adding a mechanistic understanding of compositional or functional shifts and interactions with soil microbial communities. This generalizable approach provides a common currency to compare similar microbial communities from different regions or environments with few microbial taxa in common. Microbial communities are also filtered by other processes such as global drivers, stochastic events, abiotic and biotic factors in addition to the mentioned tree traits. This environmental filtering process results in a functional microbial community structure, also with their own set of traits to increase their population size through higher performance and as response the capacity to affect their own ecosystem. Furthermore, it is expected that a particular set of microbial traits represents the life history strategies that favored a particular community under specific environmental conditions. This thesis correlates tree traits with bacterial and fungal communities by using a wide-ranged European forest platform with 64 plots of four different latitudinal regions. The SoilForEUROPE design also included multispecies and monospecific forests comprising 13 main tree species and 33 different tree species compositions. All these conditions supplied a diversity of environments to improve our knowledge of microbial soil diversity and above-belowground interactions. The here presented thesis encompasses five individual chapters. Chapter 1 provides the research context, project presentation and the main approach used. The Chapters 2 and 3 were developed in association with colleagues from the University of Freiburg and investigate four major European forest types: boreal forests (Finland), hemi‐boreal forests (Poland), mountainous beech forests (Romania) and thermophilous deciduous forests (Italy). Chapter 4 focuses purely on temperate forest plots and Chapter 5 compiles and concludes the results and presented ecological meanings. In particular, Chapter 2 evaluated the influence of tree species composition and diversity on fungal diversity and community composition, and highlights the relationships of fungal guilds and enzymatic activities with tree traits in detail, while also taking environmental variables into account. We demonstrated, how guilds like fungal saprotrophs mirror the litter quality, while tree root traits are often linked to an increasing number of fungal symbiotrophs. We found that forest types of higher latitudes, which are dominated by fast tree communities, correlated with high carbon‐cycling enzymatic activities. In contrast, Mediterranean forests with slow tree communities showed high enzymatic activities related to nitrogen and phosphorus cycles. In Chapter 3, we investigated links between bacterial communities, their functionality and root trait dispersion. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggested an increasing bacterial functionality from monospecific to multispecies forest. We also exposed that in multispecies forests, the bacterial functionality declines with the increasing functional dispersion of the roots. We further revealed important effects of the tree species identity on bacterial community composition, but we did not find significant relationships with root functional dispersion. However, bacterial network analyses indicated that multispecies forest have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. Chapter 4 aimed to explore microbial communities of different soil depths from 0 to 30 cm across forests covering deciduous, evergreen and mixtures plots. Microbial abundance and diversity were especially affected by soil depth and by the presence of evergreen trees. Results showed higher accuracy to detect niche preference by using taxonomy levels than metabolic pathways or fungal guilds as features of a machine learning model. We found that bacterial communities are primarily shaped by soil depth in contrast to fungal community, which were rather influenced by the forest composition. Results also supported the importance of mixed forest to maintain nutrient cycling and a broad diversity of metabolites compared to monospecific forest and this differences where particular perceived in the upper 10 cm of soil. Chapter 5 concludes the thesis and presents a few remarks highlighting microbial strategies that might be favored under a particular soil forest composition. Overall, this thesis not only revealed the ecological patterns of soil forest microbial communities, but also provides a practical tool with necessary information to support decision-making and enlarge the schemes to conserve soil biodiversity.

Arid and semi-arid regions, mostly found in developing countries with exponentially increasing populations, are in chronic lack of water thereby severely limiting agricultural production. Irrigation with saline water, which is available in large quantities, could be an obvious solution, but current crops are all salt sensitive. Although major efforts are underway to breed salt tolerant crops, no breakthrough results have yet been obtained. One alternative could rely on plant-interacting microbiota communities. Indeed, rhizophere and endosphere microbial communities are distinct from those of the surrounding soils, and these specific communities contribute to plant growth and health by increasing nutrient availability or plant resistance towards abiotic and biotic stresses. Here we show that plant microbe interactions induce plant tolerance to multiple stresses. From a collection of strains isolated from the desert plant Indigofera argentea, we could identify at least four different strategies to induce salt stress tolerance in Arabidopsis thaliana. A deep analysis of Enterobacter sp. SA187 showed that it induces Arabidopsis tolerance to salinity through activation of the ethylene signaling pathway. Interestingly, although SA187 does not produce ethylene as such, the association of SA187 with plants induces the expression of the methionine salvage pathway in SA187 resulting in the conversion of bacterially produced 2-keto-4-methylthiobutyric acid (KMBA) to ethylene. In addition, a metabolic network characterization of both SA187 and Arabidopsis in their free-living and endophytic state revealed that the sulfur metabolic pathways are strongly upregulated in both organisms. Furthermore, plant genetic experiments verified the essential role of the sulfur metabolism and ethylene signaling in plant salt stress tolerance. Our findings demonstrate how successful plant microbes of a given community can help other plants to enhance tolerance to abiotic stress, and reveal a part of the complex molecular communication process during beneficial plant-microbe interaction.

Cationic steroid antimicrobials (CSAs or ceragenins) are a novel class of synthetic, cholic acid-based mimics of endogenous antimicrobial peptides. These small molecule compounds display broad bactericidal activity against gram-negative and gram-positive bacteria, potent ability against fungal pathogens, and cidal effects against drug resistant and multidrug resistant microbes. Implantable medical devices provide an abiotic surface upon which bacteria and fungi can accumulate--thereby leading to localized or systemic infection. We proposed that CSA antibiotics can be incorporated into medical device surface coatings which can be optimized for the active release or elution of the CSA compounds over time to prevent device-associated infections. This report will discuss the progress of developing and testing coating systems for 3 such devices: cardiac implantable electronic devices (CIED), silicone nasal splints, and breast tissue expanders. In the case of CIEDs, an envelope material containing CSA was created using bioresorbable polymers. We found that this envelope elutes CSA antibiotics and kills all surrounding bacteria or fungi in both planktonic and biofilm forms within 1 hour of exposure. We also developed a nasal splint coating which is directly adhered to the surface of the silicone splint. This coating system demonstrated more than 8 days of protective ability (full microbicidal activity to the detection limit) against Candida albicans, and reduced microbial growth of P. aeruginosa, Candida auris, and MRSA for approximately 6 days. Lastly, in the case of tissue expanders, we developed a layered coating which displays fully-reductive antimicrobial activity against MRSA for 8 days with reintroduction of bacteria every 24 hours. Additionally, this work will discuss our investigations into the secondary properties of ceragenin compounds. On the basis of studies which have demonstrated the pro-osteogenic properties of CSA, we probed the mechanism of this effect. We studied the potential effects of ceragenins on the proliferation, differentiation, and migration of bone-derived mesenchymal stem cells (MSCs). We have determined the absence of any positive proliferative effects of ceragenins on these cells; however, we have demonstrated the significant migration-promoting chemoattractant properties of CSA. In the case of CSA-13, we have observed up to a 400% increase in migration compared to the control. Also, we demonstrated that the P2X7 receptor is strongly implicated in the cellular mechanism of this effect. Our studies of the differentiation-promoting properties of CSA on MSCs have been largely inconclusive, but further investigations are proposed in this report. Lastly, this work includes a report on our investigations into the potential synergistic interactions between CSA-131/CSA-44 with amphotericin B or caspofungin, two commonly used antifungal agents.