Microbial communities play essential roles in the intricate processes that cycle nutrients in both aquatic and terrestrial ecosystems. These microorganisms establish the very foundation that upholds ecosystem stability, supporting not only their own existence but also the survival of various other organisms, humans included. However, the intricate repercussions of global change and human-induced stressors on these communities and their intricate functions remain unclear. This lack of clarity extends to fundamental knowledge, thereby posing a challenge in determining the most appropriate methodological and experimental approaches. This dissertation aims to delve into the exploration of stressor impacts on these vital microbial communities. Additionally, it seeks to carefully analyze and compare the diverse methodological approaches available, elucidating their respective strengths and limitations in this context.
I revealed the ubiquity of microbial communities and unveiled significant geographical variations among them. In an extensive investigation covering 217 European freshwater lakes, we provided evidence that protists exhibit restricted geographical distribution patterns and that centers of high taxon richness differ from the centers of putative endemic microeukaryotes. Furthermore, the study demonstrates that lowland areas can be examined independently of high-altitude regions and are suitable for generalizable statements.

Another  study focused on individual cryptic taxa associated with Ochromonadales and mock communities when exposed to elevated temperature and salt using FISH. I revealed that, while elevated temperature alone does not affect the growth of monocultures of cryptic taxa linked to Ochromonadales, salt exposure influences Spumella growth. Yet, within mock communities, increased temperature selectively enhances Poteriospumella growth, while combined salt and increased temperature decrease growth rates overall. Thus, morphological similar protists exhibit different tolerances, suggesting that molecular data are rather appropriate to analyze protistan communities.

In another comprehensive German-wide study of 30 freshwater lakes and corresponding soil catchments I uncovered commonalities, differences, and the diffuse exchange of microeukaryotes between habitats. Aside from general variations in community composition, soil harbors greater diversity than freshwater lakes. Analyses of distribution patterns reveal that the majority of microeukaryotes exhibit specificity to particular habitats, and their co-occurrence is largely driven by random drift. This implies that freshwater and soil communities can be viewed as closed systems, supporting the idea that when studying microeukaryotes, it is valid to study these two ecosystems separately.

 

Summary in English

It is crucial to acknowledge that microbial communities thrive in dynamic environments and are interconnected with these ever-changing surroundings, actively responding to the dynamic shifts around them. The reasons behind these ever-changing environments are diverse, with a significant portion arising from human activities. On one hand, these factors include issues like global warming and deforestation, while on the other hand, they involve various non-point source inputs. Although our understanding of potential stressors on microbial communities and the environment has increased in recent decades, it is far from being comprehensive. This work further aims to identify and monitor the response of microbial diversity and functions to non-point source inputs and environmental stressors using high-throughput methods.
Following, I uncovered that the effects of tire wear proxies primarily stem from leaching substances rather than inert nanoplastics. While diversity indices remain generally unchanged due to tire wear proxies, the structure and function of the community, particularly photosynthesis, are notably impaired by zinc but not by nanoplastics. However, functional redundancy was clearly detectable since photosynthesis is performed by chlorophytes instead of bacillariophytes after exposure to tire wear proxies.
In an extensive mesocosm experiment, I further examined freshwater rivers that received treated wastewater. Utilizing 16S rRNA and strain-resolved metagenomics, I discovered that although a diverse array of bacteria and viruses is initially introduced, their numbers decline over time. This finding underscores the remarkable resilience of the river's microbial community to treated wastewater.
It was not yet investigated whether different high-throughput monitoring methods show similar patterns and exhibit similar sensitivity in detecting environmental changes. In the former large scale mesocosms experiment I additionally analyzed freshwater rivers receiving treated wastewater by means of 16S rRNA and 18S V9 rRNA metabarcoding, and non-target screening. I found that each employed high-throughput method is useful to detect treated wastewater and that the impact of treated wastewater is decreasing. Further, the obtained datasets strongly covary, but their individual strength differs. I observed that 18S V9 rRNA metabarcoding exhibited superior detection sensitivity throughout the study, while non-target screening was also effective throughout the experiments. However, 16S rRNA metabarcoding only showed a reliable detection sensitivity in the first hour.

During these experiments, I recognized that interdisciplinary work and cooperation are crucial for conducting proper research. Because of this, I introduced a measurement for interdisciplinarity based on a bibliometric approach, analyzing metadata from articles in SCOPUS in the final study of this thesis. I demonstrated that, despite being advocated as a driver of scientific progress, interdisciplinarity is rather absent or primarily conducted by a few individual scientific disciplines.