Microorganisms are ubiquitously distributed on the earth and drive the fundamental element cycling in the biosphere. Their metabolic activities serve human societies in countless areas such as biotechnological engineering, food engineering, energy production, waste disposal et cetera. For human beings, and also for animals, microorganisms are imperative for health especially as colonizers of the gut system. Microbial resource management, especially when complex communities are exploited in biotechnology is a key challenge. Therefore, communities are more and more in the focus of basic research in microbiology complementary to pure cultivation technologies. Owing to their complexity, microbial communities are almost exclusively studied on the basis of bulk parameters and empirical expert knowledge. Bulk parameters are representative for an entire community performance but do not allow a segregated analysis of subpopulations or subcommunities, let alone individuals and their disparate functions within a community. This thesis aims to resolve microbial community properties and mechanisms of assembly in managed ecosystems on the individual level (i.e. single cell). For this the flow cytometric toolbox was employed and further expanded, which phenotypically classifies microbial individuals into sub-communities according to their physiological similarities. Workflows for the fast analysis and evaluation of dynamics in community structure, assembly and interaction were developed. Stability properties of communities, i.e. resistance, resilience, displacement speed and elasticity, can now quantitatively be determined based on cytometric data. For resilience behavior an on-line tool was developed. In addition, the relative proportions of neutral and deterministic forces that structure a microbial community can now be unraveled. As consequence, microbial flow cytometry has been proven to be a powerful tool for analysing complex microbial communities, and will allow huge improvements in understanding and control of microbial communities in managed and natural ecosystems.:Contents Summary ............................................................................................................. I Zusammenfassung ........................................................................................... IV 1 Introduction ..................................................................................................... 1 1.1 Microbial community and ecology ........................................................... 1 1.1.1 What is a microbial community? ...................................................... 1 1.1.2 Flow cytometry as a tool to study microbial communities ................ 2 1.2 Community structure and diversity ........................................................ 10 1.2.1 Community structure...................................................................... 10 1.2.2 Diversity metrics ............................................................................ 10 1.2.3 Evaluating structure and diversity with flow cytometry ................... 12 1.3 Community assembly and dynamics ..................................................... 13 1.3.1 Basic assembly processes ............................................................ 13 1.3.2 Evaluating assembly processes with flow cytometry ..................... 16 1.4 Community interactions ......................................................................... 18 1.4.1 Abiotic interactions of microbes and their surroundings................. 18 1.4.2 Biotic interactions of microbial partners ......................................... 18 1.4.3 Evaluating interactions with flow cytometry ................................... 20 1.5 Community functions ............................................................................. 22 1.5.1 Omics approaches to study functions in microbial communities .... 22 1.5.2 Evaluating functions with flow cytometry ....................................... 23 1.6 Aims of this study .................................................................................. 25 2 Publications .................................................................................................. 27 2.1 Overview of publications ....................................................................... 27 2.2 Published articles .................................................................................. 28 2.2.1 Publication 1 .................................................................................. 29 2.2.2 Publication 2 .................................................................................. 42 2.2.3 Publication 3 (under review) .......................................................... 60 3 Discussion .................................................................................................... 81 3.1 The importance of perceiving ecological situations ............................... 81 3.2 Stability properties of a microbial community ........................................ 84 3.3 Assembly processes in insular environments ....................................... 87 3.3.1 Niche differentiation under balanced cultivation conditions ........... 88 3.3.2 Neutral assembly under balanced cultivation conditions ............... 89 3.3.3 From intermediate disturbance to a non‐equilibrium system ......... 90 3.4 On-line analysis of reactor data ............................................................ 93 3.5 Conclusion and outlook ......................................................................... 95 4 References ................................................................................................... 97 5 Acknowledgement ...................................................................................... 105 6 Appendix .................................................................................................... 106 6.1 Declaration of independent work ......................................................... 106 6.2 Author contributions of published articles............................................ 107 6.3 Curriculum vitae .................................................................................. 111 6.4 List of Publications and conference contributions ............................... 112 6.5 Supplementary materials .................................................................... 113 6.5.1 Supplementary material for publication 1 .................................... 113 6.5.2 Supplementary material for publication 2 .................................... 140 6.5.3 Supplementary material for publication 3 .................................... 174