Summary: Laboratory microcosm experiments using protists as model organisms have a long tradition and are widely used to investigate general concepts in population biology, community ecology and evolutionary biology. Many variables of interest are measured in order to study processes and patterns at different spatiotemporal scales and across all levels of biological organization. This includes measurements of body size, mobility or abundance, in order to understand population dynamics, dispersal behaviour and ecosystem processes. Also, a variety of manipulations are employed, such as temperature changes or varying connectivity in spatial microcosm networks. Past studies, however, have used varying methods for maintenance, measurement, and manipulation, which hinders across‐study comparisons and meta‐analyses, and the added value they bring. Furthermore, application of techniques such as flow cytometry, image and video analyses, andin situenvironmental probes provide novel and improved opportunities to quantify variables of interest at unprecedented precision and temporal resolution. Here, we take the first step towards a standardization of well‐established and novel methods and techniques within the field of protist microcosm experiments. We provide a comprehensive overview of maintenance, measurement and manipulation methods. An extensive supplement contains detailed protocols of all methods, and these protocols also exist in a community updateable online repository. We envision that such a synthesis and standardization of methods will overcome shortcomings and challenges faced by past studies and also promote activities such as meta‐analyses and distributed experiments conducted simultaneously across many different laboratories at a global scale.

Habitat fragmentation and land use changes are causing major biodiversity losses. Connectivity of the landscape or environmental conditions alone can shape biodiversity patterns. In nature, however, local habitat characteristics are often intrinsically linked to a specific connectivity. Such a link is evident in riverine ecosystems, where hierarchical dendritic structures command related scaling on habitat capacity. We experimentally disentangled the effect of local habitat capacity (i.e., the patch size) and dendritic connectivity on biodiversity in aquatic microcosm metacommunities by suitably arranging patch sizes within river-like networks. Overall, more connected communities that occupy a central position in the network exhibited higher species richness, irrespective of patch size arrangement. High regional evenness in community composition was found only in landscapes preserving geomorphological scaling properties of patch sizes. In these landscapes, some of the rarer species sustained regionally more abundant populations better tracking their own niche requirements compared to landscapes with homogeneous patch size or landscapes with spatially uncorrelated patch size. Our analysis suggests that altering the natural link between dendritic connectivity and patch size strongly affects community composition and population persistence at multiple scales. The experimental results are demonstrating a principle that can be tested in theoretical metacommunity models and eventually be projected to real riverine ecosystems.

The size of an organism matters for its metabolic, growth, mortality, and other vital rates. Scale-free community size spectra (i.e., size distributions regardless of species) are routinely observed in natural ecosystems and are the product of intra- and interspecies regulation of the relative abundance of organisms of different sizes. Intra- and interspecies distributions of body sizes are thus major determinants of ecosystems’ structure and function. We show experimentally that single-species mass distributions of unicellular eukaryotes covering different phyla exhibit both characteristic sizes and universal features over more than four orders of magnitude in mass. Remarkably, we find that the mean size of a species is sufficient to characterize its size distribution fully and that the latter has a universal form across all species. We show that an analytical physiological model accounts for the observed universality, which can be synthesized in a log-normal form for the intraspecies size distributions. We also propose how ecological and physiological processes should interact to produce scale-invariant community size spectra and discuss the implications of our results on allometric scaling laws involving body mass.

Significance: Many phytoplankton species sense light and move toward or away from it. Such directed movement, called phototaxis, has major ecological implications because it contributes to the largest biomass migration on Earth, diel vertical migration of organisms responsible for roughly one-half of the global photosynthesis. We experimentally studied phototaxis for the flagellate alga Euglena gracilis by tracking algal populations over time in accurately controlled light fields. Observations coupled with formal model comparison lead us to propose a generalized receptor law governing phototaxis of phytoplankton. Such a model accurately reproduces experimental patterns resulting from accumulation and dispersion dynamics. Direct applications concern phytoplankton migrations and vertical distribution, bioreactor optimization, and the experimental study of biological invasions in heterogeneous environments.

Significance: Biological dispersal is a key driver of several fundamental processes in nature, crucially controlling the distribution of species and affecting their coexistence. Despite its relevance for important ecological processes, however, the subject suffers an acknowledged lack of experimentation, and current assessments point at inherent limitation to predictability even in the simplest ecological settings. We show, by combining replicated experimentation on the spread of the ciliateTetrahymenasp. with a theoretical approach based on stochastic differential equations, that information on local unconstrained movement and reproduction of organisms (including demographic stochasticity) allows reliable prediction of both the propagation speed and range of variability of invasion fronts over multiple generations.