Abstract
Organisms and their resident microbial communities - the microbiome - form a complex and mostly stable ecosystem. It is known that the composition of the microbiome and bacterial species abundances can have a major impact on host health and Darwinian fitness, but the processes that lead to these microbial patterns have not yet been identified. We here apply the niche concept and trait-based approaches as a first step in understanding the patterns underlying microbial community assembly and structure in the simple metaorganism Hydra. We find that the carrying capacities in single associations do not reflect microbiota densities as part of the community, indicating a discrepancy between the fundamental and realized niche. Whereas in most cases, the realized niche is smaller than the fundamental one, as predicted by theory, the opposite is observed for Hydra’s two main bacterial colonizers. Both, Curvibacter sp. and Duganella sp. benefit from association with the other members of the microbiome and reach higher fractions as compared to when they are the only colonizer. This cannot be linked to any particular trait that is relevant for interacting with the host or by the utilization of specific nutrients but is most likely determined by metabolic interactions between the individual microbiome members.
Highlights
Microbiomes contribute to ecosystems as key engines that power system-level processes (Falkowski et al, 2008)
As the realized niche is determined by biological interactions of one species with its associate microbial community, we focus on traits that are important when competing with other species, such as growth rate, niche overlap, and niche breadth
When comparing the fundamental to the realized niche (Figure 2), we find that the realized niche of Curvibacter sp. and Duganella sp. is larger than their fundamental niche
Summary
Microbiomes contribute to ecosystems as key engines that power system-level processes (Falkowski et al, 2008). This applies to host ecosystems, where they are critical in maintaining host health, survival, and function (Kau et al, 2011; McFall-Ngai et al, 2013) Despite their importance, the mechanisms governing microbiome assembly and composition are largely unknown. The effect of biological interactions is Microbial Traits, Niches and the Metaorganism taken into account in the definition of the realized niche (Hutchinson, 1957) This is the portion of the fundamental niche in which a species has a positive population growth rate, despite the constraining effects of biological interactions, such as interspecific competition (Hutchinson, 1957; Pearman et al, 2008)
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