Substrate utilization pattern of six bacterial isolates from the Hydra microbiome measured with a BIOLOG assay. Natl. prior to each read). This suggests that metabolic overlap could be involved in promoting the extreme temporal stability of Hydra’s microbiome (Fraune and Bosch, 2007) in addition to active manipulation by Hydra through the secretion of antimicrobial peptides and neuropeptides (Franzenburg et al., 2013; Augustin et al., 2017). The microbiome inhabits the outer mucus-like layer of the glycocalyx (Fraune et al., 2015), which is hydrophilic. Trait measures of bacterial species isolated from the Hydra microbiome. U.S.A. 110, E3730–E3738. Demonstration of bacterial cells and glycocalyx in biofilms on human tonsils. Rev. Curvibacter sp. 60, 257–271. Acta Biotheor. Natl. Science 350:aac9323. (2017). You see that there can be a sharp change in abundance even with only very slight changes in species characteristics. Ga. 27, 25–38. and Duganella sp. Curvibacter sp. [ "article:topic", "showtoc:no", "license:ccbync", "niche", "authorname:lehmanlobergclark", "zonation", "Fundamental niche", "Realized niche" ], Clarence Lehman, Shelby Loberg, & Adam Clark, University of Minnesota Libraries Publishing. We also found the two main colonizers, Curvibacter sp. Consider latitude on the earth’s surface, which is connected to several parameters such as sunlight and temperature. A. Can. likely benefitted from products excreted by Curvibacter sp., it was able to outcompete Curvibacter sp. (1–2%), Acidovorax sp. Trait-based community assembly and succession of the infant gut microbiome. We therefore measured the niche overlap and resource use of the six species isolated from the Hydra microbiome. To assess the rules of assembly and coexistence of microbiota in host-associated microbiomes, we here apply the niche-assembly perspective to a metaorganism, and thus specifically extend the concept to biotic environments. Most importantly, this effect was independent of initial frequency but depended on direct contact, which might be due to competition for the same resources or due to Duganella sp. Appl. A 100 μl aliquot of each re-suspension was pipetted into 100 μl of fresh R2A medium. Sym. The “realized niche” is the real life niche—where species are restricted by interactions with other species. The origin of mucosal immunity: lessons from the holobiont Hydra. Biofilm formation was assayed and quantified as previously described (Ren et al., 2015). (2015). Figure 3. and Duganella sp., in more detail (Deines et al., 2020). (2003). Species were grown from isolate stocks in R2A medium (18°C, shaken at 250 r.p.m. Microbiol. The aim of this study is to apply the niche concept and trait-based theory to the metaorganism Hydra vulgaris (strain AEP) to gain insight into the mechanisms underlying the microbial community composition. This is not the case for Pseudomonas sp., which despite its observed niche breadth, does not seem to play a major role as part of Hydra’s microbiome. The niche-assembly perspective proposes that any ecosystem is made up of a limited number of niches, each occupied by a single species (Wennekes et al., 2012). For the relative abundance estimates, all samples were normalized to the lowest number of reads in each respective dataset. 2, 936–943. were the only two species that did not show any affinity to the hexadecane; thus their cell population can be considered homogeneous consisting of only hydrophilic cells, which significantly differs from the others, except for Pseudomonas sp. For linking the community composition in Hydra’s microbiome to specific characteristics, we used a trait-based approach focusing on traits potentially involved in microbiome assembly and stability (summarized in Figure 6). C2.2 (all Gammaproteobacteria), all of which were isolated from the Hydra vulgaris (strain AEP) microbiome (Fraune et al., 2015). (A) Cell surface hydrophobicity (Error bars are s.e.m., n = 3), and (B) Biofilm formation capacity of six bacterial isolates. Missed the LibreFest? doi: 10.1126/science.1153213, Flemming, H. C., and Wingender, J. Interestingly, from the six species tested here, the one with the highest ability to form biofilms is Pelomonas sp., whereas the two main colonizers, Curvibacter sp. Adhesion as a weapon in microbial competition. The niche concept is one of the core concepts in ecology and has been rediscovered by modern ecology for explaining biodiversity and species coexistence patterns (Pocheville, 2015). doi: 10.1016/j.cub.2019.04.024, Green, J. L., Bohannan, B. J. M., and Whitaker, R. J. 8, 623–633. Distinct antimicrobial peptide expression determines host species-specific bacterial associations.