Search for: All records

Abstract The species area relationship is a classic ecological law describing the relationship between habitat increase and the number of species. Species area relationships are resoundingly positive across macrobes such as plants and animals, and emerge through non-exclusive stochastic and deterministic processes including changes in immigration and extinction, drift, and environmental heterogeneity. Due to unique attributes of the microbial lifestyle, they may not abide by similar rules as macrobes, especially when it comes to spatial scaling. We predict that host-associated microbiomes will exhibit shallower species area relationships than free-living microbiomes due to strong host filtering, and that the species area relationships of bacteria will be shallower than fungi due primarily to differences in dispersal ability. We test these predictions in a relatively simple field system where bromeliad phytotelmata comprise aquatic ecosystems that support invertebrates and environmental substrates such as detritus. Larger phytotelmata generate larger habitat islands for microbiomes allowing us to explicitly examine their species area relationships. We find that the species area relationships of free-living and host-associated microbiomes differ, as do those of microbiome members. By assessing the relationship between environmental conditions and richness, and measuring diversity across scales, we posit that these observed differences in species area relationships are owed to differences in realized niches and dispersal abilities among microbes. These findings highlight that the classic laws of biological spatial scaling do not necessarily accurately represent microbiomes, and that the influence of area on diversity appears to be more important for some microbiomes and microbes than others. 

Abstract The potential promise of the microbiome to ameliorate a wide range of societal and ecological challenges, from disease prevention and treatment to the restoration of entire ecosystems, hinges not only on microbiome engineering but also on the stability of beneficial microbiomes. Yet the properties of microbiome stability remain elusive and challenging to discern due to the complexity of interactions and often intractable diversity within these communities of bacteria, archaea, fungi, and other microeukaryotes. Networks are powerful tools for the study of complex microbiomes, with the potential to elucidate structural patterns of stable communities and generate testable hypotheses for experimental validation. However, the implementation of these analyses introduces a cascade of dichotomies and decision trees due to the lack of consensus on best practices. Here, we provide a road map for network-based microbiome studies with an emphasis on discerning properties of stability. We identify important considerations for data preparation, network construction, and interpretation of network properties. We also highlight remaining limitations and outstanding needs for this field. This review also serves to clarify the varying schools of thought on the application of network theory for microbiome studies and to identify practices that enhance the reproducibility and validity of future work.