Emergent simplicity in microbial community assembly

Abstract

A major unresolved question in microbiome research is whether the complex taxonomic architectures observed in surveys of natural communities can be explained and predicted by fundamental, quantitative principles. Bridging theory and experiment is hampered by the multiplicity of ecological processes that simultaneously affect community assembly in natural ecosystems. We addressed this challenge by monitoring the assembly of hundreds of soil- and plant-derived microbiomes in well-controlled minimal synthetic media. Both the community-level function and the coarse-grained taxonomy of the resulting communities are highly predictable and governed by nutrient availability, despite substantial species variability. By generalizing classical ecological models to include widespread nonspecific cross-feeding, we show that these features are all emergent properties of the assembly of large microbial communities, explaining their ubiquity in natural microbiomes.

Community assembly of the native C. elegans microbiome is influenced by time, substrate and individual bacterial taxa

“…Microbiomes were more similar when collected from the same substrate. This is consistent with results on community assembly in liquid cultures (Goldford et al ., ), where environmental carbon sources determined community composition. Similarly, studies in C .…”

“…Additionally, inter-host dispersal of bacteria strongly affects the microbiome composition of different zebra fish genotypes and contributes substantially to microbiome variation (Burns et al, 2017). In a different study, bacterial community assembly in liquid cultures followed fundamental, quantitative principles (Goldford et al, 2018). Here, bacterial communities assembled in a conserved fashion on the family, but not on the strain level and independent of the starting population.…”

Ecological insights into the underlying evolutionary patterns of biofilm formation from biological wastewater treatment systems: Red or Black Queen Hypothesis?

“…Generally, a lower substrate concentration could cause more competition and reduced biofilm formation compared to higher substrate concentrations (Hibbing et al, 2010; Yan, Nadell, & Bassler, 2017). However, classic consumer‐resource models reveal that when multiple species compete for a growth‐limiting resource, the only possible outcome is competitive exclusion, unless specific circumstances are applied (Ghoul & Mitri, 2016; Goldford et al, 2018). For instance, a multispecies community, compared to a mono‐species culture, can counter substrate limitation via cross‐feeding (Goldford et al, 2018) and/or a time‐sharing strategy (Liu et al, 2017).…”

“…However, classic consumer‐resource models reveal that when multiple species compete for a growth‐limiting resource, the only possible outcome is competitive exclusion, unless specific circumstances are applied (Ghoul & Mitri, 2016; Goldford et al, 2018). For instance, a multispecies community, compared to a mono‐species culture, can counter substrate limitation via cross‐feeding (Goldford et al, 2018) and/or a time‐sharing strategy (Liu et al, 2017). Based on these previous studies, we hypothesized that the evolutionary trajectories of biofilm formation might be influenced by variations in wastewater concentration, mainly due to its indispensable role in bacteria growth.…”

Abiotic and biotic drivers of endosymbiont community assembly in Jatropha curcas

“…Environmental stresses can directly or indirectly select for divergent symbiont communities. In soil and plant surfaces, microbial community assembly has been found to be determined by the nutrient availability, specifically the carbon source available for microbial metabolism (Goldford et al 2018). Abiotic stressors causing the plant host to alter its root exudate composition can create host-mediated changes in rhizosphere bacterial composition, as has been observed with drought and altered nutrient levels (Yang andCrowley 2000, Bakker et al 2013).…”