Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems

Abstract

The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.

Machine learning analysis of microbial flow cytometry data from nanoparticles, antibiotics and carbon sources perturbed anaerobic microbiomes

“…Similar to our previous demonstration [ 17 ], there are number of papers demonstrating the effectiveness of flow cytometry in the characterization of microbial community changes [ 18 – 22 ]. However, there are very few papers illustrating the possibility of the use of machine learning models to classify microbial samples studied by flow cytometry.…”

Retracted: Building a richer understanding of diversity through causally consistent evenness measures

“…Even after decades of work on the measurement of diversity, ecologists and biologists still regularly make difficult trade‐offs whenever they reach for a measure of evenness, since common choices such as the Gini index (Gini 1912; Stensrud & Valberg, 2017; Wittebolle et al., 2009), Hill evenness (Tuomisto, 2012), or Pielou's J (Ehsani et al., 2018; Rohr et al., 2016) are not entirely convincing. These challenges around measuring the concept have not stopped researchers from recognizing the importance of evenness for regulating and impacting many different ecological processes, however.…”

The biological sink of atmospheric H2 is more sensitive to spatial variation of microbial diversity than N2O and CO2 emissions in an agroecosystem

“…This importance of evenness was elegantly supported in 100 synthetic communities with the same richness, but different evenness. Examination of microbial successions among microbial assemblies led to the identification of species favored in synthetic communities characterized by elevated or low evenness (Ehsani et al, 2018). H 2 soil uptake rate was the sole process related to spatial variation of microbial communities.…”