7 Feb 2024

Ecological Modeling of Microbial Community Composition under Variable Temperatures

Abstract: Soil microorganisms interact with one another within soil pores and respond to external conditions such as temperature. Data on microbial community composition and potential function are commonly generated in studies of soils. However, these data do not provide direct insight into the drivers of community composition and can be difficult to interpret outside the context of ecological theory. In this study, we explore the effect of abiotic environmental variation on microbial species diversity. Using a modified version of the Lotka-Volterra Competition Model with temperature-dependent growth rates, we show that environmentally relevant temperature variability may expand the set of temperature-tolerance phenotype pairs that can coexist as two-species communities compared to constant temperatures. These results highlight a potential role of temperature variation in influencing microbial diversity. This in turn suggests a need to incorporate temperature into predictive models of microbial communities in soil and other environments. We recommend future work to parameterize the model applied in this study with empirical data from environments of interest, and to validate the model predictions using field observations and experimental manipulations.

30 Aug 2021

Variation in Inhibitor Effects on qPCR Assays and implications for eDNA Surveys

Abstract: Aquatic environmental DNA (eDNA) surveys are sometimes impacted by polymerase chain reaction (PCR) inhibitors. We tested varying concentrations of different inhibitors (humic, phytic, and tannic acids; crude leaf extracts) for impacts on quantitative PCR (qPCR) assays designed for eDNA surveys of bighead and silver carp (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix). We also tested for inhibition by high concentrations of exogenous DNA, hypothesizing that DNA from increasingly closely related species would be increasingly inhibitory. All tested inhibitors impacted qPCR, though only at very high concentrations — likely a function, in part, of having used an inhibitor-resistant qPCR solution. Closer phylogenetic relatedness resulted in inhibition at lower exogenous DNA concentrations, but not at relatively close phylogenetic scales. Inhibition was also influenced by the qPCR reporter dye used. Importantly, different qPCR assays responded differently to the same inhibitor concentrations. Implications of these results are that the inclusion of more than one assay for the same target taxa in an eDNA survey may be an important countermeasure against false negatives and that internal positive controls may not, in the absence of efforts to maximize inhibition compatibility, provide useful information about the inhibition of an eDNA assay.