Macroecological laws describe variation and diversity in microbial communities

Abstract

How the coexistence of many species is maintained is a fundamental and unresolved question in ecology. Coexistence is a puzzle because we lack a mechanistic understanding of the variation in species presence and abundance. Whether variation in ecological communities is driven by deterministic or random processes is one of the most controversial issues in ecology. Here, I study the variation of species presence and abundance in microbial communities from a macroecological standpoint. I identify three macroecological laws that quantitatively characterize the fluctuation of species abundance across communities and over time. Using these three laws, one can predict species’ presence and absence, diversity, and commonly studied macroecological patterns. I show that a mathematical model based on environmental stochasticity, the stochastic logistic model, quantitatively predicts the three macroecological laws, as well as non-stationary properties of community dynamics.

Characterizing scaling laws in gut microbial dynamics from time series data: caution is warranted

“…Our results are consistent with previous findings that fluctuations in microbial abundance are mainly due to temporal stochasticity 9 , and human gut microbiota has two distinct dynamic regimes: auto-regressive and non-autoregressive 1 . In particular, most of the variance in gut microbial time series is non-autoregressive and driven by external day-to-day fluctuations in host and environmental factors (e.g., diet), with occasional internal autoregressive dynamics as the system recovered from larger shocks (e.g.…”

A macroecological description of alternative stable states reproduces intra- and inter-host variability of gut microbiome

“…The Stochastic Logistic Model with environmental noise (SLM, see Methods) is known to describe several statistical properties of abundance fluctuations for microbial species [15, 16]. In particular, it predicts that the distribution of fluctuations at stationarity is a Gamma distribution, which depends on two parameters: K i , the carrying capacity appearing in the SLM, and σ i , which can be interpreted as the amplitude of environmental noise.…”

“…As a consequence, Taylor's law on abundance fluctuation with exponent 2 [16] implies that σ i and K i are not correlated across OTUs.…”

“…Previous studies [15,16] showed that the dynamics of the relative abundance λ of a microbial species is best described by the stochastic logistic model with environmental noisė…”

“…Recent works have characterized the macroecological patterns of community composition [12,13]. Under the macroecological lens, community dynamics is characterized by large and rapid fluctuations with robust and reproducible statistical properties [14][15][16]. These regular patterns are well described by the stochastic logistic model with environmental noise, which assumes that fast environmental fluctuations perturb abundances around a taxa-specific carrying capacity [15,16].…”