Homeorhesis and ecological succession quantified in synthetic microbial ecosystems

Abstract

The dynamics of ecological change following a major perturbation, known as succession, are influenced by random processes. Direct quantitation of the degree of contingency in succession requires chronological study of replicate ecosystems. We previously found that population dynamics in carefully controlled, replicated synthetic microbial ecosystems were strongly deterministic over several months. Here, we present simplified, two-species microbial ecosystems consisting of algae and ciliates, imaged in toto at single-cell resolution with fluorescence microscopy over a period of 1 to 2 weeks. To directly study succession in these ecosystems, we deliberately varied the initial cell abundances over replicates and quantified the ensuing dynamics. The distribution of abundance trajectories rapidly converged to a nearly deterministic path, with small fluctuations, despite variations in initial conditions, environmental perturbations, and intrinsic noise, indicative of homeorhesis. Homeorhesis was also observed for certain phenotypic variables, such as partitioning of the ciliates into distinct size classes and clumping of the algae. Although the mechanism of homeorhesis observed in these synthetic ecosystems remains to be elucidated, it is clear that it must emerge from the ways each species controls its own internal states, with respect to a diverse set of environmental conditions and ecological interactions.

Keywords: contingency and determinism; ecological succession; microbial ecology.

Fig. 1.

Week-long imaging of all cells of a ciliate/algae ecosystem in a microfluidic chamber. (A) Schematic drawing of the PDMS microfluidic chamber bonded to a glass coverslip. C. reinhardtii (Cr) and T. thermophila (Tt) cells trapped in the central circular chamber (4.3 mm in diameter and 110 $\mathrm{\mu }$m in depth) are time-lapse imaged in the custom-made fluorescent microscope (SI Appendix, Fig. S1). (B) Sample image showing the entire 4.3-mm chamber (white circle boundary) containing Cr and Tt cells. Cells are pseudocolored by class (Cr in red, s-Tt in cyan, and l-Tt in yellow) to improve contrast and facilitate distinguishability. (C–H) Six small $4\times$-magnified subregions (corresponding to the white squares in B), showing Cr singlet cells, Cr clumps (E and F), s-Tt cells (smaller cyan cells in D, E, F, and H), and l-Tt cells (larger yellow cells in F–H).

Fig. 2.

Whole-chamber time-lapse images from a single ecosystem. Six images from different times show overall changes in a replicate ecosystem. With regard to timing, there is a mix of many Cr (red cells) and some Tt (cyan and yellow cells) at 15 h, followed by the temporary increase in abundance of l-Tt (yellow cells) which phagocytose Cr cells at 30 h, leading to a large reduction in Cr by 50 h, followed by persistence of both Cr and Tt (mainly s-Tt; cyan cells) through 225 h. In other replicates, similar changes occur, but at different times (Figs. 3 and 5).

Fig. 3.

The abundances of each class of organism [Top, small T. thermophila (“s-Tt”); Middle, large T. thermophila (“l-Tt”); Bottom, C. reinhardtii (“Cr”)] from 23 replicate ecosystems are plotted as time series. The abundance estimates $N_c\left(t\right)$ are plotted in Left, and the temporally aligned, normalized abundances ${Ñ}_c\left(t\right)$ are plotted in Right (Materials and Methods). In all panels, data from the reference replicate used for temporal alignment is plotted in a darker color. All counts are incremented by $\frac{1}{2}$ to avoid divergence of zero counts on the log scale.

Fig. 4.

Statistics of phase-space trajectories. In the 2D panels, population dynamics are plotted as trajectories in the space of one class’s normalized abundance vs. another’s. Black curve, geometric mean over replicates; shaded region, 68% quantile over replicates, with quantiles colored as a gradient from gray to white to show structure; red triangles, initial abundance for each replicate. The 3D panel at Lower Left shows the mean trajectory as a black curve in the space of normalized abundance of each class, with projections to each 2D subspace shown as gray curves. The red arrow indicates the direction along which the dynamics proceed with time. The classes are denoted as in the text: small T. thermophila, “s-Tt”; large T. thermophila, “l-Tt”; C. reinhardtii, “Cr.”

Fig. 5.

Time course of images from 23 replicates of the synthetic Tt/Cr ecosystem. In both Upper and Lower, each column represents the same replicate ecosystem. Each row corresponds to 12 different time points, where images are taken from the raw time (Upper) or from the aligned time (Lower) relative to a reference experiment. To show sufficient detail, we selected the most representative subimage of size $912\times 912\mu$m for that replicate and time (SI Appendix). To account for slight differences in fluorescence intensity across replicates, Cr singlets are shown by a circle of fixed size, and to allow visual identification of cell classes, all cells are pseudocolored by class (Cr in red, s-Tt in cyan, and l-Tt in yellow). Filled dark gray boxes in Upper indicate that data acquisition for that particular replicate had ended before that time. Times are indicated in hours to the left of each row (Upper, raw time; Lower, aligned time).