Figure 1.

Interactions among organisms within microbiomes change through time and space. (a) Changes in intracellular network activities or changes in genotype via random mutation and/or horizontal gene transfer (HGT) can lead to changes in microbial interactions in microbiomes. Left: On short time scales, regulatory networks govern how microbes respond to their environment. In one environment, one microbe may produce molecules that lead to a net positive impact on a second microbe (green circles and green arrow), while in a second environment the same microbe may produce molecules that lead to a net negative impact on a second microbe (purple triangles and purple arrow) due to changes in transcriptional activity. Right: On longer time scales, genetic changes due to HGT can alter microbial intracellular networks and contribute to changes in ecological relationships. In natural competence (one mechanism of HGT), extracellular DNA can be taken up by a recipient organism and integrated into the chromosome via homologous recombination. When this occurs, the functional activities of a microbe can change, manifesting as a change in the ecological network from a net positive (green arrow) to a net negative interaction (purple arrow). (b) Schematic highlighting a hypothesis about how spatial mixing (x-axis) and population density (y-axis) can alter the frequency of cheating (wherein the benefit from cooperating is disproportional to the contribution toward cooperation) and the distributions of positive/negative interactions in a microbial community. Downward arrows indicate a low frequency, and upward arrows indicate a high frequency. When population densities and spatial mixing are low, microbes are less likely to encounter one another, leading to infrequent interactions and a low frequency of cheating due to low concentrations of public goods (“low density, low mixing” box). As population densities and/or spatial mixing increase, both the frequency of interactions and frequency of cheating increase (“low density, high mixing” and “high density, low mixing” boxes). In well-mixed, dense communities, negative interactions will be especially frequent because of resource competition (“high density, high mixing” box).