<p>Natural communities form networks of species linked by interactions. Understanding the structure and dynamics of these ecological networks is pivotal to predicting species extinction risks, community stability and ecosystem functioning under global change. Traditionally, ecological network research has focused on interactions involving the flow of matter and energy, such as feeding or pollination. In nature, however, species also interact by intentionally or unintentionally exchanging information signals and cues that influence their behaviour and movement. Here we argue that this exchange of information between species constitutes an information network of nature—a crucial but largely neglected aspect of community organization. We propose to integrate information with matter flow interactions in multilayer networks. This integration reveals a novel classification of information links based on how the senders and receivers of information are embedded in food web motifs. We show that synthesizing information and matter flow interactions in multilayer networks can lead to shorter pathways connecting species and a denser aggregation of species in fewer modules. Ultimately, this tighter interconnectedness of species increases the risk of perturbation spread in natural communities, which undermines their stability. Understanding the information network of nature is thus crucial for predicting community dynamics in the era of global change.</p>