This is an interesting article on a relatively new focus of network science. While a lot of research has been done on single networks, I think that it is important to now expand what we know in both directions (larger scale and smaller scale). What I mean by that is simply that applying what we know about networks now to networks of networks (supernetworks) we can learn more about how things interact.
In terms of ecology it is especially relevant to the call for the inclusion of multiple interaction types into the study of community food webs. Trophic interactions are not the only form of interaction that generates a network. Many researchers have recently moved to the study of mutualistic networks, or those of parasites and hosts. Yet not many researchers are combining the different types of networks. We can learn so much more about an ecosystem or a community if we study the affects of multiple interactions on stability, function, and dynamics.
In the other direction, the study of the building blocks of networks, Milo et al.‘s (2002) motifs. Moving in this direction on the scale we can learn about how networks develop and why they exhibit such specific structural properties.