When we talk about “community structure” in microbial ecology we are usually referring to the composition and frequency of various species in that community, information often arrived at through rRNA sequencing and/or metagenomics.
But there is of course also a “real” structure of communities, particularly in biofilms. Some species tend to be physically associated with each other, and play different roles based on their actual location in the ecosystem. All of this structure is of course lost when we collect only the DNA from an environment.
Fluorescent imagery is a powerful tool for visualizing the in situ structure of microbial communties such as biofilms but becomes technically difficult with many colors (say one color for each major type of bacteria in a biofilm).
Work on the oral microbiome by a group at Woods Hole, MA has shown they can use new techniques to visualize 15 taxa in a single image. An article on their work claims they’re scaling up to a 100 taxa in a single image which would be a pretty good representation of the entire structure of the oral microbiome.
I would love to see this applied to biofilms found within the built environment, ranging from “soap scum” on shower curtains to the biofilms in water pipes that can house Legionella bacteria.
Of course to design the appropriate fluorescent probe we have to know what’s actually there first.