Bringing nature into the lab
Bacteria are the 'hidden majority': they pervade the Earth, coating every surface, living in soil and water, and even inside other creatures including ourselves. Although they are hidden from view because of their small size, they have a major impact on ecosystems. For example, complex communities of bacteria control the rate at which waste and dead organisms are decomposed, and therefore the rate at which nutrients are recycled to plants and other primary producers.
The paper published in Nature Microbiology is here: https://www.nature.com/articles/s41564-018-0180-0
My lab has been interested in how communities containing many different kinds of bacteria influence "ecosystem functioning", including nutrient cycling. Just a teaspoon of pond water contains hundreds of different kinds of bacteria, so the main hurdle for this type of research is the enormous complexity of bacterial communities in nature.
I believe the key to understanding these complex communities is to use experiments that simplify the communities and the environments they inhabit.
One way in which my lab has simplified this complexity is by the choice of ecosystem: we study puddles of rainwater that can form at the base of large trees. These miniature ponds have been used in my lab and others as "model ecosystems", much in the same way as fruit flies have been used in genetics research. Rain puddles are relatively simple, tractable, easy to find (especially in England!), and are as much a part of nature as a lake or stream. If we understand how a puddle works, the same general principles should apply to other ecosystems.
In my lab's previous publications, we built simple communities in laboratory puddles (bottles). By controlling the kinds of bacteria that were in each bottle, we could disentangle the role they were playing. We wanted to move beyond simple communities with just a few species to examine communities approaching natural levels of complexity.
Our innovation in the paper just published in Nature Microbiology was to take advantage of the natural variation in bacterial communities rather than individually selecting which bacteria were used. We collected hundreds of bacterial communities from puddles across the south of England and brought them back to the lab. The bacterial cells within the communities could then be inoculated into a standard environment. Since we had collected so many communities, we were able to observe how changes in ecosystem functioning were associated with changes in the abundance of specific kinds of bacteria. This allowed us to identify how each of the hundreds of different bacteria influenced ecosystem functioning in the bottles. The main finding showed that bacteria that had low abundance (rare) were influencing different components of the ecosystem compared to kinds of bacteria that were common.
The experiment is halfway between the simplicity of the lab and the full complexity of a natural system, so the task now is to extrapolate the results to nature. If it is successful, there are a lot of avenues to pursue that could make use of the method, from fecal transplants, to habitat restoration.