Vertical Stratification in Urban Green Space Aerobiomes

by Jake Robinson

“We are exposed to far more microbial species by visiting natural environments than in places where nature is kept out”.

This is important because exposure to high microbial diversity from a young age is vital for a robust immune system. But does three-dimensional space affect our exposure to microbes? If soil is one of the most biodiverse habitats on the planet, is there a decay in bacterial diversity from the ground up? Are children and smaller adults exposed to different microbes than taller adults?

During my PhD, I spent three months in Adelaide, South Australia and set out to answer these questions (along with others). I stayed in a tiny Nordic-style building about the size of a large shed, in the bottom of a garden in an Adelaide suburb. The building was perfect. It had a small private garden with tropical vegetation, carnival lights, and a stone pizza oven. I spent the first few days in the carport (Chitty-Chitty Bang-Bang style, bar my humble invention), sawing wood and tightening screws to create an army of sampling stations. I was regularly joined by a blue-tongued lizard and a couple of rosella parrots who dive-bombed below the canopy to escape the heat of the Adelaide summer, dipping their vivid emerald and scarlet feathers in the water bath, “ahh, that’s better”.

Once the sampling stations were built, I installed them in the Adelaide Parklands, which hug the boundary of the CBD. My Ecuadorian friend and research assistant Chris helped me collect samples from the air and the soil ready for processing in the lab. Each sampling station included a shelf holding Petri dishes from the ground and at regular intervals to 2 m high—they looked a bit like a hat rack. We left the sampling stations for several hours to passively collect bacterial cells. Back in the lab, we extracted the bacterial DNA from the samples and prepared them for high-throughput sequencing. This is essentially a method for reading the building blocks of the bacterial genes, thereby creating a long list of names that tell us which bacteria are in the samples.

After some bioinformatics and number crunching, we found that bacterial species diversity was much higher in the samples collected closer to the ground than those collected higher in the air column. As mentioned, diversity is considered a good thing for human health. Higher diversity towards the ground was predicted because a thimble-full of soil has more bacteria than humans roaming the planet. As such, the soil is a primary source of the bacteria floating around in the air and entering our bodies. The finding that microbial communities vary with height is important because we breathe hundreds of millions of microbes daily. Exposure during early development is crucial to children’s immune systems. But most aerobiome sampling is done at two meters above ground, so our study indicates that if we want to research what kids are breathing, we need to be sampling at half a meter above the ground. Moreover, the relative abundance of opportunistic pathogens is often lower in areas with higher alpha diversity due to competitive exclusion. This study has implications for designing and restoring urban green spaces for human health by gaining insights into exposure routes and potential.

For example, can we find ways to optimise human exposure to health-promoting biodiverse microbes in urban green spaces? Can we design our green spaces with more undulating topography to ensure an evenness of microbial diversity in the airspace? Currently, we simply flatten the ground and plonk a load of asphalt or species-poor amenity grassland on it. Yet, diversity is key when it comes to urban green spaces and human health. Diversity of species, diversity of sensory stimuli, diversity of opportunities to engage with nature, and diversity of structure—that is, diversity of topography and vegetation.

See future posts on Microbiome-Inspired Green Infrastructure (MIGI) for more on how we can design our urban environments with explicit considerations for the unseen and underappreciate life-forms—the microbes.  

Find out more about the vertical stratification study in my forthcoming book Invisible Friends.

Read the full paper here: https://ehp.niehs.nih.gov/doi/10.1289/EHP7807

Authors: Jake M. Robinson, Christian Cando-Dumancela, Craig Liddicoat, Philip Weinstein, Ross Cameron, and Martin F. Breed