Connectivity of green and blue infrastructures: living veins for biodiverse and healthy cities

Data collection for BIOVEINS: Bacteria and birds!

Collecting data on leaf bacteria and birds: what do they have in common?

BIOVEINS postdocs Nicolas Deguines and Romain Lorrillière also collected leaves for the study of bacteria living on tree leaves. According to Romain, this was the fieldwork that was “the most fun” because it was “ecology with latex gloves, scissors and disinfectant.” In other words, it seemed more like precision labwork than typical biodiversity sampling in the field. To collect the leaves without disturbing the leaf bacteria community, the researchers had to locate healthy Platanus x acerifolia trees without leaf infections in each sampled park. One person put on latex gloves, and sterilized them and a pair of scissors with ethylene. The second person used a telescopic pruner to cut a small branch 2-4 m from the ground. The person wearing the gloves had to catch the branch before it fell on the ground. If it fell on the ground, it would be contaminated with soil bacteria. The person who caught the branch then had to hold it, while the other person put on gloves, sterilized them, and cut off the individual leaves with the sterilized scissors. They rolled the leaves up and put them in sterile collection tubes, without touching the leaf to the outside of the tube, or the gloves to the inside of the tube. Then, three more leaves were cut off, without touching the leaf, and put in envelopes. The leaf samples were put in a cooler and then sent to Antwerp, where their bacterial communities will be analysed.

"How elaborate for something so random and esoteric!" might well be your reaction. Why are tree leaf bacteria interesting? According to Laforest-Lapointe et al. (2017), the global "phyllosphere", or leaf surface of all plants in the world, is 4 × 10^8 km2. This is compared to 5 x 10^8 km2 for the Earth's terrestrial surface-- that is, the global leaf surface area almost doubles the terrestrial surface area. Thus, whatever lives on the global leaf surface is significant! While microbiome studies are proliferating for the human microbiome (our gut bacteria, and so on), as well as for the bacterial fauna of the human built environment such as hospitals, we know relatively little about the microbiomes of plants, especially plants in cities. In the same way that we are learning many surprising things about how the gut microbiome affects humans, there may be much to learn about how leaf bacteria affect plant functioning in ecosystems.

Romain also collected the bird data. He did so twice, once in mid-April before the migratory birds arrived, and once in mid-May after they had arrived. Romain explained that organizing the data collection was an intensive task: he collected data at forty sites forming a gradient of urban Paris to peri-urban Orsay, and each morning he had to collect data at 10 different parks between sunrise and 11 AM. He gathered information to meticulously plan out whether the park would be open when he arrived, whether there would be a barrier preventing him from observing the park from the outside, where to stand to do the observations—this had to be at the point where three habitat types typical of each park met-- and also where to park his car. Sometimes, he said, these plans didn’t work out, but usually they did. For each observation he would stand at this point for 10 minutes and record visual and auditory observations of the birds, noting their species, sex, whether they were singing, and if they were moving. In April he made 917 separate observations. There are 41 species of birds found in the Ile-de-France region surrounding Paris, of which he observed 31 at the study sites in April. There should be 71 bird species nesting in Paris according to the most recent Atlas of birds of Paris, indicating that a large percentage of them can be found in urban and peri-urban parks.

One thing that these two data collection techniques have in common is that they are procedurally complicated. What is it about science that makes scientists carry out complicated procedures? What do we gain from this?

In the case of collecting leaf bacteria, the procedures are designed to target, separate, and isolate one thing out of the multitude of things that can be found in nature. One difficulty is that we cannot even see leaf bacteria. Because it is impossible for us to see and physically pick out the bacteria that are not leaf bacteria after the sample has been taken, we need to be sure that we can trust that the sample is only of leaf bacteria-- it needs to be pure on logical grounds. The bird data collection strategy, by contrast, isn't designed to exclude or remove anything: Romain can see the difference between a rat, a butterfly, and a bird, and exclude the first two from the sample based on his expertise. Rather, because the number of birds and parks is so large (which is also true for the number of leaves and bacteria), there isn't time to gather ALL the observations possible of ALL the birds in ALL the parks FOREVER. The sampling strategy is designed to ensure that the observations can be clearly defined (when, where, how, what, etc.) and are all strictly comparable because the method of observation was always identical. In science, identical methods = comparable data = something you can say something about.

We will think more about sampling strategies and what they mean in the next post.

Park photos (c) Romain Lorrillière.
Laforest-Lapointe, I. et al. 2017. “Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity” mSystems vol. 2,6 e00087-17. 5 doi:10.1128/mSystems.00087-17

--Meredith Root-Bernstein