Urban Life Aquatic: A Discovery In Paris Reveals A Huge Ecosystem Hidden In Plain Sight

Urban Life Aquatic: A Discovery In Paris Reveals A Huge Ecosystem Hidden In Plain Sight


For 12 days in June 2015, something rather unusual took place in Paris. Under clear skies, a team of scientists armed with toothbrushes, methodically passed through each of the city’s 20 districts searching for signs of life.

You can find many things in a busy European metropolis, but an aquatic ecology expedition isn’t usually one of them. Nevertheless, researchers from the Biology of Aquatic Organisms and Ecosystems research unit (BOREA) (CNRS / MNHN / IRD / UPMC / University of Caen / Université des Antilles) in Paris and the Max Plank Institute for Terrestrial Microbiology were on to something. They had noticed that the gutter water in Paris not only had the characteristic green and brown shades reminiscent of microbial matts, but they had also observed bubbles in the water — not the kind you get from detergent runoff, but the tiny spheres of pure oxygen that are formed during photosynthesis.

From these little bubbles came the discovery of an enormous ecosystem hidden in plain sight.

The urban biome

Understanding the ecology of cities has become increasingly important over the past few decades. Together with their associated urban sprawl, cities have essentially become the primary human habitat. More than half the global population now lives in urban areas, and by 2050 that number will increase to two-thirds.

Unsurprisingly, this comes with unprecedented environmental stresses. As major cities try to contend with air pollution, reduce carbon emissions and water use, and counteract urban heat, there has been an increasing interest in the role biology might play. This is because, despite all that steel and concrete, urban centers are also vast biomes. New York City, for example is home to more than 5.2 million trees and thousands of animal species. There are screech owls in Central Park, coyotes in the Bronx andfireflies in the West Village.

Urban ecological studies are showing how tree canopies can have a substantial impact on street temperature, water evaporation, and even flood mitigation. Other research is revealing how our highly curated urban biomes – with all their introduced plant and animal species — cause dramatic declines in local biodiversity. Only around 25% of native plant species and just 8% of native bird species manage to adapt to cosmopolitan life. As urbanization expands around many existing cities, and dramatically increases in some extremely biologically diverse areas of the world, it’s important to understand why certain plant, bird and mammal species are quite successful in cities, and others struggle to survive in the face of habitat loss.

But this isn’t the whole story. As we go smaller, the urban biome gets a lot bigger.

Under the microscope

Microbes are critical to the function of any ecosystem, and cities are no exception. Yet the extent to which urbanization stresses and distorts microbial diversity isn’t fully understood, which is kind of a problem because the microbial health of the urban biome strongly influences ecological health at the larger scale, including the health of its human inhabitants.

For example, changes in the microbe content of floral nectar can alter pollination patterns, affecting plant reproduction. Soil microbe diversity affects nutrient cycles. Meanwhile, changes in soil microbe diversity in turf grass can alter how your favorite park contributes to atmospheric nitrogen cycling.

Other microbes can corrode entire networks of concrete structures by producing tiny amounts of acid that break down calcium carbonate in cement. Even stone and granite must contend with microscopic interlopers that wear them down over time.

And there are, of course, microbes that interact directly with humans, some affecting health for the better and some for worse. As humans gather densely into urban centres, so to do our microbes. A unique ‘biogeography’ of human-associated microbes spans every city, and because urban areas tend to be highly partitioned, this can change from building to building, and even room to room.

Yet, while microbes seem to be everywhere in the urban biome, we only know about a tiny fraction of them. Which is why some urban ecologists have headed straight for the gutter.

Paris gutter.jpg

Life Aquatic

It turns out that, in the search for microscopic urbanites, gutters have been largely overlooked even though they represent a huge surface area of the biome. In New York City, gutters line the better part of more than 6,000 miles of road, conveying water runoff from surfaces that cover around 72% of the city, such as roofs, sidewalks, and streets (the Amazon river, for loose comparison, is around 4,000 miles).

Paris might be smaller, but with 6,100 streets, the gutter network is substantial and pervades the majority of the Parisian urban biome. So during those dozen rain-free days in early June 2015, the research team set out to explore the Parisian life aquatic.

“We collected water and biofilms from 90 street gutters (GMs) that cover all of the twenty districts of Paris,” they explain in their paper, published this month in the International Society for Microbial Ecology (ISME) Journal.

And the toothbrushes? Those were used for scrubbing the microbial mats that covered the gutter surfaces. If you happened to have been in Paris at the time and witnessed this, you now finally have an explanation.

Collection Sites

Collection Sites

The samples were geotagged and quickly sent back to the lab where they underwent genetic analysis.  The researchers identified 5,782 Operational Taxonomic Units (OTUs).

(A group within the same OTU share around 99% genetic similarity, so they’re very closely related. Given that there may be as many as 1 trillion microbe species in the world, with more than 99% of them yet to be discovered, an OTU is a kind of proxy for species without actually being too prescriptive.)

The discovery of nearly this many distinct OTUs indicates a significant amount of biodiversity in Parisian gutters. Remarkably, the majority of these were not found in the non-potable water sources derived from local rivers, which are usually used for street cleaning. This suggests that most gutters had established a unique ecosystem of their own. The researchers were able to classify most of the microbes and found that the majority were diatoms, photosynthetic single-celled algae.


Diatoms first showed up around 200 million years ago (and perhaps earlier), and currently they are a critical part of the global food web, and account for 20% to 25% of total global photosynthesis. Those brownish films you see in wet gutters are most likely mats of algal diatoms, quietly fixing CO2.

The researchers also found that the gutters were teeming with a large number of other algal species, as well as other unicellular organisms, like alveolates. They also found fungi, and even a freshwater sponge species and a species of mollusk.  While many of these are benign and downright fascinating, some of the organisms discovered were a concern.

While most of the fungi they found have no interest bothering humans, one of the OTUs identified may correspond to a genus of fungi that does include a human pathogen: C. neoformans, which can cause infections in immunocompromised people. While this particular species wasn’t found in the gutter study, the discovery of a close relation suggests that regular monitoring of the gutter microbiome is a good idea. So too does the discovery of an OTU that points to the presence of the Hartmannellidaefamily of amoebae. Amoebae are no strangers to natural or urban environments, the problem is that Hartmannellidae amoebae can act as hosts for some human pathogenic bacteria, including Legionella pneumophila which causes Legionnaire's diseaseThe amoeba-bacteria tenancy arrangement has probably been going on for around a billion and a half years, give or take. Bacteria find a way to evade an amoeba’s defenses and gain the advantage of its protective covering while hiding out. It lends further weight to the idea that monitoring gutter biodiversity could serve as an early warning system for public health hazards.

However, as the researchers point out in their paper, the gutter microbiome also has an important upside, “Understanding Street gutter communities’ composition and dynamic is an exciting new topic that might concern most of the urban and peri-urban areas worldwide.”

They propose that the gutter microbiome is likely to be beneficial in the treatment of water run-off, by breaking down human waste and vehicle pollutants. Given its substantial surface area in every city, it could also play a significant role in the global carbon cycle.

With this new insight into the biodiversity and structure of an often hidden layer of the urban biome, expect to see more urban ecology expeditions on a street corner near you.



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