The Rainmaking Bacteria

Thank you Keith Bell, the microbiome mind behind the Gut Club, for sending me your wonderful little book. Keith weaves the story of bacteria’s role in the weather cycle and the environment with the rainmaking ritual of Native Americans.

When I asked Keith what his take on the microbiome was, he told me he wrote a children’s book called ‘I wonder what it’s like to be a raindrop’ (2018).

Initially puzzled, I thought that was a bit mad. What could a raindrop have to do with the microbiome? Intigued, I opened the kid’s book on “rainmaking bacteria”.

Being so dug into the science world and publishings of the microbiome, I often conflate the term “microbiome” with what’s living in our gut. But actually “microbiome” – a microscopic biological community – can describe bacteria or microbes living anywhere. On plants, or even in the clouds!

What’s so great about this book is that even though it is for children, it challenges you to open your mind to imagine bacteria involved in processes as unexpected as the precipitation cycle. It certainly challenged me anyway and made me realise how close-minded and dismissive I can be towards things I don’t understand or haven’t encountered yet. Even though I’d had this epiphany before, the levels to microbial involvement in our environment continues to blow me away.

After coming away from the book skeptic that bacteria can cause rain, I was shocked after a quick bit of research that bacteria or micobes have been found to form the nuclei which ice condense around, therefore creating rain. This theory, called bioprecipitation, was first proposed by David Sands from Montana State University in 1982.

Bacteria get swept into the atmosphere by wind, travel huge distances in clouds and then fall back to earth in a heavy shower where they colonize plant surfaces to renew the cycle afresh.

Now I get that the microbiome is a global system that we are inhabiting, rather than them inhabiting a portion of us. Even though I had read about the Gaia hypothesis, I wasn’t nearly open-minded enough initially reading this book. Now I’m amazed at discovering the growing research in aerobiology, and plant-colonizing bacteria originating from inner outer space (Keith’s words not mine), some of which I will get into below.

I wonder what it’s like to be a raindrop?

The story unfolds with Chloe and Eli (the illustrator’s Brent Bludsworth’s children) playing inside by the window while it is raining heavily outside.

3 raindrops appear – Drippy, Droppy and Droopey – who offer the children their wisdom on what it’s like to be a raindrop. In a bizarre turn of events 3 ice cubes appear. They are the raindrop’s teachers and are actually bacteria frozen inside ice.

Icy, Freezy and Frozey (the bacteria) describe how they wait for wind to blow them into the sky where they can form ice clouds and then fall back to Earth as rain to start the process again.

It’s colourful, vibrant and interesting.

Asking the hard-hitting questions, Keith poses what will happen if we continue to spray our crops with pesticides which kill bacteria, when we need them to produce rain.

This is a connection I hadn’t considered before and one more jigsaw piece in the picture of how humans are disrupting the natural flow of our environment.

I also enjoyed the nod to the Native American’s rainmaking ritual and the thought experiment that dancing around and kicking up enough dust could cause rain.

Without giving away the entire story or posting screenshots of every page I will just say that this is a cute book with an important message to inspire children and adults alike.

Bacteria’s role in ice nucleation

So are bacteria really involved in ice formation and rain? I had to investigate.

This nature article points to Brent Christensen’s team’s work. A microbiologist who we are previously familiar with for profiling ancient bacteria locked up in glaciers in Lake Vostok in the Antarctic.

What his team did was test the freezing point of snow samples taken from various locations in Europe, North America and Antarctica.

At temperatures warmer than -40ºC, ice formation does not happen easily or ‘spontaneously’. For ice formation there needs to be a central particle that forms the ‘nucleus’ of the condensation. These particles can take the form of minerals or they can be biological entities or ice nucleators such as bacteria.

They found that the snow samples containing microorganisms were able to form ice at temperatures close to 0 ºC, a much higher temperature than samples containing only minerals.

Ubiquity of biological ice nucleators in snowfall

What’s most interesting about this study is that the samples were collected during seasons and in locations where no deciduous plants existed. The authors conclude that the bacteria must have been transported over large distances by the precipitation cycle while maintaining their ice nucleating ability in the atmosphere.


In the same way fungal spores and seeds can be dispersed by wind, bacteria can travel in the same way.

  • The phyllosphere (surface area of plants) is home to a multitude of bacteria and microbes.
  • Microbes living on plants can become airborne aerosols in the atmosphere.
  • The atmosphere serves as a vehicle for microbial dispersal locally and globally.
  • These airborne microbes are then deposited back to earth’s surface and soil as rain.
  • Proteobacteria followed by Bacteroidetes, Actinobacteria, and Firmicutes have been identified as the most common phyla both in the atmosphere, precipitation and in the phyllosphere.

Rain as bacterial reservoirs

Phyllosphere - Wikipedia
The phyllosphere is the total surface area of a plant where microbes can inhabit.

A paper published earlier this year titled “Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota” found that their tomato plants exposed to rain had a larger microbial population living on the leaves than the plants which hadn’t been exposed to rain.

By doing 16S rRNA sequencing of plants grown indoors vs. outdoors they found an enrichment of bacterial populations on the outdoor grown plants.

To test this finding further, they germinated plants in the lab (first sterilizing the soil by autoclaving it to prevent bacterial contamination from the soil) and separated them into 3 treatment groups by spraying the leaves with either:

  • concentrated rain microbiota (the water filter membranes were incubated at room temperature for 10 minutes to increase the number of collected bacteria present)
  • filter-sterilized rain (rainwater that passed through the filter)
  • sterile water (autoclaved rainwater)

After spraying the lab plants, their leaves were collected 7 days later for sequencing.

104 OTUs were significantly increased in the plants inoculated with concentrated rain, while there was no difference in the plants exposed to filtered or sterile water. This showed that airborne bacteria can successfully colonize plants.

Other identified sources of bacterial reservoirs for the phyllosphere include the air, insect pollinators, seed and neighbouring plants.

Plant health and microbes

This work on bacteria originating from the atmosphere colonizing plant surfaces is extremely fascinating and is clearly just getting going.

Currently these ‘rainmaking bacteria’ are considered plant pathogens and are sprayed as they can contribute to crop damage.

I would like to see more work on how or if these colonizing bacteria can contribute to plant health. Maybe some experiments profiling the metabolites produced by bacteria on the surface of plants. Or inoculate damaged or unhealthy plants with microbial rainwater to see what happens.

It really is such an exciting time for microbiome research!

the gut club

For more the gut club check out this new presentation from Keith where he drops some fantastic dietary information and microbiome facts to change your microbiome composition and health. Well worth a watch if you have the time!

Also if you are interested in learning more about constipated clouds or teaching your kids about microbial balance in our ecosystem you can get The Rainmaking bacteria book here.

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