Sampling Microbes From Redwood Groves

One of our goals in creating place-based palettes is actively noticing and thinking about the ecosystem that we live in. We especially like the parts of the ecosystem that are unique, and ground us in what makes our homes special.

For that reason, I was excited to find some discussion in the literature on the unique ecosystem of the iconic coastal redwood trees here in the San Francisco Bay Area. These trees occupy a unique niche in Coastal California that is fascinating in several ways - from their method of collecting water in a dry climate, to their ability to survive fires. There also has been some study on the microbes that live in the soil around their roots. Soil microbiome is a crucial part of how plants interact with their environment, possibly even affecting the range in which the plants can grow (Willing, 2019). Coastal redwoods, with their very limited range, may have unique microbes that can represent our relationship with these forest giants in our bioart.

 

Fig 1. The Coast Redwoods range in green (Giant Sequoia range in red). Source: USDA Forest Service <https://www.fs.usda.gov/psw/publications/documents/psw_rp082/psw_rp082.pdf>

With this in mind, I set out recently to collect some soil from a nearby redwood grove. The goal was to collect several samples and plate them, searching for any microbes that might make interesting colors or textures. In Claire Willing’s thesis, members of the order Actinomycetales were enriched in the soil near redwood roots, so I will look for species in that order in particular, since I know that Streptomyces species in that order can sometimes make brilliant colors (Nodwell, 2019). I planned to take several samples, varying the distance from the tree and the depth of the soil to have the maximum chance of encountering some of these redwood-associated genera. When I plate these samples on agar to isolate microbes I may find that all of the samples are quite similar or they could be extremely different; so I’m logging the locations I sample from in case the observations now could help with telling the story later.

I visited Reinhardt Redwood Regional Park in Oakland, because it has a unique geography, in which the Redwoods grow in a bowl that collects moisture. On the other side of the crest, the soil and weather is much dryer, resulting in totally different vegetation.

 

The biome is relatively dry on this side of the crest

Reaching the redwoods, I selected a grove that was accessible, but - crucially - not cordoned off to allow regrowth. This is a public park, so we want to be respectful of the forest and how the caretakers are helping protect it from overuse.

 

This is NOT an area that I sampled from.

I wanted a range of soil depths because the work I’ve read suggests that different conditions at different depths will lead to different microbes. To sample at these depths without digging a huge pit I used a soil core sampling device. You can order these online for a pretty reasonable price. When you push it into the ground and pull it back out, it holds the dirt at the bottom in the metal ring, while allowing all of the dirt above to fall out.

 

A soil core sampling tool was used to sample different depths of soil.

Wearing gloves, both to reduce cross-contamination and to avoid any poison oak that I might have missed, I rinsed the tool first with water, then with a little bit of isopropyl alcohol, then let it dry. This action removes some of the organisms on the surface of the tool either from the previous sample or that accumulated during storage. I don’t think it’s possible to get the working environment anywhere close to sterile - it is nature, after all - but my idea was to avoid unnecessary opportunities for contaminating my samples.

 

Sampling after cleaning the sampling tool.

Next, I took 3 samples, at different distances from the trees, and at different depths. I let the soil at the top of the tool out onto the ground, since we’re interested specifically in the soil that came from the deepest part I sampled. I placed the remaining soil core from the deepest sampling point into a ziploc bag. In order to track the distance from the tree, I laid the sampler on the ground next to the sample location, and took a photo with both the sampler and the tree in frame. Then, I estimated the depth (based on the length of the sampler) and wrote the depth on the sample bag.

 

Three sample locations in the redwood grove

On my way out of the regional park, I noticed a eucalyptus grove - another iconic California tree (although not a native one). These trees grow on the other side of the hillcrest, where it’s much dryer, so I thought we might get an interesting difference in microbes if we collected this soil as well. I sampled with the same method, and noticed that the soil itself was really different - much sandier!

At the end of the day, I drove home with the following samples:

I’ve stored the soil in the fridge, to minimize changes to the microbiome. I’m looking forward to isolating these samples in the lab. Stay tuned to hear how the isolations go and let us know if you have other ideas for locations to sample.