People, Soils, Microbes

by John Moriarty, 2019 Festival of Creative Learning Event Reporter

On Monday (18th February 2019), I headed over to the ASCUS Lab in Edinburgh for a workshop called ‘People, Soils, Microbes: the Evolution of Inhabited Landscapes’. Despite my background being in physics, I like to get out of that comfort zone whenever I can. That this event was part of the Festival of Creative Learning and was a hands-on workshop rather than a presentation was a major bonus!

ASCUS is a non-profit that tries to bring the arts and sciences together and to democratise science. The lab this session took place in was created so that anyone can have access to a basic wet lab with donated equipment from across Edinburgh.

The session was split into two parts. The first, delivered by Dr. Nikos Kourampas, was about geoarchaeology – applying geology to archaeological questions. The presence of humans and other creatures in an environment causes change in that environment, and those changes can be preserved in the ground – the geologic record. All sorts of things can be preserved, from bones and shells to tools and ash.

A sample of this sediment is like a slideshow of all the things that happened there, with more recent events at the top and older events at the bottom. If we can identify things preserved at different times, we can discover the story of a place and understand how people, other animals, plants or environmental forces have shaped the environment and in turn been shaped by it.

Perhaps the most fascinating example is bats in tropical caves. When bats roost in a cave, the CO2 that they exhale gradually dissolves the nearby rock due to its slight acidity. Over long enough time, the bats inadvertently ‘dig up’ through the rock, making more space for them to roost.

One way to study these samples is under a microscope. By injecting a sample with resin so it holds its shape and then slicing it into very thin (30 micrometres thick, about the same as a human hair) the samples become see-through. In addition to ‘normal’ microscopy, this lets us use techniques like polarised light microscopy, which makes features of the sample’s microstructure visible to the human eye.

This was our first activity of the session – to take a sample (or two, or more) and examine it under the microscopes and try and create a story to explain how the features we saw in it were laid down over time. Our experts were on hand to help with identifying specific things like bone or shell, but the idea was to stimulate creative thinking to tell the story of the places our samples were from.

For example, my sample had a central region in it that was much darker in colour and contained several fragments of bone (which by the way appears as a bright rainbow under polarised light), which I reasoned was a sign that this was an area that early humans had come to at some point in the past, lived there for a time leaving behind ash from their fires and bones from their prey or themselves, and then moved on as part of their hunter-gatherer existence.

I’ve no idea whether this is true, I’d need to know much more about the sample and others nearby to say that, but it gave me an appreciation for how geoarchaeologists use this kind of approach to investigate the ancient past before recorded history.

After we finished with our samples, we were treated to another short talk, this time by Dr. Jiří Jirout on the subject of microbes and microbiology. This was a subject we’d touched on earlier: once something has settled underground it doesn’t just stay there but rather keeps changing as microbes interact with it, much as it did above ground with humans, other animals and plants.

Microbes are amazing. They were the earliest life forms to arise on Earth and are the most numerous too – there are more microbes in a handful of soil than there are humans on Earth. If we could lay out all the microbes in the world out in a line, they’d stretch beyond the edge of the observable universe!

On top of that, most of those microbes are unknown to us. Only about 1% of microbes have been identified. From those we have identified though, we know that they serve an incredibly important function as the last step in a long chain of processes that break down organic detritus. Without microbes we’d be knee-deep in… well maybe better not to think about it.

Some of them are also incredibly tough, although if we’re giving out prizes the winner probably has to be deinococcus radiodurans.

deinococcus radiodurans

This little critter doesn’t care about acid, cold, vaccuum, starvation or – especially impressively – enough radiation to kill a human 1,000 times over! Maybe you’ve heard of tardigrades (a.k.a. water bears)? They’re kind of famous for being radiation-proof, but a dose that would kill even them doesn’t seem to phase our little friend up there. If you’ve heard of extremophiles – life forms that can thrive in extreme environments – deinococcus radiodurans is a polyextremophile – it can happily live in a mix of them.Wait, how does something evolve radiation resistance like that?

After the second presentation, we moved on to our other practical activity: making Windogradsky columns – a sort of microbial zoo! To do this we took a plastic flask, filled about a third with a pond mud and raw egg (to give the microbes some food), a third with soil (more and different microbes) and a third with pond water (more microbes and nutrients).

This forms an enclosed microbial ecosystem that over time will change as the different microbes thrive in different environments – air-breathing (aerobic) ones at the top and airless (anaerobic) at the bottom. After a long time these columns can become incredibly colourful and intricate as the microbes multiply. A great example of this is Bacteriopolis– an art installation at the San Francisco Exploratorium that is a giant Winogradsky column.

Bacteriopolis– an art installation at the San Francisco Exploratorium that is a giant Winogradsky column.
Image credit: Rhododendrites (CC BY-SA 4.0)

The pacing of the workshop was great, the talks were entertaining and detailed without ever seeming to drag and left plenty of time for the practical sessions where we could explore the concepts in more detail. The creative aspect of telling a story through the samples we examined was especially interesting to me, as it bears striking similarity to the first steps in a scientific investigation – you make your initial observations and form a working theory that you revise as more information comes to light. Being able to bring home my own little Winogradsky column was a nice touch too.

a microbe colony
My very own microbe colony! In a year or so it should be thriving in technicolour!

I found the combination of subjects in this workshop fascinating – soil forming the link between geoarchaeology and microbiology isn’t something I’d have thought of before, but like microbes soil is a near-constant presence beneath our feet. We are inextricably linked with the soil as we change it and it in turn changes us, and as we change things above ground, invisible hosts of microbes continue to shape and be shaped by the environment beneath it, gradually creating a record in the Earth that will persist for many millennia into the future.

References, Notes and Information for the Curious

1. Soil Analysis Support System for Archaeology – If you want to know more about geoarchaeological methods.

2. Geoarchaeology – Using Earth Sciences to Understand the Archaeological Record – Historic England’s guide to the subject.

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