Note from Justine: This guest post by Janani Hariharan provides a wonderful introduction to the hidden world of soil microorganisms.
“What did you do in the lab today?” my friend asked. We were both in graduate school in a tiny college town. “I spent the day extracting DNA from dozens of soil samples. I feel pretty tired!” My friend’s eyes grew wide. “Extracting DNA from soil? But where does the DNA come from?”
There’s a common misconception that soil is “dead” or static, but nothing could be further from the truth. Soil is, in fact, home to one of the largest pools of microbes across all environments. Some estimates suggest that one gram of soil could hold up to 10 billion microorganisms. Soil microbes are essential in creating healthy, flourishing soils that support many other life forms (including human beings) and in the fight against climate change. Scientists and modelers are starting to recognize the undervalued contributions of these critters, particularly when calculating the amount of carbon that is stored in soils or when working with farmers to develop farm management plans.
In this blog post, we will explore the hidden world of soil microorganisms, why we should be excited about them, and where and how they live.
Why are soil microbes exciting?
We’ve established that there are vast numbers of microbes out there in the soil—but which ones should we get to know first? Ask a soil microbiologist what their favorite microbe is, and they will have an answer. I reached out to microbiologists on Twitter, and they came up with a great list:
- Verrucomicrobia phylum or “warty microbes,” often found decomposing organic matter in grassland soils. This interesting name is derived from the Latin word ‘verruca,’ meaning warts. Visit this link to see why Verrucomicrobia are considered warty and to find a microbiome card game.
- Bacillus species, for their ability to form intricate and sometimes colorful biofilms (see photo below)
- Bradyrhizobium japonicum, a nodule former that associates with plant roots to fix nitrogen in the soil. Such bacteria can often be essential sources of nitrogen to leguminous plants.
- Streptomyces species, a genus of bacteria that produce more than two-thirds of the antibiotics we use commercially
- Chitinophaga pinensis, a bright orange bacterium that can glide on solid media
Clearly, the soil is alive with billions of tiny organisms. What are their lifestyles like? What kind of a home does the soil provide? Find out in the next two sections.
Where do soil microbes live?
Much like human civilizations, the types of microbes we find in the soil can vary drastically between different regions of the world or even between different land-use types in a single region. The microbial community in a forest soil looks different from that in an agricultural field. We’ve also found microbes in frigid places like Antarctic deserts.
Some bacterial phyla like Proteobacteria, Actinobacteria, and Acidobacteria are found in most soils globally. In some regions, soils have more characteristic communities: for example, Actinobacteria are dominant in dryland and dry-forest soils. Environments like thermal sediments harbor “extremophile” microbes like Pyrococcus furiosus, a species that produces heat-resistant enzymes.
Historically, we have assumed that microbes have no limits on migration since they are small and abundant, but this assumption is starting to come under scrutiny. For instance, we now know that hot-spring dwelling archaea are highly localized and unable to move very far. We’re also learning that glaciation has prevented microbial movement in the past, which is an important natural history lesson but also has real consequences on which microbes are found where today.
There is still a lot we don’t know about soil microbes yet. For example, we know that some plants and animals are found exclusively in certain parts of the world, but we don’t know yet if this is true for microorganisms. For instance, kangaroos and koalas are endemic to Australia, but are there soil microbes (perhaps our extremophile friends) that are found in one part of the world and not in others? It’s hard to say. Microbes can be difficult to observe and identify, and we don’t know enough about how microbes get from one place to another, or what conditions they need to settle down in their new home.
How do soil microbes live?
Soil is a complex environment, alternating between patches of high and low resource availability, aerobic (with oxygen) and anaerobic (without oxygen) conditions, all within a few centimeters. Thus, although soils may look homogenous and quiet from the outside, there is a massive, thriving microbial civilization right under our feet. As with civilizations, competition exists between different groups, but there is also a surprising amount of cooperation.
Within the soil, some microbes eat the waste of others. Some are particularly good at breaking down complex carbon compounds in the soil and produce simpler compounds that others in the community can use. For instance, a study suggests that bacteria from groups like Spartobacteria, Planctomycetes,and Chloroflexi could be involved in breaking down cellulose molecules into smaller molecules called cellodextrins or glucose, which can be easily taken up by microbes that don’t have those abilities.
The cooperation extends further than just between microbes but can occur between bacteria and plants. Various bacterial groups can fix nitrogen and make this nutrient available to plants as well as other organisms in the soil. Indeed, many soil bacteria are famous for their ability to associate with the roots of living plants and form a symbiotic partnership wherein the plants get nitrogen, and the bacteria get food.
On the flip side, soil can also be a war zone. And the weapons are antibiotics. Bacteria can produce antibiotics as a defensive weapon when a predatory microbe attacks or as an offensive weapon to gain an advantage in the complex soil environment. They may gain access to a nutrient resource or more space for a growing population. Because antibiotic production is so common among soil microbes, researchers have had great success in mining for antibiotics from those species, especially from Actinobacteria like Streptomyces species (see photo below).
Parting thoughts on soil microbes
The story of soil microbiology is that of an active, thriving, and mysterious community that is the bedrock of human civilization. These microbes drive things like food security and carbon sequestration in the soil. Bacteria isolated from the soil have been our best reservoirs of therapeutic compounds, including a new class of antibiotics called malacidins and new versions of anti-cancer agents like bleomycin. Aesthetically, they are the source of beautiful pigments that have been used to create paintings (see photo below). A world without soil bacteria might not be worth living in.
Janani Hariharan is a PhD candidate in Soil and Crop Sciences at Cornell University, where she studies the biogeography and ecology of Streptomyces bacteria in the soil. Find her on Twitter @jananiharan or at jananihariharan.com.
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