Scientists are Trying to Crack Soil’s Biological Jigsaw Puzzle

When you pick up a handful of dirt, you probably don’t see much. But biologists see an entire world. A single tablespoon of soil from your backyard contains as many cells of bacteria as there are people living in North America. 

 While we normally don’t pay much attention to the bacteria in soil, they play a major role in how plants grow. Bacteria can provide plants with the same essential nutrients found in fertilizers. They can even send signals to plants to encourage them to grow. 

Now, scientists and farmers are trying to harness the power of soil bacteria to improve the yield of major food crops like corn, lettuce, and soybeans. If spraying fields with bacteria could produce larger and faster growing plants, farmers could easily meet the world’s growing food demand. And they wouldn’t have to turn to expensive and polluting fertilizers. 

 There’s a problem, though. Not all bacteria found in soils are good for plants. Some cause diseases or suck up more nutrients than they produce. And scientists don’t yet have a way to tell good soil bacteria from bad.

The Biological Jigsaw Puzzle

power of soil bacteria

DNA sequencing is currently the best method that scientists have to identify soil bacteria and determine whether they are helping or hurting plants. By knowing what DNA a bacterial cell has, biologists can say whether it produces nutrients or acts as a dangerous invader. 

The problem is that there are so many bacteria in soil that it is impossible to separate out every individual cell and sequence its unique DNA. Instead, scientists just randomly sequence all of the DNA in the soil at the same time – a process known as metagenomics. 

Metagenomics produces millions of short snippets of DNA. Each snippet represents a tiny fraction of the DNA of one bacterium. Think of it like a single piece of a jigsaw puzzle. Putting the right pieces – DNA snippets – together in the right order paints a picture of how that bacterium might affect plant growth. 

The challenge is that scientists aren’t dealing with one big puzzle. Instead, metagenomics results in millions of small DNA puzzles to solve, with all of the pieces for all of the puzzles jumbled together. Even worse, many soil bacteria have a lot of DNA in common. That means the puzzles that scientists are trying to solve look nearly identical in certain places. 

Even today’s most powerful supercomputers can’t put all of the pieces of this puzzle together. For now, it nearly impossible to identify which bacteria could improve crop production and which could spread plant diseases. 

Technology to the Rescue

DNA sequencing

But, thanks to advances in DNA sequencing, scientists are getting closer to sorting out the mixed up soil DNA. First, new DNA sequencing methods are under development that would produce longer DNA snippets. That will make it easier for computers to detect when two snippets truly come from the same bacteria. Second, more sensitive DNA sequencing is making it increasingly possible to sequence bacteria one cell at a time instead of sequencing millions of cells all at once. 

With these improvements on the horizon, it may be only a matter of years before scientists are able to solve soil’s biological jigsaw puzzle and identify the most promising soil bacteria to improve food production. Even then, it may be some time before bacteria fully replace fertilizer. Any new potential bacteria supplements for farm fields will need to be tested on different crops and on soils around the globe. 


Bacteria – Tiny, single-celled organisms. There are an estimated one trillion species of bacteria on Earth. 

Nutrients – Chemicals that plants need to grow. 

DNA – Genetic information contained by every living cell that provides the blueprint for life. 

DNA Sequencing – Method for reading the DNA found within cells. 

Metagenomics – DNA sequencing method that involves randomly sequencing DNA from lots of cells at the same time. 


Sergaki, C., Lagunas, B., Lidbury, I., Gifford, M. L., & Schäfer, P. (2018). Challenges and Approaches in Microbiome Research: From Fundamental to Applied. Frontiers in plant science, 9, 1205. doi:10.3389/fpls.2018.01205 

Ghurye, J. S., Cepeda-Espinoza, V., & Pop, M. (2016). Metagenomic Assembly: Overview, Challenges and Applications. The Yale journal of biology and medicine, 89(3), 353-362. 

Howe, A. C., Jansson, J. K., Malfatti, S. A., Tringe, S. G., Tiedje, J. M., Brown, C. T. (2014) Tackling Soil Diversity with the Assembly of Large, Complex Metagenomes. Proceedings of the National Academy of Sciences. 


  • Michael Graw, Ph.D.
    Michael Graw is a freelance journalist and photographer based in Bellingham, Washington. He holds a PhD in oceanography from Oregon State University. Michael is excited about making scientific research easier to understand and sharing the stories behind the science. When not writing, you can find him climbing, skiing, and trail running. Writing for Smore gives Michael an opportunity to share the most exciting new developments in science today with tomorrow's scientists.

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