In just a gram of healthy garden soil, there are millions of bacteria, representatives of an estimated several thousand species. Several thousand species… just in a pinch of the soil we gardeners have our hands in most every day. That, in itself, is mind boggling.
But even stranger, in this age of cutting edge science, is that most of these bacteria haven’t even been identified yet. Why? Well, as it turns out, less than 10% of soil bacteria can be cultured (grown) in the laboratory, and even those that can be cultured might look and ‘act’ so similarly it can be difficult to tell them apart, even by looking at them under a powerful microscope.
Why can’t they be cultured? Microbiologists rely on growth media, or ‘food’ that allows one or two tiny bacteria in a sample of soil to multiply into thousands so that they can see and study them, but most soil dwellers are very picky eaters. They have trillions of neighbors to compete with, and they’ve learned to eat some very strange things to get by. Many are involved in complex food chains, needing the products of plants, fungi, or other bacteria to survive.
Then the world of DNA sequencing came along…
…And with it a new way to find new types of bacteria that have been hiding all of these years right under our feet. When searching for new bacteria, or just looking to see who’s who in a sample of soil, scientists can now look directly at their genes, often a particular gene called 16S rRNA. This gene encodes a structural component of the bacterial ribosome, but that’s not really important. What’s important about 16S rRNA, is that all bacteria have this gene, it’s always exactly the same at the beginning and the end of the gene sequence, and in the middle there are slight differences from one species to the next (called variable regions) that we can use to tell them apart.
Here, we come to a process known as PCR, or the ‘polymerase chain reaction’. This is a way to make lots of copies of one specific gene within a sample of thousands, and relatively quickly (usually within a few hours). When you watch a crime show on TV, and they put the little tube with a DNA sample into a machine and shut the lid, this is what they’re doing, only they’re trying to ID a criminal, not an obscure Bacillus that might be found clinging to a radish.
PCR works by taking advantage of DNA’s natural replication (copy making) process that happens every time a cell divides. Polymerase is an enzyme that moves along a strand of DNA, adding the correct nucleotides (building blocks) as it goes. As the PCR machine cycles through a series of temperatures, the DNA is unwound from its double helix, the polymerase attaches to newly single strand of DNA, makes a copy, falls off, and then the cycle starts again. This continues until there are thousands of copies of the gene of interest.
But wait, if our sample of soil has thousands of bacteria, each with a few thousand genes, how do we make copies of just 16S rRNA? The answer is in short pieces of DNA that are added to the reaction, called ‘primers’. These ‘primers’ match the sequence at the very beginning and very end of the gene we want to copy, and when they come across their perfect match (in this case 16S rRNA), they grab on. These short sections of now double stranded DNA are just what the polymerase needs to start making copies. So if we put primers that match the beginning and the end of 16S rRNA into the mix, we copy this specific gene so many times that it can be separated from the original sample. It can then be ‘sequenced’ by another machine, which can read the individual nucleotides as they pass by. Now the gene sequence can be compared to a database to see if it matches 16S rRNA genes from any known bacterium. If it doesn’t, a new species has most likely just been discovered!
So, now that we have PCR machines and DNA sequencers, we can go to town on discovering new species of bacteria, right? Discover them, yes, that’s the easy part. But unfortunately, it takes much longer to learn what they’re like and what they do, let alone what they eat or how they interact with other organisms.
We have some work to do…