Every step you take, you’re likely walking on a world of unseen and undescribed microbial diversity. And you don’t need to head out into nature to find these usually unnoticed microscopic organisms.
As biologists, we know this firsthand. A meetup for coffee several years ago ended with our using makeshift sampling tools – actually a coffee stirrer and a coffee cup lid – to collect some of the black gunk from between the sidewalk’s concrete slabs. In this mundane space on the Mississippi State University campus, we discovered microbes that have lived on Earth for millions of years.
Finding these charismatic organisms in the environment, while exciting, is just the first step. Our mutual interest is to better understand how organisms are related to one another. We’re using DNA to reveal their relationships in the very distant past.
By sampling organisms that are alive today, we can ask deeper questions about the evolution that happened millions of years ago in now extinct ancestors.
Piecing together the tree of life
Our simple act of collection after our 2015 coffee date started a fruitful collaboration between our labs in the field of molecular protistology. Our focus is on the microscopic single-celled organisms called protists, particularly ones that move around using tiny tentacles called pseudopodia.
Matthew W. Brown, CC BY-ND
One elusive critter we identified in our sidewalk sample is an amoeba named Amphizonella; we joke that it makes its own “leather jacket” in the form of a soft, protective outer layer.
Despite what other scientists had previously thought, we had a hunch that this organism wasn’t closely related to other amoebae that have tougher outer coverings. This other much larger group, called testate amoebae, have shells – imagine microscopic snails – instead of leather jackets.
Because testate amoebae make a hard shell, they have the potential to fossilize. In fact, their vivid fossil record represents some of the oldest unequivocal fossils of eukaryotes – the category of life whose members hold their DNA within their cells’ nuclei. Why is this important? Human beings are also eukaryotes, as are plants, fungi, other animals, kelps and protists. Because these amoebae are some of the oldest eukaryotic fossils, they can in turn tell researchers like us something about our own species’ origins.
Since the advent of DNA sequencing in the early 2000s, biologists have used a small piece of the genome, even a single gene, to examine the relationships between organisms, though with limited success. Through similarity of DNA sequences between living organisms, one can infer relationships using complex computational approaches that model evolution change over time from empirically derived data. Simply put, scientists try to piece together who’s related to whom in order to reconstruct the evolutionary tree of life, or what we call a phylogenetic tree.
In most cases the testate amoebae are quite difficult to cultivate in the laboratory, making it very hard to obtain enough material to sequence their DNA with the usual methods.
To overcome these challenges, we’re using a cutting-edge technique that allows us to take an organism directly from the environment and sequence its entire transcriptome – that’s the blueprint of all the proteins that it makes. This way, we’re able to bypass sequencing the whole genome (with its extraneous information) and sequence only the protein-coding regions. We end up with high-quality data of billions of base pairs of DNA that we can directly compare with similar data from other organisms.