Some experiments take days, some weeks or months and a few take years. In bacterial time this means multiple lifetimes!
Breaking down the microbiology world one bite at a time
Mad Scientists are starving bacteria for years.
Long term cultures teach us how bacteria evolve over time, or enable us to let the slowest growers be in enough numbers for us to study them. A recent study by Ratib and colleagues showed how they cultured E.coli for 1,200 days to study adaptation to stress.
In these 1,200 days bacteria were not fed, only samples were taken at several intervals for cell count, whole genome sequencing, and some assays to learn more about the different clones.
Bacteria replicate by binary fission, splitting in two. Each daughter cell is therefore a clone of the mother cell. But bacteria can have errors in their genome that will create mutations that will or will not be kept into further generations.
Bacteria in culture undergo several phases:
- lag phase, when they adapt to their new environment – cautious phase
- exponential phase, when they grow exponentially – happy phase
- stationary phase, when nutrients start to lack – hungry phase
- After the stationary phase cells start to die.
- But some survivors persist and enter a long stationary phase, waiting for better days – survivors!
In their study, Ratib and colleagues did not add fresh medium into the bacterial environment, thus ‘starving’ the bacteria. Therefore, bacteria had to recycle nutrients that were available. These surviving cells had to find nutrients from what was in the environment: dead cells. This shift from, for example glucose, to mostly amino acids (protein building blocks) and nucleic acids (DNA building blocks) from the dead material, forces the bacteria to adapt to utilize these resources for energy.
By doing whole genome sequencing (looking at the entire DNA sequence of the bacteria), the authors could see mutations and separations in lineages. They found two main subpopulations co-existing and adapting during the full length of the experiment. Mutations were found mostly in genes essential for long term survival and stress situations, and in genes necessary to use a new energy source.
Understanding how bacteria can adapt in stressful environments, such as starvation and stress situations, allows scientists to better understand how they survive in real world environments when subjected to these stresses.
But this study was not the longest culture experiment. The first place goes to the E. coli long-term evolution experiment (LTEE) started in 1988. Yes, 73,000 generations as of early 2020, but it had to be stopped due to the covid-19 pandemic. However, it wasn’t the first time it was interrupted and bacteria can just be frozen and unfrozen. In September 2020, it was started again and has funding for 5 more years! Long live E. coli.
Learn more about E. coli:
Original paper: Nicole R. Ratib, Fabian Seidl, Ian M. Ehrenreich, Steven E. Finkel. Evolution in Long-Term Stationary-Phase Batch Culture: Emergence of Divergent Escherichia coli Lineages over 1,200 Days mBio Jan 2021