Genomic comparison of ocean microbes reveals East-West divide in populations
By Denise Brehm
Civil & Environmental Engineering
Much as an anthropologist can study populations of people to learn about their physical attributes, their environs and social structures, some marine microbiologists read the genome of microbes to glean information about the microbes themselves, their environments and lifestyles.
Using a relatively new methodology called comparative population genomics, these scientists compare the entire genomes of different populations of the same microbe to see which genes are “housekeeping” or core genes essential to all populations and which are population-specific. (Scientists are able to read a genome and translate genes into proteins that serve particular functions.) Population-specific genes sometimes tell a very clear story about the environment, for instance the availability of light and particular elements, and over time, they can point to the microbes’ evolutionary adaptation to changes in the ecosystem.
In a recent MIT research project, the population-specific genes revealed important differences in two environments with a clarity never before reported, providing unmistakable clues about the lifestyles of two populations of the same oceanic photosynthetic bacterium, Prochlorococcus, one living in the Atlantic Ocean and one in the Pacific.
Professor Sallie (Penny) W. Chisholm and recent graduate student Maureen Coleman, now a postdoctoral scholar at Caltech, found that although a continent separates the populations, they differ significantly in only one respect: those in the Atlantic have many more genes specifically related to the scavenging of phosphorus, an essential element for these microbes. And just as the variations in the beaks of Darwin’s finches were evolutionary adaptations related to food availability, so too are the variations in the Prochlorococcus genes related to phosphorous gathering. Both are examples of a powerful evolutionary force at work.
Because the Atlantic Ocean has an order of magnitude lower concentration of phosphorus than the Pacific Ocean, the researchers expected to see some difference in the genes related to phosphorus, but they didn’t expect that to be the only difference. This indicates that phosphorus availability is the dominant selective force in defining these populations at these two sites. It also provides a benchmark the scientists can use to monitor environmental changes over time. In essence, the Prochlorococcus populations can serve as canaries to alert scientists to ecosystem-wide changes over decades.
“When you can boil controlling factors down to one element, such as phosphorus, it makes it much easier to model the ecosystem and predict its response to change,” said Chisholm. “Our guiding axiom is ‘let the organisms reveal to us what environmental factors are the most critical in regulating their growth and driving their evolution.’ This information is critical for predicting the ocean biota’s response to environmental change, and the corresponding change this will have on Earth processes.”
“Microbes have an adaptive process that responds to very subtle changes in environmental conditions,” said Coleman. “So the microbes could potentially act as miner’s canaries, telling us what they’re feeling. And what they feel matters, because they help drive the carbon cycle of the planet.”
The researchers noted that the microbes in the Atlantic Ocean had increased numbers of genes that helped them neutralize arsenic, an element they sometimes take up by mistake when they’re scavenging for phosphorus. This finding “buttresses the assertion” that this is the result of a strong selective process, Chisholm said.
They also compared the genomes of two populations of a neighboring bacterium, Pelagibacter, and found that genes related to phosphorus gathering in that bacterium appear in far greater numbers in the Atlantic Ocean population, but with a twist. These microbes have a somewhat different repertoire of phosphorus-related genes, suggesting subtle differences in how these two microbial groups scavenge phosphorus. This could reflect an adaptive behavior known as niche partitioning, which allows cells sharing a microenvironment to apportion resources according to a cell’s lifestyle rather than all competing for the same element or same form of that element.
To obtain these findings, which appeared in the Oct. 26 issue of the Proceedings of the National Academy of Sciences, the two scientists used the complete genomes of 13 strains of lab-cultured Prochlorococcus and Pelagibacter as reference genes, and compared these with the genes of well-documented wild microbe populations gathered at long-term oceanographic study stations near Bermuda (BATS) and Hawaii (HOTS). The work was funded by the Gordon and Betty Moore Foundation, the National Science Foundation and the U.S. Department of Energy.
The next step in this research is to make similar studies at different depths and locations to study the effects of light, temperature and a suite of chemical gradients on the genomes of Prochlorococcus populations.