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Amoeba that cultivate an ecosystem of edible and inedible bacteria

The smallest farmer discovered yet is the amoeba Dictyostelium discoideum, which cultivates edible bacteria that it harvests like crops. Now scientists reveal this amoeba also raises bacteria that pump out chemical weapons that protect the farmers, report findings detailed this week in the Proceedings of the National Academy of Sciences.

Chemical biologist Jon Clardy at Harvard Medical School in Boston and his colleagues investigated a farmer lineage or clone that harbored roughly equal amounts of two strains of bacteria. Although they appeared quite different, genetic analysis revealed they were the same species, Pseudomonas fluorescens. Strangely, one strain was edible while the other was not, raising the question of why the amoeba bothered raising inedible microbes.

Only a third or so of all D. discoideum clones found in the wild are farmers. The researchers discovered the inedible strain generates two chemicals — chromene, which potently enhances a farmer’s reproductive spore production and reduces a nonfarmer’s spore production, and pyrrolnitrin, a known antibiotic and antifungal molecule that probably also suppresses other soil organisms that might compete with the farmers. Experiments revealed the farmers have adapted to the chemical weapons the inedible strain produces, with non-farmers suffering in the presence of these molecules while farmers do not.

After sequencing the entire genome of both the bacterial strains, the scientists discovered one of the genes that controls both the pyrrolnitrin and chromene pathways was mutated in the edible strain, changing the expression of 10 percent of its genome. Artificially breaking this controller in the inedible strain resulted in edible bacteria with the same chemical profile as the edible strain found in the amoeba.

These findings suggest the edible strain arose from its toxic relatives. Although this edibility mutation seems harmful to any bacteria that get eaten, the investigators suggest that it still is of benefit to the strain overall — although some edible bacteria would die, the amoeba would keep others with that trait alive and safe.

“It’s totally cool that the food strain could lose its ability to defend itself but still manage to survive through its association with other bacteria and the amoebas,” Clardy says.

The scientists are now looking for genetic differences between farmer and nonfarmer amoeba. The aim is to see how exactly the farmers resist the chemical weapons of the bacteria they carry.

Future research could also reveal whether the amoeba initially harvested both the edible and inedible strains from the wild separately or if the amoeba initially kept only the inedible strain around for protection, with the edible strain evolving after the partnership began, Clardy says.

“There are many more edible and inedible bacterial strains found in the spores,” Clardy adds. “What are they doing?”

Categories: Chemistry | Ecology
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