Farming amoebas save bacteria for food

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Farming amoebas save bacteria for food
Rice researchers discover rudimentary agriculture among slime molds

Some amoebas do what many people do. Before they travel, they pack a lunch.

In a study reported this week in the journal Nature, the Rice University lab of evolutionary biologists Joan Strassmann and David Queller reported that the long-studied social amoebas Dictyostelium discoideum (commonly known as slime molds) increase their odds of survival through a rudimentary form of agriculture.

Research by lead author Debra Brock, a graduate student in the Strassmann/Queller lab, found that some amoebas sequester their food, which consists of particular strains of bacteria, for later use. These “farmer amoebas” aggregate into a slug, migrate and form a fruiting body — a stalk of dead amoebas topped by a sorus containing fertile spores — in search of nourishment. Then they release the bacteria to the environment as a feedstock for continued growth.

The findings run counter to the presumption that all “Dicty” eat everything in sight before they enter the social spore-forming stage. Nonfarmers do eat everything in sight, but farmers were found to leave food uneaten, and their slugs don’t travel as far. The advantages of going hungry now to ensure a good food supply later seem clear, as farmers are able to thrive in environments in which nonfarmers find food to be scarce.

Strassmann said Brock’s sharp eye and inquisitive mind started her on the yearslong investigation. “Debbie came from a molecular biology background, so she was coming in with a fresh eye,” Strassmann said. “She saw variations others had missed in these tiny organisms. At one point Debbie came to us with the observation that some clones consistently carried bacteria as well as spores in their sori.” Strassmann and Queller are Rice’s Harry C. and Olga K. Wiess Professors of Ecology and Evolutionary Biology.

Brock modified her research program to pursue the implications of her observation. “Once I start something, I just can’t let it go,” she said. Dozens of labs study Dicty, Brock noted, but only a few work with wild strains, including farmers. Most labs instead study a lab-adapted axenic clone that by chance is a nonfarmer, and they would not see the bacteria in the sori that caught Brock’s attention, Brock said.

The Rice researchers studying amoebas from Virginia and Minnesota found that about a third of wild-collected Dicty clones are farmers. Instead of consuming all the bacteria they encounter, these amoebas eat less and incorporate bacteria into their migratory system.

Furthermore, Dicty farmers are always farmers; nonfarmers never learn, so it is a genetic trait. Brock showed that carrying bacteria is a clone-specific characteristic by eliminating all living bacteria from four farmers and four nonfarmers (the control group) by treating them with antibiotics. They were grown on dead bacteria, and tests confirmed that they became free of live bacteria. But when the eight clones were fed live bacteria, all of the farmers regained their abilities to seed bacteria colonies, while the nonfarmers did not.

The researchers also mimicked farmer clone dispersal to environments both rich and poor in bacteria. They found spores released to areas free of bacteria but rich in nutrients soon had working bacteria colonies. Farmers made bacteria-free before dispersal were unable to raise similar crops.

Rice graduate student Tracy Douglas, who co-authored the paper with Brock, Queller and Strassmann, contributed to the research by confirming that farmers and nonfarmers belong to the same species and do not form a distinct evolved group.

Still, mysteries remain. The researchers want to know what genetic differences separate farmers from nonfarmers. They also wonder why farmer clones don’t migrate as far as their less-resourceful counterparts. It might be a consequence of bacterial interference or an evolved response, since farmers carry the seeds of their own food supply and don’t need to go as far.

Also, some useless or even harmful bacteria are not consumed as food but serve an as-yet undetermined function, Brock said. That has implications for treating disease as it may, for instance, provide clues to the way tuberculosis bacteria invade cells, infecting the host while resisting attempts by lysosomes to break them down.

Strassmann and Queller have long been interested in sociality and the maintenance of cooperation; they generated a great body of work using social wasps as their study organism. A decade or so ago they found that the model organism, D. discoideum, with its quick generation times and many genetic tools, offers advantages not found in other systems and made the switch. Both are interested in the bigger picture that can be drawn from studying the evolution of small things. “Farming could be an attribute that can only evolve in social organisms, which have already had to evolve ways to restrict benefits to close genetic relatives,” Queller said.

The new results demonstrate the importance of working in natural environments with wild organisms whose complex ties to their living environment have not been broken, Strassmann said.

The National Science Foundation supported the work.