Learning to listen to the silent majority

Image from here.

Ninety-nine percent. That is the fraction of microbes that aren’t cultivatable by microbiologists. Throughout Earth’s ecosystems, they are there, living, breathing, metabolizing…but because microbiologists can’t grow them in their labs, figuring out what this “silent majority” of microbes do has been tough.

But new lots of new research is changing that. First, microbiologists have been cooking up (literally!) new ways to grow microbes. The old recipes for growth medium turned out to be toxic for many species of bacteria. Second, in many cases, it’s turned out that cultivation is possible, with sufficient time and attention to detail. (Breaking out the microscope is almost never a bad idea.)

Lastly and most impressively, a team has demonstrably slashed the fraction of “uncultivatable” microbes from 99% to something more like 50%…by cultivating the bacteria. Their approach to this impressive success relies on a microfluidic cultivation device they call iChip. These chips are made of hydrophobic plastic arrayed with holes about 1 μL in volume. The holes are open on both top and bottom. To use it, the chip is immersed in a suspension of microbes from environmental samples, so each hole fills up with (on average) about one cell from the sample. Each side of the chip is then sealed with permeable membrane filter. The filter has pore sizes big enough to let soluble nutrients in, but small enough to block microbial cells from leaving (0.03 μm filters seems to do the trick).

Next comes the key step. The sealed chip is returned to the environment from which the sample came for several weeks — the waiting game begins. In their latest study, the team looked at soil bacteria from a grassy field in Maine, so they buried their seeded chip back into Maine soil and left there for a whole month.

New colonies of microbes, unrelated to anything previously cultivated in a lab, grow in many of iChip’s wells. In 2010, the team found an uncultured variant of the marine bacterium Maribacter polysiphoniae that would grew on the chips, but only in proximity to another bacterium they isolated, Micrococcus luteus strain KLE1011. The were able to work out the reason for the co-dependence: M. polysiphonae needed iron-binding siderophores produced by M. polysiphonae to live. In the study published today by Nature, they found a new betaproteobacterium that they called Eleftheria terrae. This bacterium turned out to be tremendously exciting because it produced a new antibiotic, as detailed very well in an accompanying News & Views article.

The chip-based cultivation is clearly useful in understanding what that supposedly “uncultivable” 99% is doing. It’s fun to speculate as to why. It could simply be that microbiologists, a patient lot by most human standards, don’t usually wait long enough for colonies to grow. (One month is a long time!). In some cases, the chip’s holes are small enough so that neighboring cells can still influence growth, such as by supplying those key siderophores. Another possibility is that isolates survive their initial seeding in the chip because it’s an environment they’re accustomed to, but over time as the microcolony grows, they adjust — either through mutation or through somatic adaptation — to life in monoculture. Or it could something else entirely, and oh yes, the answer probably varies from species to species.

Regardless, I expect to be hearing many more reports on cultivating the many “uncultivable” microbes on Earth. As many have previously observed, if we listen correctly, we should indeed be able to hear the microbial silent majority, even as they grow in our labs.


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