bacteria cultivation microbes

Finding new ways to grow bacteria to progress science

Culturing the Least Cultured Members of Society

Bacteria are everywhere, and we are very effective at growing billions of them in our guts, on our shower curtains, and on our food. But those bacteria we think about every day cover just a tiny fraction of the diversity of bacteria that exist in the world. How do we learn about all these other bacteria?

You’ve probably heard more than enough about bacteria recently. They make delicious foods such as sauerkraut and yogurt. They can rescue you from gut problems. Radioactive-resistant ones have been found on the New York subway. You can buy microbe-themed art to decorate your house with, or toys to entertain your children. And they are the “engines” which drive all the earth’s major nutrient cycles.

Despite the limelight these bacteria are presently finding themselves in, there are millions of other kinds of bacteria that we know little to nothing about. For instance, just last year 26 new phyla of bacteria were discovered in Colorado groundwater [1], which is the equivalent of discovering there are animals on Earth. These bacteria were identified by sequencing all the genes in groundwater without growing the organisms in the lab using metagenomics. If we want to learn more about these and other bacteria, however, we usually have to grow them in the lab. But doing so is difficult for many bacteria, even if we know a lot about the broad-scale environment in which they live.

This difficulty in isolating bacteria from the environment and growing them in the lab has received considerable attention as we increasingly recognize the importance of bacteria in everything from human health to Earth’s functioning. Bacteria responsible for human disease are readily cultured compared to those involved in processes such as recycling carbon in soil [2], primarily because the former’s ability to invade and dine upon the human host allows them to grow rapidly on nutrient-rich media that mimics flesh. However, organisms from soil suffer from the “great plate count anomaly”, whereby of every hundred cells seen in the soil, only one will successfully grow on media in the lab; that is, the bacterial 1% (Fig. 1).

image alt text Fig. 1 Bacterial (and fungal) cells, representing different species, show diverse morphologies. At best, one of the species in this picture could generally be cultured in the lab. Source: Science photo library/Barcroft Media

This inability to culture many bacteria in the lab can be attributed in large part to poor suitability of the media for growth. Common lab media, usually made with agar similar to jello, contains concentrations of nutrients such as proteins that are hundreds or thousands times greater than organisms experience in the environment. Some opportunistic “copiotrophic” (nutrient-loving) organisms are able to take advantage of these high levels of nutrients and grow well on the media, while other slower-growing “oligotrophic” (“low-nutrient thriving”) bacteria may even be killed by the high concentrations of nutrients [3]. Therefore, researchers have many nutrient-hungry opportunistic bacteria in culture, but few of the slower-growing ones. These slower growing organisms are more abundant in soils than the fast-growing ones, and complete many processes vital for soil and plant health, including nitrogen cycling and metal detoxification.

Culturing these slower-growing organisms is sometimes possible, but it requires both patience and adjustments to media recipes. In some instances, placing media under reduced oxygen or increased carbon dioxide conditions to better mimic the atmosphere in soil can help [4]. Making media more dilute, or diluting environmental samples so growing cells don’t face competition from neighboring cells have both proven useful in preventing the fast-growing bacteria from taking over. Indeed, Pelagibacter ubique, one of the most abundant bacteria in the ocean, was isolated in this manner [5]. In other cases, bacteria *need *other bacteria to help them grow. For instance, iron is present in the environment in dilute and insoluble forms which cannot diffuse towards bacteria, so cells must produce “siderophores” which bind and enable iron to diffuse through the media. However, not all cells can produce siderophores, and instead depend on other cells to produce them. Scientists have learned to bypass this by using diffusion chambers [Fig. 2], in which bacteria are trapped in a mesh and placed back into the environment [6]. In this way, bacteria can receive siderophores, vitamins, and minerals necessary for growth that are produced by other bacteria, but are physically separated from the producers. Some bacteria unable to initially be cultivated in the lab by traditional plating methods when taken directly from the environment can be grown in the lab after “domestication” in these diffusion chambers. A novel antibiotic producing bacteria was recently discovered in this way [7], demonstrating its utility.

image alt text Fig. 2 An iChip diffusion chamber like one used to isolate the Eleftheria terrae bacterium now famous for its ability to produce the powerful novel antibiotic, Teixobactin. A dilution of soil cells is placed between two membranes which are permeable to small molecules like vitamins but not bacteria, and the diffusion chamber is placed back into the soil or sediment. Slava Epstein/Northeastern University

The world of bacterial cultivation, once deemed a “dead” area of research, has recently undergone a renaissance. With these new methods of isolating organisms, we can not only uncover new antibiotics, but also gain insight into the diversity of pathways organisms use to recycle the carbon and nitrogen all of life depends upon or perhaps new bacteria with functions we had never realized before.


[1] Brown, Christopher T., Laura A. Hug, Brian C. Thomas, Itai Sharon, Cindy J. Castelle, Andrea Singh, Michael J. Wilkins, Kelly C. Wrighton, Kenneth H. Williams, and Jillian F. Banfield. “Unusual Biology across a Group Comprising More than 15% of Domain Bacteria.” Nature 523, no. 7559 (July 9, 2015): 208–11. doi:10.1038/nature14486.

[2] Puspita, Indun Dewi, Yoichi Kamagata, Michiko Tanaka, Kozo Asano, and Cindy H. Nakatsu. “Are Uncultivated Bacteria Really Uncultivable?” Microbes and Environments 27, no. 4 (December 2012): 356–66. doi:10.1264/jsme2.ME12092.

[3] Koch, Arthur L. “Oligotrophs versus Copiotrophs.” BioEssays 23, no. 7 (July 1, 2001): 657–61. doi:10.1002/bies.1091.

[4] Eichorst, Stephanie A, John A Breznak, and Thomas M Schmidt. “Isolation and Characterization of Soil Bacteria That Define Terriglobus Gen. Nov., in the Phylum Acidobacteria.” Applied and Environmental Microbiology 73, no. 8 (April 2007): 2708–17. doi:10.1128/AEM.02140-06.

[5] Rappé, Michael S., Stephanie A. Connon, Kevin L. Vergin, and Stephen J. Giovannoni. “Cultivation of the Ubiquitous SAR11 Marine Bacterioplankton Clade.” Nature 418, no. 6898 (August 8, 2002): 630–33. doi:10.1038/nature00917.

[6] Bollmann, Annette, Anthony V. Palumbo, Kim Lewis, and Slava S. Epstein. “Isolation and Physiology of Bacteria from Contaminated Subsurface Sediments.” Applied and Environmental Microbiology 76, no. 22 (November 2010): 7413–19. doi:10.1128/AEM.00376-10.

[7] Ling, Losee L., Tanja Schneider, Aaron J. Peoples, Amy L. Spoering, Ina Engels, Brian P. Conlon, Anna Mueller, et al. “A New Antibiotic Kills Pathogens without Detectable Resistance.” Nature 517, no. 7535 (January 22, 2015): 455–59. doi:10.1038/nature14098.

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