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 , 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 , 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).
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 . 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 . 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 . 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 . 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 , demonstrating its utility.
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.
 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.
 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.
 Koch, Arthur L. “Oligotrophs versus Copiotrophs.” BioEssays 23, no. 7 (July 1, 2001): 657–61. doi:10.1002/bies.1091.
 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.
 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.
 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.
 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.
More From Thats Life [Science]
- Who’s who? The elusive difference between butterflies and moths
- Tuberculosis - A Romantic Disease?
- Ode to a Few Arachnids
- Monotropa uniflora - This wildflower is pretty wild
- Eavesdropping in the Animal Kingdom: Sneaky Creatures Just Trying to Get Ahead
- Trypanosomes - A Weird Pathogen You Haven't Heard Of
- A Beautiful 9/11 Tribute, but a Fiasco for Migratory Birds
- Cats can have AIDS, too.
- Part 2: Does catching Pidgeys help you notice Pigeons? Interviews with Pokémon Go Researchers
- Biodiversity in my Backyard: Encounters with Pidgeys and Dratinis, Part 1
- Fins, Limbs, Rays, and Digits – A Beginner's Guide to Terrestrial Living
- Five things that really stink about the Brown Marmorated Stink Bug
- Tricks but no Treats - An Orchid’s Guide to Making a Fool of Your Pollinator
- Tracking the lost years - where do baby sea turtles grow?
- Posing as a Bird Mama: the adventures of a researcher-turned-bird-parent
- Hot moves and sexy sons · When Boys Become Men By Dancing
- The hungry caterpillar in real life
- Mantis Shrimp Vision - Seeing in Secret Code
- When It Comes to Bird Beaks - Size Matters
- Is your gut trying to kill your resolve? · Mind over microbe
- Recent talk of walls in the media has brought up a lot of emotions, but what do walls do in nature? · When a Wall is just a Wall
- Bees are more than buzzing insects around you · May the Bees Be With You: Maintaining the Sweet Balance in Life
- Neither a toad nor a worm · Nematodes: The super microscopic animal!
- Snap! Flash! Bang! Find out how ocean-dwelling pistol shrimp fire bubble ‘bullets’ to stun their unsuspecting prey. · How Pistol Shrimp Kill with Bubbles
- Who needs males after all?
- Ecology and Behavior of Woodchucks · Opposition Research on My Garden’s Greatest Nemesis
- Vision in Jumping Spiders · Watching Your Every Move
- Slimed and Consumed - The Blob is Real!
- The Evolution and Ecological Impacts of Cats · Lion in Sheep's Clothing
- What happens when frogs have to compete for acoustic space and a chance to be heard? · Struggling to be Heard - Competition in a Complex Soundscape
- Think Genghis Khan and Napoleon were the most successful invaders? Think again. · Invasive Species and Invasion: Part 1
- When, and how, terror birds invade
- 8 Reasons Plants Are Amazing
- Too Clean for Comfort · How our obsession with cleanliness might be hurting our health
- Stop, evaluate, and listen - serotonin surges when a female is present
- No Teeth, Long Tongue, No Problem - Adaptations for Ant-eating
- The Good, the Bad, and the Ugly - Predators, Parasitoids, and Parasites
- How our microbiome affects our health and vice versa · If you don't care for your microbiome, you might want to start
- Finding new ways to grow bacteria to progress science · Culturing the Least Cultured Members of Society
- Hit the Road Jack
- What Happened to Your Nose?
- Building better plants - Norman Borlaug and the Green Revolution
- Love Songs for Nobody - Birdsong in Winter
- We know we get infections from time to time. Why does this happen? · The Evolution of Virulence
- How cheese rinds may be a valuable tool for microbial discovery · The Unseen World – On Cheese?
- Find Me Where the Wild Things Are
- A commentary on how to make science more ‘clickable’ · You won’t believe this simple trick to tell if your coral is healthy or not
- Some species hide in plain sight, but scientists have ways to suss them out · Cryptic Species Hide in Plain Sight
- Minuscule Hitchhikers Pinch a Ride · Creature Feature - Pseudoscorpions
- World Fish Migration Day 2016!
- Walking With Giant Anteaters
- Why we should care about sea turtles · When A Sea Turtle Balanced Earth
- More ›