Virtually all of the life around you is invisible. We tend to forget about things we can't see, ignoring that which is literally under our noses, but it’s there: living, eating, reproducing lifeforms of incredible tenacity and surprisingly important effects on the world we can see.
Life is incredibly tenacious, fighting for and keeping its niche in just about environment it encounters. In the sky, deep underground, in the most barren habitats cold or hot anywhere on earth, there are lifeforms. The vast majority of these are microbes, so small we can’t see them, but small doesn’t mean irrelevant. In fact, the more that science understands about the invisible microbial world, the more it is clear that these uncountably numerous creatures exert a much bigger effect than we think.
Every traditional culture recognizes a role for the invisible, often translated with words like “spirit” or “life force”, sometimes with more expressive terms like “angels”, “demons”, “gods” or even, simply, “God”. Sometimes the more serious people dismiss these invisible forces as so much superstition, as though truth is made only of things we can see, but of course that’s not quite true either. With the right instruments, we can see many invisible things; some of the greatest discoveries happen when a new gadget makes people aware of a world that was previously hidden.
The invisible world of microbes is like that, with new, low-cost technologies showing us incredible, rich, living universes waiting to be explored.
The word “microbe” refers to any tiny organism that carries its own genetic information for purposes of propagating itself. Far too small to see with the naked eye, dozens could fit inside a typical human cell. Although it’s common to think of microbes and bacteria as the same thing, in fact there are at least seven different types of microorganism: bacteria, extremophile life forms called archaea that live and thrive in environments too challenging for bacteria, protozoa, algae, fungi, viruses, and some multi-cellular animal parasites such as helminths. Each of these has its own characteristic body type, means of reproduction, and ways of moving around.
Let’s look next at some of these environments and see the odd places where microbes have been found.
Microbes in the air
Even the sky contains living microbes. Pierre Amato is a staff scientist at the Institut de Chimie de Clermont-Ferrand in France who for decades has been sampling clouds to determine their precise contents, and sure enough: he finds plenty of life there, usually between 1,000 and 10,000 bacterial cells per milliliter — not all that different from the amount you’d find in alpine snow. Like every living organism, these cells must soak up water and other nutrients, converting them into energy and various by-products, which collectively have a massive effect on the overall atmosphere, more than enough to affect climate. 1
The upper atmosphere is a harsh place for life: regular freezing and thawing, constant bombardment of UV radiation from the sun during the day, cold, subzero freezing temperatures at night, high speed, unpredictable winds that quickly disperse any colonies. Plus, at any moment these organisms can find themselves flushed to the ground in a rainstorm, where they’ll need to adapt again.
These extreme conditions are just another day in the life for one species commonly found in clouds, Pseudomonas syringae, which harbors a protein in its cellular wall that reacts to cold temperatures, alternately preventing and allowing a water molecule to turn into ice and back. It doesn’t take many of these reactions to generate precipitation. With so many cells constantly floating in the atmosphere, even small changes in concentration — perhaps due to human activity on the ground — can, at least theoretically, make the difference between rainfall and drought. How much of an effect is hard to say: you can imagine how difficult it is to study bacteria floating in the sky.
Our inability to access these environments is often the biggest reason we remain ignorant of the life that is found there. Traces of plankton, for example, have been found in space, on the surface of the International Space Station, where they are believed to have floated from the upper atmosphere. 2 Why?! How did they get there! Who knows!
What is known is that between a quarter and two-thirds of microbes in the air are entirely new and undiscovered organisms. A study of the “air microbiome” above New York City found bacteria and viruses that apparently originated in water, soil, vegetation, as well as in animals and humans, but even then few patterns emerge. Although there appear to be distinct microbial environments, on the land versus water, for example, overall many of these organisms are quite hardy and seem to find themselves migrating all over the place.
Scientists studying a water-filled fracture two miles underground at the Mponeng gold mine near Johannesburg, South Africa, discovered Candidatus Desulforudis audaxviator by accident, after noticing odd levels of hydrogen compounds, by-products of the activity of an isolated bacterial colony.3 Interestingly, this organism is a member of the same Firmicutes phylum that dominates human guts, though this particular bacterium evolved quite separately from us: it hasn’t been exposed to surface water for millions of years. A systematic study of its genome revealed that, unlike other bacteria that usually live in co-dependent colonies, this one can survive all by itself, feeding on tiny bits of radioactive energy from uranium decay in an environment far removed from all other energy sources. It’s not a great life: these creatures reproduce rarely, only once every few hundred or thousand years. But at least they don’t have to worry about being consumed by predators down there.
Subglacial Lake Whillans is a lake buried under more than 800 meters of ice in the West Antarctic. A careful underground bore hole inserted by a team from Louisiana State University in 2014 found more than 4,000 different species of bacteria surviving under that ice. The total bacterial count was not that different from what you’d find in surface lakes on other parts of the planet, a fact that is especially surprising for an environment that hasn’t had a ray of light in millions of years. The bacteria instead thrive on iron, sulphur, and nitrogen as energy sources.4
Those may not be the deepest examples. A Cold War-era Soviet team drilling the world’s deepest hole, were forced to abandon the project in 1994 at 12,261 meters (or 7.5 miles) underground, when they hit temperatures above 180 °C (or 356 °F), too hot for their equipment. Apparently the conditions weren’t too hot for life, though: the nine-inch diameter Kola Superdeep Borehole5 found 24 species of fossilized plankton among the two-billion-year-old rocks down there. Of course, fossils are not the same thing as living microbes, but even dead remnants at that depth is evidence of the tenacity of life.
Still other microbes thrive in radioactive environments, like the dangerous interior of a nuclear reactor. Deinococcus radiodurans is an extremophile member of Phylum Deinococcus-Thermus that boasts an impressive built-in DNA repair mechanism that lets it survive cold, vacuum, acid, light, dehydration – you name it. It remains unbothered by radiation levels more than 1,000 times higher than would kill a human.
Microbes around you
You don’t have to go to extreme conditions to find unusual microbes. Microbes thrive whereever humans live, and they are in our everyday environment too. The recent PathoMap study of DNA collected from the New York City subway found that, like the air above, half of the microbes we walk past everyday are unknown to science. 6 Most of the organisms are apparently benign, with no obvious affect on humans one way or another. Even when known pathogens are found, including Yersinia pestis (Bubonic plague) and Bacillus anthracis (anthrax), the lack of reported infections indicates that probably these organisms are busying themselves for some other, unknown, and maybe even useful purpose.
Generally the microbes seem content to exist patiently with no apparent affect on the environment. A station flooded by Hurricane Sandy showed a similarity to a marine environment a year after the disaster.
Humans are the source of many unusual microbes in our environment. Regularly shedding 1.5 million skin cells per hour, leftover inhabitants of our bodies can colonize a hotel room in less than six hours. 7
Microbes you eat with your food
We like our food pure and clean, but microbes like it that way too. Freshly-washed produce is a just a colonization opportunity for many microbes, who like the lack of competition.
Plants are covered with them, from the flowers and branches to the roots. Seeds planted in sterilized soil will germinate, but can’t grow regardless of the nutrients, water, or sunlight you give them. The relationship between soil bacteria and plants is a complicated and understudied one, but what is known is that every plant hosts its own unique species of microbe in a symbiotic relationship as tight as any on earth. The microbes tangled in the roots of a corn or wheat plant, for example, are highly specific to that particular strain. Alter one of the microbes, or — worse — sterilize the soil, and the plant can’t take advantage of the nutrients sitting right at hand, because they are in a form that is useless until digested by microbes.
After harvest and processing, our meals still contain a surprising variety of microbes. Of course, sometimes this is deliberate: some of us eat fermented foods like sauerkraut or yogurt to ingest the microbes that were grown to make their special flavor or texture. But even every day foods, like raw vegetables, will naturally be covered with healthy levels of microbes.
You will ingest somewhere between 1.4 million and 1.3 trillion microbes per day, depending on what type of diet you follow. Eat according to USDA guidelines and you’ll be at the high end of the range, emphasizing fruits and vegetables, lean meat, dairy, and whole grains; the lower end is more typical of a vegan diet, or even a typical American convenience food-style diet of “junk food”. Interestingly, you’ll get roughly the same diversity of microbes no matter which diet you follow, although there can be a difference depending on whether the food is raw or cooked.8
We eat plants for their nutrients, but often a “nutrient” is in the eye of the beholder. Plants don’t like to be eaten any more than the rest of us, and they have developed powerful defense mechanisms to keep out predators, including microbes. In fact, it’s those anti-microbial properties that make many plants medicinally useful. One estimate showed that of 18,000 plants available to Native Americans, only 1,625 were used as food; but 2,564 were used as drugs, many of which are specifically there to manipulate microbes. 9 Extrapolate that to the estimated 500,000 different plants on earth, only about 1-10% of which are useful as foods to humans, and it becomes clear that microbes play a big role in which plants thrive and which don’t.
You’re not necessarily immune from accidental antibiotic ingestion if you simply avoid eating antibiotic-treated meat. Between 70% - 90% of the antibiotics given to farm animals are ultimately discharged in their manure, which if administered as fertilizer, can coat the soil used for growing food plants. Although antibiotics naturally degrade over time, the process can take months and under many conditions, giving ample time to be taken up in to plants that we eat, so even hard-core vegans may be getting more antibiotics than they like.
Anti-microbials in food
Plants don't like to be eaten any more than you do. Even plants that depend on pollinators, or those that spread their seeds by being ingested by birds, they don’t actually like to be eaten whole and completely. Leafy grasses attract ruminants like cows or sheep with large tasty fibrous leaves that the plant offers in order to bring in the high-nitrogen feces that will help the plants grow better.
In some foods, living microbes aren’t along just for the ride – they are the ride. Most raw foods will quickly spoil if left uneaten for too long. We say “spoiled”, but really we mean the food is consumed by bacterial species who leave by-products that are not edible or pleasant for humans.
Under the right circumstances, though, food can
Before refrigerators, the long-term preservation of food
Yes, much of that yogurt makes it past the stomach and into the gut.
3. Chivian, Dylan, Eoin L Brodie, Eric J Alm, David E Culley, Paramvir S Dehal, Todd Z DeSantis, Thomas M Gihring, et al. 2008. “Environmental Genomics Reveals a Single-Species Ecosystem Deep within Earth.” Science (New York, N.Y.) 322 (5899). American Association for the Advancement of Science: 275–78. doi:10.1126/science.1155495. ↩
6. Afshinnekoo, Ebrahim, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, et al. “Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.” Cell Systems 1, no. 1 (n.d.): 72–87. doi:10.1016/j.cels.2015.01.001. ↩
8. Lang, J. M., Eisen, J. A., & Zivkovic, A. M. (2014). The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types. PeerJ, 2, e659. http://doi.org/10.7717/peerj.659 ↩
9. Cowan, M M. 1999. “Plant Products as Antimicrobial Agents.” Clinical Microbiology Reviews 12 (4): 564–82. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=88925&tool=pmcentrez&rendertype=abstract. ↩