Microbes are everywhere

A bizarre tour of life's invisible side.

You think your life is tough?

Our bodies are bathed in living, eating, reproducing lifeforms that we can’t see but that have profound effects on all that we do. But the rest of our world is covered with microbes too. You can’t think about the human microbiome without wondering where else these invisible creatures might be hiding. Are there any limits?

We are not alone. (Photo: Wikipedia)

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.

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 consumed by predators. Or so we assume.

Subglacial Lake Whillans is a lake buried under more than 2,600 feet (800 meters) of ice in the West Antarctic. A careful underground bore hole inserted by a team from Louisiana State University in 2014 found almost 4,000 different kinds of bacteria and archaea 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 microbes instead thrive on iron, sulphur, and nitrogen as energy sources.

Figure 5.1: Go 2,600 feet further to find microbes. Photo: NASA/JPL-Caltech

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 Borehole 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.

Closer to the surface, a 2015 Chinese study showed that 32% of the variety in an ecosystem is associated with variation in the life below ground, mostly bacteria that sustain the ability of roots to take nutrients out of the soil. Just knowing the temperature or precipitation levels of an environment won’t tell you about the plants likely to be found there — the microbes matter too, and may affect the the non-living features of an ecosystem too: some of them play a role in the mineralization of copper and gold.

Even the sky contains living microbes. Scientists at the Institut de Chimie de Clermont-Ferrand in France have for decades sampled clouds to determine their precise contents, and sure enough: they find 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.

Microbes altering the climate. Source: ASMScience

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, but there have been many attempts to learn more. Formal studies about the viability of microbes in space have been conducted since the early 1960s, when Apollo-era scientists wanted to understand the dangers of space travel, both to astronauts as well as to those of us on the ground who might be exposed to any interstellar visitors.

Although new and bizarre extremophiles are discovered regularly, so far it appears that even the hardiest of known organisms have a tough time when directly exposed to solar ultraviolet radiation. But some, like the particularly resilient spore-making Bacillus subtilis, might survive for at least six years if shielded somehow from direct sunlight, say embedded inside a meteorite.

Several lichen species, including rock colonizing Rhizocarpon geographicum and Xanthoria elegans, and the vagrant Aspicilia fruticulosa, remained alive after ten days of direct UV exposure on board a European Space Agency spacecraft. Some especially hardy cyanobacteria that came with the lichens didn’t survive, so perhaps space offers a better chance for multicellular life, which has the luxury of outer protective pigmented layers.

Lichen it in space too. [Photo: J Brew]

Traces of sea 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. 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.

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.

Many “normal”, visible insects host microbes as an invisible — but vital — part of their metabolism. Termites owe their wood-eating abilities to a whole community of synergistic bacteria, archaea, and protists. Aphids can’t live off sap without Buchnera, a microbe that supplies them with essential amino acids. And when common mealworms get desperate, they’ll survive on styrofoam, thanks to Ideonella sakaiensis, which can break down and metabolize plastic.

With an astonishing range of habitats, microbes can naturally flourish everywhere in and on our bodies as well, invisible to us and seemingly benign. But with a track record of survival in the most far-flung places imaginable, what they are doing on us is anybody’s guess.

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References

Afshinnekoo, Ebrahim, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, et al. 2015. “Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.” Cell Systems 1 (1): 72–87. doi:10.1016/j.cels.2015.01.001.

Horneck, G., D. M. Klaus, and R. L. Mancinelli. 2010. “Space Microbiology.” Microbiology and Molecular Biology Reviews 74 (1): 121–56. doi:10.1128/MMBR.00016–09.

Torre, Rosa de la, Leopoldo G. Sancho, Gerda Horneck, Asunción de los Ríos, Jacek Wierzchos, Karen Olsson-Francis, Charles S. Cockell, Petra Rettberg, Thomas Berger, and Jean-Pierre P. de Vera. 2010. “Survival of Lichens and Bacteria Exposed to Outer Space Conditions — Results of the Lithopanspermia Experiments.” Icarus 208 (2): 735–48. doi:10.1016/j.icarus.2010.03.010.

Originally published at psm.personalscience.com on August 15, 2018.