Rocks and their microbes: a co-evolutionary partnership


Miles beneath our feet, Earth’s rocky crust may seem a cold, dead place. On closer inspection it’s anything but.

Microbes have been making a home on and in rocks since…well, since the beginnings of life, some 3.5 billion years ago. The traditional view of rock-dwelling microbes is one of sparse, energy-starved survivalists eking out an existence on a hostile frontier. These critters are at the mercy of their environments, their numbers dictated by physical factors – things like temperature and pH.

Geobacter, a rock-dwelling bacteria coating iron oxide minerals. Credit: Wikipedia

Geobacter, a rock-dwelling bacteria coating iron oxide minerals. Credit: Eye of Science

A study published in Geomicrobiology Journal, led by graduate student Aaron Jones at the University of Texas at Austin, challenges the assumption that subsurface microbes are passive survivalists. In a series of lab experiments, Jones demonstrates that mineral-dwelling microbial communities are uniquely adapted to their environments on the scale of individual mineral grains. Moreover, his research suggests microbes and minerals share a partnership that stretches back through geologic time.

Jones was interested in how mineralogy- the composition of the minerals that form rocks- influences the abundance and diversity of microbes. In particular, he was interested in sulfur oxidizers- bacteria that strip electrons from sulfur to acquire energy. Sulfur oxidizers are common in other subsurface environments including deep ocean vents. Their metabolism generates strong acids that eat away at certain minerals, forming cracks, pores, even caves.

In the lab, Jones set up a series of “bioreactors”- tanks in which liquid of a specific chemical composition flows over thin sheets of rock. He used a range of rocks that differ in their mineralogy. These included several rocks composed of calcium carbonate (limestone, dolostone and calcite) and several made of silica-rich minerals (albite, microcline and quartz). Jones inoculated his bioreactors with samples of a sulfur-metabolizing biofilm collected from a Wyoming cave spring.

Example of a benchtop bioreactor. Bioreactors are commonly used in microbial biotechnology for cell culturing and fermentation. Credit: Wikimedia Commons

Example of a benchtop bioreactor. Bioreactors are commonly used in microbial biotechnology for cell culturing and fermentation. Credit: Wikimedia Commons

After three weeks of incubation, he measured bacterial growth, extracted DNA and used pyrosequencing to examine the composition and diversity of the microbial communities formed on different rock types.

Different rocks, different microbes

Growth patterns differed substantially across the carbonate and silicate rocks. On carbonates, bacteria grew in thick, filamentous biofilms. By contrast, growth was much sparser on silicates, with bacteria either accumulating in small clumps or spreading out individually.

Community composition also differed among different rocks. The bacterial phyla Alphaproteobacteria dominated on most carbonates. Sulfur oxidizers that thrive at near-neutral pH were common, representing 17-45 % of the community.

A different picture emerged on the silicate rocks. Members of the phyla Firmicutes and Actinobacteria- also known as Gram-positive bacteria– were found here. While community composition was relatively similar among the carbonates, communities that grew on quartz were very different than those found on albite or microcline. Jones observed fewer sulfur oxidizers on silicates, and those he found tended to be more acid-tolerant.

Composition of bacterial communities grown on different mineral surfaces. From Jones & Bennet 2014.

Composition of bacterial communities grown on different mineral surfaces. From Jones & Bennet 2014.

Perhaps the most obvious conclusion here is that microbes do not select rocks at random. Different growth patterns among rocks tell us this. Better microbial growth on carbonates probably reflects a higher density of essential nutrients, particularly phosphorus. Moreover, two of the silicate rocks, albite and microcline, contain high concentrations of aluminum, a toxic element that restricts bacterial growth.

More subtly, however, there appears to be “selective relationship” between mineralogy and microbial ecology. In other words, the microbes making a living on any given rock are uniquely adapted to taking advantage of, or protecting themselves from, the specific chemical properties of that rock.

This relationship bears itself out in many ways. For one Jones found more acid-tolerant microbial communities on silicate rocks. Remember, acid is a byproduct of sulfur metabolism. Carbonate rocks have a high “buffering capacity”, meaning their minerals react with and neutralize acid. By contrast, silicate rocks, especially quartz, are pretty unreactive. Rather than eating away at minerals, acid accumulates at silicate surfaces. The presence of acid-loving bacteria on quartz suggests a feedback loop between sulfur metabolism, mineralogy and microbial community structure.

The presence of Gram-positive bacteria on silicates also underscores the relationship between microbial community composition and the mineral environment. The cell walls of Gram-positives possess unique chemical properties that promote bonding with silicate surfaces. This microbe-mineral binding, known as adhesion, is a key element of survival for most rock-dwelling bacteria. By adhering to a solid surface, bacteria can mine nutrients and form protective biofilms.

Even microbes living on the undesirable aluminum-rich rocks may possess unique adaptations. While few bacteria grew on albite or microcline, these sparse populations were highly diverse. The unique challenges presented by a toxic environment may serve to maintain competition, preventing any single group of organisms from gaining dominance.

Our planet’s rocky subsurface is the largest microbial habitat, but we still know very little about its inhabitants. Most microbial ecologists prefer to study environments they can see, feel and intimately relate to. Jones’s research points to complex ecological interactions between microbes and minerals in the deep, dark depths of the world. Rocks shape microbial communities, but microbes may also shape rocks in profound ways. This study lends evidence to a deep synergy between the geological and biological evolution of our planet.

Jones, A., & Bennett, P. (2014). Mineral Microniches Control the Diversity of Subsurface Microbial Populations Geomicrobiology Journal, 31 (3), 246-261 DOI: 10.1080/01490451.2013.809174


Deep but not dead: continental crust bacteria make a global impact

Scanning electron image of mineralized bacteria from a "black smoker", a deep sea hydrothermal vent. Microbes living in extreme subterranean environments such as this may be more abundant than once thought.

Scanning electron image of mineralized bacteria from a deep sea hydrothermal vent known as a “black smoker”. Microbes living in extreme subterranean environments such as this may be more abundant than once thought. Credit : SEM Images

Microbes in the deep biosphere – ocean floor sediments, subterranean aquifers, the continental crust – often get the short end of the research stick. Reproducing every few thousand years and living in perpetual starvation, life far beneath the surface beats to a different drum. The strangeness of life down deep presents numerous challenges to researchers. Getting uncontaminated samples is difficult and expensive, but once they’re back in the lab, inducing “zombie bacteria” to grow is another hurdle entirely.

Given the trouble involved, is it even worth studying the deep biosphere?

Perhaps a different way of framing that question is to ask how much the deep biosphere matters to the rest of the world. Is it simply a collection of curious survivalists, biologically impressive but of little importance to life on the surface? Or is the deep biosphere large enough that we can’t just shrug it off as too remote?

In a paper recently published in the journal FEMS Microbiology Ecology, Dr. Sean McMahon seeks to answer this question using a simple approach. How much, McMahon asks, does the deep continental biosphere weigh?

Ecosystem-scale biomass (or carbon) measurements are used to inform everything from agricultural and land management decisions to climate negotiations. But getting the numbers right is not a trivial problem. A certain amount of assuming, averaging, and extrapolating is always needed. While imperfect, such numbers carry immense value. Estimating the carbon stored in the deep continental biosphere allows scientists to evaluate the importance of subterranean bacteria on a global scale.

To determine the microbial carbon stored in the continental crust, McMahon compiled 120 cell density measurements from aquifers located anywhere from 10 meters to 3.6 km down. He also collected information on the volume of groundwater and its distribution throughout the crust, which he used to estimate the total number of cells present in groundwater worldwide.

McMahon’s groundwater data only represented “unattached” cells. Attachment to mineral particles allows bacteria to form protective biofilms and maintain a relatively stable environment. In aquifers, attached bacteria outnumber free-floaters anywhere from 100 to 1,000-fold. So McMahon scaled up his estimate accordingly. Finally, McMahon assumed that each bacterial cell in the subsurface contains 26 femtograms (10^-15 grams!) of carbon. While the carbon content of a bacteria is highly variable, ranging from 10 – 100 fg, McMahon created a low-end estimate for the weight of an average bacteria living in starvation conditions.

Shewanella oneidensis, a bacteria that attaches to iron oxide clays, using iron as an energy source

Shewanella oneidensis, a bacteria that attaches to iron oxide clays, using iron as an energy source

From all this information, McMahon estimates there are 14 – 135 petagrams of microbial carbon in the continental crust. (1 Pg = 10^15 grams). On the low end, this is approximately twice the amount of carbon that enters our atmosphere every year due to fossil fuel burning. On the high end, it’s roughly equivalent to the total annual carbon dioxide respired by vegetation and soils worldwide.

McMahon’s estimate is probably conservative. Most of his data is from aquifers bearing relatively large sand particles that serve as microbial attachment sites. Sediments consisting of smaller, clay-sized particles have larger surface areas and are likely to host more attached bacteria. McMahon also excluded coal and hydrocarbon deposits from his estimates. But these are energy-rich environments where bacteria are probably far more abundant.

Ultimately, by producing an estimate of  microbial carbon stored in the crust, McMahon is able to affirm the deep biosphere’s global significance. Taken together with new research demonstrating the role subsurface microbes play in rock weathering and nutrient cycling, perhaps the larger take home is that we should start paying a little more attention to the bacteria miles beneath our feet.

An excellent overview of life in the deep biosphere.

McMahon S, & Parnell J (2014). Weighing the deep continental biosphere. FEMS microbiology ecology, 87 (1), 113-20 PMID: 23991863

Frozen bacteria repair their DNA at -15ºC


Bacteria encased in ice can be resuscitated after thousands, perhaps even millions of years. How these hardy bugs manage to survive deep freeze is something of a mystery.  If nothing else, the low levels of radiation hitting Earth’s surface should cause any ice-bound bacterium’s DNA to break apart over time, eventually leading to irreparable damage. Some scientists think bacteria survive cryosleep by encasing their DNA in protective shells known as spores and entering a state of dormancy. Following spore formation, a bacterium can withstand harsh environmental conditions, including desiccation, strong acids, heat and UV radiation.

Spores don't actually have eyes like they do in the popular video game, but they can resist drought, fire, ice, acid, and even antibiotics.

Spores don’t actually have eyes like they do in the popular video game, but they can resist drought, fire, ice, acid, and even antibiotics.

But other researchers think we aren’t giving enough credit to the ice dwellers. Recent studies have shown that some psycrhophiles– technical-speak for cold-loving bacteria – are able to maintain basic metabolic functions at subzero temperatures. Could psychrophiles trapped in ice be repairing their DNA faster than the UV radiation bombarding our planet pulls it apart? Microbiologist Markus Dieser at Lousiana State University was interested in finding out. In a study published  in the journal Applied and Environmental Microbiology, Dieser and colleagues show for the first time that one bacteria- Psychrobacter arcticus– can repair it’s DNA at temperatures as low as -15ºC, or 5ºF. Moreover, it can do so 100,000 times faster than damage occurs.

P. articus is an innocuous little bacteria that is famous for one thing: it really likes the cold. It can grow and metabolize at -10 ºC, making it one of the most psychrophilic organisms on Earth. To investigate P. articus’’s ability to repair DNA in deep freeze, Dieser and colleagues isolated viable P. articus cells from Siberian permafrost that has been frozen for 20 to 30 thousand years. In the lab, the researchers dosed their cell cultures with a large pulse of ionizing radiation- roughly equal to what P. articus might experience over 225 thousand years of field exposure. By using such an intense burst of radiation, the team hoped to induce many “double-strand breaks”, or breaks that cause small DNA fragments to separate off from P. articus’s main chromosome.They incubated the irradiated cultures at -15ºC and monitored their survival over the course of 505 days.

Rather astoundingly, the scientists found no significant difference between the survival rates of irradiated and non-irradiated bacteria over the year and a half long study. While this finding alone suggests P. articus can repair its DNA at subzero temperatures, Dieser and colleagues wanted direct evidence.  They used pulse-field electrophoresis, a technique which separates DNA fragments by size, to determine how may DNA double-strand breaks occurred after radiation exposure, and whether the DNA fragments reassembled themselves over time. Like Humpty Dumpty rebuilding himself, the scientists could literally watch P. articus reassemble its genome. On average, P. articus was able to patch thirteen double-strand DNA breaks over the course of the study-  quite close to the roughly sixteen breaks inducted by radiation.

DNA ligase repairing a DNA molecule that has suffered a double-strand break. Credit: Wikipedia

DNA ligase repairing a DNA molecule that has suffered a double-strand break. Credit: Wikipedia

Not only can P. articus repair its DNA at subzero temperatures, it can do so really fast. Using annual radiation exposure data collected in the field, Dieser estimates that P. articus can repair double-strand breaks 100,000 times faster than they occur. The discovery has important implications for the survival of life in extreme environments, including cold extraterrestrial environments. For instance on the surface of Mars, where radiation levels are ~400 times greater than the Siberian permafrost, P. articus can still patch DNA breaks 280 times faster than they would accrue. As scientists continue exploring the “cold limit” to essential cellular functions such as DNA repair, they will continue to refine, and perhaps expand, our understanding of the fundamental boundaries for life.

Markus Dieser, John R. Battista, & Brent C. Christner (2013). DNA Double-Strand Break Repair at −15°C Applied and Environmental Microbiology DOI: 10.1128/AEM.02845-13

Crystalline nanotube-forming bacteria help crumble mountains in a tropical rainforest


Mineral weathering, the slow crumbling, dissolving, and chemical transformation of solid bedrock into smaller fragments and clays, replenishes Earth’s surface with the raw materials needed to make soil and the elements needed to support life.  In the Luquillo mountains of Puerto Rico, hot rain beats incessantly onto the ground and seeps deep into the earth, creating cracks and fissures in solid rock. While a warm, wet climate, frequent hurricanes and mudslides that shake up the landscape all contribute to the rapid weathering of these tropical mountains, a recently published study indicates crystal-forming bacteria may also be important contributors to the most rapid chemical weathering rates recorded on the planet.

Luquillo rainforest in northeast Puerto Rico- a steep, mountainous, tropical forest that has been the site of extensive ecological research for decades

Luquillo rainforest in northeast Puerto Rico- a steep, mountainous, tropical forest that has been the site of extensive ecological research for decades

Historically, scientists have studied weathering as an abiotic (i.e., non-living) process. However, there is growing evidence that living organisms, from bacteria and fungal mycelia  to treescan actively participate in the replenishment of fresh rock material to the soil. In the mid 1980’s, scientists studying geothermal sediments from Yellowstone found the some of the first evidence of biological weathering when they discovered iron-silicate minerals in association with bacterial remains. These bacterial cell fragments, the scientists hypothesized, can act as mineral “nucleation” sites – surfaces to which minerals can condense and grow. If you’ve ever made rock candy, you’ve formed sugar crystals by this same nucleation process.

Snow crystals vizualized by a scanning electron microscope. Like other types of crysals, the formation of snow crystals is promoted by nucleates- things for ice to condense and grow onto. Credit:  Agricultural Research Service, United States Department of Agriculture

Snow crystals vizualized by a scanning electron microscope. Like other types of crysals, the formation of snow crystals is promoted by nucleates- things for ice to condense and grow onto. Credit: Agricultural Research Service, United States Department of Agriculture

Why is crystal nucleation important in weathering? As primary minerals, the stuff coming directly out of rocks, are broken down, they can undergo a series of chemical transformations into a variety of secondary minerals. Many of these secondary minerals, including clays, become important raw materials for the formation of new soils.

Which brings us back to Luquillo. Here, Earth scientists from many different fields- geology, ecology, atmospheric chemistry, and hydrology to name a few, are attempting to build a holistic picture of the processes that shape landscapes. For nearly a decade, a team of scientists now affiliated with the Luquillo Critical Zone Observatory have been drilling holes in the ground to study what makes the rocks crumble. Deep holes. Mineral weathering is so rapid in these mountains that they must drill through five or even ten meters of saprolite- soft, mineral rich material, no longer solid rock but not quite soil yet- before hitting bedrock. What have they found? For one, there are more bacteria living near bedrock– at that contact zone between hard rock and soft saprolite, where weathering is actively occurring-  than higher up. Roughly a hundred times more. This led researchers to ask a simple question- if bacteria are concentrated at the so-called “weathering front”, are they just passive bystanders, or do they have an important role to play in the transformation of rock into soil?

To answer this question, a research team led by Dr. Susan Brantely, a geochemist at Penn State University, drilled several holes to bedrock, collected samples from the contact zone between saprolite and rock, and used high-resolution scanning electron and transmission electron microscopy (SEM and TEM) to investigate the structure and composition of actively weathering minerals. While SEM provides information on the 3-d structure of an object, the higher resolution TEM technique can provide information on crystal bonding structure and help determine the elemental composition of a sample.

Their findings? In most of the samples, the scientists identified halloysite, a secondary mineral that forms long, tube-like crystals. Halloysite is a natural weathering product in young soils and its presence was not entirely surprising.The really exciting part came when they identified small round and rod-shaped cells buried amidst the so-called “crystalline nanotubes”. Bacteria, sheathed in crystals.  Moreover, all of the bacterial cells observed were intact, suggesting that being coated in crystals does not damage these hardy bacteria. The presence of living bacteria within secondary minerals also implicitly suggests longevity:  halloysite crystals can take weeks or months to form.

Scanning electron microscopy image (50,000x) showing a coccus-shaped bacteria surrounded by halloysite nanotubes

Scanning electron microscopy image (50,000x) showing a coccus-shaped bacteria surrounded by halloysite nanotubes. Credit: Minyard et al. 2011.

That bacteria can serve as condensation nuclei for secondary minerals in Luquillo has important ecological implications. For instance, in this  study, halloysite minerals often occurred in higher densities around bacteria than inorganic surfaces. This may be an indication that some bacteria are evolved to be highly efficient nucleating agents. These mineral-formers may have  structures attached to their cell membranes which have a high affinity for particular mineral elements, such as silica.

Scanning electron microscope images of bacteria associated with secondary minerals nearly five meters deep in Luquillo saprolite. From Minyard et al. 2011.

Scanning electron microscope images of bacteria associated with secondary minerals nearly five meters deep in Luquillo saprolite. Credit: Minyard et al. 2011.

Bacteria that serve as mineral nucleation sites may also be able to influence mineral chemistry. Other researchers have found that sulfur, considered to be an “impurity” is more concentrated in halloysite when bacteria are present. Iron, another common impurity in halloysite, was found in many of the samples in this study. The presence of iron could indicate the crystal-forming bacteria are iron oxidizers, organisms that use iron for fuel instead of carbon. Perhaps serving as mineral nucleation sites allows these bacteria to access iron they need for energy.

Scanning electron microscope image of iron oxidizing bacteraia Acidovorax sp. BoFeN1, encrusted in iron minerals. Credit: Eye of Science, Reutlingen

Scanning electron microscope image of iron oxidizing bacteraia Acidovorax sp. BoFeN1, encrusted in iron minerals. Credit: Eye of Science, Reutlingen

Many questions remain to be answered regarding the relationship between microorganisms and weathering. What sorts of organisms can withstand being coated in minerals? What are the physiological adaptations that allow them to do so, how and when did these adaptations evolve? Traditionally, geologists have considered the lithosphere- the rocky part of the earth- to be a cold, dead place. Clearly we need to start rethinking that assumption, and considering what it may mean for our geologic understanding of the planet, if organisms can find an evolutionary space buried amidst the very rocks our biosphere sits on.

Cryogenics, gene popsicles and the oldest life on Earth


While the notion of “cryogenic freezing”, or putting a person into a state of frozen suspension, has been a common theme in science fiction for decades (think the Alien movies, Star Wars, Sleeper, Vanilla Sky) bacteria have probably been doing their own version of cryogenic sleep for billions of years.

Researchers studying ice cores from the Dry Valleys of Antarctica have found viable, frozen bacteria that are thousands to millions of years old. The ice in this region of the Dry Valleys ranges from modern to about ten million years old, making it some of the oldest known ice on earth. By analyzing the ice crystal structure and isotopic data, these researchers determined their ice samples had likely been permanently frozen (i.e., no thawing/refreezing), implying that the bacteria encased within the ice have been trapped since its formation.


The scientists incubated meltwater from ice core samples at temperatures just above freezing for up to 300 days, adding supplemental nutrients to encourage bacterial growth. The samples they incubated represented a broad range of timescales, with ages ranging from 10,000 years to 8 million years. Astoundingly, bacterial growth was observed in all samples, though growth rates declined with sample age: bacteria that had been encased in ice for shorter periods of time grew much more rapidly than bacteria frozen for millions of years.

Caveats to cryogenic

The study concluded that even bacteria cannot maintain cryogenic preservation forever. In addition to slower growth rates for older bacteria, the study found an exponential decline in the size of the community DNA pool over time, suggesting the DNA is slowly degrading, even in a deep freeze. Very slowly. The estimated half-life for the reduction in DNA pool size (i.e., the amount of time it takes to reduce the amount of DNA in a sample by 50%) was 1.1 million years. (I think I just heard the microbial ecologists breathe a collective sigh of relief.) So, it may be perfectly reasonable to find frozen bacteria that are hundreds of thousands of years, even a couple million years old, that can still be resuscitated.

{An aside: why does DNA degrade, even in a deep freeze? The jury is still out, though one suspect in the present study is cosmic radiation (high-energy particles that bombard the Earth from space). Antarctica receives the highest levels of incoming cosmic radiation on the planet.}

Gene popsicles in a melting world

Bacteria encased in ice for thousands to millions of years are literally a gene bank. Collectively, the community DNA frozen in ice can be thought of as a “gene popsicle” that provides a snapshot into the past and another clue scientists can use to piece together ancient Earth environments. Moreover, it is well known that bacteria are capable of transferring genes amongst each other in a process known as lateral gene transfer. Could the periodic melting of ice sheets, due to shifts from glacial to interglacial periods, result in an influx of ancient genes into modern bacterial communities? Could genetic information perhaps be preserved for hundreds of millions, or even billions of years, through freezing, melting, and re-uptake of ancient genes by living bacteria?

And finally, the million dollar question: what are the implications for of melting gene popsicles on present-day Earth? As glaciers and ice sheets across the world continue to melt due to climate change, will hordes of ancient bacteria start to “wake up”? Could they plague the world with ancient diseases that no modern humans have resistance to? (Hmm…sounds like a good idea for a science fiction story 🙂 The answer to the former question is, probably yes, the latter, probably not. But time, and a lot more research on the microbial ecology of melting ice sheets is needed to answer these questions.

Journal reference: Proceedings of the National Academy of Sciences (DOI: 10.1073/pnas.0702196104)

Welcome to the deep biosphere


Remember in Journey to the Center of the Earth when Hans, Lindenbrock and Axel discover giant insects, mastodons and other prehistoric creatures miles beneath the surface? While this was considered science fiction in the mid 19th century, I think most of us today would be more apt to call this story pure fantasy. We know now that such an idea is preposterous. Plants need sunlight to obtain their energy, and animals need plants for food. There is no energy source capable of sustaining complex, multicellular life far away from the sun. The biosphere as we know it can only exist on the surface, where ample sunlight and moderate temperatures prevail.

Single celled life is a bit more creative. Recent drilling expeditions beneath the surface of the continents and the ocean floor have revealed a surprisingly large number of bacteria and archaea living well beneath the surface of the earth- 3 x 10^29 cells according to current estimates!* The scientists behind these projects have coined the term “deep biosphere” to describe the areas of the earth beneath the surface that are still occupied by single-celled life. A great mystery surrounding the deep biosphere is how such communities can survive in environments that seemingly provide minimal energy. In short, how are these critters making a living?

So that we’re all on the same page here, I’ll just briefly review the three basic requirements for life as we know it on planet Earth:

1) A carbon source

2) An energy source

3) A pair of molecules that can donate and accept electrons.

More on the third one later, which relates to how organisms actually break down and harvest energy inside their cells. For now, let’s suffice it to say all life requires an energy source and a carbon source. For us, both of these requirements are satisfied by eating food. The metabolism of our food releases energy. As  we break down the complex organic molecules contained in our food, we are provided with simple carbon molecules which can be rebuilt into different molecules for growth and cellular repair. All animals use organic carbon as both an energy and a carbon source, because of the high energy yields associated with this strategy. By contrast, plants use light as an energy source and carbon dioxide from the atmosphere as a carbon source. Light energy is used to power a series of biochemical transformations, ultimately allowing plants to convert carbon dioxide into sugar: photosynthesis. Thus even in the world we are familiar with there exist two vastly different strategies for meeting life’s basic requirements.

Might the microbes of the deep biosphere choose one of these metabolic strategies? Clearly, the second one is dependent on light, which I probably don’t need to tell you is in rather short supply miles beneath the ocean floor. But what about organic carbon? Is enough organic carbon from, say, dead plant, animal and microbial bodies in the surface ocean or soils making its way into subsurface environments to sustain microbial communities?

At a first approximation, the answer is probably not. Best estimates are that < 1 % of the carbon fixed by plants on the planet’s surface is making it into the “buried organic carbon” pool- the stuff that might be available as food for deep biosphere organisms. Compared with the estimated size of the biomass inhabiting the subsurface, this flux of carbon provides, at best, enough energy to carry out only the most basic life support functions, certainly not enough for growth and reproduction.

What else could be feeding the deep biosphere? The answer is a bit complex, and something I will be exploring in much more detail throughout future posts. Many different options present themselves. Some microbes can use metals, such as iron, as an energy source, allowing them to convert carbon dioxide to sugar without light. This strategies is known as chemolithotrophy.

Dormancy might be another option for some inhabitants of the deep biosphere: in essence, forming a spore and entering a state of metabolic inertia until better conditions present themselves in the future. It is known that only certain groups of bacteria have this capability, but how widespread this strategy might be in the deep biosphere is uncertain. There is an argument to be made against dormancy in the deep biosphere; namely, that it is an evolutionary dead end. Dormancy might make sense in, for instance, a seasonal rainforest, where dry season conditions force microbes to go into hibernation but the onset of the wet season allows them to “wake up” and start growing again. But in a world that is always harsh, always lacking in energy, for thousands and millions of years, would a dormant cell ever wake up? Would it ever reproduce?

Finally, there may be sources of energy available to the deep biosphere that we simply do not understand yet. Perhaps there are microbes that can harvest energy released during the radioactive decay of elements in the earth’s crust? Or perhaps heat energy from even deeper inside the earth fuels the deep biosphere?

In short, there are many questions and many mysteries surrounding life in the deep biosphere. As scientists continue to answer these questions the answers will undoubtedly expand our understanding of what it means to be alive.

*Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C. & D’Hondt, S. Global distribution of microbial abundance and biomass in subseafloor sediment. Proc. Natl Acad. Sci. USA 109, 16213–16216 (2012).

Why we should love (or at least, respect) microbes


Hrmmm. I’ve already gone and set myself up with an ambitious title. There are so many reasons why we should respect and value microorganisms. Take your own body. Your own “microbiome”- the science word for the community of microorganisms that makes its habitat in and on your body- helps break down your food, absorb nutrients, detoxify harmful chemicals and fight off infections. Our microbiomes contribute to our long-term health in ways we are just beginning to understand.

Or, take the earth. Billions of years ago, microorganisms began respiring oxygen into our atmosphere. Plants and animals would never have evolved had microbes not “primed” our atmosphere, adding greenhouse gases that warmed the surface of the earth and oxygen that provides enough energy to support multicellular life. Today, microbes are intimately involved in the cycling of all the major elements required by life (carbon, nitrogen, phosphorus, oxygen) throughout all parts of the biosphere (air, rock, soil, water).

If nothing else, we are vastly outnumbered by them. There are as many microbes in a spoonful of dirt as there are human beings on the planet. There are more microbes on the entire earth than there are stars in the galaxy. Our own bodies contain ten times more microbial cells than human cells. In a very real sense, each and every one of us is an microbial ecosystem.

In another very real sense, Earth is a microbial planet.

But microbes don’t just outweigh us. The overwhelming majority of our planet’s genetic diversity is found in microorganisms. A rough estimate: there are approximately 150 million different species of prokaryotes (bacteria and archaea) compared with a mere 9 million species of eukaryotes (mushrooms, beetles, us).

Why is this significant? Genes encode proteins that define organisms’ functional capabilities : what they can eat, what sorts of environments they tolerate, how quickly they reproduces. We are a tiny slice of the genetic pie, thus, we are a tiny slice of the functional pie. We eat only organic (carbon-rich) compounds for food – and a limited number of organic compounds, at that. We breathe only oxygen. Microbes eat organic carbon, but also a variety of inorganic compounds including ammonium, sulfur and iron. Microbes respire using oxygen but also nitrogen, iron, sulfur, and methane, to name a few.

In short, by understanding microbes we can begin to get a handle on what is biologically possible within the context of our planet’s unique chemistry and geological history. Microbes define life’s boundaries (and often surprise us by pushing those boundaries further and further away from what we conceive to be “habitable”).

I started this microbe blog to share some of the strange and fascinating ways these tiny organisms make a living.

I’ll kick it off with a link to a BBC report on findings from the Goldschmidt research conference that took place in Florence this past August:

Miles beneath the ocean floor, scientists have discovered some very, very old bacteria. These bacteria are basically metabolically inert, reproducing on average every 10,000 years. With such slow growth rates, can they really be considered alive?