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


Probing the Aerosol Microbiome of New York City’s Subway System

River of "psychomagnotheric slime" in the NY subway from the Ghostbusters game for Wii.

River of “psychomagnotheric slime” in the NY subway from the Ghostbusters game for Wii.

If you’re a sci fi geek like me, you’ve almost certainly consumed some form of media that features perilous encounters in the New York City subway system (our AI oppressors in The Matrix, giant genetically engineered cockroaches in Mimic, negatively charged slime in Ghostbusters, lots and lots of villains in Teenage Mutant Ninja Turtles….I could go on). In reality, any non-human dangers that do exist in the subway are likely to be more insidious than the large, charismatic monsters featured by Hollywood. Do the microorganisms inhabiting subterranean bowels of New York pose any real threat? If a dangerous epidemic were to hit the metropolis, would it spread above ground or propagate below?

While zombie viruses may be a bit far-fetched, the possibility of a pathogen propagating through heavily-trafficked subway is not

While zombie viruses may be a bit far-fetched, the possibility of a pathogen propagating through the heavily-trafficked subway is not

Motivated by these sorts of public-health questions, a team of medical microbiologists led by Dr. Norman Pace at the University of Colorado, Boulder, decided to investigate the airborne microorganisms inhabiting the NYC subway. Historically, the regulatory focus on city air quality has addressed particulate materials (soot) and chemicals.  Comparably little attention is paid to the airborne microbes and other biomaterials to which we are regularly exposed. However, in heavily-trafficked public locations like the subway (with a ridership exceeding 1.5 billion per year!), airborne pathogens may represent a much greater danger than chemical pollutants.

For  nearly two years, Dr Pace and his team collected “bioaerosols” on seven NYC subway platforms and three neighboring above-ground sites, using a device known as a fluid impinger- essentially a fancy vacuum that sucks up and filters air, trapping bacteria-sized particles. They used a combination of molecular techniques to determine the genetic composition of subway bacterial communities.

Their diagnosis? Breathe easy! There appears to be no imminent danger posed by subway air. The subway microbiome is relatively simple and homogenous, both throughout the system and over time. A mere 26 taxa comprise over 75% of the bacterial populations found in the study, as compared with the millions or billions of taxa found in more diverse environments such as soils. The dominant subway species, much like their aboveground counterparts, are a mixture of bacteria characteristic of soil, water and human skin, all relatively harmless. [A fun aside: it turns out the leading mechanism by which microbes are transferred from skin to air is through heat convection! Our body temperatures are typically greater than the surrounding air, meaning we emit a constant plume of heat carrying components of our skin microbiome]

The remarkable similarity between the microbial communities of subway air and aboveground city air is testament to a highly effective air circulation system known as “passive train pumping”. It’s the same system that causes the rush of air you feel when walking over a subway grate. According to Dr. Pace, the uniformity of microbial communities throughout the subway indicates passive train pumping is doing a good job replenishing the subway with fresh air.

PathoMap, a Weil Medical School based effort to develop a map of the New York City microbiome for pathogen monitoring and predictions

PathoMap, a Weil Medical School based effort to develop a map of the New York City microbiome for pathogen monitoring and predictions

Subway microbiome research represents one component of a larger research effort known as PathoMap. Led by  Dr. Chris Mason and his lab of microbiologists at Weil Cornell Medical School in New York, PathoMap aims to use new DNA sequencing technologies to establish “pathogen weather maps” of the city. The research group collects regular environmental samples from highly trafficked regions of NYC for microbial profiling. Microbial genomic profiles are then spatially mapped using GIS-based tools. Ultimately, Dr. Mason hopes that his maps, which track the genetic dynamics of the city’s microbiome,  will be used to detect and respond to microbial dangers, thus reducing the spread of pathogens.

The original article can be found here.