Deep but not dead: how tropical subsoil microbes could affect the carbon cycle


It’s no exaggeration to say the tropics drive our planet’s carbon cycle – the constant transfer of carbon back and forth, on a global scale, between living things and the environment. Understanding the dynamics of the carbon cycle is increasingly important because more carbon in the atmosphere increases the warming greenhouse effect.

Rainforests are known for their unparalleled biodiversity, but they also pull more CO2 from the atmosphere than any other terrestrial ecosystem, helping to keep our climate in the stable state we’ve enjoyed for the past 10,000 years. But overlooked beneath the lush green canopies lies a big piece of the carbon puzzle: the soil.

Carbon cycles through living things and the environment.
Sahmed1890, CC BY-SA

Tropical forest soils contain more carbon than all living vegetation on Earth. And we’d like to keep it that way. Not only does organic matter — a mixture of decomposed plant, animal and microbial molecules — build soil fertility, it locks up carbon that might otherwise end up in our atmosphere. Keeping soil carbon in the ground, particularly in the tropics, is critically important to maintaining Earth’s climatic stability.

In some parts of the soil, notably the deep soil, carbon seems to be doing a pretty good job staying put on its own. Here, you’re apt to find soil organic matter that’s been sitting around for hundreds to thousands of years. It’s appealing, then, to call these subsoils a long-term carbon sink.

But a critical question remains with regard to how locked away that soil carbon really is: can microorganisms — the biological engine that drives the soil carbon cycle — actually decompose this ancient organic matter? If the soil microbes can decompose some of it, metabolizing it for energy, some of the previously sequestered carbon would eventually wind up in the atmosphere as carbon dioxide. And that could be a big problem for the climate.

The view above the canopy in Luquillo.
Joe Spurr, CC BY-NC-SA

To answer that question, I traveled to the Luquillo Critical Zone Observatory, an environmental “laboratory” located in the world’s most extensively studied tropical forest, in northeast Puerto Rico. Here, I investigated how microbial metabolism changes as we dig deeper.

Beneath organic-rich surface soils, the subsoil contains small amounts of very old – and potentially very stable – carbon that’s been there for thousands of years. What sorts of microbes live down there? What controls their activity? And if tropical subsoils are biologically active, is subsoil carbon really as stable as we think?

Collecting a soil core in the clay-rich tropics.
Madeleine Stone, CC BY-NC

Digging for data in the dirt

First, my colleagues and I spent weeks traipsing up and down the mountains, identifying sites with distinct geologies and plant communities at different elevations. Within each site, we dug holes a meter and a half deep, collecting samples from discrete depth layers for chemical and microbiological analysis back in the lab.

Everywhere we dug, microbial activity, soil carbon and nutrients dwindled rapidly with depth. This we expected: Over large areas, subsoils hold vast pools of carbon, but actual carbon concentrations dwindle rapidly away from the surface. And as their food supply diminishes, so does the amount of microbes.

Performing a respiration experiment to assess the metabolic potential of soils.
Madeleine Stone, CC BY-NC

What surprised us was that even in the deepest, most carbon-starved soils, microbial activity didn’t disappear. Rather, subsoil microbes were ready and waiting to cycle soil carbon and nutrients. Exoenzymes — proteins that break down large, complex molecules into smaller ones that can pass through cell membranes — remained active. On a per-microbe basis, soil respiration – the collective CO2 “exhale” of microbial metabolism – was equal or greater in subsoils than at the surface.

Microbes at the ready

In total numbers, the subsoil contained less carbon and fewer microbes. But on a per-capita basis, subsoil microbes were capable of cycling carbon and nutrients, at rates equal — or even exceeding — their surface counterparts.

How could this be? In resource-poor subsoils, any metabolic process comes at a steep energetic cost. In such environments, microbes often go dormant and wait for fairer weather. So what’s causing microbes to maintain their metabolic machinery here?

For one, deep soil microbes may have adapted to exploit resource-poor environments. High per-capita microbial activity in subsoils could also be a stress response. Much like car engines, biological systems perform less efficiently as conditions get worse. Microbes that are stressed due to low energy availability may, paradoxically, respire more carbon as CO2 for each molecule they actually use. Or they may produce more enzymes to harvest increasingly scarce resources.

Iron-breathing microbes, Geobacter, are a major component of tropical soils.
Derek Lovley, Kelly Nevin & Ben Barnhart, University of Massachusetts

Climate implications

Soil microbes are critical drivers of Earth’s carbon cycle. But in deep tropical soils, we still don’t know what controls them.

My research shows how tropical subsoil carbon, typically considered stable, may in fact be biologically vulnerable. Small changes in microbial carbon metabolism could have a huge effect, integrated over all the carbon present in tropical subsoils. Releasing as CO2 all the carbon currently locked up in these subsoils would have devastating effects on the planet’s climate.

What sorts of environmental changes might amp up subsoil metabolism? Climate-induced soil warming, for one, which makes it easier for enzymatic reactions to occur. A recent modeling study shows how soil carbon losses over the 21st century vary dramatically depending on the microbial response to temperature. Other climate change feedbacks, including increased root carbon production under elevated atmospheric CO2, could also stimulate soil biota.

Land use change is another persistent threat in the tropics. Conversion of forests to pasture can expose subsoils that haven’t seen the light of day in hundreds or thousands of years. Will ancient, “stable” carbon become susceptible to loss?

These are the questions that need to be answered. Compared with temperate and boreal regions, tropical forests remain a poorly studied microbial ecosystem. Field experiments that simulate anthropogenic drivers — climate change, deforestation — are virtually nonexistent. Until we can predict how tropical microbes will respond to global climate change, we can only guess at how the vast carbon pools beneath our planet’s most productive forests will shift over the 21st century and beyond.

The Conversation

This article was originally published on The Conversation.
Read the original article.


Volcano bacteria uses rare earth metals to survive in acid hot springs

Rare earth elements, highly coveted in the technology industry, are difficult to mine because of their low concentrations in most rocks. Clockwise from top center: praseodymium, cerium, lanthanum, neodymium, samarium, and gadolinium. Credit: Wikipedia

Rare earth elements, highly coveted in the tech industry, are difficult to mine because of their low concentrations in the Earth’s crust. Clockwise from top center: praseodymium, cerium, lanthanum, neodymium, samarium, and gadolinium.
Credit: Wikipedia

Most of us pay little heed to rare earth elements, found in trace quantities throughout Earth’s crust and sporting unpronounceable names like lanthanum and praseodymium. However, REEs are ubiquitous in our lives, a key ingredient in technological wonders such as cell phones, laptop computers, and solar cells. While our anthropocentric bias may lead us to assume we are the only organisms smart enough to take advantage of REEs, not so, according to a study published last week in the journal Environmental Microbiology. New research indicates that at least one bacteria- perhaps many- use REEs to turn methane into fuel. By doing so, they are able to survive in some of the most extreme environments on Earth.

Just west of Naples, Italy, lies the Solfatara crater: a dormant volcano that spews jets of sulfurous steam from fissures in the Earth. In addition to being the mythological home of Vulcan, the Roman god of fire, Solfatara harbors an unusual member of the bacterial phyla Verrumicrobia known as Methylacidophilum fumariolicum . Discovered in 2007, M. fumariolicum has proven astounding in many ways: it thrives in high heat (120-140 ºF), in strong acid (pH < 1), and with nothing to eat except for methanol, a very simple carbon-containing alcohol. But the ability of scientists to study the unique physiology of M. fumariolicum has been limited by the bacteria’s very slow growth in the lab.

Also known as fumaroles, openings in the planet's crust such as this one emit steam containing a mixture of noxious gases. They are also home to extremeophilic microbes that can tolerate both high heat and acid. Credit: Wikipedia

Also known as fumaroles, openings in the planet’s crust such as this one emit steam containing a mixture of noxious gases. They are also home to extremeophilic microbes that can tolerate both high heat and acid.
Credit: Wikipedia

Until, that is, Dr. Arjan Pol and colleagues from Radboud University decided to add a dash of volcanic mudpot water, M.fumariolicum’s natural habitat, to the petri dish. And, eureka! M.fumariolicum started to grow, at a rate directly proportional to the amount of mud water added.

But this was puzzling to the researchers. They couldn’t find a single element with known biological importance that could replace the mudpot water. In order to narrow down what was causing M.fumariolicum’s growth, the scientists heated the mudpot water to 550ºC to ash off all organic materials. Adding the ashed residue to their cell cultures still caused M.fumariolicum to grow. This clued Dr. Pol in that whatever ingredient M.fumariolicum needed to grow was capable of withstanding high heat- a mineral.

To determine the identity this essential mineral, the scientists further analyzed the mudpot water using inductive coupled plasma mass spectrometry, a technique that allows quantification of different element concentrations. As it turns out, several rare earth elements known as lanthanides were ten times more abundant than usual. By experimentally adding each of these metals to their cultures, the researchers quickly confirmed lanthanides were causing M.fumariolicum to multiply.

Lanthanides are sometimes observed to have positive effects on plant growth, and are commonly used in fertilizers. Scientists speculate that lanthanides boost growth by interacting with Rubisco, the ubiquitous photosynthesis enzyme that binds carbon dioxide and begins the process of turning it into sugar. Metals are often associated with enzymes as cofactors, switches that turn an enzyme on or off by binding or releasing. If a plant’s Rubisco operates more efficiently in the presence of lanthanides, that would mean the plant could turn carbon into sugar faster.

In an analogous manner, Dr. Pol and colleagues guessed lanthanides might be interacting with some protein involved in helping M.fumariolicum acquire energy. To investigate this hypothesis, they extracted and separated different proteins present in their microbe. Lanthanides were most abundant in association with methanol dehydrogenase (MDH), an enzyme that helps break methanol down into methane. Thus it appears this volcanic bacteria requires lanthanide metals in order to metabolize methane, its primary food source.

But why would a bacteria depend on rare earth metals for a crucial component of its metabolism? Most organisms would use more common elements like calcium, zinc or magnesium. It turns out MDH produced by M.fumariolicum has an extraordinarily high affinity for its substrate, methanol. Lanthanides, by slightly altering the enzyme’s 3-D structure, may be responsible for this high affinity. In resource-limited volcanic mud pots, any adaptations that increase an organism’s ability to acquire energy would provide an enormous advantage.

While this study provides the first direct evidence of an organism requiring REEs to grow, use of REEs may not be limited to extreme environments. Certain plants are known to hyperaccumulate REEs in their leaves. Bacteria living on the surface of REE-enriched leaves may be adapted to use these metals. Beaches or ocean sediments are another place for REE lovers might thrive- sand represents a virtually inexhaustible source of these metals.

It's not always easy getting microbes to grow. We can only culture <1% of the bacteria present earth. Bacteria that live in environments very different from our own are poorly represented in the catalog of culturable organisms.

It’s not always easy getting microbes to grow. Currently, scientsts can only culture <1% of the bacteria present earth. Bacteria that live in environments very different from our own are poorly represented in the catalog of culturable organisms.

A major challenge for scientists studying unusual or uncommon microorganisms is growing these critters in the lab. This is often because we are unaware of key ingredients they require. The finding that REEs are essential for some microbes will undoubtedly help future scientists to grow and study more of our planet’s vast unseen diversity.

Arjan Pol,, Thomas R. M. Barends,, Andreas Dietl,, Ahmad F. Khadem,, Jelle Eygensteyn,, Mike S. M. Jetten, & Huub J. M. Op den Camp (2014). Rare earth metals are essential for methanotrophic life in volcanic mudpots Environmental Microbiology, 16 (1), 255-264 DOI: 10.1111/1462-2920.12249

Combing sloth hair for rainforest fungi, scientists uncover anti-malaria, anti-cancer and antibiotic activity


Hosting the highest biodiversity of any biome on Earth, tropical rainforests may represent a goldmine of “bioactive” compounds- medicinal chemicals produced naturally by plants, insects and microorganisms. Given a full 50% of all medicines introduced between 1981 and 2006 came directly from nature, the notion of “bioprospecting”, or combing the diversity of tropical forests for new drugs, has enticed imaginations for decades. But Big Pharma’s interest in bioprospecting has waned in recent decades due to the slow pace of discovery. However, hope is still alive amongst microbiologists working in the field.  And for good reason. In a study published last week in the journal PLOS ONE, scientists report on a new, highly promising source of bioactive compounds from a rather unusual suspect: the three toed sloth.

Sloths are famous for their green coloration, a result of the algae that live in their hair and help provide camoflauge

Sloths are famous for their green coloration, a result of the algae that live in their hair and help provide camoflauge

Sloths host entire ecosystems in their thick, coarse hair, including plants (green algae), arthropods (cockroaches, moths and roundworms), bacteria and fungi. Microbiologist Sarah Higgingbotham at the Smithsonian Tropical Research Institute in Panama was interested in finding out whether any of this diversity was medicinally valuable. Of particular interest to Higgingbotham and colleagues were the numerous species of fungi living in sloth hair. Fungi have made substantial contributions to the pool of natural drug products since the discovery of penicillin over 80 years ago.

Fungi are a diverse kingdom of organism from which have come a variety of natural products, including food supplements, antibiotics such as penicillin, and anti-cancer agents.  Credit: National Geographic

Fungi are a diverse kingdom of organisms that produce a variety of economically valuable compounds, such as antioxidants, antibiotics and anti-cancer agents.
Credit: National Geographic

To uncover potential drug-producing fungi, Higgingbotham and colleagues collected samples of the coarse, outer hair from nine unsuspecting three toed sloths found moseying along a road in Soberanía National Park, Panama (yes, aspiring microbiologists, this is something you can actually get paid to do). The hair samples were taken back to their lab, incubated on petri dishes, and checked regularly for fungal growth. Following growth, the researchers collected fungal hyphae from the plates, extracted and sequenced their DNA in order to determine identity. In total, 84 unique fungi were isolated. Although these fungi are a highly diverse group, including several potentially novel species, most fell into the taxonomic class Sordariomycetes – a well documented source of bioactive compounds.

Samples of 70 isolated fungal strains were grown in liquid culture media and tested for “bioactivity” against malaria, Chagas disease and the breast cancer cell line MCF-7, in addition to 15 human pathogenic bacteria. A strain was considered “highly bioactive” if it inhibited growth of a disease by 50% or more. For 50 of these strains, the researchers also constructed “antibiotic activity profiles” – scorecards indicating the degree to which a given fungal strain inhibits a range of bacterial pathogens. Antibiotic activity profiles are commonly used in medicine to determine the efficacy of a particular drug against an infection. Creating antibiotic activity profiles allows scientists to compare novel antibiotics to databases of antibiotics currently on the market and identify new disease-fighting drugs.

Malaria parasite P. falciparum eats its way through the hemoglobin in red blood cells.  Credit: National Geographic

Malaria parasite P. falciparum eats its way through the hemoglobin in red blood cells.
Credit: National Geographic

Overall, two of the fungal isolates were highly bioactive against the malaria parasite Plasmodium falciparum and eight were active against the Chagas parasite Trypanosoma cruzi. Fifteen fungal isolates were highly active against the MCF-7 cell line. Bioactivity against T. cruzi is particularly rare and represents a promising alternative to the two currently used drugs, nitrofurane and benznidazole, both of which can have toxic side effects.

Twenty of the fifty fungal isolates screened were bioactive against at least one bacterial pathogen. An exceptionally promising isolate, Lasiodiplodia sp.1, aggressively reduced the growth of several pathogenic Gram-negative bacteria. Infections caused by multi drug-resistant (MDR) Gram-negative bacteria, such as E.coli and Pseudomonas aeruginosa, are on the rise worldwide due to the overuse of antibiotics in hospitals and clean rooms. There is currently a paucity of drugs in development against MDR Gram-negative bacteria compared with their Gram-positive counterparts. Lasiodiplodia’s bioactivity profile did not match that of any known antibiotics, suggesting a potentially novel disease-fighting mechanism.

What do hospital clean rooms and factory farms have in common? Both use lots of antibiotics, leading to an increase in multidrug-resistant bacteria

What do hospital clean rooms and factory farms have in common? Both use lots of antibiotics, leading to an increase in multidrug-resistant bacteria

Twenty nine of the fungal strains isolated by Higgingbotham and colleagues are known endophytes– fungi that make a home living on plants. Endophytic rainforest fungi have recently made news for other remarkable metabolic features such as the capacity to metabolize plastic . The discovery of endophytic fungi on sloth hair increases our understanding of the habitat range occupied by these diverse organisms. Higgingbotham speculates some her fungi living may be associated with the algae present in sloth hair, forming a symbiosis analogous to that seen in lichen.

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.

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?

Thanks for checking out this little microbe blog


I’m a microbial ecologist and biogeochemist. That’s a mouthful! In a nutshell, I study how microorganisms make a living in strange environments while contributing to global cycles of carbon and nutrients. Microbes are nature’s unsung heroes, and I hope to show you some of the bizarre and wonderful ways these tiny creatures make a living. Thanks for checking out my blog- I’d love to hear your feedback!