Don’t treat soil like dirt!

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Soil is a precious resource, yet most of us pay little attention to the stuff under our feet.  It is the medium in which we grow our food and the foundation on which we build our cities. Soils filter our water, detoxify our pollutants, decompose our waste and hold vast reserves of the nutrients required for life. Soils are also fragile, taking thousands to million of years to develop but destroyed in minutes by human development.

For the past three years, myself and my fellow soil enthusiast Aurora have spent our Saturdays in December showing kids how awesome soil and the microbes that inhabit it actually are. We’ve developed a number of soil and microbiology activities to teach kids of all ages what soil actually is, who lives in it, and why we should value it. The take-home message? Don’t treat soil like dirt! Human beings (and nearly ever other species on earth) depend on soil for our very survival.

Here are some highlights from the last two weeks of the workshop:

Checking out some protozoa under the microscope!
Making a hypothesis before conducting an experiment!
Making a hypothesis before conducting an experiment!
MAKING SOIL! This is always a favorite. Want to make soil at home with your kids? Check out my homebrew recipe below...
MAKING SOIL! This is always a favorite. Want to make soil at home with your kids? Check out my homebrew recipe below…
Probably the coolest thing I've ever made in photoshop.
Probably the coolest thing I’ve ever made in photoshop.

We are even participating in an international, crowd-sourced science experiment known as the Tea Bag Index experiment to measure rates of decomposition in different soil types! This is a fun and easy experiment you can do in your backyard. All you need is a few teabags and a scale.  Decomposition, the breakdown of once-living organic matter and conversion into soil organic matter, is an important step in the global carbon cycle that is driven primarily by soil microorganisms. Ultimately, decomposed carbon is respired back to the atmosphere as carbon dioxide. Scientists are currently trying to understand how global climate change will affect decomposition and the microbial “respiration” of CO2 from soils. Projects such as the Tea Bag Index experiment provide scientists with valuable data that can be used to inform predictions about changes to the global carbon cycle. For more information on the Tea Bag Index experiment check out the website:

Or click here to access the protocol and get involved directly!

Most importantly, our workshop strives to underscore the importance of soils in our everyday lives.  Kids (and parents) often come unsure of what exactly soil is or why it should matter to them, and often enjoy the experience so much that they return week after week.

Live in the Philly area and got kids? Check us out, every Saturday for the rest of the month!

And since I can’t seem to stop geeking out about this stuff, here are some more cool resources to check out on soil science education:

USDA NRCS Healthy Soil Fact Sheets

Lovely animated gif of some sort of protist. #beautiful

Microbes are beautiful. I am not much of an expert on protozoa but I’ve seen a lot of these little guys under the microscope in soil samples. Protozoa are single celled but eukaryotic microbes, which basically means they are distinguished from other single celled microbes by their complex internal structure and generally larger size. Protozoa are an important indicator of soil fertility and, by consuming smaller bacteria and excreting nutrients, play an important role in delivering nutrients to plant roots in a complex process known as the microbial loop.


From gifovea, via Fresh Photons.

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microbes improve carbon cycle models

Microorganisms are key drivers of the global carbon cycle both on the land and in the ocean. Through a diverse array of metabolic strategies, microbes decompose organic and recycle organic carbon. Just as we respire a fraction of the carbon we consume as CO2, so do microbes. Globally, vast quantities of organic carbon are funneled through many billions of microbes every year: to be decomposed, recycled, and respired into the atmosphere. In spite of this, microbial activity has historically been ignored in attempts to model the global carbon cycle and predict climate change-related feedbacks. Instead, our models rely on untested assumptions that microbes and their carbon cycle activities will respond in uniform, predictable manners to increases in temperature, and as such, can essentially be ignored.

A recent paper in Nature Geoscience paper challenges this assumption by explicitly integrating microbial physiology into a new model of the soil carbon cycle. Compared with traditional models, the new model more accurately matches current observations of carbon stocks and fluxes across ecosystems. Regarding future carbon cycling in a warming world, the model produces several widely different scenarios that vary due to the potential response of microbes to rising temperatures. In short, if microbes respond negatively to warming by decreasing their “growth efficiency”; that is, if warming slows down their growth rates, no additional carbon is released to the atmosphere as the soil warms. But if microbes are able to adapt to higher temperatures and maintain their current growth efficiencies, higher temperatures will accelerate carbon decomposition rates and lead to potentially huge additional losses of carbon dioxide from soils.

The integration of biological mechanisms into earth system models is an important step forward in our ability to forecast future climates. Future research that empirically measures microbial community responses to long-term warming is desperately needed in order to accurately model and predict this potentially huge feedback to the global carbon cycle.


The end of the evolutionary road on a far future earth

The question of how life first came to be on early earth  has been of fascination to scientists for decades. By stark contrast, the question of how life may end on Earth in the distant future has received little attention, probably because the question itself forces us to face the rather depressing reality that one day, our star will die, our planet’s center will cool, and Earth will no longer be capable of supporting life. But the end of the road for life on Earth will not dawn on us overnight. Just as it took billions of years for our earliest prokaryotic ancestors to evolve into complex, multicellular life (these early microbial communities, spread far and wide across the earth, had the big responsibility of oxidizing the atmosphere so that multicellular organisms could have something to breathe) it will likely take millions if not billions of years for life on Earth to devolve as the planetary systems that allow complex ecosystems to exist slowly shut down.

How will the end of life happen?  On present day Earth, the weathering of silicate rocks draws carbon dioxide out of the atmosphere and returns it to the continental and oceanic crusts. This process occurs quite slowly (millions – billions of year timescales), but ultimately if there were no source of carbon to replenish the CO2 drawn out of the atmosphere by weathering, it would eventually be depleted. This would make our planet inhospitable to plant life, which requires CO2 to do photosynthesis. Unfortunately this is exactly what will happen when our star begins to die. As the Sun ages, its luminosity will increase, meaning Earth’s surface is going to get hotter. This will speed up silicate weathering and the speed with which CO2 leaves our atmosphere. Normally, this CO2 would be replenished with carbon recycled through the crust and mantle due to tectonic activity. However, the heating up of the planet’s surface will also increase surface water loss due to evaporation, which will increase the friction between the plates until eventually plate tectonics shuts down entirely.

When atmospheric CO2 concentrations drop below a critical threshold (< 10 ppm), plants will begin to die off. With the plants will go both the food and oxygen source for animals. Large ectotherms (large mammals and birds) will likely go first, due to their high oxygen requirements, followed by smaller ectotherms (i.e., small birds, rodents). Reptiles, amphibians and fish will likely outlast the rest of us due to their lower oxygen requirements, with marine species lasting longer in general because the oceans will likely heat up less rapidly than the land. Eventually, within perhaps 100 million years of the end of plant life, the world will be returned to the microbes.

And what might the final microbes on Earth be? In all likelihood, they will be extremophiles capable of tolerating multiple environmental stressors (polyextremophiles)- low oxygen concentrations and high temperatures, for example. They will recede from the planet’s surface where high heat and rapid evaporation will be too stressful. In all likelihood, they will return to deep ocean vents and similar subsurface environments that are both buffered from surface temperatures and capable of supplying their own source of energy.

I’ve just described the devolving (or perhaps mass extinction occurring on along a trajectory of evolutionary complexity over geologic timescales) of life of Earth in broad brushstrokes. As with most scientific theories, there are details, nuances, unanswered questions and questionable assumptions. Of course, this is also assuming that some anthropogenic force doesn’t end life on Earth far sooner (nuclear war, chemical warfare, climate change, GMOs, encountering an unfriendly and technologically superior alien race, creation and subsequent uprising of AI, zombie apocalypse). And it’s also possible that I’m being far too pessimistic, and some future technological or geoengineering solution will be able to keep our planet liveable far beyond its natural lifetime.

I’ll leave you with a plug for SpaceRip, a really awesome astronomy youtube show that has several episodes focused on questions of planetary habitability. These guys know way more than I do.

The Search for Earth-Like Planets

Amazonian fungi that will eat your plastic

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The Amazon rainforest has been a poster-child for many aspects of the environmental movement over the past 50 years. Deforestation, soil erosion, land degradation, resource exploitation, anthropogenic climate change and the rights of indigenous peoples are all major issues that have repeatedly brought the world’s largest tropical rainforest to our attention.

It turns out that environmental scientists and activists may have yet another reason to focus their attention on the Amazon: bioremediation. Several years ago, a research team from Yale University took an exploratory trip to the tropical forests of eastern Ecuador with the goal of isolating and characterizing novel species of fungi. Fungi are a diverse group of organisms possessing a range of unique life strategies and metabolic capabilities. They are of major ecological importance in many forest ecosystems as the primary degraders of lignocellulose, a class of carbon-rich biopolymers that make up woody tissue and other tough, structural parts of plants. This research team brought fungal samples back to the lab, cultured them, and set out to grow them on a variety of different carbon sources to figure out how these organisms make a living. What they found was nothing short of astonishing: several strains of endophytic fungi (fungi that live symbiotically within plant tissue, such as endomycorrhizal fungi that associate with plant roots) with the capacity to grow using the plastic polyester polyurethane, or PUR, as their sole carbon source. PUR is a synthetic polymer that is widely used in industry and manufacturing, and is known to most of us in the form of foam insulation or synthetic fibers.

So, maybe don’t bring your Spandex next time you decide to take a trip down to eastern Amazonia.

To me, this discovery poses several interesting questions. The first is, simply, why would an organism have such a capability, to which my knee-jerk response as a biologist is  “because there was evolutionary pressure to do so”. This would of course mean that  a) something in the environment of these endophytic fungi is similar enough to polyurethane plastic that the PUR-degrading enzymes can also break it down and (more importantly) b) whatever natural compound this PUR-degrading enzyme is meant to degrade is a good enough source of food that a fungus would expend energy and resources producing an enzyme to digest it. The first part of this may not be as surprising as it sounds- plants, particularly in the tropics, produce a host of resins,waxes, and other tough, carbon-rich, chemically recalcitrant (i.e., hard to break down) polymers that are in many ways quite analogous to plastics. But the fact that there are fungi that have seemingly found a niche making a living off such substances, is, to me, highly significant, as it speaks to both the incredible resilience and adaptability of nature in the face of intense resource competition. And nowhere is the competition for resources likely to be more intense than in the world’s most biodiverse forest.

Whether or not the metabolic gift of these plastic-eating fungi could be harnessed for, say, bioremediation purposes, is an open question. But the mere possibility provides another powerful incentive for preserving our forests. Many of the environmental challenges and questions facing human societies today, such as waste management, resource depletion and finding viable non-fossil fuel energy sources, may have analogs and answers waiting for us in the natural world. To deplete and destroy that world without fully exploring the knowledge it has to offer us seems to me to be not just a shameful waste, but a death wish.

“Destroying rainforest for economic gain is like burning a Renaissance painting to cook a meal.”  -EO Wilson

PS- I’ve done a bit more research and it turns out the capacity to degrade a synthetic plastic, while remarkable, is not unique to these Amazonian endophytes. In fact, enzymatic degradation of PUR in other fungal species and some bacteria has been observed by research teams around the world.

For more information check out: Russel et al. 2011. Biodegradation of polyester polyurethane by endophytic fungi. Applied and Environmental Microbiology, Vol. 77, No. 17, pp 6076-6084.

American Gut

American Gut

Most of us have heard at some point or another that we have entire ecosystems of microbes living in our gut. Mostly of these microbes are happy symbionts that help us digest our food, but some can occasionally becoming pathogenic and cause health problems. Have you ever wondered what your gut microbial community looks like? Now you can find out! The Earth Microbiome Project (, founded several years ago with the ambitious goal of “sequencing the microbiome of planet earth”, (or, in other words, characterizing basically all of the genetic diversity that exists on our planet), has begun a smaller, more targeted project with the aim of characterizing the gut communities of human populations.

Some of the key science questions driving this project : to what extent do gut microbial communities vary among people? At what scales can we discern patterns in microbial community composition? Are similar microbial communities found among people from similar geographic regions, with shared genetic history, or with a shared diet? And, perhaps more interestingly to most of us, to what extent does the composition of our gut community impact our own health? Once we have enough data to start answering some of these basic questions, perhaps we can even start making predictions about what sorts of lifestyles will lead to what sorts of gut flora, and how these communities, in turn, will impact our overall health.

It costs just $100 to join and get your microbiome sequenced. And the information could change your life!

A draft of the national climate report has been released for review by the American people. Please take a moment to look it over. It’s a lengthy report, but the message is clear from the opening letter: our climate is warming, faster than we anticipated even three years ago. We have many lines of evidence pointing to this conclusion. To name a few, hotter summers with periods of extreme heat lasting longer than any living American has ever experienced. More frequent, extreme weather events, such as superstorm Sandy that devastated coastal regions of the northeast this past year. Global sea level has risen approximately 8 inches since the end of the 19th century, and is projected to rise another 1-4 feet by the end of this one. The Greenland ice sheet is melting more rapidly than scientists have anticipated, and the north pole is expected to be completely ice free in the summer by mid-century. Massive die-offs of coral reefs are being observed, species distributions are shifting in time and space.

In deciding whether to try to massively reduce our carbon emissions and prevent some of the most dramatic consequences of climate change from being born out, or implementing a comprehensive global adaptation strategy, I believe that humanity faces its single greatest challenge yet as a species. The decisions we make now and in the coming decades will alter the environment we experience and the fundamental way our planet functions for thousands, if not hundreds of thousands of years to come.

On this post-Thanksgiving day of rest, digestion, and reflection on the ability of food to bring families and friends together, I thought it would be appropriate to share some information I learned this past week about food and its ability to bring other, more disparate groups together. The largest migration on planet Earth is not, as I would have guessed, a seasonal migration. It is a daily migration of numerous species of marine organisms, from tiny zooplankton to the largest marine predators. Across the world, entire marine ecosystems migrate from the ocean surface at dawn to anywhere from hundreds to thousands of meters depth. They then return back to the surface at dusk. The motivation for this massive migration? Well, that depends on where you are in the food chain. Smaller organisms migrate to the dark depths of the ocean to avoid predation, while larger organisms generally follow in hopes of catching a meal.

The hunt for food mobilizes entire ecosystems on a daily basis! But why does this migration make any sense if the little creatures driving it are constantly being pursued? Turns out that smaller animals require less oxygen than larger ones, and so the depth of migration depends on where in the ocean oxygen limitation begins to occur. Small animals hoping to avoid becoming someone’s next meal migrate just far enough into this zone that larger predators cannot follow.

Just a lil’ piece of science to put everyone’s turkey day in perspective. Happy Thanksgiving to all!

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