Tag Archives: soil

Don’t treat soil like dirt!

Check out my new blog here

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

Reconstructing the proteome of ancient peoples in soils

Soils are often one of the most common archaeological artifacts, and the clay minerals contained within soils have a unique ability to tightly bind proteins, slowing or preventing their decomposition. For this reason, a fraction of proteins added to a soil during human occupation can potentially be retained for hundreds or thousands of years, serving as a “protein fingerprint” that may shed light on the diet, agricultural activities, livestock, or even human populations themselves that inhabited region.

A recent study attempts to use mass spectrometry techniques to characterize the proteinaceous matter residing in soils from excavated farmhouses of Roman origin in the present-day Netherlands. Using a novel approach termed “peptide-mass fingerprinting”, the researchers were able to uncover a suite of keratinaceous proteins commonly found in human hair and skin fragments.

Characterizing the proteins present in living tissues has been common practice in the biomedical world for at least two decades. The application of proteomics to complex environments such as soils is, by contrast, novel, and this study represents the first published attempt to use proteomics as a fingerprinting tool in an archaeological soil. I could easily see this technique becoming valuable in reconstructing the history of not just soils, but any structures or artifacts produced from clays, as clay minerals in soils are one of the key protein-binding agents. If certain protein classes in soils, for instance keratinaceous skin proteins, could be distinguished into different isoforms, or classes, based on their molecular weight, then these protein fingerprints could be related to extant proteins.Taking this one step further, different protein isoforms are often associated with genetically distinct populations of organisms. If we could begin relating ancient protein fingerprints to their extant counterparts, we might be able to indirectly trace the human genetic history of a site or an object.

Oonk et al. 2012. Soil proteomics: An assessment of its potential for archaeological site interpretation. Organic Geochemistry, 50, 57-67.

The history beneath your feet

I think about dirt a lot more than most people. Probably this is the result of my background in ecosystem science, the study of how nutrients and energy flow throughout the biosphere. The soil represents a huge sink for all major nutrients that sustain life on earth, and an important source of nutrients such as carbon and nitrogen that are naturally recycled to the atmosphere.

But it’s not economic, or really even environmental value that makes soil so fascinating to me. It’s history. In the forests of northeastern Puerto Rico where I’m currently conducting research, the historic record deposited in soil is up to 8, 10 or 15 meters thick and stretches back 300,000 years into the past, to a time when the island itself was shooting up out of the Gulf of Mexico due to rising magmatic rock deep beneath the ocean floor.

If you start looking closely at the composition of soil, you will quickly discover a wealth of information recorded within it. Tiny grains of minerals, produced from thousands to millions of years of water dissolving rock, form the physical matrix on which life has developed. As these clean, crystalline minerals slowly rot, they are chemically transformed into new compounds such as clays. Clays and other secondary minerals add stickiness to the soil, allowing decomposing organic materials to adhere. Slowly, a strange collection of organic materials that were once living and the inorganic ingredients that supported their existence begins to accumulate. As this assortment of the dead and rotting grows, so does the living biomass that it sustains. Most of the soil microfauna is involved in feeding off dead (or other living) organic materials and ultimately recycling nutrients that would otherwise be locked away forever. Embracing death is a way of life in the world’s most biologically diverse ecosystem.

But wait- I was talking about history. Yes, living organisms, dead organic materials, clays and minerals are all important components of the soil, but how do we piece together a history (and of what? The geology that the soil formed over? The forest that once stood atop it? The long-dead animals whose traces still linger within it?) from such a complex and dynamic system?

The answer is not entirely clear. But I am convinced that history is sitting in the dirt, rotting away, waiting patiently for someone to find a way to unwrap the stories contained within.


In an unpredictable environment, trees network for stability

In the highly variable ridge, slope and valley mosaic that forms the Luquillo Mountains of northeastern Puerto Rico, Dacroydes excelsa, commonly known as Tabnuco, dominates the landscape. Though tropical forests are generally quite diverse and seen as ideal environments for plant growth, life in this rainforest can actually be quite challenging. Powerful hurricanes pass through the Caribbean annually and hit the Puerto Rican mainland every few years. Large swatches of the Luquillo forest were flattened several years back when hurricane Hugo struck in 1989.  Aside from directly damaging or wiping out forest stands, hurricanes cause landslides that severly erode the already shallow, nutrient depauperate soils.

On steep, harsh slopes that experience such frequent disturbance, what allows one tree species to gain a competitive advantage over the hundreds of others struggling to survive? Rather than compete fiercely for limited resources only to be at the mercy of the next devastating hurricane, Tabunuco trees have adopted an alternative strategy- cooperation and resource sharing through root grafting.

Root grafting, the joining of neighboring tree roots to produce a network, is a phenomenon that scientists have been aware of for decades, though the extent of its occurrence and the benefits that it provides trees are largely unknown. In Tabunuco forests, however, root grafting is widespread and many of its benefits obvious.

Tabunuco trees grow in dense stands and will graft roots with neighboring trees as they mature, forming unions that comprise anywhere from two to over a dozen trees. A clear advantage of this strategy in an environment that experiences powerful storms is structural stability. Trees that have entered unions increase their base of support and are less likely to be uprooted during a wind event or landslide. In increasing their wind-firmness, individual trees boost their survival chances during a storm. Fewer uprooting events also reduces the probability of a major landslide and helps ensure the retention of the surface organic matter that contains most of the forest’s available nutrients.

Root networks can also improve soil conditions during the off-season. Densely packed surface roots form “organic benches” which trap leaves and other decaying plant matter rather than allowing these important nutrient sources be washed downslope. Roots aerate the soil, facilitating decomposition and nutrient flow. They also “prime” the surrounding soil for productivity by releasing sugary compounds that stimulate beneficial microbial activity (the interaction between plants and microbes in the root zone known as the “rhizosphere” is another fascinating topic entirely, which I will do attempt to do justice to in the future).

Scientists are now discovering previously undetectable advantages of Tabunuco grafting that underscore the high degree of sophistication and evolutionary purpose in the development of these networks. It is now known that root networks can actually serve as conduits for the transfer of carbon and essential nutrients between trees. This can provide an immense competitive advantage over non-networked trees. Tabunuco trees that receive the most sunlight and produce the most carbon through photosynthesis can transfer carbon to neighboring Tabunucos to ensure the long-term health and survival of the community. Individuals of less common species, such as the Caribbean palm and Colorado tree are excluded from Tabunuco networks and must compete for growth given only the resources available in the vicinity of their roots.

Though in Tabunucos root grafting precludes the need for inter-tree competition, it is theoretically possible that trees could use grafting for more selfish purposes. Ecologists have speculated whether trees can gain a competitive advantage over their neighbors by leeching a neighbor’s nutrients, much as the fungal organisms that associate symbiotically with plant roots can become greedy and actually sap nutrients from their host under stressful conditions. Root networks may even serve as a conduit for disease or herbicide transfer, allowing trees that produce or tolerate a harmful compound to efficiently clear out their competitors.

Basnet, K., F.N. Scatena, G.E. Likens, and A.E. Lugo. 1992. Ecological consequences of root grafting in tabonuco (Dacryodes excelsa) trees in the Luquillo Experimental Forest, Puerto Rico. Biotropica 25:28-35.

enzymes in the environment

enzymes are the catalysts of life. they are the link between higher forms of biological structure- cells, organisms, ecosystems- and the physical universe. they form such links by allowing incredible reactions to occur, reactions that strip complex molecules down into simple components that our cells can harvest energy from, reactions that detoxify harmful substances, reactions that take nonliving compounds and turn them into something organic. they have ugly names. ribulose-1,5-bisphosphate carboxylase oxygenase is a name that most eyes would glaze over while reading, but what if i told you that RuBisCO (it has a nickname!) is the only thing on earth that can add electrons to carbon dioxide? if that doesn’t seem to impressive, look out your window. not a single tree, flower, blade of grass, animal or human being (or man-made structure, for that matter) would exist if RuBisCO had not evolved to turn carbon dioxide into sugars.

there is a less appreciated truth about enzymes that i find to be equally intriguing, almost poetic. enzymes not only build and maintain life, they destroy it. or, to be a bit more accurate, they recycle its components. enzymes are largely responsible for decomposing organic matter, breaking down trees and blades of grass and human beings into the tiny carbon-rich compounds that RuBisCO created. in fact, if you take a small handful of soil from your garden, you are holding billions of free floating enzymes. they have been constructed by plants and microbes and were released into the environment to acquire something that their creator needs (i hate to use the word “creator”, when writing about science, if you have a better word, please do share). most often, this is an essential nutrient or a small sugar that can be used for energy. imagine if you could take your stomach out, and send it off to wendy’s to eat a chicken sandwich for you. not the prettiest analogy, perhaps, but this is in essence this is what microbes and plants do in the soil.

while intellectually it may be somewhat interesting to imagine billions of microbial exo-stomachs scouring the earth for their lunch, why should anyone really care about enzymes in the environment? well, truth be told, very few people do. but i’m going to tell you why an increasing number of environmental scientists are taking an interest in enzymes, not only in order to understand a process, but with the growing realization that understanding how enzymes shape our planet may be essential to averting looming environmental catastrophes.

as the agents responsible for the breakdown of organic, carbon containing compounds (and this is true in soils and aquatic ecosystems), enzymes are gatekeepers. they regulate how quickly carbon is broken down and taken up anew by living organisms. if you want to think realistically about any form of carbon sequestration in soils (an idea that has exploded in popularity in the last several years), or understand how global warming is altering ecosystems and the balance of carbon and nutrients within them, you simply cannot ignore enzymes.

the fact is, much as we would like to find a way to store the huge amounts of  carbon our activities are releasing into the atmosphere back in the earth, adding carbon feeds the soil. and just as human populations increase during times of food surplus, microbial populations explode, produce more enzymes and cycle that carbon at a faster rate.

another aspect of enzyme behavior that makes global climate change scenarios even stickier is that enzymes are very, very sensitive to changes in their environment. the activity and efficiency of enzymes in the environment is closely linked to temperature, moisture, and pH conditions. my own research on soil enzymes from northeastern forests is showing that even a few degrees of temperature increase can cause a dramatic increase in the rate of the carbon-cycling reactions that these enzymes perform. droughts, on the other hand, can quickly kill demolish enzyme communities and cause carbon cycling in a system to drop off.

the behavior of enzymes in the environment, we are discovering, is far more complex and nuanced than the story i’ve outlined here. moreover, ecologists know that enzymes must be understood within a broad context. the plants, animals and environmental processes that interact to form complex ecosystems, which enzymes regulate on a very fundamental level, must be somehow integrated if we are to fully understand how these tiny reaction machines keep our earth running.

Maybe we should reconsider raking our leaves

I recently learned a fascinating fact about leaf raking that should be painfully obvious to a forest ecologist- it’s bad for trees! Every spring, deciduous trees produce leaves that they use throughout the growing season for photosynthesis and sugar production.  Plants concentrate essential nutrients such as nitrogen, potassium, calcium and magnesium in their leaves, as these nutrients are all required in relatively high amounts to perform photosynthesis.

As winter approaches and the growing season ends, trees withdraw many of the proteins and nutrients they have stockpiled in leaves back into their woody tissue, so that these nutrients can be recycled to make new leaves the following year. However, most trees are able to do even better than this- after their leaves have fallen, the nutrients that couldn’t be recaptured in time are decomposed into the surface soil surrounding the tree, and will be available for uptake through the roots several years later. This regular flux of plant essential nutrients back to the soil through leaf litter means that plants depend on those same nutrients, year after year, to grow new leaves.

In fact, if you look at the typical architecture of a deciduous tree, it is no accident that probably appears like two umbrellas attached together at their handles. The top umbrella is the above ground parts of a tree from the base of the trunk to its canopy. The bottom umbrella is inverted and planted into the ground. It is composed of a main taproot that drives straight down into the earth, and lateral roots that branch out horizontally. Of these lateral roots are branching networks of finer and finer “root hairs” and associated fungi that are able, through their enormous surface area, to mine the soil underneath a tree for nutrients. Everything that is dropped from the top umbrella should theoretically be recoverable by this root system.

I’d imagine most of you can already see where this is going, but I find that sometimes simple truths are quite elusive. When we rake our leaves in the fall to maintain our clean, grassy lawns, we are removing loads of nutrients that our trees are expecting to get back! We are creating an artificially open, leaky system, that trees have spent millions of evolutionary years refining. A recent paper in a relatively esoteric research journal, “Nutrient Cycling in Agroecosystems” (who reads that??) attempted to quantify the impact of historic leaf raking on old agricultural towns in central Europe. The fascinating bit of historical information in this paper is that centuries ago, medieval farmers actually knew that leaves were a great nutrient source- farmers removed leaves from nearby forests specifically to use as fertilizer on their fields. This paper claims that the result of historic leaf raking is that the “majority of central European forests were severely depleted of nutrients…when modern long-term rotation forestry became the dominant form of forest land use”.

So next fall, when you’re pulling out your rakes or enlisting your kids to do so for a few dollars, think carefully about your trees. In all likelihood, the average patch of suburban lawn is already so nutrient depauperate from numerous land use changes (deforestation, asphalt paving, over-fertilization, the cultivation of a monoculture of non-native grasses, to name a few) that removing a few leaves isn’t going to make a big difference. But if I’ve learned anything from Malcom Gladwell, it’s that little changes that add up to produce big effects, and if medieval Europeans were knowingly removing nutrients from their forests, I figured modern suburbanites should at least be aware.