Tag Archives: decomposition

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:

Shahada_microscope
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:

http://decolab.org/tbi/concept.html

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

http://decolab.org/tbi/protocol.html

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

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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.

 

A forest on glass beads

Defying all expectations,  a forest has grown on the beach. Just east of Philadelphia is  the New Jersey Pine Barrens- a vast wilderness almost completely ignored outside of a small group of park rangers, volunteer fire fighters and hardy locals whose families have eked out a subsistence living here for generations. And yet is is considered the largest undisturbed wilderness in the northeastern corridor with a incredibly unique ecology and a set of rare endemic species.

The Pine Barrens region spans most of southeastern New Jersey from the Atlantic coast inland across the mid-Atlantic coastal Plain. The coastal plain is essentially a huge wedge of sand that has accumulated over 5 million years of sedimentary deposition from the Applalachian mountains and southerly flowing rivers such as the Hudson. A long history of sedimentary accumulation has created a flat, unvarying topography. 18 feet of height divide the highest point in the Pine Barrens “uplands” region and the lowest point in the “lowlands”, and yet this seemingly homogeneous landscape has produced broad environmental gradients over incredibly short distances.

The reason for these gradients seems to relate to the unique nature of the sandy, nutrient depauperate soil. Sand can act as either a sieve or a water trap depending on its spatial position. At higher elevations,  rain drains freely through the sandy soils, leaching away any nutrients that accumulate and producing highly acid conditions that few plants can survive on. The uplands forests are dominated by drought-resistant, fire-tolerant pitch pine trees with a smattering of oaks. A few scrubby, low-nutrient requiring members of the Ericaceae family, such as huckleberry and highbush blueberry, dominate the understory. At low elevations, rain accumulates and has nowhere to go. The water table is generally high, producing soils that are saturated year-round. In the most saturated places, one finds peat bogs and white cedar swamps more reminiscent of the deep south than the mid-Atlantic. Swamps grade into tall, shady oak-dominated forests dotted with an occasional pine in the drier lowlands.

The stark contrast between uplands and lowlands vegetation is not just a product of  the soil conditions. The uplands and lowlands communities produce feedbacks on the environment that maintain the land in precisely the same condition for generations, such that nothing new can manage to gain a competitive edge.

In the uplands,  pine trees exude organic acids into the soils, maintaining their soils in a state of poor nutrient quality that nothing else can survive on. Every few years pines drop their needles, but not before sucking nearly all the nutrients out and back into the branches, ensuring that few nutrients are added back to the soil. The low nutrient-quality of this leaf litter slows microbial decomposition, causing years of litter to accumulate on the surface. This litter serves as kindle that enhances the spread of forest fires the pine trees require to sprout. These forest fires keep the less fire-resistant oaks at bay.

In the lowlands, wet conditions prevent forest fires from scorching the landscape with regular ferocity seen in the uplands. Oak trees are able to gain a firmer footing here, and once established, produce a shady understory that pine saplings cannot survive in. The oak trees drop their leaves annually, adding more nutrients to the ground and producing a soil richer in organic matter than enhances the development of a herbaceous understory, which helps crowd out pine saplings.

I stood over a pit we had just dug in the ground, staring down into what resembled a layer cake of dark chocolate, vanilla and red velvet. Distinct stratification in the soil profile  generally indicates a long history of mobilization processes. Organic matter leached down through the chocolately topsoil will sometimes produce a white, organic-free layer beneath, known to soil scientists as an E-horizon. Deeper still, weathering products from the underlying bedrock will accumulate in the subsoil and form complexes with the organic matter that has been transported down. The reddish layer I was seeing in the deep soil was the result of iron accumulation and subsequent oxidization by microbes in need of an energy source. In fact, the entire soil profile, from brown to white to red, is very typical of a class of soils known as Spodosols that dominate the New England and Canadian boreal forests, where low temperatures cause decomposition and other soil-forming processes to occur slowly, resulting in a surface buildup of organic matter and eventually the formation of distinct, colorful stratified layers. What, then, was such a soil doing in the Pine Barrens, a much warmer climate than New England, and a region with few soil nutrients and barely any organic matter inputs?

It turns out that the Pine Barrens soils which so closely resemble Spodosols may in fact be a relic from a much earlier time and different climate. At the height of the Last Glacial Maximum approximately 18,000 years ago, a large continental ice sheet known as the Wisconsan Glacier ended a mere 40 miles north of the Pine Barrens.  The New Jersey climate probably resembled those seen in the high Canadian boreal today, and there is little doubt that the soils that formed were some version of Spodosols. It is entirely possible that, given the state of extreme stasis that the Pine Barrens have existed in since the beginning of the Holocene, not much has occurred to alter the soils from their former state.  A forest that grows today on glass beads has thrived because of its ability to maintain stasis. Peeling back the layers of that forest reveals this stasis to be true, but only for a fleeting moment in the geologic record.

Carbon sequestration in soils: sources, sinks and pitfalls

When we talk about “sequestering” carbon in the soil to mitigate anthropogenic climate change, what are we really saying as scientists, and what is the public getting from it?  And perhaps even more importantly, what implicit assumptions are we as scientists making that may affect the validity of the widely held belief that increased C storage in soils is a good thing, and can offset our CO2 emissions?

In a recent soil carbon series in the European Journal of Soil Science, one review paper attempts to address these issues. “Carbon sequestration” has become a popular idea among policy makers and scientists alike. As anyone who keeps up on ecosystem science literature will know, C sequestration has also become an explicit motivation for numerous studies of soil and ecosystem properties.

Current best estimates claim that worldwide, soils store 684-720 Pg of C within the upper 30 cm, and 1462-1548 Pg to a depth of 1m. (For anyone not familiar with these terms, 1Pg = 1×10ˆ15 gram). The upper 30% of the soil profile to 1m clearly stores a disproportionate amount of C; this ecologists know to be the zone where continuous inputs from roots and organic matter replenish C. To put these numbers in an ecosystem context, the amount of C stored globally in soils to 30cm is twice the amount  of C stored as CO2 in the atmosphere and three times the amount of C stored in above ground vegetation. Clearly, soils represent a huge pool in global C budgets and should be managed with the knowledge that changes may represent a powerful feedback on the global C cycle. This vast storage potential is what has popularized the idea of sequestering even more C in soils and has spurred a myriad of different research approaches, from ecosystem-scale reforestation efforts to molecular studies of C-mineral binding interactions.

Given the amount of hope that has already been invested in this powerful idea, it is important for scientists interested in soil C to keep several caveats in mind when planning and conducting their research, and when communicating that research to a broader audience at a science or policy conference.

Caveat #1) Carbon sequestration does not necessarily mean climate change mitigation.

Increasing the amount of C stored in a particular ecosystem’s soil does not by default decrease the amount of CO2 released to the atmosphere. This is partially an issue of scale. If policy makers choose to set aside a certain amount of pasture land for reforestation (with the assumption that this will increase the net C storage in these systems), it is often the case that new land will have to be cleared somewhere else to compensate for the lost agricultural production.  The clearest way around this problem is to be selective in land use changes: land that is more fertile should be exploited for farming, and land that is less fertile should be reforested to boost C storage. However, an increasing global population poses obvious constraints to this line of reasoning. Ultimately, the fact remains that in the upcoming decades, we will need to boost our agricultural yields to meet global demand, and furthermore, climate change is predicted to decrease the fertility of some of the world’s most productive regions.

Moreover, allowing land to go back to its “natural” state does not necessarily lead to a net accumulation of C. A forest respires far more CO2 per acre than a wheat field. Due to the high water demands of forests relative to crops, it can sometimes be the case that trees dry up otherwise inundated subsurface soils, and in doing so create a soil environment that accelerates the decomposition of C.  One must have a refined understanding of the sources and sinks of CO2 in any particular ecosystem to claim that it will or will not “sequester” C.

Finally, management changes leading to increased C storage may increase or decrease the flux of other greenhouse gases, most notably N2O and methane. Given that these gases have 298 and 25 times the global warming potential of CO2, respectively, they are not a trivial consideration. Forests often hold less nitrogen than pastures (due to the different C:N demands of woody vs. non-woody tissue), and consequently release more N2O through the microbial process known as denitrification.

Caveat #2) The amount of carbon that can be locked up in soil in finite

Our understanding of how C is actually “stabilized” in soil on a molecular scale is still evolving. Scientists are using powerful technologies such as x-ray crystallography to understand in detail the chemical interactions between soil minerals and carbon-rich compounds that cause C to be tightly bound and inaccessible to microbes. As a general rule, the more mineral surface area available for C binding, the more tightly C is bound. In subsurface soils lower levels of C mean higher (mineral surface area: C) ratios and thus tighter binding of the C that is present.

However, mineral stabilization has its limits. Laboratory experiments are finding that as C is added to soils, “steady states” are sequentially reached. Careful manipulation of the  chemical and thermodynamic parameters of a soil may bump that soil from a lower steady state to a higher one, but whether such techniques can be applied on a whole-ecosystem scale remains to be seen.

To repeat, caveat #2 is that the amount of carbon that can be locked up in soil is finite, which leads to caveat #3.
At present, the amount of CO2 we put in the atmosphere does not seem to be.

Powlson et al. 2011. Soil carbon sequestration to mitigate climate change: a critical re-examination to identify the true and the false. European Journal of Soil Science 62: 42-55.

Earthworms play key role in regulating carbon storage in tropical ecosystems

A principle frontier in our understanding of global carbon budgets is tropical forests, on which research is historically scarce. At temperate and high latitudes, a warmer climate is predicted to increase the rate of decomposition and soil carbon turnover, resulting in a positive feedback on atmospheric carbon as CO2 is released from soils at increasing rates. A better understanding of the mechanisms regulating tropical carbon storage is needed in order to develop a holistic picture of global carbon cycling and feedbacks due to climate change.

Earthworms are important regulators of many ecological properties of soils. Their burrowing activity increases soil pore space and contributes to soil structure and drainage. Most importantly, earthworms can digest a huge quantity of dead and partially decomposed plant material. This digestion causes chemical transformations that ultimately produce nutrient-rich soil organic matter, or SOM. SOM helps ensure soil fertility, and contributes to numerous physical and chemical soil properties such as soil structure, porosity, water retention, and the capacity of soils to buffer pH changes. SOM’s aggregate structure causes it to have high water stability. This is an essential property in tropical forests, which have the highest rainfall levels of any biome on Earth.

SOM produced by earthworms is also rich in both carbon and nitrogen. A detailed biochemical and molecular analysis of earthworm casts suggests that these creatures may in fact play a key role in controlling tropical carbon storage.

Casts are clumps of digested organic matter excreted by earthworms that aggregate into large and distinctive structures. Researchers working in the rain forest neighboring the Dong Cao village in Northeast Vietnam studied the effect of cast production by Amynthas Khami on soil C storge. A. Khami is a species of tropical earthworm that can grow up to 50 cm long and produce tower-like casts. The researchers first used a “simulated rainfall” experiment to determine the relative stability of casts versus control soils. They then measured total carbon content, lignin and mineral-bound SOM content of casts and control soils.

An earthworm cast produced by A. Khami, a large tropical species found in Northeast Vietnam.

The study found striking differences in the chemical composition of earthworm casts versus control soils that ubiquitously indicate higher carbon storage in casts. Casts are more structurally stable and can withstand at least twice as long a rainfall event as control soils without compromising their structural integrity. They are enriched in carbon compared with controls, and particularly in carbon compounds such as lignin that have a high “carbon storage” potential. Lignin, a primary constituent of woody plant tissue, is a complex and heterogeneous molecule that is both carbon-rich and difficult for microbes to decompose. Earthworms probably excrete high quantities of lignin after obtaining the more digestible carbon sources from the roots and leaves that they eat. Finally, high levels of mineral associated-SOM were found in casts. Soil minerals bind to organic matter through electrostatic interactions, and in doing so make it unavailable for decomposers.

Though it well known that earthworm digestion initially speeds up decomposition, this new study suggests that casts may in fact contribute to long-term carbon stabilization. In tropical soils, which tend to cycle carbon quite rapidly, this mechanism should not go unappreciated. Future tropical land-use decisions may want to account for the welfare of this often-unappreciated soil organism.

Hong et al. 2011. How do earthworms influence organic matter quantity and quality in tropical soils? Soil Biology and Biochemistry 43: 223-230.

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.