Tag Archives: nutrient cycling

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.

GeoChip: linking genetics with environmental processes

Over the past decade, environmental scientists have been casting a wider net in their attempts to understand complex environmental processes on a molecular scale. Once fascinating new line of research involves co-opting techniques developed by geneticists, largely for the biomedical industry, in order to understand how genes are important regulators of earth-scale processes as carbon and nitrogen cycling.

The GeoChip is a clear example of this search for new methods to answer old questions. Microbiologists  are working on remote Antarctic islands to understand some of the simplest nutrient cycling pathways in the world. The ecosystems they study are often composed of only a handful of fungal and microbial species. These simple food chains allow resarchers to contruct basic models of how energy and nutrients (such as carbon and nitrogen) are transferred.

This is where GeoChip comes in. GeoChip is a gene microarray chip designed to identify “functional genes” involved in important nutrient cycles. It allows the identification of genes in an environmental sample that regulate carbon fixation, decomposition, and atmospheric nitrogen fixation, to name a few.  Understanding what functional genes are available in a system allows scientists to both understand the potential of that system for cycling nutrients and better predict how that system will respond to environmental change.

Imagine a glass floor divided into hundreds of indentical squares. Each of these squares contains a different fragment of DNA, reconstructed by geneticists from known DNA sequences. When scientists want to probe an environmental sample for specific DNA sequences, they “wash” their sample over the floor. Fragments of DNA will stick to their complementary sequence on the floor, causing a square to light up. Scientists can “read” a GeoChip by identifying fluroescently lit spots where environmental DNA has attached. They use this information to develop a picture of the functional genes present in that system.

In Antarctica, GeoChip is already been used to answer important ecological questions. For example, scientists are finding that genes for nitrogen fixation, the crucial ecosystem process that produces plant-useable nitrogen in the soil, occur in lichen-rich areas. Lichens are believed to be among the earliest land colonizers, and the ability of lichen-dominated systems to add nitrogen to the soil may be an important finding in reconstructing the early colonization of terrestrial systems. Other findings include carbon-fixation genes in plots that lack vegetation, indicating microbial communities that are able to perform some sort of photosythesis in the absence of plants.


Yergeau et al. 2007. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. The ISME Journal 1: 163–179

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.