Tag Archives: biogeochemistry

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 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.


Whats up with nitrogen at Hubbard Brook?

Buried deep in the White Mountains of New Hampshire, the Hubbard Brook experimental forest has provided ecologists with questions and answers for over four decades.  And more questions.

Hubbard Brook was founded on the principle that it was the ideal location for “small watershed” experiments: it is a forest ecosystem whose energetic inputs and outputs could be fully accounted for and directly measured. Ecologists have been able to ask many broad and profound questions at Hubbard Brook, and the forest has told them a story from which many fundamental ecological principles have been distilled. What causes forests to grow? Where do they get their nutrients? What sort of energy enters and leaves an ecosystem? How are human activities impacting forests? Are they resistant to change, and are they resilient in the wake of disturbance?

Before tackling any of these big questions, you may well wonder about my first statement: that the energetic inputs and outputs of the forest can be fully accounted for and measured. How can one possibly measure all the energy that enters and leaves a forest? In the case of Hubbard Brook, there is a deceptively simple answer: it’s all in the streams. Keep a record of what enters and leaves the streams, and you’ll have a good idea of what is entering and leaving the forest as a whole.

Plants need three things to grow: sunlight, nutrients and water. Of the plant essential nutrients, nitrogen is the most important in temperate deciduous forests, but phosphorous, calcium, magnesium and sulfur, among others, are also essential.  In describing where  nutrients and energy come from, ecologists like to talk about autochthonous and allochthonous inputs. Autochthonous inputs come from within the system. Allochthonous inputs come from elsewhere. In the case of nitrogen, an autochthonous source would be a leguminous plant, or a plant that can convert atmospheric nitrogen into a plant useable form through the biochemical process known as nitrogen fixation. An allochthonous input might be a nitrogen fertilizer sprayed on a field.

Hubbard Brook has plentiful rain and sunlight to support a healthy forest. The first unknown that ecologists tackled was nitrogen, and I’ll focus on it from here on out because understanding nitrogen at Hubbard Brook has proved more challenging than anyone ever imagined.

Where are the plants getting their nitrogen? It turns out that for the last 14,000 years (since the retreat of the North American glacier that allowed the northeastern US to re-vegetate), all nitrogen that has entered and fed Hubbard Brook has come from the atmosphere. From the rain. No nitrogen fixing plants, no weatherable rock-derived nutrients. All that plant nourishment has entered the forest silently, dissolved in the summer rains or the winter snow.

It also turns out that all nitrogen eventually leaves  Hubbard Brook by water as well, in a readily soluble form known as nitrate, or NO3-. Streams cut across the forest, forming discrete, independent watersheds over a relatively small space. (A watershed simply refers to a region whose hydrologic inputs and outputs are well defined and accounted for). Streams are an integral part of the Hubbard Brook forest. Much as your bloodstream carries essential nutrients to your tissue and allows your body to flush out toxins, streams transport nutrients to different parts of the forest and flush away excess chemicals that the system doesn’t use. Through long term monitoring of the stream chemistry at Hubbard Brook, including measurements of headwater inputs and lowland outputs, ecologists have developed an accurate record of how much nitrogen enters and leaves the system annually.

In an unpolluted forest, how much nitrogen enters, and how much nitrate leaves, tells ecologists a lot about the forest’s growth and nutrient requirements. At Hubbard Brook, scientists have found an annual cycle of stream nitrate that reflects a strategy the trees have evolved in response to a predictable environment.

When leaves  drop in autumn, nitrate export in streams peaks. Leaves fall both directly into the stream and onto the surrounding soil, where they are decomposed and their nutrients can be leached away. Over time, this process would lead to a dramatic reduction in the nitrogen held in the system, if not for the annual winter replenishment of nitrogen through snowfall. Snow contains nitrogen just like rain does, and as it builds up on the forest floor during the winter, a stockpile is created for the next growing season. Trees have timed their first buds to break in the spring just as this snow is melting and releasing a pulse of nitrogen into the earth. This is essentially how things work at Hubbard Brook, in the absence of human influence.

However, Hubbard Brook, situated just north of the Washington-New York-Boston urban corridor, is by no means isolated from human pollution. Nitrous oxide gases emitted from fossil fuel combustion dissolve in the atmosphere and are rained out across the world, often at great distances from the source. Since at least the 1960’s, excess nitrogen has been entering Hubbard Brook as nitrate through this process. As a negatively charged anion, nitrate often picks up a hydrogen cation, H+, to balance its charge. “Hydrogen cation” is basically a fancy term for acid (remember ocean acidification?) The greater the concentration of hydrogen in solution, the more acid a solution is. Nitrogen pollution, ecologists realized, was doing something very strange to rainwater chemistry at Hubbard Brook. The concept of acid rain was born.

Thus is should not be surprising that another more powerful trend overlies the annual nitrogen cycle at Hubbard Brook. From first measurements in the late 1950’s until 1970, scientists observed a steady, annual rise in stream water nitrogen export. Since 1970, however, nitrate concentrations have been dropping. This has been attributed in large part to the passage of the Clean Air Act and the subsequent reduction in nitrous oxide emissions from automobiles.

Here’s what is causing ecologists to scratch their heads. Nitrogen levels in Hubbard Brook streams have now been dropping steadily for forty years. They are approximately at their 1960 level, and this downward trend shows no indication of leveling off. This reduction is dramatic, unexpected, and not accounted for by the emissions reductions enforced through the Clean Air Act. It is becoming increasingly clear that something else about the ecosystem has fundamentally changed.

What exactly is happening to cause reduced nitrogen outflow from Hubbard Brook forests concerns ecologists for a variety of reasons. The main reason ecologists are concerned is because the forest has stopped growing. In fact, it is now thought that Hubbard Brook may be losing biomass.

Could reduced nitrogen loss reflect increased nutrient limitation in the forest, and a need for trees to hold tightly to the nutrients they have? Could it mean rainfall is no longer supplying the nitrogen the forest needs? Could the soil microbial community no longer be decomposing and transforming nitrogen in the manner that the forest has depended on for thousands of years? Could it possibly reflect some other fundamental hydrologic shift, perhaps induced by climate change?

The most compelling theories in my view are that the phenomenon of “missing nitrate” is climate change driven, or driven by changes in soil chemistry and loss of important soil cations. I’ll explain both of these ideas briefly and leave you to ponder.

Climate change is certainly causing other weird stuff to happen at Hubbard Brook. The forest typically experiences sub-freezing temperatures all winter and builds up a healthy snowpack. Snow insulates the soil and streams alike, preventing them from freezing. This allows frogs, salamanders and some fish to hibernate over winter without freezing. Recently, warmer and more varied winter weather patterns have lead to reduced snow cover, with the consequence that the soil and stream water are now freezing instead. (The number of frozen salamander bodies discovered in the winter of 2006 was apparently unprecendented). Loss of snow cover is also disrupting the annual nitrogen cycle, which could well be leading to a springtime nitrogen limitation for growing trees.

Calcium, which typically takes the form Ca2+ in soils, turns out have a high affinity for nitrate. The two ions balance each other’s charge, and when nitrate leaches out of soil, it often brings a calcium ion along with it. Actually, it often requires the charge-balancing association provided by calcium to leave the soil in the first place. Well, calcium turns out to be another very important plant nutrient, and unfortunately is not as quickly replenished through rain as nitrogen. Declining soil calcium levels will, over time, produce soil that leaches nitrate less readily. Nitrate loss in streams could thus be indicative of a serious calcium deficiency. Incidentally, sugar maple, a common species in New Hampshire forests and a calcium-accumulating tree, is dying out and may be entirely lost these forests within the next several decades.

What’s up with nitrogen at Hubbard Brook? No one really knows yet, but we’d sure like to figure it out.

In trying to paint a picture of the dynamic nature of nitrogen at Hubbard Brook, I’ve left quite a bit of detail out and haven’t discussed some of the fascinating experimental manipulations that have been conducted at the forest. Hopefully I’ve touched on enough of the important ideas that this ramble provides some sense of the many layers of complexity that ecologists must piece through to understand a system or solve a problem.


The title and much of the content of this article I’m crediting to Dr. Gene Likens, a senior ecologist at the Hubbard Brook experimental forest who provided fascinating information on the forest during a conversation and a guest lecture at the University of Pennsylvania.

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.