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.

Breathing Earth

Most of us learned at some point in our lives that when we exhale, we are releasing carbon dioxide, or CO­2, an invisible gas generated as waste through the millions of metabolic processes that maintain business-as-usual in our cells every day. But rarely do we pause to consider the significance of this unconsciously routine activity. In fact, few other activities allow us to participate so intimately in a global cycle that sustains all life on earth. If you’re the type of person who is inclined to be intrigued by the profundity of mundane truths, read on!

CO2 is fascinating in that it represents a beginning and an end in the most fundamental sense. As our cells’ mitochondria break down complex sugars to produce energy, CO2 is formed- a forgotten leftover once all the juicy electrons have been stripped away. But much as any gardener or urban composter knows, leftovers can sustain new life. Once expelled from its indifferent host, CO2 is free to reenter the atmosphere, where it resides for hours to decades, disappearing into a vast sea of nitrogen. Eventually, each molecule of CO2 respired will be absorbed by the biosphere again, sucked up through the tiny pores in a plant leaf or diffused across a bacterial cell membrane where it will be incorporated into sugar anew.

It is not just humans and animals that participate in the cycle of energy and breath. If you start looking for it, you’ll find evidence of electron-stripping, energy and CO2– releasing activities in nearly every corner of your life. Your houseplants respire CO2 as a byproduct of metabolizing the very same sugars they work to hard to photosynthesize. Soil, water, air and nearly every other non-sterile surface or media is filled with microorganisms that need sugars just like you and your plants, and likewise participate in the flow of energy. Even our machines strip electrons from once-living carbon-rich compounds, in a process not so different from what happens in your mitochondria (though cars and jet engines require much greater supplies of energy than humans or cats, thus we find ourselves extracting concentrated, fossilized plant remains from the bowels of the earth in order to keep them chugging).

Thus, as you zoom out a bit from your individual perspective, and it becomes remarkably easy to start aggregating breathers. Humans in a neighborhood. Cars on a highway. Blades of grass in a lawn. The soil beneath a cornfield. The amazing fact of the matter is, in fact, a very simple truth- we are all carbon-combusting machines, steadily chugging away at the biosphere’s second great energy source (sunlight is, quite arguably, the first). All of us except a fascinatingly weird little cult of microorganisms that I’ll have to touch on another time.

Okay, so maybe Morpheus cleared this all up a decade ago when describing the post-apocalyptic fields of human babies that serve as a primary energy source for our robot overlords. But our collective role in the global cycles of carbon and energy are important enough that I think it’s worth reiterating every once in a while.

Iron reducing bacteria fertilize tropical forests with phosphorus

A classic paradigm in ecosystem science is the concept of nutrient limitation. Simply put, nutrient limitation theory states that the total plant productivity of an ecosystem (ie, plant biomass produced via photosynthesis) is always limited by the scarcest nutrient. This concept makes intuitive sense- plants require a suite of different nutrients in specific proportions to produce new tissue (animals including humans do, too, we just are fortunate enough to eat other living organisms whose tissue contains all the nutrients we require). For plants, the “big three” nutrients are carbon, nitrogen and phosphorus. Organic carbon, produced during photosynthesis using light energy and CO2 from the atmosphere, is the most important in terms of total amount required, but it is actually N and P that plants are believed to be limited by most often.

It turns out that the question of which nutrient, N or P, is going to be more limiting in a particular environment is not a trivial one.There is a long-held notion that temperate forests are more N-limited, while tropical forests are more P-limited. The reason for this is that the primary source of phosphorus for plants is found in rocks- their slow decay into soil releases phosphorus in a form that plants can readily take up and use. Tropical forests sit on ancient soils and even more ancient rocks that have had nearly all the phosphorus sucked out of them millions of years ago. By contrast, temperate forest soils are quite young, having only started developing at the end of the last glacial period ~11,000 years ago, and are relatively rich in rock-derived P. The lack of P in tropical forest soils has also led scientists to conclude that these forests are less resilient to human disturbance than their temperate counterparts. A patch of Amazon that is converted into cattle pasture has scant levels of essential nutrients in its soil to begin with, and typically erodes into desert in a matter of years.

This simple paradigm of temperate forest N-limiation and tropical forest P-limitation makes good sense until you start going out in the forest and taking measurements. On the island of Puerto Rico, soils are at least 10 million years old and  up to 30 meters deep, making the forests that grow upon them perfect candidates for P-limitation. Scientists were thus surprsised several decades ago to find that there is abundant P in both the soils and plant biomass of Puerto Rican forests. Moreover, the forests of Puerto Rico experience frequent natural disturbances- hurricanes that occasionally flatten an entire landscape- and yet, within a growing season or two, things start returning to normal. Clearly, these forests are highly resilient, which begs the question of whether our classic model of tropical P limitation is completely off base.

As is often the case in science, it appears that the devil may be in the details. Puerto Rican forest soils may contain a lot of phosphorus, but they contain even more iron, a “garbage” element that’s found abundantly in soils that have long since had most other mineral-derived elements consumed or eroded away . It turns out that mineral-derived iron loves to bind P and make it inaccessible to plants. This much has been known for a long time. In fact, iron-phosphorus binding is often cited as auxillary evidence for tropical P limitation. However, recent research indicates that  a special group of bacteria know as iron reducers can actually use iron in soil for metabolic energy, much as we and other aerobic organisms use oxygen to fuel our metabolism. In the process of “breathing iron”, these bacteria release iron-bound phosphorus, which plants are then free to take up.

So, are iron-reducing bacteria saving Puerto Rican, and perhaps other tropical forests from being P-limited? The answer appears to be yes, but only sometimes. Iron reduction in soils is a rather specialized process that only occurs under conditions of anoxia (no oxygen), which in turn only occurs when a soil is completely inundated with water. Sounds like just the type of scenario that we’d see when a hurricane strikes. In flattening a forest, hurricanes may not be wreaking havoc at all, but simply playing their part in a natural cycle that provides just the right conditions for an essential but plant-limiting nutrient to be pulsed into the soil.

So, P limitation? Still an open debate, but in my view forests are incredibly complex, self-regulatory systems that have evolved to attain everything they need from their environment. Furthermore, nature is messy and doesn’t like to fit into nice little paradigms. I’ll give it a “maybe” and a “sometimes” and call it a day.

The end of the line

Fish has been an important source of protein, essential amino acids and oils to human societies for tens of thousands of years. However, in the last 50 years many of our important fish stocks have become depleted. Some have vanished entirely.

In his recent book and documentary film The End of the Line, Charles Clover, investigative reporter and prominent environmental spokesperson, outlines the social, political, technological and environmental choices that have pushed many of our favorite types of seafood to the brink of extinction, and have transformed most of the world’s biologically productive marine habitats.

Cod, a predatory fish once so common in the North Atlantic that early European pilgrims to the New World left accounts of their ships pushing through thick seas of fish, was declared commercially extinct in 1990. Estimated to contain 7.7 million tons of fish before significant human depletion, the spawning stock of the North Sea in 2005 was a meager 45,100 tons. Bluefin tuna, perhaps an even more impressive top predator reaching weights of over 1200 pounds, began disappearing from the North Sea in the 1950s.

As the oceans top predators have become rarer, fisheries have turned their attention down- down the food chain, and into deeper waters. Smaller fish that feed at a lower on the food chain, such as anchovies and herring, are now being harvested both for human consumption and as feed for fish farming operations, which focus mainly on raising big predators like salmon and tuna.

Fishing down the food chain would be a disturbing trend on its own, given its implications about our concern for maintaining the integrity of marine ecosystems. A possibly even more ecologically dangerous trend, however, is the heightened interest among fishermen in the slow-breeding, long-lived species that inhabit deeper waters. The technology to fish at depths greater than 1,000 meters is relatively new, and government regulations are virtually non-existent. Enterprising fishermen are now catching fish  such as the orange roughy, a creature that lives up to 150 years, does not reproduce until about 30 years of age, and produces far less offspring than common shallow water species, at depths down to 10,000 feet. As consumers are most familiar with fish from shallow continental shelves, many of these deep catches are fileted to look like any other more familiar white fish, and brandished with exciting new names (empereur in the case of the orange roughy).

The countries that are the largest culprits in global fishery depletion are also those that travel furthest from home to ensure plentiful delivery of seafood to their citizens. For instance Spain, which has traditionally depended on seafood more than most other European countries as a principle source of protein, is currently in the process of stripping West African countries of their coastal stocks, hiring out just enough locals to make their operations legal to the European Commission. 

In a Earth whose population is expected to peak around 10 billion in another four decades, is there any way to halt the accelerating demise of our world’s fisheries? According to Clover, a fundamental paradigm shift needs to occur in the way we view our oceans. Fishing is the only type of food production carried out on an industrial scale that follows a hunter-gatherer tradition. Agricultural yields have been vastly improved by investments in technology. As Clover puts it, “the trajectory of modern technological hunter-gathering goes in the opposite direction. Increased effort produces less fish”.

To maintain the integrity and heritage of our oceans, to ensure that our descendants have access to this resource, we need to put away the steamrollers and heavy artillery. If we continue to treat the oceans as a battlefield, it is a war that we have already won. However, the short term gains of industrial fishing technology, gains enjoyed by only a privileged few, will not be remembered when the oceans have been scraped clean. The time is ripe to change the way we interact with this precious resource. Already, smart management decisions including restricted fishing seasons, maximum allowable catches based on scientifically-determined safe population sizes, and larger nets to avoid catching the youngest fish that have not had a chance to spawn, are transforming some of the world’s fisheries into what could one day be a truly renewable resource.

As a consumer, your choices have as much of a voice in the ocean’s future as fishermen or politicians. There is good documentation on several websites about what popular seafoods are the most environmentally-friendly or the most endangered. At the very least, it’s important to know where your fish came from. If every consumer insisted on knowing where his or her fish came from, even what ocean it came from, it would force fisheries to become more accountable and transparent about their catches. A can of light, dolphin safe tuna (a label which, by the way, does not mean that no dolphins are killed as bycatch, and moreover does nothing to protect the thousands of seaturtles and birds caught in nets intended for tuna every year) might as well have come from mars for all the fisheries tell us.

Scientists predict that if we continue fishing as we are now, we will see the end of most seafood by 2048. Let’s ring in the new year with a resolution to not let that happen.

– Good, up to date seafood guide that rates fish and shellfish based on the sustainability of their fisheries

-Monteray Bay Aquarium fish guide

-Red List of threatened or endangered species by the International Union for the conservation of Nature and Natural Resources.

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.


Back to the future- ecosystem memory in environmental metagenomes

Over the past two decades, the study of ecology has been revolutionized by the advent of molecular genetics techniques. Originally developed with only biomedical applications in mind, some forward thinking ecologists quickly realized the possibilities that these technologies could offer. One of the fastsest growing areas of environmental research is metagenomics, the study of pooled genetic material from an environmental sample. In a gram of soil or a droplet of seawater, millions of unique species of bacteria exist with their own unique genetic make-up. Combine an enormous number of bacteria with even more abundant viruses- naked fragments of DNA encased in a protein coat that serve no other purpose than to infect living cells and hijack their DNA replication machinery- and you have a metagenome.

Thanks to a handful of pioneering scientists, scientists can now take a sample from practically any environment- soil, ocean water, subsurface rocks, or cloud water, to name a few, and sequence its “genome”. The genes obtained from an environmental sample indicate the total potential that the sample is biologically capable of.

What sorts of information is metagenomics providing us? Genes present in environmental samples encode proteins that perform numerous ecosystem functions- enzymes that decompose organic matter and release carbon, nitrogen and phosphorus, as well as numerous important micronutrients. Proteins that detoxify organic wastes, or convert inorganic gases such as carbon dioxide into sugar.

A major challenge moving forward from genomic information to understanding, at the most fundamental level, how an environmental system functions, relates to the fact that a genome is not a reflection of every process going on in a system, but rather an indication of what that system is capable of. Only a fraction of your body’s genes are being translated into proteins at any given time- some are turned on or off at certain points in your life, and some are only activated under the proper environmental conditions.

The mechanisms underlying gene expression in humans are still  largely unknown, but it is becoming increasingly clear that in microbial metagenomics, gene expression is highly sensitive  to external stimuli. The emerging framework for microbial gene expression is actually strikingly similar to economic resource allocation theory. Why waste time and energy producing a protein to degrade cellulose if there is no cellulose in your vicinity? Why produce nitrogenase, the protein responsible for taking inert atmospheric nitrogen and converting it into a form useable by plants, if there is already abundant organic nitrogen in the soil? Proteins represent an energetic cost, and microbes exist in a competitive, resource limited environment where any misallocation of resources almost certainly compromises your chances of survival.

Given that microbes will only express those genes that provide the maximum return on investment, what does a metagenome really tell us? Memory. As ecologists begin to push forward from examining metagenomes to studying gene expression and protein expression in environmental samples, Mary Firestone, one of the pioneers of the field of molecular microbial ecology, encourages her colleagues to look “back to the future”. All the genes present in a sample, she argues, provide a written history of what the environment has been like in the past. Resource allocation theory and evolutionary theory tell us this. Why would a gene be present, if there wasn’t a selective advantage to it at some point? Much as paleontologists can study changes in dinosaur morphology over time and infer changing environmental conditions, microbial ecologists can use metagenomics to infer what must have been the conditions at some point in the past. And if something occurred in the past to select for a bacteria carrying a particular gene, it may well happen in the future. Carbonic anhydrase is a protein commonly found in surface seawaters that is responsible for converting dissolved CO2 into bicarbonate, and in doing so acidifies the environment. The presence of carbonic anhydrase encoding genes in a seawater sample may indicate a past in which CO2 concentrations were much higher. Forward thinking about how to deal with new genomic information may in fact be a history lesson.

Quorum sensing: an understudied control in plant nutrient availability

It is a well known fact that many bacteria like to live in groups. Moreover, just as human societies strive to facilitate group living, (through grocery stores that provide food for otherwise unsustainably crowded cities, and municipal waste centers to ensure that our concentrated living spaces are kept clean enough to remain livable), bacterial populations employ a variety of strategies that enhance collective life.

The bacterial analog to human group-living strategies is called quorum sensing.  Quorum sensing, or QS, is really an umbrella term used to describe a range of bacterial behaviors that enhance group life. QS behaviors are considered common to all bacteria and have likely been tracking bacterial evolution since the first true cells of Precambrian earth crawled out of their prebiotic soup. Here I’ll focus on a particular group of bacteria that employ some very ecologically important QS strategies.

Bacteria are broadly divided into several distinct phyla that occupy a range of earth habitats and employ an enormous variety of survival strategies. Proteobacteria are one such major group that is particularly interesting to me because of their posited dominance in the zone of plant-nutrient uptake known as the rhizosphere. The significance of proteobacteria in rhizosphere microbial populations has really only been examined in temperate forests, and hopefully some of my own work will bring a tropical perspective to our understanding of rhizosphere community composition.

It turns out that proteobacteria release a specific signal molecule known as N-acyl-homoserine lactone, or (AHL) in order to alert other proteobacteria of their existence. Thus proteobacteria are able to “quorum sense” their environment and receive information of the relative density of their fellow quorum members. Moreover, the release of AHLs operates via a positive feedback mechanism- higher concentrations of AHLs attract more bacteria, resulting in even higher concentrations of AHLs.

Bacteria don’t employ quorum sensing simply because they enjoy each other’s company. In fact, there are almost certainly trade offs associated with group life, including higher levels of predation, lower oxygen availability and buildups of toxic waste products. However, the benefits that can be obtained by living in groups are also significant. Soil bacteria produce extracellular enzymes that release soluble, digestible molecules into their environment. A greater concentration of bacteria results in a greater concentration of free enzymes and thus a more nutrient-rich environment.  In the rhizosphere, high concentrations of bacteria can also exert positive feedbacks on rhizosphere priming, the mechanism by which plants release sugars into the soil to nourish the bacterial community.

Though bacterial QS behavior has been well studied for decades, most research has been in the field of disease ecology and few studies have experimentally demonstrated QS to be an important phenomenon in soils. One recent study tackled this problem through a detailed examination of bacterial populations in rhizosphere soil, using controlled pot experiments. The authors found that AHL, the QS signal specific to proteobacteria, was 10 times more concentrated in rhizosphere soils compared to bulk soil. Similarly, bacterial densities in the rhizosphere were about 10 times higher. Furthermore, the researchers discovered a tight correlation between QS and enzyme activity. In particular, enzymes involved in acquiring nitrogen were closely linked to QS expression. Nitrogen is considered the major plant-limiting nutrient in temperate ecosystems, and it is believed that one of the primary motivations for a plant to “prime” the soil around its roots is to access soluble nitrogen from microbial decomposers.

I knew almost nothing about quorum sensing before reading this paper. As always, I found myself overwhelmed by the nuanced mechanisms that bacteria employ in order to explore and shape their environment, coupled with the interactions of plants that can manipulate this complex community for their own nutrition. Quorum sensing could well be an important control in rhizosphere nitrogen availability, and will have to be studied in more detail to fully assess its role in controlling ecosystem productivity.

DeAngelis, K.M., Lindow, S.E. & Firestone, M.K. Bacterial quorum sensing and nitrogen cycling in rhizosphere soil. FEMS Microbiology Ecology 66, 197-207 (2008).

Protozoa drive growth enhancing hormone release in the rhizosphere: where biochemistry meets ecology

Though numbering far fewer in the soil than the bacteria they prey on, protozoa are an indispensible link in the transfer of nutrients through the food web that drives forest productivity. These single celled, eukaryotic “bactivores” concentrate themselves in regions of high bacterial activity, notably in the vicinity of plant roots. I’ve previously discussed the “microbial loop theory”, a paradigm for understanding plant nutrient acquisition in terms of the interactions between root exudates, protozoan predators and bacterial prey. To summarize briefly, plant roots exude sugary compounds to “prime” the surrounding soil, making it a highly suitable habitat for bacterial populations. Protozoans naturally move in, too. As quickly as bacteria decompose organic matter to recycle nutrients for their own growth and metabolism, protozoans eat bacteria and excrete those very same nutrients in a form readily available for plants. This “microbial loop” of nutrients is essentially an ecological fertilization system built on a very simple predator-prey model.
Given the advantage plant obtain by maintaining a large and healthy microbial (bacterial + protozoan) community, what strategies can plants employ to ensure that they are supporting the largest and best community possible? (Note that best, from the plants perspective, means the community that mineralizes the most plant-available nutrients in the rhizosphere.) A first obvious strategy for a growing plant would be to release more food- to exude more sugary carbon from its fine root tips. But another, possibly more important step precedes this, and it has to do with root architecture.
Most plants begin their foray into the earth as a seedling, by sending a long, primary taproot straight down like a sledgehammer. Lateral roots begin branching off this main taproot slightly later, and from these lateral roots networks of fine roots, or root hairs, spread out like tiny fingers to penetrate the smallest nooks and crannies in the soil matrix. It is these root hairs which become the site of almost all nutrient and water acquisition and can end up covering an enormous surface area in a mature plant. And it is in the narrow band around these root hairs known as the rhizosphere that a microbial food web has evolved to provide those nutrients.
But plants don’t just grow root hairs everywhere. That would be a waste of energy. Root growth is highly plastic and sensitive to environmental parameters such as soil moisture and nutrient availability. If, for instance, a calcium deposit exists several inches from a primary lateral root, root hairs will likely develop in the direction of that deposit to access as many nutrients as possible. How can plants regulate their growth so precisely in order to ensure themselves the best chance of survival?
It turns out that a complex set of biochemical pathways drive plant growth, and that these pathways can be switched “on” or “off” according to the presence or absence of growth hormones. Auxins are a class of hormones that are particularly important in mediating the growth of plastic stem cells in response to the environment. They are largely responsible for phototropism, the phenomenom that anyone with a windowsill plant has observed, that plants tend to concentrate their above-ground growth in the direction of the most sunlight. Belowground, auxins are largely responsible for root branching and the selective production of root hairs.
At this point you might be wondering why I’ve diverged from my original topic (the microbial loop) to discussing the biochemistry of plant growth. Well, recent research suggests that these two subjects may be even more intricately linked than previously imagined. Growth hormones such as auxins are responsible for the production of fine roots, and by the same token responsible for the maintenance of a rhizosphere in which microbial communities thrive. Though they are hardly aware of it, microbes desperately need auxins to ensure the continued maintenance of the roots they depend upon as a primary food source. A recent study conducted by rhizosphere ecologists (there aren’t very many of them, in case you were wondering) in Germany has found that protozoa selectively “graze” on certain bacteria in the rhizosphere while largely ignoring others. Which bacteria do they choose to ignore? The ones that produce auxins that promote root growth. By selectively removing amoebae, a key bacterial predator, from experimental plant roots, the researchers found a marked decrease in plant auxin concentrations compared to treatments that contained amoebae. Soils with amoebae predators maintained plants with higher auxin concentrations and increased root branching.
It is becoming clear that the interspecies interactions that plants, protozoa and bacteria all depend on may be far more nuanced than we previously understood. Future research to characterize the specific players in this complex web would allow scientists to develop a more holistic picture of exactly who and what is driving plant growth and ecosystem nutrient cycling.
Krome et al. 2010. Soil bacteria and protozoa affect root branching via effects on the auxin and cytokinin balance in plants. Plant Soil: 328, 191-201.

Applying equations to forests- carbon storage across environmental gradients in northeastern Puerto Rico

If you’ve ever read about carbon storage or sequestration (and if you’ve read my blog before, there’s a good chance you have), have you ever wondered how scientists come up with the numbers they love to throw around? How do we “know” that there are 684-724 petagrams of carbon to a depth of 30 cm in all the soils across the whole wide world? How could anyone possibly know that?

We don’t. And we can’t. But there are those crazy enough to try, and trying essentially boils down to  sampling, sampling, sampling, then a whole lot of extrapolating. If you imagine a landscape in which there is a continuous but highly variable distribution of carbon, the only way we’re gong to get any sort of meaningful estimate of the total is to dig a lot of holes. The points you see below represent a lot of holes that I actually helped dig! (I’m one of those crazies). I’ve thrown them up over this topographical surface to give you a sense of just how variable carbon can be across space.

Rather than subject you to a discussion of a ecosystem carbon storage, I’d like to share some pretty pictures I’ve been putting together. I’m attempting to create a model for carbon storage across a roughly 10 km area of forest in northeastern Puerto Rico that is underlain by two bedrock types, contains three distinct forests dominated by different tree species, and has broad gradients in temperature and rainfall across the topographically varied landscape.

Bluer regions represent areas of greater carbon storage while yellower regions store less carbon. Essentially I’ve created an image made of a series of pixels -here, the resolution is coarse enough that you can distinguish individual pixels around the edges. For each pixel, a predicted carbon value has been calculated from a very simple equation that takes bedrock, forest type and elevation into account.

Breaking it down by forest type…



That’s all for now, hopefully I’ll have more and more interesting pictures to show in the future.

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.

microbes, carbon, energy, the planet. life is a struggle for order in a disorderly world.

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Wellcome Trust Blog

Life from a Wellcome Trust perspective

microbes, carbon, energy, the planet. life is a struggle for order in a disorderly world.

Green Grid Radio

Engaging and transformative reporting on the environment, energy, and sustainability

Reflections from Spyglass Hill

A Window into my Research Notebook


The latest oceanography literature, explained

Cosmic Chatter

microbes, carbon, energy, the planet. life is a struggle for order in a disorderly world.

Animal Behavior Research Oddities

Musings on Matings and the Evolutionary Biology of Sex


Science interest, advocacy, and explanation

UNder the C

An Ocean Science Blog by Grad Students in Marine Science at UNC- Chapel Hill


the curious lives of microbes on the edge

Writing Science

How to write papers that get cited and proposals that get funded

Sci-fi interfaces

IxD Lessons from Sci-Fi

Chicken Mushrooms

What's Orange and Green?

Kuhan Chandru's

Astrobiology blog