Tag Archives: ecology

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.

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.

Loss of top predators reduces Black Sea ecosystem’s resilience to eutrophication

Human activities are having profound effects on marine ecosystems. Since the mid 20th century, marine food webs have undergone dramatic changes due to the emergence of industrial fishing. Humans tend to feed on fish with “high trophic status”- those that are near the top of the food chain. In many systems, top predators have been severely reduced or even lost entirely due to overfishing. More recently, increased nutrient loads due to agriculture are fertilizing marine ecosystems, particularly in the more delicate and high-productivity coastal habitats. This often results in explosions of phytoplankton, the tiny photosynthetic bacteria that forms the bottom of most marine food chains. In recent years these phytoplankton blooms have been further facilitated by warmer sea surface temperatures and increased runoff levels due to climate change. Taken together, overfishing and anthropogenic nutrient loading are resulting in both top-down and bottom-up forcing that is fundamentally altering the the structure of marine communities.

A recent study in Global Change Biology examined the impacts of eutrophication and overfishing on a marine community in the Black Sea, a land-locked basin in Eastern Europe. Marine communities in the Black Sea are largely isolated, and offer ecologists the opportunity to study how removal of key organisms in a food web affect the broader community. Decades of overfishing have led to a loss of several traditional apex predators, which has disturbed the structure of the system from the top down. Recent eutrophication has further altered community structure. In particular, once-restricted jellyfish species have been able to make inroads, in some cases coming to dominate the oxygen-depleted waters that result from phytoplankton blooms.

The native marine community at this research group’s study site had difficulty adapting to increased productivity at the bottom of its food web. The researchers concluded that the community as a whole would likely have fared much better if top predators had not also been removed. The inclusion of top predators would have prevented jellyfish and other minor players from becoming dominant and in turn pushing out other mid-trophic level species. These results indicate that ecosystems-based fisheries management must take into account the role of top predators in structuring communities and offering resilience to other profound changes such as nutrient loading and warming. Whether the Black Sea will recover from the major disturbances it has suffered, or revert to a low-diversity, eutrophic state will depend in large part on the economic and political decisions of the countries whose fishing and agriculture practices have so profoundly affected it.

Llope et al. 2011. Overfishing of top predators eroded the resilience of the Black Sea system regardless of the climate and anthropogenic conditions. Global Change Biology 17: 1251-1265.


Tree girdling reveals that photosynthates drives soil activity late in the growing season

The role of trees in nourishing the soil has long been understood by ecologists, but the extent to which trees control belowground processes remains unclear. This is due in large part to the difficulties associated with measuring root activity and the dynamic interactions between roots, mycorrhizal fungi, and the soil environment.

To develop a better understanding of how photosynthates, the sugars produced by photosynthesis, influence patterns of growth and metabolic activity in the soil, a group of ecologists in Sweden decided to conduct a large scale girdling experiment. Tree girlding involves stripping tree bark all the way to the depth of the tree’s xylem, the long tubes that transport water from the soil to the leaves using negative pressure and the difference in water potential between the soil and the atmosphere. Xylem is located well inside the living tissue of a tree, but most importantly for a girdling experiment, it is located directly inside the phloem. Phloem is the piping that runs down the tree and transports photosynthates produced in the leaves via gravity into the rest of the plant. Thus by stripping a tree down to its xylem, the researchers are removing phloem and cutting off the supply of photosynthates to the roots and the soil. This allows them to study the effect of photosynthate removal on the soil without influencing roots, water transport or any other soil parameters.

In this large-scale experiment conducted in a boreal Scots pine forest in northern Sweden, six 900m2 plots were chosen and rouglhy 120 trees per plot were girdled.  In each plot, half of the trees were girdled early in June and half in late August. Early and late girdling were used to detect whether phenological (seasonal) differences affected root photosynthate production.

The results of this experiment were striking. In the early-girdled plots, soil respiration declined by 27% compared to control plots within the first five days of girdling. (Remember, “soil respiration” refers to the amount of CO2 released by the soil. It is a proxy for total soil metabolic activity, including the respiration of microbes, fungi, nematodes and other small soil invertebrates, and even roots themselves! Thus more respiration = healthier, more metabolically active soil.) By the end of the growing season, roughly 50% less respiration had occurred in the early-girdled plots. The occurrence of ectomychorizal fungi, an essential nutrient-acquiring symbiote for most plants, was also dramatically reduced. The late-girdled plots responded even faster, with respiration declining almost 40% within the first 5 days of girdling. Interestingly, the researchers found less response to girdling toward the edge of the girdled plots, indicating that soil organisms here were acquiring some photosynthates from neighboring, ungirdled trees.

The more rapid declines of soil respiration in the late girdling plots fit with our current understanding of how trees use their photosynthates. Early in the growing season, and especially in conifer forests, trees allocate most new photosynthates towards shoot, bud and needle production. Simultaneously, trees begin tapping their root carbon stores to enhance above ground growth. Later in the growing season more photosynthates are sent belowground to nourish the soil community. By this point root carbon stores are also diminished.  Girdling trees later in the growing season cuts off carbon supply to the soil at precisely the moment when it is being ramped up.

The flux of photosynthates to the roots has a big impact on belowground processes, with a clear seasonal component. In moving forward in our understanding of whole ecosystem carbon balances, understanding that trees are conduit, connecting the earth to the atmosphere and transforming both in the process, will, I believe, be an essential paradigm to adopt.



Ho¨gberg P, Nordgren A, Buchmann N et al. (2001) Large-scale forest girdling shows that photosynthesis drives soil respiration. Nature, 411, 789–792.




Frog invasions successful when family is involved

Darwin’s famous naturalization hypothesis states that the probability of an invasive species successfully introducing itself to a new environment  decreases due to competition if closely related species are already present. Though this has proven true for many invasives, the opposite appears true for frogs. Researchers at the University of Sydeny, Australia, recently published a study examining a suite of successful and unsuccessful amphibian invasions across 162 species. It turns out that chance of a successful invasion increases significantly as the number of related species increases. Invader success is also higher on islands than mainlands, and higher in areas with abiotic conditions similar to the invader’s natural habitat.

Why would invaders be more likely to succeed if closely related species, who undoubtedly use similar resources and occupy similar habitats, are present? The “preadaptation hypothesis” suggests that the very attributes of an ecosystem that allow an invader’s relatives to thrive allow the invader to establish itself as well- that is to say, the resource competition between relatives is not as important as the suitability of the habitat for both species. (Could humans learn a thing or two from frogs?) Preadaptation is known to be true for some invasive plants, but these findings represent the first example of support for the preadaptation hypothesis in an animal. For conservationists interested in endangered frogs, this information will no doubt be valuable in searching for suitable new habitats.



The microbial loop theory: 30 years of cross-Atlantic communication barriers

The more forest ecologists learn about plant nutrients, the more evidence accumulates that plants are not simply passive organisms whose chances of survival are based on environmental factors outside of their control.  In acquiring basic nutrients from the soil, one may well imagine that a plant’s success is dependent on chemical properties of the soil alone. By simple “luck of the draw”, plants that seed in nutrient-rich spots will grow faster and larger than plants seeding in nutrient poor regions.

In several of my previous posts, I’ve addressed this issue one way or another, talking about plant-mychorrizhal associations and root-grafting as strategies that allow less fortunately placed plants to acquire sufficient nutrients to survive. I’d like to now address an entirely different theory concerning plant nutrient acquisition, one which, despite thirty years of European research, remains hotly contested and represents one of the major theoretical divides between European and American soil/plant ecologists.

The microbial-loop theory is a paradigm developed several decades ago and has become a cornerstone of European thinking about how plants interact with other soil organisms. In essence a relatively simple idea, the microbial loop would, if proved, require the reevaluation of a huge body of North American literature about plant nutrient acquisition, which generally argues that that basic nutrient demands and stoichiometric constraints- most notably nitrogen limitation in temperate forests and phosphorous limitation in the tropics, exert a fundamental control over forest productivity.

It is well known that plants exert significant control over the processes that occur in the rhizosphere, a narrow zone of soil and pore space that surrounds their roots. Here, plants dump simple sugars such as glucose in order to nourish an active microbial community. They apparently do so because microbes exhibit a diverse array of metabolic capabilities that plants themselves do not have. Microbial processes release essential nutrients, such as nitrogen, from complex organic matter in a plant-soluble form. This much about plant-microbe symbioses- trading carbon for nitrogen or another plant-limiting nutrient- is agreed upon by American and European scientists.

We start entering hot water when we look more closely at the actual microbial players in this game- who are they and what exactly are they doing? “Microbe” is really a very generic term that can refer to pretty much any organism that is invisible to the unaided eye. Within this umbrella grouping, two slightly more specific classess of organisms seem to be important in the rhizosphere: protozoa and bacteria. Bacteria are the tiny prokaryotic organisms that are largely responsible for decomposition and the release of plant-available nutrients. Protozoa, however, are single celled eukaryotes. They are larger, have more complex cellular organization, and importantly, feed on their smaller bacterial neighbors. Any soil sample that contains bacteria almost certainly contains protozoa as well. The relationship between these two groups of microorganisms represents a classic and well-studied predatory-prey model.

So, given that plants are feeding microbes by dumping sugar into the soil, who is the sugar intended for? The bacteria, or the protozoa? The classic paradigm would argue that the bacteria, as the important nutrient-acquiring organisms, are the intended recipients of plant carbon exudates.

But what does this make the protozoa? Are they just thieves, stealing a farmer’s corn that was intended to feed his cattle? Numerous studies have shown that protozoan populations increase dramatically in the presence of plant carbon exudates because they are using the carbon themselves. A high-energy, readily available food source is just as appealing to protozoa as it is to bacteria.  Why would plants, that have perfected so many survival strategies over evolutionary time, allow this to happen?

The microbial loop theory argues that it is the protozoa that plants are “cultivating”. Why? Protozoa prey on bacteria, and bacteria, remember, are full of the nutrients that plants need. After eating a bacteria filled meal, a protozoa will likely excrete those same nutrients, making them available for plants. The protozoa are a conduit, passing nutrients to plants that would otherwise be locked up in the bacterial community.

There is mounting evidence from various lines of research in support of the microbial loop theory. Experiments have shown that early in development, plant root architecture is dramatically altered in the presence of protozoa. Increased root branching increases surface area, or “real estate” that protozoa can inhabit. “Tracer” studies, using a labeled isotope of a nutrient, are now providing evidence for a flow of soil nutrients from bacteria to protozoa before becoming plant-available. Finally, molecular studies of bacterial communities reveal an increased abundance of less-palatable bacterial species in the presence of protozoa, and an increased frequency of genes involved with bacterial defense. This genetic evidence underscores the importance of protozoan predation in structuring bacterial communities. Soon, perhaps, nano-cameras will be available to visualize what is actually happening in the rhizosphere between plants, bacteria and protozoa.

The importance of understanding this interaction is not trivial.  The means by which plants get their nutrients has ramifications for ecosystem productivity, ecosystem nutrient cycling, and responses to environmental change. Should we progress forward in the field of ecosystem science, a critical reexamination (and open discussion!) of what exactly is going on in the rhizosphere between plants and they critters they cultivate is necessary.

A detailed review of microbial loop theory and a paper that addresses some of the important counter-arguments:

1.    Bonkowski, M. Protozoa and plant growth: the microbial loop in soil revisited. NEW PHYTOLOGIST 162, 617-631 (2004).
2.    Ekelund, F., Saj, S., Vestergard, M., Bertaux, J. & Mikola, J. The “soil microbial loop” is not always needed to explain protozoan stimulation of plants. SOIL BIOLOGY & BIOCHEMISTRY 41, 2336-2342 (2009).



A term thrown in so many different fields of science but never really successfully explained outside the realm of the super nerdy. They’re pretty simple, really- essentially just flavors of the same atom with different numbers of neutrons. More neutrons, heavier isotope. Too many neutrons, and your isotope becomes unstable, radioactively decaying over time to a different version of that element or perhaps another element entirely. With that brief introduction I’d like to explain one stable isotope system that is particularly interesting to me because it allows scientists to take a piece of the earth and reconstruct ancient environments.

C12 and C13 are stable isotopes of carbon- they both occur naturally in the environment and do not undergo any natural physical transformations over time. However, because of a small difference in their molecular weights due to the “extra” neutron in the C13 isotope, these two isotopes are processed quite differently in the environment.

Being slightly heavier means that C13 is a bit more difficult for biological systems to process. Most biological processes are adapted to using the lighter isotope, which is far more abundant.  When air diffuses into plant leaves via stomates, the tiny pores that suck up carbon dioxide for photosynthesis, CO2 is tightly bound by an enzyme before it can diffuse out again. In most cases this enzyme is Rubisco (see post: enzymes in the environment) . It turns out that Rubisco preferentially binds to C12, causing C13-enriched air to be released back into the atmosphere. Since most plants take up CO2 via Rubisco (this is known as the C3 photosynthetic pathway), most plant tissue on Earth is depleted in C13 relative to the atmosphere.

However, when a plant keeps its stomata open to take up CO2, a problem emerges- transpiration. Water loss occurs primarily through these same pores that plants must keep open if they want to feed themselves. In hot, arid environments, this puts your normal C3 plants in a sticky situation. They must open their stomata to eat, but risk losing dangerous amounts of water when they do so.

Millions of years ago, a group of plants evolved a rather elegant solution to this problem, known as the C4 photosynthetic pathway. They co-opted an enzyme already present in mitochondria for cellular respiration and gave it Rubisco’s job. This enzyme, known as PEP-carboxylase (I’ll call it PEPC here for simplicity), has a much higher affinity for CO2 than Rubisco- in fact, it binds CO2 so tightly that leaf stomata only need to be open for a fraction of the time they would otherwise. The high affinity of PEPC for CO2 also means that it doesn’t “distinguish” C12 from C13- it grabs whatever CO2 molecule is closest and binds tightly.

What does it matter that two classes of plants fractionate C13 differently? Scientists now have the tools to analyze the molecular composition of plant tissue and can determine a plant’s specific C13/C12 ratio.  C3 and C4 plants have distinct C13/C12 ratios and are easy to distinguish once isotopic analysis has been performed. For living plants, this would not be a terribly illuminating exercise- there are other anatomical and taxonomical ways to distinguish C3 and C4 plants that would be much more straightforward and less expensive.

But what about dead plants? Soil organic matter is composed principally of decomposed plant material, but even the most knowledgeable soil scientists aren’t able to look at a soil and say exactly what plants produced it. If we could, however, the soil would tell us numerous things. Accumulating over hundreds to tens of thousands of years, the soil profile from bedrock to the surface essentially represents a continuum of accumulated material that represents different floral and faunal assemblages, climate regimes and major environmental disturbances.

However, a complex series of transformation processes take place as plant material is decomposed and moved down the soil profile, some of which lead to C13 accumulation while others lead to C13 depletion. Carbon compounds are sorbed to surfaces, eaten by microbes, recycled, taken up by plants, leached, oxidized, and protected, to name a few. Given the inherent complexity of these systems, how can scientists can’t always sample down a soil pit and accurately describe species assemblages at different times using carbon isotopes alone.

A more fruitful path has involved obtaining environmental  samples that have undergone relatively little decomposition, such as cores of sediment from the bottom of a lake, or a core of peat from an inundated field. The plant material within samples that have been buried or otherwise protected from decomposition will be relatively similar, at least at the molecular level, to the original plant tissue, and can thus provide meaningful information about a past environment. For example, a sudden switch from C3 to C4 dominated plant material could indicate a transition from a cooler, wetter climate to a warmer, drier one. Stable carbon isotopes have proved incredibly valuable in tracing the spread of human agriculture, which can often lead to rather dramatic changes in the isotopic signature of a sample.

Still don’t think isotopes are interesting? If you have a friend whose fidelity to vegetarianism is in question, sending a sample of their hair to an isotope lab should resolve the situation. Chances are, if you’re a vegetarian your C13 levels will be relatively high, indicating a more plant-rich diet (a disproportionate number of the world’s major crops are C4 plants).

Bacteria using “silicate sunscreen” provide a glimpse into Archean Earth

If you had the misfortune of becoming stranded for any length of time in the Atacama desert, you’d probably like nothing better than to see a clear blue pools of water stretching out across the landscape. Upon closer examination, however, these pools may begin to look a bit funny, perhaps a tad too crystalline. Known as el Tatio, this strange geyser field used to be a popular site for guides to stop and allow sweltering groups of tourists to get a refreshing drink of clean, clear Chilean water. It was only recently discovered that el Tatio contains the highest natural concentrations of arsenic on Earth- hundreds of times higher than the World Health Organization’s “recommended maximum limit” of ten micrograms/liter.

el Tatio geyserfield, Atacama desert, Chile

An abundance of arsenic is not the only strange thing about el Tatio- high concentrations of silicate minerals give the geyser an unusually glassy look (another good reason that the water is really not fit for human consumption!) Strange environments produce strange biology. Scientists studying el Tatio are now discovering some of the strangest- and perhaps oldest- microbial adaptations on Earth to cope with the stress on a dessicatingly dry, blazingly sunny environment awash in arsenic.

The microbes that have chosen to reside in this harsh environment are primarily arsenic reducers- they use energy from redox reactions involving arsenic to synthesize organic compounds. If this sounds at all familiar to you, it should. Plants do something very similar when they allow sunlight to stimulate their photosystems, releasing electrons that are later used to reduce carbon dioxide into organic carbon sugars. These bugs belong to a rare collection of microbes known as chemolithautotrophs- organisms that produce their own food, much like plants, using an alternate electron acceptors to eventually fix carbon dioxide.

Taking advantage of an abundance of arsenic to produce their own organic food source solves one of the problems associated with living in el Tatio- a scarcity of bioavailable carbon in the environment. It doesn’t, however, solve the problem of the intense sunlight that literally bombards the Atacama desert with powerful UV radiation all day. If the microbes in el Tatio didn’t have some way to protect themselves, their photoreceptors would quickly bleach and their DNA would be destroyed.

It turns out that this problem is solved by taking advantage of the peculiarly high levels of silica in el Tatio’s water. For most microorganisms, silicate mineral concentrations at these levels would be fatal- the precipitation of sharp silicious minerals would literally puncture any soft, free floating cell that tried to make a living. (Imagine living suspended in water, with giant, jagged pieces of glass floating around everywhere). These hardy microbes, however, precipitate a tough polysaccharide on their outer cell membranes that is actually able to capture silica particles and assemble them into a protective coating. Rather then let shards of silicate minerals destroy them, they assemble a house. This protective silicate coating serves two essential defensive purposes. Building silica shells protects the microbes from the silica itself, but it also deflects damaging UV radiation, preventing UV rays from damaging their cellular machinery.

Sounds creative, right? Actually, it may just be one of the oldest tricks in the book. Dr. Philip Bennett and colleagues at the University of Texas, Austin, are now  suggesting that sunscreening oneself up with silica may be  an ancient adaptation to survive in a world with a very thin atmosphere. Remember, when microbes first appeared some 3.5 billion years ago, the world was a very different place. There was very little oxygen in the atmosphere to absorb and deflect harmful UV radiation. Anyone alive today would have suffered acute radiation poisoning. Before the oxygenation of the atmosphere, some strange defenses must have been in place to allow early life to survive. The isolated bugs of the Atcama desert may be giving us clues as to how autotrophy originated on Archean Earth.

Credit: Dr. Philip Bennett, University of Texas at Austin. “Microbial Geochemistry: Coupling microbial ecology and mineral chemistry” . Oral presentation.

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.