Category Archives: Jabberwocky

Finding meaning in the chaos.

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.

 

Advertisements

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.

Reference
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).

Isotopes?

Isotopes?

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).

Carbon sequestration in soils: sources, sinks and pitfalls

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

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

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

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

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

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

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

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

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

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

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

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

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

the meaning of life

when most people hear the word “virus”, the first image that comes to mind is generally something along the lines of a sick person, an epidemic, trips to the doctors office, vaccinations, or, for those with some biology background, a crystalline, nightmarish spider-alien injecting DNA into a defenseless cell. viruses are generally perceived as perpetrators of malaise, a scourge to society that modern science can and will eventually eradicate. only in the past decade, since the advent of fast and relatively cheap genetic sequencing technology, have scientists begun to recognize the staggering diversity of viruses in the world, many of which are entirely benign and have no known ecological function. the dawning realization that really are just about everywhere- they are ten times more abundant than bacteria in the ocean- indicates an incredibly effective strategy for self-propagation. this strategy in turn represents  a form of existence so simple that scientists have been debating for decades whether or not viruses can be classified as life.

despite their apparent simplicity, understanding viruses has been one of biology’s greatest challenges since the beginnings of the molecular revolution. the traits that we have discovered to be ubiquitous among viruses are relatively straightforward. generally, a virus consists of a single piece of naked DNA, encapsulated in some sort of protein-based coat. viruses cannot be considered cells because they contain none of the internal machinery necessary for growth or self-replication. instead, many viruses replicate by inserting their DNA into the cells of a host. this invading DNA is able to co-opt the host cell’s own replication proteins, and turn the host into a small factory for new viruses.

many but not all of the viruses that cause human disease use this strategy, and they often do so with alarming efficiency. another common viral replication strategy is to insert DNA into a host, and integrate that DNA into the hosts own DNA. viruses that employ this strategy are effectively choosing symbiosis inside a host, and replicate themselves in step with the host cell’s own cycle.

it may seem strange that some viruses act aggressively- invading, replicating and moving on once they have plundered all the resources available, while others choose a life of harmless symbiosis within their host. how can we come up with a general definition for all viruses if this is the case? shouldn’t we classify these critters as two unique types – neither truly alive perhaps, but fundamentally different in their non-living existence?

to answer this question, one must think carefully not about what viruses are doing but why. in both cases, a fragment of DNA is simply trying to replicate itself in the most effective way possible. for some, this means integrating itself into an organism, and reproducing in concert with the organisms own generations. for others, it means rape, kill, pillage and burn. viruses  are the ultimate narcissists- no ambitions for complex structure or function,, simply a raw, unabashed need for self-propagation.

if existence driven entirely by the need to replicate and produce more of oneself what it means to be a virus, i don’t think it’s a far stretch of the imagination to draw parallels with organisms that we officially classify as “alive”. with simple single-celled life, the similarity is easy to see. unicellular bacteria are essentially DNA vessels, but with extra compartments for the tools and machinery required to replicate. some single-celled bacteria do reproduce sexually and, in exchanging DNA, produce offspring that are not genetic clones. nevertheless, the idea is essentially still simple propagation of genes, but given one more level of complexity in that the replication process is self-sufficient.

but how much similarity can there possibly be between a complex, multi-cellular organism, and a single replicating strand of DNA? try thinking of a complex organism, like a cat, horse, or even human, as a nation of cells. each cell is an individual citizen, and each citizen has a specialized job that he must perform as an effective member of the community. if too many citizens dissent, or get lazy, and choose not to perform their allocated jobs, the community falls apart. and what do these citizens, many of whom look and act very different, and would certainly never be caught getting coffee or drinks together, all have in common? dependency on each other for replication.

a human being is orders of magnitude more complex than a virus, and I am not trying to diminish that complexity, or even to claim that it can be reduced to aggregate of cells driven by a simple process. but the common purpose of genes, in everything from their rawest form that do not even consider living, to the most complex organism evolution has produced, speaks to the ancestry we all share.

wyrd evolution

A population essentially evolves through the accumulation of random changes in its genetic makeup over time. These genetic changes modify organisms’ phenotypes, and over time change the distribution of traits in a population. Many traits which become prevalent in a population do so because they make the population more “evolutionarily fit”- better able survive and reproduce in its environment. Darwin coined the famous term “natural selection”to describe this phenomenon, though he wasn’t aware of the complex genetic mechanisms underlying it.

Evolutionary theory is anchored on the principle that the biology of the past has shaped the diversity we see today. Though countless examples in nature substantiate the important role of natural selection in evolution, it is important to understand that natural selection itself is not a conscious force. Rather, it is it is a pattern that produces predictable outcomes. Stochastic probability tells us that, over a long enough time and with large enough populations, traits that allow organisms to produce more offspring will come to dominate a population, simply because the individuals possessing these traits will pass along more of their genes into the next generation.

Because evolution by natural selection is not a conscious force, and because it must work to improve upon what already exists in nature, evolution cannot rapidly produce superanimals that are perfectly adapted to their environments. As the French biochemist Francois Jacob once eloquently described it, evolution is a tinkerer that works to improve upon what is already there, but its creative freedom is heavily constrained by existing body plans and biochemical pathways. Moreover, natural selection works to optimize organisms, not isolated systems. A trait that may seem advantageous, such as a genetic mutation producing enhanced night vision, may be helpful for a large predator on the Savannah, but useless for a cave fish that is rarely exposed to any sunlight and must use other sensory systems to perceive its environment. The cave fish would not develop improved eyesight because the selective advantage conferred by this ability would not outweigh its energetic costs.

As this last example begins to illustrate, natural selection is often working in concert with another force known as selective constraint. When a gene, biochemical pathway, or phenotypic trait is under selective constraint, it is maintained over evolutionary time. There are many reasons that selective constraint could operate. A biochemical pathway could be so fundamental to an organisms ability to survive that any small alterations to that pathway would be lethal. A limb or sensory organ could already be well suited for its environment, or the benefits of  making any changes to it may not outweigh the costs. A single mutation event in a gene encoding an essential protein could alter the protein’s structure and make it useless.

Natural selection and selective constraint are two important paradigms for understanding evolution. They are not the entire story, but they do help us to understand how evolution produces produces change but also propagates sameness. An alien visiting earth 3 billion years ago could not have imagined that the simple life he discovered would lead to the overwhelming diversity we see today. And yet in spite of all the novelty and innovation that has appeared over evolutionary time, this diversity has drawn upon itself, reaching outwards without  breaking its ties to the past.

what is ‘wyrd’?

etymology of “wryd”: an old English word that primarily means “that which comes to pass”. wyrdscience describes natural phenomena and pressing scientific questions which provide us not only with a mechanical understanding of the world, but insight into the social, cultural, and environmental changes that are coming to pass on our planet.

a more metaphysical interpretation of wyrd is that everything in the universe is constantly changing and moving towards some other state, but simultaneously being drawn into itself. all changes an object goes through can be understood through its past, and the myriad of possible trajectories of a change event tend to converge to a single, predictable outcome. wyrd as interpreted this way is useful in understanding many fundamental scientific concepts.