Tag Archives: carbon cycle

microbes improve carbon cycle models

Microorganisms are key drivers of the global carbon cycle both on the land and in the ocean. Through a diverse array of metabolic strategies, microbes decompose organic and recycle organic carbon. Just as we respire a fraction of the carbon we consume as CO2, so do microbes. Globally, vast quantities of organic carbon are funneled through many billions of microbes every year: to be decomposed, recycled, and respired into the atmosphere. In spite of this, microbial activity has historically been ignored in attempts to model the global carbon cycle and predict climate change-related feedbacks. Instead, our models rely on untested assumptions that microbes and their carbon cycle activities will respond in uniform, predictable manners to increases in temperature, and as such, can essentially be ignored.

A recent paper in Nature Geoscience paper challenges this assumption by explicitly integrating microbial physiology into a new model of the soil carbon cycle. Compared with traditional models, the new model more accurately matches current observations of carbon stocks and fluxes across ecosystems. Regarding future carbon cycling in a warming world, the model produces several widely different scenarios that vary due to the potential response of microbes to rising temperatures. In short, if microbes respond negatively to warming by decreasing their “growth efficiency”; that is, if warming slows down their growth rates, no additional carbon is released to the atmosphere as the soil warms. But if microbes are able to adapt to higher temperatures and maintain their current growth efficiencies, higher temperatures will accelerate carbon decomposition rates and lead to potentially huge additional losses of carbon dioxide from soils.

The integration of biological mechanisms into earth system models is an important step forward in our ability to forecast future climates. Future research that empirically measures microbial community responses to long-term warming is desperately needed in order to accurately model and predict this potentially huge feedback to the global carbon cycle.



The end of the evolutionary road on a far future earth

The question of how life first came to be on early earth  has been of fascination to scientists for decades. By stark contrast, the question of how life may end on Earth in the distant future has received little attention, probably because the question itself forces us to face the rather depressing reality that one day, our star will die, our planet’s center will cool, and Earth will no longer be capable of supporting life. But the end of the road for life on Earth will not dawn on us overnight. Just as it took billions of years for our earliest prokaryotic ancestors to evolve into complex, multicellular life (these early microbial communities, spread far and wide across the earth, had the big responsibility of oxidizing the atmosphere so that multicellular organisms could have something to breathe) it will likely take millions if not billions of years for life on Earth to devolve as the planetary systems that allow complex ecosystems to exist slowly shut down.

How will the end of life happen?  On present day Earth, the weathering of silicate rocks draws carbon dioxide out of the atmosphere and returns it to the continental and oceanic crusts. This process occurs quite slowly (millions – billions of year timescales), but ultimately if there were no source of carbon to replenish the CO2 drawn out of the atmosphere by weathering, it would eventually be depleted. This would make our planet inhospitable to plant life, which requires CO2 to do photosynthesis. Unfortunately this is exactly what will happen when our star begins to die. As the Sun ages, its luminosity will increase, meaning Earth’s surface is going to get hotter. This will speed up silicate weathering and the speed with which CO2 leaves our atmosphere. Normally, this CO2 would be replenished with carbon recycled through the crust and mantle due to tectonic activity. However, the heating up of the planet’s surface will also increase surface water loss due to evaporation, which will increase the friction between the plates until eventually plate tectonics shuts down entirely.

When atmospheric CO2 concentrations drop below a critical threshold (< 10 ppm), plants will begin to die off. With the plants will go both the food and oxygen source for animals. Large ectotherms (large mammals and birds) will likely go first, due to their high oxygen requirements, followed by smaller ectotherms (i.e., small birds, rodents). Reptiles, amphibians and fish will likely outlast the rest of us due to their lower oxygen requirements, with marine species lasting longer in general because the oceans will likely heat up less rapidly than the land. Eventually, within perhaps 100 million years of the end of plant life, the world will be returned to the microbes.

And what might the final microbes on Earth be? In all likelihood, they will be extremophiles capable of tolerating multiple environmental stressors (polyextremophiles)- low oxygen concentrations and high temperatures, for example. They will recede from the planet’s surface where high heat and rapid evaporation will be too stressful. In all likelihood, they will return to deep ocean vents and similar subsurface environments that are both buffered from surface temperatures and capable of supplying their own source of energy.

I’ve just described the devolving (or perhaps mass extinction occurring on along a trajectory of evolutionary complexity over geologic timescales) of life of Earth in broad brushstrokes. As with most scientific theories, there are details, nuances, unanswered questions and questionable assumptions. Of course, this is also assuming that some anthropogenic force doesn’t end life on Earth far sooner (nuclear war, chemical warfare, climate change, GMOs, encountering an unfriendly and technologically superior alien race, creation and subsequent uprising of AI, zombie apocalypse). And it’s also possible that I’m being far too pessimistic, and some future technological or geoengineering solution will be able to keep our planet liveable far beyond its natural lifetime.

I’ll leave you with a plug for SpaceRip, a really awesome astronomy youtube show that has several episodes focused on questions of planetary habitability. These guys know way more than I do.

The Search for Earth-Like Planets

deep sea carbon cycling: more dynamic than we thought?

For years, scientists have speculated that deep sea carbon may have played an essential role in past climate change episodes. Specifically, it has been suggested that the C bound in seafloor sediment has undergone thermodynamic alterations in the past to due upwellings of molten magma from the mantle. Magma may have triggered the release of CO2 and methane into the upper ocean and eventually the atmosphere. Evidence suggests that the Paleocene-Eocene thermal maximum, which lasted approximately 100,000 years, may have been triggered in part by the release of greenhouse gases from the seaflooor.

Despite these speculations about deep sea carbon influencing past climate, little research has been done on the role of seafloor carbon in the present day C cycle. In some ways, this is surprising given the enormous amount of attention being payed to global C budgets and possible means of C sequestration. It is generally assumed that the deep sea represents a huge “carbon sink”, to which organic C from the upper ocean enters and does not emerge again for thousands to millions of years. This would suggest that whatever carbon-cycling processes are occuring at the seafloor are not powerful enough to cause a net carbon release.

Recent research published in Nature Geoscience suggests otherwise. Several case studies have demonstrated dynamic processes occurring on the ocean floor can in fact lead to a net release of greenhouse gases. Spreading seafloor centers- regions where oceanic plates pull apart-  are a site of magma activity and hydrothermal venting. Hydrothermal vents release a variety of hot, mineral-rich fluids that can support a diverse microbial and invertebrate community. At one such spreading center in the Gulf of California, magma is intruding into thick organic basin sediments. These sediments have long been thought to sequester C, however, it now appears tht their heating is causing the release of methane into the upper ocean.

In the Northeast Pacific, another intriguing deep ocean C cycling system has been discovered. Here, microbes are converting ancient inorganic C into dissolved organic C, which is subsequently released to the overlying ocean. This discovery contradicts the general belief that ancient deep-sea C is highly stable and not accessible to microbes.

Other distinct seafloor C sources are rapidly emerging around the world, as improved technology and a heightened interest in seafloor processes are accelerate the pace of discovery. However, the contribution of such “point sources” to global C budgets is still highly uncertain and far more research is needed to come up with even a rough estimate of global deep sea C sources. Nonetheless, it would seem that we can no longer consider the deep ocean a black box of C sequestration, and that we should think carefully about the ramifications of introducing more carbon- either accidentally through the introduction of dissolved greenhouse gases to the ocean, or intentionally as part of a climate change mitigation strategy- to a system that is clearly more dynamic than we once thought.,

Reference : “Deep Sea Discoveries.” 2011. Nature Geoscience: Letters. Volume 4, Page 1.

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.

GeoChip: linking genetics with environmental processes

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

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

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

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

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


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