Ronald Amundson

Rapid exchange between soil carbon and atmospheric carbon dioxide driven by temperature change

Comparison of 14C (carbon-14) in archived (pre-1963) and contemporary soils taken along an elevation gradient in the Sierra Nevada, California, demonstrates rapid (7 to 65 years) turnover for 50 to 90 percent of carbon in the upper 20 centimeters of soil (A horizon soil carbon). Carbon turnover times increased with elevation (decreasing temperature) along the Sierra transect. This trend was consistent with results from other locations, which indicates that temperature is a dominant control of soil carbon dynamics. When extrapolated to large regions, the observed relation between carbon turnover and temperature suggests that soils should act as significant sources or sinks of atmospheric carbon dioxide in response to global temperature changes.

A new view of the tree of life

The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of lifes diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

The isotopic composition of soil and soil-respired CO2

Abstract The isotopic composition of soil CO 2 has been investigated for the past three decades by earth scientists in a variety of disciplines. Carbon dioxide is produced in soil through biological processes (organic matter decomposition and root respiration) and is transported to the overlying atmosphere via molecular diffusion. Research has focused on both the isotopic composition of respired CO 2 (CO 2 that diffuses across the soil–atmosphere interface) and soil CO 2 (CO 2 that exists at any given soil depth). It is recognized that most soils are at quasi-steady state, and that the C isotopic composition of respired CO 2 is the same as that of the biological sources in the soil. Research on the isotopic composition of soil CO 2 has successfully used steady-state production/diffusion models to explain the common observation that the isotopic composition of soil CO 2 generally shows a gradual change from atmospheric isotopic values at the soil surface to values closer to biological sources with increasing depth. The complexity of the production/diffusion models needed to describe soil CO 2 is simplest with stable C isotopes, and increases in complexity and uncertainty with radiocarbon and O isotopes. For radiocarbon and O isotopes this is due to the fact that there can be a variety of isotopic sources within a given soil. Furthermore, for O isotopes, equilibration processes can alter the composition of the CO 2 as it diffuses through the soil. While much remains to be learned about the natural variations in the isotopic composition of soil and respired CO 2 , interest in this topic will likely increase due to the magnitude of soil respiration on a global scale, and its role in the processes controlling the isotopic composition of atmospheric CO 2 .

Can C3 plants faithfully record the carbon isotopic composition of atmospheric carbon dioxide

Abstract Atmospheric carbon dioxide is the raw material for the biosphere. Therefore, changes in the carbon isotopic composition of the atmosphere will influence the terrestrial δ13C signals we interpret. However, reconstructing the atmospheric δ13C value in the geologic past has proven challenging. Land plants sample the isotopic composition of CO2 during photosynthesis. We use a model of carbon isotopic fractionation during C3 photosynthesis, in combination with a meta–data set (519 measurements from 176 species), to show that the δ13C value of atmospheric CO2 can be reconstructed from the isotopic composition of plant tissue. Over a range of pCO2 (198–1300 ppmv), the δ13C value of plant tissue does not vary systematically with atmospheric carbon dioxide concentration. However, environmental factors, such as water stress, can influence the δ13C value of leaf tissue. These factors explained a relatively small portion of variation in the δ13C value of plant tissue in our data set and emerged strongly only when the carbon isotopic composition of the atmosphere was held constant. Members of the Poaceae differed in average δ13C value, but we observed no other differences correlated with plant life form (herbs, trees, shrubs). In contrast, over 90% of the variation the carbon isotopic composition of plant tissue was explained by variation in the δ13C value of the atmosphere under which it was fixed. We use a subset of our data spanning a geologically reasonable range of atmospheric δ13C values (−6.4‰ to −9.6‰) and excluding C3 Poaceae to develop an equation to reconstruct the δ13C value of atmospheric CO2 based on plant values. Reconstructing the δ13C value of atmospheric CO2 in geologic time will facilitate chemostratigraphic correlation in terrestrial sediments, calibrate pCO2 reconstructions based on soil carbonates, and offer a window into the physiology of ancient plants.

Biogeochemistry: Soil warming and organic carbon content

Soils store two or three times more carbon than exists in the atmosphere as CO2, and it is thought that the temperature sensitivity of decomposing organic matter in soil partly determines how much carbon will be transferred to the atmosphere as a result of global warming. Giardina and Ryan have questioned whether turnover times of soil carbon depend on temperature, however, on the basis of experiments involving isotope analysis and laboratory incubation of soils. We believe that their conclusions are undermined by methodological factors and also by their turnover times being estimated on the assumption that soil carbon exists as a single homogeneous pool, which can mask the dynamics of a smaller, temperature-dependent soil-carbon fraction. The real issue about release of carbon from soils to the atmosphere, however, is how temperature, soil water content and other factors interact to influence decomposition of soil organic matter. And, contrary to one interpretation of Giardina and Ryans results, we believe that positive feedback to global warming is still a concern.

Terrestrial record of methane hydrate dissociation in the Early Cretaceous

Reconstruction of changing C isotopic composition of Early Cretaceous atmospheric CO2 from fossilized C3 vascular land-plant tissue revealed a brief and striking negative excursion (D 25‰) in atmospheric d 13 C, followed by a rapid positive compensation (D 15‰) during the Aptian (ca. 117 Ma). Mass-balance calculations show that dissociation of a small amount of methane gas hydrate is the most tenable cause of the negative excursion; this would also result in an increased CO2:O2 mixing ratio as O2 is consumed during CH4 oxidation to CO2, spurring the exponential phase of angiosperm biogeographic expansion.

Soil warming and organic carbon content.

Soils store two or three times more carbon than exists in the atmosphere as CO2, and it is thought that the temperature sensitivity of decomposing organic matter in soil partly determines how much carbon will be transferred to the atmosphere as a result of global warming. Giardina and Ryan have questioned whether turnover times of soil carbon depend on temperature, however, on the basis of experiments involving isotope analysis and laboratory incubation of soils. We believe that their conclusions are undermined by methodological factors and also by their turnover times being estimated on the assumption that soil carbon exists as a single homogeneous pool, which can mask the dynamics of a smaller, temperature-dependent soil-carbon fraction. The real issue about release of carbon from soils to the atmosphere, however, is how temperature, soil water content and other factors interact to influence decomposition of soil organic matter. And, contrary to one interpretation of Giardina and Ryans results, we believe that positive feedback to global warming is still a concern.

Soil development along an elevational transect in the western Sierra Nevada, California

Soil development along an elevational transect on the western slopes of the the central Sierra Nevada was investigated to assess the effects of climate on soil properties and processes. The transect of seven soils formed in granitic residuum spans elevations from 198 to 2865 m with mean annual temperature and precipitation differences of 13°C (3.9–16.7) and 94 cm (33–127), respectively. Soil pH decreased by about two units and base saturation decreased from 90 to 10% with increasing elevation. Concentrations of organic C in the solum increased with elevation, with the largest single increase occurring between the oak woodland (5–6 kg C/m2) and mixed-conifer sites (10–15 kg C/m2). Clay mineralogy showed a general trend of desilication and hydroxy-Al interlayering of 2:1 layer silicates with increasing elevation. The degree of chemical weathering, based on clay and secondary Fe oxide concentration in the solum, showed a maximum (clay = 536 kg/m2 and Fe oxides = 24 kg/m2) at mid-elevations having intermediate levels of precipitation and temperature. While some soil properties show a continuous progression (e.g., organic carbon, base saturation, clay mineralogy) with elevation, other properties (e.g., pH, soil color, clay and secondary Fe oxide concentrations) show a pronounced change (threshold-type step over a short distance at about 1600 m. The explanation for the abrupt nature of this shift is not known; however, it coincides with the approximate elevation of the present-day average effective winter snow-line.

Soil and human security in the 21st century

Global soil resources under stress The future of humanity is intertwined with the future of Earths soil resources. Soil provides for agriculture, improves water quality, and buffers greenhouse gases in the atmosphere. Yet human activities, including agricultural soil erosion, are rapidly degrading soil faster than it is naturally replenished. At this rate, human security over the next century will be severely threatened by unsustainable soil management practices. Amundson et al. review recent advances in understanding global soil resources, including how carbon stored in soil responds to anthropogenic warming. Translating this knowledge into practice is the biggest challenge remaining. Science, this issue 10.1126/science.1261071 BACKGROUND Earth’s soil has formed by processes that have maintained a persistent and expansive global soil mantle, one that in turn provided the stage for the evolution of the vast diversity of life on land. The underlying stability of soil systems is controlled by their inherent balance between inputs and losses of nutrients and carbon. Human exploitation of these soil resources, beginning a few thousand years ago, allowed agriculture to become an enormous success. The vastness of the planet and its soil resources allowed agriculture to expand, with growing populations, or to move, when soil resources were depleted. However, the practice of farming greatly accelerated rates of erosion relative to soil production, and soil has been and continues to be lost at rates that are orders of magnitude greater than mechanisms that replenish soil. Additionally, agricultural practices greatly altered natural soil carbon balances and feedbacks. Cultivation thus began an ongoing slow ignition of Earth’s largest surficial reservoir of carbon—one that, when combined with the anthropogenic warming of many biomes, is capable of driving large positive feedbacks that will further increase the accumulation of atmospheric greenhouse gases and exacerbate associated climate change. ADVANCES The study of soil is now the domain of diverse schools of physical and biological science. Rapid advances in empirical and theoretical understanding of soil processes are occurring. These advances have brought an international, and global, perspective to the study of soil processes and focused the implications of soil stewardship for societal well-being. Major advances in the past decade include our first quantitative understanding of the natural rates of soil production, derived from isotopic methods developed by collaboration of geochemists and geomorphologists. Proliferation of research by soil and ecological scientists in the northern latitudes continues to illuminate and improve estimates of the magnitude of soil carbon storage in these regions and its sensitivity and response to warming. The role of soil processes in global carbon and climate models is entering a period of growing attention and increasing maturity. These activities in turn reveal the severity of soil-related issues at stake for the remainder of this century—the need to rapidly regain a balance to the physical and biological processes that drive and maintain soil properties, and the societal implications that will result if we do not. OUTLOOK Both great challenges and opportunities exist in regards to maintaining soil’s role in food, climate, and human security. Erosion continues to exceed natural rates of soil renewal even in highly developed countries. The recent focus by economists and natural scientists on potential future shortages of phosphorus fertilizer offers opportunities for novel partnerships to develop efficient methods of nutrient recycling and redistribution systems in urban settings. Possibly the most challenging issues will be to better understand the magnitude of global soil carbon feedbacks to climate change and to mitigating climate change in a timely fashion. The net results of human impacts on soil resources this century will be global in scale and will have direct impacts on human security for centuries to come. Large-scale erosion forming a gully system in the watershed of Lake Bogoria, Kenya. Accelerated soil erosion here is due to both overgrazing and improper agricultural management, which are partially due to political-social impacts of past colonization and inadequate resources and infrastructure. The erosion additionally affects the long-term future of Lake Bogoria because of rapid sedimentation. This example illustrates the disruption of the natural balance of soil production and erosion over geological time scales by human activity and the rapidity of the consequences of this imbalance. CREDIT: BRENT STIRTON/GETTY IMAGES Human security has and will continue to rely on Earth’s diverse soil resources. Yet we have now exploited the planet’s most productive soils. Soil erosion greatly exceeds rates of production in many agricultural regions. Nitrogen produced by fossil fuel and geological reservoirs of other fertilizers are headed toward possible scarcity, increased cost, and/or geopolitical conflict. Climate change is accelerating the microbial release of greenhouse gases from soil organic matter and will likely play a large role in our near-term climate future. In this Review, we highlight challenges facing Earth’s soil resources in the coming century. The direct and indirect response of soils to past and future human activities will play a major role in human prosperity and survival.

Function without purpose

Philosophers of evolutionary biology favor the so-called “etiological concept” of function according to which the function of a trait is its evolutionary purpose, defined as the effect for which that trait was favored by natural selection. We term this the selected effect (SE) analysis of function. An alternative account of function was introduced by Robert Cummins in a non-evolutionary and non-purposive context. Cumminss account has received attention but little support from philosophers of biology. This paper will show that a similar non-purposive concept of function, which we term causal role (CR) function, is crucial to certain research programs in evolutionary biology, and that philosophical criticisms of Cumminss concept are ineffective in this scientific context. Specifically, we demonstrate that CR functions are a vital and ineliminable part of research in comparative and functional anatomy, and that biological categories used by anatomists are not defined by the application of SE functional analysis. Causal role functions are non-historically defined, but may themselves be used in an historical analysis. Furthermore, we show that a philosophical insistence on the primary of SE functions places practicing biologists in an untenable position, as such functions can rarely be demonstrated (in contrast to CR functions). Biologists who study the form and function of organismal design recognize that it is virtually impossible to identify the past action of selection on any particular structure retrospectively, a requirement for recognizing SE functions.