Scott R Saleska

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• Chorover, J. D., Gavaert, A., Tueling, A. J., Uijlenhoet, R., DeLong, S. B., Huxman, T. E., Pangle, L., Brashears, D. D., Pelletier, J. D., Saleska, S. R., Zeng, X., & Troch, P. A. (2014). Hillslope-scale experiment demonstrates the role of convergence during two-step saturation. Hydrol. Earth Syst. Sci., 18, 1-12.
• Christoffersen, B. O., Restrepo-Coupe, N., Arain, M. A., Baker, I. T., Cestaro, B. P., Ciais, P., Fisher, J. B., Galbraith, D., Guan, X., Gulden, L., van den Hurk, B., Ichii, K., Imbuzeiro, H., Jain, A., Levine, N., Miguez-Machor, G., Poulter, B., Roberti, D. R., Sakaguchi, K., , Sahoo, A., et al. (2014). Mechanisms of water supply and vegetation demand govern the seasonality and magnitude of evapotranspiration in Amazonia and Cerrado. AGRICULTURAL AND FOREST METEOROLOGY, 191, 33-50.
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  Evapotranspiration (E) in the Amazon connects forest function and regional climate via its role in precipitation recycling However, the mechanisms regulating water supply to vegetation and its demand for water remain poorly understood, especially during periods of seasonal water deficits In this study, we address two main questions: First, how do mechanisms of water supply (indicated by rooting depth and groundwater) and vegetation water demand (indicated by stomatal conductance and intrinsic water use efficiency) control evapotranspiration (E) along broad gradients of climate and vegetation from equatorial Amazonia to Cerrado, and second, how do these inferred mechanisms of supply and demand compare to those employed by a suite of ecosystem models? We used a network of eddy covariance towers in Brazil coupled with ancillary measurements to address these questions With respect to the magnitude and seasonality of E, models have much improved in equatorial tropical forests by eliminating most dry season water limitation, diverge in performance in transitional forests where seasonal water deficits are greater, and mostly capture the observed seasonal depressions in E at Cerrado However, many models depended universally on either deep roots or groundwater to mitigate dry season water deficits, the relative importance of which we found does not vary as a simple function of climate or vegetation In addition, canopy stomatal conductance (g's) regulates dry season vegetation demand for water at all except the wettest sites even as the seasonal cycle of E follows that of net radiation In contrast, some models simulated no seasonality in gs, even while matching the observed seasonal cycle of E. We suggest that canopy dynamics mediated by leaf phenology may play a significant role in such seasonality, a process poorly represented in models Model bias in gs and E, in turn, was related to biases arising from the simulated light response (gross primary productivity, GPP) or the intringic water use efficiency of photosynthesis (iWUE). We identified deficiencies in models which would not otherwise be apparent based on a simple comparison of simulated and observed rates of E. While some deficiencies can be remedied by parameter tuning, in most models they highlight the need for continued process development of belowground hydrology and in particular, the biological processes of root dynamics and leaf phenology, which via their controls on E, mediate vegetation-climate feedbacks in the tropics. (C) 2014 Elsevier B.V. All rights reserved.
• Hodgkins, S. B., Tfaily, M. M., McCalley, C. K., Logan, T. A., Crill, P. M., Saleska, S. R., Rich, V. I., & Chanton, J. P. (2014). Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(16), 5819-5824.
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  Carbon release due to permafrost thaw represents a potentially major positive climate change feedback. The magnitude of carbon loss and the proportion lost as methane (CH4) vs. carbon dioxide (CO2) depend on factors including temperature, mobilization of previously frozen carbon, hydrology, and changes in organic matter chemistry associated with environmental responses to thaw. While the first three of these effects are relatively well understood, the effect of organic matter chemistry remains largely un-studied. To address this gap, we examined the biogeochemistry of peat and dissolved organic matter (DOM) along a similar to 40-y permafrost thaw progression from recently- to fully thawed sites in Stordalen Mire (68.35 degrees N, 19.05 degrees E), a thawing peat plateau in northern Sweden. Thaw-induced subsidence and the resulting inundation along this progression led to succession in vegetation types accompanied by an evolution in organic matter chemistry. Peat C/N ratios decreased whereas humification rates increased, and DOM shifted toward lower molecular weight compounds with lower aromaticity, lower organic oxygen content, and more abundant microbially produced compounds. Corresponding changes in decomposition along this gradient included increasing CH4 and CO2 production potentials, higher relative CH4/CO2 ratios, and a shift in CH4 production pathway from CO2 reduction to acetate cleavage. These results imply that subsidence and thermokarst-associated increases in organic matter lability cause shifts in biogeochemical processes toward faster decomposition with an increasing proportion of carbon released as CH4. This impact of permafrost thaw on organic matter chemistry could intensify the predicted climate feedbacks of increasing temperatures, permafrost carbon mobilization, and hydrologic changes.
• Hodgkins, S. B., Tfaily, M. M., McCalley, C. K., Logan, T., Crill, P. M., Saleska, S. R., Rich, V. I., & Chanton, J. P. (2014). Journal article: Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production. Proceedings of the National Academy of Sciences, 111(16), 5819–5824.
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  PNAS | April 22, 2014 | vol. 111 | no. 16 | 5819–5824
• McCalley, C. K., Woodcroft, B. J., Hodgkins, S. B., Wehr, R. A., Kim, E., Mondav, R., Crill, P. M., Chanton, J. P., Rich, V. I., Tyson, G. W., & Saleska, S. R. (2014). Journal article: Methane dynamics regulated by microbial community response to permafrost thaw. Nature.
• McCalley, C. K., Woodcroft, B. J., Hodgkins, S. B., Wehr, R. A., Kim, E., Mondav, R., Crill, P. M., Chanton, J. P., Rich, V. I., Tyson, G. W., & Saleska, S. R. (2014). Methane dynamics regulated by microbial community response to permafrost thaw. NATURE, 514(7523), 478-+.
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  Permafrost contains about 50% of the global soil carbon(1). It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions(2,3). The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown(3) and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the delta C-13 signature (1015 parts per thousand) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden(4,5) as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus Methanoflorens stordalenmirensis(6) is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models(3,7). By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.
• Mondav, R., Woodcroft, B. J., Kim, E., McCalley, C. K., Hodgkins, S. B., Crill, P. M., Chanton, J., Hurst, G. B., VerBerkmoes, N. C., Saleska, S. R., Hugenholtz, P., Rich, V. I., & Tyson, G. W. (2014). Discovery of a novel methanogen prevalent in thawing permafrost. NATURE COMMUNICATIONS, 5.
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  Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov. belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.
• Mondav, R., Woodcroft, B. J., Kim, E., Mccalley, C. K., Hodgkins, S. B., Crill, P. M., Chanton, J., Hurst, G. B., Verberkmoes, N. C., Saleska, S. R., Hugenholtz, P., Rich, V. I., & Tyson, G. W. (2014). Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5.
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  Abstract: Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming. © 2014 Macmillan Publishers Limited.
• Mondav, R., Woodcroft, B., Kim, E., McCalley, C. K., Hodgkins, S. B., Crill, P. M., Chanton, J. P., Hurst, G. B., Verberkmoes, N., Saleska, S. R., Hugenholtz, P., Rich, V. I., & Tyson, G. W. (2014). Journal article: Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5, 3212.
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  Mondav* R, Woodcroft* BJ, Kim E-H, McCalley CK, Hodgkins SB, Crill PM, Chanton JP, Hurst GB, VerBerkmoes N, Saleska SR, Hugenholtz P, Rich VI, Tyson GW. 2014. Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications. 5: 3212. doi:10.1038/ncomms4212
• Niu, G., Pasetto, D., Scudeler, C., Paniconi, C., Putti, M., Troch, P. A., DeLong, S. B., Dontsova, K., Pangle, L., Breshears, D. D., Chorover, J., Huxman, T. E., Pelletier, J., Saleska, S. R., & Zeng, X. (2014). Incipient subsurface heterogeneity and its effect on overland flow generation – insight from a modeling study of the first experiment at the Biosphere 2 Landscape Evolution Observatory. Hydrology and Earth System Sciences.
• Baker, I. T., Harper, A. B., da Rocha, H. R., Denning, A. S., Araujo, A. C., Borma, L. S., Freitas, H. C., Goulden, M. L., Manzi, A. O., Miller, S. D., Nobre, A. D., Restrepo-Coupe, N., Saleska, S. R., Stoeckli, R., von Randow, C., & Wofsy, S. C. (2013). Surface ecophysiological behavior across vegetation and moisture gradients in tropical South America. AGRICULTURAL AND FOREST METEOROLOGY, 182, 177-188.
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  Surface ecophysiology at five sites in tropical South America across vegetation and moisture gradients is investigated. From the moist northwest (Manaus) to the relatively dry southeast (Pe de Gigante, state of Sao Paulo) simulated seasonal cycles of latent and sensible heat, and carbon flux produced with the Simple Biosphere Model (SiB3) are confronted with observational data. In the northwest, abundant moisture is available, suggesting that the ecosystem is light-limited. In these wettest regions, Bowen ratio is consistently low, with little or no annual cycle. Carbon flux shows little or no annual cycle as well; efflux and uptake are determined by high-frequency variability in light and moisture availability. Moving downgradient in annual precipitation amount, dry season length is more clearly defined. In these regions, a dry season sink of carbon is observed and simulated. This sink is the result of the combination of increased photosynthetic production due to higher light levels, and decreased respiratory efflux due to soil drying. The differential response time of photosynthetic and respiratory processes produce observed annual cycles of net carbon flux. In drier regions, moisture and carbon fluxes are in-phase; there is carbon uptake during seasonal rains and efflux during the dry season. At the driest site, there is also a large annual cycle in latent and sensible heat flux. Published by Elsevier B.V.
• Baker, I. T., Harper, A. B., da Rocha, H. d., Denning, A. S., Araújo, A. C., Borma, L. S., Freitas, H. C., Goulden, M. L., Manzi, A. O., Miller, S. D., Nobre, A. D., Restrepo-Coupe, N., Saleska, S. R., Stöckli, R., von Randow, C., & Wofsy, S. C. (2013). Surface ecophysiological behavior across vegetation and moisture gradients in tropical South America. Agricultural and Forest Meteorology, 182, 177-188.
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  Abstract: Surface ecophysiology at five sites in tropical South America across vegetation and moisture gradients is investigated. From the moist northwest (Manaus) to the relatively dry southeast (Pé de Gigante, state of São Paulo) simulated seasonal cycles of latent and sensible heat, and carbon flux produced with the Simple Biosphere Model (SiB3) are confronted with observational data. In the northwest, abundant moisture is available, suggesting that the ecosystem is light-limited. In these wettest regions, Bowen ratio is consistently low, with little or no annual cycle. Carbon flux shows little or no annual cycle as well; efflux and uptake are determined by high-frequency variability in light and moisture availability. Moving downgradient in annual precipitation amount, dry season length is more clearly defined. In these regions, a dry season sink of carbon is observed and simulated. This sink is the result of the combination of increased photosynthetic production due to higher light levels, and decreased respiratory efflux due to soil drying. The differential response time of photosynthetic and respiratory processes produce observed annual cycles of net carbon flux. In drier regions, moisture and carbon fluxes are in-phase; there is carbon uptake during seasonal rains and efflux during the dry season. At the driest site, there is also a large annual cycle in latent and sensible heat flux. © 2012.
• Coe, M. T., Marthews, T. R., Costa, M. H., Galbraith, D. R., Greenglass, N. L., Imbuzeiro, H. M., Levine, N. M., Malhi, Y., Moorcroft, P. R., Muza, M. N., Powell, T. L., Saleska, S. R., Solorzano, L. A., & Wang, J. (2013). Deforestation and climate feedbacks threaten the ecological integrity of south-southeastern Amazonia. Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1619).
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  PMID: 23610166;PMCID: PMC3638426;Abstract: A mosaic of protected areas, including indigenous lands, sustainable-use production forests and reserves and strictly protected forests is the cornerstone of conservation in the Amazon, with almost 50 per cent of the region now protected. However, recent research indicates that isolation from direct deforestation or degradation may not be sufficient to maintain the ecological integrity of Amazon forests over the next several decades. Large-scale changes in fire and drought regimes occurring as a result of deforestation and greenhouse gas increases may result in forest degradation, regardless of protected status. How severe or widespread these feedbacks will be is uncertain, but the arc of deforestation in south-southeastern Amazonia appears to be particularly vulnerable owing to high current deforestation rates and ecological sensitivity to climate change. Maintaining forest ecosystem integrity may require significant strengthening of forest conservation on private property, which can in part be accomplished by leveraging existing policy mechanisms. © 2013 The Author(s) Published by the Royal Society. All rights reserved.
• Coe, M. T., Marthews, T. R., Costa, M. H., Galbraith, D. R., Greenglass, N. L., M, H., Levine, N. M., Malhi, Y., Moorcroft, P. R., Muza, M. N., Powell, T. L., Saleska, S. R., Solorzano, L. A., & Wang, J. (2013). Deforestation and climate feedbacks threaten the ecological integrity of south-southeastern Amazonia.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 368(1619), 20120155-.
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  PMID: 23610166;Abstract: A mosaic of protected areas, including indigenous lands, sustainable-use production forests and reserves and strictly protected forests is the cornerstone of conservation in the Amazon, with almost 50 per cent of the region now protected. However, recent research indicates that isolation from direct deforestation or degradation may not be sufficient to maintain the ecological integrity of Amazon forests over the next several decades. Large-scale changes in fire and drought regimes occurring as a result of deforestation and greenhouse gas increases may result in forest degradation, regardless of protected status. How severe or widespread these feedbacks will be is uncertain, but the arc of deforestation in south-southeastern Amazonia appears to be particularly vulnerable owing to high current deforestation rates and ecological sensitivity to climate change. Maintaining forest ecosystem integrity may require significant strengthening of forest conservation on private property, which can in part be accomplished by leveraging existing policy mechanisms.
• Goncalves de Goncalves, L. G., Borak, J. S., Costa, M. H., Saleska, S. R., Baker, I., Restrepo-Coupe, N., Muza, M. N., Poulter, B., Verbeeck, H., Fisher, J. B., Arain, M. A., Arkin, P., Cestaro, B. P., Christoffersen, B., Galbraith, D., Guan, X., van den Hurk, B. J., Ichii, K., Imbuzeiro, H. M., , Jain, A. K., et al. (2013). Overview of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia Data Model Intercomparison Project (LBA-DMIP). AGRICULTURAL AND FOREST METEOROLOGY, 182, 111-127.
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  A fundamental question connecting terrestrial ecology and global climate change is the sensitivity of key terrestrial biomes to climatic variability and change. The Amazon region is such a key biome: it contains unparalleled biological diversity, a globally significant store of organic carbon, and it is a potent engine driving global cycles of water and energy. The importance of understanding how land surface dynamics of the Amazon region respond to climatic variability and change is widely appreciated, but despite significant recent advances, large gaps in our understanding remain. Understanding of energy and carbon exchange between terrestrial ecosystems and the atmosphere can be improved through direct observations and experiments, as well as through modeling activities. Land surface/ecosystem models have become important tools for extrapolating local observations and understanding to much larger terrestrial regions. They are also valuable tools to test hypothesis on ecosystem functioning. Funded by NASA under the auspices of the LBA (the Large-Scale Biosphere-Atmosphere Experiment in Amazonia), the LBA Data Model Intercomparison Project (LBA-DMIP) uses a comprehensive data set from an observational network of flux towers across the Amazon, and an ecosystem modeling community engaged in ongoing studies using a suite of different land surface and terrestrial ecosystem models to understand Amazon forest function. Here an overview of this project is presented accompanied by a description of the measurement sites, data, models and protocol. (C) 2013 Elsevier B.V. All rights reserved.
• Hutyra, L. R., Munger, J. W., Hammond-Pyle, E., Saleska, S. R., Restrepo-Coupe, N., Daube, B. C., de Camargo, P. B., & Wofsy, S. C. (2013). Resolving systematic errors in estimates of net ecosystem exchange of CO2 and ecosystem respiration in a tropical forest biome. AGRICULTURAL AND FOREST METEOROLOGY, 148(8-9), 1266-1279.
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  The controls on uptake and release Of CO2 by tropical rainforests, and the responses to a changing climate, are major uncertainties in global climate change models. Eddy-covariance measurements potentially provide detailed data on CO2 exchange and responses to the environment in these forests, but accurate estimates of the net ecosystem exchange of CO2 (NEE) and ecosystem respiration (R-eco) require careful analysis of data representativity, treatment of data gaps, and correction for systematic errors. This study uses the comprehensive data from our study site in an old-growth tropical rainforest near Santarem, Brazil, to examine the biases in NEE and R-eco potentially associated with the two most important sources of systematic error in Eddy-covariance data: lost nighttime flux and missing canopy storage measurements. We present multiple estimates for the net carbon balance and Reco at our site, including the conventional "u* filter", a detailed bottom-up budget for respiration, estimates by similarity with Rn-122, and an independent estimate of respiration by extrapolation of daytime Eddy flux data to zero light. Eddy-covariance measurements between 2002 and 2006 showed a mean net ecosystem carbon loss of 0.25 +/- 0.04 mu mol m(-2) s(-1), with a mean respiration rate of 8.60 +/- 10.11 mu mol m(-2) s(-1) at our site. We found that lost nocturnal flux can potentially introduce significant bias into these results. We develop robust approaches to correct for these biases, showing that, where appropriate, a site-specific u* threshold can be used to avoid systematic bias in estimates of carbon exchange. Because of the presence of gaps in the data and the day-night asymmetry between storage and turbulence, inclusion of canopy storage is essential to accurate assessments of NEE. We found that short-terrn measurements of storage may be adequate to accurately model storage for use in obtaining ecosystem carbon balance, at sites where storage is not routinely measured. The analytical framework utilized in this study can be applied to other Eddy-covariance sites to help correct and validate measurements of the carbon cycle and its components. (C) 2008 Elsevier B.V. All rights reserved.
• Powell, T. L., Galbraith, D. R., Christoffersen, B. O., Harper, A., Imbuzeiro, H., Rowland, L., Almeida, S., Brando, P. M., da Costa, A., Costa, M. H., Levine, N. M., Malhi, Y., Saleska, S. R., Sotta, E., Williams, M., Meir, P., & Moorcroft, P. R. (2013). Confronting model predictions of carbon fluxes with measurements of Amazon forests subjected to experimental drought. New Phytologist, 200(2), 350-364.
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  PMID: 23844931;Abstract: Summary: Considerable uncertainty surrounds the fate of Amazon rainforests in response to climate change. Here, carbon (C) flux predictions of five terrestrial biosphere models (Community Land Model version 3.5 (CLM3.5), Ecosystem Demography model version 2.1 (ED2), Integrated BIosphere Simulator version 2.6.4 (IBIS), Joint UK Land Environment Simulator version 2.1 (JULES) and Simple Biosphere model version 3 (SiB3)) and a hydrodynamic terrestrial ecosystem model (the Soil-Plant-Atmosphere (SPA) model) were evaluated against measurements from two large-scale Amazon drought experiments. Model predictions agreed with the observed C fluxes in the control plots of both experiments, but poorly replicated the responses to the drought treatments. Most notably, with the exception of ED2, the models predicted negligible reductions in aboveground biomass in response to the drought treatments, which was in contrast to an observed c. 20% reduction at both sites. For ED2, the timing of the decline in aboveground biomass was accurate, but the magnitude was too high for one site and too low for the other. Three key findings indicate critical areas for future research and model development. First, the models predicted declines in autotrophic respiration under prolonged drought in contrast to measured increases at one of the sites. Secondly, models lacking a phenological response to drought introduced bias in the sensitivity of canopy productivity and respiration to drought. Thirdly, the phenomenological water-stress functions used by the terrestrial biosphere models to represent the effects of soil moisture on stomatal conductance yielded unrealistic diurnal and seasonal responses to drought. © 2013 New Phytologist Trust.
• Restrepo-Coupe, N., da Rocha, H. R., Hutyra, L. R., da Araujo, A. C., Borma, L. S., Christoffersen, B., Cabral, O. M., de Camargo, P. B., Cardoso, F. L., Lola da Costa, A. C., Fitzjarrald, D. R., Goulden, M. L., Kruijt, B., Maia, J. M., Malhi, Y. S., Manzi, A. O., Miller, S. D., Nobre, A. D., von Randow, C., , Abreu Sa, L. D., et al. (2013). What drives the seasonality of photosynthesis across the Amazon basin? A cross-site analysis of eddy flux tower measurements from the Brasil flux network. AGRICULTURAL AND FOREST METEOROLOGY, 182, 128-144.
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  We investigated the seasonal patterns of Amazonian forest photosynthetic activity, and the effects thereon of variations in climate and land-use, by integrating data from a network of ground-based eddy flux towers in Brazil established as part of the large-Scale Biosphere Atmosphere Experiment in Amazonia' project. We found that degree of water limitation, as indicated by the seasonality of the ratio of sensible to latent heat flux (Bowen ratio) predicts seasonal patterns of photosynthesis. In equatorial Amazonian forests (5 degrees N-5 degrees S), water limitation is absent, and photosynthetic fluxes (or gross ecosystem productivity, GEP) exhibit high or increasing levels of photosynthetic activity as the dry season progresses, likely a consequence of allocation to growth of new leaves. In contrast, forests along the southern flank of the Amazon, pastures converted from forest, and mixed forest-grass savanna, exhibit dry-season declines in GEP, consistent with increasing degrees of water limitation. Although previous work showed tropical ecosystem evapotranspiration (ET) is driven by incoming radiation, GEP observations reported here surprisingly show no or negative relationships with photosynthetically active radiation (PAR). Instead, GEP fluxes largely followed the phenology of canopy photosynthetic capacity (Pc), with only deviations from this primary pattern driven by variations in PAR. Estimates of leaf flush at three non-water limited equatorial forest sites peak in the dry season, in correlation with high dry season light levels. The higher photosynthetic capacity that follows persists into the wet season, driving high GEP that is out of phase with sunlight, explaining the negative observed relationship with sunlight. Overall, these patterns suggest that at sites where water is not limiting, light interacts with adaptive mechanisms to determine photosynthetic capacity indirectly through leaf flush and litterfall seasonality. These mechanisms are poorly represented in ecosystem models, and represent an important challenge to efforts to predict tropical forest responses to climatic variations. (C) 2013 Elsevier B.V. All rights reserved.
• Restrepo-Coupe, N., da Roche, H., Hutyra, L. R., da Araujo, A., Borma, L. S., Christoffersen, B., Cabral, O. M., de Camargo, P., Cardoso, F. L., Lola da Costa, A., Fitzjarrald, D. R., Goulden, M. L., Kruijt, B., Maia, J. M., Malhi, Y. S., Manzi, A. O., Miller, S. D., Nobre, A. D., von Randow, C., , Abreu Sa, L., et al. (2013). What drives the seasonality of photosynthesis across the Amazon basin? A cross-site analysis of eddy flux tower measurements from the Brasil flux network. Agricultural and Forest Meteorology, 182-183, 128-144.
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  Abstract: We investigated the seasonal patterns of Amazonian forest photosynthetic activity, and the effects thereon of variations in climate and land-use, by integrating data from a network of ground-based eddy flux towers in Brazil established as part of the 'Large-Scale Biosphere Atmosphere Experiment in Amazonia' project. We found that degree of water limitation, as indicated by the seasonality of the ratio of sensible to latent heat flux (Bowen ratio) predicts seasonal patterns of photosynthesis. In equatorial Amazonian forests (5° N-5° S), water limitation is absent, and photosynthetic fluxes (or gross ecosystem productivity, GEP) exhibit high or increasing levels of photosynthetic activity as the dry season progresses, likely a consequence of allocation to growth of new leaves. In contrast, forests along the southern flank of the Amazon, pastures converted from forest, and mixed forest-grass savanna, exhibit dry-season declines in GEP, consistent with increasing degrees of water limitation. Although previous work showed tropical ecosystem evapotranspiration (ET) is driven by incoming radiation, GEP observations reported here surprisingly show no or negative relationships with photosynthetically active radiation (PAR). Instead, GEP fluxes largely followed the phenology of canopy photosynthetic capacity (Pc), with only deviations from this primary pattern driven by variations in PAR. Estimates of leaf flush at three non-water limited equatorial forest sites peak in the dry season, in correlation with high dry season light levels. The higher photosynthetic capacity that follows persists into the wet season, driving high GEP that is out of phase with sunlight, explaining the negative observed relationship with sunlight. Overall, these patterns suggest that at sites where water is not limiting, light interacts with adaptive mechanisms to determine photosynthetic capacity indirectly through leaf flush and litterfall seasonality. These mechanisms are poorly represented in ecosystem models, and represent an important challenge to efforts to predict tropical forest responses to climatic variations. © 2013 Elsevier B.V.
• Van Haren, J. L., Oliveira, R. C., Beldini, P. T., de Camargo, P. B., Keller, M., & Saleska, S. R. (2013). Tropical tree species effects on soil properties and greenhouse gas fluxes in monoculture and diverse forests. Biotropica, 45(6), 709-718.
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  Abstract: Tropical plantations are considered a viable option to sequester carbon on abandoned agricultural lands, but implications of tree species selection for overall greenhouse gas budgets on plantations have been little studied. During three wet seasons, we investigated the influence of nine tree species on soil pH, temperature (ST), bulk density (BD), moisture content water filled pore space (WFPS), and greenhouse gas fluxes in diverse forest sites and monoculture plantation plots. All sites were on clay-rich soils of the Barreiras formation, in east-central Amazônia, Brazil. We found that ST and BD were 0.6°C and 0.2 g/cm3 higher in the plantation relative to the forest, and soil CH4, CO,2 and N2O fluxes were, respectively, 38, 12, 62, percent lower in the plantation. Tree growth rates were highly variable on the plantation, with the mean comparable to the forest sites. Tree species identity mattered (P < 0.01) for all soil properties and gas fluxes on the plantation, but only for pH, BD, WFPS, and N2O fluxes in the forest. The species rank order of pH and N2O fluxes in the forest, however, were unlike the plantation. Tree growth rates were a strong predictor for soil WFPS, and together with location, they also explained 75 percent of the mean N2O flux variation. Our study indicates that: (1) tree species influence soil processes; and (2) high tree growth and low soil gas emissions imply a reduced climate forcing effect from plantations, especially when planted with fast-growing legume species on abandoned farmland.
• Wehr, R., Munger, J. W., Nelson, D. D., McManus, J. B., Zahniser, M. S., Wofsy, S. C., & Saleska, S. R. (2013). Long-term eddy covariance measurements of the isotopic composition of the ecosystem-atmosphere exchange of CO₂ in a temperate forest. Agricultural and Forest Meteorology, 181, 69-84.
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  Abstract: Measurements of the isotopic composition of the net ecosystem-atmosphere exchange of CO2 (NEE) have been desired as a means to probe ecosystem carbon cycling and in particular to partition NEE into gross ecosystem photosynthesis and respiration. Several attempts at such measurements have combined eddy covariance (EC) measurements of the total net CO2 flux with flask measurements of the isotopic composition of CO2 in ambient air - an indirect method that has never been validated. Direct EC measurements of the isotopic composition of NEE (i.e. of the net exchanges of 12C16O2, 13C16O2, and 18O12C16O) have been made only twice, in short-term (2-month and 1-month) campaigns.Here we present a full growing season of direct EC measurements of the isotopic composition of NEE in a temperate deciduous forest, and we use these data: (1) to rigorously assess their limiting sources of error, (2) to test the indirect EC/flask method, and (3) to give an indication of the potential for ecological analyses. We describe the method and instrumentation, including the new cryogen-free, continuous-wave, quantum cascade laser spectrometer, which can determine δ13C and δ18O in ambient CO2 with unprecedented noise levels of ±0.02‰ and ±0.03‰ (1 standard deviation), respectively, for a 100s integration time and a 1-h calibration interval. We find: (1) that precision is jointly limited by the instrumentation and by horizontal ecosystem or landscape heterogeneity, so that there is little to be gained by further improvements to instrument performance; (2) that the isotopic composition of NEE obtained by the EC/flask method can be biased, on a monthly timescale, by 2‰; and (3) that the present measurements are precise enough to elucidate biological mechanisms controlling the ecosystem-scale carbon balance. © 2013 Elsevier B.V.
• van Haren, J., de Oliveira, R. C., Beldini, P. T., de Camargo, P. B., Keller, M., & Saleska, S. (2013). Tree Species Effects on Soil Properties and Greenhouse Gas Fluxes in East-central Amazonia: Comparison between Monoculture and Diverse Forest. BIOTROPICA, 45(6), 709-718.
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  Tropical plantations are considered a viable option to sequester carbon on abandoned agricultural lands, but implications of tree species selection for overall greenhouse gas budgets on plantations have been little studied. During three wet seasons, we investigated the influence of nine tree species on soil pH, temperature (ST), bulk density (BD), moisture content water filled pore space (WFPS), and greenhouse gas fluxes in diverse forest sites and monoculture plantation plots. All sites were on clay-rich soils of the Barreiras formation, in east-central Amazonia, Brazil. We found that ST and BD were 0.6 degrees C and 0.2g/cm(3) higher in the plantation relative to the forest, and soil CH4, CO,(2) and N2O fluxes were, respectively, 38, 12, 62, percent lower in the plantation. Tree growth rates were highly variable on the plantation, with the mean comparable to the forest sites. Tree species identity mattered (P
• von Randow, C., Zeri, M., Restrepo-Coupe, N., Muza, M. N., de Goncalves, L. G., Costa, M. H., Araujo, A. C., Manzi, A. O., da Rocha, H. R., Saleska, S. R., Arain, M. A., Baker, I. T., Cestaro, B. P., Christoffersen, B., Ciais, P., Fisher, J. B., Galbraith, D., Guan, X., Van den Hurk, B., , Ichii, K., et al. (2013). Inter-annual variability of carbon and water fluxes in Amazonian forest, Cerrado and pasture sites, as simulated by terrestrial biosphere models. AGRICULTURAL AND FOREST METEOROLOGY, 182, 145-155.
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  This study analyzes the inter-annual variability (IAV) of simulations of 21 different land surface model formulations, driven by meteorological conditions measured at 8 flux towers, located in rain forest, forest-savanna ecotone and pasture sites in Amazonia, and one in savanna site in Southeastern Brazil. Annual totals of net ecosystem exchange (NEE) of carbon and evapotranspiration (ET), measured and simulated by each model for each site-year, were compared in terms of year-to-year variability and possible relation to climate drivers. Results have shown that most of models simulations for annual totals of NEE and ET, and IAV of these fluxes, are frequently different from measurements. The average of the model simulations of annual fluxes tend to respond to climatic drivers similarly to the observations, but with noticeable discrepancies. Annual measurements of NEE are negatively correlated to annual rainfall in the forest sites group. Although the ensemble of all models yields a similar result, only three model formulations reproduce a significant negative correlation of simulated NEE with rainfall. For the IAV of ET, tower measurements are controlled by annual variations of radiation and this feature is captured by the ensemble of the models, both at individual sites and when all forest sites are grouped. However, simulated ET values are also significantly correlated to the amount of precipitation in many models and in the model ensemble, while there is no significant correlation in the observations. In general, the surface models are able to reproduce the responses of fluxes to climatic drivers, but improvements are still needed to better capture their inter-annual variability. (C) 2013 Elsevier B.V. All rights reserved.
• von Randow, C., Zeri, M., Restrepo-Coupe, N., Muza, M. N., de Goncalves, L., Costa, M. H., Araujo, A. C., Manzi, A. O., da Rocha, H., Saleska, S. R., Arain, M. A., Baker, I. T., Cestaro, B. P., Christoffersen, B., Ciais, P., Fisher, J. B., Galbraith, D., Guan, X., van den Hurk, B., , Ichii, K., et al. (2013). Inter-annual variability of carbon and water fluxes in Amazonian forest, Cerrado and pasture sites, as simulated by terrestrial biosphere models. Agricultural and Forest Meteorology, 182, 145-155.
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  Abstract: This study analyzes the inter-annual variability (IAV) of simulations of 21 different land surface model formulations, driven by meteorological conditions measured at 8 flux towers, located in rain forest, forest-savanna ecotone and pasture sites in Amazonia, and one in savanna site in Southeastern Brazil. Annual totals of net ecosystem exchange (NEE) of carbon and evapotranspiration (ET), measured and simulated by each model for each site-year, were compared in terms of year-to-year variability and possible relation to climate drivers. Results have shown that most of models simulations for annual totals of NEE and ET, and IAV of these fluxes, are frequently different from measurements. The average of the model simulations of annual fluxes tend to respond to climatic drivers similarly to the observations, but with noticeable discrepancies. Annual measurements of NEE are negatively correlated to annual rainfall in the forest sites group. Although the ensemble of all models yields a similar result, only three model formulations reproduce a significant negative correlation of simulated NEE with rainfall. For the IAV of ET, tower measurements are controlled by annual variations of radiation and this feature is captured by the ensemble of the models, both at individual sites and when all forest sites are grouped. However, simulated ET values are also significantly correlated to the amount of precipitation in many models and in the model ensemble, while there is no significant correlation in the observations. In general, the surface models are able to reproduce the responses of fluxes to climatic drivers, but improvements are still needed to better capture their inter-annual variability. © 2013 Elsevier B.V..
• Ivanov, V. Y., Hutyra, L. R., Wofsy, S. C., Munger, J. W., Saleska, S. R., & de Camargo, P. B. (2012). Root niche separation can explain avoidance of seasonal drought stress and vulnerability of overstory trees to extended drought in a mature Amazonian forest. Water Resources Research, 48(12).
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  Abstract: Large areas of Amazonian evergreen forest experience seasonal droughts extending for three or more months, yet show maximum rates of photosynthesis and evapotranspiration during dry intervals. This apparent resilience is belied by disproportionate mortality of the large trees in manipulations that reduce wet season rainfall, occurring after 2-3 years of treatment. The goal of this study is to characterize the mechanisms that produce these contrasting ecosystem responses. A mechanistic model is developed based on the ecohydrological framework of TIN (Triangulated Irregular Network)-based Real Time Integrated Basin Simulator + Vegetation Generator for Interactive Evolution (tRIBS+VEGGIE). The model is used to test the roles of deep roots and soil capillary flux to provide water to the forest during the dry season. Also examined is the importance of "root niche separation," in which roots of overstory trees extend to depth, where during the dry season they use water stored from wet season precipitation, while roots of understory trees are concentrated in shallow layers that access dry season precipitation directly. Observational data from the Tapajós National Forest, Brazil, were used as meteorological forcing and provided comprehensive observational constraints on the model. Results strongly suggest that deep roots with root niche separation adaptations explain both the observed resilience during seasonal drought and the vulnerability of canopy-dominant trees to extended deficits of wet season rainfall. These mechanisms appear to provide an adaptive strategy that enhances productivity of the largest trees in the face of their disproportionate heat loads and water demand in the dry season. A sensitivity analysis exploring how wet season rainfall affects the stability of the rainforest system is presented. © 2012. American Geophysical Union. All Rights Reserved.
• Jardine, K. J., Monson, R. K., Abrell, L., Saleska, S. R., Arneth, A., Jardine, A., Ishida, F. Y., Serrano, A. M., Artaxo, P., Karl, T., Fares, S., Goldstein, A., Loreto, F., & Huxman, T. (2012). Within-plant isoprene oxidation confirmed by direct emissions of oxidation products methyl vinyl ketone and methacrolein. Global Change Biology, 18(3), 973-984.
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  Abstract: Isoprene is emitted from many terrestrial plants at high rates, accounting for an estimated 1/3 of annual global volatile organic compound emissions from all anthropogenic and biogenic sources combined. Through rapid photooxidation reactions in the atmosphere, isoprene is converted to a variety of oxidized hydrocarbons, providing higher order reactants for the production of organic nitrates and tropospheric ozone, reducing the availability of oxidants for the breakdown of radiatively active trace gases such as methane, and potentially producing hygroscopic particles that act as effective cloud condensation nuclei. However, the functional basis for plant production of isoprene remains elusive. It has been hypothesized that in the cell isoprene mitigates oxidative damage during the stress-induced accumulation of reactive oxygen species (ROS), but the products of isoprene-ROS reactions in plants have not been detected. Using pyruvate-2- 13C leaf and branch feeding and individual branch and whole mesocosm flux studies, we present evidence that isoprene (i) is oxidized to methyl vinyl ketone and methacrolein (i ox) in leaves and that i ox/i emission ratios increase with temperature, possibly due to an increase in ROS production under high temperature and light stress. In a primary rainforest in Amazonia, we inferred significant in plant isoprene oxidation (despite the strong masking effect of simultaneous atmospheric oxidation), from its influence on the vertical distribution of i ox uptake fluxes, which were shifted to low isoprene emitting regions of the canopy. These observations suggest that carbon investment in isoprene production is larger than that inferred from emissions alone and that models of tropospheric chemistry and biota-chemistry-climate interactions should incorporate isoprene oxidation within both the biosphere and the atmosphere with potential implications for better understanding both the oxidizing power of the troposphere and forest response to climate change. © 2012 Blackwell Publishing Ltd.
• Stark, S. C., Leitold, V., Wu, J. L., Hunter, M. O., Lefsky, M. A., Keller, M., Alves, L. F., Mcmahon, S. M., Parker, G. G., Castilho, C. V., Schietti, J., Costa, F. R., Shimabukuro, Y. E., Brandão, D. O., Oliveira, R. C., Shimabukuro, M. T., Higuchi, N., Woodcock, T. K., Camargo, P. B., & Saleska, S. R. (2012). Differences in Amazon forest growth and carbon dynamics predicted by profiles of canopy leaf area and light environment. Ecology Letters, 15(12), 1406-1414.
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  PMID: 22994288;Abstract: Tropical forest structural variation across heterogeneous landscapes may control above-ground carbon dynamics. We tested the hypothesis that canopy structure (leaf area and light availability) - remotely estimated from LiDAR - control variation in above-ground coarse wood production (biomass growth). Using a statistical model, these factors predicted biomass growth across tree size classes in forest near Manaus, Brazil. The same statistical model, with no parameterisation change but driven by different observed canopy structure, predicted the higher productivity of a site 500 km east. Gap fraction and a metric of vegetation vertical extent and evenness also predicted biomass gains and losses for one-hectare plots. Despite significant site differences in canopy structure and carbon dynamics, the relation between biomass growth and light fell on a unifying curve. This supported our hypothesis, suggesting that knowledge of canopy structure can explain variation in biomass growth over tropical landscapes and improve understanding of ecosystem function. © 2012 Blackwell Publishing Ltd/CNRS.
• Jardine, K., Monson, R. K., Abrell, L. M., Saleska, S. R., Arneth, A., Jardine, A., Karl, T., Fares, S., Goldstein, A., Loreto, F., & Huxman, T. E. (2012). Within-plant isoprene oxidation confirmed by direct emissions of oxidation products methyl vinyl ketone and methacrolein. Global Change Biology, 18, 973-984.
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  Keywords: Amazon; biosphere&amp;#8211;atmosphere interactions; isoprene oxidation; methacrolein; methyl vinyl ketone; reactive oxygen species; temperature stress; thermotoleranceAbstractIsoprene is emitted from many terrestrial plants at high rates, accounting for an estimated 1/3 of annual global volatile organic compound emissions from all anthropogenic and biogenic sources combined. Through rapid photooxidation reactions in the atmosphere, isoprene is converted to a variety of oxidized hydrocarbons, providing higher order reactants for the production of organic nitrates and tropospheric ozone, reducing the availability of oxidants for the breakdown of radiatively active trace gases such as methane, and potentially producing hygroscopic particles that act as effective cloud condensation nuclei. However, the functional basis for plant production of isoprene remains elusive. It has been hypothesized that in the cell isoprene mitigates oxidative damage during the stress-induced accumulation of reactive oxygen species (ROS), but the products of isoprene-ROS reactions in plants have not been detected. Using pyruvate-2-13C leaf and branch feeding and individual branch and whole mesocosm flux studies, we present evidence that isoprene (i) is oxidized to methyl vinyl ketone and methacrolein (iox) in leaves and that iox/i emission ratios increase with temperature, possibly due to an increase in ROS production under high temperature and light stress. In a primary rainforest in Amazonia, we inferred significant in plant isoprene oxidation (despite the strong masking effect of simultaneous atmospheric oxidation), from its influence on the vertical distribution of iox uptake fluxes, which were shifted to low isoprene emitting regions of the canopy. These observations suggest that carbon investment in isoprene production is larger than that inferred from emissions alone and that models of tropospheric chemistry and biota&amp;#8211;chemistry&amp;#8211;climate interactions should incorporate isoprene oxidation within both the biosphere and the atmosphere with potential implications for better understanding both the oxidizing power of the troposphere and forest response to climate change.
• Jardine, K., Serrano, A. Y., Arneth, A., Abrell, L., Jardine, A., Artaxo, P., Alves, E., Kesselmeier, J., Taylor, T., Saleska, S., & Huxman, T. (2011). Ecosystem-scale compensation points of formic and acetic acid in the central Amazon. Biogeosciences, 8(12), 3709-3720.
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  Abstract: Organic acids, central to terrestrial carbon metabolism and atmospheric photochemistry, are ubiquitous in the troposphere in the gas, particle, and aqueous phases. As the dominant organic acids in the atmosphere, formic acid (FA, HCOOH) and acetic acid (AA, CH3COOH) control precipitation acidity in remote regions and may represent a critical link between the terrestrial carbon and water cycles by acting as key intermediates in plant carbon and energy metabolism and aerosol-cloud-precipitation interactions. However, our understanding of the exchange of these acids between terrestrial ecosystems and the atmosphere is limited by a lack of field observations, the existence of biogenic and anthropogenic primary and secondary sources whose relative importance is unclear, and the fact that vegetation can act as both a source and a sink. Here, we first present data obtained from the tropical rainforest mesocosm at Biosphere 2 which isolates primary vegetation sources. Strong light and temperature dependent emissions enriched in FA relative to AA were simultaneously observed from individual branches (FA/AA Combining double low line 3.0 ± 0.7) and mesocosm ambient air (FA/AA Combining double low line 1.4 ± 0.3). We also present long-term observations of vertical concentration gradients of FA and AA within and above a primary rainforest canopy in the central Amazon during the 2010 dry and 2011 wet seasons. We observed a seasonal switch from net ecosystem-scale deposition during the dry season to net emissions during the wet season. This switch was associated with reduced ambient concentrations in the wet season (FA < 1.3 nmol molg -1, AA < 2.0 nmol molg -1) relative to the dry season (FA up to 3.3 nmol molg -1, AA up to 6.0 nmol molg -1), and a simultaneous increase in the FA/AA ambient concentration ratios from 0.3-0.8 in the dry season to 1.0-2.1 in the wet season. These observations are consistent with a switch between a biomass burning dominated source in the dry season (FA/AA < 1.0) to a vegetation dominated source in the wet season (FA/AA > 1.0). Our observations provide the first ecosystem-scale evidence of bidirectional FA and AA exchange between a forest canopy and the atmosphere controlled by ambient concentrations and ecosystem scale compensation points (estimated to be 1.3 ± 0.3 nmol molg -1: FA, and 2.1 ± 0.4 nmol molg -1: AA). These results suggest the need for a fundamental change in how future biosphere-atmosphere exchange models should treat FA and AA with a focus on factors that influence net exchange rates (ambient concentrations and ecosystem compensation points) rather than treating emissions and deposition separately. © Author(s) 2011. CC Attribution 3.0 License.
• Jardine, K., Serrano, A. Y., Arneth, A., Abrell, L., Jardine, A., van Haren, J., Artaxo, P., Rizzo, L. V., Ishida, F. Y., Karl, T., Kesselmeier, J., Saleska, S., & Huxman, T. (2011). Within-canopy sesquiterpene ozonolysis in Amazonia. JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, 116.
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  Through rapid reactions with ozone, which can initiate the formation of secondary organic aerosols, the emission of sesquiterpenes from vegetation in Amazonia may have significant impacts on tropospheric chemistry and climate. Little is known, however, about sesquiterpene emissions, transport, and chemistry within plant canopies owing to analytical difficulties stemming from very low ambient concentrations, high reactivities, and sampling losses. Here, we present ambient sesquiterpene concentration measurements obtained during the 2010 dry season within and above a primary tropical forest canopy in Amazonia. We show that by peaking at night instead of during the day, and near the ground instead of within the canopy, sesquiterpene concentrations followed a pattern different from that of monoterpenes, suggesting that unlike monoterpene emissions, which are mainly light dependent, sesquiterpene emissions are mainly temperature dependent. In addition, we observed that sesquiterpene concentrations were inversely related with ozone (with respect to time of day and vertical concentration), suggesting that ambient concentrations are highly sensitive to ozone. These conclusions are supported by experiments in a tropical rain forest mesocosm, where little atmospheric oxidation occurs and sesquiterpene and monoterpene concentrations followed similar diurnal patterns. We estimate that the daytime dry season ozone flux of -0.6 to -1.5 nmol m(-2) s(-1) due to in-canopy sesquiterpene reactivity could account for 7%-28% of the net ozone flux. Our study provides experimental evidence that a large fraction of total plant sesquiterpene emissions (46%-61% by mass) undergo within-canopy ozonolysis, which may benefit plants by reducing ozone uptake and its associated oxidative damage.
• Mercado, L. M., Patiño, S., Domingues, T. F., Fyllas, N. M., Weedon, G. P., Sitch, S., Quesada, C. A., Phillips, O. L., Aragao, L. E., Malhi, Y., Dolman, A. J., Restrepo-Coupe, N., Saleska, S. R., Baker, T. R., Almeida, S., Higuchi, N., & Lloyd, J. (2011). Variations in Amazon forest productivity correlated with foliar nutrients and modelled rates of photosynthetic carbon supply. Philosophical Transactions of the Royal Society B: Biological Sciences, 366(1582), 3316-3329.
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  PMID: 22006971;PMCID: PMC3179632;Abstract: The rate of above-ground woody biomass production, W P, in some western Amazon forests exceeds those in the east by a factor of 2 or more. Underlying causes may include climate, soil nutrient limitations and species composition. In this modelling paper, we explore the implications of allowing key nutrients such as N and P to constrain the photosynthesis of Amazon forests, and also we examine the relationship between modelled rates of photosynthesis and the observed gradients in W P. We use a model with current understanding of the underpinning biochemical processes as affected by nutrient availability to assess: (i) the degree to which observed spatial variations in foliar [N] and [P] across Amazonia affect stand-level photosynthesis; and (ii) how these variations in forest photosynthetic carbon acquisition relate to the observed geographical patterns of stem growth across the Amazon Basin. We find nutrient availability to exert a strong effect on photosynthetic carbon gain across the Basin and to be a likely important contributor to the observed gradient in W P. Phosphorus emerges as more important than nitrogen in accounting for the observed variations in productivity. Implications of these findings are discussed in the context of future tropical forests under a changing climate. © 2011 The Royal Society.
• Miller, S. D., Goulden, M. L., Hutyra, L. R., Keller, M., Saleska, S. R., Wofsy, S. C., Silva Figueira, A. M., da Rocha, H. R., & de Camargo, P. B. (2011). Reduced impact logging minimally alters tropical rainforest carbon and energy exchange. Proceedings of the National Academy of Sciences of the United States of America, 108(48), 19431-19435.
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  PMID: 22087005;PMCID: PMC3228459;Abstract: We used eddy covariance and ecological measurements to investigate the effects of reduced impact logging (RIL) on an old-growth Amazonian forest. Logging caused small decreases in gross primary production, leaf production, and latent heat flux, which were roughly proportional to canopy loss, and increases in heterotrophic respiration, tree mortality, and wood production. The net effect of RIL was transient, and treatment effects were barely discernable after only 1 y. RIL appears to provide a strategy for managing tropical forest that minimizes the potential risks to climate associated with large changes in carbon and water exchange.
• Nobre, A. D., Cuartas, L. A., Hodnett, M., Rennó, C. D., Rodrigues, G., Silveira, A., Waterloo, M., & Saleska, S. (2011). Height Above the Nearest Drainage - a hydrologically relevant new terrain model. Journal of Hydrology, 404(1-2), 13-29.
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  Abstract: This paper introduces a new terrain model named HAND, and reports on the calibration and validation of landscape classes representing soil environments in Amazonia, which were derived using it. The HAND model normalizes topography according to the local relative heights found along the drainage network, and in this way, presents the topology of the relative soil gravitational potentials, or local draining potentials. The HAND model has been demonstrated to show a high correlation with the depth of the water table, providing an accurate spatial representation of soil water environments. Normalized draining potentials can be classified according to the relative vertical flowpath-distances to the nearest drainages, defining classes of soil water environments. These classes have been shown to be comparable and have verifiable and reproducible hydrological significance across the studied catchment and for surrounding ungauged catchments. The robust validation of this model over an area of 18,000km2 in the lower Rio Negro catchment has demonstrated its capacity to map expansive environments using only remotely acquired topography data as inputs. The classified HAND model has also preliminarily demonstrated robustness when applied to ungauged catchments elsewhere with contrasting geologies, geomorphologies and soil types. The HAND model and the derived soil water maps can help to advance physically based hydrological models and be applied to a host of disciplines that focus on soil moisture and ground water dynamics. As an original assessment of soil water in the landscape, the HAND model explores the synergy between digital topography data and terrain modeling, presenting an opportunity for solving many difficult problems in hydrology. © 2011 Elsevier B.V.
• Sakaguchi, K., Zeng, X., Christoffersen, B. J., Restrepo-Coupe, N., Saleska, S. R., & Brando, P. M. (2011). Natural and drought scenarios in an east central Amazon forest: Fidelity of the Community Land Model 3.5 with three biogeochemical models. JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 116.
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  Recent development of general circulation models involves biogeochemical cycles: flows of carbon and other chemical species that circulate through the Earth system. Such models are valuable tools for future projections of climate, but still bear large uncertainties in the model simulations. One of the regions with especially high uncertainty is the Amazon forest where large-scale dieback associated with the changing climate is predicted by several models. In order to better understand the capability and weakness of global-scale land-biogeochemical models in simulating a tropical ecosystem under the present day as well as significantly drier climates, we analyzed the off-line simulations for an east central Amazon forest by the Community Land Model version 3.5 of the National Center for Atmospheric Research and its three independent biogeochemical submodels (CASA', CN, and DGVM). Intense field measurements carried out under Large Scale Biosphere-Atmosphere Experiment in Amazonia, including forest response to drought from a throughfall exclusion experiment, are utilized to evaluate the whole spectrum of biogeophysical and biogeochemical aspects of the models. Our analysis shows reasonable correspondence in momentum and energy turbulent fluxes, but it highlights three processes that are not in agreement with observations: (1) inconsistent seasonality in carbon fluxes, (2) biased biomass size and allocation, and (3) overestimation of vegetation stress to short-term drought but underestimation of biomass loss from long-term drought. Without resolving these issues the modeled feedbacks from the biosphere in future climate projections would be questionable. We suggest possible directions for model improvements and also emphasize the necessity of more studies using a variety of in situ data for both driving and evaluating land-biogeochemical models.
• Adams, H. D., MacAlady, A. K., Breshears, D. D., Allen, C. D., Stephenson, N. L., Saleska, S. R., Huxman, T. E., & McDowell, N. G. (2010). Climate-induced tree mortality: Earth system consequences. Eos, 91(17), 153-154.
• Jardine, K. J., Sommer, E. D., Saleska, S. R., Huxman, T. E., Harley, P. C., & Abrell, L. (2010). Gas phase measurements of pyruvic acid and its volatile metabolites. Environmental Science and Technology, 44(7), 2454-2460.
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  PMID: 20210357;Abstract: Pyruvic acid, central to leaf carbon metabolism, is a precursor of many volatile organic compounds (VOCs) that impact air quality and climate. Although the pathways involved in the production of isoprenoids are well-known, those of several oxygenated VOCs remain uncertain. We present concentration and flux measurements of pyruvic acid and other VOCs within the tropical rainforest (TRF) biome at Biosphere 2. Pyruvic acid concentrations varied diurnally with midday maxima up to 15 ppbv, perhaps due to enhanced production rates and suppression of mitochondrial respiration in the light. Branch fluxes and ambient concentrations of pyruvic acid correlated with those of acetone, acetaldehyde, ethanol, acetic acid, isoprene, monoterpenes, and sesquiterpenes. While pyruvic acid is a known substrate for isoprenoid synthesis, this correlation suggests that the oxygenated VOCs may also derive from pyruvic acid, an idea supported by leaf feeding experiments with sodium pyruvate which resulted in large enhancements in emissions of both isoprenoids and oxygenated VOCs. While feeding with sodium pyruvate-2-13C resulted in large emissions of both 13C-labeled isoprenoids and oxygenated VOCs, feeding with sodium pyruvate-1-l3C resulted in only relabeled isoprenoids. This suggests that acetaldehyde, ethanol, and acetic acid are produced from pyruvic acid via the pyruvate dehydrogenase (PDH) bypass system (in which the 1-C carbon of pyruvic acid is lost as CO2) and that acetone is also derived from the decarboxylation of pyruvic acid. © 2010 American Chemical Society.
• Martin, S. T., Andreae, M. O., Artaxo, P., Baumgardner, D., Chen, Q., Goldstein, A. H., Guenther, A., Heald, C. L., Mayol-Bracero, O. L., McMurry, P. H., Pauliquevis, T., Poschl, U., Prather, K. A., Roberts, G. C., Saleska, S. R., Dias, M. S., Spracklen, D. V., Swietlicki, E., & Trebs, I. (2010). Sources and properties of Amazonian aerosol particles. Reviews of Geophysics, 48(2).
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  Abstract: This review provides a comprehensive account of what is known presently about Amazonian aerosol particles and concludes by formulating outlook and priorities for further research. The review is organized to follow the life cycle of Amazonian aerosol particles. It begins with a discussion of the primary and secondary sources relevant to the Amazonian particle burden, followed by a presentation of the particle properties that characterize the mixed populations present over the Amazon Basin at different times and places. These properties include number and mass concentrations and distributions, chemical composition, hygroscopicity, and cloud nucleation ability. The review presents Amazonian aerosol particles in the context of natural compared to anthropogenic sources as well as variability with season and meteorology. This review is intended to facilitate an understanding of the current state of knowledge on Amazonian aerosol particles specifically and tropical continental aerosol particles in general and thereby to enhance future research in this area. Copyright © 2010 by the American Geophysical Union.
• Rosolem, R., Shuttleworth, W. J., Zeng, X., Saleska, S. R., & Huxman, T. E. (2010). Land surface modeling inside the Biosphere 2 tropical rain forest biome. JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 115.
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  Tropical rain forests contribute substantially to regional and global energy, water, and carbon exchanges between the land surface and the atmosphere, and better understanding of the mechanisms of vegetation response to different environmental stresses is needed. The Biosphere 2 facility provides an opportunity to link laboratory-scale and plot-scale studies in a controllable environment. We compiled a consistent quality-controlled time series of climate data from Biosphere 2 and used it to drive the Simple Biosphere model (SiB3) to test how well it represented the behavior of soils and vegetation inside the tropical rain forest biome of Biosphere 2 (B2-TRF). We found that soil respiration parameterization in SiB3 was not suitable for use in B2-TRF, so several alternative parameterizations were tested. None gave outstanding results, but a modified version of the parameterization originally proposed for SiB3 gave the best results. With this modification, SiB3 well simulated the observed net ecosystem exchange in B2-TRF but, significantly, only after additionally modifying parameters describing the thermal tolerance of plants so that photosynthetic capacity was reduced on average but maintained to higher temperatures. This implies either that tropical rain forest species can acclimate to higher temperatures than allowed for by vegetation models or that the plant community assembly in B2-TRF has shifted to allow continued functioning at higher temperatures, and plants in natural ecosystems could also. In either case, this suggests that the Amazon rain forest may be more resilient to climate change than hitherto thought.
• van Haren, J. L., Cosme de Oliveira, R., Restrepo-Coupe, N., Hutyra, L., de Camargo, P. B., Keller, M., & Saleska, S. R. (2010). Do plant species influence soil CO2 and N2O fluxes in a diverse tropical forest?. JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES, 115.
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  To test whether plant species influence greenhouse gas production in diverse ecosystems, we measured wet season soil CO2 and N2O fluxes close to similar to 300 large (>35 cm in diameter at breast height (DBH)) trees of 15 species at three clay-rich forest sites in central Amazonia. We found that soil CO2 fluxes were 38% higher near large trees than at control sites >10 m away from any tree (P < 0.0001). After adjusting for large tree presence, a multiple linear regression of soil temperature, bulk density, and liana DBH explained 19% of remaining CO2 flux variability. Soil N2O fluxes adjacent to Caryocar villosum, Lecythis lurida, Schefflera morototoni, and Manilkara huberi were 84%-196% greater than Erisma uncinatum and Vochysia maxima, both Vochysiaceae. Tree species identity was the most important explanatory factor for N2O fluxes, accounting for more than twice the N2O flux variability as all other factors combined. Two observations suggest a mechanism for this finding: (1) sugar addition increased N2O fluxes near C. villosum twice as much (P < 0.05) as near Vochysiaceae and (2) species mean N2O fluxes were strongly negatively correlated with tree growth rate (P = 0.002). These observations imply that through enhanced belowground carbon allocation liana and tree species can stimulate soil CO2 and N2O fluxes (by enhancing denitrification when carbon limits microbial metabolism). Alternatively, low N2O fluxes potentially result from strong competition of tree species with microbes for nutrients. Species-specific patterns in CO2 and N2O fluxes demonstrate that plant species can influence soil biogeochemical processes in a diverse tropical forest.
• Fisher, J. B., Malhi, Y., Bonal, D., R., H., C., A., Gamo, M., Goulden, M. L., Rano, T. H., Huete, A. R., Kondo, H., Kumagai, T., Loescher, H. W., Miller, S., Nobre, A. D., Nouvellon, Y., Oberbauer, S. F., Panuthai, S., Roupsard, O., Saleska, S., , Tanaka, K., et al. (2009). The land-atmosphere water flux in the tropics. Global Change Biology, 15(11), 2694-2714.
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  Abstract: Tropical vegetation is a major source of global land surface evapotranspiration, and can thus play a major role in global hydrological cycles and global atmospheric circulation. Accurate prediction of tropical evapotranspiration is critical to our understanding of these processes under changing climate. We examined the controls on evapotranspiration in tropical vegetation at 21 pan-tropical eddy covariance sites, conducted a comprehensive and systematic evaluation of 13 evapotranspiration models at these sites, and assessed the ability to scale up model estimates of evapotranspiration for the test region of Amazonia. Net radiation was the strongest determinant of evapotranspiration (mean evaporative fraction was 0.72) and explained 87% of the variance in monthly evapotranspiration across the sites. Vapor pressure deficit was the strongest residual predictor (14%), followed by normalized difference vegetation index (9%), precipitation (6%) and wind speed (4%). The radiation-based evapotranspiration models performed best overall for three reasons: (1) the vegetation was largely decoupled from atmospheric turbulent transfer (calculated from Ω decoupling factor), especially at the wetter sites; (2) the resistance-based models were hindered by difficulty in consistently characterizing canopy (and stomatal) resistance in the highly diverse vegetation; (3) the temperature-based models inadequately captured the variability in tropical evapotranspiration. We evaluated the potential to predict regional evapotranspiration for one test region: Amazonia. We estimated an Amazonia-wide evapotranspiration of 1370mmyr-1, but this value is dependent on assumptions about energy balance closure for the tropical eddy covariance sites; a lower value (1096mmyr-1) is considered in discussion on the use of flux data to validate and interpolate models. © 2009 The Authors Journal compilation © 2009 Blackwell Publishing Ltd.
• Grant, R. F., Hutyra, L. R., Oliveira, R. D., Munger, J. W., Saleska, S. R., & Wofsy, S. C. (2009). Modeling the carbon balance of Amazonian rain forests: Resolving ecological controls on net ecosystem productivity. Ecological Monographs, 79(3), 445-463.
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  Abstract: There is still much uncertainty about ecological controls on the rate and direction of net CO2 exchange by tropical rain forests, in spite of their importance to global C cycling. These controls are thought to arise from hydrologic and nutrient constraints to CO2 fixation caused by seasonality of precipitation and adverse chemical properties of some major tropical soil types. Using the ecosystem model ecosys, we show that water uptake to a depth of 8 m avoids constraints to CO2 and energy exchange from soil drying during five-month dry seasons typical for eastern Amazonian forests. This avoidance in the model was tested with eddy covariance (EC) measurements of CO2 and energy fluxes during 2003 and 2004 over an old-growth forest on an acidic, nutrient-poor oxisol in the Tapajós National Forest (TNF) in Pará, Brazil. Modeled CO2 fixation was strongly constrained by slow phosphorus (P) uptake caused by low soil pH. Daytime CO2 influxes in the model were in close agreement with EC measurements (R2 > 0.8) during both wet and dry seasons. Both modeled and measured fluxes indicated that seasonality of precipitation affected CO2 and energy exchange more through its effect on radiation and air temperature than on soil water content. When aggregated to a yearly scale, modeled and gap-filled EC CO2 fluxes indicated that old-growth forest stands in the TNF remained within 100 g C·m-2·yr -1 of C neutrality in the absence of major disturbance. Annual C transformations in ecosys were further corroborated by extensive biometric measurements taken in the TNF and elsewhere in the Amazon basin, which also indicated that old-growth forests were either small C sources or small C sinks. Long-term model runs suggested that rain forests could be substantial C sinks for several decades while regenerating after stand-replacing disturbances, but would gradually decline toward C neutrality thereafter. The time course of net ecosystem productivity (NEP) in the model depended upon annual rates of herbivory and tree mortality, which were based on site observations as affected by weather (e.g., El Niño Southern Oscillation [ENSO] events). This dependence suggests that rain forest NEP is strongly controlled by disturbance as well as by weather. © 2009 by the Ecological Society.
• R., H., Manzi, A. O., Cabral, O. M., Miller, S. D., Goulden, M. L., Saleska, S. R., Coupe, N. R., Wofsy, S. C., Borma, L. S., Artaxo, R., Vourlitis, G., Nogueira, J. S., Cardoso, F. L., Nobre, A. D., Kruijt, B., Freitas, H. C., Randow, C. V., Aguiar, R. G., & Maia, J. F. (2009). Patterns of water and heat flux across a biome gradient from tropical forest to savanna in brazil. Journal of Geophysical Research G: Biogeosciences, 114(1).
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  Abstract: We investigated the seasonal patterns of water vapor and sensible heat flux along a tropical biome gradient from forest to savanna. We analyzed data from a network of flux towers in Brazil that were operated within the Large-Scale Biosphere-Atmosphere Experiment in Amazonia (LBA). These tower sites included tropical humid and semideciduous forest, transitional forest, floodplain (with physiognomies of cerrado), and cerrado sensu stricto. The mean annual sensible heat flux at all sites ranged from 20 to 38 Wm-2, and was generally reduced in the wet season and increased in the late dry season, coincident with seasonal variations of net radiation and soil moisture. The sites were easily divisible into two functional groups based on the seasonality of evaporation: tropical forest and savanna. At sites with an annual precipitation above 1900 mm and a dry season length less than 4 months (Manaus, Santarém and Rondonia), evaporation rates increased in the dry season, coincident with increased radiation. Evaporation rates were as high as 4.0 mm d-1 in these evergreen or semidecidous forests. In contrast, ecosystems with precipitation less than 1700 mm and a longer dry season (Mato Grosso, Tocantins and São Paulo) showed clear evidence of reduced evaporation in the dry season. Evaporation rates were as low as 2.5 mm d-1 in the transitional forests and 1 mm d-1 in the cerrado. The controls on evapotranspiration seasonality changed along the biome gradient, with evaporative demand (especially net radiation) playing a more important role in the wetter forests, and soil moisture playing a more important role in the drier savannah sites. Copyright 2009 by the American Geophysical Union.
• Gu, L., Falge, E., Boden, T., Baldocchi, D., Black, T., Saleska, ., Suni, T., Verma, S., Vesala, T., Wofsy, S., & Xu, L. (2008). Objective threshold determination for nighttime eddy flux filtering. AGRICULTURAL AND FOREST METEOROLOGY, 128(3-4), 179-197.
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  We recommend an automated statistical method (Moving Point Test, or MPT) to determine the friction velocity (u(*)) thresholds in nighttime eddy flux filtering. Our intention is to make the determination of the u* thresholds objective and reproducible and to keep flux treatment consistent over time and across sites. In developing the MPT method, we recognize that both ecosystem respiration and u* exhibit diurnal and seasonal cycles and there are potential correlative changes between them, which must be removed before u* can be used as a filter criterion. MPT uses an iterative approach to simultaneously determine a valid temperature response function, which is used to normalize nighttime flux measurements, and identify u* thresholds based on the normalized fluxes. Tests show that MPT works well for a variety of scenarios and vegetation types. We also recommend that in order to increase the reliability of nighttime flux filters, a detailed measurement of mean CO2 concentration profiles need to be employed to calculate canopy storage changes accurately. Preferably, multiple profiles at different locations within the nighttime flux footprint should be used so that volume-averaged storage changes can be made. In addition, efforts should be made to minimize measurement gaps in summer nights as much as possible because of the short-time duration and frequent calm conditions, which greatly limit the amount of reliable data. We emphasize that the MPT method is not meant to be a final solution to the nighttime flux issue. Continuous theoretical and experimental researches are still needed to overcome the challenges in measuring nighttime fluxes accurately. (C) 2004 Elsevier B.V. All rights reserved.
• Huete, A. R., Restrepo-Coupe, N., Ratana, P., Didan, K., Saleska, S. R., Ichii, K., Panuthai, S., & Gamo, M. (2008). Multiple site tower flux and remote sensing comparisons of tropical forest dynamics in Monsoon Asia. AGRICULTURAL AND FOREST METEOROLOGY, 148(5), 748-760.
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  The spatial and temporal dynamics of tropical forest functioning are poorly understood, partly attributed to a weak seasonality and high tree species diversity at the landscape scale. Recent neotropical rainforest studies with local tower flux measurements have revealed strong seasonal carbon fluxes that follow the availability of sunlight in intact forests, while in areas of forest disturbance, carbon fluxes more closely tracked seasonal water availability. These studies also showed a strong seasonal correspondence of satellite measures of greenness, using the Enhanced Vegetation index (E-VI) with ecosystem carbon fluxes in both intact and disturbed forests, which may enable larger scale extension of tower flux measurements.
• Huete, A. R., Restrepo-Coupe, N., Ratana, P., Didan, K., Saleska, S. R., Ichii, K., Panuthai, S., & Gamo, M. (2008). Multiple site tower flux and remote sensing comparisons of tropical forest dynamics in Monsoon Asia. Agricultural and Forest Meteorology, 148(5), 748-760.
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  Abstract: The spatial and temporal dynamics of tropical forest functioning are poorly understood, partly attributed to a weak seasonality and high tree species diversity at the landscape scale. Recent neotropical rainforest studies with local tower flux measurements have revealed strong seasonal carbon fluxes that follow the availability of sunlight in intact forests, while in areas of forest disturbance, carbon fluxes more closely tracked seasonal water availability. These studies also showed a strong seasonal correspondence of satellite measures of greenness, using the Enhanced Vegetation Index (EVI) with ecosystem carbon fluxes in both intact and disturbed forests, which may enable larger scale extension of tower flux measurements. In this study, we investigated the seasonal patterns and relationships of local site tower flux measures of gross primary productivity (Pg) with independent Moderate Resolution Imaging Spectroradiometer (MODIS) satellite greenness measures across three Monsoon Asia tropical forest types, encompassing drought-deciduous, dry evergreen, and humid evergreen secondary tropical forests. In contrast to neotropical forests, the tropical forests of Monsoon Asia are more extensively degraded and heterogeneous due to intense land use pressures, and therefore, may exhibit unique seasonal patterns of ecosystem fluxes that are more likely water-limited and drought-susceptible. Our results show significant phenologic variability and response to moisture and light controls across the three tropical forest sites and at the regional scale. The drier tropical forests were primarily water-limited, while the wet evergreen secondary forest showed a slight positive trend with light availability. Satellite EVI greenness observations were generally synchronized and linearly related with seasonal and inter-annual tower flux Pg measurements at the multiple sites and provided better opportunities for tower extension of carbon fluxes than other satellite products, such as the MODIS Pg product. Satellite EVI-derived Pg images revealed strong seasonal variations in photosynthetic activity throughout the Monsoon Asia tropical region. © 2008 Elsevier B.V. All rights reserved.
• Hutyra, L. R., Munger, J. W., Hammond-Pyle, E., Saleska, S. R., Restrepo-Coupe, N., Daube, B. C., B., P., & Wofsy, S. C. (2008). Resolving systematic errors in estimates of net ecosystem exchange of CO₂ and ecosystem respiration in a tropical forest biome. Agricultural and Forest Meteorology, 148(8-9), 1266-1279.
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  Abstract: The controls on uptake and release of CO2 by tropical rainforests, and the responses to a changing climate, are major uncertainties in global climate change models. Eddy-covariance measurements potentially provide detailed data on CO2 exchange and responses to the environment in these forests, but accurate estimates of the net ecosystem exchange of CO2 (NEE) and ecosystem respiration (Reco) require careful analysis of data representativity, treatment of data gaps, and correction for systematic errors. This study uses the comprehensive data from our study site in an old-growth tropical rainforest near Santarem, Brazil, to examine the biases in NEE and Reco potentially associated with the two most important sources of systematic error in Eddy-covariance data: lost nighttime flux and missing canopy storage measurements. We present multiple estimates for the net carbon balance and Reco at our site, including the conventional "u* filter", a detailed bottom-up budget for respiration, estimates by similarity with 222Rn, and an independent estimate of respiration by extrapolation of daytime Eddy flux data to zero light. Eddy-covariance measurements between 2002 and 2006 showed a mean net ecosystem carbon loss of 0.25 ± 0.04 μmol m-2 s-1, with a mean respiration rate of 8.60 ± 0.11 μmol m-2 s-1 at our site. We found that lost nocturnal flux can potentially introduce significant bias into these results. We develop robust approaches to correct for these biases, showing that, where appropriate, a site-specific u* threshold can be used to avoid systematic bias in estimates of carbon exchange. Because of the presence of gaps in the data and the day-night asymmetry between storage and turbulence, inclusion of canopy storage is essential to accurate assessments of NEE. We found that short-term measurements of storage may be adequate to accurately model storage for use in obtaining ecosystem carbon balance, at sites where storage is not routinely measured. The analytical framework utilized in this study can be applied to other Eddy-covariance sites to help correct and validate measurements of the carbon cycle and its components. © 2008 Elsevier B.V. All rights reserved.
• Hutyra, L. R., Munger, J. W., Saleska, S. R., Gottlieb, E., Daube, B. C., Dunn, A. L., Amaral, D. F., B., P., & Wofsy, S. C. (2007). Seasonal controls on the exchange of carbon and water in an Amazonian rain forest. Journal of Geophysical Research G: Biogeosciences, 112(3).
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  Abstract: The long-term resilience of Amazonian forests, to climate changes and the fate of their large stores of organic carbon depend on the ecosystem response to climate and weather. This study presents 4 years of eddy covariance data for CO2 and water fluxes in an evergreen, old-growth tropical rain forest examining the forest's response to seasonal variations and to short-term weather anomalies. Photosynthetic efficiency declined late in the wet season, before appreciable leaf litter fall, and increased after new leaf production midway through the dry season. Rates of evapotranspiration were inelastic and did not depend on dry season precipitation. However, ecosystem respiration was inhibited by moisture, limitations on heterotrophic respiration during the dry season. The annual carbon balance for this ecosystem was very close to neutral, with mean net loss of 890 ± 220 kg C ha-1 yr-1, and a range of -221 ± 453 (C uptake) to +2677 ± 488 (C loss) kg C ha-1 yr-1 over 4 years. The trend from large net carbon release in 2002 towards net carbon uptake in 2005 implies recovery from prior disturbance. The annual carbon balance was sensitive to weather anomalies, particularly the timing of the dry-to-wet season transition, reflecting modulation of light inputs and respiration processes. Canopy carbon uptake rates were largely controlled by phenology and light with virtually no indication of seasonal water limitation during the 5-month dry season, indicating ample supplies of plant-available-water and ecosystem adaptation for maximum light utilization. Copyright 2007 by the American Geophysical Union.
• Saleska, S. R., Didan, K., Huete, A. R., & R., H. (2007). Amazon forests green-up during 2005 drought. Science, 318(5850), 612-.
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  PMID: 17885095;
• Harte, J., Saleska, S., & Shih, T. (2006). Shifts in plant dominance control carbon-cycle responses to experimental warming and widespread drought. Environmental Research Letters, 1(1).
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  Abstract: Global climate change is predicted to increase the intensity and frequency of future drought, which in turn may be expected to induce a range of biogeochemical climate feedbacks. A combination of model simulations and observational studies of a recent wide-scale drought, suggested that the drought induced substantial terrestrial ecosystem carbon loss, but hypothesized mechanisms could not be evaluated via comparison to a control. Here, we investigated carbon-cycle responses to climate changes by combining results from a controlled 15-year ecosystem warming experiment in montane grassland with observational data from before and during the recent drought. We found that both experimental warming and real-world drought induced substantial soil carbon loss in our study system, and that the same mechanism, a drying-induced shift in plant species composition and an associated decline in community productivity, provides a common explanation for these declines in soil carbon. © IOP Publishing Ltd.
• Huete, A. R., Didan, K., Shimabukuro, Y. E., Ratana, P., Saleska, S. R., Hutyra, L. R., Yang, W., Nemani, R. R., & Myneni, R. (2006). Amazon rainforests green-up with sunlight in dry season. Geophysical Research Letters, 33(6).
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  Abstract: Metabolism and phenology of Amazon rainforests significantly influence global dynamics of climate, carbon and water, but remain poorly understood. We analyzed Amazon vegetation phenology at multiple scales with Moderate Resolution Imaging Spectroradiometer (MODIS) satellite measurements from 2000 to 2005. MODIS Enhanced Vegetation Index (EVI, an index of canopy photosynthetic capacity) increased by 25% with sunlight during the dry season across Amazon forests, opposite to ecosystem model predictions that water limitation should cause dry season declines in forest canopy photosynthesis. In contrast to intact forests, areas converted to pasture showed dry-season declines in EVI-derived photosynthetic capacity, presumably because removal of deep-rooted forest trees reduced access to deep soil water. Local canopy photosynthesis measured from eddy flux towers in both a rainforest and forest conversion site confirm our interpretation of satellite data, and suggest that basin-wide carbon fluxes can be constrained by integrating remote sensing and local flux measurements. Copyright 2006 by the American Geophysical Union.
• Liu, W. H., Bryant, D. M., Hutyra, L. R., Saleska, S. R., Hammond-Pyle, E., Curran, D., & Wofsy, S. C. (2006). Woody debris contribution to the carbon budget of selectively logged and maturing mid-latitude forests. Oecologia, 148(1), 108-117.
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  PMID: 16463056;Abstract: Woody debris (WD) is an important component of forest C budgets, both as a C reservoir and source of CO2 to the atmosphere. We used an infrared gas analyzer and closed dynamic chamber to measure CO2 efflux from downed coarse WD (CWD; diameter≥7.5 cm) and fine WD (FWD; 7.5 cm > diameter≥2 cm) to assess respiration in a selectively logged forest and a maturing forest (control site) in the northeastern USA. We developed two linear regression models to predict WD respiration: one based on WD temperature, moisture, and size (R2 = 0.57), and the other on decay class and air temperature (R2 = 0.32). WD respiration (0.28±0.09 Mg C ha-1 year-1) contributed only ≈2% of total ecosystem respiration (12.3±0.7 Mg C ha-1 year-1, 1999-2003), but net C flux from CWD accounted for up to 30% of net ecosystem exchange in the maturing forest. C flux from CWD on the logged site increased modestly, from 0.61±0.29 Mg C ha-1 year-1 prior to logging to 0.77±0.23 Mg C ha-1 year-1 after logging, reflecting increased CWD stocks. FWD biomass and associated respiration flux were ≈7 times and ≈5 times greater, respectively, in the logged site than the control site. The net C flux associated with CWD, including inputs and respiratory outputs, was 0.35±0.19 Mg C ha-1 year-1 (net C sink) in the control site and -0.30±0.30 Mg C ha-1 year-1 (net C source) in the logged site. We infer that accumulation of WD may represent a small net C sink in maturing northern hardwood forests. Disturbance, such as selective logging, can enlarge the WD pool, increasing the net C flux from the WD pool to the atmosphere and potentially causing it to become a net C source. © Springer-Verlag 2006.
• Saleska, S. R., Shorter, J. H., Herndon, S., Jiménez, R., McManus, J. B., Munger, J. W., Nelson, D. D., & Zahniser, M. S. (2006). What are the instrumentation requirements for measuring the isotopic composition of net ecosystem exchange of CO₂ using eddy covariance methods?. Isotopes in Environmental and Health Studies, 42(2), 115-133.
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  PMID: 16707314;Abstract: Better quantification of isotope ratios of atmosphere-ecosystem exchange of CO2 could substantially improve our ability to probe underlying physiological and ecological mechanisms controlling ecosystem carbon exchange, but the ability to make long-term continuous measurements of isotope ratios of exchange fluxes has been limited by measurement difficulties. In particular, direct eddy covariance methods have not yet been used for measuring the isotopic composition of ecosystem fluxes. In this article, we explore the feasibility of such measurements by (a) proposing a general criterion for judging whether a sensor's performance is sufficient for making such measurements (the criterion is met when the contribution of sensor error to the flux measurement error is comparable to or less than the contribution of meteorological noise inherently associated with turbulence flux measurements); (b) using data-based numerical simulations to quantify the level of sensor precision and stability required to meet this criterion for making direct eddy covariance measurements of the 13C/12C ratio of CO2 fluxes above a specific ecosystem (a mid-latitude temperate forest in central Massachusetts, USA); (c) testing whether the performance of a new sensor - a prototype pulsed quantum cascade laser (QCL) based isotope-ratio absorption spectrometer (and plausible improvements thereon) - is sufficient for meeting the criterion in this ecosystem. We found that the error contribution from a prototype sensor (∼0.2‰, 1 SD of 10s integrations) to total isoflux measurement error was comparable to (1.5 to 2×) the irreducible 'meteorological' noise inherently associated with turbulent flux measurements above this ecosystem (daytime measurement error SD of ∼60% of flux versus meteorological noise of 30-40% for instantaneous half-hour fluxes). Our analysis also shows that plausible instrument improvements (increase of sensor precision to ∼0.1‰, 1 SD of 10s integrations, and increased sensor stability during the half-hour needed to integrate eddy covariance measurements) should decrease the contribution of sensor error to the point where it is less than the contribution from meteorological noise. This suggests that new sensors using QCL-based isotope ratio absorption spectroscopy should make continuous long-term observations of the isotopic composition of CO2 fluxes via eddy covariance methods feasible. © 2006 Taylor & Francis.
• Turner, D. P., Ritts, W. D., Cohen, W. B., Gower, S. T., Running, S. W., Zhao, M., Costa, M. H., Kirschbaum, A. A., Ham, J. M., Saleska, S. R., & Ahl, D. E. (2006). Evaluation of MODIS NPP and GPP products across multiple biomes. Remote Sensing of Environment, 102(3-4), 282-292.
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  Abstract: Estimates of daily gross primary production (GPP) and annual net primary production (NPP) at the 1 km spatial resolution are now produced operationally for the global terrestrial surface using imagery from the MODIS (Moderate Resolution Imaging Spectroradiometer) sensor. Ecosystem-level measurements of GPP at eddy covariance flux towers and plot-level measurements of NPP over the surrounding landscape offer opportunities for validating the MODIS NPP and GPP products, but these flux measurements must be scaled over areas on the order of 25 km2 to make effective comparisons to the MODIS products. Here, we report results for such comparisons at 9 sites varying widely in biome type and land use. The sites included arctic tundra, boreal forest, temperate hardwood forest, temperate conifer forest, tropical rain forest, tallgrass prairie, desert grassland, and cropland. The ground-based NPP and GPP surfaces were generated by application of the Biome-BGC carbon cycle process model in a spatially-distributed mode. Model inputs of land cover and leaf area index were derived from Landsat data. The MODIS NPP and GPP products showed no overall bias. They tended to be overestimates at low productivity sites - often because of artificially high values of MODIS FPAR (fraction of photosynthetically active radiation absorbed by the canopy), a critical input to the MODIS GPP algorithm. In contrast, the MODIS products tended to be underestimates in high productivity sites - often a function of relatively low values for vegetation light use efficiency in the MODIS GPP algorithm. A global network of sites where both NPP and GPP are measured and scaled over the local landscape is needed to more comprehensively validate the MODIS NPP and GPP products and to potentially calibrate the MODIS NPP/GPP algorithm parameters. © 2006 Elsevier Inc. All rights reserved.
• Engel, K. H., & Saleska, S. R. (2005). Subglobal regulation of the global commons: The case of climate change. Ecology Law Quarterly, 32(2), 183-233.
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  Abstract: In this Article, the authors challenge the conventional wisdom in the legal, economics, and policy literature that unilateral (as opposed to collective) action by individual countries to restrain despoliation of the global commons is presumptively irrational. The conventional view flows from Garrett Hardin's classic "Tragedy of the Commons" analysis, in which commons preservation, though collectively desirable, is economically irrational when undertaken by individuals, hence the tragedy. Motivated by the unexpected actions of many individual nations and states to address climate change (a classic global commons problem) even in the absence of an unambiguous global framework, the authors show that the market imperfections that characterize some global commons problems, including those of climate change, can diverge from those underpinning the standard "Tragedy of the Commons." The authors argue that this divergence makes room for significant rational unilateral action towards commons preservation, and that this has been underappreciated by many scholars who instinctively disparage unilateral action. In place of the conventional wisdom, the authors suggest that short of the ideal "full glass" of optimal collective action, there exists a "glass half full" of suboptimal unilateral action by larger subglobal governments that is better than no regulation (and hence no benefits) at all, and, indeed, the evidence shows that some larger subglobal governments, the United States in particular, should actually be doing more to address climate change. Furthermore, action by both large and small subglobal governments may function as a mechanism by which individual governments can help trigger the implementation of the preferred solution of an international framework for collective action. Copyright © 2005 by the Regents of the University of California.
• Hutyra, L. R., Munger, J. W., Nobre, C. A., Saleska, S. R., Vieira, S. A., & Wofsy, S. C. (2005). Climatic variability and vegetation vulnerability in Amazǒnia. Geophysical Research Letters, 32(24), 1-4.
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  Abstract: Models of climate change predict close coupling between increases in aridity and conversion of Amazonian forests to savanna. Here we assess the vulnerability and resilience of Amazonian vegetation to climate change by analyzing observed climate-vegetation relationships using climate data, observed vegetation distributions, and evapotranspiration rates inferred from eddy flux data. We found that drought frequency is an excellent predictor of the forest-savanna boundary, indicating the key role of extreme climatic events for inducing vegetation change, and highlighting particularly vulnerable regions of Amazônia. Copyright 2005 by the American Geophysical Union.
• Lianhong, G. u., Falge, E. M., Boden, T., Baldocchi, D. D., Black, T. A., Saleska, S. R., Suni, T., Verma, S. B., Vesala, T., Wofsy, S. C., & Liukang, X. u. (2005). Objective threshold determination for nighttime eddy flux filtering. Agricultural and Forest Meteorology, 128(3-4), 179-197.
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  Abstract: We recommend an automated statistical method (Moving Point Test, or MPT) to determine the friction velocity (u*) thresholds in nighttime eddy flux filtering. Our intention is to make the determination of the u* thresholds objective and reproducible and to keep flux treatment consistent over time and across sites. In developing the MPT method, we recognize that both ecosystem respiration and u* exhibit diurnal and seasonal cycles and there are potential correlative changes between them, which must be removed before u* can be used as a filter criterion. MPT uses an iterative approach to simultaneously determine a valid temperature response function, which is used to normalize nighttime flux measurements, and identify u* thresholds based on the normalized fluxes. Tests show that MPT works well for a variety of scenarios and vegetation types. We also recommend that in order to increase the reliability of nighttime flux filters, a detailed measurement of mean CO 2 concentration profiles need to be employed to calculate canopy storage changes accurately. Preferably, multiple profiles at different locations within the nighttime flux footprint should be used so that volume-averaged storage changes can be made. In addition, efforts should be made to minimize measurement gaps in summer nights as much as possible because of the short-time duration and frequent calm conditions, which greatly limit the amount of reliable data. We emphasize that the MPT method is not meant to be a final solution to the nighttime flux issue. Continuous theoretical and experimental researches are still needed to overcome the challenges in measuring nighttime fluxes accurately. © 2004 Elsevier B.V. All rights reserved.
• McManus, J. B., Nelson, D. D., Shorter, J. H., Jimenez, R., Herndon, S., Saleska, S., & Zahniser, M. (2005). A high precision pulsed quantum cascade laser spectrometer for measurements of stable isotopes of carbon dioxide. Journal of Modern Optics, 52(16), 2309-2321.
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  Abstract: We describe a prototype instrument using a Peltier cooled quantum cascade laser for precise measurement of stable carbon ( 13 C/ 12 C) isotopologue ratios in atmospheric CO 2 . Using novel optics and signal processing techniques in a compact instrument, we are able to detect the difference between sample and reference with a precision of 0.1‰ (2 standard error of mean of 11 samples) in 10min of analysis time. The standard deviation of 0.18‰ for individual 30s measurements shows that this prototype instrument already approaches the best reported literature values using continuous wave lead alloy tunable diode lasers. The application of pulsed near room-temperature quantum cascade lasers to this demanding problem opens the possibility of field worthy rapid response isotopic instrumentation and attests to the maturity of these lasers as spectroscopic sources.
• Wehr, R., Munger, J. W., Nelson, D. D., McManus, J. B., Zahniser, M. S., Wofsy, S. C., & Saleska, S. R. (2005). Long-term eddy covariance measurements of the isotopic composition of the ecosystem-atmosphere exchange of CO2 in a temperate forest. AGRICULTURAL AND FOREST METEOROLOGY, 181, 69-84.
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  Measurements of the isotopic composition of the net ecosystem-atmosphere exchange of CO2 (NEE) have been desired as a means to probe ecosystem carbon cycling and in particular to partition NEE into gross ecosystem photosynthesis and respiration. Several attempts at such measurements have combined eddy covariance (EC) measurements of the total net CO2 flux with flask measurements of the isotopic composition of CO2 in ambient air - an indirect method that has never been validated. Direct EC measurements of the isotopic composition of NEE (i.e. of the net exchanges of (CO2)-C-12-O-16, (CO2)-C-13-O-16, and (OCO)-O-18-C-12-O-16) have been made only twice, in short-term (2-month and 1-month) campaigns.
• Xiao, X., Zhang, Q., Saleska, S., Hutyra, L., Camargo, P. D., Wofsy, S., Frolking, S., Boles, S., Keller, M., & III, B. M. (2005). Satellite-based modeling of gross primary production in a seasonally moist tropical evergreen forest. Remote Sensing of Environment, 94(1), 105-122.
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  Abstract: A CO 2 eddy flux tower study has recently reported that an old-growth stand of seasonally moist tropical evergreen forest in Santarém, Brazil, maintained high gross primary production (GPP) during the dry seasons [Saleska, S. R., Miller, S. D., Matross, D. M., Goulden, M. L., Wofsy, S. C., da Rocha, H. R., de Camargo, P. B., Crill, P., Daube, B. C., de Freitas, H. C., Hutyra, L., Keller, M., Kirchhoff, V., Menton, M., Munger, J. W., Pyle, E. H., Rice, A. H., & Silva, H. (2003). Carbon in amazon forests: Unexpected seasonal fluxes and disturbance-induced losses. Science, 302, 1554-1557]. It was proposed that seasonally moist tropical evergreen forests have evolved two adaptive mechanisms in an environment with strong seasonal variations of light and water: deep roots system for access to water in deep soils and leaf phenology for access to light. Identifying tropical forests with these adaptive mechanisms could substantially improve our capacity of modeling the seasonal dynamics of carbon and water fluxes in the tropical zone. In this paper, we have analyzed multi-year satellite images from the VEGETATION (VGT) sensor onboard the SPOT-4 satellite (4/1998-12/2002) and the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard the Terra satellite (2000-2003). We reported temporal analyses of vegetation indices and simulations of the satellite-based vegetation photosynthesis model (VPM). The Enhanced Vegetation Index (EVI) identified subtle changes in the seasonal dynamics of leaf phenology (leaf emergence, leaf aging and leaf fall) in the forest, as suggested by the leaf litterfall data. The land surface water index (LSWI) indicated that the forest experienced no water stress in the dry seasons of 1998-2002. The VPM model, which uses EVI, LSWI and site-specific climate data (air temperature and photosynthetically active radiation, PAR) for 2001-2002, predicted high GPP in the late dry seasons, consistent with observed high evapotranspiration and estimated GPP from the CO 2 eddy flux tower. © 2004 Elsevier Inc. All rights reserved.
• Dunne, J. A., Saleska, S. R., Fischer, M. L., & Harte, J. (2004). Integrating experimental and gradient methods in ecological climate change research. Ecology, 85(4), 904-916.
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  Abstract: Field-based research on the responses of ecosystems to anthropogenic climate change has primarily used either natural gradient or experimental methods. Taken separately, each approach faces methodological, spatial, and temporal limitations that potentially constrain the generality of results and predictions. Integration of the two approaches within a single study can overcome some of those limitations and provide ways to distinguish among consistent, dynamic, and context-dependent ecosystem responses to global warming. A simple conceptual model and two case studies that focus on climate change impacts on flowering phenology and carbon cycling in a subalpine meadow ecosystem illustrate the utility of this type of integration.
• Martens, C. S., Shay, T. J., Mendlovitz, H. P., Matross, D. M., Saleska, S. R., Wofsy, S. C., Woodward, W. S., Menton, M. C., M.S., J., Crill, P. M., L.L., O., & Lima, R. L. (2004). Radon fluxes in tropical forest ecosystems of Brazilian Amazonia: Night-time CO₂ net ecosystem exchange derived from radon and eddy covariance methods. Global Change Biology, 10(5), 618-629.
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  Abstract: Radon-222 (Rn-222) is used as a transport tracer of forest canopy-atmosphere CO2 exchange in an old-growth, tropical rain forest site near km 67 of the Tapajós National Forest, Pará, Brazil. Initial results, from month-long periods at the end of the wet season (June-July) and the end of the dry season (November-December) in 2001, demonstrate the potential of new Rn measurement instruments and methods to quantify mass transport processes between forest canopies and the atmosphere. Gas exchange rates yield mean canopy air residence times ranging from minutes during turbulent daytime hours to greater than 12h during calm nights. Rn is an effective tracer for net ecosystem exchange of CO2 (CO2 NEE) during calm, night-time hours when eddy covariance-based NEE measurements are less certain because of low atmospheric turbulence. Rn-derived night-time CO2 NEE (9.00 ± 0.99 μmol m-2 s-1 in the wet season, 6.39 ± 0.59 in the dry season) was significantly higher than raw uncorrected, eddy covariance-derived CO2 NEE (5.96 ± 0.51 wet season, 5.57 ± 0.53 dry season), but agrees with corrected eddy covariance results (8.65 ± 1.07 wet season, 6.56 ± 0.73 dry season) derived by filtering out lower NEE values obtained during calm periods using independent meteorological criteria. The Rn CO2 results suggest that uncorrected eddy covariance values underestimate night-time CO2 loss at this site. If generalizable to other sites, these observations indicate that previous reports of strong net CO2 uptake in Amazonian terra firme forest may be overestimated. © 2004 Blackwell Publishing Ltd.
• Rice, A. H., Pyle, E. H., Saleska, S. R., Hutyra, L., Palace, M., Keller, M., B., P., Portilho, K., Marques, D. F., & Wofsy, S. C. (2004). Carbon balance and vegetation dynamics in an old-growth Amazonian forest. Ecological Applications, 14(4 SUPPL.), S55-S71.
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  Abstract: Amazon forests could be globally significant sinks or sources for atmospheric carbon dioxide, but carbon balance of these forests remains poorly quantified. We surveyed 19.75 ha along four 1-km transects of well-drained old-growth upland forest in the Tapajós National Forest near Santarém, Pará, Brazil (2°51' S, 54°58' W) in order to assess carbon pool sizes, fluxes, and climatic controls on carbon balance. In 1999 there were, on average, 470 live trees per hectare with diameter at breast height (dbh) ≥ 10 cm. The mean (and 95% CI) aboveground live biomass was 143.7 ± 5.4 Mg C/ha, with an additional 48.0 ± 5.2 Mg C/ha of coarse woody debris (CWD). The increase of live wood biomass after two years was 1.40 ± 0.62 Mg C·ha-1·yr-1, the net result of growth (3.18 ± 0.20 Mg C·ha-1·yr -1 from mean bole increment of 0.36 cm/yr), recruitment of new trees (0.63 ± 0.09 Mg C·ha-1·yr-1, reflecting a notably high stem recruitment rate of 4.8 ± 0.9%), and mortality (-2.41 ± 0.53 Mg C·ha-1·yr -1 from stem death of 1.7% yr-1). The gain in live wood biomass was exceeded by respiration losses from CWD, resulting in an overall estimated net loss from total aboveground biomass of 1.9 ± 1.0 Mg C·ha-1·yr-1. The presence of large CWD pools, high recruitment rate, and net accumulation of small-tree biomass, suggest that a period of high mortality preceded the initiation of this study, possibly triggered by the strong El Niño Southern Oscillation events of the 1990s. Transfer of carbon between live and dead biomass pools appears to have led to substantial increases in the pool of CWD, causing the observed net carbon release. The data show that biometric studies of tropical forests neglecting CWD are unlikely to accurately determine carbon balance. Fur-thermore, the hypothesized sequestration flux from CO2 fertilization (
• Saleska, S. R., Miller, S. D., Matross, D. M., Goulden, M. L., Wofsy, S. C., R., H., B., P., Crill, P., Daube, B. C., C., H., Hutyra, L., Keller, M., Kirchhoff, V., Menton, M., Munger, J. W., Pyle, E. H., Rice, A. H., & Silva, H. (2003). Carbon in Amazon Forests: Unexpected Seasonal Fluxes and Disturbance-Induced Losses. Science, 302(5650), 1554-1557.
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  PMID: 14645845;Abstract: The net ecosystem exchange of carbon dioxide was measured by eddy covariance methods for 3 years in two old-growth forest sites near Santarém, Brazil. Carbon was lost in the wet season and gained in the dry season, which was opposite to the seasonal cycles of both tree growth and model predictions. The 3-year average carbon loss was 1.3 (confidence interval: 0.0 to 2.0) megagrams of carbon per hectare per year. Biometric observations confirmed the net loss but imply that it is a transient effect of recent disturbance superimposed on long-term balance. Given that episodic disturbances are characteristic of old-growth forests, it is Likely that carbon sequestration is lower than has been inferred from recent eddy covariance studies at undisturbed sites.
• Malhi, Y., Phillips, O. L., Lloyd, J., Baker, T., Wright, J., Almeida, S., Arroyo, L., Frederiksen, T., Grace, J., Higuchi, N., Killeen, T., Laurance, W. F., Leaño, C., Lewis, S., Meir, P., Monteagudo, A., Neill, D., Vargas, P. N., Panfil, S. N., , Patiño, S., et al. (2002). An international network to monitor the structure, composition and dynamics of Amazonian forests (RAINFOR). Journal of Vegetation Science, 13(3), 439-450.
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  Abstract: The Amazon basin is likely to be increasingly affected by environmental changes: higher temperatures, changes in precipitation, CO2 fertilization and habitat fragmentation. To examine the important ecological and biogeochemical consequences of these changes, we are developing an international network, RAINFOR, which aims to monitor forest biomass and dynamics across Amazonia in a co-ordinated fashion in order to understand their relationship to soil and climate. The network will focus on sample plots established by independent researchers, some providing data extending back several decades. We will also conduct rapid transect studies of poorly monitored regions. Field expeditions analysed local soil and plant properties in the first phase (2001-2002). Initial results suggest that the network has the potential to reveal much information on the continental-scale relations between forest and environment. The network will also serve as a forum for discussion between researchers, with the aim of standardising sampling techniques and methodologies that will enable Amazonian forests to be monitored in a coherent manner in the coming decades.
• Saleska, S. R., Shaw, M. R., Fischer, M. L., Dunne, J. A., Still, C. J., Holman, M. L., & Harte, J. (2002). Plant community composition mediates both large transient decline and predicted long-term recovery of soil carbon under climate warming. Global Biogeochemical Cycles, 16(4), 3-1.
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  Abstract: We integrated two methods, experimental heating and observations across natural climate gradients, to elucidate both short- and long-term climatic controls on ecosystem carbon storage and to investigate carbon-cycle feedbacks to climate in montane meadows. A 10-year heating experiment warmed and dried heated plot soils and substantially decreased (by ∼200 ± 150 g C m-2) the amount of carbon stored in soil organic matter, a positive feedback to warming. In situ CO2 flux measurements, laboratory soil incubations, and a heating-induced shift in vegetation community composition from high- to low-productivity species indicate that a decline in community productivity and resultant decrease in soil inputs from plant litter caused most of the soil carbon decrease. An alternative widely hypothesized mechanism for soil carbon decrease under warming is stimulation of soil respiration, but we observed no increase in seasonally integrated soil respiration in our experiment (soil drying inhibited microbial decomposition even as soil warming stimulated it). To extend our analysis from the short-term transient response represented by the heating experiment to the presumed long-term approximate steady state represented by natural climate gradients, we tested a hypothesized relation between vegetation community composition (which controls both litter input rate and average litter quality) and soil carbon along the climate gradient. The gradient analysis implies that the experimentally induced decline in soil carbon is transient and will eventually reverse as lower quality litter inputs from the increasingly dominant low-productivity species reduce soil respiration losses. This work shows that ecological processes can control both short- and long-term responses to climate change, confirming some model-based predictions about the importance of vegetation shifts, but challenging the widely held hypothesis that the effect of temperature change on respiration will dominate soil carbon changes.
• Barford, C. C., Wofsy, S. C., Munger, J. W., Goulden, M. L., Pyle, H. E., Urbanski, S. P., Hutyra, L., Saleska, S. R., Fitzjarrald, D., & Moore, K. (2001). Factors controlling long- and short-term sequestration of atmospheric CO₂ in a mid-latitude forest. Science, 294(5547), 1688-1691.
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  PMID: 11721047;Abstract: Net uptake of carbon dioxide (CO2) measured by eddy covariance in a 60- to 80-year-old forest averaged 2.0 ± 0.4 megagrams of carbon per hectare per year during 1993 to 2000, with interannual variations exceeding 50%. Biometry indicated storage of 1.6 ± 0.4 megagrams of carbon per hectare per year over 8 years, 60% in live biomass and the balance in coarse woody debris and soils, confirming eddy-covariance results. Weather and seasonal climate (e.g., variations in growing-season length or cloudiness) regulated seasonal and interannual fluctuations of carbon uptake. Legacies of prior disturbance and management, especially stand age and composition, controlled carbon uptake on the decadal time scale, implying that eastern forests could be managed for sequestration of carbon.
• Saleska, S. R., Harte, J., & Torn, M. S. (1999). The effect of experimental ecosystem warming on CO₂ fluxes in a montane meadow. Global Change Biology, 5(2), 125-141.
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  Abstract: Climatic change is predicted to alter rates of soil respiration and assimilation of carbon by plants. Net loss of carbon from ecosystems would form a positive feedback enhancing anthropogenic global warming. We tested the effect of increased heat input, one of the most certain impacts of global warming, on net ecosystem carbon exchange in a Rocky Mountain montane meadow. Overhead heaters were used to increase the radiative heat flux into plots spanning a moisture and vegetation gradient. We measured net whole-ecosystem CO2 fluxes using a closed-path chamber system, relatively nondisturbing bases, and a simple model to compensate for both slow chamber leaks and the CO2 concentration-dependence of photosynthetic uptake, in 1993 and 1994. In 1994, we also measured soil respiration separately. The heating treatment altered the timing and magnitude of net carbon fluxes into the dry zone of the plots in 1993 (reducing uptake by ~100 g carbon m-2), but had an undetectable effect on carbon fluxes into the moist zone. During a strong drought year (1994), heating altered the timing, but did not significantly alter the cumulative magnitude, of net carbon uptake in the dry zone. Soil respiration measurements showed that when differences were detected in dry zone carbon fluxes, they were caused by changes in carbon input from photosynthesis, not by temperature-driven changes in carbon output from soil respiration. When differences were detected in dry-zone carbon fluxes, they were caused by changes in carbon input from photosynthesis, not by a temperature-driven changes in carbon output from soil respiration. Regression analysis suggested that the reduction in carbon inputs from plants was due to a combination of two soil moisture effects: a direct physiological response to decreased soil moisture, and a shift in plant community composition from high-productivity species to low-productivity species that are more drought tolerant. These results partially support predictions that warming may cause net carbon losses from some terrestrial ecosystems. They also suggest, however, that changes in soil moisture caused by global warming may be as important in driving ecosystem response as the direct effects of increased soil temperature.
• Lashof, D. A., DeAngelo, B. J., Saleska, S. R., & Harte, J. (1997). Terrestrial ecosystem feedbacks to global climate change. Annual Review of Energy and the Environment, 22(1), 75-118.
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  Abstract: Anthropogenic greenhouse gases are expected to induce changes in global climate that can alter ecosystems in ways that, in turn, may further affect climate. Such climate-ecosystem interactions can generate either positive or negative feedbacks to the climate system, thereby either enhancing or diminishing the magnitude of global climate change. Important terrestrial feedback mechanisms include CO2 fertilization (negative feedbacks), carbon storage in vegetation and soils (positive and negative feedbacks), vegetation albedo (positive feedbacks), and peatland methane emissions (positive and negative feedbacks). While the processes involved are complex, not readily quantifiable, and demonstrate both positive and negative feedback potential, we conclude that the combined effect of the feedback mechanisms reviewed here will likely amplify climate change relative to current projections that have not yet adequately incorporated these mechanisms.

Proceedings Publications

• Crill, P. M., McCalley, C. K., Hodgkins, S., Wehr, R., Kim, E., Logan, T., Chanton, J., Rich, V. I., Mondav, R., Woodcroft, B., Tyson, G., & Saleska, S. R. (2013, January). Measurements of CH4 fluxes and isotopes reveal changing mechanisms of production and consumption across a thaw gradient in an arctic wetland. In Geophysical Research Abstracts: EGU General Assembly 2013, 15, 8928.

Presentations

• Crill, P., McCalley, C., Hodkins, S., Wehr, R., Kim, E., Logan, T., Chanton, J., Mondav, R., Rich, V. I., Woodcroft, B., Tyson, G., & Saleska, S. R. (2013, April). Presentation co-author: Measurements of CH4 fluxes and isotopes reveal changing mechanisms of production and consumption across a thaw gradient in an arctic wetland. European Geophysical Union General Meeting. Vienna, Austria.: uropean Geophysical Union.
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  Measurements of CH4 fluxes and isotopes reveal changing mechanisms of production and consumption across a thaw gradient in an arctic wetlandAuthors: Crill, Patrick; McCalley, Carmody; Hodgkins, Suzanne; Wehr, Richard; Kim, Eun-Hae; Logan, Tyler; Chanton, Jeff; Rich, Virginia; Mondav, Rhiannon; Woodcroft, Ben; Tyson, Gene; Saleska, ScottEGU General Assembly 2013, held 7-12 April, 2013 in Vienna, Austria, id. EGU2013-8928Publication Date: 04/2013
• Rich, V. I., McCalley, C., Woodcroft, B., Hodgkins, S., Kim, E., Mondav, R., Wehr, R., Logan, T., Jones, R., Li, C., Frolking, S., Crill, P., Chanton, J., Tyson, G., & Saleska, S. R. (2013, April). Presentation (lead author): A systems approach to understanding methane emissions from thawing permafrost. American Society for Microbiology, Southwest Regional Mtg. Tucson, AZ: American Society for Microbiology, Southwest Division.
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  Talk, American Society for Microbiology, Southwest Regional Mtg, Tucson, AZ, 4/13/13. V Rich, C McCalley, B Woodcroft, S Hodgkins, E-H Kim, R Mondav, R Wehr, T Logan, R Jones, C Li, S Frolking, P Crill, J Chanton, G Tyson and S Saleska. A systems approach to understanding methane emissions from thawing permafrost.
• Rich, V. I., McCalley, C., Woodcroft, B., Kim, E., Hodgkins, S., Tfaily, M., Wehr, R., Logan, T., Jones, R., Mondav, R., Hurst, G., Verberkmoes, N., Li, C., Frolking, S., Crill, P., Chanton, J., Saleska, S. R., & Tyson, G. (2013, December). Invited Talk: A systems approach to understanding subarctic critical zone changes in a warming climate. American Geophysical Union Fall Meeting. San Francisco, CA: American Geophysical Union.
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  Invited talk: A systems approach to understanding subarctic critical zone changes in a warming climate. Virginia Rich, Carmody McCalley, Ben Woodcroft, Eun-Hae Kim, Suzanne Hodgkins, Malak Tfailly, Richard Wehr, Tyler Logan, Robert Jones, Rhiannon Mondav, Greg Hurst, Nathan Verberkmoes, Changsheng Li, Steve Frolking, Patrick Crill, Jeff Chanton, Scott Saleska and Gene Tyson
• Saleska, S. R., McCalley, C. K., Woodcroft, B. J., Hodgkins, S. B., Mondav, R., Wehr, R., Kim, E., Crill, P., Rich, V. I., Chanton, J. P., & Tyson, G. W. (2013, December). Presentation co-author: Shifting microbial communities dynamically mediate the effect of permafrost thaw on atmospheric methane isotopes. American Geophysical Union Fall Meeting. San Francisco, CA: American Geophysical Union.
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  Shifting microbial communities dynamically mediate the effect of permafrost thaw on atmospheric methane isotopes. Scott R. Saleska, Carmody K McCalley, Ben J Woodcroft, Suzanne B Hodgkins, Rhiannon Mondav, Richard Wehr, Eun-Hae Kim, Patrick M Crill, Virginia I Rich, Jeffrey P Chanton, Gene W Tyson

Poster Presentations

• Hodgkins, S. B., Tfaily, M. M., McCalley, C. K., Logan, T., Crill, P. M., Saleska, S. R., Rich, V. I., & Chanton, J. (2013, December). Poster presentation co-author: Changes in Soil Chemistry Help Drive Higher Greenhouse Gas Emissions from Thawing Permafrost. American Geophysical Union Fall Meeting. San Francisco, CA: American Geophysical Union.
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  Poster: Changes in Soil Chemistry Help Drive Higher Greenhouse Gas Emissions from Thawing Permafrost. Suzanne B. Hodgkins; Malak M. Tfaily; Carmody K. McCalley; Tyler Logan; Patrick M. Crill; Scott R. Saleska; Virginia I. Rich; Jeffrey Chanton
• Hodgkins, S., McCalley, C., Tfaily, M., Wehr, R., Logan, T., Tyson, G., Rich, V. I., Crill, P., Saleska, S. R., & Chanton, J. (2013, February). Poster presentation co-author: Examining the controls on CH4 dynamics along a permafrost thaw gradient: carbon isotopes and organic matter structure. Department of Energy Genomic Sciences Meeting. Washington, DC: Department of Energy.
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  Poster, DOE Genomic Science Mtg. Washington DC 2/24-27/13. S Hodgkins, C McCalley, M Tfaily, R Wehr, T Logan, G Tyson, V Rich, P Crill, S Saleska, and J Chanton. "Examining the controls on CH4 dynamics along a permafrost thaw gradient: carbon isotopes and organic matter structure".
• Kim, E., Woodcroft, B. J., McCalley, C. K., Hodgkins, S., Jones, R. M., Wehr, R. A., Logan, T., Varner, R., Chanton, J. P., Crill, P. M., Verberkmoes, N. C., Saleska, S. R., Tyson, G. W., & Rich, V. I. (2013, May). Poster Presentation senior author: Microbial carbon cycling across a natural permafrost thaw gradient, via biogeochemistry and metaproteomics-inferred microbial activity. American Society for Microbiology Annual General Meeting. Denver, CO: American Society for Microbiology.
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  Poster, American Society of Microbiology Meeting, Denver, May 2013. E-H Kim, BJ Woodcroft, CK McCalley, S Hodgkins, RM Jones, RA Wehr, T Logan, R Varner, JP Chanton, PM Crill, NC Verberkmoes, SR Saleska, GW Tyson, VI Rich. Microbial carbon cycling across a natural permafrost thaw gradient, via biogeochemistry and metaproteomics-inferred microbial activity
• Rich, V. I., Kim, E., Woodcroft, B. J., Mondav, R., McCalley, C. K., Jones, R. M., Hodgkins, S., Wehr, R. A., Logan, T., Chanton, J. P., Crill, P. M., Verberkmoes, N. C., Saleska, S. R., & Tyson, G. W. (2013, February). Poster Presentation first author: Examining the controls on CH4 dynamics along a permafrost thaw gradient: microbial community composition and expression. Department of Energy Genomic Sciences Meeting. Washington, DC: Department of Energy.
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  Poster, DOE Genomic Science Mtg. Washington DC 2/24-27/13. VI Rich, E-H Kim, BJ Woodcroft, R Mondav, CK McCalley, RM Jones, S Hodgkins, RA Wehr, T Logan, JP Chanton, PM Crill, NC VerBerkmoes, SR Saleska, GW Tyson. Examining the controls on CH4 dynamics along a permafrost thaw gradient: microbial community composition and expression