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1.  Spatial and Seasonal CH4 Flux in the Littoral Zone of Miyun Reservoir near Beijing: The Effects of Water Level and Its Fluctuation 
PLoS ONE  2014;9(4):e94275.
Wetlands, and especially their littoral zones, are considered to be CH4 emissions hotspots. The recent creation of reservoirs has caused a rapid increase in the area of the world’s littoral zones. To investigate the effects of water depth and water level fluctuation on CH4 fluxes, and how these are coupled with vegetation and nutrients, we used static closed chamber and gas chromatography techniques to measure CH4 fluxes in the littoral zone of a large reservoir near Beijing, China, from November 2011 to October 2012. We found that CH4 flux decreased significantly along a transect from open water to dry land, from 3.1 mg m−2 h−1 at the deep water site to approximately 1.3 mg m−2 h−1 at the shallow water site, and less than 0.01 mg m−2 h−1 in the non-flooded area. Water level influenced CH4 flux by affecting soil properties including soil redox potential, soil carbon and nitrogen, and bulk density. The largest emission of all was from the seasonally flooded site after a flooding event (up to 21.1 mg m−2 h−1), which may have been caused by vegetation decomposition. Submerged sites had greater emissions, while the driest site had lower emissions. Immediately after the monthly measurements had been made, we removed the aboveground vegetation to enable an assessment of the gas transportation per unit of biomass. Removal of biomass decreased emissions by up to 53%. These results indicated the dominant effect of water depth on CH4 flux through effects of soil conditions, plant species composition and distribution. This study suggests that temporally flooded wetlands, including littoral zones, contribute significantly to the global CH4 burden. However, the current challenge is to capture their spatial extent and temporal variation in the fluxes.
doi:10.1371/journal.pone.0094275
PMCID: PMC3978027  PMID: 24710279
2.  Role of Megafauna and Frozen Soil in the Atmospheric CH4 Dynamics 
PLoS ONE  2014;9(4):e93331.
Modern wetlands are the world’s strongest methane source. But what was the role of this source in the past? An analysis of global 14C data for basal peat combined with modelling of wetland succession allowed us to reconstruct the dynamics of global wetland methane emission through time. These data show that the rise of atmospheric methane concentrations during the Pleistocene-Holocene transition was not connected with wetland expansion, but rather started substantially later, only 9 thousand years ago. Additionally, wetland expansion took place against the background of a decline in atmospheric methane concentration. The isotopic composition of methane varies according to source. Owing to ice sheet drilling programs past dynamics of atmospheric methane isotopic composition is now known. For example over the course of Pleistocene-Holocene transition atmospheric methane became depleted in the deuterium isotope, which indicated that the rise in methane concentrations was not connected with activation of the deuterium-rich gas clathrates. Modelling of the budget of the atmospheric methane and its isotopic composition allowed us to reconstruct the dynamics of all main methane sources. For the late Pleistocene, the largest methane source was megaherbivores, whose total biomass is estimated to have exceeded that of present-day humans and domestic animals. This corresponds with our independent estimates of herbivore density on the pastures of the late Pleistocene based on herbivore skeleton density in the permafrost. During deglaciation, the largest methane emissions originated from degrading frozen soils of the mammoth steppe biome. Methane from this source is unique, as it is depleted of all isotopes. We estimated that over the entire course of deglaciation (15,000 to 6,000 year before present), soils of the mammoth steppe released 300–550 Pg (1015 g) of methane. From current study we conclude that the Late Quaternary Extinction significantly affected the global methane cycle.
doi:10.1371/journal.pone.0093331
PMCID: PMC3973675  PMID: 24695117
3.  Landscape Heterogeneity–Biodiversity Relationship: Effect of Range Size 
PLoS ONE  2014;9(3):e93359.
The importance of landscape heterogeneity to biodiversity may depend on the size of the geographic range of species, which in turn can reflect species traits (such as habitat generalization) and the effects of historical and contemporary land covers. We used nationwide bird survey data from Japan, where heterogeneous landscapes predominate, to test the hypothesis that wide-ranging species are positively associated with landscape heterogeneity in terms of species richness and abundance, whereas narrow-ranging species are positively associated with landscape homogeneity in the form of either open or forest habitats. We used simultaneous autoregressive models to explore the effects of climate, evapotranspiration, and landscape heterogeneity on the richness and abundance of breeding land-bird species. The richness of wide-ranging species and the total species richness were highest in heterogeneous landscapes, where many wide-ranging species showed the highest abundance. In contrast, the richness of narrow-ranging species was not highest in heterogeneous landscapes; most of those species were abundant in either open or forest landscapes. Moreover, in open landscapes, narrow-ranging species increased their species richness with decreasing temperature. These results indicate that heterogeneous landscapes are associated with rich bird diversity but that most narrow-ranging species prefer homogeneous landscapes—particularly open habitats in colder regions, where grasslands have historically predominated. There is a need to reassess the generality of the heterogeneity-biodiversity relationship, with attention to the characteristics of species assemblages determined by environments at large spatiotemporal scales.
doi:10.1371/journal.pone.0093359
PMCID: PMC3968173  PMID: 24675969
4.  Short-Term Effect of Nutrient Availability and Rainfall Distribution on Biomass Production and Leaf Nutrient Content of Savanna Tree Species 
PLoS ONE  2014;9(3):e92619.
Changes in land use may lead to increased soil nutrient levels in many ecosystems (e.g. due to intensification of agricultural fertilizer use). Plant species differ widely in their response to differences in soil nutrients, and for savannas it is uncertain how this nutrient enrichment will affect plant community dynamics. We set up a large controlled short-term experiment in a semi-arid savanna to test how water supply (even water supply vs. natural rainfall) and nutrient availability (no fertilisation vs. fertilisation) affects seedlings’ above-ground biomass production and leaf-nutrient concentrations (N, P and K) of broad-leafed and fine-leafed tree species. Contrary to expectations, neither changes in water supply nor changes in soil nutrient level affected biomass production of the studied species. By contrast, leaf-nutrient concentration did change significantly. Under regular water supply, soil nutrient addition increased the leaf phosphorus concentration of both fine-leafed and broad-leafed species. However, under uneven water supply, leaf nitrogen and phosphorus concentration declined with soil nutrient supply, this effect being more accentuated in broad-leafed species. Leaf potassium concentration of broad-leafed species was lower when growing under constant water supply, especially when no NPK fertilizer was applied. We found that changes in environmental factors can affect leaf quality, indicating a potential interactive effect between land-use changes and environmental changes on savanna vegetation: under more uneven rainfall patterns within the growing season, leaf quality of tree seedlings for a number of species can change as a response to changes in nutrient levels, even if overall plant biomass does not change. Such changes might affect herbivore pressure on trees and thus savanna plant community dynamics. Although longer term experiments would be essential to test such potential effects of eutrophication via changes in leaf nutrient concentration, our findings provide important insights that can help guide management plans that aim to preserve savanna biodiversity.
doi:10.1371/journal.pone.0092619
PMCID: PMC3965441  PMID: 24667837
5.  How Does Tree Density Affect Water Loss of Peatlands? A Mesocosm Experiment 
PLoS ONE  2014;9(3):e91748.
Raised bogs have accumulated more atmospheric carbon than any other terrestrial ecosystem on Earth. Climate-induced expansion of trees and shrubs may turn these ecosystems from net carbon sinks into sources when associated with reduced water tables. Increasing water loss through tree evapotranspiration could potentially deepen water tables, thus stimulating peat decomposition and carbon release. Bridging the gap between modelling and field studies, we conducted a three-year mesocosm experiment subjecting natural bog vegetation to three birch tree densities, and studied the changes in subsurface temperature, water balance components, leaf area index and vegetation composition. We found the deepest water table in mesocosms with low tree density. Mesocosms with high tree density remained wettest (i.e. highest water tables) whereas the control treatment without trees had intermediate water tables. These differences are attributed mostly to differences in evapotranspiration. Although our mesocosm results cannot be directly scaled up to ecosystem level, the systematic effect of tree density suggests that as bogs become colonized by trees, the effect of trees on ecosystem water loss changes with time, with tree transpiration effects of drying becoming increasingly offset by shading effects during the later phases of tree encroachment. These density-dependent effects of trees on water loss have important implications for the structure and functioning of peatbogs.
doi:10.1371/journal.pone.0091748
PMCID: PMC3954773  PMID: 24632565
6.  Ion Uptake in Tall Fescue as Affected by Carbonate, Chloride, and Sulfate Salinity 
PLoS ONE  2014;9(3):e91908.
Turfgrass nutrient uptake may be differentially affected by different salts. The objective of this study was to compare nutrient uptake in tall fescue (Festuca arundinacea Schreb.) as affected by carbonate, chloride, and sulfate under iso-osmotic, iso-Na+ strength conditions. ‘Tar Heel II’ and ‘Wolfpack’ cultivars were subjected to NaCl, Na2CO3, Na2SO4, CaCl2, NaCl+ CaCl2, Na2CO3+ CaCl2, and Na2SO4+ CaCl2, in the range of 0 to 225 mM. There was no cultivar difference regarding K, Na, Mg, and Mn content in shoots. ‘Tar Heel II’ had higher shoot Ca content than ‘Wolfpack’, which were 6.9 and 5.7 g kg−1, respectively. In general, K+/Na+ ratio decreased with increasing salt concentrations, which reached <1 at about 87.5 mM in Na2CO3 treatment. All salt treatments decreased Mg content in shoot tissues, especially in Na2CO3 and treatments containing CaCl2. Both Ca and Mg content in shoot were higher in the NaCl treatment than the Na2SO4 and Na2CO3 treatments. All salt treatments except Na2CO3 had higher Mn content in shoots compared to the control. In conclusion, nutrient uptake was differently affected by carbonate, chloride, and sulfate which are different in pH, electrical conductivity (EC), and osmotic potential at the same concentration. Adding Ca to the sodium salts increased Ca content and balanced K+/Na+ in shoots, but did not increase Mg content, which was below sufficient level. Maintaining Mg content in shoots under salinity stress was recommended. The physiological impact of elevated Mn content in shoot under salinity stress requires further study.
doi:10.1371/journal.pone.0091908
PMCID: PMC3953601  PMID: 24626173
7.  Carbon Sequestration and Fertility after Centennial Time Scale Incorporation of Charcoal into Soil 
PLoS ONE  2014;9(3):e91114.
The addition of pyrogenic carbon (C) in the soil is considered a potential strategy to achieve direct C sequestration and potential reduction of non-CO2 greenhouse gas emissions. In this paper, we investigated the long term effects of charcoal addition on C sequestration and soil physico-chemical properties by studying a series of abandoned charcoal hearths in the Eastern Alps of Italy established in the XIX century. This natural setting can be seen as an analogue of a deliberate experiment with replications. Carbon sequestration was assessed indirectly by comparing the amount of pyrogenic C present in the hearths (23.3±4.7 kg C m−2) with the estimated amount of charcoal that was left on the soil after the carbonization (29.3±5.1 kg C m−2). After taking into account uncertainty associated with parameters’ estimation, we were able to conclude that 80±21% of the C originally added to the soil via charcoal can still be found there and that charcoal has an overall Mean Residence Time of 650±139 years, thus supporting the view that charcoal incorporation is an effective way to sequester atmospheric CO2. We also observed an overall change in the physical properties (hydrophobicity and bulk density) of charcoal hearth soils and an accumulation of nutrients compared to the adjacent soil without charcoal. We caution, however, that our site-specific results should not be generalized without further study.
doi:10.1371/journal.pone.0091114
PMCID: PMC3948733  PMID: 24614647
8.  Use of Spatial Analysis to Test Hypotheses on Plant Recruitment in a Hyper-Arid Ecosystem 
PLoS ONE  2014;9(3):e91184.
Mounds originating from wind-blown sediment accumulation beneath vegetation (nebkhas) often indicate land degradation in dry areas. Thus far, most nebkha research has focused on individual plants. Here, we aimed to explore population-scale processes (up to scales of about 100 m) that might explain an observed nebkha landscape pattern. We mapped the Rhazya stricta Decne. population in a 3 ha study site in a hyper-arid region of Saudi Arabia. We compared the spatial patterns of five different cohorts (age classes) of observed nebkha host plants to those expected under several hypothesized drivers of recruitment and intraspecific interaction. We found that all R. stricta cohorts had a limited fractional vegetation cover and established in large-scale clusters. This clustering weakened with cohort age, possibly indicating merging of neighboring vegetation patches. Different cohort clusters did not spatially overlap in most cases, indicating that recruitment patterns changed position over time. Strong indications were found that the main drivers underlying R. stricta spatial configurations were allogenic (i.e. not driven by vegetation) and dynamic. Most likely these drivers were aeolian-driven sand movement or human disturbance which forced offspring recruitment in spatially dynamic clusters. Competition and facilitation were likely active on the field site too, but apparently had a limited effect on the overall landscape structure.
doi:10.1371/journal.pone.0091184
PMCID: PMC3948780  PMID: 24614307
9.  Winter Soil CO2 Flux from Different Mid-Latitude Sites from Middle Taihang Mountain in North China 
PLoS ONE  2014;9(3):e91589.
Winter soil respiration is a very important component of the annual soil carbon flux in some ecosystems. We hypothesized that, with all other factors being equal, shorter winter SR result in reduced contribution to annual soil C flux. In this study, the contribution of winter soil respiration to annual soil respiration was measured for three sites (grassland: dominated by Artemisia sacrorum, Bothriochloa ischaemum and Themeda japonica; shrubland: dominated by Vitex negundo var. heterophylla; plantation: dominated by Populus tomatosa) in a mountainous area of north China. Diurnal and intra-annual soil CO2 flux patterns were consistent among different sites, with the maximum soil respiration rates at 12∶00 or 14∶00, and in July or August. The lowest respiration rates were seen in February. Mean soil respiration rates ranged from 0.26 to 0.45 µmol m−2 s−1 in the winter (December to February), and between 2.38 to 3.16 µmol m−2 s−1 during the growing season (May-September). The winter soil carbon flux was 24.6 to 42.8 g C m−2, which contributed 4.8 to 7.1% of the annual soil carbon flux. Based on exponential functions, soil temperature explained 73.8 to 91.8% of the within year variability in soil respiration rates. The Q10 values of SR against ST at 10 cm ranged from 3.60 to 4.90 among different sites. In addition, the equation between soil respiration and soil temperature for the growing season was used to calculate the “modeled” annual soil carbon flux based on the actual measured soil temperature. The “measured” annual value was significantly higher than the “modeled” annual value. Our results suggest that winter soil respiration plays a significant role in annual soil carbon balance, and should not be neglected when soil ecosystems are assessed as either sinks or sources of atmospheric CO2.
doi:10.1371/journal.pone.0091589
PMCID: PMC3948914  PMID: 24614868
10.  Input-Output Modeling for Urban Energy Consumption in Beijing: Dynamics and Comparison 
PLoS ONE  2014;9(3):e89850.
Input-output analysis has been proven to be a powerful instrument for estimating embodied (direct plus indirect) energy usage through economic sectors. Using 9 economic input-output tables of years 1987, 1990, 1992, 1995, 1997, 2000, 2002, 2005, and 2007, this paper analyzes energy flows for the entire city of Beijing and its 30 economic sectors, respectively. Results show that the embodied energy consumption of Beijing increased from 38.85 million tonnes of coal equivalent (Mtce) to 206.2 Mtce over the past twenty years of rapid urbanization; the share of indirect energy consumption in total energy consumption increased from 48% to 76%, suggesting the transition of Beijing from a production-based and manufacturing-dominated economy to a consumption-based and service-dominated economy. Real estate development has shown to be a major driving factor of the growth in indirect energy consumption. The boom and bust of construction activities have been strongly correlated with the increase and decrease of system-side indirect energy consumption. Traditional heavy industries remain the most energy-intensive sectors in the economy. However, the transportation and service sectors have contributed most to the rapid increase in overall energy consumption. The analyses in this paper demonstrate that a system-wide approach such as that based on input-output model can be a useful tool for robust energy policy making.
doi:10.1371/journal.pone.0089850
PMCID: PMC3940614  PMID: 24595199
11.  Does Animal-Mediated Seed Dispersal Facilitate the Formation of Pinus armandii-Quercus aliena var. acuteserrata Forests? 
PLoS ONE  2014;9(2):e89886.
The Pinus armandii and Quercus aliena var. acuteserrata mixed forest is one of the major forest types in the Qinling Mountains, China. P. armandii is considered to be a pioneer species during succession and it is usually invaded by late successional Q. aliena var. acuteserrata. However, the mechanism that underlies its invasion remains unclear. In the present study, we tracked seed dispersal of P. armandii and Q. aliena var. acuteserrata using coded plastic tags in the western, middle and eastern Qinling Mountains to elucidate the invasion process in the mixed forests. Our results indicated that the seeds of both P. armandii and Q. aliena var. acuteserrata were removed rapidly in the Qinling Mountains, and there were no differences in the seed removal rates between the two species. There were significant differences in rodent seed-eating and caching strategies between the two tree species. For P. armandii, seeds were more likely to be eaten in situ than those of Q. aliena var. acuteserrata in all plots. By contrast, the acorns of Q. aliena var. acuteserrata were less frequently eaten in situ, but more likely to be removed and cached. Q. aliena var. acuteserrata acorns had significantly longer dispersal distances than P. armandii seeds in all plots. Although P. armandii seeds were less likely to be dispersed into the Q. aliena var. acuteserrata stands, over 30% of the released acorns were transported into the P. armandii stands where they established five seedlings. Based on the coupled recruitment patterns of P. armandii and Q. aliena var. acuteserrata, we suggest that the animal-mediated seed dispersal contributes to the formation of Pinus armandii-Quercus aliena var. acuteserrata forests.
doi:10.1371/journal.pone.0089886
PMCID: PMC3938510  PMID: 24587099
12.  An Integrated Framework for Assessing Vulnerability to Climate Change and Developing Adaptation Strategies for Coffee Growing Families in Mesoamerica 
PLoS ONE  2014;9(2):e88463.
The Mesoamerican region is considered to be one of the areas in the world most vulnerable to climate change. We developed a framework for quantifying the vulnerability of the livelihoods of coffee growers in Mesoamerica at regional and local levels and identify adaptation strategies. Following the Intergovernmental Panel on Climate Change (IPCC) concepts, vulnerability was defined as the combination of exposure, sensitivity and adaptive capacity. To quantify exposure, changes in the climatic suitability for coffee and other crops were predicted through niche modelling based on historical climate data and locations of coffee growing areas from Mexico, Guatemala, El Salvador and Nicaragua. Future climate projections were generated from 19 Global Circulation Models. Focus groups were used to identify nine indicators of sensitivity and eleven indicators of adaptive capacity, which were evaluated through semi-structured interviews with 558 coffee producers. Exposure, sensitivity and adaptive capacity were then condensed into an index of vulnerability, and adaptation strategies were identified in participatory workshops. Models predict that all target countries will experience a decrease in climatic suitability for growing Arabica coffee, with highest suitability loss for El Salvador and lowest loss for Mexico. High vulnerability resulted from loss in climatic suitability for coffee production and high sensitivity through variability of yields and out-migration of the work force. This was combined with low adaptation capacity as evidenced by poor post harvest infrastructure and in some cases poor access to credit and low levels of social organization. Nevertheless, the specific contributors to vulnerability varied strongly among countries, municipalities and families making general trends difficult to identify. Flexible strategies for adaption are therefore needed. Families need the support of government and institutions specialized in impacts of climate change and strengthening of farmer organizations to enable the adjustment of adaptation strategies to local needs and conditions.
doi:10.1371/journal.pone.0088463
PMCID: PMC3935832  PMID: 24586328
13.  The Physiological and Biochemical Responses of a Medicinal Plant (Salvia miltiorrhiza L.) to Stress Caused by Various Concentrations of NaCl 
PLoS ONE  2014;9(2):e89624.
Salvia miltiorrhiza, which is commonly known as Danshen, is a traditional Chinese herbal medicine. To illustrate its physiological and biochemical responses to salt stress and to evaluate the feasibility of cultivating this plant in saline coastal soils, a factorial experiment under hydroponic conditions was arranged on the basis of a completely randomised design with three replications. Five salinity treatments (0, 25, 50, 75 and 100 mM NaCl) were employed in this experiment. The results showed that salinity treatments of <100 mM NaCl did not affect the growth of Salvia miltiorrhiza in a morphological sense, but significantly inhibit the accumulation of dry matter. Salinity treatments significantly decreased the Chl-b content but caused a negligible change in the Chl-a content, leading to a conspicuous overall decrease in the T-Chl content. The Na+ content significantly increased with increasing hydroponic salinity but the K+ and Ca2+ contents were reversed, indicating that a high level of external Na+ resulted in a decrease in both K+ and Ca2+ concentrations in the organs of Salvia miltiorrhiza. Salt stress significantly decreased the superoxide dismutase (SOD) activity of Salvia miltiorrhiza leaves in comparison with that of the control. On the contrary, the catalase (CAT) activity in the leaves markedly increased with the increasing salinity of the hydroponic solution. Moreover, the soluble sugar and protein contents in Salvia miltiorrhiza leaves dramatically increased with the increasing salinity of the hydroponic solution. These results suggested that antioxidant enzymes and osmolytes are partially involved in the adaptive response to salt stress in Salvia miltiorrhiza, thereby maintaining better plant growth under saline conditions.
doi:10.1371/journal.pone.0089624
PMCID: PMC3934908  PMID: 24586918
14.  Biophysical Controls on Light Response of Net CO2 Exchange in a Winter Wheat Field in the North China Plain 
PLoS ONE  2014;9(2):e89469.
To investigate the impacts of biophysical factors on light response of net ecosystem exchange (NEE), CO2 flux was measured using the eddy covariance technique in a winter wheat field in the North China Plain from 2003 to 2006. A rectangular hyperbolic function was used to describe NEE light response. Maximum photosynthetic capacity (Pmax) was 46.6±4.0 µmol CO2 m−2 s−1 and initial light use efficiency (α) 0.059±0.006 µmol µmol−1 in April−May, two or three times as high as those in March. Stepwise multiple linear regressions showed that Pmax increased with the increase in leaf area index (LAI), canopy conductance (gc) and air temperature (Ta) but declined with increasing vapor pressure deficit (VPD) (P<0.001). The factors influencing Pmax were sorted as LAI, gc, Ta and VPD. α was proportional to ln(LAI), gc, Ta and VPD (P<0.001). The effects of LAI, gc and Ta on α were larger than that of VPD. When Ta>25°C or VPD>1.1−1.3 kPa, NEE residual increased with the increase in Ta and VPD (P<0.001), indicating that temperature and water stress occurred. When gc was more than 14 mm s−1 in March and May and 26 mm s−1 in April, the NEE residuals decline disappeared, or even turned into an increase in gc (P<0.01), implying shifts from stomatal limitation to non-stomatal limitation on NEE. Although the differences between sunny and cloudy sky conditions were unremarkable for light response parameters, simulated net CO2 uptake under the same radiation intensity averaged 18% higher in cloudy days than in sunny days during the year 2003−2006. It is necessary to include these effects in relevant carbon cycle models to improve our estimation of carbon balance at regional and global scales.
doi:10.1371/journal.pone.0089469
PMCID: PMC3930739  PMID: 24586800
15.  Value Assessment of Ecosystem Services in Nature Reserves in Ningxia, China: A Response to Ecological Restoration 
PLoS ONE  2014;9(2):e89174.
Changes in land use can cause significant changes in the ecosystem structure and process variation of ecosystem services. This study presents a detailed spatial, quantitative assessment of the variation in the value of ecosystem services based on land use change in national nature reserves of the Ningxia autonomous region in China. We used areas of land use types calculated from the remote sensing data and the adjusted value coefficients to assess the value of ecosystem services for the years 2000, 2005, and 2010, analyzing the fluctuations in the valuation of ecosystem services in response to land use change. With increases in the areas of forest land and water bodies, the value of ecosystem services increased from 182.3×107 to 223.8×107 US$ during 2000–2010. Grassland and forest land accounted for 90% of this increase. The values of all ecosystem services increased during this period, especially the value of ecosystem services for biodiversity protection and soil formation and protection. Ecological restoration in the reserves had a positive effect on the value of ecosystem services during 2000–2010.
doi:10.1371/journal.pone.0089174
PMCID: PMC3929645  PMID: 24586571
16.  Application of Organic Amendments to a Coastal Saline Soil in North China: Effects on Soil Physical and Chemical Properties and Tree Growth 
PLoS ONE  2014;9(2):e89185.
The ability of the following four organic amendments to ameliorate saline soil in coastal northern China was investigated from April 2010 to October 2012 in a field experiment: green waste compost (GWC), sedge peat (SP), furfural residue (FR), and a mixture of GWC, SP and FR (1∶1∶1 by volume) (GSF). Compared to a non-amended control (CK), the amendments, which were applied at 4.5 kg organic matter m−3, dramatically promoted plant growth; improved soil structure; increased the cation exchange capacity (CEC), organic carbon, and available nutrients; and reduced the salt content, electrical conductivity (EC), and exchangeable sodium percentage (ESP). At the end of the experiment in soil amended with GSF, bulk density, EC, and ESP had decreased by 11, 87, and 71%, respectively, and total porosity and organic carbon had increased by 25 and 96% respectively, relative to the CK. The GSF treatment resulted in a significantly lower Na++K+ content than the other treatments. CEC and the contents of available N, P, and K were significantly higher in the GSF-treated soil than in the CK and were the highest in all treatments. The FR treatment resulted in the lowest pH value and Ca2+ concentration, which decreased by 8% and 39%, respectively, relative to the CK. Overall, the results indicate that a combination of green waste compost, sedge peat and furfural residue (GSF treatment) has substantial potential for ameliorating saline soils in the coastal areas of northern China, and it works better than each amendment alone. Utilization of GWC and FR can be an alternative organic amendment to substitute the nonrenewable SP in saline soil amelioration.
doi:10.1371/journal.pone.0089185
PMCID: PMC3928440  PMID: 24558486
17.  A Tale of Two “Forests”: Random Forest Machine Learning Aids Tropical Forest Carbon Mapping 
PLoS ONE  2014;9(1):e85993.
Accurate and spatially-explicit maps of tropical forest carbon stocks are needed to implement carbon offset mechanisms such as REDD+ (Reduced Deforestation and Degradation Plus). The Random Forest machine learning algorithm may aid carbon mapping applications using remotely-sensed data. However, Random Forest has never been compared to traditional and potentially more reliable techniques such as regionally stratified sampling and upscaling, and it has rarely been employed with spatial data. Here, we evaluated the performance of Random Forest in upscaling airborne LiDAR (Light Detection and Ranging)-based carbon estimates compared to the stratification approach over a 16-million hectare focal area of the Western Amazon. We considered two runs of Random Forest, both with and without spatial contextual modeling by including—in the latter case—x, and y position directly in the model. In each case, we set aside 8 million hectares (i.e., half of the focal area) for validation; this rigorous test of Random Forest went above and beyond the internal validation normally compiled by the algorithm (i.e., called “out-of-bag”), which proved insufficient for this spatial application. In this heterogeneous region of Northern Peru, the model with spatial context was the best preforming run of Random Forest, and explained 59% of LiDAR-based carbon estimates within the validation area, compared to 37% for stratification or 43% by Random Forest without spatial context. With the 60% improvement in explained variation, RMSE against validation LiDAR samples improved from 33 to 26 Mg C ha−1 when using Random Forest with spatial context. Our results suggest that spatial context should be considered when using Random Forest, and that doing so may result in substantially improved carbon stock modeling for purposes of climate change mitigation.
doi:10.1371/journal.pone.0085993
PMCID: PMC3904849  PMID: 24489686
18.  Dynamics and Sources of Soil Organic C Following Afforestation of Croplands with Poplar in a Semi-Arid Region in Northeast China 
PLoS ONE  2014;9(1):e86640.
Afforestation of former croplands has been proposed as a promising way to mitigate rising atmospheric CO2 concentration in view of the commitment to the Kyoto Protocol. Central to this C sequestration is the dynamics of soil organic C (SOC) storage and stability with the development of afforested plantations. Our previous study showed that SOC storage was not changed after afforestation except for the 0–10 cm layer in a semi-arid region of Keerqin Sandy Lands, northeast China. In this study, soil organic C was further separated into light and heavy fractions using the density fractionation method, and their organic C concentration and 13C signature were analyzed to investigate the turnover of old vs. new SOC in the afforested soils. Surface layer (0–10 cm) soil samples were collected from 14 paired plots of poplar (Populus × xiaozhuanica W. Y. Hsu & Liang) plantations with different stand basal areas (the sum of the cross-sectional area of all live trees in a stand), ranging from 0.2 to 32.6 m2 ha−1, and reference maize (Zea mays L.) croplands at the same sites as our previous study. Soil ΔC stocks (ΔC refers to the difference in SOC content between a poplar plantation and the paired cropland) in bulk soil and light fraction were positively correlated with stand basal area (R2 = 0.48, p<0.01 and R2 = 0.40, p = 0.02, respectively), but not for the heavy fraction. SOCcrop (SOC derived from crops) contents in the light and heavy fractions in poplar plantations were significantly lower as compared with SOC contents in croplands, but tree-derived C in bulk soil, light and heavy fraction pools increased gradually with increasing stand basal area after afforestation. Our study indicated that cropland afforestation could sequester new C derived from trees into surface mineral soil, but did not enhance the stability of SOC due to a fast turnover of SOC in this semi-arid region.
doi:10.1371/journal.pone.0086640
PMCID: PMC3900571  PMID: 24466183
19.  Land-Use History and Contemporary Management Inform an Ecological Reference Model for Longleaf Pine Woodland Understory Plant Communities 
PLoS ONE  2014;9(1):e86604.
Ecological restoration is frequently guided by reference conditions describing a successfully restored ecosystem; however, the causes and magnitude of ecosystem degradation vary, making simple knowledge of reference conditions insufficient for prioritizing and guiding restoration. Ecological reference models provide further guidance by quantifying reference conditions, as well as conditions at degraded states that deviate from reference conditions. Many reference models remain qualitative, however, limiting their utility. We quantified and evaluated a reference model for southeastern U.S. longleaf pine woodland understory plant communities. We used regression trees to classify 232 longleaf pine woodland sites at three locations along the Atlantic coastal plain based on relationships between understory plant community composition, soils (which broadly structure these communities), and factors associated with understory degradation, including fire frequency, agricultural history, and tree basal area. To understand the spatial generality of this model, we classified all sites together and for each of three study locations separately. Both the regional and location-specific models produced quantifiable degradation gradients–i.e., progressive deviation from conditions at 38 reference sites, based on understory species composition, diversity and total cover, litter depth, and other attributes. Regionally, fire suppression was the most important degrading factor, followed by agricultural history, but at individual locations, agricultural history or tree basal area was most important. At one location, the influence of a degrading factor depended on soil attributes. We suggest that our regional model can help prioritize longleaf pine woodland restoration across our study region; however, due to substantial landscape-to-landscape variation, local management decisions should take into account additional factors (e.g., soil attributes). Our study demonstrates the utility of quantifying degraded states and provides a series of hypotheses for future experimental restoration work. More broadly, our work provides a framework for developing and evaluating reference models that incorporate multiple, interactive anthropogenic drivers of ecosystem degradation.
doi:10.1371/journal.pone.0086604
PMCID: PMC3900602  PMID: 24466167
20.  A 50-m Forest Cover Map in Southeast Asia from ALOS/PALSAR and Its Application on Forest Fragmentation Assessment 
PLoS ONE  2014;9(1):e85801.
Southeast Asia experienced higher rates of deforestation than other continents in the 1990s and still was a hotspot of forest change in the 2000s. Biodiversity conservation planning and accurate estimation of forest carbon fluxes and pools need more accurate information about forest area, spatial distribution and fragmentation. However, the recent forest maps of Southeast Asia were generated from optical images at spatial resolutions of several hundreds of meters, and they do not capture well the exceptionally complex and dynamic environments in Southeast Asia. The forest area estimates from those maps vary substantially, ranging from 1.73×106 km2 (GlobCover) to 2.69×106 km2 (MCD12Q1) in 2009; and their uncertainty is constrained by frequent cloud cover and coarse spatial resolution. Recently, cloud-free imagery from the Phased Array Type L-band Synthetic Aperture Radar (PALSAR) onboard the Advanced Land Observing Satellite (ALOS) became available. We used the PALSAR 50-m orthorectified mosaic imagery in 2009 to generate a forest cover map of Southeast Asia at 50-m spatial resolution. The validation, using ground-reference data collected from the Geo-Referenced Field Photo Library and high-resolution images in Google Earth, showed that our forest map has a reasonably high accuracy (producer's accuracy 86% and user's accuracy 93%). The PALSAR-based forest area estimates in 2009 are significantly correlated with those from GlobCover and MCD12Q1 at national and subnational scales but differ in some regions at the pixel scale due to different spatial resolutions, forest definitions, and algorithms. The resultant 50-m forest map was used to quantify forest fragmentation and it revealed substantial details of forest fragmentation. This new 50-m map of tropical forests could serve as a baseline map for forest resource inventory, deforestation monitoring, reducing emissions from deforestation and forest degradation (REDD+) implementation, and biodiversity.
doi:10.1371/journal.pone.0085801
PMCID: PMC3899076  PMID: 24465714
21.  Land Use Compounds Habitat Losses under Projected Climate Change in a Threatened California Ecosystem 
PLoS ONE  2014;9(1):e86487.
Given the rapidly growing human population in mediterranean-climate systems, land use may pose a more immediate threat to biodiversity than climate change this century, yet few studies address the relative future impacts of both drivers. We assess spatial and temporal patterns of projected 21st century land use and climate change on California sage scrub (CSS), a plant association of considerable diversity and threatened status in the mediterranean-climate California Floristic Province. Using a species distribution modeling approach combined with spatially-explicit land use projections, we model habitat loss for 20 dominant shrub species under unlimited and no dispersal scenarios at two time intervals (early and late century) in two ecoregions in California (Central Coast and South Coast). Overall, projected climate change impacts were highly variable across CSS species and heavily dependent on dispersal assumptions. Projected anthropogenic land use drove greater relative habitat losses compared to projected climate change in many species. This pattern was only significant under assumptions of unlimited dispersal, however, where considerable climate-driven habitat gains offset some concurrent climate-driven habitat losses. Additionally, some of the habitat gained with projected climate change overlapped with projected land use. Most species showed potential northern habitat expansion and southern habitat contraction due to projected climate change, resulting in sharply contrasting patterns of impact between Central and South Coast Ecoregions. In the Central Coast, dispersal could play an important role moderating losses from both climate change and land use. In contrast, high geographic overlap in habitat losses driven by projected climate change and projected land use in the South Coast underscores the potential for compounding negative impacts of both drivers. Limiting habitat conversion may be a broadly beneficial strategy under climate change. We emphasize the importance of addressing both drivers in conservation and resource management planning.
doi:10.1371/journal.pone.0086487
PMCID: PMC3897708  PMID: 24466116
22.  Spatial Variation in Soil Properties among North American Ecosystems and Guidelines for Sampling Designs 
PLoS ONE  2014;9(1):e83216.
Soils are highly variable at many spatial scales, which makes designing studies to accurately estimate the mean value of soil properties across space challenging. The spatial correlation structure is critical to develop robust sampling strategies (e.g., sample size and sample spacing). Current guidelines for designing studies recommend conducting preliminary investigation(s) to characterize this structure, but are rarely followed and sampling designs are often defined by logistics rather than quantitative considerations. The spatial variability of soils was assessed across ∼1 ha at 60 sites. Sites were chosen to represent key US ecosystems as part of a scaling strategy deployed by the National Ecological Observatory Network. We measured soil temperature (Ts) and water content (SWC) because these properties mediate biological/biogeochemical processes below- and above-ground, and quantified spatial variability using semivariograms to estimate spatial correlation. We developed quantitative guidelines to inform sample size and sample spacing for future soil studies, e.g., 20 samples were sufficient to measure Ts to within 10% of the mean with 90% confidence at every temperate and sub-tropical site during the growing season, whereas an order of magnitude more samples were needed to meet this accuracy at some high-latitude sites. SWC was significantly more variable than Ts at most sites, resulting in at least 10× more SWC samples needed to meet the same accuracy requirement. Previous studies investigated the relationship between the mean and variability (i.e., sill) of SWC across space at individual sites across time and have often (but not always) observed the variance or standard deviation peaking at intermediate values of SWC and decreasing at low and high SWC. Finally, we quantified how far apart samples must be spaced to be statistically independent. Semivariance structures from 10 of the 12-dominant soil orders across the US were estimated, advancing our continental-scale understanding of soil behavior.
doi:10.1371/journal.pone.0083216
PMCID: PMC3894938  PMID: 24465377
23.  Plasticity in Dendroclimatic Response across the Distribution Range of Aleppo Pine (Pinus halepensis) 
PLoS ONE  2013;8(12):e83550.
We investigated the variability of the climate-growth relationship of Aleppo pine across its distribution range in the Mediterranean Basin. We constructed a network of tree-ring index chronologies from 63 sites across the region. Correlation function analysis identified the relationships of tree-ring index to climate factors for each site. We also estimated the dominant climatic gradients of the region using principal component analysis of monthly, seasonal, and annual mean temperature and total precipitation from 1,068 climatic gridpoints. Variation in ring width index was primarily related to precipitation and secondarily to temperature. However, we found that the dendroclimatic relationship depended on the position of the site along the climatic gradient. In the southern part of the distribution range, where temperature was generally higher and precipitation lower than the regional average, reduced growth was also associated with warm and dry conditions. In the northern part, where the average temperature was lower and the precipitation more abundant than the regional average, reduced growth was associated with cool conditions. Thus, our study highlights the substantial plasticity of Aleppo pine in response to different climatic conditions. These results do not resolve the source of response variability as being due to either genetic variation in provenance, to phenotypic plasticity, or a combination of factors. However, as current growth responses to inter-annual climate variability vary spatially across existing climate gradients, future climate-growth relationships will also likely be determined by differential adaptation and/or acclimation responses to spatial climatic variation. The contribution of local adaptation and/or phenotypic plasticity across populations to the persistence of species under global warming could be decisive for prediction of climate change impacts across populations. In this sense, a more complex forest dynamics modeling approach that includes the contribution of genetic variation and phenotypic plasticity can improve the reliability of the ecological inferences derived from the climate-growth relationships.
doi:10.1371/journal.pone.0083550
PMCID: PMC3877073  PMID: 24391786
24.  Relationships between Nutrient-Related Plant Traits and Combinations of Soil N and P Fertility Measures 
PLoS ONE  2013;8(12):e83735.
Soil fertility and nutrient-related plant functional traits are in general only moderately related, hindering the progress in trait-based prediction models of vegetation patterns. Although the relationships may have been obscured by suboptimal choices in how soil fertility is expressed, there has never been a systematic investigation into the suitability of fertility measures. This study, therefore, examined the effect of different soil fertility measures on the strength of fertility–trait relationships in 134 natural plant communities. In particular, for eight plot-mean traits we examined (1) whether different elements (N or P) have contrasting or shared influences, (2) which timescale of fertility measures (e.g. mineralization rates for one or five years) has better predictive power, and (3) if integrated fertility measures explain trait variation better than individual fertility measures. Soil N and P had large mutual effects on leaf nutrient concentrations, whereas they had element-specific effects on traits related to species composition (e.g. Grime's CSR strategy). The timescale of fertility measures only had a minor impact on fertility–trait relationships. Two integrated fertility measures (one reflecting overall fertility, another relative availability of soil N and P) were related significantly to most plant traits, but were not better in explaining trait variation than individual fertility measures. Using all fertility measures together, between-site variations of plant traits were explained only moderately for some traits (e.g. 33% for leaf N concentrations) but largely for others (e.g. 66% for whole-canopy P concentration). The moderate relationships were probably due to complex regulation mechanisms of fertility on traits, rather than to a wrong choice of fertility measures. We identified both mutual (i.e. shared) and divergent (i.e. element-specific and stoichiometric) effects of soil N and P on traits, implying the importance of explicitly considering the roles of different elements to properly interpret fertility–trait relationships.
doi:10.1371/journal.pone.0083735
PMCID: PMC3877083  PMID: 24391815
25.  Spatial Distribution of Soil Organic Carbon and Total Nitrogen Based on GIS and Geostatistics in a Small Watershed in a Hilly Area of Northern China 
PLoS ONE  2013;8(12):e83592.
The spatial variability of soil organic carbon (SOC) and total nitrogen (STN) levels is important in both global carbon-nitrogen cycle and climate change research. There has been little research on the spatial distribution of SOC and STN at the watershed scale based on geographic information systems (GIS) and geostatistics. Ninety-seven soil samples taken at depths of 0–20 cm were collected during October 2010 and 2011 from the Matiyu small watershed (4.2 km2) of a hilly area in Shandong Province, northern China. The impacts of different land use types, elevation, vegetation coverage and other factors on SOC and STN spatial distributions were examined using GIS and a geostatistical method, regression-kriging. The results show that the concentration variations of SOC and STN in the Matiyu small watershed were moderate variation based on the mean, median, minimum and maximum, and the coefficients of variation (CV). Residual values of SOC and STN had moderate spatial autocorrelations, and the Nugget/Sill were 0.2% and 0.1%, respectively. Distribution maps of regression-kriging revealed that both SOC and STN concentrations in the Matiyu watershed decreased from southeast to northwest. This result was similar to the watershed DEM trend and significantly correlated with land use type, elevation and aspect. SOC and STN predictions with the regression-kriging method were more accurate than those obtained using ordinary kriging. This research indicates that geostatistical characteristics of SOC and STN concentrations in the watershed were closely related to both land-use type and spatial topographic structure and that regression-kriging is suitable for investigating the spatial distributions of SOC and STN in the complex topography of the watershed.
doi:10.1371/journal.pone.0083592
PMCID: PMC3877373  PMID: 24391791

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