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1.  Evaluating the Relationship between Competition and Productivity within a Native Grassland 
PLoS ONE  2012;7(8):e43703.
Ideas about how plant competition varies with productivity are rooted in classic theories that predict either increasing (Grime) or invariant (Tilman) competition with increasing productivity. Both predictions have received experimental support, although a decade-old meta-analysis supports neither. Attempts to reconcile the conflicting predictions and evidence include: expanding the theory to include other conditions (e.g. stress gradient hypothesis), development of indices to differentiate either the ‘intensity’ or ‘importance’ of competition, a focus on resource supply and demand, and explicit recognition that both growth and survival may exhibit different relationships with productivity. To determine which of these theories accurately predict how competition varies with productivity within a native grassland site, we estimated competitive intensity and relative competitive importance using 22 species across the range of productivity naturally occurring within that site. Plant performance was measured as survival and size with and without neighbours and the local environment was quantified according to variability in standing crop, gross water supply, and net water supply. On average, neighbours weakly facilitated seedling survival, but strongly reduced seedling growth. For both seedling survival and growth, relative competitive importance and competitive intensity declined with some measure of productivity; neighbour effects on survival declined with standing crop, while effects on growth declined with gross water supply. These results add to the growing evidence that plant-plant interactions vary among life history components with different life history components contingent upon separate environmental factors. Although the range of productivity measured in this study was not large, our results do not support the theories of Grime or Tilman. However, our results are consistent with the meta-analysis and parts of other theories, although no single theory is capable of explaining the entirety of these results. This suggests that, at least in moderately productive grasslands, new theory needs to be developed.
doi:10.1371/journal.pone.0043703
PMCID: PMC3424220  PMID: 22928021
2.  Biomass Allocation Patterns across China’s Terrestrial Biomes 
PLoS ONE  2014;9(4):e93566.
Root to shoot ratio (RS) is commonly used to describe the biomass allocation between below- and aboveground parts of plants. Determining the key factors influencing RS and interpreting the relationship between RS and environmental factors is important for biological and ecological research. In this study, we compiled 2088 pairs of root and shoot biomass data across China’s terrestrial biomes to examine variations in the RS and its responses to biotic and abiotic factors including vegetation type, soil texture, climatic variables, and stand age. The median value of RS (RSm) for grasslands, shrublands, and forests was 6.0, 0.73, and 0.23, respectively. The range of RS was considerably wide for each vegetation type. RS values for all three major vegetation types were found to be significantly correlated to mean annual precipitation (MAP) and potential water deficit index (PWDI). Mean annual temperature (MAT) also significantly affect the RS for forests and grasslands. Soil texture and forest origin altered the response of RS to climatic factors as well. An allometric formula could be used to well quantify the relationship between aboveground and belowground biomass, although each vegetation type had its own inherent allometric relationship.
doi:10.1371/journal.pone.0093566
PMCID: PMC3977935  PMID: 24710503
3.  Sensitivity of Soil Respiration to Variability in Soil Moisture and Temperature in a Humid Tropical Forest 
PLoS ONE  2013;8(12):e80965.
Precipitation and temperature are important drivers of soil respiration. The role of moisture and temperature are generally explored at seasonal or inter-annual timescales; however, significant variability also occurs on hourly to daily time-scales. We used small (1.54 m2), throughfall exclusion shelters to evaluate the role soil moisture and temperature as temporal controls on soil CO2 efflux from a humid tropical forest in Puerto Rico. We measured hourly soil CO2 efflux, temperature and moisture in control and exclusion plots (n = 6) for 6-months. The variance of each time series was analyzed using orthonormal wavelet transformation and Haar-wavelet coherence. We found strong negative coherence between soil moisture and soil respiration in control plots corresponding to a two-day periodicity. Across all plots, there was a significant parabolic relationship between soil moisture and soil CO2 efflux with peak soil respiration occurring at volumetric soil moisture of approximately 0.375 m3/m3. We additionally found a weak positive coherence between CO2 and temperature at longer time-scales and a significant positive relationship between soil temperature and CO2 efflux when the analysis was limited to the control plots. The coherence between CO2 and both temperature and soil moisture were reduced in exclusion plots. The reduced CO2 response to temperature in exclusion plots suggests that the positive effect of temperature on CO2 is constrained by soil moisture availability.
doi:10.1371/journal.pone.0080965
PMCID: PMC3846571  PMID: 24312508
4.  Field Evidence of Colonisation by Holm Oak, at the Northern Margin of Its Distribution Range, during the Anthropocene Period 
PLoS ONE  2013;8(11):e80443.
A major unknown in the context of current climate change is the extent to which populations of slowly migrating species, such as trees, will track shifting climates. Niche modelling generally predicts substantial northward shifts of suitable habitats. There is therefore an urgent need for field-based forest observations to corroborate these extensive model simulations. We used forest inventory data providing presence/absence information from just over a century (1880–2010) for a Mediterranean species (Quercus ilex) in forests located at the northern edge of its distribution. The main goals of the study were (i) to investigate whether this species has actually spread into new areas during the Anthropocene period and (ii) to provide a direct estimation of tree migration rate. We show that Q. ilex has colonised substantial new areas over the last century. However, the maximum rate of colonisation by this species (22 to 57 m/year) was much slower than predicted by the models and necessary to follow changes in habitat suitability since 1880. Our results suggest that the rates of tree dispersion and establishment may also be too low to track shifts in bioclimatic envelopes in the future. The inclusion of contemporary, rather than historical, migration rates into models should improve our understanding of the response of species to climate change.
doi:10.1371/journal.pone.0080443
PMCID: PMC3832392  PMID: 24260391
5.  Comparative Patterns of Plant Invasions in the Mediterranean Biome 
PLoS ONE  2013;8(11):e79174.
The objective of this work was to compare and contrast the patterns of alien plant invasions in the world’s five mediterranean-climate regions (MCRs). We expected landscape age and disturbance history to have bearing on levels of invasion. We assembled a database on naturalized alien plant taxa occurring in natural and semi-natural terrestrial habitats of all five regions (specifically Spain, Italy, Greece and Cyprus from the Mediterranean Basin, California, central Chile, the Cape Region of South Africa and Southwestern - SW Australia). We used multivariate (hierarchical clustering and NMDS ordination) trait and habitat analysis to compare characteristics of regions, taxa and habitats across the mediterranean biome. Our database included 1627 naturalized species with an overall low taxonomic similarity among the five MCRs. Herbaceous perennials were the most frequent taxa, with SW Australia exhibiting both the highest numbers of naturalized species and the highest taxonomic similarity (homogenization) among habitats, and the Mediterranean Basin the lowest. Low stress and highly disturbed habitats had the highest frequency of invasion and homogenization in all regions, and high natural stress habitats the lowest, while taxonomic similarity was higher among different habitats in each region than among regions. Our analysis is the first to describe patterns of species characteristics and habitat vulnerability for a single biome. We have shown that a broad niche (i.e. more than one habitat) is typical of naturalized plant species, regardless of their geographical area of origin, leading to potential for high homogenization within each region. Habitats of the Mediterranean Basin are apparently the most resistant to plant invasion, possibly because their landscapes are generally of relatively recent origin, but with a more gradual exposure to human intervention over a longer period.
doi:10.1371/journal.pone.0079174
PMCID: PMC3828305  PMID: 24244443
6.  Beyond Precipitation: Physiographic Gradients Dictate the Relative Importance of Environmental Drivers on Savanna Vegetation 
PLoS ONE  2013;8(8):e72348.
Background
Understanding the drivers of large-scale vegetation change is critical to managing landscapes and key to predicting how projected climate and land use changes will affect regional vegetation patterns. This study aimed to improve our understanding of the role, magnitude and spatial distribution of the key environmental factors driving vegetation change in southern African savanna, and how they vary across physiographic gradients.
Methodology/Principal Findings
We applied Dynamic Factor Analysis (DFA), a multivariate times series dimension reduction technique to ten years of monthly remote sensing data (MODIS-derived normalized difference vegetation index, NDVI) and a suite of environmental covariates: precipitation, mean and maximum temperature, soil moisture, relative humidity, fire and potential evapotranspiration. Monthly NDVI was described by cyclic seasonal variation with distinct spatiotemporal patterns in different physiographic regions. Results support existing work emphasizing the importance of precipitation, soil moisture and fire on NDVI, but also reveal overlooked effects of temperature and evapotranspiration, particularly in regions with higher mean annual precipitation. Critically, spatial distributions of the weights of environmental covariates point to a transition in the importance of precipitation and soil moisture (strongest in grass-dominated regions with precipitation<750 mm) to fire, potential evapotranspiration, and temperature (strongest in tree-dominated regions with precipitation>950 mm).
Conclusions/Significance
We quantified the combined spatiotemporal effects of an available suite of environmental drivers on NDVI across a large and diverse savanna region. The analysis supports known drivers of savanna vegetation but also uncovers important roles of temperature and evapotranspiration. Results highlight the utility of applying the DFA approach to remote sensing products for regional analyses of landscape change in the context of global environmental change. With the dramatic increase in global change research, this methodology augurs well for further development and application of spatially explicit time series modeling to studies at the intersection of ecology and remote sensing.
doi:10.1371/journal.pone.0072348
PMCID: PMC3758306  PMID: 24023616
7.  Soil Respiration and Organic Carbon Dynamics with Grassland Conversions to Woodlands in Temperate China 
PLoS ONE  2013;8(8):e71986.
Soils are the largest terrestrial carbon store and soil respiration is the second-largest flux in ecosystem carbon cycling. Across China's temperate region, climatic changes and human activities have frequently caused the transformation of grasslands to woodlands. However, the effect of this transition on soil respiration and soil organic carbon (SOC) dynamics remains uncertain in this area. In this study, we measured in situ soil respiration and SOC storage over a two-year period (Jan. 2007–Dec. 2008) from five characteristic vegetation types in a forest-steppe ecotone of temperate China, including grassland (GR), shrubland (SH), as well as in evergreen coniferous (EC), deciduous coniferous (DC) and deciduous broadleaved forest (DB), to evaluate the changes of soil respiration and SOC storage with grassland conversions to diverse types of woodlands. Annual soil respiration increased by 3%, 6%, 14%, and 22% after the conversion from GR to EC, SH, DC, and DB, respectively. The variation in soil respiration among different vegetation types could be well explained by SOC and soil total nitrogen content. Despite higher soil respiration in woodlands, SOC storage and residence time increased in the upper 20 cm of soil. Our results suggest that the differences in soil environmental conditions, especially soil substrate availability, influenced the level of annual soil respiration produced by different vegetation types. Moreover, shifts from grassland to woody plant dominance resulted in increased SOC storage. Given the widespread increase in woody plant abundance caused by climate change and large-scale afforestation programs, the soils are expected to accumulate and store increased amounts of organic carbon in temperate areas of China.
doi:10.1371/journal.pone.0071986
PMCID: PMC3751950  PMID: 24058408
8.  Ecosystem Consequences of Tree Monodominance for Nitrogen Cycling in Lowland Tropical Forest 
PLoS ONE  2013;8(7):e70491.
Understanding how plant functional traits shape nutrient limitation and cycling on land is a major challenge in ecology. This is especially true for lowland forest ecosystems of the tropics which can be taxonomically and functionally diverse and rich in bioavailable nitrogen (N). In many tropical regions, however, diverse forests occur side-by-side with monodominant forest (one species >60% of canopy); the long-term biogeochemical consequences of tree monodominance are unclear. Particularly uncertain is whether the monodominant plant-soil system modifies nutrient balance at the ecosystem level. Here, we use chemical and stable isotope techniques to examine N cycling in old-growth Mora excelsa and diverse watershed rainforests on the island of Trinidad. Across 26 small watershed forests and 4 years, we show that Mora monodominance reduces bioavailable nitrate in the plant-soil system to exceedingly low levels which, in turn, results in small hydrologic and gaseous N losses at the watershed-level relative to adjacent N-rich diverse forests. Bioavailable N in soils and streams remained low and remarkably stable through time in Mora forests; N levels in diverse forests, on the other hand, showed high sensitivity to seasonal and inter-annual rainfall variation. Total mineral N losses from diverse forests exceeded inputs from atmospheric deposition, consistent with N saturation, while losses from Mora forests did not, suggesting N limitation. Our measures suggest that this difference cannot be explained by environmental factors but instead by low internal production and efficient retention of bioavailable N in the Mora plant-soil system. These results demonstrate ecosystem-level consequences of a tree species on the N cycle opposite to cases where trees enhance ecosystem N supply via N2 fixation and suggest that, over time, Mora monodominance may generate progressive N draw-down in the plant-soil system.
doi:10.1371/journal.pone.0070491
PMCID: PMC3723728  PMID: 23936215
9.  Species Richness Patterns and Water-Energy Dynamics in the Drylands of Northwest China 
PLoS ONE  2013;8(6):e66450.
Dryland ecosystems are highly vulnerable to climatic and land-use changes, while the mechanisms underlying patterns of dryland species richness are still elusive. With distributions of 3637 native vascular plants, 154 mammals, and 425 birds in Xinjiang, China, we tested the water-energy dynamics hypothesis for species richness patterns in Central Asian drylands. Our results supported the water-energy dynamics hypothesis. We found that species richness of all three groups was a hump-shaped function of energy availability, but a linear function of water availability. We further found that water availability had stronger effects on plant richness, but weaker effects on vertebrate richness than energy availability. We conducted piecewise linear regressions to detect the breakpoints in the relationship between species richness and potential evapotranspiration which divided Xinjiang into low and high energy regions. The concordance between mammal and plant richness was stronger in high than in low energy regions, which was opposite to that between birds and plants. Plant richness had stronger effects than climate on mammal richness regardless of energy levels, but on bird richness only in high energy regions. The changes in the concordance between vertebrate and plant richness along the climatic gradient suggest that cautions are needed when using concordance between taxa in conservation planning.
doi:10.1371/journal.pone.0066450
PMCID: PMC3688736  PMID: 23840472
10.  Prediction of Soil Organic Carbon at the European Scale by Visible and Near InfraRed Reflectance Spectroscopy 
PLoS ONE  2013;8(6):e66409.
Soil organic carbon is a key soil property related to soil fertility, aggregate stability and the exchange of CO2 with the atmosphere. Existing soil maps and inventories can rarely be used to monitor the state and evolution in soil organic carbon content due to their poor spatial resolution, lack of consistency and high updating costs. Visible and Near Infrared diffuse reflectance spectroscopy is an alternative method to provide cheap and high-density soil data. However, there are still some uncertainties on its capacity to produce reliable predictions for areas characterized by large soil diversity. Using a large-scale EU soil survey of about 20,000 samples and covering 23 countries, we assessed the performance of reflectance spectroscopy for the prediction of soil organic carbon content. The best calibrations achieved a root mean square error ranging from 4 to 15 g C kg−1 for mineral soils and a root mean square error of 50 g C kg−1 for organic soil materials. Model errors are shown to be related to the levels of soil organic carbon and variations in other soil properties such as sand and clay content. Although errors are ∼5 times larger than the reproducibility error of the laboratory method, reflectance spectroscopy provides unbiased predictions of the soil organic carbon content. Such estimates could be used for assessing the mean soil organic carbon content of large geographical entities or countries. This study is a first step towards providing uniform continental-scale spectroscopic estimations of soil organic carbon, meeting an increasing demand for information on the state of the soil that can be used in biogeochemical models and the monitoring of soil degradation.
doi:10.1371/journal.pone.0066409
PMCID: PMC3686688  PMID: 23840459
11.  How Spatial Variation in Areal Extent and Configuration of Labile Vegetation States Affect the Riparian Bird Community in Arctic Tundra 
PLoS ONE  2013;8(5):e63312.
The Arctic tundra is currently experiencing an unprecedented combination of climate change, change in grazing pressure by large herbivores and growing human activity. Thickets of tall shrubs represent a conspicuous vegetation state in northern and temperate ecosystems, where it serves important ecological functions, including habitat for wildlife. Thickets are however labile, as tall shrubs respond rapidly to both abiotic and biotic environmental drivers. Our aim was to assess how large-scale spatial variation in willow thicket areal extent, configuration and habitat structure affected bird abundance, occupancy rates and species richness so as to provide an empirical basis for predicting the outcome of environmental change for riparian tundra bird communities. Based on a 4-year count data series, obtained through a large-scale study design in low arctic tundra in northern Norway, statistical hierarchical community models were deployed to assess relations between habitat configuration and bird species occupancy and community richness. We found that species abundance, occupancy and richness were greatly affected by willow areal extent and configuration, habitat features likely to be affected by intense ungulate browsing as well as climate warming. In sum, total species richness was maximized in large and tall willow patches of small to intermediate degree of fragmentation. These community effects were mainly driven by responses in the occupancy rates of species depending on tall willows for foraging and breeding, while species favouring other vegetation states were not affected. In light of the predicted climate driven willow shrub encroachment in riparian tundra habitats, our study predicts that many bird species would increase in abundance, and that the bird community as a whole could become enriched. Conversely, in tundra regions where overabundance of large herbivores leads to decreased areal extent, reduced height and increased fragmentation of willow thickets, bird community richness and species-specific abundance are likely to be significantly reduced.
doi:10.1371/journal.pone.0063312
PMCID: PMC3653927  PMID: 23691020
12.  Tree Species Composition Influences Enzyme Activities and Microbial Biomass in the Rhizosphere: A Rhizobox Approach 
PLoS ONE  2013;8(4):e61461.
Monoculture causes nutrient losses and leads to declines in soil fertility and biomass production over successive cultivation. The rhizosphere, a zone of usually high microbial activities and clearly distinct from bulk soil, is defined as the volume of soil around living roots and influenced by root activities. Here we investigated enzyme activities and microbial biomass in the rhizosphere under different tree compositions. Six treatments with poplar, willow, and alder mono- or mixed seedlings were grown in rhizoboxes. Enzyme activities associated with nitrogen cycling and microbial biomass were measured in all rhizosphere and bulk soils. Both enzyme activities and microbial biomass in the rhizosphere differed significantly tree compositions. Microbial biomass contents were more sensitive to the changes of the rhizosphere environment than enzyme activities. Tree species coexistence did not consistently increase tested enzyme activities and microbial biomass, but varied depending on the complementarities of species traits. In general, impacts of tree species and coexistence were more pronounced on microbial composition than total biomass, evidenced by differences in microbial biomass C/N ratios stratified across the rhizosphere soils. Compared to poplar clone monoculture, other tree species addition obviously increased rhizosphere urease activity, but greatly reduced rhizosphere L-asparaginase activity. Poplar growth was enhanced only when coexisted with alder. Our results suggested that a highly productive or keystone plant species in a community had greater influence over soil functions than the contribution of diversity.
doi:10.1371/journal.pone.0061461
PMCID: PMC3630193  PMID: 23637838
13.  Forest Canopy Gap Distributions in the Southern Peruvian Amazon 
PLoS ONE  2013;8(4):e60875.
Canopy gaps express the time-integrated effects of tree failure and mortality as well as regrowth and succession in tropical forests. Quantifying the size and spatial distribution of canopy gaps is requisite to modeling forest functional processes ranging from carbon fluxes to species interactions and biological diversity. Using high-resolution airborne Light Detection and Ranging (LiDAR), we mapped and analyzed 5,877,937 static canopy gaps throughout 125,581 ha of lowland Amazonian forest in Peru. Our LiDAR sampling covered a wide range of forest physiognomies across contrasting geologic and topographic conditions, and on depositional floodplain and erosional terra firme substrates. We used the scaling exponent of the Zeta distribution (λ) as a metric to quantify and compare the negative relationship between canopy gap frequency and size across sites. Despite variable canopy height and forest type, values of λ were highly conservative (λ mean  = 1.83, s  = 0.09), and little variation was observed regionally among geologic substrates and forest types, or at the landscape level comparing depositional-floodplain and erosional terra firme landscapes. λ-values less than 2.0 indicate that these forests are subjected to large gaps that reset carbon stocks when they occur. Consistency of λ-values strongly suggests similarity in the mechanisms of canopy failure across a diverse array of lowland forests in southwestern Amazonia.
doi:10.1371/journal.pone.0060875
PMCID: PMC3626694  PMID: 23613748
14.  Phylogenetic Responses of Forest Trees to Global Change 
PLoS ONE  2013;8(4):e60088.
In a rapidly changing biosphere, approaches to understanding the ecology and evolution of forest species will be critical to predict and mitigate the effects of anthropogenic global change on forest ecosystems. Utilizing 26 forest species in a factorial experiment with two levels each of atmospheric CO2 and soil nitrogen, we examined the hypothesis that phylogeny would influence plant performance in response to elevated CO2 and nitrogen fertilization. We found highly idiosyncratic responses at the species level. However, significant, among-genetic lineage responses were present across a molecularly determined phylogeny, indicating that past evolutionary history may have an important role in the response of whole genetic lineages to future global change. These data imply that some genetic lineages will perform well and that others will not, depending upon the environmental context.
doi:10.1371/journal.pone.0060088
PMCID: PMC3617192  PMID: 23593164
15.  Changing Climate and Overgrazing Are Decimating Mongolian Steppes 
PLoS ONE  2013;8(2):e57599.
Satellite observations identify the Mongolian steppes as a hotspot of global biomass reduction, the extent of which is comparable with tropical rainforest deforestation. To conserve or restore these grasslands, the relative contributions of climate and human activities to degradation need to be understood. Here we use a recently developed 21-year (1988–2008) record of satellite based vegetation optical depth (VOD, a proxy for vegetation water content and aboveground biomass), to show that nearly all steppe grasslands in Mongolia experienced significant decreases in VOD. Approximately 60% of the VOD declines can be directly explained by variations in rainfall and surface temperature. After removing these climate induced influences, a significant decreasing trend still persists in the VOD residuals across regions of Mongolia. Correlations in spatial patterns and temporal trends suggest that a marked increase in goat density with associated grazing pressures and wild fires are the most likely non-climatic factors behind grassland degradation.
doi:10.1371/journal.pone.0057599
PMCID: PMC3581472  PMID: 23451249
16.  Regional Contingencies in the Relationship between Aboveground Biomass and Litter in the World’s Grasslands 
PLoS ONE  2013;8(2):e54988.
Based on regional-scale studies, aboveground production and litter decomposition are thought to positively covary, because they are driven by shared biotic and climatic factors. Until now we have been unable to test whether production and decomposition are generally coupled across climatically dissimilar regions, because we lacked replicated data collected within a single vegetation type across multiple regions, obfuscating the drivers and generality of the association between production and decomposition. Furthermore, our understanding of the relationships between production and decomposition rests heavily on separate meta-analyses of each response, because no studies have simultaneously measured production and the accumulation or decomposition of litter using consistent methods at globally relevant scales. Here, we use a multi-country grassland dataset collected using a standardized protocol to show that live plant biomass (an estimate of aboveground net primary production) and litter disappearance (represented by mass loss of aboveground litter) do not strongly covary. Live biomass and litter disappearance varied at different spatial scales. There was substantial variation in live biomass among continents, sites and plots whereas among continent differences accounted for most of the variation in litter disappearance rates. Although there were strong associations among aboveground biomass, litter disappearance and climatic factors in some regions (e.g. U.S. Great Plains), these relationships were inconsistent within and among the regions represented by this study. These results highlight the importance of replication among regions and continents when characterizing the correlations between ecosystem processes and interpreting their global-scale implications for carbon flux. We must exercise caution in parameterizing litter decomposition and aboveground production in future regional and global carbon models as their relationship is complex.
doi:10.1371/journal.pone.0054988
PMCID: PMC3566150  PMID: 23405103
17.  Watershed Sediment Losses to Lakes Accelerating Despite Agricultural Soil Conservation Efforts 
PLoS ONE  2013;8(1):e53554.
Agricultural soil loss and deposition in aquatic ecosystems is a problem that impairs water quality worldwide and is costly to agriculture and food supplies. In the US, for example, billions of dollars have subsidized soil and water conservation practices in agricultural landscapes over the past decades. We used paleolimnological methods to reconstruct trends in sedimentation related to human-induced landscape change in 32 lakes in the intensively agricultural region of the Midwestern United States. Despite erosion control efforts, we found accelerating increases in sediment deposition from erosion; median erosion loss since 1800 has been 15.4 tons ha−1. Sediment deposition from erosion increased >6-fold, from 149 g m−2 yr−1 in 1850 to 986 g m−2 yr−1 by 2010. Average time to accumulate one mm of sediment decreased from 631 days before European settlement (ca. 1850) to 59 days mm−1 at present. Most of this sediment was deposited in the last 50 years and is related to agricultural intensification rather than land clearance or predominance of agricultural lands. In the face of these intensive agricultural practices, traditional soil conservation programs have not decelerated downstream losses. Despite large erosion control subsidies, erosion and declining water quality continue, thus new approaches are needed to mitigate erosion and water degradation.
doi:10.1371/journal.pone.0053554
PMCID: PMC3541183  PMID: 23326454
18.  A Space-For-Time (SFT) Substitution Approach to Studying Historical Phenological Changes in Urban Environment 
PLoS ONE  2012;7(12):e51260.
Plant phenological records are crucial for predicting plant responses to global warming. However, many historical records are either short or replete with data gaps, which pose limitations and may lead to erroneous conclusions about the direction and magnitude of change. In addition to uninterrupted monitoring, missing observations may be substituted via modeling, experimentation, or gradient analysis. Here we have developed a space-for-time (SFT) substitution method that uses spatial phenology and temperature data to fill gaps in historical records. To do this, we combined historical data for several tree species from a single location with spatial data for the same species and used linear regression and Analysis of Covariance (ANCOVA) to build complementary spring phenology models and assess improvements achieved by the approach. SFT substitution allowed increasing the sample size and developing more robust phenology models for some of the species studied. Testing models with reduced historical data size revealed thresholds at which SFT improved historical trend estimation. We conclude that under certain circumstances both the robustness of models and accuracy of phenological trends can be enhanced although some limitations and assumptions still need to be resolved. There is considerable potential for exploring SFT analyses in phenology studies, especially those conducted in urban environments and those dealing with non-linearities in phenology modeling.
doi:10.1371/journal.pone.0051260
PMCID: PMC3517568  PMID: 23236460
19.  Extensive Management Promotes Plant and Microbial Nitrogen Retention in Temperate Grassland 
PLoS ONE  2012;7(12):e51201.
Leaching losses of nitrogen (N) from soil and atmospheric N deposition have led to widespread changes in plant community and microbial community composition, but our knowledge of the factors that determine ecosystem N retention is limited. A common feature of extensively managed, species-rich grasslands is that they have fungal-dominated microbial communities, which might reduce soil N losses and increase ecosystem N retention, which is pivotal for pollution mitigation and sustainable food production. However, the mechanisms that underpin improved N retention in extensively managed, species-rich grasslands are unclear. We combined a landscape-scale field study and glasshouse experiment to test how grassland management affects plant and soil N retention. Specifically, we hypothesised that extensively managed, species-rich grasslands of high conservation value would have lower N loss and greater N retention than intensively managed, species-poor grasslands, and that this would be due to a greater immobilisation of N by a more fungal-dominated microbial community. In the field study, we found that extensively managed, species-rich grasslands had lower N leaching losses. Soil inorganic N availability decreased with increasing abundance of fungi relative to bacteria, although the best predictor of soil N leaching was the C/N ratio of aboveground plant biomass. In the associated glasshouse experiment we found that retention of added 15N was greater in extensively than in intensively managed grasslands, which was attributed to a combination of greater root uptake and microbial immobilisation of 15N in the former, and that microbial immobilisation increased with increasing biomass and abundance of fungi. These findings show that grassland management affects mechanisms of N retention in soil through changes in root and microbial uptake of N. Moreover, they support the notion that microbial communities might be the key to improved N retention through tightening linkages between plants and microbes and reducing N availability.
doi:10.1371/journal.pone.0051201
PMCID: PMC3515579  PMID: 23227252
20.  The Potential of Aspen Clonal Forestry in Alberta: Breeding Regions and Estimates of Genetic Gain from Selection 
PLoS ONE  2012;7(8):e44303.
Background
Aspen naturally grows in large, single-species, even-aged stands that regenerate clonally after fire disturbance. This offers an opportunity for an intensive clonal forestry system that closely emulates the natural life history of the species. In this paper, we assess the potential of genetic tree improvement and clonal deployment to enhance the productivity of aspen forests in Alberta. We further investigate geographic patterns of genetic variation in aspen and infer forest management strategies under uncertain future climates.
Methodology/Principal Findings
Genetic variation among 242 clones from Alberta was evaluated in 13 common garden trials after 5–8 growing seasons in the field. Broad-sense heritabilities for height and diameter at breast height (DBH) ranged from 0.36 to 0.64, allowing 5–15% genetic gains in height and 9–34% genetic gains in DBH. Geographic partitioning of genetic variance revealed predominant latitudinal genetic differentiation. We further observed that northward movement of clones almost always resulted in increased growth relative to local planting material, while southward movement had a strong opposite effect.
Conclusion/Significance
Aspen forests are an important natural resource in western Canada that is used for pulp and oriented strandboard production, accounting for ∼40% of the total forest harvest. Moderate to high broad-sense heritabilities in growth traits suggest good potential for a genetic tree improvement program with aspen. Significant productivity gains appear possible through clonal selection from existing trials. We propose two breeding regions for Alberta, and suggest that well-tested southern clones may be used in the northern breeding region, accounting for a general warming trend observed over the last several decades in Alberta.
doi:10.1371/journal.pone.0044303
PMCID: PMC3431317  PMID: 22957006
21.  Post-Disturbance Plant Community Dynamics following a Rare Natural-Origin Fire in a Tsuga canadensis Forest 
PLoS ONE  2012;7(8):e43867.
Opportunities to directly study infrequent forest disturbance events often lead to valuable information about vegetation dynamics. In mesic temperate forests of North America, stand-replacing crown fire occurs infrequently, with a return interval of 2000–3000 years. Rare chance events, however, may have profound impacts on the developmental trajectories of forest ecosystems. For example, it has been postulated that stand-replacing fire may have been an important factor in the establishment of eastern hemlock (Tsuga canadensis) stands in the northern Great Lakes region. Nevertheless, experimental evidence linking hemlock regeneration to non-anthropogenic fire is limited. To clarify this potential relationship, we monitored vegetation dynamics following a rare lightning-origin crown fire in a Wisconsin hemlock-hardwood forest. We also studied vegetation in bulldozer-created fire breaks and adjacent undisturbed forest. Our results indicate that hemlock establishment was rare in the burned area but moderately common in the scarified bulldozer lines compared to the reference area. Early-successional, non-arboreal species including Rubus spp., Vaccinium angustifolium, sedges (Carex spp.), grasses, Epilobium ciliatum, and Pteridium aquilinium were the most abundant post-fire species. Collectively, our results suggest that competing vegetation and moisture stress resulting from drought may reduce the efficacy of scarification treatments as well as the usefulness of fire for preparing a suitable seedbed for hemlock. The increasing prevalence of growing-season drought suggests that silvicultural strategies based on historic disturbance regimes may need to be reevaluated for mesic species.
doi:10.1371/journal.pone.0043867
PMCID: PMC3424231  PMID: 22928044
22.  Avian Species Richness in Relation to Intensive Forest Management Practices in Early Seral Tree Plantations 
PLoS ONE  2012;7(8):e43290.
Background
Managers of landscapes dedicated to forest commodity production require information about how practices influence biological diversity. Individual species and communities may be threatened if management practices truncate or simplify forest age classes that are essential for reproduction and survival. For instance, the degradation and loss of complex diverse forest in young age classes have been associated with declines in forest-associated Neotropical migrant bird populations in the Pacific Northwest, USA. These declines may be exacerbated by intensive forest management practices that reduce hardwood and broadleaf shrub cover in order to promote growth of economically valuable tree species in plantations.
Methodology and Principal Findings
We used a Bayesian hierarchical model to evaluate relationships between avian species richness and vegetation variables that reflect stand management intensity (primarily via herbicide application) on 212 tree plantations in the Coast Range, Oregon, USA. Specifically, we estimated the influence of broadleaf hardwood vegetation cover, which is reduced through herbicide applications, on bird species richness and individual species occupancy. Our model accounted for imperfect detection. We used average predictive comparisons to quantify the degree of association between vegetation variables and species richness. Both conifer and hardwood cover were positively associated with total species richness, suggesting that these components of forest stand composition may be important predictors of alpha diversity. Estimates of species richness were 35–80% lower when imperfect detection was ignored (depending on covariate values), a result that has critical implications for previous efforts that have examined relationships between forest composition and species richness.
Conclusion and Significance
Our results revealed that individual and community responses were positively associated with both conifer and hardwood cover. In our system, patterns of bird community assembly appear to be associated with stand management strategies that retain or increase hardwood vegetation while simultaneously regenerating the conifer cover in commercial tree plantations.
doi:10.1371/journal.pone.0043290
PMCID: PMC3419709  PMID: 22905249

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