Validating module network learning algorithms using simulated data

In recent years, several authors have used probabilistic graphical models to learn expression modules and their regulatory programs from gene expression data. Here, we demonstrate the use of the synthetic data generator SynTReN for the purpose of testing and comparing module network learning algorithms. We introduce a software package for learning module networks, called LeMoNe, which incorporates a novel strategy for learning regulatory programs. Novelties include the use of a bottom-up Bayesian hierarchical clustering to construct the regulatory programs, and the use of a conditional entropy measure to assign regulators to the regulation program nodes. Using SynTReN data, we test the performance of LeMoNe in a completely controlled situation and assess the effect of the methodological changes we made with respect to an existing software package, namely Genomica. Additionally, we assess the effect of various parameters, such as the size of the data set and the amount of noise, on the inference performance. Overall, application of Genomica and LeMoNe to simulated data sets gave comparable results. However, LeMoNe offers some advantages, one of them being that the learning process is considerably faster for larger data sets. Additionally, we show that the location of the regulators in the LeMoNe regulation programs and their conditional entropy may be used to prioritize regulators for functional validation, and that the combination of the bottom-up clustering strategy with the conditional entropy-based assignment of regulators improves the handling of missing or hidden regulators.Comment: 13 pages, 6 figures + 2 pages, 2 figures supplementary informatio

Carbon dioxide fluxes across the Sierra de Guadarrama, Spain

Understanding the spatial and temporal variation in soil respiration within small geographic areas is essential to accurately assess the carbon budget on a global scale. In this study, we investigated the factors controlling soil respiration in an altitudinal gradient in a southern Mediterranean mixed pine–oak forest ecosystem in the north face of the Sierra de Guadarrama in Spain. Soil respiration was measured in five Pinus sylvestris L. plots over a period of 1 year by means of a closed dynamic system (LI-COR 6400). Soil temperature and water content were measured at the same time as soil respiration. Other soil physico-chemical and microbiological properties were measured during the study. Measured soil respiration ranged from 6.8 to 1.4 lmol m-2 s-1, showing the highest values at plots situated at higher elevation. Q10 values ranged between 1.30 and 2.04, while R10 values ranged between 2.0 and 3.6. The results indicate that the seasonal variation of soil respiration was mainly controlled by soil temperature and moisture. Among sites, soil carbon and nitrogen stocks regulate soil respiration in addition to soil temperature and moisture. Our results suggest that application of standard models to estimate soil respiration for small geographic areas may not be adequate unless other factors are considered in addition to soil temperature

Climate Change Alters Seedling Emergence and Establishment in an Old-Field Ecosystem

Background: Ecological succession drives large-scale changes in ecosystem composition over time, but the mechanisms whereby climatic change might alter succession remain unresolved. Here, we asked if the effects of atmospheric and climatic change would alter tree seedling emergence and establishment in an old-field ecosystem, recognizing that small shifts in rates of seedling emergence and establishment of different species may have long-term repercussions on the transition of fields to forests in the future. Methodology/Principal Findings: We introduced seeds from three early successional tree species into constructed old-field plant communities that had been subjected for 4 years to altered temperature, precipitation, and atmospheric CO 2 regimes in an experimental facility. Our experiment revealed that different combinations of atmospheric CO2 concentration, air temperature, and soil moisture altered seedling emergence and establishment. Treatments directly and indirectly affected soil moisture, which was the best predictor of seedling establishment, though treatment effects differed among species. Conclusions: The observed impacts, coupled with variations in the timing of seed arrival, are demonstrated as predictors o

Foliar δ15N values characterize soil N cycling and reflect nitrate or ammonium preference of plants along a temperate grassland gradient

The natural abundance of stable 15N isotopes in soils and plants is potentially a simple tool to assess ecosystem N dynamics. Several open questions remain, however, in particular regarding the mechanisms driving the variability of foliar δ15N values of non-N2 fixing plants within and across ecosystems. The goal of the work presented here was therefore to: (1) characterize the relationship between soil net mineralization and variability of foliar Δδ15N (δ15Nleaf − δ15Nsoil) values from 20 different plant species within and across 18 grassland sites; (2) to determine in situ if a plant’s preference for NO3− or NH4+ uptake explains variability in foliar Δδ15N among different plant species within an ecosystem; and (3) test if variability in foliar Δδ15N among species or functional group is consistent across 18 grassland sites. Δδ15N values of the 20 different plant species were positively related to soil net mineralization rates across the 18 sites. We found that within a site, foliar Δδ15N values increased with the species’ NO3− to NH4+ uptake ratios. Interestingly, the slope of this relationship differed in direction from previously published studies. Finally, the variability in foliar Δδ15N values among species was not consistent across 18 grassland sites but was significantly influenced by N mineralization rates and the abundance of a particular species in a site. Our findings improve the mechanistic understanding of the commonly observed variability in foliar Δδ15N among different plant species. In particular we were able to show that within a site, foliar δ15N values nicely reflect a plant’s N source but that the direction of the relationship between NO3− to NH4+ uptake and foliar Δδ15N values is not universal. Using a large set of data, our study highlights that foliar Δδ15N values are valuable tools to assess plant N uptake patterns and to characterize the soil N cycle across different ecosystems

Comparing the Effect of Naturally Restored Forest and Grassland on Carbon Sequestration and Its Vertical Distribution in the Chinese Loess Plateau

Vegetation restoration has been conducted in the Chinese Loess Plateau (CLP) since the 1950s, and large areas of farmland have been converted to forest and grassland, which largely results in SOC change. However, there has been little comparative research on SOC sequestration and distribution between secondary forest and restored grassland. Therefore, we selected typical secondary forest (SF-1 and SF-2) and restored grassland (RG-1 and RG-2) sites and determined the SOC storage. Moreover, to illustrate the factors resulting in possible variance in SOC sequestration, we measured the soil δ13C value. The average SOC content was 6.8, 9.9, 17.9 and 20.4 g kg−1 at sites SF-1, SF-2, RG-1 and RG-2, respectively. Compared with 0–100 cm depth, the percentage of SOC content in the top 20 cm was 55.1%, 55.3%, 23.1%, and 30.6% at sites SF-1, SF-2, RG-1 and RG-2, suggesting a higher SOC content in shallow layers in secondary forest and in deeper layers in restored grassland. The variation of soil δ13C values with depth in this study might be attributed to the mixing of new and old carbon and kinetic fractionation during the decomposition of SOM by microbes, whereas the impact of the Suess effect (the decline of 13C atmospheric CO2 values with the burning of fossil fuel since the Industrial Revolution) was minimal. The soil δ13C value increased sharply in the top 20 cm, which then increased slightly in deeper layers in secondary forest, indicating a main carbon source of surface litter. However the soil δ13C values exhibited slow increases in the whole profile in the restored grasslands, suggesting that the contribution of roots to soil carbon in deeper layers played an important role. We suggest that naturally restored grassland would be a more effective vegetation type for SOC sequestration due to higher carbon input from roots in the CLP

Altitudinal variation in soil organic carbon stock in coniferous subtropical and broadleaf temperate forests in Garhwal Himalaya

<p>Abstract</p> <p>Background</p> <p>The Himalayan zones, with dense forest vegetation, cover a fifth part of India and store a third part of the country reserves of soil organic carbon (SOC). However, the details of altitudinal distribution of these carbon stocks, which are vulnerable to forest management and climate change impacts, are not well known.</p> <p>Results</p> <p>This article reports the results of measuring the stocks of SOC along altitudinal gradients. The study was carried out in the coniferous subtropical and broadleaf temperate forests of Garhwal Himalaya. The stocks of SOC were found to be decreasing with altitude: from 185.6 to 160.8 t C ha^-1and from 141.6 to 124.8 t C ha^-1in temperature (<it>Quercus leucotrichophora</it>) and subtropical (<it>Pinus roxburghii</it>) forests, respectively.</p> <p>Conclusion</p> <p>The results of this study lead to conclusion that the ability of soil to stabilize soil organic matter depends negatively on altitude and call for comprehensive theoretical explanation</p

The Contribution of Occult Precipitation to Nutrient Deposition on the West Coast of South Africa

The Strandveld mediterranean-ecosystem of the west coast of South Africa supports floristically diverse vegetation growing on mostly nutrient-poor aeolian sands and extending from the Atlantic Ocean tens of kilometers inland. The cold Benguela current upwelling interacts with warm onshore southerly winds in summer causing coastal fogs in this region. We hypothesized that fog and other forms of occult precipitation contribute moisture and nutrients to the vegetation. We measured occult precipitation over one year along a transect running inland in the direction of the prevailing wind and compared the nutrient concentrations with those in rainwater. Occult deposition rates of P, N, K, Mg, Ca, Na, Al and Fe all decreased with distance from the ocean. Furthermore, ratios of cations to Na were similar to those of seawater, suggesting a marine origin for these. In contrast, N and P ratios in occult precipitation were higher than in seawater. We speculate that this is due to marine foam contributing to occult precipitation. Nutrient loss in leaf litter from dominant shrub species was measured to indicate nutrient demand. We estimated that occult precipitation could meet the demand of the dominant shrubby species for annual N, P, K and Ca. Of these species, those with small leaves intercepted more moisture and nutrients than those with larger leaves and could take up foliar deposits of glycine, NO3-, NH4 + and Li (as tracer for K) through leaf surfaces. We conclude that occult deposition together with rainfall deposition are potentially important nutrient and moisture sources for the Strandveld vegetation that contribute to this vegetation being floristically distinct from neighbouring nutrient-poor Fynbos vegetation

Stable Isotope Biogeochemistry of Seabird Guano Fertilization: Results from Growth Chamber Studies with Maize (Zea Mays)

Stable isotope analysis is being utilized with increasing regularity to examine a wide range of issues (diet, habitat use, migration) in ecology, geology, archaeology, and related disciplines. A crucial component to these studies is a thorough understanding of the range and causes of baseline isotopic variation, which is relatively poorly understood for nitrogen (δ(15)N). Animal excrement is known to impact plant δ(15)N values, but the effects of seabird guano have not been systematically studied from an agricultural or horticultural standpoint.This paper presents isotopic (δ(13)C and δ(15)N) and vital data for maize (Zea mays) fertilized with Peruvian seabird guano under controlled conditions. The level of (15)N enrichment in fertilized plants is very large, with δ(15)N values ranging between 25.5 and 44.7‰ depending on the tissue and amount of fertilizer applied; comparatively, control plant δ(15)N values ranged between -0.3 and 5.7‰. Intraplant and temporal variability in δ(15)N values were large, particularly for the guano-fertilized plants, which can be attributed to changes in the availability of guano-derived N over time, and the reliance of stored vs. absorbed N. Plant δ(13)C values were not significantly impacted by guano fertilization. High concentrations of seabird guano inhibited maize germination and maize growth. Moreover, high levels of seabird guano greatly impacted the N metabolism of the plants, resulting in significantly higher tissue N content, particularly in the stalk.The results presented in this study demonstrate the very large impact of seabird guano on maize δ(15)N values. The use of seabird guano as a fertilizer can thus be traced using stable isotope analysis in food chemistry applications (certification of organic inputs). Furthermore, the fertilization of maize with seabird guano creates an isotopic signature very similar to a high-trophic level marine resource, which must be considered when interpreting isotopic data from archaeological material