Quantitative assessment of soil parameters in Western Tajikistan using a soil spectral library approach

Soil degradation is a major problem in the agriculturally dominated country of Tajikistan, which makes it necessary to determine and monitor the state of soils. For this purpose a soil spectral library was established as it enables the determination of soil properties with relatively low costs and effort. A total of 1465 soil samples were collected from three 10x10 km test sites in western Tajikistan. The diffuse reflectance of the samples was measured with a FieldSpec PRO FR from ASD in the spectral range from 380 to 2500 nm in laboratory. 166 samples were finally selected based on their spectral information and analysed on total C and N, organic C, pH, CaCO₃, extractable P, exchangeable Ca, Mg and K, and the fractions clay, silt and sand. Multiple linear regression was used to set up the models. Two third of the chemically analysed samples were used to calibrate the models, one third was used for hold-out validation. Very good prediction accuracy was obtained for total C (R² = 0.76, RMSEP = 4.36 g kg⁻¹), total N (R² = 0.83, RMSEP = 0.30 g kg⁻¹) and organic C (R² = 0.81, RMSEP = 3.30 g kg⁻¹), good accuracy for pH (R² = 0.61, RMSEP = 0.157) and CaCO3(R² = 0.72, RMSEP = 4.63 %). No models could be developed for extractable P, exchangeable Ca, Mg and K, and the fractions clay, silt and sand. It can be concluded that the spectral library approach has a high potential to substitute standard laboratory methods where rapid and inexpensive analysis is required.

Modelling susceptibility of grassland soil to macropore flow

Investigating preferential flow, including macropore flow, is crucial to predicting and preventing point sources of contamination in soil, for example in the vicinity of pumping wells. With a view to advancing groundwater protection, this study aimed (i) to quantify the strength of macropore flow in four representative natural grassland soils on the Swiss plateau, and (ii) to define the parameters that significantly control macropore flow in grassland soil. For each soil type we selected three measurement points on which three successive irrigation experiments were carried out, resulting in a total of 36 irrigations. The strength of macropore flow, parameterized as the cumulated water volume flowing from macropores at a depth of 1 m in response to an irrigation of 60 mm h−1 intensity and 1 h duration, was simulated using the dual-permeability MACRO model. The model calibration was based on the key soil parameters and fine measurements of water content at different depths. Modelling results indicate high performance of macropore flow in all investigated soil types except in gleysols. The volume of water that flowed from macropores and was hence expected to reach groundwater varied between 81% and 94% in brown soils, 59% and 67% in para-brown soils, 43% and 56% in acid brown soils, and 22% and 35% in gleysols. These results show that spreading pesticides and herbicides in pumping well protection zones poses a high risk of contamination and must be strictly prohibited. We also found that organic carbon content was not correlated with the strength of macropore flow, probably due to its very weak variation in our study, while saturated water content showed a negative correlation with macropore flow. The correlation between saturated hydraulic conductivity (Ks) and macropore flow was negative as well, but weak. Macropore flow appears to be controlled by the interaction between the bulk density of the uppermost topsoil layer (0–0.10 m) and the macroporosity of the soil below. This interaction also affects the variations in Ks and saturated water content. Further investigations are needed to better understand the combined effect of all these processes including the exchange between micropore and macropore domains.

Differences in Soil Fungal Communities between European Beech (Fagus sylvatica L.) Dominated Forests Are Related to Soil and Understory Vegetation

Fungi are important members of soil microbial communities with a crucial role in biogeochemical processes. Although soil fungi are known to be highly diverse, little is known about factors influencing variations in their diversity and community structure among forests dominated by the same tree species but spread over different regions and under different managements. We analyzed the soil fungal diversity and community composition of managed and unmanaged European beech dominated forests located in three German regions, the Schwäbische Alb in Southwestern, the Hainich-Dün in Central and the Schorfheide Chorin in the Northeastern Germany, using internal transcribed spacer (ITS) rDNA pyrotag sequencing. Multiple sequence quality filtering followed by sequence data normalization revealed 1655 fungal operational taxonomic units. Further analysis based on 722 abundant fungal OTUs revealed the phylum Basidiomycota to be dominant (54%) and its community to comprise 71.4% of ectomycorrhizal taxa. Fungal community structure differed significantly (p≤0.001) among the three regions and was characterized by non-random fungal OTUs co-occurrence. Soil parameters, herbaceous understory vegetation, and litter cover affected fungal community structure. However, within each study region we found no difference in fungal community structure between management types. Our results also showed region specific significant correlation patterns between the dominant ectomycorrhizal fungal genera. This suggests that soil fungal communities are region-specific but nevertheless composed of functionally diverse and complementary taxa.

Using plant functional traits and phylogenies to understand patterns of plant community assembly in a seasonal tropical forest in Lao PDR

Plant functional traits reflect different evolutionary responses to environmental variation, and among extant species determine the outcomes of interactions between plants and their environment, including other plant species. Thus, combining phylogenetic and trait-based information can be a powerful approach for understanding community assembly processes across a range of spatial scales. We used this approach to investigate tree community composition at Phou Khao Khouay National Park (18°14’-18°32’N; 102°38’- 102°59’E), Laos, where several distinct forest types occur in close proximity. The aim of our study was to examine patterns of plant community assembly across the strong environmental gradients evident at our site. We hypothesized that differences in tree community composition were being driven by an underlying gradient in soil conditions. Thus, we predicted that environmental filtering would predominate at the site and that the filtering would be strongest on sandier soil with low pH, as these are the conditions least favorable to plant growth. We surveyed eleven 0.25 ha (50x50 m) plots for all trees above 10 cm dbh (1221 individual trees, including 47 families, 70 genera and 123 species) and sampled soils in each plot. For each species in the community, we measured 11 commonly studied plant functional traits covering both the leaf and wood economic spectrum traits and we reconstructed a phylogenetic tree for 115 of the species in the community using rbcL and matK sequences downloaded from Genebank (other species were not available). Finally we compared the distribution of trait values and species at two scales (among plots and 10x10m subplots) to examine trait and phylogenetic community structures. Although there was strong evidence that an underlying soil gradient was determining patterns of species composition at the site, our results did not support the hypothesis that the environmental filtering dominated community assembly processes. For the measured plant functional traits there was no consistent pattern of trait dispersion across the site, either when traits were considered individually or when combined in a multivariate analysis. However, there was a significant correlation between the degree of phylogenetic dispersion and the first principle component axis (PCA1) for the soil parameters.Moreover, the more phylogenetically clustered plots were on sandier soils with lower pH. Hence, we suggest that the community assembly processes across our sitemay reflect the influence ofmore conserved traits that we did not measure. Nevertheless, our results are equivocal and other interpretations are possible. Our study illustrates some difficulties in combining trait and phylogenetic approaches that may result from the complexities of integrating spatial and evolutionary processes that vary at different scales.

Combined effects of heterogeneity, anisotropy, and saturation on steady state flow and transport: A laboratory sand tank experiment

Field soils show rather different spreading behavior at different water saturations, frequently caused by layering of the soil material. We performed tracer experiments in a laboratory sand tank. Such experiments complement and help comprehension of field investigations. We estimated, by image analysis, the first two moments of small plumes traveling through a two-dimensional, heterogeneous medium with strongly anisotropic correlation structure. Three steady state regimes were analyzed. Two main conclusions were drawn. First, low saturation led to very large heterogeneity and to strong preferential flow. Thus the description of the flow paths and the prediction of the solute arrival times require, in this case, more accurate knowledge about the topological structure. Second, saturation-dependent macroscopic anisotropy is an essential element of transport in unsaturated media. For this reason, small structural soil features should be properly upscaled to give appropriate effective soil parameters to be input in transport models.

“Sweating meteorites”-Water-soluble salts and temperature variation in ordinary chondrites and soil from the hot desert of Oman

The common appearance of hygroscopic brine (“sweating”) on ordinary chondrites (OCs) from Oman during storage under room conditions initiated a study on the role of water-soluble salts on the weathering of OCs. Analyses of leachates from OCs and soils, combined with petrography of alteration features and a 11-month record of in situ meteorite and soil temperatures, are used to evaluate the role of salts in OC weathering. Main soluble ions in soils are Ca2+, SO42−, HCO3−, Na+, and Cl−, while OC leachates are dominated by Mg2+ (from meteoritic olivine), Ca2+ (from soil), Cl− (from soil), SO42− (from meteoritic troilite and soil), and iron (meteoritic). “Sweating meteorites” mainly contain Mg2+ and Cl−. The median Na/Cl mass ratio of leachates changes from 0.65 in soils to 0.07 in meteorites, indicating the precipitation of a Na-rich phase or loss of an efflorescent Na-salt. The total concentrations of water-soluble ions in bulk OCs ranges from 600 to 9000 μg g−1 (median 2500 μg g−1) as compared to 187–14140 μg g−1 in soils (median 1148 μg g−1). Soil salts dissolved by rain water are soaked up by meteorites by capillary forces. Daily heating (up to 66.3 °C) and cooling of the meteorites cause a pumping effect, resulting in a strong concentration of soluble ions in meteorites over time. The concentrations of water-soluble ions in meteorites, which are complex mixtures of ions from the soil and from oxidation and hydrolysis of meteoritic material, depend on the degree of weathering and are highest at W3. Input of soil contaminants generally dominates over the ions mobilized from meteorites. Silicate hydrolysis preferentially affects olivine and is enhanced by sulfide oxidation, producing local acidic conditions as evidenced by jarosite. Plagioclase weathering is negligible. After completion of troilite oxidation, the rate of chemical weathering slows down with continuing Ca-sulfate contamination.

Gene expression variation between distinct areas of breast cancer measured from paraffin-embedded tissue cores

BACKGROUND: Diagnosis and prognosis in breast cancer are mainly based on histology and immunohistochemistry of formalin-fixed, paraffin-embedded (FFPE) material. Recently, gene expression analysis was shown to elucidate the biological variance between tumors and molecular markers were identified that led to new classification systems that provided better prognostic and predictive parameters. Archived FFPE samples represent an ideal source of tissue for translational research, as millions of tissue blocks exist from routine diagnostics and from clinical studies. These should be exploited to provide clinicians with more accurate prognostic and predictive information. Unfortunately, RNA derived from FFPE material is partially degraded and chemically modified and reliable gene expression measurement has only become successful after implementing novel and optimized procedures for RNA isolation, demodification and detection. METHODS: In this study we used tissue cylinders as known from the construction of tissue microarrays. RNA was isolated with a robust protocol recently developed for RNA derived from FFPE material. Gene expression was measured by quantitative reverse transcription PCR. RESULTS: Sixteen tissue blocks from 7 patients diagnosed with multiple histological subtypes of breast cancer were available for this study. After verification of appropriate localization, sufficient RNA yield and quality, 30 tissue cores were available for gene expression measurement on TaqMan(R) Low Density Arrays (16 invasive ductal carcinoma (IDC), 8 ductal carcinoma in situ (DCIS) and 6 normal tissue), and 14 tissue cores were lost. Gene expression values were used to calculate scores representing the proliferation status (PRO), the estrogen receptor status and the HER2 status. The PRO scores measured from entire sections were similar to PRO scores determined from IDC tissue cores. Scores determined from normal tissue cores consistently revealed lower PRO scores than cores derived from IDC or DCIS of the same block or from different blocks of the same patient. CONCLUSION: We have developed optimized protocols for RNA isolation from histologically distinct areas. RNA prepared from FFPE tissue cores is suitable for gene expression measurement by quantitative PCR. Distinct molecular scores could be determined from different cores of the same tumor specimen.

High-resolution computer simulation of the dynamics of isoelectric focusing: in quest of more realistic input parameters for carrier ampholytes

The impact of the systematic variation of either DeltapK(a) or mobility of 140 biprotic carrier ampholytes on the conductivity profile of a pH 3-10 gradient was studied by dynamic computer simulation. A configuration with the greatest DeltapK(a) in the pH 6-7 range and uniform mobilities produced a conductivity profile consistent with that which is experimentally observed. A similar result was observed when the neutral (pI = 7) ampholyte is assigned the lowest mobility and mobilities of the other carriers are systematically increased as their pI's recede from 7. When equal DeltapK(a) values and mobilities are assigned to all ampholytes a conductivity plateau in the pH 5-9 region is produced which does not reflect what is seen experimentally. The variation in DeltapK(a) values is considered to most accurately reflect the electrochemical parameters of commercially available mixtures of carrier ampholytes. Simulations with unequal mobilities of the cationic and anionic species of the carrier ampholytes show either cathodic (greater mobility of the cationic species) or anodic (greater mobility of the anionic species) drifts of the pH gradient. The simulated cationic drifts compare well to those observed experimentally in a capillary in which the focusing of three dyes was followed by whole column optical imaging. The cathodic drift flattens the acidic portion of the gradient and steepens the basic part. This phenomenon is an additional argument against the notion that focused zones of carrier ampholytes have no electrophoretic flux.

A 700-year paleoecological record of boreal ecosystem responses to climatic variation from Alaska

Recent observations and model simulations have highlighted the sensitivity of the forest - tundra ecotone to climatic forcing. In contrast, paleoecological studies have not provided evidence of tree-line fluctuations in response to Holocene climatic changes in Alaska, suggesting that the forest - tundra boundary in certain areas may be relatively stable at multicentennial to millennial time scales. We conducted a multiproxy study of sediment cores from an Alaskan lake near the altitudinal limits of key boreal-forest species. Paleoecological data were compared with independent climatic reconstructions to assess ecosystem responses of the forest - tundra boundary to Little Ice Age (LIA) climatic. uctuations. Pollen, diatom, charcoal, macrofossil, and magnetic analyses provide the first continuous record of vegetation -. re - climate interactions at decadal to centennial time scales during the past 700 years from southern Alaska. Boreal-forest diebacks characterized by declines of Picea mariana, P. glauca, and tree Betula occurred during the LIA ( AD 1500 - 1800), whereas shrubs ( Alnus viridis, Betula glandulosa/nana) and herbaceous taxa (Epilobium, Aconitum) expanded. Marked increases in charcoal abundance and changes in magnetic properties suggest increases in. re importance and soil erosion during the same period. In addition, the conspicuous reduction or disappearance of certain aquatic ( e. g., Isoetes, Nuphar, Pediastrum) and wetland ( Sphagnum) plants and major shifts in diatom assemblages suggest pronounced lake-level. uctuations and rapid ecosystem reorganization in response to LIA climatic deterioration. Our results imply that temperature shifts of 1 - 2 degrees C, when accompanied by major changes in moisture balance, can greatly alter high-altitudinal terrestrial, wetland, and aquatic ecosystems, including conversion between boreal-forest tree line and tundra. The climatic and ecosystem variations in our study area appear to be coherent with changes in solar irradiance, suggesting that changes in solar activity contributed to the environmental instability of the past 700 years.

Variation in hepatic regulation of metabolism during the dry period and in early lactation in dairy cows

The purpose of this study was to investigate variations in hepatic regulation of metabolism during the dry period, after parturition, and in early lactation in dairy cows. For this evaluation, cows were divided into 2 groups based on the plasma concentration of beta-hydroxybutyric acid (BHBA) in wk 4 postpartum (PP; group HB, BHBA >0.75 mmol/L; group LB, BHBA <0.75 mmol/L, respectively). Liver biopsies were obtained from 28 cows at drying off (mean 59 +/- 8 d antepartum), on d 1, and in wk 4 and 14 PP. Blood samples were collected every 2 wk during this entire period. Liver samples were analyzed for mRNA abundance of genes related to carbohydrate metabolism (pyruvate carboxylase, PC; phosphoenolpyruvate carboxykinase, PEPCK; citrate synthase, CS), fatty acid biosynthesis (ATP citrate lyase, ACLY) and oxidation (acyl-CoA synthetase long-chain, ACSL; carnitine palmitoyltransferase 1A, CPT 1A; carnitine palmitoyltransferase 2, CPT 2; acyl-coenzyme A dehydrogenase very long chain, ACADVL), cholesterol biosynthesis (3-hydroxy-3-methylglutaryl-coenzyme A synthase 1, HMGCS1), ketogenesis (3-hydroxy-3-methylglutaryl-coenzyme A synthase 2, HMGCS2), and of genes encoding the transcription factors peroxisome proliferator-activated receptor alpha (PPARalpha), peroxisome proliferator-activated receptor gamma (PPARgamma), and sterol regulatory element binding factor 1 (SREBF1). Blood plasma was assayed for concentrations of glucose, BHBA, nonesterified fatty acids, cholesterol, triglycerides, insulin, insulin-like growth factor-I, and thyroid hormones. In both groups, plasma parameters followed a pattern usually observed in dairy cows. However, changes were moderate and the energy balance in cows turned positive in wk 7 PP for both groups. Additionally, the energy balance and milk yield were similar for both groups after parturition onwards. Significant group effects were found at drying off, when plasma concentrations of triglycerides were higher in LB than in HB, and in wk 4 PP, when plasma concentrations of glucose and IGF-I were lower in HB than in LB. Similarly, moderate changes in mRNA expression of hepatic genes between the different time points were observed, although HB cows showed more adaptive performance than LB cows based on changes in mRNA expression of PEPCKc, PEPCKm, CS, CPT 1A, CPT 2, and PPARalpha. Part of the variation measured in this study was explained by parity. Significant Spearman rank correlation coefficients between the variables were not similar at each time point and were not similar between the groups at each time point, suggesting that metabolic regulation differs between cows. In conclusion, metabolic regulation in dairy cows is a dynamic system, and differs obviously between cows at different metabolic stages related to parturition.

Does organic grassland farming benefit plant and arthropod diversity at the expense of yield and soil fertility?

Organic management is one of the most popular strategies to reduce negative environmental impacts of intensive agriculture. However, little is known about benefits for biodiversity and potential worsening of yield under organic grasslands management across different grassland types, i.e. meadow, pasture and mown pasture. Therefore, we studied the diversity of vascular plants and foliage-living arthropods (Coleoptera, Araneae, Heteroptera, Auchenorrhyncha), yield, fodder quality, soil phosphorus concentrations and land-use intensity of organic and conventional grasslands across three study regions in Germany. Furthermore, all variables were related to the time since conversion to organic management in order to assess temporal developments reaching up to 18 years. Arthropod diversity was significantly higher under organic than conventional management, although this was not the case for Araneae, Heteroptera and Auchenorrhyncha when analyzed separately. On the contrary, arthropod abundance, vascular plant diversity and also yield and fodder quality did not considerably differ between organic and conventional grasslands. Analyses did not reveal differences in the effect of organic management among grassland types. None of the recorded abiotic and biotic parameters showed a significant trend with time since transition to organic management, except soil organic phosphorus concentrations which decreased with time. This implies that permanent grasslands respond slower and probably weaker to organic management than crop fields do. However, as land-use intensity and inorganic soil phosphorus concentrations were significantly lower in organic grasslands, overcoming seed and dispersal limitation by re-introducing plant species might be needed to exploit the full ecological potential of organic grassland management. We conclude that although organic management did not automatically increase the diversity of all studied taxa, it is a reasonable and useful way to support agro-biodiversity.

Isotopes Trace Biogeochemistry and Sources of Cu and Zn in an intertidal soil

River floodplain soils are sinks and potential sources for toxic trace metals like Cu and Zn. We hypothesize that stable Cu and Zn isotope ratios reflect both the mobilization and the sources of metals. We determined the soil properties, the concentrations and partitioning of Cu and Zn, and variations in δ65Cu and δ66Zn values in a core obtained from an Aquic Udifluvent developed on a freshwater intertidal mudflat of the River Elbe, Germany. The core was sampled at 2 cm intervals to a depth of 34 cm, which corresponds to approximately 9 yr of sedimentation. Elevated concentrations of Cu (up to 320 μg g−1) and Zn (up to 2080 μg g−1) indicated anthropogenic pollution. At the time of sampling the redox conditions changed from oxic (Eh 200 to 400 mV, above 22 cm deep) to strongly anoxic conditions (-100 to -200 mV, below 22 cm deep). The δ65Cu values varied systematically with depth (from -0.02 to 0.16‰) and were correlated with the Fe, C, and N concentrations. Although pre-depositional variations cannot be ruled out, the systematic variation with depth suggests post-sedimentation fractionation of δ65Cu in response to seasonally variable organic matter deposition and redox conditions. In contrast, the δ66ZnIRMM values were uniform (from -0.07 to 0.01‰) throughout the core, indicating that the Zn isotopes did not significantly fractionate after deposition and that the Zn sources were homogeneous throughout the sedimentation.

Soil property and management effects on grassland microbial communities across a latitudinal gradient in Germany

There is much interest in the identification of the main drivers controlling changes in the microbial community that may be related to sustainable land use. We examined the influence of soil properties and land-use intensity (N fertilization, mowing, grazing) on total phospholipid fatty acid (PLFA) biomass, microbial community composition (PLFA profiles) and activities of enzymes involved in the C, N, and P cycle. These relationships were examined in the topsoil of grasslands from three German regions (Schorfheide-Chorin (SCH), Hainich-Dun (HAI), Schwabische Alb (ALB)) with different parent material. Differences in soil properties explained 60% of variation in PLFA data and 81% of variation in enzyme activities across regions and land-use intensities. Degraded peat soils in the lowland areas of the SCH with high organic carbon (OC) concentrations and sand content contained lower PLFA biomass, lower concentrations of bacterial, fungal, and arbuscular mycorrhizal PLFAs, but greater enzyme activities, and specific enzyme activities (per unit microbial biomass) than mineral soils in the upland areas of the HAI and ALB, which are finer textured, drier, and have smaller OC concentrations. After extraction of variation that originated from large-scale differences among regions and differences in land-use intensities between plots, soil properties still explained a significant amount of variation in PLFA data (34%) and enzyme activities (60%). Total PLFA biomass and all enzyme activities were mainly related to OC concentration, while relative abundance of fungi and fungal to bacterial ratio were mainly related to soil moisture. Land-use intensity (LUI) significantly decreased the soil C:N ratio. There was no direct effect of LUI on total PLFA biomass, microbial community composition, N and P cycling enzyme activities independent of study region and soil properties. In contrast, the activities and specific activities of enzymes involved in the C cycle increased significantly with LUI independent of study region and soil properties, which can have impact on soil organic matter decomposition and nutrient cycling. Our findings demonstrate that microbial biomass and community composition as well as enzyme activities are more controlled by soil properties than by grassland management at the regional scale. (C) 2013 Elsevier B.V: All rights reserved.