The force needed to move an atom on a surface

Manipulation of individual atoms and molecules by scanning probe microscopy offers the ability of controlled assembly at the single-atom scale. However, the driving forces behind atomic manipulation have not yet been measured. We used an atomic force microscope to measure the vertical and lateral forces exerted on individual adsorbed atoms or molecules by the probe tip. We found that the force that it takes to move an atom depends strongly on the adsorbate and the surface. Our results indicate that for moving metal atoms on metal surfaces, the lateral force component plays the dominant role. Furthermore, measuring spatial maps of the forces during manipulation yielded the full potential energy landscape of the tip-sample interaction.     

Soil condition classification using infrared spectroscopy: A proposition for assessment of soil condition along a tropical forest-cropland chronosequence

Soil fertility depletion in smallholder agricultural systems in sub-Saharan Africa presents a formidable challenge both for food production and environmental sustainability. A critical constraint to managing soils in sub-Saharan Africa is poor targeting of soil management interventions. This is partly due to lack of diagnostic tools for screening soil condition that would lead to a robust and repeatable spatially explicit case definition of poor soil condition. The objectives of this study were to: (i) evaluate the ability of near infrared spectroscopy to detect changes in soil properties across a forest-cropland chronosequence; and (ii) develop a heuristic scheme for the application of infrared spectroscopy as a tool for case definition and diagnostic screening of soil condition for agricultural and environmental management. Soil reflectance was measured for 582 topsoil samples collected from forest-cropland chronosequence age classes namely; forest, recently converted, RC (17 years) and historically converted, HC (ca.70 years). 130 randomly selected samples were used to calibrate soil properties to soil reflectance using partial least-squares regression (PLSR). 64 randomly selected samples were withheld for validation. A proportional odds logistic model was applied to chronosequence age classes and 10 principal components of spectral reflectance to determine three soil condition classes namely; “good”, “average” and “poor” for 194 samples. Discriminant analysis was applied to classify the remaining 388 “unknown” samples into soil condition classes using the 194 samples as a training set. Validation r² values were: total C, 0.91; total N, 0.90; effective cation exchange capacity (ECEC), 0.90; exchangeable Ca, 0.85; clay content, 0.77; silt content, 0.77 exchangeable Mg, 0.76; soil pH, 0.72; and K, 0.64. A spectral based definition of “good”, “average” and “poor” soil condition classes provided a basis for an explicitly quantitative case definition of poor or degraded soils. Estimates of probabilities of membership of a sample in a spectral soil condition class presents an approach for probabilistic risk-based assessments of soil condition over large spatial scales. The study concludes that reflectance spectroscopy is rapid and offers the possibility for major efficiency and cost saving, permitting spectral case definition to define poor or degraded soils, leading to better targeting of management interventions.     

Specific respiration rates, adenylates, and energy budgets of soil microorganisms after addition of transgenic Bt-maize straw

An arable soil was incubated with straw (stem+leaves) of two transgenic Bt-maize varieties (Novelis: event MON810 and Valmont: event Bt176) and the two corresponding near-isogenic varieties (Nobilis and Prelude). The aim was to evaluate the use of these substrates for microbial growth and maintenance in soil during early decomposition. The addition of Bt-maize straw increased CO₂ production rates and the specific respiration rates CO₂-C/microbial biomass C and CO₂-C/ATP significantly compared with the addition of non-Bt maize straw. This extra energy in the Bt-maize straw could not be used for microbial biomass or ATP and ADP production, and was lost for maintenance. In addition, increased death rates of microbial biomass occurred in the soils treated with the Bt-maize straw from day 3 to 21. Generally, most of the energy was stored in microbial biomass, whereas only 10% of energy was stored in ATP, and only 1-2% in ADP. The AEC (adenylate energy charge: (ATP+0.5×ADP)/(AMP+ADP+ATP)) was not affected by any treatment. The reasons for the lower efficiency of microbial substrate use after adding Bt-maize straw cannot be fully explained by the present experiment. However, a risk assessment has to look at the impact of transgenic plant material on soil microorganisms at different maturity stages.     

Application of two-dimensional gel electrophoresis to interrogate alterations in the proteome of gentically modified crops. 3. Assessing unintended effects

The current procedures to assess the safety of food and feed derived from modern biotechnology include the investigation of possible unintended effects. To improve the probability of detecting unintended effects, profiling techniques such as proteomics are currently tested as complementary analytical tools to the existing safety assessment. An optimized two-dimensional gel electrophoresis (2DE) method was used as a proteomics approach to investigate insertional and pleiotropic effects on the proteome due to genetic engineering. Twelve transgenic Arabidopsis thaliana lines were analyzed by 2DE, and their seed proteomes were compared to that of their parental line as well as to 12 Arabidopsis ecotype lines. The genetic modification of the Arabidopsis lines, using three different genes and three different promoters, did not cause unintended changes to the analyzed seed proteome. Differences in spot quantity between transgenic and nontransgenic lines fell in the range of values found in the 12 Arabidopsis ecotype lines or were related to the introduced gene.     

N-linked glycosylation of folded proteins by the bacterial oligosaccharyltransferase

N-linked protein glycosylation is found in all domains of life. In eukaryotes, it is the most abundant protein modification of secretory and membrane proteins, and the process is coupled to protein translocation and folding. We found that in bacteria, N-glycosylation can occur independently of the protein translocation machinery. In an in vitro assay, bacterial oligosaccharyltransferase glycosylated a folded endogenous substrate protein with high efficiency and folded bovine ribonuclease A with low efficiency. Unfolding the eukaryotic substrate greatly increased glycosylation. We propose that in the bacterial system, glycosylation sites are located in flexible parts of folded proteins, whereas the eukaryotic cotranslational glycosylation evolved to a mechanism presenting the substrate in a flexible form before folding.     

Erratum to: Woody habitats promote pollinators and complexity of plant–pollinator interactions in homegardens located in rice terraces of the Philippine Cordilleras

Paddy and Water Environment -     

Assessment of trace element phytoavailability in compost amended soils using different methodologies

Purpose

This study evaluates the effects of two soil amendments and the growth of two plant species on labile trace element (TE) fractions in two different contaminated soils.

Materials and methods

We studied the effects of two organic amendments (biosolid compost and alperujo compost) and two plant species (Medicago polymorpha and Poa annua) on pH, total organic carbon (TOC), and TE availability, by three extraction methods (CaCl₂ aqueous solution, soil pore water (SPW), and diffusive gradient in thin film (DGT)), in two contaminated soils with contrasting pH values (Aznalcázar, 6.53, and Vicario, 3.48) in a 118-day pot experiment. The effects of the composts on labile TE fractions were compared with element concentrations in plants.

Results and discussion

No relevant effects of amendments and plants were found on the physical and chemical characteristics of the Aznalcázar soil. However, the addition of amendments was essential for plant species growing in the acid Vicario soil. In this soil, amendments and plant growth increased pH and TOC and reduced substantially TE bioavailability. Although absolute values of bioavailable TE contents obtained by the three methods were very different and followed the trend CaCl₂ extraction?>?SPW?>?DGT, these values follow a similar behavior in the two studied soils and for the two species.

Conclusions

The results demonstrate that the application of organic amendments are suitable for remediating acid TE-contaminated soils, for the establishment of a vegetation cover on previously bare soils for reducing wind and water erosion and for reducing labile TE fractions to prevent leaching of pollutants into subsoil or groundwater layers. Moreover, the results obtained in this study pointed out that under microcosm conditions, the three methods tested (CaCl₂ extraction, SPW, and DGT) to predict TE bioavailability were highly correlated.

     

The role of soil chemical properties,land use and plant diversity for microbial phosphorus in forest and grassland soils

Management intensity modifies soil properties, e.g., organic carbon (C_org) concentrations and soil pH with potential feedbacks on plant diversity. These changes might influence microbial P concentrations (P_mic) in soil representing an important component of the P cycle. Our objectives were to elucidate whether abiotic and biotic variables controlling P_mic concentrations in soil are the same for forests and grasslands, and to assess the effect of region and management on P_mic concentrations in forest and grassland soils as mediated by the controlling variables. In three regions of Germany, Schwäbische Alb, Hanich‐Dün, and Schorfheide‐Chorin, we studied forest and grassland plots (each n = 150) differing in plant diversity and land‐use intensity. In contrast to controls of microbial biomass carbon (C_mic), P_mic was strongly influenced by soil pH, which in turn affected phosphorus (P) availability and thus microbial P uptake in forest and grassland soils. Furthermore, P_mic concentrations in forest and grassland soils increased with increasing plant diversity. Using structural equation models, we could show that soil C_org is the profound driver of plant diversity effects on P_mic in grasslands. For both forest and grassland, we found regional differences in P_mic attributable to differing environmental conditions (pH, soil moisture). Forest management and tree species showed no effect on P_mic due to a lack of effects on controlling variables (e.g., C_org). We also did not find management effects in grassland soils which might be caused by either compensation of differently directed effects across sites or by legacy effects of former fertilization constraining the relevance of actual practices. We conclude that variables controlling P_mic or C_mic in soil differ in part and that regional differences in controlling variables are more important for P_mic in soil than those induced by management.     

Exploring the future use of forests: perceptions from non-industrial private forest owners in Finland

The transformation of the forest sector toward a bioeconomy calls for finding new sources of competitive advantage for the whole sector to retain its future viability. Non-industrial private forest owners are an important group of actors in the Finnish forest-based sector, as they supply 80% of industrial roundwood and control numerous other tangible and intangible forest-based ecosystem services. Our study analyzes forest owner views on the future use of forests in Finland, their perceptions on the evolving sectorial interlinkages and the position of the forest sector now and in the future bioeconomy. The data were collected in two phases: through telephone interviews of forest owners (n?=?278) and four focus group (FG) discussions (n?=?17), and were analyzed both qualitatively and quantitatively. The interviews showed that forest owners consider the highest potential for strengthening the sector toward bioeconomy to come from collaboration with energy and construction businesses. During the FG phase, we identified new possibilities founded on forest-based recreational services, cooperation with nature-based tourism and in increasing value-added wood products. In total, forest owners as a high-involvement group emphasized future value creation to be based upon forest ecosystem services and in diversifying the utilization of forests beyond the dominant raw material-driven mindset.