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.     

Carbon storage in loess derived surface soils from Central Germany: Influence of mineral phase variables

The influence of the soil mineral phase on organic matter storage was studied in loess derived surface soils of Central Germany. The seven soils were developed to different genetic stages. The carbon content of the bulk soils ranged from 8.7 to 19.7 g kg^—1. Clay mineralogy was confirmed to be constant, with illite contents > 80 %. Both, specific surface area (SSA, BET‐N₂‐method) and cation exchange capacity (CEC) of bulk soils after carbon removal were better predictors of carbon content than clay content or dithionite‐extractable iron. SSA explained 55 % and CEC 54 % of the variation in carbon content. The carbon loadings of the soils were between 0.57 and 1.06 mg C m^—2, and therefore in the ”︁monolayer equivalent” (ME) level. The increase in SSA after carbon removal (ΔSSA) was significantly and positively related to carbon content (r² = 0.77). Together with CEC of carbon‐free samples, ΔSSA explained 90 % of the variation in carbon content. Clay (< 2 μm) and fine silt fractions (2—6.3 μm) contained 68—82 % of the bulk soil organic carbon. A significantly positive relationship between carbon content in the clay fraction and in the bulk soil was observed (r² = 0.95). The carbon pools of the clay and fine silt fractions were characterized by differences in C/N ratio, δ¹³C ratio, and enrichment factors for carbon and nitrogen. Organic matter in clay fractions seems to be more altered by microbes than organic matter in fine silt fractions. The results imply that organic matter accumulates in the fractions of smallest size and highest surface area, apparently intimately associated with the mineral phase. The amount of cations adhering to the mineral surface and the size of a certain and specific part of the surface area (ΔSSA) are the mineral phase properties which affect the content of the organic carbon in loess derived arable surface soils in Central Germany most. There is no monolayer of organic matter on the soil surfaces even if carbon loadings are in the ME level.     

Phytoextraction of heavy metal contaminated soils with Thlaspi goesingense and Amaranthus hybridus: Rhizosphere manipulation using EDTA and ammonium sulfate

Selection of appropriate plant species and rhizosphere manipulation to enhance metal uptake are considered key factors in the development of phytoextraction technologies. A pot trial was conducted with two contaminated soils to investigate the effect of EDTA and ammonium sulfate on the accumulation of heavy metals into shoots of the low‐biomass hyperaccumlator Thlaspi goesingense Hálácsy (Brassicaceae) and the high‐biomass non‐hyperaccumulating plant Amaranthus hybridus (Amaranthaceae). Upon application of 1 g EDTA (kg soil)^—1 metal extractability with 1 M NH₄NO₃ increased substantially, whereas the application of (NH₄)₂SO₄ was less effective. The EDTA treatment increased the heavy metal concentrations in both plant species, however, the difference to the control was larger for A. hybridus. EDTA enhanced shoot concentrations in A. hybridus grown on soil Arnoldstein from 32.7 mg kg^—1 to 1140 mg kg^—1 for Pb and from 3.80 mg kg^—1 to 10.3 mg kg^—1 for Cd. Cd concentrations in shoots of T. goesingense were also increased by EDTA application, however, a slight decrease was observed for Pb. T. goesingense accumulated 2840 mg Pb kg^—1 without any treatment. This is the first report of Pb hyperacumulation by T. goesingense. A decrease of shoot Pb concentration was observed in T. goesingense upon treatment with ammonium sulfate. Although metal concentrations in the shoots were rather large and significantly increased upon application of EDTA, plant growth and heavy metal removal were still too small to obtain reasonable extraction rates in soils heavily polluted by metals. It should be also noted that metal lability largely increased in EDTA‐treated soils and this lability persisted for several weeks after the application of the chelating agent, which is likely to be associated with the risk of groundwater contamination.