Four Swedish long-term field experiments with sewage sludge reveal a limited effect on soil microbes and on metal uptake by crops

Purpose

This study aims to study the effect of sewage sludge amendment on crop yield and on microbial biomass and community structure in Swedish agricultural soils.

Materials and methods

Topsoil samples (0–0.20 m depth) from four sites where sewage sludge had been repeatedly applied during 14–53 years were analysed for total C, total N, pH and phospholipid fatty acids (PLFAs). Heavy metals were analysed in both soil and plant samples, and crop yields were recorded.

Results and discussion

At all four sites, sewage sludge application increased crop yield and soil organic carbon. Sludge addition also resulted in elevated concentrations of some heavy metals (mainly Cu and Zn) in soils, but high concentrations of metals (Ni and Zn) in plant materials were almost exclusively found in the oldest experiment, started in 1956. PLFA analysis showed that the microbial community structure was strongly affected by changes in soil pH. At those sites where sewage sludge had caused low pH, Gram-positive bacteria were more abundant. However, differences in community structure were larger between sites than between the treatments.

Conclusions

At all four sites, long-term sewage sludge application increased the soil organic carbon and nitrogen content, microbial biomass and crop yield. Long-term sewage sludge application led to a decrease in soil pH. Concentrations of some metals had increased significantly with sewage sludge application at all sites, but the amounts of metals added to soil with sewage sludge were found not to be toxic for microbes at any site.     

Role of a ubiquitin-like modification in polarized morphogenesis

Type I ubiquitin-like proteins constitute a family of protein modifiers. Here we report the identification of a posttranslational protein modifier from Saccharomyces cerevisiae, Hub1. Overexpression of Hub1 resulted in enhanced conjugate formation when its carboxyl-terminal residue was deleted, suggesting that mature Hub1 may be produced by proteolytic processing. In vivo targets of Hub1 conjugation included cell polarity factors Sph1 and Hbt1. In the hub1Delta mutant, the subcellular localization of both Hbt1 and Sph1 was disrupted, and cell polarization during the formation of mating projections was defective. Consistent with these polarization defects, the hub1Delta mutant was deficient in mating.     

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and approximately 4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.     

Deeply inverted electron-hole recombination in a luminescent antibody-stilbene complex

The blue-emissive antibody EP2-19G2 that has been elicited against trans-stilbene has unprecedented ability to produce bright luminescence and has been used as a biosensor in various applications. We show that the prolonged luminescence is not stilbene fluorescence. Instead, the emissive species is a charge-transfer excited complex of an anionic stilbene and a cationic, parallel pi-stacked tryptophan. Upon charge recombination, this complex generates exceptionally bright blue light. Complex formation is enabled by a deeply penetrating ligand-binding pocket, which in turn results from a noncanonical interface between the two variable domains of the antibody.     

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.     

The mineral content affects vertebral morphology in underyearling smolt of Atlantic salmon (Salmo salar L.)

This study investigated the individual variation in vertebral morphology and mineral content (as % of bone dry weight) in rapid growing underyearling smolt (n = 33) twelve weeks after transfer to seawater. The smolt, which were reared in triplicate tanks, had a large individual variation in vertebral bone mineral content (Tank A: 36.2% min, 45.2% max, 39.6% mean. Tank B: 32.6% min, 46.6% max, 40.0% mean. Tank C: 38.5% min, 47.9% max, 42.4% mean), and were subdivided into two groups based on mean within each tank: high mineral content (HMC, above tank mean, n = 15) and low mineral content (LMC, below tank mean, n = 18). Vertebrae of smolt with a low mineral content were more compressed in the anterior–posterior direction (HMC vertebral length/dorso-ventral diameter ratio 0.83, LMC 0.80). This was related to a change in the growth direction of the vertebral cone. This change occurred around transfer to seawater and was characterised by an increased angle between the wall of the cone of the vertebrae and the cranial–caudal axis, and gave the vertebrae a compressed appearance. Smolt with a high mineral content were significantly longer (HMC 28.1 cm, LMC 26.5 cm) and heavier (HMC 270 g, LMC 210 g) twelve weeks after transfer to seawater.