Development of SNP assays for genotyping the puroindoline b gene for grain hardness in wheat using pyrosequencing

Grain hardness is one of the most important quality characteristics of cultivated bread wheat (Triticum aestivum L.) and has been reported to result from either a failure to express puroindoline a (Pina) or single-nucleotide mutations in puroindoline b (Pinb). Up to now, seven alleles from Pinb-D1a to Pinb-D1g were identified in bread wheat. Compared to the DNA coding region of Pinb-D1a (allele for softness), six single-nucleotide polymorphisms (SNPs) were detected in six alleles for Pinb-D1. In this study, we used pyrosequencing technology to develop two SNP assays for identification of the seven Pinb alleles and characterized SNP variations in the Pinb of 493 European wheat varieties. Of the three hardness alleles Pinb-D1b, Pinb-D1c, and Pinb-D1d detected in this study, Pinb-D1b was the most predominant hardness allele in European hard wheats. The hardness genotypes of partial German wheat varieties available confirmed the reliability and validation of the SNP assays developed for the Pinb locus. Therefore, pyrosequencing technology offers an efficient, precise, and reliable concept for high-throughout genotyping to assist selection of grain hardness genes in wheat quality breeding programs.     

Real-time monitoring of growing nanoparticles

One challenge in the production of nanometer-sized objects with given properties is to control their growth at a macroscopic scale in situ and in real time. A dedicated ultrahigh-vacuum grazing-incidence small-angle x-ray scattering setup has been developed, yielding high sensitivity and dynamics. Its capabilities to derive the average particle shape and size and the film growth mode and ordering and to probe both surfaces and buried interfaces are illustrated for two prototypical cases: the model catalyst Pd/MgO(100) and the self-organized Co/Au(111) system. A wide range of technologically important systems can potentially be investigated in various gaseous environments.     

Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds

The evolving global threat of antimicrobial resistance requires a deep renewal of the antibiotic arsenal including the isolation and characterization of new drugs. Underexplored marine ecosystems may represent an untapped reservoir of novel bioactive molecules. Deep-sea fungi isolated from a record-depth sediment core of almost 2000 m below the seafloor were investigated for antimicrobial activities. This antimicrobial screening, using 16 microbial targets, revealed 33% of filamentous fungi synthesizing bioactive compounds with activities against pathogenic bacteria and fungi. Interestingly, occurrence of antimicrobial producing isolates was well correlated with the complexity of the habitat (in term of microbial richness), as higher antimicrobial activities were obtained at specific layers of the sediment core. It clearly highlights complex deep-sea habitats as chemical battlefields where synthesis of numerous bioactive compounds appears critical for microbial competition. The six most promising deep subseafloor fungal isolates were selected for the production and extraction of bioactive compounds. Depending on the fungal isolates, antimicrobial compounds were only biosynthesized in semi-liquid or solid-state conditions as no antimicrobial activities were ever detected using liquid fermentation. An exception was made for one fungal isolate, and the extraction procedure designed to extract amphipathic compounds was successful and highlighted the amphiphilic profile of the bioactive metabolites.     

Influence of pH on the redox chemistry of metal (hydr)oxides and organic matter in paddy soils

Purpose

The primary purpose of this study was to determine how flooding and draining cycles affect the redox chemistry of metal (hydr)oxides and organic matter in paddy soils and how the pH influences these processes. Our secondary purpose was to determine to what extent a geochemical thermodynamic equilibrium model can be used to predict the solubility of Mn and Fe during flooding and draining cycles in paddy soils.

Material and methods

We performed a carefully designed column experiment with two paddy soils with similar soil properties but contrasting pH. We monitored the redox potential (Eh) continuously and took soil solution samples regularly at four depths along the soil profile during two successive flooding and drainage cycles. To determine dominant mineral phases of Mn and Fe under equilibrium conditions, stability diagrams of Mn and Fe were constructed as a function of Eh and pH. Geochemical equilibrium model calculations were performed to identify Mn and Fe solubility-controlling minerals and to compare predicted total dissolved concentrations with their measured values.

Results and discussion

Flooding led to strong Eh gradients in the columns of both soils. In the acidic soil, pH increased with decreasing Eh and vice versa, whereas pH in the alkaline soil was buffered by CaCO₃. In the acidic soil, Mn and Fe solubility increased during flooding due to reductive dissolution of their (hydr)oxides and decreased during drainage because of re-oxidation. In the alkaline soil, Mn and Fe solubility did not increase during flooding due to Mn(II) and Fe(II) precipitation as MnCO₃, FeCO₃, and FeS. The predicted levels of soluble Mn and Fe in the acidic soil were much higher than their measured values, but predictions and measurements were rather similar in the alkaline soil. This difference is likely due to kinetically limited reductive dissolution of Mn and Fe (hydr)oxides in the acidic soil. During flooding, the solubility of dissolved organic matter increased in both soils, probably because of reductive dissolution of Fe (hydr)oxides and the observed increase in pH.

Conclusions

Under alternating flooding and draining conditions, the pH greatly affected Mn and Fe solubility via influencing either reductive dissolution or carbonate formation. Comparison between measurements and geochemical equilibrium model predictions revealed that reductive dissolution of Mn and Fe (hydr)oxides was kinetically limited in the acidic soil. Therefore, when applying such models to systems with changing redox conditions, such rate-limiting reactions should be parameterized and implemented to enable more accurate predictions of Mn and Fe solubility.     

Mass mortality of native anuran tadpoles in tropical Australia due to the invasive cane toad (Bufo marinus)

Specific pathways of the ecological impact of invasive species remain poorly known. Although the spread of toxic cane toads (Bufo marinus) through tropical Australia is widely believed to have caused extensive mortality of native reptiles and mammals, effects of toad ingestion on native anurans have been virtually ignored. Our studies on the Adelaide River floodplain show that the most numerous vertebrate victims of toad invasion are native tadpoles that die when they attempt to consume toad eggs. We documented 11 episodes of mass mortality, totalling >1300 tadpoles of 10 species, in five waterbodies within a single wet-season shortly after the toads invaded. A causal link between toad breeding and tadpole mortality is supported by observations that: (1) in at least 9 of the 11 waterbodies involved, toads bred immediately prior to mortality events; (2) water quality was indistinguishable from that of control ponds, and tadpoles placed in that water remained healthy; (3) dead tadpoles showed no sign of disease; and (4) laboratory trials showed rapid, 100% mortality in native tadpoles exposed to freshly-laid toad eggs. Despite these high mortality rates, toad invasion does not appear to threaten the viability of anuran populations because frogs often breed in ponds not used by toads, and because density-dependent growth and survival within tadpole communities mean that additional mortality may not reduce the total effective recruitment of metamorph frogs from a waterbody.     

Harvesting fodder trees in montane forests in Kenya: species,techniques used and impacts

There has been an increasing interest in fodder trees and their potential to help the rural poor. However, few studies have addressed the ecological impacts of fodder tree harvesting. We investigated the species harvested and the techniques used, and the effects of fodder harvesting on (1) species’ populations and (2) forest carbon stocks in three montane forests in Kenya. Focus-group discussions were organized in 36 villages to determine which species were harvested and with which techniques. Field observations were made on vegetation plots: stem diameter, tree height, species and extent of harvest were recorded. Carbon stocks were calculated using an allometric equation with (1) observed height of harvested trees, and (2) potential height estimated with a power model, and results were compared. Eight tree species were commonly harvested for fodder using different techniques (some branches, main stem, most branches except stem apex). Fodder harvesting (together with other uses for some species) negatively affected one species populations (Olea europaea), it did not negatively affect four (Drypetes gerrardii, Gymnosporia heterophylla, Pavetta gardeniifolia, Xymalos monospora), and more information is needed for three species (Olea capensis, Prunus africana, Rinorea convallarioides). Fodder harvesting did not significantly reduce forest carbon stocks, suggesting that local communities could continue using these fodder trees if a carbon project is established. Among the fodder species studied, X. monospora could be used in reforestation programs, as it has multiple uses and can withstand severe pruning. Although our study is only a snapshot, it is a baseline which can be used to monitor changes in fodder harvesting and its impacts related to increasing droughts in northern Kenya and increasing human populations.     

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.