Controlled experimental acidification of lake sediments and resulting trace metal behavior

Severe stream water acidification occurs at higher altitudes (> 600 m a.s.l.) in the Western Harz mountains in Northern Germany. Since 1986 an interdisciplinary research team has followed the fate of pollutants in the 50 km² catchment of an important drinking water reservoir (Lake Söse). An acidification experiment has estimated the role of the remobilization of selected elements from the lake sediments via acidification. Aquaria were used to monitor the effects of a stepwise acidification (from the natural pH of 6.5 to 5.0, 4.0 and 3.0) of the water column over a reconstituted sediment layer. The sediment chemistry has been analyzed before and after the acidification by XRF. The water chemistry was sampled at time intervals and analyzed by ICP-MS. With a pH drop from 6.5 to 3.0, many elements increase in concentration in the water of the acidified basins. Enrichment factors were: Al (5000), Ba (10), Cd (220), Co (800), Cu (170), Ni (90), Pb (5000), and Zn (400). This corresponds fairly well with the field data. Al, Cd, Fe, Mn, and Pb exceed German drinking water limits at pH 4.0. The combined high concentrations (μg L^?1) of Al (1000–2600), Cd (2–4), Cu (4–7), Pb (30–60), and Zn (100–300) in the water column of the acidified streams are not only toxic for fish but also for many other aquatic organisms. Chemical changes in the sediment are not significant within the experimental setup.     

Effects of acid irrigation and liming in a norway spruce stand (Picea abies [L.] KARST.)

Acid irrigation (pH 2.7 to 2.8; mean annual input 4.1 kmol H⁺ ha^?1 as H₂SO₄) has caused significant changes in the chemistry of the soil of a mature Norway spruce stand (Picea abies [L.] KARST.) after 4 years of treatment. In the surface humus layer around 20% of the exchangeable Ca, Mg, K and Mn ions were leached. This was connected with a decrease of pH and cation exchange capacity. In the mineral soil no changes of pH and cation adsorption were observed. However there was a significant increase of Al³⁺ ions in the soil solution, exceeding 20 mg L^?1, mainly caused by dissolution of Al-hydroxides and Al-hydroxosulphates. Also the concentrations of ionic Cu, Zn and Cd were nearly doubled. Manganese concentrations are fluctuating according to periods with and without acid irrigation, showing reduction and oxidation phases. In contrast to microorganisms, certain moss species and Oxalis acetosella, the mature spruce stand was not severely damaged up to now. It is hypothesized that Ca/Al and Mg/Al ratios of single horizons are insufficient for characterizing Al stress in the field. Liming (4 Mg ha^?1) led to a significant increase of dissolved organic C, which is associated with mobilization of metals such as Pb, Cu and Al in organic complexation. Also nitrification increased in the surface humus layer. As a consequence the nitrate concentrations in the seepage water exceeded 250 mg NO₃ L^?1.     

Studies of Atmospheric Nitrogen Deposition in a Mire of the German National Park Hochharz Mountains Using Two Different Methods

The purpose of this study was to determine the nitrogen (N) deposition in a mire of the German National Park Hochharz Mountains in regard to different input pathways of open area and forest stand deposition. High N deposition rates strongly affect the development and growth of mires in general. For determination of the open area N deposition two methods were applied: the bulk deposition method and the Integral Total Nitrogen Input (ITNI) method. This method is based on the ¹⁵N isotope dilution technique and was adapted at this study to evaluate its applicability for natural ecosystems as well as to compare with the traditional bulk method. The forest stand deposition included canopy throughfall, stemflow and fog was measured by means of bulk collectors. On the test site, bulk deposition measurements showed an input of 27 kg N ha^{? 1} yr^{? 1} in the open area and 47 kg N ha^{? 1} yr^{? 1} in the forest stand. The higher N input in the forest stand is caused by interception of fog by the canopy. N concentrations in fog were up to more than six times higher than in rain. The ITNI system yielded a total N deposition of 30 kg N ha^{? 1} yr^{? 1} on average in the open area. The small differences between the two simultaneously applied measuring techniques were caused by a minimum biomass development of the autochthonous plant Calamagrostis villosa in the ITNI system. With increasing biomass production the influence of plants on the atmospheric N input also increased. It can be concluded that the ITNI system is beneficial for the application in a natural ecosystem when using more robust and biomass producing plants. The measured atmospheric N deposition exceeds the critical load for nutrient poor mires and represents therefore a potential risk for the continuity of this ecosystem.     

Incorporating parameter uncertainty into prediction intervals for spatial data modeled via a parametric variogram

In spatial predictions, researchers usually treat the estimated theoretical variogram parameters as known without error and ignore the variability of the parameter estimators. Although the prediction is still unbiased, the prediction error is usually underestimated. Therefore, the coverage probability of the prediction interval usually is lower than the nominal probability. A simulation study is performed to show how the coverage probability for prediction relates to the true range and sill of an exponential variogram. This article proposes two parametric bootstrap methods to incorporate the variability of the corresponding parameter estimators. A simulation study is performed to evaluate the coverage probability of these proposed methods. Finally, we apply the parametric bootstrap methods to a real dataset and compare the results with those from naive (i.e., treating estimated parameters as known) and Bayesian methods.     

QTL mapping of sheath blight resistance in a deep-water rice cultivar

Sheath blight, caused by the pathogen Rhizoctonia solani Kühn, is one of the most serious diseases of rice and leads to severe yield loss worldwide. A recombinant inbred line (RIL) population consisting of 121 lines was constructed from a cross between HH1B and RSB03, the latter of which is a deep-water rice variety. Five traits were used to evaluate sheath blight resistance, namely disease rating (DR), lesion length (LL), lesion height (LH), relative lesion length [RLL, the ratio of LL to plant height (PH)], and relative LH (RLH, the ratio of LH to PH). Using the RIL population and 123 molecular markers, we identified 28 quantitative trait loci (QTLs) for the five traits in two environments. These QTLs are located on nine chromosomes and most of them are environment specific. A major QTL for DR (qSBR1) on chromosome 1 was identified with contributions of 12.7% at Shanghai and 42.6% at Hainan, and it collocated with a QTL for PH. The allele at this locus from RSB03 enhances sheath blight resistance and increases PH. Another QTL for DR on chromosome 7 was adjacent to QTLs for heading date (HD) and four other disease traits. RSB03 also carries the resistant allele at this locus and shortens HD. The susceptible parent, HH1B, provides the resistance allele at the locus qSBR8, where QTLs for four other disease traits were identified. QTL mapping results showed that most QTLs for LL, LH, RLL, and RLH are collocated with QTLs for DR. Three QTLs for DR are independent from HD, PH, and four other disease traits, while four QTLs are closely related to HD and PH. Four QTLs for LL, LH, RLL, and RLH are independent from DR, HD, and PH, while there is only one region harboring QTLs for these four traits and HD. Correlation analysis and QTL mapping results indicated that LL, LH, RLL, and RLH might be important indices, like DR, for evaluating the level of resistance to rice sheath blight.     

Allele mining and haplotype discovery in barley candidate genes for drought tolerance

In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately 1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for 9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound information about the natural variation in the tested drought related candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait.     

Molecular genetics of race non-specific rust resistance in wheat

Over 150 resistance genes that confer resistance to either leaf rust, stripe rust or stem rust have been catalogued in wheat or introgressed into wheat from related species. A few of these genes from the ‘slow-rusting’ adult plant resistance (APR) class confer partial resistance in a race non-specific manner to one or multiple rust diseases. The recent cloning of two of these genes, Lr34/Yr18, a dual APR for leaf rust and stripe rust, and Yr36, a stripe rust APR gene, showed that they differ from other classes of plant resistance genes. Currently, seven Lr34/Yr18 haplotypes have been identified from sequencing the encoding ATP Binding Cassette transporter gene from diverse wheat germplasm of which one haplotype is commonly associated with the resistance phenotype. The paucity of well characterised APR genes, particularly for stem rust, calls for a focused effort in developing critical genetic stocks to delineate quantitative trait loci, construct specific BAC libraries for targeted APR genes to facilitate robust marker development for breeding applications, and the eventual cloning of the encoding genes.     

Development of simple PCR-based markers linked to the <Emphasis Type="Italic">Ms</Emphasis> locus,a restorer-of-fertility gene in onion (<Emphasis Type="Italic">Allium cepa</Emphasis> L.)

In order to implement reliable marker-assisted selection systems for the restorer-of-fertility locus (Ms) in onions (Allium cepa L.), simple PCR-based codominant markers linked to the Ms locus were developed. Based on the EST probe sequences of previously reported RFLP markers, full-length genomic sequences of the gene encoding putative oligopeptide transporter (OPT) was obtained by RACE. The first intron contained two 108 and 439-bp indel polymorphisms between the two Ms allele-linked OPT alleles. A simple PCR marker for OPT was developed by designing a primer pair on the flanking regions of the 108-bp indel which is created by two tandem repeats. The second simple PCR marker was developed from the EST probe encoding photosystem I subunit O (PsaO). Two 14 and 39-bp tandem repeats were identified from the 5′ upstream sequences of the PsaO-coding gene, which were isolated by genome walking. Three different compositions of these tandem repeats were identified from diverse onion germplasm. A primer set binding to the flanking sequence of these polymorphic repeats was used to amplify three different marker haplotypes. The OPT marker was tightly linked to the Ms locus at a distance of 1.5 cM, but the analysis of the linkage relationship showed little linkage disequilibrium between the marker and the Ms locus. Even so, these simple PCR markers are valuable tools for the marker-assisted selection of segregating individuals in onion F₁ hybrid breeding programs.