Using bulked AFLP analysis to assess genetic diversity in Echinacea species

Echinacea is an allogamous genus, thus its cultivars or populations are genetically heterogeneous. Using amplified fragment length polymorphism (AFLP) to estimate the genetic diversity of Echinacea is generally limited by the large number of individual plants and the higher cost that need to be processed. In the present study, effectiveness of several sizes of DNA bulking (10, 15, 20, 25 and 30 individuals) with 20, 36 and 55 primer pairs was compared using AFLP in determining the genetic diversity of Echinacea species. The results indicated that the use of bulked DNA-based AFLP analysis by using the selected eight primer pairs was capable of detecting genetic diversity between the tested Echinacea species, provided that the potential presence of low frequency variants was ignored and a possible bias in the estimates of genetic similarity was accepted. The assessments showed that a bulk of 15 individuals could detect sufficient AFLP variations at most genomic sites. Additionally, 20 primer pairs could generate sufficient polymorphic fragments to achieve high resolving power of AFLP for the tested Echinacea species.     

Organic carbon sequestration in earthworm burrows

Earthworms strongly affect soil organic carbon cycling. The aim of this study was to determine whether deep burrowing anecic earthworms enhance carbon storage in soils and decrease C turnover. Earthworm burrow linings were separated into thin cylindrical sections with different distances from the burrow wall to determine gradients from the burrow wall to the surrounding soil. Organic C, total N, radiocarbon (¹⁴C) concentration, stable isotope values (δ¹³C, δ¹⁵N) and extracellular enzyme activities were measured in these samples. Anecic earthworms increased C stocks by 270 and 310 g m^?2 accumulated in the vertical burrows. C-enrichment of the burrow linings was spatially highly variable within a distance of millimetres around the burrow walls. It was shown that C accumulation in burrows can be fast with C sequestration rates of about 22 g C m^?2 yr^?1 in the burrow linings, but accumulated C in the burrows may be mineralised fast with turnover times of only 3–5 years. Carbon stocks in earthworm burrows strongly depended on the earthworm activity which maintains continuous C input into the burrows. The enhanced extracellular enzyme activity of fresh casts was not persistent, but was 47% lower in inhabited burrows and 62% lower in abandoned burrows. Enzyme activities followed the C concentrations in the burrows and were not further suppressed due to earthworms. Radiocarbon concentrations and stable isotopes in the burrow linings showed an exponential gradient with the youngest and less degraded organic matter in the innermost part of the burrow wall. Carbon accumulation by anecic earthworm is restricted to distinct burrows with less influence to the surrounding soil. Contrary to the initial hypothesis, that organic C is stabilised due to earthworms, relaxation time experiments with nuclear magnetic resonance spectroscopy (NMR) did not reveal any enhanced adsorption of C on iron oxides with C stabilising effect. Our results suggest that earthworm activity does not substantially increase subsoil C stocks but burrows serve as fast ways for fresh C transport into deep soil horizons.     

Storage and stability of organic matter and fossil carbon in a Luvisol and Phaeozem with continuous maize cropping: A synthesis

Quantitative information about the amount and stability of organic carbon (OC) in different soil organic‐matter (OM) fractions and in specific organic compounds and compound‐classes is needed to improve our understanding of organic‐matter sequestration in soils. In the present paper, we summarize and integrate results performed on two different arable soils with continuous maize cropping (a) Stagnic Luvisol with maize cropping for 24 y, b) Luvic Phaeozem with maize cropping for 39 y) to identify (1) the storage of OC in different soil organic‐matter fractions, (2) the function of these fractions with respect to soil‐OC stabilization, (3) the importance and partitioning of fossil‐C deposits, and (4) the rates of soil‐OC stabilization as assessed by compound‐specific isotope analyses. The fractionation procedures included particle‐size fractionation, density fractionation, aggregate fractionation, acid hydrolysis, different oxidation procedures, isolation of extractable lipids and phospholipid fatty acids, pyrolysis, and the determination of black C. Stability of OC was determined by ¹³C and ¹⁴C analyses. The main inputs of OC were plant litter (both sites) and deposition of fossil C likely from coal combustion and lignite dust (only Phaeozem).     

Exchangeable cations in rock fractions and fine earth in soil profiles of different genesis

Data on accumulated exchangeable H, Al, Fe and Mn (M_a) cations in rock fractions in German soil profiles are scarce. The objective of this study was to describe the sum of accumulated M_a cations of fine earth and rock fragments in 11 deep soil profiles of varying genesis. Soil profiles were laid out at the sites Solling, Eifel, Harz mountains and the Erzgebirge and the parent materials included sandstones, siltstones, quartzite, slate, greywacke, diabase, gneiss and quartz porphyry. Exchangeable cations in the fine earth and rock fragments were measured in depths down to 6 m. Additionally, effective porosity and specific surface of rock fragments were determined. The effective porosity of the different rock fragments ranged from 4 to 28% (v/v), indicating that the rocks were accessible to solutions. For most samples, the cation exchange capacities (CEC) of the fine earth fractions were larger than those of the rock fragments, and the CEC (fine earth)/CEC (rock) ratios decreased with depth. All 11 profiles had small (<40%) amounts of exchangeable Na, K, Mg and Ca (M_b) cations in the fine earth fraction. Exchangeable M_a and M_b cations in the rock fragments changed similarly with depth as in the fine earth fractions for all profiles. Cumulative (rock + fine earth) M_a cations from 0—200 cm ranged from 474 to 1592 kmol_c ha⁻¹. The contribution of the rock fraction to the cumulative exchangeable M_a cations accounted for 13 to 85% of the total. The sum of exchangeable M_a cations was much higher than the cumulative acid deposition in western Germany since the beginning of industrialization, suggesting that carbonic acid and organic acids contributed largely to soil acidification. The rocks contribute significantly to buffering the acidity of the seepage water by silicate weathering and cation exchange. Therefore, acidification models which consider the fine earth fraction only, may lead to an overestimation of the rate of soil and groundwater acidification.     

Die Baumschule

Ohne Zusammenfassung     

Bovine mycoplasmas: classification of groups related to Mycoplasma mycoides.

Mycoplasmas which had in various ways proved to be related to Mycoplasma mycoides were studied with a view to classification and nomenclature. Representative strains of M. mycoides — subspecies mycoides (PG1) and subspecies capri (PG3) — and of the as yet unclassified bovine serogroups 7 (PG50) and L (B144P) were compared serologically and by DNA-DNA hybridization. The serological methods used (metabolism inhibition, growth inhibition and immunofluorescence) are usually considered to be species-specific.

1. The two subspecies of M. mycoides can be clearly separated by all three serological methods, whereas the hybridization studies revealed great similarity between them, the relatedness value being 0.70.
2. The two serogroups (7 and L) cross-reacted with each other in all three serological tests, and their relatedness value was 0.83. The relatedness value between group 7 and M. mycoides subsp. mycoides was found to be 0.72, and only limited cross-reactions were demonstrated by immunofluorescence and growth inhibition.
3. Although groups 7 and L were found only to a slight degree to be genetically related to M. bovigenitalium with a DNA homology of 20 % or less, a serological cross-reaction between group 7 and M. bovigenitalium has been demonstrated by growth inhibition in previous studies.

Conclusions drawn on the basis of the premises just mentioned give rise to a dilemma, because three different situations exist. In (1), significant serological differences were disclosed, but the DNA homology was great. In (2), the serogroups 7 and L showed conformity between hybridization and serological findings, whereas, in (3), hybridization showed a distinct separation, but a serological cross-reaction does occur. If the results of hybridization are regarded as decisive, the two subspecies of M. mycoides can be preserved, but this is at variance with the general perception that the serological methods used here are species-specific. If, on the other hand, the serological results are chosen to be decisive, PG1 and PG3 must be regarded as two separate species, and consequently Group L/7 may also be a separate species.As regards the relation between group L/7 and M. bovigenitalium, the results of hybridization clearly show that they are two different species. As a consequence of this, it must be accepted that cross-reactions may occur — also in growth inhibition — between different species which, genetically, are even far removed from each other.On account of the fundamental nature of these problems, the authors prefer to leave the decisions — also as to the nomenclature — to the Subcommittee on the Taxonomy of Mycoplasmatales.     

Escherichia coli, but not Staphylococcus aureus triggers an early increased expression of factors contributing to the innate immune defense in the udder of the cow

The outcome of an udder infection is influenced by the pathogen species. We established a strictly defined infection model to better analyze the unknown molecular causes for these pathogen-specific effects, using Escherichia coli and Staphylococcus aureus strains previously asseverated from field cases of mastitis. Inoculation of quarters with 500 CFU of E. coli (n = 4) was performed 6 h, 12 h, and 24 h before culling. All animals showed signs of acute clinical mastitis 12 h after challenge: increased somatic cell count (SCC), decreased milk yield, leukopenia, fever, and udder swelling. Animals inoculated with 10 000 CFU of S. aureus for 24 h (n = 4) showed no or only modest clinical signs of mastitis. However, S. aureus caused clinical signs in animals, inoculated for 72 h-84 h. Real-time PCR proved that E. coli inoculation strongly and significantly upregulated the expression of beta-defensins, TLR2 and TLR4 in the pathogen inoculated udder quarters as well as in mammary lymph nodes. TLR3 and TLR6 were not significantly regulated by the infections. Immuno-histochemistry identified mammary epithelial cells as sites for the upregulated TLR2 and beta-defensin expression. S. aureus, in contrast, did not significantly regulate the expression of any of these genes during the first 24 h after pathogen inoculation. Only 84 h after inoculation, the expression of beta-defensins, but not of TLRs was significantly (> 20 fold) upregulated in five out of six pathogen inoculated quarters. Using the established mastitis model, the data clearly demonstrate a pathogen-dependent difference in the time kinetics of induced pathogen receptors and defense molecules.     

Mutations in Cyp51 of Venturia inaequalis and their effects on DMI sensitivity

Journal of Plant Diseases and Protection - DMIs (sterol demethylation inhibitors) provide an important mode of action for control of Venturia inaequalis. They target the enzyme 14a-demethylase,...     

Geochemical analysis of Lake Bant sediments to ascertain inorganic and organic indicators for warfare residues

Purpose  

The immediate time period after the Second World War (1945–1946) was characterised by an urgent need to dispose large amounts of ammunition residues. Although the environmental relevance of explosives released to soils is intensively investigated, to date, their fate and effects in marine ecosystems are not well known. Surface sediments from Lake Bant, Germany, for which deposition of an enhanced amount of ammunition after World War II has been reported, were analysed to identify organic and inorganic indicators for warfare residues. Additionally, samples of ammunition residues collected from the Wadden Sea, Germany, were analysed in order to obtain information on the long-term behaviour of explosives in undamaged ammunition left in the aquatic environment and to obtain first insights into the spectrum of organic substances which are possibly released to the aquatic environment by such ammunition residues.     

Direct and indirect effects of tree diversity drive soil microbial diversity in temperate deciduous forest

We investigated the link between aboveground and belowground diversity in temperate deciduous forest ecosystems. To this end, we determined the effects of the tree species composition on the biomass and composition of the soil microbial community using phospholipid fatty acid (PLFA) profiles in the Hainich National Park, a deciduous mixed forest on loess over limestone in Central-Germany. We investigated the effects of the leaf litter composition on the microbial community, hypothesizing that distinctive leaf litter compositions increase signature PLFAs. In addition, we studied the impact of clay content, pH and nutrient status of the soil on the microbial community in different surface soil layers. Consequently, soil was sampled from depths of 0-5 cm, 5-10 cm and 10-20 cm. Plots with highest leaf litter diversity had the largest total amounts of fatty acids, but only PLFA 16:1ω5, which is a common marker for arbuscular mycorrhizal fungi, was significantly increased. In the uppermost soil layer, the pH explained most of the variance in microbial composition. In the deeper surface soil layers, nutrients such as carbon, nitrogen and phosphorus determined the microbial abundances and composition. Our results suggest that the soil microbial community is mainly indirectly influenced by aboveground diversity. Changes in soil pH or the soil nutrient status that are driven by specific plant traits like leave litter quality drive these indirect changes. Specific direct interactions are most reasonable for mycorrhizal fungi.