A commentary on current approaches to forest population genetics

Some of the most frequently chosen approaches to forest population genetics as reflected in the present volume are discussed, and some topics possibly deserving more attention are addressed. Among the first are studies of self-fertilization as a characteristic of forest tree mating systems, gene markers as indicators of adaptive or phylogenetic differentiation, and methodological aspects of the measurement of genetic differentiation. The latter mainly concern generalizable methods of analysis and the involvement of gene markers in the determination of mating systems, detection of mechanisms of frequency dependent selection, and the incorporation of genetic profiles (characteristics of frequency distributions of genetic types) into population genetic analysis.     

Influence of long-term fertilization with farmyard manure on soil organic matter: Characteristics of particle-size fractions

Summary The influence of more than 100 years of fertilization with farmyard manure on soil organic matter in comparison to unfertilized soil was studied in particle-size fractions using elemental (C and N) analyses and pyrolysis-field ionization mass spectrometry. Distinct differences in C and N concentrations and distribution and in the quality of organic matter between the size fractions and the fertilization treatments were observed. Clay-associated C and N were relatively higher in the unfertilized treatment, whereas the application of farmyard manure preferentially increased soil organic matter associated with the fine and medium silt fractions. Pyrolysis-field ionization mass spectrometry of soil fractions <20 m showed increasing values for lignin monomers and dimers and fatty acids with larger equivalent diameters, whereas the proportion of N compounds, mono- and polysaccharides and phenolics decreased in the larger size fractions. Sand fractions were particularly rich in lignin fragments, mono- and polysaccharides, and alkanes/alkenes. These relationships seemed to be independent of management practices. In the same size fractions of the different treatments, however, a higher relative abundance of N-compounds, mono- and polysaccharides, phenolics, lignin monomers, and alkanes/alkenes was observed in the unfertilized variant. Lignin dimers and fatty acids were more abundant in the farmyard manure treatment. Both trends together imply that soil enrichment in organic matter due to the application of farmyard manure largely reflects an increase in lignin building blocks and partly reflects an increase in lipids such as fatty acids in the silt fractions. Therefore these constituents are of particular importance in assessing the positive effects of farmyard manure on soil fertility.     

Characterization of cultivation effects on soil organic matter

Humus properties in various Ap horizons from field plots, that have been cultivated in long-term experiments under different management conditions, were investigated by pyrolysis-field ionization mass spectrometry (Py-FIMS) and ¹³C-NMR spectroscopy. The results of Py-FIMS were evaluated by correlation and principal component analysis from reproducible data sets of bulk soil samples and extracted humic substances, and allowed a distinct discrimination on the basis of humus quality and composition. The chemical subunits suitable for discrimination are the major plant constituents carbohydrates, lignin, and proteinaceous materials as well as their humification products. The contribution of these compound classes to soil organic matter decreased with the intensity of management. CPMAS and solution ¹³C NMR spectra of soils and humic substances demonstrated that with more intense management, both the intensities of the phenolic region (140–160 ppm) and the aromatic region (110–140 ppm) decreased. The combination of both independent methods MS and NMR, together with microbiological and biochemical data, yields the general result that intensive soil management leads to a less active humus.     

A structural mechanism for MscS gating in lipid bilayers

The mechanosensitive channel of small conductance (MscS) is a key determinant in the prokaryotic response to osmotic challenges. We determined the structural rearrangements associated with MscS activation in membranes, using functorial measurements, electron paramagnetic resonance spectroscopy, and computational analyses. MscS was trapped in its open conformation after the transbilayer pressure profile was modified through the asymmetric incorporation of lysophospholipids. The transition from the closed to the open state is accompanied by the downward tilting of the transmembrane TM1-TM2 hairpin and by the expansion, tilt, and rotation of the TM3 helices. These movements expand the permeation pathway, leading to an increase in accessibility to water around TM3. Our open MscS model is compatible with single-channel conductance measurements and supports the notion that helix tilting is associated with efficient pore widening in mechanosensitive channels.     

Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction

Despite the recent advances in single-molecule manipulation techniques, purely mechanical approaches cannot detect subtle conformational changes in the biologically important regime of weak forces. We developed a hybrid scheme combining force and fluorescence that allowed us to examine the effect of subpiconewton forces on the nanometer scale motion of the Holliday junction (HJ) at 100-hertz bandwidth. The HJ is an exquisitely sensitive force sensor whose force response is amplified with an increase in its arm lengths, demonstrating a lever-arm effect at the nanometer-length scale. Mechanical interrogation of the HJ in three different directions helped elucidate the structures of the transient species populated during its conformational changes. This method of mapping two-dimensional reaction landscapes at low forces is readily applicable to other nucleic acid systems and their interactions with proteins and enzymes.     

Structural studies on soil nitrogen by Curie-point pyrolysis — gas chromatography/mass spectrometry with nitrogen-selective detection

Curie-point pyrolysis-gas chromatography mass spectrometry with N-selective detection was used to characterize the structure of organic N compounds in four mineral soils. The technique was found suitable for the fast, sensitive, and highly specific identification of N-containing pyrolysis products from whole soils with total N contents between 0.08 and 0.46%. In order to optimize the methodology, one agricultural soil was pyrolyzed at final temperatures of 573, 773, and 973 K. Almost no chemical alterations to identifiable pyrolysis products were observed when the final pyrolysis temperature was increased from 573 to 973 K. More than 50 N-containing pyrolysis products were identified, and were divided into compound classes chracterized by specific molecular-chemical structures. These included pyrroles, imidazoles, pyrazoles, pyridines, pyrimidines, pyrazines, indoles, quinolines, N derivatives of benzene, alkyl nitriles, and aliphatic amines. Three additional soil samples different in origin and N content were analyzed at 773 K and each showed a specific thermosensitive N-selective chromatogram. Many N-containing pyrolysis products were identified in all samples, which indicated general qualitative regularities in the thermal release of N-containing pyrolysis products from the four soils. In the pyrolyzates of the investigated soils a number of compounds were identified, which is usually not detectable in pyrolysis-gas chromatography spectrometry analyses with N-selective detection of plants and microorganisms. Among these were N derivatives of benzene and long-chain alkyl nitriles, which appear to be soil-specific and suggest significant transformations of organic N in soils. Thus, our results contribute to a better understanding of the molecular-chemical structure of unknown N.     

Thermal stability and composition of mineral-bound organic matter in density fractions of soil

Heavy density fractions of soil contain organic matter tightly bound to the surface of soil minerals. The chemical composition and ecological meaning of non-metabolic decomposition products and microbial metabolites in organic–mineral bonds is poorly understood. Therefore, we investigated the heavy fraction (density > 2 g cm^–3) from the topsoil of a Gleysol (Bainsville, Ottawa, Canada). It accounted for 952 g kg^–1 of soil and contained 19 g kg^–1 of organic C. Pyrolysis-field ionization mass spectra showed intensive signals of carbohydrates, and phenols and lignin monomers, alkylaromatics (mostly aromatic) N-containing compounds, and peptides. These classes of compound have been proposed as structural building blocks of soil organic matter. In comparison, the light fraction (density > 2 g cm^–3) was richer in lignin dimers, lipids, sterols, suberin and fatty acids which clearly indicate residues of plants and biota. To confirm the composition and stability of mineral-bound organic matter, we also investigated the heavy fraction (density > 2.2 g cm^–3) from clay-, silt- and sand-sized separates of the topsoil of a Chernozem (Bad Lauchstädt, Germany). These heavy size separates differed in their mass spectra but were generally characterized by volatilization maxima of alkylaromatics, lipids and sterols at about 500°C. We think that the observed high-temperature volatilization of these structural building blocks of soil organic matter is indicative of the organic–mineral bonds. Some unexpected low-temperature volatilization of carbohydrates, N-containing compounds, peptides, and phenols and lignin monomers was assigned to hot-water-extractable organic matter which accounted for 7–27% of the carbon and nitrogen in the heavy fractions. As this material is known to be mineralizable, our study indicates that these constituents of the heavy density fractions are degradable by micro-organisms and involved in the turnover of soil organic matter.     

Litter decomposition and humification in acidic forest soils studied by chemical degradation,IR and NMR spectroscopy and pyrolysis field ionization mass spectrometry

Two forest soils (Typic Dystrochrept, Entic Haplorthod) with mor and moder were investigated by chemical degradation, IR and CPMAS ¹³C NMR spectroscopy and pyrolysis (Py) field ionization (FI) mass spectrometry (MS). Chemical analyses show that during litter decomposition, humification, and podzolisation, cellulose and lignin structures decrease considerably, whereas no distinct changes were found for the hemicellulose and protein fractions. These results are consistent with current hypotheses on the conversion of plant residues to stable humic substances, but the sum of chemically identified organic soil components of the litter layers only accounts for 40–50% of total organic carbon. The amounts of different carbon types were estimated by the integration of CPMAS ¹³C NMR spectra. For the L layers this calculation assigns 56–58% as O-alkyl-C, 20–22% as alkyl-C, 14–16% as aryl-C, and 6–8% as carboxyl-C. With increasing soil depth O-alkyl-C (with polysaccharides as main source) decrease to 31–42%, aliphatic C increases to 36–43%, and aryl- and carboxyl-C show no distinct changes. The hypothesis of an increasing aromaticity during humification in soils therefore is questionable. Data from Py-FIMS confirm and extend the results' of chemical methods as well as IR and ¹³C NMR spectroscopy. In particular, the Fi mass spectra of the generated pyrolysates show that the increase in polymethylene carbon during the biodegradation and humification of beech and spruce litter is partly due to an increase of saturated fatty acids. This means, Py-FIMS is able to describe the structure of wet-chemically unaccounted, individual humus constituents and thus improves the knowledge about the genesis of humic substances.