Testing hypotheses on interlinks between silicon and organic matter cycling in rice ecosystems

Recent studies demonstrated that sufficient Si supply enhances the resistance of rice plants against biotic and abiotic stresses. The mechanisms by which Si supports the stress resistance are still under debate. One hypothesis assumes that phytoliths exert similar eco-physiological functions as organic structural compounds. The formation of amorphous Si oxide bodies (`phytoliths`) within the plant tissue, therefore, represents an energy-saving alternative to synthesis of organic structural compounds, such as cellulose and lignin. Hence, Si availability may interact with the recycling of organic matter because rates of plant litter decomposition are regulated by contents of structural organic compounds. We currently test the hypothesis using a large set of rice straw samples collected at 70 paddy fields in Vietnam and the Philippines. Due to the differing portions of weatherable silicate minerals in soil, Si availability varies largely between the fields; the Si concentrations in the straw samples, thus, range from 1.6 to 10.7%. The Si concentrations are significantly negatively related to carbon concentrations, which range from 31.1 to 42.5% (the R2 of the linear relationship is 0.83). In turn, no relationships between Si and nitrogen concentrations were found. These findings support the assumption that Si substitutes N-poor structural compounds in rice plants. Currently, we apply cupric oxide oxidation analysis to the straw samples in order to test for relationships between concentrations Si and lignin. The results will be included into the proposed presentation

A flowering-time gene network model for association analysis in Arabidopsis thaliana

In our project we want to determine a set of single nucleotide polymorphisms (SNPs), which have a major effect on the flowering time of Arabidopsis thaliana. Instead of performing a genome-wide association study on all SNPs in the genome of Arabidopsis thaliana, we examine the subset of SNPs from the flowering-time gene network model. We are interested in how the results of the association study vary when using only the ascertained subset of SNPs from the flowering network model, and when additionally using the information encoded by the structure of the network model. The network model is compiled from the literature by manual analysis and contains genes which have been found to affect the flowering time of Arabidopsis thaliana [Far+08; KW07]. The genes in this model are annotated with the SNPs that are located in these genes, or in near proximity to them. In a baseline comparison between the subset of SNPs from the graph and the set of all SNPs, we omit the structural information and calculate the correlation between the individual SNPs and the flowering time phenotype by use of statistical methods. Through this we can determine the subset of SNPs with the highest correlation to the flowering time. In order to further refine this subset, we include the additional information provided by the network structure by conducting a graph-based feature pre-selection. In the further course of this project we want to validate and examine the resulting set of SNPs and their corresponding genes with experimental methods

Highlights from the Student Council Symposium 2011 at the International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology

The Student Council (SC) of the International Society for Computational Biology (ISCB) organized their annual symposium in conjunction with the Intelligent Systems for Molecular Biology (ISMB) conference

Persistence of dissolved organic matter explained by molecular changes during its passage through soil

Dissolved organic matter affects fundamental biogeochemical processes in the soil such as nutrient cycling and organic matter storage. The current paradigm is that processing of dissolved organic matter converges to recalcitrant molecules (those that resist degradation) of low molecular mass and high molecular diversity through biotic and abiotic processes. Here we demonstrate that the molecular composition and properties of dissolved organic matter continuously change during soil passage and propose that this reflects a continual shifting of its sources. Using ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, we studied the molecular changes of dissolved organic matter from the soil surface to 60 cm depth in 20 temperate grassland communities in soil type Eutric Fluvisol. Applying a semi-quantitative approach, we observed that plant-derived molecules were first broken down into molecules containing a large proportion of low-molecular-mass compounds. These low-molecular-mass compounds became less abundant during soil passage, whereas larger molecules, depleted in plant-related ligno-cellulosic structures, became more abundant. These findings indicate that the small plant-derived molecules were preferentially consumed by microorganisms and transformed into larger microbial-derived molecules. This suggests that dissolved organic matter is not intrinsically recalcitrant but instead persists in soil as a result of simultaneous consumption, transformation and formation

No depth-dependence of fine root litter decomposition in temperate beech forest soils

Aims Subsoil organic carbon (OC) tends to be older and is presumed to be more stable than topsoil OC, but the reasons for this are not yet resolved. One hypothesis is that decomposition rates decrease with increasing soil depth. We tested whether decomposition rates of beech fine root litter varied with depth for a range of soils using a litterbag experiment in German beech forest plots. Methods In three study regions (Schorfheide-Chorin, Hainich-Dün and Schwäbische-Alb), we buried 432 litterbags containing 0.5 g of standardized beech root material (fine roots with a similar chemical composition collected from 2 year old Fagus sylvatica L. saplings, root diameter<2mm) at three different soil depths (5, 20 and 35 cm). The decomposition rates as well as the changes in the carbon (C) and nitrogen (N) concentrations of the decomposing fine root litter were determined at a 6 months interval during a 2 years field experiment. Results The amount of root litter remaining after 2 years of field incubation differed between the study regions (76 ± 2 % in Schorfheide-Chorin, 85 ± 2 % in Schwäbische-Alb, and 88±2 % in Hainich-Dün) but did not vary with soil depth. Conclusions Our results indicate that the initial fine root decomposition rates are more influenced by regional scale differences in environmental conditions including climate and soil parent material, than by changes in microbial activities with soil depth. Moreover, they suggest that a similar potential to decompose new resources in the form of root litter exists in both surface and deep soils

Processes controlling the production of aromatic water-soluble organic matter during litter decomposition

Dissolved organic matter (DOM) plays a fundamental role for many soil processes. For instance, production, transport, and retention of DOM control properties and long-term storage of organic matter in mineral soils. Production of water-soluble compounds during the decomposition of plant litter is a major process providing DOM in soils. Herein, we examine processes causing the commonly observed increase in contribution of aromatic compounds to WSOM during litter decomposition, and unravel the relationship between lignin degradation and the production of aromatic WSOM. We analysed amounts and composition of water-soluble organic matter (WSOM) produced during 27 months of decomposition of leaves and needles (ash, beech, maple, spruce, pine). The contribution of aromatic compounds to WSOM, as indicated by the specific UV absorbance of WSOM, remained constant or increased during decomposition. However, the contribution of lignin-derived compounds to the total phenolic products of 13C-labelled tetramethylammonium hydroxide (13C-TMAH) thermochemolysis increased strongly (by >114%) within 27 months of decomposition. Simultaneous changes in contents of lignin phenols in solid litter residues (cupric oxide method as well as 13C-TMAH thermochemolysis) were comparably small (−39% to +21% within 27 months). This suggests that the increasing contribution of lignin-derived compounds to WSOM during decomposition does not reflect compositional changes of solid litter residues, but rather the course of decomposition processes. In the light of recently published findings, these processes include: (i) progressive oxidative alteration of lignin that results in increasing solubility of lignin, (ii) preferential degradation of soluble, non-lignin compounds that limits their contribution to WSOM during later phases of decomposition