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Soils are important for ecosystem functions and services. However, soil processes are complex and changes of solid phase soil properties, such as soil organic matter contents are slow. As a consequence, a comprehensive understanding of the role of soil in the biodiversity-ecosystem functioning (BEF) relationship is still lacking. Thus, long-term observations and experiments are needed in biodiversity research in order to better understand how biodiversity influences soil properties and thus the BEF relationships. To elucidate the integrated response of soil-related functions and processes to plant diversity, we reviewed literature on the water, nutrient and carbon cycles in biodiversity research with specific focus on the Jena Experiment. Furthermore, we took advantage of the long-term observations of water, nutrient and carbon dynamics gathered in the Jena Experiment to investigate changes of the plant diversity effect over time on theses cycles and the accompanying plant-microbial interactions. We found that soil organic carbon and soil nitrogen stocks in the top 15 cm constantly increased over time and that this increase was positively related to plant species richness. In contrast, the concentrations of the quantitatively most important nutrient ions nitrate and phosphate in soil solution decreased with time, likely because of the ongoing removal of nutrients by plant biomass harvest. We furthermore observed a shift in the microbial community composition, which was triggered by an increased availability of plant-derived carbon at higher plant species richness over time, suggesting that plant communities compensated for nutrient losses by stimulating the microbial nutrient cycling. In addition, water including dissolved nutrients and carbon percolated deeper in plots of higher plant diversity. Thereby, higher plant diversity spatially extended the nutrient cycling through the microbial communities to deeper soil layers from which nutrients are transferred to the topsoil by deep-rooting plants. Although microbial nutrient cycling cannot fully compensate for negative plant diversity effects on nutrient availability in soil solution, this suggests that over time the role of plant-derived inputs becomes increasingly important for ecosystem functioning. It furthermore implies that plant species richness tightens plant-microbial interactions, which in the long-term feed back on other ecosystem functions, such as productivity.

During the last decades, a number of biodiversity experiments have been established to study the effects of plant diversity on ecosystem functioning. This research has been accompanied by a controversial discussion how “diversity effects” in experimental communities are related to the role of biodiversity in “real-world” ecosystems. To explore potential relationships, we compared plant community characteristics of 12 semi-natural managed reference grasslands to selected 10-year old communities of a large grassland biodiversity experiment (Jena Experiment): two communities initially sown with 60 species (JE60), and two communities assembled naturally during succession from bare soil (JESuc). Compared to semi-natural grasslands (17.6 ± 5.6), JE60 had higher species richness (27.5 ± 0.8), while species richness in JESuc (15.2 ± 0.5) was not different on subplots of 0.64 m2 size. Evenness and spatial heterogeneity were similar among grassland types, but biomass proportions of legumes and forbs were higher in JE60, while JESuc and semi-natural grasslands were dominated by grasses. Structural equation modelling applied to identify the drivers of biomass production in mixtures of the Jena Experiment with similar species richness (sown with 8, 16, and 60 species) and reference grasslands, showed no direct relationships between observed species richness and biomass production. In contrast, functional characteristics related to nitrogen acquisition and use were the most important variables explaining community biomass production. These functional characteristics were either driven by management intensity (fertilisation) in the “real world” reference grasslands or established by sowing in the experimental grasslands. Our results imply that species functional characteristics are key for a better understanding of the mechanisms underlying community assembly and ecosystem functioning and that the drivers of ecosystem functioning are not fundamentally different between experimental and “real-world” grasslands. Thus, experimental studies with designed extinction scenarios may help to predict the consequences of species loss for ecosystem functioning in “real-world” ecosystems.

Forest management is known to influence species diversity of various taxa but inconsistent or even contrasting effects are reported for arthropods. Regional differences in management as well as differences in regional species pools might be responsible for these inconsistencies, but, inter-regional replicated studies that account for regional variability are rare. We investigated the effect of forest type on the abundance, diversity, community structure and composition of two important ground-dwelling beetle families, Carabidae and Staphylinidae, in 149 forest stands distributed over three regions in Germany. In particular we focused on recent forestry history, stand age and dominant tree species, in addition to a number of environmental descriptors. Overall management effects on beetle communities were small and mainly mediated by structural habitat parameters such as the cover of forest canopy or the plant diversity on forest stands. The general response of both beetle taxa to forest management was similar in all regions: abundance and species richness of beetles was higher in older than in younger stands and species richness was lower in unmanaged than in managed stands. The abundance ratio of forest species-to-open habitat species differed between regions, but generally increased from young to old stands, from coniferous to deciduous stands and from managed to unmanaged stands. The response of both beetle families to dominant tree species was variable among regions and staphylinid richness varied in the response to recent forestry history. Our results suggest that current forest management practices change the composition of ground-dwelling beetle communities mainly by favoring generalists and open habitat species. To protect important forest beetle communities and thus the ecosystem functions and services provided by them, we suggest to shelter remaining ancient forests and to develop near-to-nature management strategies by prolonging rotation periods and increasing structural diversity of managed forests. Possible geographic variations in the response of beetle communities need to be considered in conservation-orientated forest management strategies. (C) 2014 Elsevier B.V. All rights reserved.

Publisher Summary Functional genomics, the science of deciphering DNA sequence structure, variation, and function have become the engine driving the discovery of traits and helps to solve intractable problems in crop production. The chapter discusses that the completion of rice draft genome sequences represents an enormous pool of information for rice improvement through marker-aided selection or genetic engineering. It also helps to understand the biological functions encoded by the sequenced DNA. A genome-wide experimental approach is instrumental in dissecting metabolic pathways important for increasing rice productivity and nutritional content. The chapter focuses on progress toward the elucidation of specific metabolic pathways linked to key quality traits in rice. Future research needs to identify direct interactions among starch biosynthetic enzymes, as well as modifying factors that regulate enzyme activity. Comparative genomics will help to distinguish components of the starch synthesizing machinery that are conserved among all plant species from those that are unique to cereals and to identify those components that differ among the various cereal species.

Publisher Summary The peppermint oil gland secretory cell (complimentary) cDNA library has proven to provide a highly enriched source of candidate genes involved in essential oil biosynthesis. A functional genomics approach has successfully been employed to clone genes involved in the mevalonate-independent pathway of isoprenoid biosynthesis and in the peppermint-specific steps producing (-)-menthol and (-)-menthone. The optimization of (liquid chromatography mass spectrography ) LC-MS technology to profile phosphorylated carbohydrates and prenyl diphosphates has helped to establish that the reaction catalyzed by 1-deoxy-D-xylulose 5- phosphate reductoisomerase (DXR) is a slow step of the mevalonate-independent pathway in peppermint. Transgenic plants with either increased or decreased steady-state DXR transcript accumulation or enzyme activity have confirmed the correlation of DXR expression rate and essential oil yield, thus providing evidence for the utility of profiling biosynthetic intermediates to predict flux control through metabolic pathways.