Effects of simulated drought and nitrogen fertilizer on plant productivity and nitrous oxide (N2O) emissions of two pastures

Aims: As a consequence of global climate change, increases in the frequencies and severities of drought are anticipated for many parts of the world. Soil moisture and nitrogen (N) are among the major factors limiting grassland productivity. In pastures, N fertilizer returns by grazing animals are spatially and temporally heterogenous, and we therefore hypothesized that responses of plants and soil processes to drought may differ at the patch level. Methods: Using rain-exclusion roofs, we simulated severe summer drought in a three-year field experiment replicated at two grassland sites contrasting in climate and management intensity. The study included a factorial N application treatment encompassing the application of cattle urine and mineral nitrogen. Responses of plants, soil microbes, and soil organic matter were assessed (carbon and nitrogen pools). N2O emissions were measured on 72 dates, and soil N2O concentration profiles on 44 dates. Results: Plant productivity responded negatively to drought and positively to N application. Interestingly, no or only small drought-effect were found on plant productivity when cumulated over the entire experimental duration, despite large effects during and shortly after the period when rain-exclusion roofs were installed. We further did not find evidence for compensatory growth after drought, and drought-effects did not differ between fertilizer hot spots and unaffected areas. In the short-term, soil microbial biomass responded positively to drought, but no long-term effects were detected. Nitrous oxide (N2O) emissions originated primarily from fertilizer hot spots, and these emissions were massively reduced under drought, with effects lasting throughout most of the growing season. On a growing season basis, N2O emissions were estimated to be 1 to 2 orders of magnitude lower under drought. Conclusions: Overall, our data suggest that even severe summer drought may have relatively little effect on plant productivity in the type of grassland and climate investigated, at least when considered on an annual basis. In contrast, drought may result in a large and sustained reduction of N2O emission

Identification of GPI anchor attachment signals by a Kohonen self-organizing map

Motivation: Anchoring of proteins to the extracytosolic leaflet of membranes via C-terminal attachment of glycosylphosphatidylinositol (GPI) is ubiquitous and essential in eukaryotes. The signal for GPI-anchoring is confined to the C-terminus of the target protein. In order to identify anchoring signals in silico, we have trained neural networks on known GPI-anchored proteins, systematically optimizing input parameters. Results: A Kohonen self-organizing map, GPI-SOM, was developed that predicts GPI-anchored proteins with high accuracy. In combination with SignalP, GPI-SOM was used in genome-wide surveys for GPI-anchored proteins in diverse eukaryotes. Apart from specialized parasites, a general trend towards higher percentages of GPI-anchored proteins in larger proteomes was observed. Availability: GPI-SOM is accessible on-line at http://gpi.unibe.ch. The source code (written in C) is available on the same website. Contact: [email protected] Supplementary information: Positive training set, performance test sets and lists of predicted GPI-anchored proteins from different eukaryotes in fasta forma

Effects of Plant Species Diversity and Composition on Nitrogen Cycling and the Trace Gas Balance of Soils

Experiments addressing the role of plant species diversity for ecosystem functioning have recently proliferated. Most studies have focused on plant biomass responses. However, microbial processes involved in the production of N2O and the oxidation of atmospheric CH4 could potentially be affected via effects on N cycling, on soil diffusive properties (due to changes in water relations and root architecture) and by more direct interactions of plants with soil microbes. We studied ecosystem-level CH4 and N2O fluxes in experimental communities assembled from two pasture soils and from combinations of 1, 3, 6, 8 or 9 species typical for these pastures. The soils contrasted with respect to texture and fertility. N2O emissions decreased with diversity and increased in the presence of legumes. Soils were sinks for CH4 at all times; legume monocultures were a smaller sink for atmospheric CH4 than non-legume monocultures, but no effect of species richness per se was detected. However, both the exchange of CH4 and N2O strongly depended on plant community composition, and on the interaction of composition with soil type, indicating that the functional role of species and their interactions differed between soils. N2O fluxes were mainly driven by effects on soil nitrate and on nitrification while soil moisture had less of an effect. Soil microbial C and N and N mineralisation rates were not altered. The driver of the interactive soil type×plant community composition-effects was less clear. Because soil methanotrophs may take longer to respond to alterations of N cycling than the 1/2year treatment in this study, we also tested species richness-effects in two separate 5-year field studies, but results were ambiguous, indicating complex interactions with soil disturbance. In conclusion, our study demonstrates that plant community composition can affect the soil trace gas balance, whereas plant species richness per se was less important; it also indicates a potential link between the botanical composition of plant communities and global warmin

A study of soil methane sink regulation in two grasslands exposed to drought and N fertilization

Oxidation by soil bacteria is the only biological sink for atmospheric methane (CH4). There are substantial uncertainties regarding the global size of this sink, in part because the ecological controls of the involved processes are not well understood to date. We have investigated effects of severe summer drought and of nitrogen inputs (ammonium nitrate or cattle urine) on soil CH4 fluxes in a field experiment. Soil moisture was the most important factor regulating the temporal dynamics of CH4 fluxes. Simulated drought episodes altered the soil's water balance throughout the year, increasing CH4 oxidation by 50% on an annual basis. N fertilizers exerted only small and transient effects at the ecosystem level. Laboratory incubations suggested that effects differed between soil layers, with larger effects of drought and N application in the top soil than in deeper layers. With soil moisture being the primary controlling factor of methanotrophy, a detailed understanding of the ecosystem's water balance is required to predict CH4 budgets under future climatic condition

Forest soil respiration reflects plant productivity across a temperature gradient in the Alps

Soil respiration (R s) plays a key role in any consideration of ecosystem carbon (C) balance. Based on the well-known temperature response of respiration in plant tissue and microbes, R s is often assumed to increase in a warmer climate. Yet, we assume that substrate availability (labile C input) is the dominant influence on R s rather than temperature. We present an analysis of NPP components and concurrent R s in temperate deciduous forests across an elevational gradient in Switzerland corresponding to a 6K difference in mean annual temperature and a considerable difference in the length of the growing season (174 vs. 262days). The sum of the short-lived NPP fractions ("canopy leaf litter,” "understory litter,” and "fine root litter”) did not differ across this thermal gradient (+6% from cold to warm sites, n.s.), irrespective of the fact that estimated annual forest wood production was more than twice as high at low compared to high elevations (largely explained by the length of the growing season). Cumulative annual R s did not differ significantly between elevations (836±5g C m−2 a−1 and 933±40g C m−2 a−1 at cold and warm sites, +12%). Annual soil CO2 release thus largely reflected the input of labile C and not temperature, despite the fact that R s showed the well-known short-term temperature response within each site. However, at any given temperature, R s was lower at the warm sites (downregulation). These results caution against assuming strong positive effects of climatic warming on R s, but support a close substrate relatedness of R

Erratum to: Effects of drought and N-fertilization on N cycling in two grassland soils

Changes in frequency and intensity of drought events are anticipated in many areas of the world. In pasture, drought effects on soil nitrogen (N) cycling are spatially and temporally heterogeneous due to N redistribution by grazers. We studied soil N cycling responses to simulated summer drought and N deposition by grazers in a 3-year field experiment replicated in two grasslands differing in climate and management. Cattle urine and NH4NO3 application increased soil NH4 + and NO3 − concentrations, and more so under drought due to reduced plant uptake and reduced nitrification and denitrification. Drought effects were, however, reflected to a minor extent only in potential nitrification, denitrifying enzyme activity (DEA), and the abundance of functional genes characteristic of nitrifying (bacterial and archaeal amoA) and denitrifying (narG, nirS, nirK, nosZ) micro-organisms. N2O emissions, however, were much reduced under drought, suggesting that this effect was driven by environmental limitations rather than by changes in the activity potential or the size of the respective microbial communities. Cattle urine stimulated nitrification and, to a lesser extent, also DEA, but more so in the absence of drought. In contrast, NH4NO3 reduced the activity of nitrifiers and denitrifiers due to top-soil acidification. In summary, our data demonstrate that complex interactions between drought, mineral N availability, soil acidification, and plant nutrient uptake control soil N cycling and associated N2O emissions. These interactive effects differed between processes of the soil N cycle, suggesting that the spatial heterogeneity in pastures needs to be taken into account when predicting changes in N cycling and associated N2O emissions in a changing climat

Ecological principles to guide the development of crop variety mixtures

Crop variety mixtures can provide many benefits, including pathogen suppression and increased yield and yield stability. However, these benefits do not necessarily occur in all mixtures, and the benefits of diversity may be compromised by disadvantages due to increased crop heterogeneity. In-field development of mixtures by assembling many combinations of crop genotypes without prior expectation about which genotypes need to be combined to produce well-performing mixtures results in prohibitively large designs. Therefore, effective tools are required to narrow down the number of promising variety mixtures, and to then identify in experiments which of these deliver the highest benefits. Here, we first review current knowledge about the mechanisms underlying effects in ecological diversity experiments and in current agricultural applications. We then discuss some of the principal difficulties arising in the application of this knowledge to develop good variety mixtures. We also discuss non-conventional approaches to solve some of these issues. In particular, we highlight the potential and limitations of trait-based methods to determine good variety mixing partners, and argue that nontraditional traits and trait-derived metrics may be needed for the trait-based approach to deliver its full potential. Specifically, we argue that good mixing partners can be identified using modern genetic and genomic approaches. Alternatively, good mixtures may be obtained by combining varieties that respond differently to environmental variation; such varieties could easily be identified in standard variety testing trials. Preliminary analyses show that niche differences underlying the different environmental responses can indicate functional complementarity and promote mixture yield and yield stability

Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats

<p>Abstract</p> <p>Background</p> <p>Many parasitic organisms, eukaryotes as well as bacteria, possess surface antigens with amino acid repeats. Making up the interface between host and pathogen such repetitive proteins may be virulence factors involved in immune evasion or cytoadherence. They find immunological applications in serodiagnostics and vaccine development. Here we use proteins which contain perfect repeats as a basis for comparative genomics between parasitic and free-living organisms.</p> <p>Results</p> <p>We have developed Reptile <url>http://reptile.unibe.ch</url>, a program for proteome-wide probabilistic description of perfect repeats in proteins. Parasite proteomes exhibited a large variance regarding the proportion of repeat-containing proteins. Interestingly, there was a good correlation between the percentage of highly repetitive proteins and mean protein length in parasite proteomes, but not at all in the proteomes of free-living eukaryotes. Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites.</p> <p>Conclusion</p> <p>Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance. An on-line tool is available at <url>http://genomics.unibe.ch/dora</url>.</p

Nutrient relations in calcareous grassland under elevated CO2

Plant nutrient responses to 4 years of CO2 enrichment were investigated in situ in calcareous grassland. Beginning in year 2, plant aboveground C:N ratios were increased by 9% to 22% at elevated CO2 (P > 0.01), depending on year. Total amounts of N removed in biomass harvests during the first 4 years were not affected by elevated CO2 (19.9 +/- 1.3 and 21.1 +/- 1.3 g N m(-2) at ambient and elevated CO2), indicating that the observed plant biomass increases were solely attained by dilution of nutrients. Total aboveground P and tissue N:P ratios also were not altered by CO2 enrichment (12.5 +/- 2 g N g(-1) P in both treatments). In contrast to non-legumes (<98% of community aboveground biomass), legume C/N was not reduced at elevated CO2 and legume N:P was slightly increased. We attribute the less reduced N concentration in legumes at elevated CO2 to the fact that virtually all legume N originated from symbiotic N-2 fixation (%N-dfa approximate to 90%), and thus legume growth was not limited by soil N. While total plant N was not affected by elevated CO2, microbial N pools increased by +18% under CO2 enrichment (P = 0.04) and plant available soil N decreased. Hence, there was a net increase in the overall biotic N pool, largely due increases in the microbial N pool. In order to assess the effects of legumes for ecosystem CO2 responses and to estimate the degree to which plant growth was P-limited, two greenhouse experiments were conducted, using firstly undisturbed grassland monoliths from the field site, and secondly designed 'microcosm' communities on natural soil. Half the microcosms were planted with legumes and half were planted without. Both monoliths and microcosms were exposed to elevated CO2 and P fertilization in a factored design. After two seasons, plant N pools in both unfertilized monoliths and microcosm communities were unaffected by CO2 enrichment, similar to what was found in the field. However, when P was added total plant N pools increased at elevated CO2. This community-level effect originated almost solely from legume stimulation. The results suggest a complex interaction between atmospheric CO2 concentrations, N and P supply. Overall ecosystem productivity is N-limited, whereas CO2 effects on legume growth and their N2 fixation are limited by P

A plant biodiversity effect resolved to a single chromosomal region

Despite extensive evidence that biodiversity promotes plant community productivity, progress towards understanding the mechanistic basis of this effect remains slow, impeding the development of predictive ecological theory and agricultural applications. Here, we analysed non-additive interactions between genetically divergent Arabidopsis accessions in experimental plant communities. By combining methods from ecology and quantitative genetics, we identify a major effect locus at which allelic differences between individuals increase the above-ground productivity of communities. In experiments with near-isogenic lines, we show that this diversity effect acts independently of other genomic regions and can be resolved to a single region representing less than 0.3% of the genome. Using plant–soil feedback experiments, we also demonstrate that allelic diversity causes genotype-specific soil legacy responses in a consecutive growing period, even after the original community has disappeared. Our work thus suggests that positive diversity effects can be linked to single Mendelian factors, and that a range of complex community properties can have a simple cause. This may pave the way to novel breeding strategies, focusing on phenotypic properties that manifest themselves beyond isolated individuals; that is, at a higher level of biological organization