Global Data Set (global + data_set)

Distribution by Scientific Domains

Selected Abstracts

Global phenotypic characterization of bacteria

Barry R. Bochner
Abstract The measure of the quality of a systems biology model is how well it can reproduce and predict the behaviors of a biological system such as a microbial cell. In recent years, these models have been built up in layers, and each layer has been growing in sophistication and accuracy in parallel with a global data set to challenge and validate the models in predicting the content or activities of genes (genomics), proteins (proteomics), metabolites (metabolomics), and ultimately cell phenotypes (phenomics). This review focuses on the latter, the phenotypes of microbial cells. The development of Phenotype MicroArrays, which attempt to give a global view of cellular phenotypes, is described. In addition to their use in fleshing out and validating systems biology models, there are many other uses of this global phenotyping technology in basic and applied microbiology research, which are also described. [source]

Trends and methodological impacts in soil CO2 efflux partitioning: A metaanalytical review

Abstract Partitioning soil carbon dioxide (CO2) efflux (RS) into autotrophic (RA; including plant roots and closely associated organisms) and heterotrophic (RH) components has received considerable attention, as differential responses of these components to environmental change have profound implications for the soil and ecosystem C balance. The increasing number of partitioning studies allows a more detailed analysis of experimental constraints than was previously possible. We present results of an exhaustive literature search of partitioning studies and analyse global trends in flux partitioning between biomes and ecosystem types by means of a metaanalysis. Across all data, an overall decline in the RH/RS ratio for increasing annual RS fluxes emerged. For forest ecosystems, boreal coniferous sites showed significantly higher (P<0.05) RH/RS ratios than temperate sites, while both temperate or tropical deciduous forests did not differ in ratios from any of the other forest types. While chronosequence studies report consistent declines in the RH/RS ratio with age, no difference could be detected for different age groups in the global data set. Different methodologies showed generally good agreement if the range of RS under which they had been measured was considered, with the exception of studies estimating RH by means of root mass regressions against RS, which resulted in consistently lower RH/RS estimates out of all methods included. Additionally, the time step over which fluxes were partitioned did not affect RH/RS ratios consistently. To put results into context, we review the most common techniques and point out the likely sources of errors associated with them. In order to improve soil CO2 efflux partitioning in future experiments, we include methodological recommendations, and also highlight the potential interactions between soil components that may be overlooked as a consequence of the partitioning process itself. [source]

Global-scale patterns of nutrient resorption associated with latitude, temperature and precipitation

GLOBAL ECOLOGY, Issue 1 2009
Z. Y. Yuan
ABSTRACT Aim Nutrient resorption from senescing leaves is an important mechanism of nutrient conservation in plants, but the patterns of nutrient resorption at the global scale are unknown. Because soil nutrients vary along climatic gradients, we hypothesize that nutrient resorption changes with latitude, temperature and precipitation. Location Global. Methods We conducted a meta-analysis on a global data set collected from published literature on nitrogen (N) and phosphorus (P) resorption of woody plants. Results For all data pooled, both N resorption efficiency (NRE) and P resorption efficiency (PRE) were significantly related to latitude, mean annual temperature (MAT) and mean annual precipitation (MAP): NRE increased with latitude but decreased with MAT and MAP. In contrast, PRE decreased with latitude but increased with MAT and MAP. When functional groups (shrub versus tree, coniferous versus broadleaf and evergreen versus deciduous) were examined individually, the patterns of NRE and PRE in relation to latitude, MAT and MAP were generally similar. Main conclusions The relationships between N and P resorption and latitude, MAT and MAP indicate the existence of geographical patterns of plant nutrient conservation strategies in relation to temperature and precipitation at the global scale, particularly for PRE, which can be an indicator for P limitation in the tropics and selective pressure shaping the evolution of plant traits. Our results suggest that, although the magnitude of plant nutrient resorption might be regulated by local factors such as substrate, spatial patterns are also controlled by temperature or precipitation. [source]

Testing the role of genetic factors across multiple independent invasions of the shrub Scotch broom (Cytisus scoparius)

Abstract Knowledge of the introduction history of invasive plants informs on theories of invasiveness and assists in the invasives management. For the highly successful invasive shrub Scotch broom, Cytisus scoparius, we analysed a combination of nuclear and chloroplast microsatellites for eight native source regions and eight independent invasion events in four countries across three continents. We found that two exotic Australian populations came from different sources, one of which was derived from multiple native populations, as was an invasive sample from California. An invasive population from New Zealand appeared to be predominantly sourced from a single population, either from the native or exotic ranges. Four invasive populations from Chile were genetically differentiated from the native range samples analysed here and so their source of introduction could not be confirmed, but high levels of differentiation between the Chilean populations suggested a combination of different sources. This extensive global data set of replicated introductions also enabled tests of key theories of invasiveness in relation to genetic diversity. We conclude that invasive populations have similar levels of high genetic diversity to native ranges; levels of admixture may vary across invasive populations so admixture does not appear to have been an essential requirement for invasion; invasive and native populations exhibit similar level of genetic structure indicating similar gene flow dynamics for both types of populations. High levels of diversity and multiple source populations for invasive populations observed here discount founder effects or drift as likely explanations for previously observed seed size differences between ranges. The high levels of genetic diversity, differential and source admixture identified for most exotic populations are likely to limit the ability to source biocontrol agents from the native region of origin of invasive populations. [source]

Shifts in leaf N : P ratio during resorption reflect soil P in temperate rainforest

Sarah J. Richardson
Summary 1Large-scale syntheses of leaf and litter N and P concentrations have demonstrated that leaf and litter N : P ratios both decline with latitude, that litter N : P ratios are generally greater than those of fresh leaves, and that the difference between these two ratios increases towards the tropics. These patterns have been ascribed to either a direct effect of temperature on plant growth rates and leaf-level physiology, or a decline in soil P towards the tropics. We test the hypothesis that global patterns of leaf and litter N : P ratios reflect a soil-P gradient by examining leaf and litter N : P in all species from a temperate rainforest along a soil-P gradient. 2The soil P gradient followed a toposequence of 20 plots. There was > 50-fold variation in soil total P from ridges (23,136 mg kg,1), through faces and terraces (32,744 mg kg,1), to gullies (440,1214 mg kg,1). 3The N : P ratios of leaves and litter both declined as soil total P increased, and the N : P ratio of litter was greater than that of fresh leaves. The difference between litter N : P and fresh leaf N : P declined with increasing soil total P supporting the hypothesis that global patterns of N : P ratios reflect gradients of soil P. 4Compositional turnover with soil P partly contributed to the total plant community leaf and litter nutrient concentration responses. However, consistent within-species responses pointed to a soil-based mechanism for determining responses by the total plant community. 5Comparisons of our litter data to global data sets suggest that the vegetation was well adapted to low soil nutrient concentrations with 37% of litter N and 24% of litter P samples being below published thresholds for highly proficient nutrient resorption. 6The range of leaf N and leaf P concentrations at our site captured a large portion of the range reported in global leaf trait data sets. 7Highly proficient P resorption was responsible for the divergence in leaf and litter N : P ratios on P-poor soils. These results emphasize the significance of proficient nutrient resorption as an advantageous plant trait for nutrient conservation on P-poor soils. [source]