Qualitative simulation of the carbon starvation response in Escherichia coli

In case of nutritional stress, like carbon starvation, Escherichia coli cells abandon their exponential-growth state to enter a more resistant, non-growth state called stationary phase. This growth-phase transition is controlled by a genetic regulatory network integrating various environmental signals. Although E. coli is a paradigm of the bacterial world, it is little understood how its response to carbon starvation conditions emerges from the interactions between the different components of the regulatory network. Using a qualitative method that is able to overcome the current lack of quantitative data on kinetic parameters and molecular concentrations, we model the carbon starvation response network and simulate the response of E. coli cells to carbon deprivation. This allows us to identify essential features of the transition between exponential and stationary phase and to make new predictions on the qualitative system behavior following a carbon upshift.     

Evidence at hand: Diversity, functional implications, and locomotor prediction in intrinsic hand proportions of diprotodontian marsupials

Knowledge about the diversity, locomotor adaptations, and evolution of the marsupial forelimb is limited, resulting in an underrepresentation of marsupials in comparative anatomical literature on mammalian forelimb anatomy. This study investigated hand proportions in the diverse marsupial order Diprotodontia. Fifty-two measurements of 95 specimens representing 47 species, as well as 6 non-diprotodontian specimens, were explored using principal components analysis (PCA). Bootstrapping was used to assess the reliability of the loadings. Phylogenetically independent contrasts and phylogenetic ANOVA were used to test for correlation with size and functional adaptation of forelimbs for locomotor habit, scored as arboreal vs. terrestrial. Analysis of first principal component (PC1) scores revealed significant differences between arboreal and terrestrial species, and was related to relative slenderness of their phalangeal elements. Both locomotor groups displayed allometry along PC1 scores, but with different intercepts such that PC1 discriminated between the two locomotor habits almost completely. PC2 separated some higher-level clades and burrowing species. Analysis of locomotor predictors commonly applied by palaeontologists indicates that ratios between proximal and intermediate phalanges were unsuitable as predictors of arboreality/terrestriality, but the phalangeal index was more effective. From PCA results, a phalangeal slenderness ratio was developed which proved to be a useful discriminator, suggesting that a single unallocated phalanx can be used for an impression of locomotor mode in fossils. Most Diprotodontia are laterally paraxonic or ectaxonic, with the exception of digging species whose hands are medially paraxonic. Our results complement those of studies on placental mammals, suggesting that the demands of arboreality, terrestriality, or frequent digging on intrinsic hand proportions are met with similar anatomical adaptations in marsupials.     

Do carbon-based defences reduce foliar damage? Habitat-related effects on tree seedling performance in a temperate rainforest of Chiloé Island, Chile

Carbon-based secondary compounds (CBSCs), such as phenols or tannins, have been considered as one of the most important and general chemical barriers of woody plants against a diverse array of herbivores. Herbivory has been described as a critical factor affecting the growth and survival of newly established tree seedlings or juveniles then, the presence of secondary metabolites as defences against herbivores should be a primary strategy to reduce foliar damage. We examined whether light-induced changes in leaf phenolic chemistry affected insect herbivory on seedlings of two rainforest tree species, Drimys winteri (Winteraceae) and Gevuina avellana (Proteaceae). Seedlings of both species were planted under closed canopy and in a canopy gap within a large remnant forest patch. Half of the seedlings in each habitat were disinfected with a wide-spectrum systemic insecticide and the other half were used as controls. Seedling growth, survival, and foliar damage (estimated by an herbivory index) due to insect herbivores were monitored over a period of 16 months (December 2001–April 2003). The total leaf content of phenols and condensed tannins were assessed in seedlings from both habitats. As expected, access to light induced a greater production of CBSCs in seedlings of both tree species, but these compounds did not seem to play a significant defensive role, as seedlings grown in gaps suffered greater leaf damage than those planted in forest interior. In addition, in both habitats, seedlings without insecticide treatment suffered a greater foliar damage than those with insecticide, especially 16 months after the beginning of the experiment. Canopy openness and herbivory had positive and negative effects, respectively, on seedling growth and survival in both tree species. In conclusion, despite the higher levels of defence in tree-fall gap, the higher densities of herbivore override this and lead to higher damage levels.     

Response of soil properties and maize yield to simulated erosion by artificial topsoil removal

The study was aimed at identifying the soil properties responsible for maize yield decline on eroded soils and at quantifying their relationship with yield. Topsoil was artificially removed to incremental depths of 0, 5, 10, 15 and 20 cm to simulate various degrees of erosion. Maize growth and yield were monitored on the plots and soil physical and chemical properties were determined after two years (4 seasons) of cultivation. Soil pH was significantly higher on the control plot and decreased with increased depth of topsoil removal. Bulk density (BD) increased with depth of topsoil removal from a mean value of 1.38 g cm⁻³ under control to 1.55 g cm⁻³ at 20 cm depth of removal, while cone index of penetrometer resistance (CI) correspondingly increased from 1.09 g cm⁻² to 1.37 g cm⁻². Maize yield significantly decreased in the first year from 3.2 t ha⁻¹ on the control plot to 0.12 t ha⁻¹ where 20 cm of topsoil was removed and correspondingly from 1.85 to 0.09 t ha⁻¹ in the second year of cropping. Maize yield decreased exponentially with increase in depth of topsoil removal (r ²=0.99, P<0.01) with an average of 55% yield loss on the removal of just 5 cm topsoil. Soil organic carbon (SOC), BD, CI, field capacity (FC), pH and exchangeable Mg²⁺ were significantly correlated to maize yield parameters. However, factor analysis showed that the combination of SOC and exchangeable Mg²⁺ with soil physical properties (BD, FC, CI and depth of topsoil removal) explained 99% of variation in maize grain yield. The need for conservation farm practices is recommended on the soil to prevent soil degradation. Section Editor: L. Wade     

From Flooded to Aerobic Conditions in Rice Cultivation: Consequences for Zinc Uptake

Scarcity of water causes a shift from flooded to aerobic conditions for rice production in zinc deficient areas in Northern China. This shift alters soil conditions that affect zinc availability to the crop. This paper concerns the effect of aerobic compared to flooded conditions on crop biomass production, grain yield and zinc content. A field experiment was done with six rice genotypes (Oryza sativa L.) grown on a calcareous soil, both with (23 kg Zn ha⁻¹) and without Zn fertilization. Sampling was conducted at tillering and physiological mature stage. Zn concentration in the shoots was significantly lower at both stages in plants grown in the aerobic field. At maturity, Zn uptake, biomass production, grain yield and Zn-harvest index [grain Zn/(shoot + grain Zn)] were lower under aerobic cultivation. Rice genotypes including aerobic rice and lowland rice differ in degree of response to low Zn supply. A twofold difference was found among aerobic genotypes in grain yield and Zn uptake. Also Zn-harvest index varied significantly. Zn application affected neither grain yield nor grain Zn content, although it significantly improved biomass production in both systems in most genotypes. These results demonstrate that introduction of aerobic rice systems on calcareous soils may increase Zn deficiency problems.     

Soil CO2 efflux in uneven-aged managed forests: temporal patterns following harvest and effects of edaphic heterogeneity

Increased nutrient availability can have a large impact in Australian woodland ecosystems, many of which are very poor in nutrients, particularly phosphorus. A study was conducted in an urban Banksia woodland remnant in Perth, southwest Western Australia to test the hypothesis that the soil nutrient status in areas in good condition (GC), poor condition invaded by the perennial grass Ehrharta calycina (PCe), and poor condition invaded by the perennial herb Pelargonium capitatum (PCp), is reflected in the nutrient status of the native and introduced species. Leaf concentrations of P, K, N, Na, Ca, Mg, S, B, Cu, Fe, Mn and Zn of six native (Banksia attenuata, Banksia menziesii, Allocasuarina humilis, Melaleuca systena, Macrozamia fraseri and Conostylis aculeata) and four introduced species (Ehrharta calycina, Pelargonium capitatum, Gladiolus caryophyllaceus and Briza maxima), were measured. Soil pH, electrical conductivity, N (total), P (total), available P, K, S and organic C were assessed beneath all species on all sites. Significantly higher concentrations of soil P (total) and P (HCO₃) were found at PCe and PCp sites than GC sites, while PCp sites also had significantly higher soil concentrations for N (total) and S. Principal Components Analysis of the leaf analyses showed (a) individual species have characteristically different nutrient concentrations; (b) the introduced species Ehrharta calycina and Pelargonium capitatum clustered separately from each other and by vegetation condition. Leaf concentrations of P were significantly (P<0.05) higher, and K and Cu were significantly lower in PCe and PCp sites compared with those at GC sites. Introduced species leaf nutrient concentrations were significantly greater than native species for all nutrients except Mn which was significantly lower, with no differences for Mg and B. The results indicate a key role for P in the Banksia woodland, and we conclude that higher levels of available P at invaded sites are having a detrimental impact on the ecosystem. These results provide new knowledge to enhance conservation practices for the management of the key threatening process of invasion within a biodiversity hot spot. Section Editor: T. Kalapos     

Foraminiferal assemblages and the confinement index as tools for assessment of saline intrusion and human impact in the Mekong Delta and neighbouring areas (Vietnam)

Foraminiferal assemblages have been studied in 33 samples from the Can Gio region to the north of the Mekong Delta and from two regions of the Delta: the Tra Vinh province, in the middle part of the Delta; and the Ca Mau peninsula, to the south. Two plates, including 117 pictures, illustrate the species. These assemblages, either through the nature of the test or through the calculation of the confinement index Ic, clearly indicate differences in the balance between continental and marine influences, the Tra Vinh province being subject to the strongest freshwater influence. The decrease of calcareous specimens and the increase of Ic indicate the impact of deforestation in the Ca Mau peninsula, the influence of organic matter in shrimp ponds, and the impact of pollution in a tidal channel. The distribution of foraminiferal assemblages described in this study should be used as part of a reference point for further observations with a view to assessing environmental impacts of increasing human activities and/or global change.     

Uncertainty in Diatom Assessment: Sampling, Identification and Counting Variation

Despite the widespread application of periphytic diatoms to water quality assessment at a regional level, there is no standard European sampling protocol or associated assessment metrics. Furthermore, relatively little is known about the uncertainty in the results of such assessments. One of the objectives of the European project for the Standardisation of River Classifications (STAR) is to improve and standardise diatom assessment methods. An extensive diatom ring test, together with an audit of the project results, provided a better understanding and quantification of the uncertainty in quality assessment of running waters using diatoms. The variation in multimetric analysis shows that the choice of site and substrate for sampling, the inter-operator differences in diatom taxonomy and the counting techniques are the primary sources of uncertainty. To some extent, this variation also reveals the robustness of specific metrics in relation to the sources of uncertainty. Of the three most common substrate types tested (stone, macrophyte and sediment), macrophytes emerge as the most preferred substrate for diatom sampling when performing multimetric water quality assessment.     

Assessing ant assemblages: pitfall trapping versus nest counting (Hymenoptera, Formicidae)

Pitfall trapping and nest counting are the most common census methods for ant assemblages. We examined the concordance between pitfall catches and nest counts on dry grassland. Spearman rank correlations and non-metric multidimensional scaling of the Bray Curtis similarity index revealed moderate concordance between the data collated by the two methods, but overall method-related differences were considerable. The dissimilarity was influenced by the type of land management, but not by trapping period or plot shape. Trapping success depended on nest density, ground vegetation cover and species-specific traits (inhabited stratum, colony size, foraging distance). Even when these factors were taken into account, the convertibility of pitfall trap and nest density values was unsatisfactory: the census method proved to be crucial in designing ant-ecological studies and interpreting literature data. Received 11 November 2005; revised 9 February 2006; accepted 1 March 2006.