The interactive effects of elevated CO<Subscript>2</Subscript>, temperature and initial size on growth and competition between a native C<Subscript>3</Subscript> and an invasive C<Subscript>3</Subscript> grass

A controlled environment experiment was conducted to determine the impact of enhanced carbon dioxide and temperature on competition between the C₃ grasses Austrodanthonia eriantha and Vulpia myuros. Plants were grown in mixtures and monocultures to compare the responses both with and without an interspecific competitor. Temperature and CO₂ were set at current levels (350 ppm CO₂; 20 °C day and 10 °C night temperature), in factorial combination with enhanced levels (700 ppm CO₂; 23 °C day and 13 °C night temperature). To examine the potential impact of initial seedling size on competition under elevated CO₂ and temperature, the two species were combined in mixtures of differing initial sizes. Above-ground growth of all plants was enhanced by increased CO₂ and temperature alone, however the combined temperature and CO₂ treatment showed a sub-additive effect, where growth was less than expected based on the responses to each factor independently. Austrodanthonia in mixture with Vulpia plants of the same initial size experienced a 27 reduction in growth. Austrodanthonia grown in the presence of an initially larger Vulpia plant experienced a 58 reduction in growth. When the Vulpia plant was initially smaller than Austrodanthonia, growth of the Austrodanthonia was reduced by 16%. The growth of Vulpia appeared to be largely unaffected by the presence of Austrodanthonia. Variation in the CO₂ and temperature environment did not affect the pattern of these interspecific interactions, although there was some evidence to suggest that the degree of suppression of Austrodanthonia by Vulpia was less under elevated CO₂. These results do not support the initial advantage hypothesis, as Vulpia was always able to suppress Austrodanthonia, regardless of the initial relative sizes of the competitors. Furthermore, the lack of an effect of changing the CO₂ or temperature environment on the direction of interspecific competition suggests that the competitiveness of the invasive Vulpia will be minimally affected by changes in atmospheric CO₂ concentration or temperature.     

Cardiolipin synthase is required for Streptomyces coelicolor morphogenesis

The fluid mosaic model has recently been amended to account for the existence of membrane domains enriched in certain phospholipids. In rod-shaped bacteria, the anionic phospholipid cardiolipin is enriched at the cell poles but its role in the morphogenesis of the filamentous bacterium Streptomyces coelicolor is unknown. It was impossible to delete clsA (cardiolipin synthase; SCO1389) unless complemented by a second copy of clsA elsewhere in the chromosome. When placed under the control of an inducible promoter, clsA expression, phospholipid profile and morphogenesis became inducer dependent. TLC analysis of phospholipid showed altered profiles upon depletion of clsA expression. Analysis of cardiolipin by mass spectrometry showed two distinct cardiolipin envelopes that reflected differences in acyl chain length; the level of the larger cardiolipin envelope was reduced in concert with clsA expression. ClsA-EGFP did not localize to specific locations, but cardiolipin itself showed enrichment at hyphal tips, branch points and anucleate regions. Quantitative analysis of hyphal dimensions showed that the mycelial architecture and the erection of aerial hyphae were affected by the expression of clsA. Overexpression of clsA resulted in weakened hyphal tips, misshaped aerial hyphae and anucleate spores and demonstrates that cardiolipin synthesis is a requirement for morphogenesis in Streptomyces.     

Timing of disturbance alters competitive outcomes and mechanisms of coexistence in an annual plant model

Ecological disturbance is inherently a multi-faceted phenomenon; disturbance events can differ in distinct quantifiable aspects, such as intensity, duration, spatial extent, and time since last disturbance. Though effects of disturbance timing (specifically, time within a season) have been investigated empirically, theoretical work is lacking, in part because effects of disturbance may depend on the timing relative to the life cycle of the species in question. To demonstrate a theoretical basis for the effects of timing, we develop a model of annual plants subject to soil disturbance. We show that timing of disturbance can have significant effects on community composition. In addition, we quantify the mechanisms of coexistence acting under different timing regimes and show that differences in timing lead to different coexistence mechanisms. Specifically, we find that early disturbance (which enhances germination from the seed bank) generates the storage effect, whereas coexistence under late disturbance (which reduces adult fecundity and contributions to the soil seed bank) depends more on relative nonlinearity of competition. We discuss these two distinct mechanisms within the context of the underlying ecological processes, and we also briefly consider the broader implications of our analyses for disturbance timing in real communities. Our findings extend ecological disturbance theory by linking timing to specific competitive outcomes and can be applied to a wide range of disturbance-prone communities. Because we identify the underlying mechanisms resulting from different disturbance timings, our results can potentially inform theory for conservation and invasive species management practice.     

Diversity-disturbance relationships: frequency and intensity interact

An influential ecological theory, the intermediate disturbance hypothesis (IDH), predicts that intermediate levels of disturbance will maximize species diversity. Empirical studies, however, have described a wide variety of diversity-disturbance relationships (DDRs). Using experimental populations of microbes, we show that the form of the DDR depends on an interaction between disturbance frequency and intensity. We find that diversity shows a monotonically increasing, unimodal or flat relationship with disturbance, depending on the values of the disturbance aspects considered. These results confirm recent theoretical predictions, and potentially reconcile the conflicting body of empirical evidence on DDRs.     

Response of instream animal communities to a short-term extreme event and to longer-term cumulative impacts in a strategic water resource area,South Africa

Disturbance plays an integral part in generating heterogeneity required for ecosystem persistence, but the increased amplitude and duration of disturbances linked to drivers of global change could result in ecosystem shifts or collapse. Biomonitoring over time provides insights into trajectories of ecosystem change. The responses of two instream animal taxa to two contrasting disturbance events, a major flood event and the long-term cumulative effects of land-use changes, were assessed in 1999–2012 by quantifying variation and change in abundance of functional groups based on flow rate sensitivity, water quality and metrics of ecological condition. All metrics recovered to pre-flood conditions within seven months after the flood event. Similarly, cumulative impacts of land use effected significant decreases in some but not all metrics. Indices that did not change, including SASS total score and ASPT, were the result of insufficient consideration of the decrease in the abundance of sensitive taxa specifically, and the abundance of all taxa in general. The decrease in abundance of sensitive taxa could signal imminent collapse in certain metrics. Evidence is also provided for a shift in the structure of fish assemblages linked to the decrease and loss of taxa sensitive to ecosystem degradation caused by the longer-term impacts of land-use change.     

Species-area relations in a New Zealand tussock grassland,with implications for nature reserve design and for community structure

Abstract. A tussock grassland, in Blackrock Reserve, New Zealand, was sampled thoroughly at scales ranging from 0.01 m x 0.01 m to 20 m x 20 m, to investigate species-area relations of relevance to plant community structure, and to offer a pointer to reserve design. In total, 96 species were found. Of the native vascular species among these, 20% were new records for the reserve. For the total and the native vascular flora the observed points fell midway between the Arrhenius and Gleason fitted curves. Cryptogams fitted the Arrhenius model well, with z close to the 0.26 value expected for isolates under Preston's Canonical hypothesis. Extrapolation of the Arrhenius curve to the whole of the New Zealand uplands gave values far too large; the Gleason curve gave values much too low. A General Root model is introduced. It fits the observed species richnesses at various quadrat sizes considerably better than previous models. When biogeographic limitations on species richness are included, extrapolation of the General Root curve accurately predicts the size of the upland flora. This fit, the lack of an asymptote, and the rarity structure, are compatible with a random and individualistic model of community structure. However, there are differences in species-area relation between vascular and cryptogamic plants, which cautions against expecting any universal type of community structure. Extrapolations using the General Root model suggest that if the ideal is a 10 km x 10 km reserve, a reserve one tenth that size would contain 81% of the native species in that ideal, and the present Blackrock Reserve contains 67%.     

Analysis for amide nitrogen in proteins

Existing procedures for amide analysis of soluble proteins have been studied. Use of the automatic amino acid analyser for the determination of released ammonia gave greatly increased sensitivity over the distillation procedure and more reliable blank values. For the insoluble fibrous proteins, wool and silk hydrolysis in vacuo was found to remove the need for an extrapolation procedure; prolonged hydrolysis was required with hydrochloric acid but not with hydriodic acid.     

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples

Background

DNA methylation plays crucial roles in epigenetic gene regulation in normal development and disease pathogenesis. Efficient and accurate quantification of DNA methylation at single base resolution can greatly advance the knowledge of disease mechanisms and be used to identify potential biomarkers. We developed an improved pipeline based on reduced representation bisulfite sequencing (RRBS) for cost-effective genome-wide quantification of DNA methylation at single base resolution. A selection of two restriction enzymes (Taq^αI and MspI) enables a more unbiased coverage of genomic regions of different CpG densities. We further developed a highly automated software package to analyze bisulfite sequencing results from the Solexa GAIIx system.

Results

With two sequencing lanes, we were able to quantify ~1.8 million individual CpG sites at a minimum sequencing depth of 10. Overall, about 76.7% of CpG islands, 54.9% of CpG island shores and 52.2% of core promoters in the human genome were covered with at least 3 CpG sites per region.

Conclusions

With this new pipeline, it is now possible to perform whole-genome DNA methylation analysis at single base resolution for a large number of samples for understanding how DNA methylation and its changes are involved in development, differentiation, and disease pathogenesis.     

Stability and coexistence in a lawn community: mathematical prediction of stability using a community matrix with parameters derived from competition experiments

Community matrix theory has been proposed as a means of predicting whether a particular set of species will form a stable mixture. However, the approach has rarely been used with data from real communities. Using plant competition experiments, we use community matrix theory to predict the stability and competitive structuring of a lawn community. Seven species from the lawn, including the six most abundant, were grown in boxes, in conditions very similar to those on the lawn. They were grown alone (monocultures), and in all possible pairs. The species formed a transitive hierarchy of competitive ability, with most pairs of species showing asymmetric competition. Relative competitive ability (competitive effect) was positively correlated with published estimates of the maximum relative growth rate (RGR_max) for the same species. A seven-species community matrix predicted the mixture of species to be unstable. Simulations revealed two topological features of this community matrix. First, the matrix was closer to the stability/instability boundary than predicted from a range of null (random) models, suggesting that the lawn may be close to stability. Second, the tendencies of the lawn species to compete asymmetrically, and to be arranged in competitive hierarchies, were found to be positively associated with stability, and hence may be contributing factors to the near-stability seen in the matrix. The limitations of using competition experiments for constructing community matrices are discussed.