Determination of the impact of continuous defoliation of Lolium perenne and Trifolium repens on bacterial and fungal community structure in rhizosphere soil

To determine the effects of defoliation on microbial community structure, rhizosphere soil samples were taken pre-, and post-defoliation from the root tip and mature root regions of Trifolium repens L. and Lolium perenne L. Microbial DNA isolated from samples was used to generate polymerase chain reaction-denaturing gradient gel electrophoresis molecular profiles of bacterial and fungal communities. Bacterial plate counts were also obtained. Neither plant species nor defoliation affected the bacterial and fungal community structures in both the root tip and mature root regions, but there were significant differences in the bacterial and fungal community profiles between the two root regions for each plant. Prior to defoliation, there was no difference between plants for bacterial plate counts of soils from the root tip regions; however, counts were greater in the mature root region of L. perenne than T. repens. Bacterial plate counts for T. repens were higher in the root tip than the mature root region. After defoliation, there was no effect of plant type, position along the root or defoliation status on bacterial plate counts, although there were significant increases in bacterial plate counts with time. The results indicate that a general effect existed during maturation in the root regions of each plant, which had a greater impact on microbial community structure than either plant type or the effect of defoliation. In addition there were no generic consequences with regard to microbial populations in the rhizosphere as a response to plant defoliation.

Use of an artificial root to examine the influence of 8-hydroxyquinoline on soil microbial activity and bacterial community structure

Invasive plant species have been shown to alter the microbial community composition of the soils they invade and it is suggested that this below-ground perturbation of potential pathogens, decomposers or symbionts may feedback positively to allow invasive success. Whether these perturbations are mediated through specific components of root exudation are not understood. We focussed on 8-hydroxyquinoline, a putative allelochemical of Centaurea diffusa (diffuse knapweed) and used an artificial root system to differentiate the effects of 8-hydroxyquinoline against a background of total rhizodeposition as mimicked through supply of a synthetic exudate solution. In soil proximal (0-10 cm) to the artificial root, synthetic exudates had a highly significant (P < 0.001) influence on dehydrogenase, fluorescein diacetate hydrolysis and urease activity. in addition, 8-hydroxyquinoline was significant (p = 0.003) as a main effect on dehydrogenase activity and interacted with synthetic exudates to affect urease activity (p = 0.09). Hierarchical cluster analysis of 16S rDNA-based DGGE band patterns also identified a primary affect of synthetic exudates and a secondary affect of 8-hydroxyquinoline on bacterial community structure. Thus, we show that the artificial rhizosphere produced by the synthetic exudates was the predominant effect, but, that the influence of the 8-hydroxyquinoline signal on the activity and structure of soil microbial communities could also be detected. (C) 2009 Elsevier Ltd. All rights reserved.

Modelling the lava dome extruded at Soufrière Hills Volcano, Montserrat, August 2005–May 2006. Part I: Dome shape and internal structure

Lava domes comprise core, carapace, and clastic talus components. They can grow endogenously by inflation of a core and/or exogenously with the extrusion of shear bounded lobes and whaleback lobes at the surface. Internal structure is paramount in determining the extent to which lava dome growth evolves stably, or conversely the propensity for collapse. The more core lava that exists within a dome, in both relative and absolute terms, the more explosive energy is available, both for large pyroclastic flows following collapse and in particular for lateral blast events following very rapid removal of lateral support to the dome. Knowledge of the location of the core lava within the dome is also relevant for hazard assessment purposes. A spreading toe, or lobe of core lava, over a talus substrate may be both relatively unstable and likely to accelerate to more violent activity during the early phases of a retrogressive collapse. Soufrière Hills Volcano, Montserrat has been erupting since 1995 and has produced numerous lava domes that have undergone repeated collapse events. We consider one continuous dome growth period, from August 2005 to May 2006 that resulted in a dome collapse event on 20th May 2006. The collapse event lasted 3 h, removing the whole dome plus dome remnants from a previous growth period in an unusually violent and rapid collapse event. We use an axisymmetrical computational Finite Element Method model for the growth and evolution of a lava dome. Our model comprises evolving core, carapace and talus components based on axisymmetrical endogenous dome growth, which permits us to model the interface between talus and core. Despite explicitly only modelling axisymmetrical endogenous dome growth our core–talus model simulates many of the observed growth characteristics of the 2005–2006 SHV lava dome well. Further, it is possible for our simulations to replicate large-scale exogenous characteristics when a considerable volume of talus has accumulated around the lower flanks of the dome. Model results suggest that dome core can override talus within a growing dome, potentially generating a region of significant weakness and a potential locus for collapse initiation.

A benchmark method for global optimization problems in structure determination from powder diffraction data

Quasi-Newton-Raphson minimization and conjugate gradient minimization have been used to solve the crystal structures of famotidine form B and capsaicin from X-ray powder diffraction data and characterize the chi(2) agreement surfaces. One million quasi-Newton-Raphson minimizations found the famotidine global minimum with a frequency of ca 1 in 5000 and the capsaicin global minimum with a frequency of ca 1 in 10 000. These results, which are corroborated by conjugate gradient minimization, demonstrate the existence of numerous pathways from some of the highest points on these chi(2) agreement surfaces to the respective global minima, which are passable using only downhill moves. This important observation has significant ramifications for the development of improved structure determination algorithms.

Linking bees and flowers: How do floral communities structure pollinator communities?

Pollinators provide essential ecosystem services, and declines in some pollinator communities around the world have been reported. Understanding the fundamental components defining these communities is essential if conservation and restoration are to be successful. We examined the structure of plant-pollinator communities in a dynamic Mediterranean landscape, comprising a mosaic of post-fire regenerating habitats, and which is a recognized global hotspot for bee diversity. Each community was characterized by a highly skewed species abundance distribution, with a few dominant and many rare bee species, and was consistent with a log series model indicating that a few environmental factors govern the community. Floral community composition, the quantity and quality of forage resources present, and the geographic locality organized bee communities at various levels: (1) The overall structure of the bee community (116 species), as revealed through ordination, was dependent upon nectar resource diversity (defined as the variety of nectar volume-concentration combinations available), the ratio of pollen to nectar energy, floral diversity, floral abundance, and post-fire age. (2) Bee diversity, measured as species richness, was closely linked to floral diversity (especially of annuals), nectar resource diversity, and post-fire age of the habitat. (3) The abundance of the most common species was primarily related to post-fire age, grazing intensity, and nesting substrate availability. Ordination models based on age-characteristic post-fire floral community structure explained 39-50% of overall variation observed in bee community structure. Cluster analysis showed that all the communities shared a high degree of similarity in their species composition (27-59%); however, the geographical location of sites also contributed a smaller but significant component to bee community structure. We conclude that floral resources act in specific and previously unexplored ways to modulate the diversity of the local geographic species pool, with specific disturbance factors, superimposed upon these patterns, mainly affecting the dominant species.

Genetic diversity and structure of natural and managed populations of Cedrus atlantica (Pinaceae) assessed using random amplified polymorphic DNA

Cedrus atlantica (Pinaceae) is a large and exceptionally long-lived conifer native to the Rif and Atlas Mountains of North Africa. To assess levels and patterns of genetic diversity of this species. samples were obtained throughout the natural range in Morocco and from a forest plantation in Arbucies, Girona (Spain) and analyzed using RAPD markers. Within-population genetic diversity was high and comparable to that revealed by isozymes. Managed populations harbored levels of genetic variation similar to those found in their natural counterparts. Genotypic analyses Of Molecular variance (AMOVA) found that most variation was within populations. but significant differentiation was also found between populations. particularly in Morocco. Bayesian estimates of F,, corroborated the AMOVA partitioning and provided evidence for Population differentiation in C. atlantica. Both distance- and Bayesian-based Clustering methods revealed that Moroccan populations comprise two genetically distinct groups. Within each group, estimates of population differentiation were close to those previously reported in other gymnosperms. These results are interpreted in the context of the postglacial history of the species and human impact. The high degree of among-group differentiation recorded here highlights the need for additional conservation measures for some Moroccan Populations of C. atlantica.

Host niches and defensive extended phenotypes structure parasitoid wasp communities

Oak galls are spectacular extended phenotypes of gallwasp genes in host oak tissues and have evolved complex morphologies that serve, in part, to exclude parasitoid natural enemies. Parasitoids and their insect herbivore hosts have coevolved to produce diverse communities comprising about a third of all animal species. The factors structuring these communities, however, remain poorly understood. An emerging theme in community ecology is the need to consider the effects of host traits, shaped by both natural selection and phylogenetic history, on associated communities of natural enemies. Here we examine the impact of host traits and phylogenetic relatedness on 48 ecologically closed and species-rich communities of parasitoids attacking gall-inducing wasps on oaks. Gallwasps induce the development of spectacular and structurally complex galls whose species- and generation-specific morphologies are the extended phenotypes of gallwasp genes. All the associated natural enemies attack their concealed hosts through gall tissues, and several structural gall traits have been shown to enhance defence against parasitoid attack. Here we explore the significance of these and other host traits in predicting variation in parasitoid community structure across gallwasp species. In particular, we test the "Enemy Hypothesis,'' which predicts that galls with similar morphology will exclude similar sets of parasitoids and therefore have similar parasitoid communities. Having controlled for phylogenetic patterning in host traits and communities, we found significant correlations between parasitoid community structure and several gall structural traits (toughness, hairiness, stickiness), supporting the Enemy Hypothesis. Parasitoid community structure was also consistently predicted by components of the hosts' spatiotemporal niche, particularly host oak taxonomy and gall location (e.g., leaf versus bud versus seed). The combined explanatory power of structural and spatiotemporal traits on community structure can be high, reaching 62% in one analysis. The observed patterns derive mainly from partial niche specialisation of highly generalist parasitoids with broad host ranges (>20 hosts), rather than strict separation of enemies with narrower host ranges, and so may contribute to maintenance of the richness of generalist parasitoids in gallwasp communities. Though evolutionary escape from parasitoids might most effectively be achieved via changes in host oak taxon, extreme conservatism in this trait for gallwasps suggests that selection is more likely to have acted on gall morphology and location. Any escape from parasitoids associated with evolutionary shifts in these traits has probably only been transient, however, due to subsequent recruitment of parasitoid species already attacking other host galls with similar trait combinations.

Intra-specific variation affects the structure of the natural enemy assemblage attacking pea aphid colonies

1. Intra-specific variation in plant defence traits has been shown to profoundly affect herbivore community structure. Here we describe two experiments designed to test whether similar effects occur at higher trophic levels, by studying pea aphid–natural enemy interactions in a disused pasture in southern England. 2. In the first experiment, the numbers and identity of natural enemies attacking different monoclonal pea aphid colonies were recorded in a series of assays throughout the period of pea aphid activity. 3. In the summer assay, there was a significant effect of clone on the numbers of aphidophagous hoverfly larvae and the total number of non-hoverfly natural enemies recruited. Clone also appeared to influence the attack rate suffered by the primary predator in the system, the hoverfly Episyrphus balteatus, by Diplazon laetatorius, an ichneumonid parasitoid. Colonies were generally driven to extinction by hoverfly attack, resulting in the recording of low numbers of parasitoids and entomopathogens, suggesting intense intra-guild predation. 4. To further examine the influence of clonal variation on the recruitment of natural enemies, a second experiment was performed to monitor the temporal dynamics of community development. Colonies were destructively sampled every other day and the numbers of natural enemies attacking aphid colonies were recorded. These data demonstrated that clonal variation influenced the timing, abundance, and identity of natural enemies attacking aphid colonies. 5. Taken together, these data suggest that clonal variation may have a significant influence on the patterns of interactions between aphids and their natural enemies, and that such effects are likely to affect our understanding of the ecology and biological control of these insect herbivores.

Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments

MOTIVATION: The accurate prediction of the quality of 3D models is a key component of successful protein tertiary structure prediction methods. Currently, clustering or consensus based Model Quality Assessment Programs (MQAPs) are the most accurate methods for predicting 3D model quality; however they are often CPU intensive as they carry out multiple structural alignments in order to compare numerous models. In this study, we describe ModFOLDclustQ - a novel MQAP that compares 3D models of proteins without the need for CPU intensive structural alignments by utilising the Q measure for model comparisons. The ModFOLDclustQ method is benchmarked against the top established methods in terms of both accuracy and speed. In addition, the ModFOLDclustQ scores are combined with those from our older ModFOLDclust method to form a new method, ModFOLDclust2, that aims to provide increased prediction accuracy with negligible computational overhead. RESULTS: The ModFOLDclustQ method is competitive with leading clustering based MQAPs for the prediction of global model quality, yet it is up to 150 times faster than the previous version of the ModFOLDclust method at comparing models of small proteins (<60 residues) and over 5 times faster at comparing models of large proteins (>800 residues). Furthermore, a significant improvement in accuracy can be gained over the previous clustering based MQAPs by combining the scores from ModFOLDclustQ and ModFOLDclust to form the new ModFOLDclust2 method, with little impact on the overall time taken for each prediction. AVAILABILITY: The ModFOLDclustQ and ModFOLDclust2 methods are available to download from: http://www.reading.ac.uk/bioinf/downloads/ CONTACT: l.j.mcguffin@reading.ac.uk.

Bryophyte diversity and community structure on thatched roofs of the Holnicote Estate, Somerset, U.K.

We investigated patterns of bryophyte species richness and community structure, and their relation to roof variables, on thatched roofs of the Holnicote Estate, South Somerset. Thirty-two bryophyte species were recorded from 28 sampled roofs, including the globally rare and endangered thatch moss, Leptodontium gemmascens. Multiple regression analyses revealed that thatch age has a highly significant positive effect on the number of species present, accounting for nearly half the observed variation in species richness after removal of outliers. Aspect has a slight and marginally significant effect on species diversity (accounting for an additional 6% of variation), with north-facing samples having slightly more species. Age also has a significant impact on total bryophyte cover after removal of outlying observations. TWINSPAN analysis of bryophyte cover data suggests the existence of at least five discrete communities. Simple Discriminant Analyses indicate that these communities occupy different ecological subspaces as defined by the measured roof variables, with pitch, aspect and thatch age emerging as especially significant attributes. Contingency Analysis indicates that some communities are disfavoured by water reed as compared to wheat straw. The findings are significant for understanding the structure of bryophyte communities, for evaluating the effect of bryophyte cover on thatch performance, and for conservation of thatch communities, especially those harbouring rare species.

Effect of heat treatment on changes in texture, structure and properties of Thai indigenous chicken muscle

Changes in texture, microstructure, colour and protein solubility of Thai indigenous and broiler chicken Pectoralis muscle stripes cooked at different temperatures were evaluated. The change in shear value of both chicken muscles was a significant increase from 50 to 80 degrees C but no change from 80 to 100 degrees C. A significant decrease in fibre diameter was obtained in samples heated to an internal temperature of 60 degrees C and the greatest shrinkage of sarcomeres was observed with internal temperatures of 70-100 and 80-100 C for broiler and indigenous chicken muscles, respectively (P < 0.05). Cooking losses of indigenous chicken muscles increased markedly in the temperature range 80-100 C and were significantly higher than those of the broiler (P < 0.001). With increasing temperature, from 50 to 70 degrees C, cooked chicken muscle became lighter and yellower. Relationships between changes in sarcomere length, fibre diameter, shear value, cooking loss and solubility of muscle proteins were evaluated. It was found that the solubility of muscle protein was very highly correlated with the texture of cooked broiler muscle while sarcomere length changes and collagen solubility were important factors influencing the cooking loss and texture of cooked indigenous chicken muscle. (c) 2004 Elsevier Ltd. All rights reserved.

Recent patterns of change in vegetation structure and tree composition of British broadleaved woodland: evidence from large-scale surveys

Evidence is presented of widespread changes in structure and species composition between the 1980s and 2003–2004 from surveys of 249 British broadleaved woodlands. Structural components examined include canopy cover, vertical vegetation profiles, field-layer cover and deadwood abundance. Woods were located in 13 geographical localities and the patterns of change were examined for each locality as well as across all woods. Changes were not uniform throughout the localities; overall, there were significant decreases in canopy cover and increases in sub-canopy (2–10 m) cover. Changes in 0.5–2 m vegetation cover showed strong geographic patterns, increasing in western localities, but declining or showing no change in eastern localities. There were significant increases in canopy ash Fraxinus excelsior and decreases in oak Quercus robur/petraea. Shrub layer ash and honeysuckle Lonicera periclymenum increased while birch Betula spp. hawthorn Crataegus monogyna and hazel Corylus avellana declined. Within the field layer, both bracken Pteridium aquilinum and herbs increased. Overall, deadwood generally increased. Changes were consistent with reductions in active woodland management and changes in grazing and browsing pressure. These findings have important implications for sustainable active management of British broadleaved woodlands to meet silvicultural and biodiversity objectives.

The structure of the mixed OH+H2O overlayer on Pt{111}

The structure of the mixed p(3x3)-(3OH+3H(2)O) phase on Pt{111} has been investigated by low-energy electron diffraction-IV structure analysis. The OH+H2O overlayer consists of hexagonal rings of coplanar oxygen atoms interlinked by hydrogen bonds. Lateral shifts of the O atoms away from atop sites result in different O-O separations and hexagons with only large separations (2.81 and 3.02 angstrom) linked by hexagons with alternating separations of 2.49 and 2.81/3.02 A. This unusual pattern is consistent with a hydrogen-bonded network in which water is adsorbed in cyclic rings separated by OH in a p(3x3) structure. The topmost two layers of the Pt atoms relax inwards with respect to the clean surface and both show vertical buckling of up to 0.06 angstrom. In addition, significant shifts away from the lateral bulk positions have been found for the second layer of Pt atoms. (C) 2005 American Institute of Physics.

The surface geometries of the medium and high coverage carbon monoxide structures c(2 × 4)–(2CO) and p(root7- x root7)R19°–(4CO) structure

The surface geometries of the p (root7- x root7)R19degrees-(4CO) and c(2 x 4)-(2CO) layers on Ni {111} and the clean Ni {111} surface were determined by low energy electron diffraction structure analysis. For the clean surface small but significant contractions of d(12) and d(23) (both 2.02 Angstrom) were found with respect to the bulk interlayer distance (2.03 Angstrom). In the c(2 x 4)-(2CO) structure these distances are expanded, with values of d(12) = 2.08 Angstrom and d(23) = 2.06 Angstrom and buckling of 0.08 and 0.02 Angstrom, respectively, in the first and second layer. CO resides near hcp and fcc hollow sites with relatively large lateral shifts away from the ideal positions leading to unequal C-Ni bond lengths between 1.76 and 1.99 Angstrom. For the p(root7- x root7-)R19'-(4CO) layer two best fit geometries were found, which agree in most of their atomic positions, except for one out of four CO molecules, which is either near atop or between bridge and atop. The remaining three molecules reside near hcp and fcc sites, again with large lateral deviations from their ideal positions. The average C Ni bond length for these molecules is, however, the same as for CO on hollow sites at low coverage. The average CNi bond length at hollow sites, the interlayer distances, and buckling in the first Ni layer are similar to the c(2 x 4)(2CO) geometry, only the buckling in the second layer (0.08 Angstrom) is significantly larger. Lateral and vertical shifts of the Ni atoms in the first layer lead to unsymmetric environments for the CO molecules, which can be regarded as an imprint of the chiral p(root7- x root7-)R19degrees lattice geometry onto the substrate.

The synthesis, structure, and electrochemical properties of Fe(C CC N)(dppe)Cp and related compounds

The cyanoacetylide complex Fe(CCCN)(dppe)Cp (3) is readily obtained from sequential reaction of Fe(CCSiMe3)(dppe)Cp with methyllithium and phenyl cyanate. Complex 3 is a good metalloligand, and coordination to the metal fragments [RhCl(CO)(2)], [Ru(PPh3)(2)Cp](+), and [Ru(dppe)Cp*](+) affords the corresponding cyanoaceylide-bridged heterobimetallic complexes. In the case of the 36-electron complexes [Cp(dppe)Fe-CCCN-MLn](n+), spectroscopic and structural data are consistent with a degree of charge transfer from the iron centre to the rhodium or ruthenium centre via the C3N bridge, giving rise to a polarized ground state. Electrochemical and spectroelectrochemical methods reveal significant interactions between the metal centres in the oxidized (35 electron) derivatives, [Cp(dppe)Fe-CCCN-MLn]((n+1)+).