Effects of AM colonization on “wild tobacco” plants grown in zinc-contaminated soil

This greenhouse study aimed to determine the effect of colonization by the arbuscular mycorrhizal (AM) fungus (Glomus intraradices Schenck & Smith) on the “wild” tobacco (Nicotiana rustica L. var. Azteca), under soil–zinc (Zn) conditions. Plants of N. rustica were grown in AM or non-AM inoculated substrate and subjected to four soil–[Zn] concentrations (0, 50, 100, and 250 mg Zn kg⁻¹ dry soil). The AM root colonization increased markedly from 14 to 81% with the increasing soil–[Zn] and the mycorrhizal structures were significantly more abundant at the highest soil–[Zn], suggesting that Zn may be involved directly or indirectly in AM root colonization. In addition, total Zn content or Zn concentrations in shoots and roots were shown to increase as soil–[Zn] increased in both AM and non-AM plants. As for the growth parameters studied, there were no significant differences between treatments despite the increase in Zn content or concentration. The AM roots subjected to the highest soil–[Zn] had a significant reduction by about 50% of total Zn content and Zn concentration compared to non-AM roots. Still, the relative extracted Zn percentage decreased dramatically as soil–[Zn] increased. Soil pH was significantly lower in non-AM than AM treatments at the highest soil–[Zn]. In summary, AM plants (particularly roots) showed lower Zn content and concentration than non-AM plants. In this regard, the AM fungi have a protective role for the host plant, thus playing an important role in soil-contaminant immobilization processes; and, therefore, are of value in phytoremediation, especially when heavy metals approach toxic levels in the soil.     

Effects of habitat configuration on host–parasitoid food web structure

The dispersal of organisms among patches affects community structure in spatially heterogeneous habitats. The enhancement of dispersal frequency among patches can be expected to increase potential interaction between organisms in food webs. However, it has been difficult to fairly evaluate the effects of dispersal on the food web structure because the quantification of actual dispersal is difficult. In this study, in order to manipulate the dispersal frequency, two oak plantations (each with 100 oak trees) were established as high-patch connectivity (1-m interval) and low-patch connectivity (3-m interval) plots. Quantitative food webs of herbivores and their parasitoids were constructed for the high- and low-connectivity plots, and quantitative measures of food web metrics as indices of structure were calculated for both webs to examine dispersal effects on food web complexity. In the entire web, 86 herbivore species (Lepidoptera and Coleoptera) were attacked by 50 parasitoid species (Hymenoptera and Diptera). As a result, although we found no significant difference in herbivore abundance between high- and low-connectivity plots, a higher parasitism rate and greater complexity in web structure were observed in many food web metrics for the high-connectivity plot. Furthermore, the parasitoid overlap diagram showed a higher potential for indirect interactions among herbivore species in the high-connectivity plot. These results imply that the increase in dispersal frequency among habitat patches facilitates food web complexity, and the role of dispersal as a determinant of food web structure should be considered in food web ecology.     

Effects of plant species on each other's pollination: Is community structure influenced?

Pollination is one of the most important aspects of the life histories of most vascular plants. Until recently, there has been a broad consensus that heterospecific neighbors compete for pollinators, that this competition leads to phenological divergence, and that divergence leads to structured communities. New work is revealing a more complex web of interactions.     

Evaluation of apple replant problems based on different soil disinfection treatments—links to soil microbial community structure?

Background and aims

Replant problems or soil sickness are known phenomena but still unsolved. The aims of this study were (i) to set up a test system for detecting replant problems using in vitro propagated apple rootstocks (M26) based on different soil disinfection treatments and (ii) to explore the treatment effects on root morphology and soil microbial community structure.

Methods

The bio-test involved soil with apple replant problems (apple sick) and healthy soil from an adjacent plot, both either untreated, or submitted to treatments of 50 and 100 °C, or the chemical soil disinfectant Basamid. Histological analyses of roots and denaturing gradient gel electrophoresis (DGGE) fingerprints in rhizosphere soil collected at the final evaluation were performed.

Results

After 10 weeks, shoot dry mass on apple sick soil was 79, 108 and 124 % higher for soil treated at 50 °C, 100 °C and with Basamid, respectively, compared to the untreated soil. Roots in untreated apple sick soil showed destroyed epidermal and cortical layers. DGGE fingerprints revealed treatment dependent differences in community composition and relative abundance of total bacteria, Bacillus, Pseudomonas and total fungi.

Conclusions

The clear differences detected in soil microbial communities are the first steps towards a better understanding of the causes for apple replant problems.     

Nitrogen enrichment modifies plant community structure via changes to plant–soil feedback

We tested the hypothesis that N enrichment modifies plant-soil feedback relationships, resulting in changes to plant community composition. This was done in a two-phase glasshouse experiment. In the first phase, we grew eight annual plant species in monoculture at two levels of N addition. Plants were harvested at senescence and the effect of each species on a range of soil properties was measured. In the second phase, the eight plant species were grown in multi-species mixtures in the eight soils conditioned by the species in the first phase, at both levels of N addition. At senescence, species performance was measured as aboveground biomass. We found that in the first phase, plant species identity strongly influenced several soil properties, including microbial and protist biomass, soil moisture content and the availability of several soil nutrients. Species effects on the soil were mostly independent of N addition and several were strongly correlated with plant biomass. In the second phase, both the performance of individual species and overall community structure were influenced by the interacting effects of the species identity of the previous soil occupant and the rate of N addition. This indicates that N enrichment modified plant-soil feedback. The performance of two species correlated with differences in soil N availability that were generated by the species formerly occupying the soil. However, negative feedback (poorer performance on the soil of conspecifics relative to that of heterospecifics) was only observed for one species. In conclusion, we provide evidence that N enrichment modifies plant-soil feedback relationships and that these modifications may affect plant community composition. Field testing and further investigations into which mechanisms dominate feedback are required before we fully understand how and when feedback processes determine plant community responses to N enrichment.     

Effects of benomyl on reproduction and population structure of enchytraeid oligochaetes (Annelida)—Sublethal tests on agar and soil

• 1.1. The toxicity of the fungicide benomyl to terrestrial enchytraeid species was tested under different conditions.
• 2.2. Despite a relatively low acute response even to higher concentrations in agar media, sensitive effects were observed for cocoon production and hatching success at the recommended concentration for agricultural application (5.9 ppm in the test medium).
• 3.3. These sublethal effects could be reconciled with population tests in larger quantities of soil: lower abundance was due to a very low number of juveniles in the benomyl-treated cultures.

     

Effects of freeze–thaw and micro-computed tomography irradiation on structure–property relations of porcine trabecular bone

We study the effects of freeze–thaw and irradiation on structure–property relations of trabecular bone. We measure the porosity, apparent density, mineral content, trabecular orientation, trabecular thickness, fractal dimension, surface area, and connectivity of trabecular bone using micro-computed tomography (micro-CT) and relate them to Young?s modulus and ultimate strength measured by uniaxial compression testing. The analysis is done on six-month porcine trabecular bone from femoral heads. The effects of freeze–thaw are studied by using bones from three different groups: fresh bone and bones frozen for one and five years. We find that the porosity and apparent density have most dominant influence on the elastic modulus and strength of fresh bone. Also, five years of freezing lowers both Young?s modulus and ultimate strength of trabecular bone. Additionally, the effects of radiation are investigated by comparing Young?s modulus before and after micro-CT exposure. We find that the micro-CT irradiation has a negligible effect on the Young?s modulus of trabecular bone. These findings provide insights on the effects of tissue preservation and imaging on properties of trabecular bone.     

Impacts of methamidophos, copper, and their combinations on bacterial community structure and function in black soil

The potential ecotoxicologial risks of methamidophos, copper, and their combinations on microbial community of black soil ecosystem in the Northeast China were assessed in species richness and structures by using 16S rDNA-PCR-DGGE analysis approach, and functional characteristics at community levels by using BIOLOGGN system analysis method as well as two conventional methods(DHA and SIR). All results of DGGE banding fingerprint pat-terns(amplified by bacterial specific 16S rDNA V3 high variable region universal primer) indicated that the species richness of bacterial community in tested soil was significantly decreased to different extents by using different concentrations of single methamidophos, copper, especially some of their combinations had worse effects than their corresponding single factors. In addition, the structures of soil bacterial community had been disturbed under all stresses applied in this study because of the enrichment of some species and the disappearance of other species from the b     

A comparison of the refractile bodies (R-bodies) of certain bacteria—II. Effects of pH on the structure

The ‘R-bodies’ of Caedibacter taeniospiralis, an endosymbiont of Paramecium tetraurelia and Pseudomonas avenae, have been examined under a wide range of pH. They both unroll over a small range, but in both cases the process does not always proceed to completion. Acid pHs cause both to unroll. All the R-bodies of P. avenae at high pHs are wound which is not the case with Caedibacter. There are differences between the two bodies in the details of their unrolling. Caedibacter taenospiralis unwinds from the inside, whereas P. avenae unwinds from the outside. Detailed study of the unwound ribbon shows a difference in terms of roughness and smoothness of the two surfaces.     

Effects of Hofmeister ions on the α-helical structure of proteins

The molecular conformation of proteins is sensitive to the nature of the aqueous environment. In particular, the presence of ions can stabilize or destabilize (denature) protein secondary structure. The underlying mechanisms of these actions are still not fully understood. Here, we combine circular dichroism (CD), single-molecule Förster resonance energy transfer, and atomistic computer simulations to elucidate salt-specific effects on the structure of three peptides with large α-helical propensity. CD indicates a complex ion-specific destabilization of the α-helix that can be rationalized by using a single salt-free computer simulation in combination with the recently introduced scheme of ion-partitioning between nonpolar and polar peptide surfaces. Simulations including salt provide a molecular underpinning of this partitioning concept. Furthermore, our single-molecule Förster resonance energy transfer measurements reveal highly compressed peptide conformations in molar concentrations of NaClO₄ in contrast to strong swelling in the presence of GdmCl. The compacted states observed in the presence of NaClO₄ originate from a tight ion-backbone network that leads to a highly heterogeneous secondary structure distribution and an overall lower α-helical content that would be estimated from CD. Thus, NaClO₄ denatures by inducing a molten globule-like structure that seems completely off-pathway between a fully folded helix and a coil state.     

Microbial population index and community structure in saline–alkaline soil using gene targeted metagenomics

Population indices of bacteria and archaea were investigated from saline–alkaline soil and a possible microbe–environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline–alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling.     

Effects of supercoiling on enhancer–promoter contacts

Using Brownian dynamics simulations, we investigate here one of possible roles of supercoiling within topological domains constituting interphase chromosomes of higher eukaryotes. We analysed how supercoiling affects the interaction between enhancers and promoters that are located in the same or in neighbouring topological domains. We show here that enhancer–promoter affinity and supercoiling act synergistically in increasing the fraction of time during which enhancer and promoter stay in contact. This stabilizing effect of supercoiling only acts on enhancers and promoters located in the same topological domain. We propose that the primary role of recently observed supercoiling of topological domains in interphase chromosomes of higher eukaryotes is to assure that enhancers contact almost exclusively their cognate promoters located in the same topological domain and avoid contacts with very similar promoters but located in neighbouring topological domains.     

Effects of epibiosis on consumer–prey interactions

In many benthic communities predators play a crucialrole in the population dynamics of their prey. Surfacecharacteristics of the prey are important forrecognition and handling by the predator. Because theestablishment of an epibiotic assemblage on thesurface of a basibiont species creates a new interfacebetween the epibiotized organism and its environment,we hypothesised that epibiosis should have an impacton consumer–prey interactions. In separateinvestigations, we assessed how epibionts onmacroalgae affected the susceptibility of the latterto herbivory by the urchin Arbacia punctulataand how epibionts on the blue mussel Mytilusedulis affected its susceptibility to predation bythe shore crab Carcinus maenas.Some epibionts strongly affected consumer feedingbehavior. When epibionts were more attractive thantheir host, consumer pressure increased. Whenepibionts were less attractive than their host or whenthey were repellent, consumer pressure decreased. Insystems that are controlled from the top-down,epibiosis can strongly influence community dynamics.For the Carcinus/Mytilus system that westudied, the in situ distribution of epibiontson mussels reflected the epibiosis-determinedpreferences of the predator. Both direct and indirecteffects are involved in determining theseepibiont-prey–consumer interactions.     

Effects of non-linearity on cell–ECM interactions

Filamentous biopolymers such as F-actin, vimentin, fibrin and collagen that form networks within the cytoskeleton or the extracellular matrix have unusual rheological properties not present in most synthetic soft materials that are used as cell substrates or scaffolds for tissue engineering. Gels formed by purified filamentous biopolymers are often strain stiffening, with an elastic modulus that can increase an order of magnitude at moderate strains that are relevant to cell and tissue deformation in vivo. This review summarizes some experimental studies of non-linear rheology in biopolymer gels, discusses possible molecular mechanisms that account for strain stiffening, and explores the possible relevance of non-linear rheology to the interactions between cell and extracellular matrices.     

Linking microbial community structure to β-glucosidic function in soil aggregates

To link microbial community 16S structure to a measured function in a natural soil, we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-Glucosidase activity was assayed in 450 individual aggregates, which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differences in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be observed that functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to the presence or absence of particular taxonomic groups.     

Patterns of grassland community composition and structure along an elevational gradient on the Qinghai–Tibet Plateau

青藏高原草地群落组成和结构的海拔梯度格局 青藏高原高寒草地是维持区域生态安全的天然屏障,也在一定程度上造就了该区域较高的生物多样性。然而,我们对青藏高原高寒草地植物群落组成和结构的海拔分布格局及其自身维持机制仍知之甚少。本研究在青藏高原东北部沿公路形成的海拔梯度设置了39个实验样地(海拔跨度为2800–5100m),每个样地设5个调查样方进行群落调查,包括物种组成、高度、盖度,评估青藏高原高寒草地植物群落的α和β多样性的海拔梯度格局及其影响因素。研究结果发现草地群落高度随着海拔的增加而显著降低,而群落盖度变化却不显著。随着海拔的增加,植物物种丰富度(α多样性)显著增加,而群落变异性(β多样性)显著降低。约束聚类分析表明,随海拔增加草地群落结构逐渐发生变化,基于此,在这种变化过程中,我们监测到3个渐变的海拔间断点,分别在海拔3640、4252和4333 m处。结构方程模型(SEM)表明,降水增加和温度降低对α多样性有显著的正向作用,但植物群落α多样性的变化显著改变群落变异性。以上结果表明,青藏高原的群落组成和结构沿海拔梯度发生了从量变到质变的过程。     

Chemical warfare? Effects of uropygial oil on feather‐degrading bacteria

Anti-microbial activity is a commonly suggested but rarely tested property of avian uropygial oil. Birds may defend themselves against feather-degrading and other potentially harmful bacteria using this oil. We preliminarily identified 13 bacterial isolates taken from the plumage of wild house finches Carpodacus mexicanus , measured bacterial production of the enzyme keratinase as an index of feather-degrading activity, and used the disc-diffusion method to test bacterial response to uropygial oil of house finches. For comparison, we performed the same tests on a type strain of the known feather-degrading bacterium Bacillus licheniformis . Uropygial oil inhibited the growth of three strongly feather-degrading isolates (including Bacillus licheniformis ), as well as one weakly feather-degrading isolate and one non-feather-degrading isolate. Uropygial oil appeared to enhance the growth of one weakly feather-degrading isolate. Growth of the remaining isolates was unaffected by uropygial oil. These results suggest that birds may defend themselves against some feather-degrading bacteria using uropygial oil.     

Impact of soil salinity on the plant-growth – promoting and biological control abilities of root associated bacteria

The effectiveness of plant growth – promoting bacteria is variable under different biotic and abiotic conditions. Abiotic factors may negatively affect the beneficial properties and efficiency of the introduced PGPR inoculants. The aim of this study was to evaluate the effect of plant growth – promoting rhizobacteria on plant growth and on the control of foot and root rot of tomatoes caused by Fusarium solani under different soil salinity conditions. Among the five tested strains, only Pseudomonas chlororaphis TSAU13, and Pseudomonas extremorientalis TSAU20 were able to stimulate plant growth and act as biological controls of foot and root rot disease of tomato. The soil salinity did not negatively affect the beneficial impacts of these strains, as they were able to colonize and survive on the roots of tomato plants under both saline and non-saline soil conditions. The improved plant height and fruit yield of tomato was also observed for plants inoculated with P. extremorientalis TSAU20. Our results indicated that, saline condition is not crucial factor in obtaining good performance with respect to the plant growth stimulating and biocontrol abilities of PGPR strains. The bacterial inoculant also enhanced antioxidant enzymes activities thereby preventing ROS induced oxidative damage in plants, and the proline concentrations in plant tissue that play an important role in plant stress tolerance.