Soil microbial community analysis using two-dimensional polyacrylamide gel electrophoresis of the bacterial ribosomal internal transcribed spacer regions

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of digested genomic DNA has been previously used in comparative genomics studies of closely related bacteria species. However, a two-dimensional gel electrophoresis approach for examining microbial community structures in environmental samples has not yet been developed. We determined that it is theoretically possible to separate internal transcribed spacer regions (ITS) of bacterial communities into hundreds of operational taxonomic units (OTUs) using 2D-PAGE. Application of 2D-PAGE for separating Bacterial ITS sequences that have been PCR-amplified from replicate soil samples taken from along a Zn gradient resulted in reproducible gels containing hundreds of spots. Clear differences in spot patterns were observed between soil samples that differed in both sampling location and Zn content. The number of OTUs detected using 2D-PAGE of ITS regions was much greater than that observed using Automated Ribosomal Internal Transcribed Spacer Analysis (ARISA), Terminal Restriction Fragment Length Polymorphism (T-RFLP), or Denaturing Gradient Gel Electrophoresis (DGGE). Principal Component Analysis (PCA) of community spot patterns resulted in similar groupings of samples as those obtained using other molecular methods, however, excised spots were found to contain a far lower diversity of different sequences than excised ITS bands of the same length, as determined by RFLP analysis of excision clone libraries and subsequent sequencing of DNA eluted from excised spots. This increase in resolution makes 2D-PAGE of Bacteria ITS fragments from complex microbial communities a viable method for detecting differences between highly similar communities, as well as in streamlining follow-on sequencing efforts by reducing the level of homoplasy (co-migration of heterogeneous sequences) often seen in band-based community fingerprinting methods.     

X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells,tissues, and organs

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.

Lab-based X-ray microscopy allows high-resolution 3D imaging of intact plant samples over a wide range of sample types and sizes, filling the imaging gap between light and electron microscopy.     

Folding and association of the antibody domain CH3: prolyl isomerization preceeds dimerization.

The simplest naturally occurring model system for studying immunoglobulin folding and assembly is the non-covalent homodimer formed by the C-terminal domains (CH3) of the heavy chains of IgG. Here, we describe the structure of recombinant CH3 dimer as determined by X-ray crystallography and an analysis of the folding pathway of this protein.Under conditions where prolyl isomerization does not contribute to the folding kinetics, formation of the beta-sandwich structure is the rate-limiting step. beta-Sheet formation of CH3 is a slow process, even compared to other antibody domains, while the subsequent association of the folded monomers is fast. After long-time denaturation, the majority of the unfolded CH3 molecules reaches the native state in two serial reactions, involving the re-isomerization of the Pro35-peptide bond to the cis configuration. The species with the wrong isomer accumulate as a monomeric intermediate. Importantly, the isomerization to the correct cis configuration is the prerequisite for dimerization of the CH3 domain. In contrast, in the Fab fragment of the same antibody, prolyl isomerization occurs after dimerization demonstrating that within one protein, comprised of highly homologous domains, both the kinetics of beta-sandwich formation and the stage at which prolyl isomerization occurs during the folding process can be completely different.     

Agricultural intensification and cereal aphid–parasitoid–hyperparasitoid food webs: network complexity, temporal variability and parasitism rates

Agricultural intensification (AI) is currently a major driver of biodiversity loss and related ecosystem functioning decline. However, spatio-temporal changes in community structure induced by AI, and their relation to ecosystem functioning, remain largely unexplored. Here, we analysed 16 quantitative cereal aphid–parasitoid and parasitoid–hyperparasitoid food webs, replicated four times during the season, under contrasting AI regimes (organic farming in complex landscapes vs. conventional farming in simple landscapes). High AI increased food web complexity but also temporal variability in aphid–parasitoid food webs and in the dominant parasitoid species identity. Enhanced complexity and variability appeared to be controlled bottom-up by changes in aphid dominance structure and evenness. Contrary to the common expectations of positive biodiversity–ecosystem functioning relationships, community complexity (food-web complexity, species richness and evenness) was negatively related to primary parasitism rates. However, this relationship was positive for secondary parasitoids. Despite differences in community structures among different trophic levels, ecosystem services (parasitism rates) and disservices (aphid abundances and hyperparasitism rates) were always higher in fields with low AI. Hence, community structure and ecosystem functioning appear to be differently influenced by AI, and change differently over time and among trophic levels. In conclusion, intensified agriculture can support diverse albeit highly variable parasitoid–host communities, but ecosystem functioning might not be easy to predict from observed changes in community structure and composition.     

EFFECTS OF SHADING BY ADULTS ON THE GROWTH OF BLADE-STAGE MACROCYSTIS PYRZFERA (PHAEOPHYTA) DURING AND AFTER THE 1982–1984 EL NIÑO1

The effect of shading by an adult canopy on blade-stage Macrocystis pyrifera (L.) C. A. Agardh was estimated by comparing the average growth rate of individuals under a canopy to that of individuals in a canopy gap. This comparison was made in 1983 during a strong El Niño and again in 1986 after the El Niño. Estimated nutrient concentrations in 1983 were two orders of magnitude below those in 1986, whereas ambient light levels were over 3 times higher. The kelp canopy caused similar proportional light reductions (20–30%) during both years. Blades grew 18% slower under the canopy than in the clearing in 1983 and about 77% slower under the canopy in 1986. Blade-stage individuals grew at the same rates in clearings in 1983 and 1986. Regardless of shading, the average growth rate of blade-stage kelp under the ambient, low-nutrient conditions of 1983 was higher than that later observed for multifronded juveniles during the same El Niño. The growth of blade-stage kelp was more like that of larger juveniles growing under high-nutrient conditions. The difference may be due to greater concentrations of nutrients very near the sea floor where single blades are growing compared to concentrations higher in the water column where larger kelp have most of their tissues.     

Innovative combination strategy to enhance effect and diminish adverse effects of glucocorticoids: another promise?

In a paper by Zimmermann and colleagues in this issue of Arthritis Research & Therapy, results of extended laboratory research with the drug combination of prednisolone and dipyridamole are reported. There seems to be a boost and extension of the glucocorticoid effect by the combination, without a clear increase of adverse effects, potentially allowing the application of lower dosages. However, laboratory models are not patients and the glucocorticoid mechanisms leading to effects and adverse effects are manifold. The next required step will be to demonstrate the improved therapeutic window in patients in adequate comparative clinical trials, assessing predefined beneficial effects and adverse effects in a standardized way.     

Macroinvertebrate Diversity in Alpine Lakes: Effects of Altitude and Catchment Properties

Lakes are common features of alpine landscapes, and the attention given to alpine lakes has increased recently in response to increased recognition of the important role that these freshwaters play as sensible indicators of climate change. Despite this general research interest, there is nevertheless a general lack of information about zoobenthos especially of lakes in the Alps, and only few published data are available, which has made it nearly impossible to draw general conclusions in respect to benthic community structure, profundal and/or littoral food webs. This paper aims to explore the relationships between main environmental/catchment properties of 55 lakes and their littoral benthic fauna across three regions of the Alps. We provide updated information on relative abundance, species richness, distribution and ecology of macroinvertebrates which occur and are typical in the littoral of high-mountain lakes of the Alps. These lakes were located in the Lago-Maggiore Watershed (Italy and Switzerland), in South Tyrol (Italy) and in North/East Tyrol (Austria), between 1840 and 2796 m a.s.l., in catchments undisturbed by human activities. As the studied lakes are situated above the tree line, they were characterised by low nutrient levels indicating an oligotrophic status. Lake water chemistry corresponded closely to the geo-lithology of the catchment and some parameters (especially nutrient concentrations) differed between the regions. The macroinvertebrates were dominated by insects which to a high degree were chironomid larvae and pupae. Other insect orders were typical cold stenotherm species of Ephemeroptera, Plecoptera and Trichoptera. Non-insect macroinvertebrates contributed to the 144 taxa found. Other than lake size and catchment area, the faunal parameters exhibited a clearer pattern along altitude. Macroinvertebrates per sample increased with higher elevation, reached their maximum in lakes between 2400 and 2600 m a.s.l., but decreased strongly above 2600 m. The altitudinal pattern of species richness and Shannon diversity resembled each other being highest between 2001 and 2200 m a.s.l., but decreased when going lower and higher, respectively. Various patterns and trends along altitude were also evident when individual groups were analysed within the individual sampling regions. The somewhat conflicting trends of various biocoenotic indices let assume that factors other than altitude are also responsible for the structure of faunal assemblages in the littoral of alpine lakes. Six variables (“bare rocks” and “nitrate”, “alkalinity”, “ammonia” and “peat bog”) were selected by the CCA analysis where these three groups of lakes were identified: (1) lakes with a higher alkalinity (higher pH, conductivity, ion concentration), a higher relative vegetation cover (compared to the “bare rocks” on the opposite side) and lower nitrate levels; (2) lakes with a higher portion of “bare rocks” in their catchments and higher nitrate levels; and (3) a smaller group of lakes with higher ammonia levels and a boggy environment. Geographical patterns seemed to have weak effects on the presence of taxa while catchment properties had evident impacts on macroinvertebrate communities in these lakes. In this way, the present study contributes to the overall understanding of environmental settings and effects on high mountain lake ecosystems and assists in refining research and conservation strategies for an important landscape aspect in the Alps.     

Analysis of T-RFLP data using analysis of variance and ordination methods: a comparative study

The analysis of T-RFLP data has developed considerably over the last decade, but there remains a lack of consensus about which statistical analyses offer the best means for finding trends in these data. In this study, we empirically tested and theoretically compared ten diverse T-RFLP datasets derived from soil microbial communities using the more common ordination methods in the literature: principal component analysis (PCA), nonmetric multidimensional scaling (NMS) with Sørensen, Jaccard and Euclidean distance measures, correspondence analysis (CA), detrended correspondence analysis (DCA) and a technique new to T-RFLP data analysis, the Additive Main Effects and Multiplicative Interaction (AMMI) model. Our objectives were i) to determine the distribution of variation in T-RFLP datasets using analysis of variance (ANOVA), ii) to determine the more robust and informative multivariate ordination methods for analyzing T-RFLP data, and iii) to compare the methods based on theoretical considerations. For the 10 datasets examined in this study, ANOVA revealed that the variation from Environment main effects was always small, variation from T-RFs main effects was large, and variation from T-RF × Environment (T × E) interactions was intermediate. Larger variation due to T × E indicated larger differences in microbial communities between environments/treatments and thus demonstrated the utility of ANOVA to provide an objective assessment of community dissimilarity. The comparison of statistical methods typically yielded similar empirical results. AMMI, T-RF-centered PCA, and DCA were the most robust methods in terms of producing ordinations that consistently reached a consensus with other methods. In datasets with high sample heterogeneity, NMS analyses with Sørensen and Jaccard distance were the most sensitive for recovery of complex gradients. The theoretical comparison showed that some methods hold distinct advantages for T-RFLP analysis, such as estimations of variation captured, realistic or minimal assumptions about the data, reduced weight placed on rare T-RFs, and uniqueness of solutions. Our results lead us to recommend that method selection be guided by T-RFLP dataset complexity and the outlined theoretical criteria. Finally, we recommend using binary or relativized peak height data with soil-based T-RFLP data for ordination-based exploratory microbial analyses.