Bacterial community structures in rhizosphere microsites of ryegrass (Lolium perenne var. Nui) as revealed by pyrosequencing

Management of soils to facilitate plant beneficial microbial interactions requires basic knowledge of the species composition and microbial community structures in the plant rhizosphere. Here, we examined composition of bacterial communities associated with rhizosphere microsites located at the root tips and mature root zones of Lolium perenne when grown in Chilean ash-derived volcanic soils (Andisols: Freire and Piedras Negras soil series). Community structures were analyzed by pyrosequencing of 16S ribosomal RNA (rRNA) genes followed by in silico analysis for phylogenetic assignments (MOTHUR and Visualization tool for Taxonomic Compositions of Microbial Community (VITCOMIC)). Analysis of the community structure revealed significant differences in community structures in relation to the soil series, which differed particularly in the relative abundance of Cyanobacteria and Firmicutes. However, no significant differences were observed with respect to root microsite location in the same Andisol series. Predominant taxa included members of the Proteobacteria, Actinobacteria, and Acidobacteria. Analysis by VITCOMIC showed that dominant bacterial groups comprised only 5 to 10 % of the total bacterial community and the remaining majority of bacteria included low-abundant taxa (Fusobacteria, Thermotogae, Lentisphaerae, Tenericutes, Deferribacteres Spirochaetes, Planctomycetes, Thermotogae, and Deinococcus-Thermus), most of which have not been previously reported or associated with the plant rhizosphere according to GenBank database. The results indicate that most of bacteria in the Chilean Andisols have not been described to the rhizosphere plants and their functional traits are still largely unknown.     

Global topology analysis of the Escherichia coli inner membrane proteome

The protein complement of cellular membranes is notoriously resistant to standard proteomic analysis and structural studies. As a result, membrane proteomes remain ill-defined. Here, we report a global topology analysis of the Escherichia coli inner membrane proteome. Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins. By constraining a topology prediction algorithm with this data, we derived high-quality topology models for the 601 proteins, providing a firm foundation for future functional studies of this and other membrane proteomes. We also estimated the overexpression potential for 397 green fluorescent protein fusions; the results suggest that a large fraction of all inner membrane proteins can be produced in sufficient quantities for biochemical and structural work.     

Identifying declines in waterbirds: The effects of missing data, population variability and count period on the interpretation of long-term survey data

To manage and conserve wildlife populations effectively it is necessary to use methods that identify the often non-linear trends in populations, have an inbuilt assessment of trend quality and can analyse count data from a range of spatial scales. We present a method of trend analysis using generalised additive models. These produce smoothed indices of abundance that can be used to assess population change from one or more sites or time periods, with any number of estimates of abundance per index period. We apply this method to count data collected under the Wetland Bird Survey, a national scheme that monitors waterbirds in the United Kingdom. To highlight declining populations, ‘alerts’ were raised if the population decline was equal to or greater than 50%. Significance was determined using bootstrapped confidence intervals for analyses that included many sites, or a novel Monte-Carlo method for single site analyses. The impact of missing data, species count variability and the number of months used to calculate the population change was greater at individual sites than for national datasets, which were relatively insensitive to changes in the above parameters. For single sites it is essential that three or more counts be made per index period if reliable estimates of population change are required. We propose that the method presented could be applied to a wide range of national or other monitoring schemes for a variety of taxa.     

Determination of the secondary structure of Kluyveromyces lactis beta-galactosidase by circular dichroism and its structure-activity relationship as a function of the pH

The secondary structure of Kluyveromyces lactis beta-galactosidase was determined by circular dichroism. It is mainly a beta-type protein, having 22% beta-turns, 14% parallel beta-sheet, 25% antiparallel beta-sheet, 34% unordered structure, and only 5% alpha-helix. The structure-activity relationship as a function of the pH was also studied. The pH conditions leading to the highest secondary structure content (100% ellipticity) of the enzyme was found at pH 7.0; at pH 6.5-7.0, the percent ellipticity decreased slightly, suggesting little structural change, but the activity decreased significantly, probably because of variations in critical residues. On the other hand, at pH's above 7.0, a more noticeable change in ellipticity was observed due to structural changes; the CD analysis showed a small increase in the helical content toward higher pH, whereas the maximum activity was found at pH 7.5, meaning that the changes produced in the secondary structure at this pH favored the interaction between the enzyme and the substrate.     

Beobachtungen über die Symptombildung bei virusinfizierten Kartoffelsorten

Zusammenfassung An den Kartoffelsorten Bintje, Ulla und Jetta wurde in der Klimakammer und unter Freilandbedingungen die Symptomauspr?gung von Einzel- und Mischinfektionen mit den Viren Y, M und S geprüft. Bei der Sorte Bintje wurde nach Einzel- und Mischinfektionen in der Klimakammer bei 12°C eine Symptomverst?rkung beobachtet. Dasselbe galt für die Viren M und S bei der Sorte Ulla, w?hrend diese Sorte nach Infektion mit dem Virus Y^N bei 20°C am st?rksten reagierte. Die Sorte Jetta bildete im Temperaturbereich von 12 bis 16°C bei allen Verfahren die st?rksten Symptome aus. Unter Feldbedingungen führten Mischinfektionén bei der Sorte Bintje zu keinerlei Symptomverst?rkung gegenüber der reinen Y^N-Infektion. Die Ertragsreduktion lag je nach Verfahren zwischen 39,3 und 53,3%. Die Sorten Ulla und Jetta reagierten auf Einzel- und Mischinfektionen uneinheitlich. Bei Bintje-Importgut franz?sischer und holl?ndischer Herkunft zeigte das Saatgut aus Frankreich eine um zwei Bonitierungsnoten st?rkere Symptomausbildung. Dabei war der Stamm Y^A h?ufiger vertreten als in holl?ndischem Saatgut. Die Arbeit wurde mit Hilfe eines Stipendiums der Kommission für ausl?ndische Studenten an der Eidg. Forschungsanstalt für landwirtschaftlichen Pflanzenbau in CH-8046 Zürich-Reckenholz ausgeführt.     

Enzymes of Nitrogen Metabolism and Proteases Activity in Hairy Roots of Clover and Carrots,with and without Arbuscular Mycorrhizal Fungi

Hairy roots can be used for metabolic studies and also as a substrate for arbuscular mycorrhizal fungi (AMF). However, little is known about the behavior of these roots when infected with AMF. The metabolism of hairy roots grown with or without AMF, on two culture media, was investigated. An increase in protease activity was observed when the roots were cultured on medium with high nitrogen (N)-content. Glutamate synthase (GOGAT) and glutamate dehydrogenase (GDH) activities increased along the development in both carrot and clover hairy roots. With the advancement of root senescence (at 132 d) a greater degradation of root tissue occurred, which was characterized by an increase in catabolic enzymes activity (proteases and GDH deamination). The results indicate that the glutamine synthetase/GOGAT pathway, characteristic of plant tissues, ceases to act in synchronism and is replaced by the GDH/GOGAT system under conditions of stress or senescence when excess ammonium is present.     

Nitrogen and organic matter of volcanic ash soils of Santa Bárbara Association in Chile

Santa Bárbara association is a group of Andosols widely distributed on the western foothills of the Andes Mountains in the Central Valley of Chile from about 36° to 40° south latitude. The soils of this association may be divided into two groups—south and north—by the characteristics of soil organic matter, although they are much alike in morphology. The line of demarcation between the groups lies at about 38° south latitude.

The potential nitrogen fertility or , the content of easily decomposable organic nitrogen is greater in the south soils than in the north soils of which humic matter is at a more advanced stage of humification, as compared with that of the south soils. Dry summers have caused the north soils to lessen in their potential nitrogen fertility and to stimulate humification of organic matter, altering the organic matter in quantity as well as in nature. It is evident that the analysis of soil organic matter is an effectual measure for the characterization of Andosols, and hence for the classification of the soils.

It is very probable that a considerable water erosion has occurred in the soils of this association, transporting the fine soil particles from the mid-slope to the foot of the hills.     

Integrating stakeholders’ demands and scientific knowledge on ecosystem services in landscape planning

The conflict between conservation and timber production is shifting in regions such as Biscay (Basque Country, northern Spain) where planted forests are no longer profitable without public subsidies and environmentalist claim that public subsidies should be reoriented to the regeneration of natural forest. This paper develops an approach that integrates scientific knowledge and stakeholders’ demands to provide decision-making guidelines for the development of new landscape planning strategies while considering ecosystem services. First, a participatory process was conducted to develop a community vision for the region’s sustainable future considering the opportunities and constrains provided by the landscape and its ecosystems. In the participatory process forest management was considered an important driver for the region`s landscape development and forest multi-functionality was envisioned as a feasible attractive alternative. The participatory process identified a knowledge gap on the synergies and trade-offs between biodiversity and carbon storage and how these depend on different forest types. Second, to study the existing synergies and trade-offs between biodiversity and carbon storage and disentangle the identified knowledge gap, a GIS-based research was conducted based on spatially explicit indicators. Our spatial analysis results showed that natural forests’ contribution to biodiversity and carbon storage is higher than that of the plantations with exotic species in the region. The results from the spatial analysis converged with those from the participatory process in the suitability of promoting, where possible and appropriate, natural forest ecosystems restoration. This iterative learning and decision making process is already showing its effectiveness for decision making, with concrete examples of how the results obtained with the applied approach are being included in planning and decision-making processes.     

Qualitative and quantitative risk assessment for human salmonellosis due to multi-resistant Salmonella Typhimurium DT104 from consumption of Danish dry-cured pork sausages

Salmonella Typhimurium DT104 (DT104) is unwanted in products for human consumption due to its antibiotic resistance and ability to cause disease. We intended to set up an improved monitoring and management program to aid in deciding when to use pork contaminated with DT104 for production of sausages without jeopardizing consumer safety. We started by carrying out two assessments of the risk for human health associated with consumption of sausages produced by: (1) Danish pork from average slaughter days; (2) imported pork (IMP) with average prevalence of DT104. The assessments showed that, if Salmonella is present, it is usually in lower numbers (≤50 per 400 cm² surface). Additionally, during processing, the numbers will be reduced by at least 2 log-units. In Danish (DK) pork, DT104 constitutes 0.2–1.0% of the Salmonella isolates reported, while in imported pork (IMP), 18%. We estimated that out of one million, 25 g servings of DK dry-cured sausages, up to two DT104 bacteria could be found in each of 245 servings. Out of one million servings of 25 g IMP dry-cured sausages, up to two DT104 bacteria would occur in each of 19,260 servings.