Genetic diversity of livestock-associated MRSA isolates obtained from piglets from farrowing until slaughter age on four farrow-to-finish farms

During a previous longitudinal study, performed on four farrow-to-finish farms (A to D), samples were taken from twelve sows, their offspring, and the environment on various occasions over six months to study the MRSA presence. During the present study, a selection of the obtained MRSA isolates were typed by multiple-locus variable-number tandem-repeat analysis (MLVA), Pulsed Field Gel Electrophoresis (PFGE), spa typing, and SCCmec typing to study the genetic diversity of LA-MRSA isolates and to determine possible MRSA sources for pig(let)s. PFGE, spa typing, and SCCmec typing revealed the presence of one or few dominant genotype(s) per farm. In contrast, 212 MLVA types were detected on the four farms, forming one cluster on farm A, three on farm B, four on farm C and two on farm D. The genotype, found on farm A was unique for this farm. Farms B, C and D shared one cluster. In general, MLVA types from these clusters were isolated from piglets, sows, and the environment on various sampling events. Piglets carried MLVA types both related and unrelated to their mother sows’ MLVA types at farrowing and onwards. In conclusion, molecular typing revealed that within a farm one or a few dominant strain(s) are widespread. Potential MRSA sources for piglets were mother sows, the environment and other piglets.

Electronic supplementary material

The online version of this article (doi:10.1186/s13567-014-0089-4) contains supplementary material, which is available to authorized users.     

A high virulence and pathotype diversity of Puccinia striiformis f.sp. tritici at its centre of diversity,the Himalayan region of Pakistan

Information on the pathogen virulence profile and diversity across locations is crucial for host germplasm improvement and deployment. The rapid acquisition of virulence to host resistance by the wheat yellow/stripe rust pathogen (Puccinia striiformis f.sp. tritici: PST), makes it crucial to know about its virulence and pathotype diversity. Recent studies have shown the plausible centre of origin of the pathogen in the Himalayan region, with Pakistan being the most ancestral to all other worldwide populations. To assess the status of virulence and pathotype diversity in the Himalayan region of Pakistan, a set of 127 PST infected wheat samples from eight locations were collected, multiplied and pathotyped using a set of 36 differential lines from the world set, European and Chinese sets, and 9 Avocet Yr isolines. Virulence (Vr) was recorded to 18 out of 24 tested yellow rust resistance (Yr) genes, while a total of 53 pathotypes were detected out of 127 isolates tested. Virulence was found to the resistance genes rarely deployed in Pakistan (Vr8) or even worldwide level (Vr5), while virulence to Vilmorin 23 (Yr3+) was absent in Pakistan, which is common in Europe. None of the pathotypes was dominant across all locations, however, no clear spatial structuring was observed for the studied locations. Our results suggested a high virulence and pathotype diversity in line with the previously proposed potential role of sexual recombination in the temporal maintenance of PST in the Himalayan region of Pakistan. This information should be useful in host resistance gene improvement and deployment.     

Soil Characteristics Overwhelm Cultivar Effects on the Structure and Assembly of Root-Associated Microbiomes of Modern Maize

Modern breeding primarily targets crop yield traits and is likely to influence root-associated microbiomes, which play significant roles in plant growth and health. The relative importance of soil and cultivar factors in shaping root-associated microbiomes of modern maize (Zea mays L.) remains uncertain. We conducted a pot experiment in a controlled environment using three soils (Mollisol, Inceptisol, and Ultisol) and four contrasting cultivars, Denghai 605, Nonghua 816, Qiaoyu 8, and Zhengdan 958, which are widely planted in China. We used 16S rRNA gene amplicon sequencing to characterize the bacterial communities in the bulk soil, rhizosphere, and endosphere. Our results showed that the four cultivars had different shoot biomass and root exudate total organic carbon and organic acid contents. The microbiomes in the bulk soil, rhizosphere, and endosphere were different. We observed apparent community divergence between soils rather than cultivars, within which edaphic factors substantially contributed to microbiome variation. Moreover, permutational multivariate analysis of variance corroborated significant contributions of soil type but not cultivar on the root-associated microbiome structure. Differential abundance analysis confirmed that each soil presented a distinct root microbiome, while network analysis indicated different co-occurrence patterns of the root microbiome among the three soils. The core root microbiome members are implicated in plant growth promotion and nutrient acquisition in the roots. In conclusion, root-associated microbiomes of modern maize are much more controlled by soil characteristics than by cultivar root exudation. Our study is anticipated to help improve breeding strategies through integrative interactions of soils, cultivars, and their associated microbiomes.     

Geochemistry of mercury in pristine and flooded ferralitic soils of a tropical rain forest in French Guiana,South America

In ferralitic soils of the dense Guianese forest, mercury (Hg) concentrations of the surface horizons varied from 122 to 318 ng/g d.w. The behaviour and accumulation of Hg is not related to the accumulation of organic matter but to the penetration of humic substances and the progressive adsorption onto iron (Fe) oxy-hydroxydes in the mineral horizons. The flooding of such soils with the creation of a small reservoir has lead to a release of 20% of the Hg initially present. This observation is related to the reduction of the Fe oxy-hydroxydes and to the migration of the organo-metallic complexes to the water column. Although physico-chemical conditions are appropriate for bacterial methylation, methyl Hg (MeHg) levels of these soils are very low. The process regulating MeHg production and its possible loss from the soil are unknown.     

Physical carbon‐sequestration mechanisms under special consideration of soil wettability

The protective impact of aggregation on microbial degradation through separation has been described frequently, especially for biotically formed aggregates. However, to date little information exists on the effects of organic‐matter (OM) quantity and OM quality on physical protection, i.e., reduced degradability by microorganisms caused by physical factors. In the present paper, we hypothesize that soil wettability, which is significantly influenced by OM, may act as a key factor for OM stabilization as it controls the microbial accessibility for water, nutrients, and oxygen in three‐phase systems like soil. Based on this hypothesis, the first objective is to evaluate new findings on the organization of organo‐mineral complexes at the nanoscale as one of the processes creating water‐repellent coatings on mineral surfaces. The second objective is to quantify the degree of alteration of coated surfaces with regard to water repellence. We introduce a recently developed trial that combines FTIR spectra with contact‐angle data as the link between chemical composition of OM and the physical wetting behavior of soil particles. In addition to characterizing the wetting properties of OM coatings, we discuss the implications of water‐repellent surfaces for different physical protection mechanisms of OM. For typical minerals, the OM loading on mineral surfaces is patchy, whereas OM forms nanoscaled micro‐aggregates together with metal oxides and hydroxides and with layered clay minerals. Such small aggregates may efficiently stabilize OM against microbial decomposition. However, despite the patchy structure of OM coating, we observed a relation between the chemical composition of OM and wettability. A higher hydrophobicity of the OM appears to stabilize the organic C in soil, either caused by a specific reduced biodegradability of OM or indirectly caused by increased aggregate stability. In partly saturated nonaggregated soil, the specific distribution of the pore water appears to further affect the mineralization of OM as a function of wettability. We conclude that the wettability of OM, quantified by the contact angle, links the chemical structure of OM with a bundle of physical soil properties and that reduced wettability results in the stabilization of OM in soils.     

Microbial immobilisation of C rhizodeposits in rhizosphere and root-free soil under continuous C labelling of oats

A greenhouse experiment was conducted by growing oats (Avenasativa L.) in a continuously ¹³CO₂ labeled atmosphere. The allocation of ¹³C-labeled photosynthates in plants, microbial biomass in rhizosphere and root-free soil, pools of soil organic C, and CO₂ emissions were examined over the plant's life cycle. To isolate rhizosphere from root-free soil, plant seedlings were placed into bags made of nylon monofilament screen tissue (16 μm mesh) filled with soil. Two peaks of ¹³C in rhizosphere pools of microbial biomass and dissolved organic carbon (DOC), as well as in CO₂ emissions at the earing and ripeness stages were revealed. These ¹³C maxima corresponded to: (i) the end of rapid root growth and (ii) beginning of root decomposition, respectively. The δ¹³C values of microbial biomass were higher than those of DOC and of soil organic matter (SOM). The microbial biomass C accounted for up to 56 and 39% of ¹³C recovered in the rhizosphere and root-free soil, respectively. Between 4 and 28% of ¹³C assimilated was recovered in the root-free soil. Depending on the phenological stage, the contribution of root-derived C to total CO₂ emission from soil varied from 61 to 92% of total CO₂ evolved, including 4-23% attributed to rhizomicrobial respiration. While 81-91% of C substrates used for microbial growth in the root-free soil and rhizosphere came from SOM, the remaining 9-19% of C substrates utilized by the microbial biomass was attributable to rhizodeposition. The use of continuous isotopic labelling and physical separation of root-free and rhizosphere soil, combined with natural ¹³C abundance were effective in gaining new insight on soil and rhizosphere C-cycling.     

Effect of moisture content during dry-heating on selected physicochemical and functional properties of dried egg white

This article addresses the effect of moisture content (0.8-9.9%) during dry-heating (80 degrees C) on selected physicochemical (solubility, turbidity, residual denaturation enthalpy, aggregation, surface hydrophobicity, and sulfhydryl content) and functional (foaming ability, foam density, and stability) properties of freeze-dried egg white (FDEW). Moisture content during dry-heating proved to be a parameter determining the functionality of the resulting egg white powder. The degree of conformational changes induced in the egg white proteins by dry-heating was strongly dependent on the amount of water present. Preferentially, dry-heating at 80 degrees C should be performed on egg white powder with a moisture content below 6.8%, as the loss of protein solubility above this value is extensive. In addition to insoluble aggregates, soluble, strongly stabilized aggregates were also formed, especially at higher moisture contents. The decrease in denaturation enthalpy, increase in surface hydrophobicity, and exposure of SH groups previously hidden in the protein core and their subsequent oxidation were more pronounced at prolonged dry-heating times and at higher moisture contents. These conformational changes resulted in improved foaming ability and foams with lower density. No effect of dry-heating on the foam stability was observed.     

Infrared spectroscopy of comet 81P/Wild 2 samples returned by Stardust

Infrared spectra of material captured from comet 81P/Wild 2 by the Stardust spacecraft reveal indigenous aliphatic hydrocarbons similar to those in interplanetary dust particles thought to be derived from comets, but with longer chain lengths than those observed in the diffuse interstellar medium. Similarly, the Stardust samples contain abundant amorphous silicates in addition to crystalline silicates such as olivine and pyroxene. The presence of crystalline silicates in Wild 2 is consistent with mixing of solar system and interstellar matter. No hydrous silicates or carbonate minerals were detected, which suggests a lack of aqueous processing of Wild 2 dust.     

Diagnostic imaging for the assessment of acquired abdominal vascular diseases in small animals: A pictorial review

Advances in interventional radiology and surgical techniques now allow complex abdominal diseases to be more successfully treated in small animals. Abdominal vascular alterations, acquired as individual process or as complication of other lesions such as neoplasia, can be life‐threatening or at least greatly limit curative interventions of underlying diseases. Computed tomography (CT) and high‐definition ultrasonography are now readily available in veterinary referral centers. Yet, there is little information currently available on the use of these modalities for the diagnosis and characterization of these vascular alterations. The purpose of this article is to review the CT and ultrasonographic findings of acquired vascular diseases in the abdomen of dogs and cats, using both the veterinary and human medicine literature as references, and highlighting essential concepts through figures.     

Agronomic performance of no-tillage relay intercropping with maize under smallholder conditions in Central Brazil

In the context of conservation agriculture on small scale farms of the Brazilian Cerrado, we hypothesized that planting a cover crop in relay with a commercial crop improves the efficiency of use of available natural resources, increasing biomass for use as fodder without reducing the grain yield of the main crop. The objective of this study was to measure the performance of two intercropped systems in terms of total above-ground biomass production and maize (Zea mays) grain yield: pigeon pea (Cajanus cajan) and Brachiaria (Brachiaria ruziziensis) sown as cover crops in established maize under a no-tillage management. The cover crops were sown at two different dates and a comparison was made with the three crops sown as a sole crop at the early sowing date. The experiment was conducted during the 2007-2008 and 2008-2009 growing seasons. Maize grain yield was not reduced by the presence of the relay cover crops in comparison with maize as the sole crop, even when the cover crop was sown soon after maize emergence. In contrast, the production of above-ground biomass by the cover crop was significantly lower when grown with maize than it was when grown as a sole crop. In the intercropped systems, when sown early, the cover crop produced higher total biomass than when sown late. Total above-ground biomass production of maize intercropped with a cover crop was much higher than that of any of the crops sown alone: the total biomass (average of the two growing seasons) produced by maize and pigeon pea was more than double that of maize grown alone. The land equivalent ratio (LER) of maize grain yield and biomass production was higher than one whatever the intercropped system used. It was particularly high when maize was intercropped with early sown pigeon pea; grain yield LER and biomass LER reaching, respectively, 1.72 and 1.73 in 2007-2008 and 2.02 and 2.03 in 2008-2009. These high LER values provide evidence for the complementary and the high efficiency of use of available resources by the intercropped plants and thus the advantage of such systems to produce both maize grain and cover crop forage under the conditions of our study.