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.     

Phage and MLVA Typing of Salmonella Enteritidis Isolated from Layers and Humans in Belgium from 2000–2010, A Period in which Vaccination of Laying Hens was Introduced

The aim of the study was to characterize isolates of Salmonella enterica serovar Enteritidis (S. Enteritidis) obtained from humans and layer farms in Belgium collected during 2000–2010. Three periods were compared, namely (i) before implementation of vaccination (2000–2004), (ii) during voluntary vaccination (2005–2006) and (iii) during implementation of the national control program (NCP) for Salmonella including mandatory vaccination against S. Enteritidis (2007–2010). The characteristics compared across time periods were distributions of phage type and multiple‐locus variable number tandem‐repeat assay (MLVA). While PT4 and PT21 were predominantly isolated in Belgium in layers and humans before 2007, a significant reduction of those PTs was observed in both populations in the period 2007–2010. The relative proportion of PT4b, PT21c and PT6c was found to have increased considerably in the layer population since 2007. In the human population, PT8, PT1 and the group of ‘other’ PTs were more frequently isolated compared to the previous periods. When comparing the proportion of the predominant MLVA types Q2 and U2, no significant difference was found between the layer and human population in the three periods and between periods within each category (layer and human). A significant difference in isolate distribution among MLVA clusters I and II was found between human and layer isolates recovered during Period 3 and in the human population between Period 1 and 3. Results suggest that the association between S. Enteritidis in layers and the occurrence of the pathogen in humans changed since implementation of the NCP in 2007.     

Somatic hybridization as a tool for tomato breeding

Protoplast fusion can be used to produce somatic hybrids of species that cannot be obtained by sexual hybridization. The possibility to introgress genes from Solanum species into the cultivated tomato species Lycopersicon esculentum, and to obtain novel cytoplasm-nucleus combinations (cybrids) was considered as an important strategy to extend the genetic variation available for tomato breeding. Somatic hybrids between L. esculentum and other Lycopersicon species, as well as between L. esculentum and Solanum or Nicotiana species, have been produced. Specific mutants, genotypes with antibiotic resistances, and metabolic inhibition by iodoacetate or iodoacetamide and irradiation were used for the selection of hybrids. In addition, the improvement of protoplast culture techniques and the use of the favourable tissue culture traits derived from species such as L. peruvianum, which have been introduced into tomato by classical breeding, allowed the efficient recovery of somatic hybrids. However, the occurrence of somatic incongruity in fusion combinations of L. esculentum and Solanum and even more in L. esculentum and Nicotiana, did not allow the production of true cybrids and/or fertile hybrids, indicating the importance of both cytoplasm-nucleus and nucleus-nucleus interactions in somatic incongruity. Another problem with fusions between distantly related species is the strongly reduced fertility of the hybrids and the very limited homoeologous recombination between chromosomes of the parental species. Partial genome transfer from donor to recipient through microprotoplast (+) protoplast fusion, and the production of monosomic or disomic chromosome addition lines, light overcome some of these problems. In symmetric somatic hybrids between L. esculentum and S. tuberosum the occurrence of limited somatic and meiotic recombination was demonstrated. Fertile progeny plants could be obtained, though at a low frequency, when embryo rescue was performed on a large scale after backcrossing hexaploid somatic tomato (+) potato hybrids with a tetraploid potato genotype. The potential value of genomic in situ hybridization (GISH) and RFLPs for the analysis of the genome/chromosome composition of the hybrids has been demonstrated for intergeneric somatic hybrids between Lycopersicon and Solanum.Abbreviations cpDNA chloroplast DNA - mtDNA mitochondrial DNA     

Dry deposition loading of Lake Michigan by airborne particulate matter

A transport model as a function of particle size is presented which couples Chicago area meteorological data through the mixed layer with laboratory and field data on water surface dry deposition. The model is used to (a) estimate a minimum mass transfer efficiency by dry deposition from the Chicago area to Lake Michigan, (b) compare this minimum with the maximum wet deposition likely, and (c) estimate the transfer efficiency of trace metals. Dry deposition is found to cause 15% or more mass transfer efficiency of aerosols to the Lake. This value is considered to be equal to or greater than the efficiency of precipitation scavenging mass transfer. However, dry deposition as a function of particle size is such that the transfer of trace metals by this mechanism appears to be a few percent or less. Consequently, precipitation scavenging appears to be the dominant mechanism for trace metal transfer to Lake Michigan.     

Abatement of High Concentrated Ammonia Loaded Waste Gases in Compost Biofilters

The performance of lab-scale compostbiofilters for the purification of waste gasescontaining high (>70 mg m^-3) ammoniaconcentrations was studied. When using fresh compostmaterial, no effect of inoculating the compostmaterial with a nitrifying culture was observed sincehigh elimination capacities (up to 350 gNH₃ m^-3 d^-1) were obtained in both theinoculated and the non-inoculated biofilter. Due tothe physico-chemical interaction of NH₃ with thecompost material at the start of the experiment, nomicrobiological start-up period was observed and highremoval efficiencies were obtained from the first dayon. Next to this, no NH₃-toxicity was observedeven at concentrations up to 550 mg NH₃ m^-3.About 50% of the NH₃-removal was found to benitrified, while the other 50% remained in thebiofilter as NH ⁺₄ . As a result of this, noacidification of the carrier material was observed andNH₄NO₃ accumulated in the biofilter. Due toosmotic effects, however, a complete inhibition innitrification and NH₃-removal was obtained at ameasured NH₄NO₃-concentration in the compostmaterial of 6–7 g N kg^-1, corresponding to acumulative NH₃-removal in the biofilter of ±6000 g m^-3. Finally, it was illustrated that theremoval of the odorant dimethyl sulfide (Me₂S) ina Hyphomicrobium MS3-inoculated compostbiofilter is completely inhibited due toNH₃-toxicity at a waste gas concentration of 100 mg NH₃ m^-3. Next to this, theNH ⁺₄ - and NO ^?₃ -concentrations inthe compost material that were shown to inhibit thenitrification, also strongly affected theMe₂S-degrading activity of Hyphomicrobium MS3.

     

Comparison of depth- and mass-based approaches for estimating changes in forest soil carbon stocks: A case study in young plantations and secondary forests in West Java, Indonesia

Soil carbon (C) stocks in forest ecosystems have been widely estimated to a fixed soil depth (i.e., 0-30 cm) to clarify temporal changes in the C pool. However, surface elevations change as a result of compaction or expansion of the soil under forest management and land use. On the other hand, the calculation of soil C stocks based on “equivalent soil mass” is not affected by compaction or expansion of forest soil. To contribute to the development of a forest C accounting methodology, we compared changes in soil C stocks over 4 years between depth- and mass-based approaches using original soil data collected at 0-30 cm depths in young plantations and secondary forests in West Java, Indonesia. Our methodology expanded on the mass-based approach; rather than using one representative value for the mass-based calculation of soil C stocks, we adjusted individual values, maintaining the coefficient of variance in soil mass. We also considered the effect of an increase or decrease in soil organic matter on equivalent soil mass. Both increasing and decreasing trends in soil C stocks became clearer when the mass-based approach was used rather than the depth-based approach. The trends in soil C stocks based on equivalent soil mass were particularly evident in the surface soil layers (0-5 cm) and in plantation sites, compared with those for soil profiles including subsurface soil layers (0-30 cm) and in secondary forests. These trends in soil C stocks corresponded with temporal trends in litter stocks. We suggest that equivalent mass-basis soil C stock for the upper 30 cm of soil be calculated based on multiple soil layers to reduce estimation errors. Changes in soil organic matter mass had little effect on the estimation of soil C stock on an equivalent mass basis. For the development of a forest C accounting system, the mass-based approach should be used to characterize temporal trends in soil C stocks and to improve C cycle models, rather than simpler methods of calculating soil C stocks. These improvements will help to increase the tier level of country-specific forest C accounting systems.     

The effect of Lumbricus rubellus and Lumbricus terrestris on zinc distribution and availability in artificial soil columns

This study investigated the impact of epigeic and (epi)anecic earthworms on the distribution and availability of zinc in the soil profile. Experiments were carried out with Lumbricus rubellus and Lumbricus terrestris in perspex columns (Ø 10 cm), filled with 20 to 23 cm non-polluted soil [organic matter 2%, clay 2.9%, pH 6.4 (0.01 M CaCl₂)], that was covered by a 3- to 5-cm layer of aged zinc-spiked soil (500 mg Zn/kg dry soil) and another 2 cm non-polluted soil on top. After 80 days, columns were sacrificed and sampled in a depth profile. Earthworm casts, deposited on top of the soil, were collected. Each sample was analyzed for total and 0.01 M CaCl₂-exchangeable zinc concentrations. L. rubellus did not go deeper than 3 cm into the soil and therefore no effect on zinc distribution in the soil could be detected. For L. terrestris, total zinc concentrations in the non-polluted layers were slightly but significantly higher in columns with earthworms, and so were the CaCl₂-exchangeable zinc concentrations in the polluted layers of these columns. Casts of L. terrestris collected from the soil surface showed higher total zinc concentrations than those from non-polluted soil. Casts were mainly placed on top of the soil. This study showed that these epigeic and (epi)anecic species have only a slight effect on zinc availability, and that deep burrowing species, like L. terrestris, are able to transport polluted soil from deeper layers to the soil surface.