Dynamics of the Apple Fruit Microbiome after Harvest and Implications for Fruit Quality

The contribution of the apple microbiome to the production chain of apple was so far largely unknown. Here, we describe the apple fruit microbiome and influences on its composition by parameters such as storage season, storage duration, storage technology, apple variety, and plant protection schemes. A combined culturing and metabarcoding approach revealed significant differences in the abundance, composition, and diversity of the apple fruit microbiome. We showed that relatively few genera contribute a large portion of the microbiome on fruit and that the fruit microbiome changes during the storage season depending on the storage conditions. In addition, we show that the plant protection regime has an influence on the diversity of the fruit microbiome and on the dynamics of pathogenic fungal genera during the storage season. For the genus Neofabraea, the quantitative results from the metabarcoding approach were validated with real-time PCR. In conclusion, we identified key parameters determining the composition and temporal changes of the apple fruit microbiome, and the main abiotic driving factors of microbiome diversity on apple fruit were characterized

Restricted streptomycin use in apple orchards did not adversely alter the soil bacteria communities

Streptomycin has been authorized for restricted use in the prevention of the fire blight disease of pome fruit orchards in the EU and Switzerland. This study addresses the important topic of the influence of the use of streptomycin in agriculture on the total bacteria community within the soil ecosystem. Soil samples were taken from soils under apple trees, prior to streptomycin application and 2 weeks post streptomycin application or water application (untreated control). High throughput 16S rRNA gene amplicon sequencing was used to generate datasets from the soils under apple trees in apple orchards from three different locations in Switzerland. We hypothesized that the use of streptomycin would reduce the bacterial diversity within the soil samples and enhance a reduction in the variety of taxa present. Bacterial species such as Pseudomonas, Burkholderia, and Stenotrophomonas are intrinsically resistant to many antibiotics and as such it is of interest to investigate if the use of streptomycin provided a selective advantage for these bacteria in the soil ecosystem. The application of streptomycin did not influence the abundance and diversities of major bacteria taxa of the soils or the Pseudomonas, Burkholderia, and Stenotrophomonas species. We also discovered that apple orchards under the same management practices, did not harbor the same bacterial communities. The restricted application of streptomycin in the protection of apple orchards from the fire blight pathogen Erwinia amylovora under the guidelines in Switzerland did not alter either the bacterial diversity or abundance within these soil ecosystems

Real-time PCR methods for quantitative monitoring of streptomycin and tetracycline resistance genes in agricultural ecosystems

Antibiotic application in plant agriculture is primarily used to control fire blight caused by Erwinia amylovora in pome fruit orchards. In order to facilitate environmental impact assessment for antibiotic applications, we developed and validated culture-independent quantitative real-time PCR multiplex assays for streptomycin (strA, strB, aadA and insertion sequence IS1133) and tetracycline (tetB, tetM and tetW) resistance elements in plant and soil samples. The qPCR were reproducible and consistent whether the DNA was extracted directly from bacteria, plant and soil samples inoculated with bacteria or soil samples prior to and after manure slurry treatment. The genes most frequently identified in soils pre- and post-slurry treatment were strB, aadA, tetB and tetM. All genes tested were detected in soils pre-slurry treatment, and a decrease in relative concentrations of tetB and the streptomycin resistance genes was observed in samples taken post-slurry treatment. These multiplex qPCR assays offer a cost-effective, reliable method for simultaneous quantification of antibiotic resistance genes in complex, environmental sample matrices

Einfluss von Streptomycin in Apfelanlagen auf Antibiotika-Resistenzen in der Umwelt

Das Bundesamt für Landwirtschaft (BLW) liess 2008 den Einsatz von Streptomycin zur Bekämpfung von Feuerbrand unter kontrollierten Bedingungen zu. Es knüpfte diese Zulassung an die Auflage, die behandelten Flächen auf die Entwicklung von Antibiotikaresistenzen hin zu beobachten. Agroscope in Wädenswil führte dazu eine erste quantitative Analyse von mobilen Streptomycin-, Tetrazyklin-Resistenzgenen (strA, strB, aadA, tetB, tetM, tetW) und der Insertionssequenz IS1133 in Streptomycinbehandelten Kernobstanlagen durch. Von drei Streptomycinbehandelten Apfelanlagen wurden in den Jahren 2010, 2011 und 2012 Blüten-, Blätter- und Bodenproben entnommen. Die Häufigkeit und Verteilung der Resistenzgene wurden zu verschiedenen Zeitpunkten und in Abhängigkeit der Behandlung untersucht. Die mobilen Streptomycin- und Tetrazyklinresistenzgene konnten bereits vor der Streptomycin-Applikation in fast allen Proben nachgewiesen werden, was das Vorkommen dieser Resistenzgene in der Natur dokumentiert. Statistisch relevante Anstiege in der Häufigkeit der Resistenzgene traten gelegentlich auf, waren aber nicht konstant und traten im Folgejahr nicht wieder auf. Zusätzlich wurde in der Studie die bakterielle Zusammensetzung in Bodenproben mit und ohne Streptomycin-Applikation untersucht. Es zeigten sich ebenfalls keine signifikanten und konstanten Veränderungen

Einfluss von Streptomycin in Apfelanlagen auf Antibiotika-Resistenzen in der Umwelt

Das Bundesamt für Landwirtschaft (BLW) liess 2008 den Einsatz von Streptomycin zur Bekämpfung von Feuerbrand unter kontrollierten Bedingungen zu. Es knüpfte diese Zulassung an die Auflage, die behandelten Flächen auf die Entwicklung von Antibiotikaresistenzen hin zu beobachten. Agroscope in Wädenswil führte dazu eine erste quantitative Analyse von mobilen Streptomycin-, Tetrazyklin-Resistenzgenen (strA, strB, aadA, tetB, tetM, tetW) und der Insertionssequenz IS1133 in Streptomycinbehandelten Kernobstanlagen durch. Von drei Streptomycinbehandelten Apfelanlagen wurden in den Jahren 2010, 2011 und 2012 Blüten-, Blätter- und Bodenproben entnommen. Die Häufigkeit und Verteilung der Resistenzgene wurden zu verschiedenen Zeitpunkten und in Abhängigkeit der Behandlung untersucht. Die mobilen Streptomycin- und Tetrazyklinresistenzgene konnten bereits vor der Streptomycin-Applikation in fast allen Proben nachgewiesen werden, was das Vorkommen dieser Resistenzgene in der Natur dokumentiert. Statistisch relevante Anstiege in der Häufigkeit der Resistenzgene traten gelegentlich auf, waren aber nicht konstant und traten im Folgejahr nicht wieder auf. Zusätzlich wurde in der Studie die bakterielle Zusammensetzung in Bodenproben mit und ohne Streptomycin-Applikation untersucht. Es zeigten sich ebenfalls keine signifikanten und konstanten Veränderungen

Analysis of the bacterial epiphytic microbiota of oak leaf lettuce with 16S ribosomal RNA gene analysis

The leaf microbiota has major influences on the quality of ready-to-eat lettuce. While studies investigating the epi- and endophytic microbiota of lettuce have been published, no protocols focusing only on the epiphytic microbiota exist. As the epiphytic microbiota may be especially influenced by technological steps in the production of ready-to-eat lettuce, an in-depth knowledge of these microorganisms is essential with regard to consumer safety and spoilage. Currently it is not clear to what extent results gained from single samples are representative of the community composition. A technique for the separation of bacterial cells from the leaf surface was applied to green oak leaf lettuce. The bacterial diversity was analysed in triplicate with high throughput Roche 454 sequencing of prokaryotic 16S rRNA genes to analyse the intra-sample variation. Sequence analysis revealed members of the phyla Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, Proteobacteria and Verrucomicrobia, and of the candidate division WYO. The ten most abundant proteobacterial genera in all three samples were Alkanindiges (24.6%), Pseudomonas (11.3%), Sphingomonas (8.6%), Janthinobacterium (8.3%), Acinetobacter (4.3%), Polaromonas (1.3%), Erwinia (1.1%), and Methylobacterium (1.1%). The genera Pedobacter (2.5%) and Hymenobacter (1.4%) dominated the phylum Bacteroidetes. The intra-sample variation was less than 0.7% for seven of these most abundant genera with the exception of Pseudomonas, Janthinobacterium and Alkanindiges, where larger standard deviations were obtained. This low intra-sample variation demonstrates that the established technique based on oak leaf lettuce is suitable for the culture-independent analysis of the epiphytic bacterial microbiota of produce

Transverse momentum and pseudorapidity distributions of charged hadrons in pp collisions at (s)\sqrt(s) = 0.9 and 2.36 TeV

Measurements of inclusive charged-hadron transverse-momentum and pseudorapidity distributions are presented for proton-proton collisions at sqrt(s) = 0.9 and 2.36 TeV. The data were collected with the CMS detector during the LHC commissioning in December 2009. For non-single-diffractive interactions, the average charged-hadron transverse momentum is measured to be 0.46 +/- 0.01 (stat.) +/- 0.01 (syst.) GeV/c at 0.9 TeV and 0.50 +/- 0.01 (stat.) +/- 0.01 (syst.) GeV/c at 2.36 TeV, for pseudorapidities between -2.4 and +2.4. At these energies, the measured pseudorapidity densities in the central region, dN(charged)/d(eta) for |eta| < 0.5, are 3.48 +/- 0.02 (stat.) +/- 0.13 (syst.) and 4.47 +/- 0.04 (stat.) +/- 0.16 (syst.), respectively. The results at 0.9 TeV are in agreement with previous measurements and confirm the expectation of near equal hadron production in p-pbar and pp collisions. The results at 2.36 TeV represent the highest-energy measurements at a particle collider to date