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  • Article  (41)
  • 2018  (41)
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  • 2018  (41)
  • 11
    Language: English
    In: Vadose Zone Journal, 01 March 2018, Vol.17(1)
    Description: X-ray radiography is a suitable approach to study water dynamics in undisturbed soil. However, beam hardening impairs the deduction of soil moisture changes from X-ray attenuation, especially when studying infiltration of water into cylindrical soil columns. We developed a calibration protocol to correct for beam hardening effects that enables the quantitative determination of changing average water content in two-dimensional projections. The method works for a broad range of materials and is easy to implement. Moreover, we studied the drift of X-ray attenuation values due to the detector latency and eliminated its contribution to the quantitative analysis. Finally we could visualize the dynamics of infiltrating water into undisturbed cylindrical soil samples.
    Keywords: Agriculture
    ISSN: 1539-1663
    E-ISSN: 1539-1663
    Source: Directory of Open Access Journals (DOAJ)
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  • 12
    Language: English
    In: GigaScience, 01 September 2018, Vol.7(9)
    Description: To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.
    Keywords: Archaea–Genetics ; Bacteria–Genetics ; Genome, Archaeal–Methods ; Genome, Bacterial–Genetics ; Molecular Sequence Annotation–Genetics ; RNA, Archaeal–Genetics ; RNA, Bacterial–Genetics ; RNA, Untranslated–Genetics ; Software–Genetics ; RNA, Archaeal ; RNA, Bacterial ; RNA, Untranslated;
    E-ISSN: 2047-217X
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  • 13
    Language: English
    In: https://doi.org/10.1371/journal.pgen.1007401
    Description: Invasion of epithelial cells by Salmonella enterica requires expression of genes located in the pathogenicity island I (SPI-1). The expression of SPI-1 genes is very tightly regulated and activated only under specific conditions. Most studies have focused on the regulatory pathways that induce SPI-1 expression. Here, we describe a new regulatory circuit involving CRP-cAMP, a widely established metabolic regulator, in silencing of SPI-1 genes under non-permissive conditions. In CRP-cAMP-deficient strains we detected a strong upregulation of SPI-1 genes in the mid-logarithmic growth phase. Genetic analyses revealed that CRP-cAMP modulates the level of HilD, the master regulator of Salmonella invasion. This regulation occurs at the post-transcriptional level and requires the presence of a newly identified regulatory motif within the hilD 3'UTR. We further demonstrate that in Salmonella the Hfq-dependent sRNA Spot 42 is under the transcriptional repression of CRP-cAMP and, when this transcriptional repression is relieved, Spot 42 exerts a positive effect on hilD expression. In vivo and in vitro assays indicate that Spot 42 targets, through its unstructured region III, the 3'UTR of the hilD transcript. Together, our results highlight the biological relevance of the hilD 3'UTR as a hub for post-transcriptional control of Salmonella invasion gene expression.
    Keywords: Salmonel·La ; Expressió Gènica ; Salmonella ; Gene Expression
    ISSN: 1553-7390
    Source: Universitat de Barcelona
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  • 14
    Language: English
    In: Frontiers in Environmental Science, 01 April 2018, Vol.6
    Description: Soil-borne nitrous oxide (N2O) emissions have a high spatial and temporal variability which is commonly attributed to the occurrence of hotspots and hot moments for microbial activity in aggregated soil. Yet there is only limited information about the biophysical processes that regulate the production and consumption of N2O on microscopic scales in undisturbed soil. In this study, we introduce an experimental framework relying on simplified porous media that circumvents some of the complexities occuring in natural soils while fully accounting for physical constraints believed to control microbial activity in general and denitrification in particular. We used this framework to explore the impact of aggregate size and external oxygen concentration on the kinetics of O2 consumption, as well as CO2 and N2O production. Model aggregates of different sizes (3.5 vs. 7 mm diameter) composed of porous, sintered glass were saturated with a defined growth medium containing roughly 109 cells ml−1 of the facultative anaerobic, nosZ-deficient denitrifier Agrobacterium tumefaciens with N2O as final denitrification product and incubated at five different oxygen levels (0–13 vol-%). We demonstrate that the onset of denitrification depends on the amount of external oxygen and the size of aggregates. Smaller aggregates were better supplied with oxygen due to a larger surface-to-volume ratio, which resulted in faster growth and an earlier onset of denitrification. In larger aggregates, the onset of denitrification was more gradual, but with comparably higher N2O production rates once the anoxic aggregate centers were fully developed. The normalized electron flow from the reduced carbon substrate to N-oxyanions (edenit-/etotal- ratio) could be solely described as a function of initial oxygen concentration in the headspace with a simple, hyperbolic model, for which the two empirical parameters changed with aggregate size in a consistent way. These findings confirm the important role of soil structure on N2O emissions from denitrification by shaping the spatial patterns of microbial activity and anoxia in aggregated soil. Our dataset may serve as a benchmark for constraining or validating spatially explicit, biophysical models of denitrification in aggregated soil.
    Keywords: Greenhouse Gas Emissions ; Denitrification Kinetics ; Microbial Hotspots ; Microsites ; Anoxic Aggregate Centers ; Agrobacterium Tumefaciens ; Environmental Sciences
    E-ISSN: 2296-665X
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  • 15
    Language: English
    In: Environmental Technology, 01 February 2018, Vol.39(3), pp.264-276
    Description: Municipal wastewater treatment commonly involves mechanical, biological and chemical treatment steps to protect humans and the environment from adverse effects. Membrane technology has gained increasing attention as an alternative to conventional...
    Keywords: Biogas Production ; Forward Osmosis ; Membrane Filtration ; Seawater ; Wastewater Treatment ; Engineering
    ISSN: 0959-3330
    E-ISSN: 1479-487X
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  • 16
    Language: English
    In: PLoS Genetics, 01 June 2018, Vol.14(6), p.e1007401
    Description: Invasion of epithelial cells by Salmonella enterica requires expression of genes located in the pathogenicity island I (SPI-1). The expression of SPI-1 genes is very tightly regulated and activated only under specific conditions. Most studies have focused on the regulatory pathways that induce SPI-1 expression. Here, we describe a new regulatory circuit involving CRP-cAMP, a widely established metabolic regulator, in silencing of SPI-1 genes under non-permissive conditions. In CRP-cAMP-deficient strains we detected a strong upregulation of SPI-1 genes in the mid-logarithmic growth phase. Genetic analyses revealed that CRP-cAMP modulates the level of HilD, the master regulator of Salmonella invasion. This regulation occurs at the post-transcriptional level and requires the presence of a newly identified regulatory motif within the hilD 3'UTR. We further demonstrate that in Salmonella the Hfq-dependent sRNA Spot 42 is under the transcriptional repression of CRP-cAMP and, when this transcriptional repression is relieved, Spot 42 exerts a positive effect on hilD expression. In vivo and in vitro assays indicate that Spot 42 targets, through its unstructured region III, the 3'UTR of the hilD transcript. Together, our results highlight the biological relevance of the hilD 3'UTR as a hub for post-transcriptional control of Salmonella invasion gene expression.
    Keywords: Biology
    ISSN: 1553-7390
    E-ISSN: 1553-7404
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  • 17
    Language: English
    In: Frontiers in Microbiology, 2018, Vol.9, p.1929
    Description: Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the usual bulk, macroscopic parameters used to characterize soils (e.g., granulometry, pH, soil organic matter and biomass contents) provide insufficient information to describe quantitatively...
    Keywords: Life Sciences ; X-Ray Computed ; Upscaling ; Biodiversity ; Soil Microbiology ; Tomography ; Single-Cell Genomics ; Nanosims Imaging ; Biology
    ISSN: 1664-302X
    E-ISSN: 1664-302X
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  • 18
    Language: English
    In: Science of the Total Environment, 15 December 2018, Vol.645, pp.192-204
    Description: Riverbank filtration systems are important structures that ensure the cleaning of infiltrating surface water for drinking water production. In our study, we investigated the potential risk for a breakthrough of environmentally aged silver nanoparticles (Ag NP) through these systems. Additionally, we identified factors leading to the remobilization of Ag NP accumulated in surficial sediment layers in order to gain insights into remobilization mechanisms. We conducted column experiments with Ag NP in an outdoor pilot plant consisting of water-saturated sediment columns mimicking a riverbank filtration system. The NP had previously been aged in river water, soil extract, and ultrapure water, respectively. We investigated the depth-dependent breakthrough and retention of NP. In subsequent batch experiments, we studied the processes responsible for a remobilization of Ag NP retained in the upper 10 cm of the sediments, induced by ionic strength reduction, natural organic matter (NOM), and mechanical forces. We determined the amount of remobilized Ag by ICP-MS and differentiated between particulate and ionic Ag after remobilization using GFAAS. The presence of Ag-containing heteroaggregates was investigated by combining filtration with single-particle ICP-MS. Single and erratic Ag breakthrough events were mainly found in 30 cm depth and Ag NP were accumulated in the upper 20 cm of the columns. Soil-aged Ag NP showed the lowest retention of only 54%. Remobilization was induced by the reduction of ionic strength and the presence of NOM in combination with mechanical forces. The presence of calcium in the aging- as well as the remobilizing media reduced the remobilization potential. Silver NP were mainly remobilized as heteroaggregates with natural colloids, while dissolution played a minor role. Our study indicates that the breakthrough potential of Ag NP in riverbank filtration systems is generally low, but the aging in soil increases their mobility. Remobilization processes are associated to co-mobilization with natural colloids.
    Keywords: Heteroaggregation ; Nanoparticle Transformation ; Breakthrough ; Mobility ; Reversibility ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 19
    Language: English
    In: Nature, 22 February 2018, Vol.554(7693), pp.423
    Keywords: Soil ; Plant Roots -- Chemistry
    ISSN: 00280836
    E-ISSN: 1476-4687
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  • 20
    Language: English
    In: Geoderma, 01 June 2018, Vol.319, pp.132-141
    Description: Irrigation with treated waste water (TWW) is a common practice in agriculture, mainly in arid and semiarid areas as it provides a sustainable water resource available at all-season in general and at freshwater shortage in particular. However, TWW still contains abundant organic material which is known to decrease soil wettability, which in turn may promote flow instabilities that lead to the formation of preferential flow paths. We investigate the impact of long-term TWW irrigation on water wettability and infiltration into undisturbed soil cores from two commercially used orchards in Israel. Changes of water content during infiltration were quantitatively analysed by X-ray radiography. One orchard (sandy clay loam) had been irrigated with TWW for more than thirty years. In the other orchard (loamy sand) irrigation had been changed from freshwater to TWW in 2008 and switched back in some experimental plots to freshwater in 2012. Undisturbed soil cores were taken at the end of the dry and the rainy season to investigate the seasonal effect on water repellency and on infiltration dynamics in the laboratory. The irrigation experiments were done on field moist samples. A test series with different initial water contents was run to detect the influence on water movement at different wettabilities. In this study we show that the infiltration front stability is dependent on the history of waste water irrigation at the respective site and on the initial water content.
    Keywords: Soil Water Repellency ; Treated Waste Water Irrigation ; Unstable Flow ; Preferential Flow ; Water Infiltration ; X-Ray Analysis ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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