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  • 1
    Language: English
    In: Plant and Soil, 2011, Vol.341(1), pp.221-232
    Description: The root-zone of wetland rice was monitored in a paddy soil throughout a vegetation period with the aid of a rhizotron experiment. For this purpose (a) digital images of the root-zone were taken daily, and (b) the redox potential was measured in situ every day. The images were processed by image analysis in order to display areas of oxidation and reduction in the soil. Therefore, thresholds were set to simplify the localization and quantification of discrete areas which were colourized due to the redox potential. Both, images and measured redox potentials, provide the basis for the visualization of the root and redox dynamics in the root-zone. The anaerobic root-zone of flooded paddy soils is significantly influenced by the aerenchymal transport of oxygen to rice roots. The release of oxygen into the rhizosphere, which causes different patterns of oxidized and reduced areas in the course of the vegetation period, also affects microbial communities such as methane producing archaea or methane oxidizing bacteria. The visualization of redox dynamics may, therefore, be useful to localize potential hotspots for the microorganisms in the root-zone of paddy soils. The reduced and oxidized conditions changed spatiotemporally. Oxidized areas were mostly found in the surrounding of active roots and in a distinct layer next to the soil surface. Reduced areas shifted from beneath the oxidized surface layer into sparsely-rooted soil. The ratio of the analyzed oxidized and reduced areas was oscillating with increasing intensity throughout the monitored vegetation period.
    Keywords: Rhizotron ; Paddy soil ; Rhizosphere ; Root-zone ; Redox potential ; Image analysis
    ISSN: 0032-079X
    E-ISSN: 1573-5036
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  • 2
    Language: English
    In: Soil Biology and Biochemistry, 2008, Vol.40(7), pp.1883-1891
    Description: In recent years, methods of molecular microbiology have been used for the investigation of soil microbial diversity. Fluorescence hybridization (FISH) represents a method which allows a specific staining and enumeration of soil microorganisms by using fluorescent-labelled oligonucleotide probes. However, the detection of FISH-stained cells is often affected by strong autofluorescence of the background, especially in samples of the top soils. In this study a more efficient FISH-approach coupled with catalyzed reporter deposition (CARD) was adapted to soils. Due to tyramide signal amplification (TSA) the fluorescence intensity has been considerably increased at the target binding site of a probe. Six different soils were investigated to evaluate the effect of sample preparation and pre-treatments, TSA, and the procedure of detection. The results show that both cell permeabilization and TSA are two important factors which improve hybridization of soil microorganisms. Soils with higher clay contents have shown better results when prepared on polycarbonate filters rather than on glass slides. Using specific fluorescence filter systems and dye combinations the detection of hybridized cells was extensively increased compared with the application of monolabelled oligonucleotide probes in regular FISH-analysis. As a result, CARD-FISH-stained cells were suitable for automated counting using digital image analysis. Nevertheless, the counterstain with DAPI had to be analyzed manually as it was strongly affected by autofluorescence.
    Keywords: Fluorescence in Situ Hybridization ; Catalyzed Reporter Deposition ; Soil Microorganisms ; Fluorescence Microscopy ; Soil Molecular Microbiology ; CARD-FISH ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 3
    Language: English
    In: Soil Biology and Biochemistry, June, 2008, Vol.40(6), p.1284(10)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2007.06.019 Byline: Thilo Eickhorst, Rolf Tippkotter Keywords: Fish; Microorganisms; Undisturbed soil; Fluorescence microscopy; Fluorescence in situ hybridization; Soil molecular microbiology; Micropedology Abstract: In contrast to conventional approaches molecular microbiology leads to a deeper understanding of the biodiversity of soil microorganisms. Nevertheless, there is a lack of knowledge regarding the spatial distribution of microbiota in the complex soil matrix and the interaction between the soil structure and microorganisms. DNA analytical methods such as fluorescence in situ hybridization (FISH) are being utilized to improve the characterization of microbial biocoenosis. Micropedological procedures which preserve the soil structure by embedding it with resin, in combination with FISH, allow the localization and identification of soil microorganism diversity in relation to the specific properties of their microhabitats. In this study, FISH was used prior to resin embedding in undisturbed soil samples of four different soils. The polished sections provided visualization of the bound probes as well as the undisturbed soil matrix via fluorescence microscopy. Furthermore, cell counts of active bacteria, locating of hot spots and their relationship to microsites rich in nutrients and water, such as humus or clay minerals, are now easy to perform. This will lead to a better understanding of how soil structure can affect soil microorganisms and vice versa. Derived from the use of 16S rRNA targeted oligonucleotide probes, EUB338 and NON338, the cell counts of FISH-detected bacteria were in the same order of magnitude in the undisturbed and the suspended soil samples. Counterstaining with DAPI showed varying detection rates caused by differing activities of the soil microorganisms. Author Affiliation: Institute of Soil Science, University of Bremen, Leobener Street, UFT, D-28359 Bremen, Germany Article History: Received 28 October 2006; Revised 8 May 2007; Accepted 10 June 2007
    Keywords: Microbiology -- Methods ; Microbiology -- Analysis ; Fluorescence -- Methods ; Fluorescence -- Analysis ; Microorganisms -- Methods ; Microorganisms -- Analysis
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 4
    In: Nature, 2012, Vol.488(7409), p.91
    Description: The plant root defines the interface between amulticellular eukaryote and soil, one of the richest microbial ecosystems on Earth1. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development2, with implications ranging from enhanced crop productivity3 to phytoremediation4. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbeassociated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication5. Several studies attempted to describe the structure of bacterial root endophytes6; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describemethodology to characterize and compare soil- and rootinhabiting bacterial communities, which reveals not only a function formetabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization.We showthat the roots ofArabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabitingmicrobiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not beArabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells. [PUBLICATION ]
    Keywords: Actinobacteria–Isolation & Purification ; Arabidopsis–Classification ; Arabidopsis–Microbiology ; Bacteria–Classification ; Bacteria–Genetics ; Bacteria–Isolation & Purification ; Bacteria–Ultrastructure ; Bacteroidetes–Isolation & Purification ; Biodiversity–Metabolism ; Cell Wall–Microbiology ; Cell Wall–Classification ; Ecosystem–Genetics ; Endophytes–Growth & Development ; Endophytes–Isolation & Purification ; Endophytes–Microbiology ; Endophytes–Microbiology ; Host Specificity–Isolation & Purification ; In Situ Hybridization, Fluorescence–Genetics ; Metagenome–Analysis ; Plant Cells–Chemistry ; Plant Roots–Chemistry ; Proteobacteria–Chemistry ; RNA, Ribosomal, 16s–Chemistry ; Rhizosphere–Chemistry ; Ribotyping–Chemistry ; Soil–Chemistry ; Soil–Chemistry ; Soil Microbiology–Chemistry ; Microbiology ; Classification ; Taxonomy ; Bacteria ; Data Bases ; Community ; Cluster Analysis ; Hypothesis Testing ; Genetic Testing ; Gene Amplification ; RNA, Ribosomal, 16s ; Soil;
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 5
    Language: English
    In: Soil Biology and Biochemistry, 2015, Vol.84, p.21(7)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2015.02.010 Byline: Hannes Schmidt, Doris Vetterlein, John M. Kohne, Thilo Eickhorst Abstract: X-ray Microfocused Computed Tomography (X-ray [mu]-CT) allows a non-destructive and three-dimensional observation of microbial habitats (i.e. pore space) in soil. A major premise for microbiological studies integrating X-ray [mu]-CT is that soil microorganisms are not affected by irradiation dose in terms of physiology and composition. However, the compatibility of X-ray [mu]-CT and soil biological experiments has been evaluated controversially. We performed an incubation experiment with packed microcosms to assess the effect of X-ray [mu]-CT on native microbial populations with emphasis on soil archaea and bacteria. Before (14 days) and after (1 and 14 days) scanning we analyzed (i) respiration, (ii) enzyme activity, (iii) microbial biomass, (iv) abundance and (v) community structure in scanned and control treatments. None of the microbial parameters exhibited significant differences among scanned and unscanned soil samples at all sampling times with the exception of lower archaeal cell numbers subsequent to X-ray [mu]-CT. Incubation time was the main factor that induced a significant alteration of microbial soil populations while irradiation had no or only very little effect thereupon. Taken together, three-dimensional in situ data obtained via X-ray [mu]-CT may well be combined with microbiological analyses in soil. Author Affiliation: (a) Soil Microbial Ecology, University of Bremen, 28359 Bremen, Germany (b) Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria (c) Department of Soil Physics, UFZ - Helmholtz Center for Environmental Research, 06120 Halle, Germany Article History: Received 18 November 2014; Revised 7 February 2015; Accepted 9 February 2015
    Keywords: Enzymes – Physiological Aspects ; Enzymes – Analysis ; Soil Microbiology – Physiological Aspects ; Soil Microbiology – Analysis ; Bacteria – Physiological Aspects ; Bacteria – Analysis ; Cat Scans – Physiological Aspects ; Cat Scans – Analysis ; Ecosystems – Physiological Aspects ; Ecosystems – Analysis
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 6
    In: FEMS Microbiology Ecology, 2014, Vol. 87(2), pp.390-402
    Description: Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was applied to detect microbial cells on the rhizoplane of wetland rice ( Oryza sativa L.). Fluorescent signals of high intensity and specificity allowed for a reliable quantification of selected microbial phyla. Absolute cell numbers of archaea and bacteria were observed to be highest at flowering stage of rice plant development ( P 〈 0.05) showing values of 1.32 and 6.26 × 10 4 cells mm −2 rhizoplane, respectively. Highest colonization densities shifted from the root tip toward more mature regions with increasing plant age. Significant differences between cell numbers observed within a short distance (0–15 mm) indicated irregular distribution patterns of microbiota. Root tips, elongation zones, and openings at the base of lateral roots represented preferential areas for microbial colonization, which were often covered with iron coatings and densely colonized with potential iron-oxidizing Betaproteobacteria (59% of bacteria). Methanogenic archaea were abundant on the rhizoplane (up to 0.96 × 10 3 cells mm −2 rhizoplane), and the decline of their relative abundance with plant age was also found in the associated rhizosphere soil. Cell numbers of methanotrophic bacteria significantly increased at flowering (6.38 × 10 3 cells mm −2 rhizoplane; P 〈 0.05), indicating their stimulation by root-derived substrates which was less pronounced in the rhizosphere soil. 〈p〉〈fig id="fig0" position="float"〉 〈graphic alt-version="no" position="float" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="fem12232-toc-0001" xlink:type="simple"/〉〈/fig〉 〈/p〉
    Keywords: Rhizosphere ; Rhizoplane ; Wetland Rice ; Archaea ; Bacteria ; Methanogenic
    E-ISSN: 1574-6941
    Source: Oxford University Press
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  • 7
    Language: English
    In: Soil Biology and Biochemistry, May 2015, Vol.84, pp.21-27
    Description: X-ray Microfocused Computed Tomography (X-ray μ-CT) allows a non-destructive and three-dimensional observation of microbial habitats (i.e. pore space) in soil. A major premise for microbiological studies integrating X-ray μ-CT is that soil microorganisms are not affected by irradiation dose in terms of physiology and composition. However, the compatibility of X-ray μ-CT and soil biological experiments has been evaluated controversially. We performed an incubation experiment with packed microcosms to assess the effect of X-ray μ-CT on native microbial populations with emphasis on soil archaea and bacteria. Before (14 days) and after (1 and 14 days) scanning we analyzed (i) respiration, (ii) enzyme activity, (iii) microbial biomass, (iv) abundance and (v) community structure in scanned and control treatments. None of the microbial parameters exhibited significant differences among scanned and unscanned soil samples at all sampling times with the exception of lower archaeal cell numbers subsequent to X-ray μ-CT. Incubation time was the main factor that induced a significant alteration of microbial soil populations while irradiation had no or only very little effect thereupon. Taken together, three-dimensional data obtained via X-ray μ-CT may well be combined with microbiological analyses in soil.
    Keywords: X-Ray Microfocused Computed Tomography ; Microbial Habitat ; Microbial Biomass ; Enzyme Activity ; Fluorescence in Situ Hybridization ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
    Source: ScienceDirect Journals (Elsevier)
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  • 8
    Language: English
    In: Plant and Soil, 2016, Vol.408(1), pp.357-368
    Description: Background and Aims Biochar amendment to soil is a promising practice of enhancing productivity of agricultural systems. The positive effects on crop are often attributed to a promotion of beneficial soil microorganisms while suppressing pathogens e.g. This study aims to determine the influence of biochar feedstock on (i) spontaneous and fungi inoculated microbial colonisation of biochar particles and (ii) physical pore space characteristics of native and fungi colonised biochar particles which impact microbial habitat quality. Methods Pyrolytic biochars from mixed woods and Miscanthus were investigated towards spontaneous colonisation by classical microbiological isolation, phylogenetic identification of bacterial and fungal strains, and microbial respiration analysis. Physical pore space characteristics of biochar particles were determined by X-ray [mu]-CT. Subsequent 3D image analysis included porosity, surface area, connectivities, and pore size distribution. Results Microorganisms isolated from Wood biochar were more abundant and proliferated faster than those from the Miscanthus biochar. All isolated bacteria belonged to gram-positive bacteria and were feedstock specific. Respiration analysis revealed higher microbial activity for Wood biochar after water and substrate amendment while basal respiration was on the same low level for both biochars. Differences in porosity and physical surface area were detected only in interaction with biochar-specific colonisation. Miscanthus biochar was shown to have higher connectivity values in surface, volume and transmission than Wood biochars as well as larger pores as observed by pore size distribution. Differences in physical properties between colonised and non-colonised particles were larger in Miscanthus biochar than in Wood biochar. Conclusions Vigorous colonisation was found on Wood biochar compared to Miscanthus biochar. This is contrasted by our findings from physical pore space analysis which suggests better habitat quality in Miscanthus biochar than in Wood biochar. We conclude that (i) the selected feedstocks display large differences in microbial habitat quality as well as physical pore space characteristics and (ii) physical description of biochars alone does not suffice for the reliable prediction of microbial habitat quality and recommend that physical and surface chemical data should be linked for this purpose.
    Keywords: Biochar ; Microbial colonisation ; Pore geometry ; Habitat quality
    ISSN: 0032-079X
    E-ISSN: 1573-5036
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  • 9
    Language: English
    In: Nature, Sept 26, 2013, Vol.501(7468), p.S20(5)
    Description: Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation (1-3). Colonization of the root occurs despite a sophisticated plant immune system (4,5), suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant-microbe interactions derived from complex soil communities.
    Keywords: Arabidopsis Thaliana -- Genetic Aspects ; Rna Sequencing -- Research ; Microbiota (Symbiotic Organisms) -- Observations ; Host-Bacteria Relationships -- Observations
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 10
    Language: English
    In: Nature, 02 August 2012, Vol.488(7409), pp.86-90
    Description: Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. Colonization of the root occurs despite a sophisticated plant immune system, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant-microbe interactions derived from complex soil communities.
    Keywords: Metagenome ; Soil Microbiology ; Arabidopsis -- Microbiology ; Endophytes -- Classification ; Plant Roots -- Microbiology
    ISSN: 00280836
    E-ISSN: 1476-4687
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