The preparation of soil thin sections for biological studies

Tippkötter, Rolf; Ritz, Karl; Darbyshire, John F.

doi:10.1111/j.1365-2389.1986.tb00396.x

Cited by 47 publications

(16 citation statements)

References 13 publications

(3 reference statements)

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“…All attempts at refrigeration of impregnation components failed to decrease this reaction. However, this result was in line with the findings of Tippkotter et al (1986) that the control of polymerization is exceedingly difficult in resin mixtures with short curing times.…”

Section: Resin Impregnationsupporting

confidence: 92%

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Development of a technique for the measurement of root geometry in the soil using resin‐impregnated blocks and image analysis

Commins

McBratney

Koppi

1991

Journal of Soil Science

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A method is described that permits the measurement of roots in situ in the soil using computerized image analysis to process images obtained from planar faces cut from a resin-fixed pot. Soil sample pots are initially impregnated with rapid-curing epoxy resin. Blocks are then cut from the impregnated pot with a diamond saw to expose a planar face. Modification of the present resin-impregnation procedure is necessary as impregnation results were mostly unsatisfactory. Roots are contrasted from the soil matrix by enhancing autofluorescence using longwave ultraviolet light and appropriate filters. After image capture and segmentation to show regions of root material, measurements of volume fraction of roots, volumetric surface area, horizontal root length and horizontal root separation, were made with a larger resolution with soil depth than previously.

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Section: Resin Impregnationsupporting

confidence: 92%

“…Treatment with toluidine blue was seen to quench autofluorescence, which was also found by Smith & McCully (1978). Generally, it has been found that non-fluorescent stains tend to quench autofluorescence (Tippkotter et al, 1986).…”

Section: Stainingmentioning

confidence: 93%

Development of a technique for the measurement of root geometry in the soil using resin‐impregnated blocks and image analysis

Commins

McBratney

Koppi

1991

Journal of Soil Science

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“…To obtain quantitative data about the distribution of microorganisms, researchers found it necessary to return to staining cells in thin sections that could be georeferenced easily and viewed in their entirety (e.g., Jones and Griffiths, 1964; White et al, 1994; Nunan et al, 2001, 2002, 2003; Li et al, 2003, 2004). Aside from non-specific stains like calcofluor white M2R applied before impregnation (Postma and Altemuller, 1990), or basic fuchsin and methylene blue applied after impregnation (Tippkötter et al, 1986), researchers also have been interested in selective staining techniques of specific cells, e.g., using fluorescence-conjugated antibody techniques (Postma and Altemuller, 1990), to observe the distribution of bacteria and fungal hyphae in soils. In some cases, problem arose because of the crystallization of the stains when in contact with soils (Harris et al, 2002, 2003).…”

Section: The Microbiological Scenementioning

confidence: 99%

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

et al. 2018

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Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

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“…Water was removed from the soil by wet dehydration applying a graded series of acetone (Tippkötter et al, 1986). Unsaturated polyester resin (Palatal P50-01, Büfa) with acetone as a thinner was used for the embedding of these samples (Tippkötter and Ritz, 1996).…”

Section: Preparation Of Soil Thin Sectionsmentioning

confidence: 99%

Structure and pore system in differently managed clayey surface soil as described by micromorphology and image analysis

et al. 2012

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The preparation of soil thin sections for biological studies

Cited by 47 publications

References 13 publications

Development of a technique for the measurement of root geometry in the soil using resin‐impregnated blocks and image analysis

Development of a technique for the measurement of root geometry in the soil using resin‐impregnated blocks and image analysis

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Structure and pore system in differently managed clayey surface soil as described by micromorphology and image analysis

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