Soil aggregation dynamics and carbon sequestration

The quantity and quality of residues determine the formation and stabilization of aggregate structure for soil organic carbon (SOC) sequestration. Plant roots and residues are the primary organic skeleton to enmesh the inorganic particles together and build macro- and microaggregates while sequestering SOC. There are three major organic binding agents of aggregation: temporary (plant roots, fungal hyphae, and bacterial cells), transient (polysaccharides), and persistent (humic compounds and polymers). Conversion of natural ecosystems into agricultural lands for intensive cultivation severely depletes SOC pools. Magnitude of SOC sequestration in the soil system depends on the residence time of SOC in aggregates. Microaggregates are bound to old organic C, whereas macroaggregates contain younger organic material. Many techniques have been used to assess the SOC distribution in aggregates. Classical methods include SOC determination in aggregate fractions by wet and dry sieving of bulk soil. Isotopic methods including the determination of 13C and 14C with mass spectrometry are techniques to quantify the turnover and storage of organic materials in soil aggregates. Other techniques involve the use of computed tomography, X-ray scattering, and X-ray microscopy to examine the internal porosity and interaggregate attributes of macro- and microaggregates. Current state-of-knowledge has not unravelled completely the underlying complex processes involved in the sequestration, stability, dynamics, and residence times of SOC in macro- and microaggregates. There is a need to develop a unique conceptual model of aggregate hierarchy.

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Nanoscale STXM imaging of soil fungal exudates and organo-mineral interfaces

10.5194/egusphere-egu2020-4733 ◽

2020 ◽

Author(s):

Milda Pucetaite ◽

Per Persson ◽

Edith Hammer

Keyword(s):

Light Source ◽

Soil Aggregates ◽

Decisive Role ◽

Arbuscular Mycorrhizal ◽

Fungal Hypha ◽

Organic C ◽

X Ray ◽

Mineral Particles ◽

Silicon Nitride Membrane ◽

Mineral Interfaces

Soils act as a major sink for atmospheric carbon (C) and, correctly managed, can help counterbalance the excessive CO2 emissions. Organic C in soils can be physically stabilized and &#8216;hidden&#8217; from its decomposers within soil aggregates and it is thought that soil fungi play a decisive role in &#8220;gluing together&#8221; and redistributing soil mineral particles and existing organic matter to form them (M. W. I. Schmidt et al., Nature 478(7367), 49&#8211;56, 2011). A significant contribution to the early aggregation process is adsorption of fungal exudates to the reactive surfaces of mineral particles. To uncover the mechanisms of C stabilization processes and to be able to increase the C sink potential of our soils, we need a deepened understanding of which fungi play key roles in the process, what mineral properties promote it, and what type of fungal exudates are involved.For this purpose, we have grown saprotrophic and symbiotic (both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM)) fungi under sterile conditions in contact with different principal soil components: quartz, goethite and muscovite, on top of X-ray transparent silicon nitride membrane windows and analyzed fungal hyphae by high lateral resolution synchrotron based scanning transmission X-ray microscopy (STXM) in combination with near edge X-ray fine structure (NEXAFS) spectroscopy at absorption edges of C(K), K(L), N(K) and Fe(L). We performed our experiments in the SM beamline at Canadian Light Source, Saskatoon, Canada and I08 beamline at Diamond Light Source, Oxfordshire, UK. In the resultant chemical images, we were able to differentiate the mostly proteinaceous hyphal material, the exudate layer constituting of mixtures of polysaccharides and proteins, and the organo-mineral interfaces consisting of a higher protein and carboxyl to sugar ratio than in the exudate layer. We also observed heterogeneous distributions of the exudate materials around the fungal hypha, indicating presence of exudation channels in the cell wall. Finally, we specifically analyzed NEXAFS spectra at Fe(L) absorption edge of goethite containing samples and were able to show changes in iron speciation in the mineral particles that were in contact with the fungal exudates. These results provide us with better insights to both nanoscale processes of fungal exudation and their role in the formation of organo-mineral interfaces subsequently responsible for soil aggregation.

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Faculty Opinions recommendation of Elemental and redox analysis of single bacterial cells by x-ray microbeam analysis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1022145.253694 ◽

2004 ◽

Author(s):

Janet Morrow

Keyword(s):

Bacterial Cells ◽

X Ray ◽

Microbeam Analysis

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Influence of soil organic matter on sulfate retention in two Podzols in Quebec, Canada

Canadian Journal of Soil Science ◽

10.4141/s98-024 ◽

1999 ◽

Vol 79 (1) ◽

pp. 103-109 ◽

Cited By ~ 5

Author(s):

F. Courchesne ◽

J.-F. Laberge ◽

A. Dufresne

Keyword(s):

Organic Matter ◽

Soil Organic Matter ◽

Ammonium Oxalate ◽

X Ray Diffraction ◽

Weighted Mean ◽

Fine Silt ◽

Mineral Horizon ◽

Organic C ◽

X Ray

The role of soil organic matter (OM) on SO4 retention was investigated by comparing OM content, SO4 retention, and the distribution of Fe, Al and Si compounds in OM-poor (Grands-Jardins, PGJ) and OM-rich (Hermine, HER) Podzols from Québec, Canada. At both sites, four pedons were sampled by horizon; soil pH in H2O, organic C, phosphate-extractable SO4 and, sodium pyrophosphate, acid ammonium oxalate and dithionite-citrate-bicarbonate (DCB) extractable Fe, Al and Si were measured for each mineral horizon. The mineralogy of the clay (<2 µm) and fine silt (2–20 µm) fractions of selected horizons was determined by X-ray diffraction (XRD) and infrared spectroscopy (IR). Weighted mean organic C and pyrophosphate extractable Fe and Al contents were significantly higher in the HER than in the PGJ sola, while the PGJ soils were richer in amorphous inorganic Al. No trends were observed for inorganic Fe compounds. Chemical dissolution and IR allowed the identification of short-range ordered aluminosilicates, probably allophane, in the OM-poor and slightly acidic to neutral PGJ soils. These materials were absent from the OM-rich and acidic HER soils. Phosphate extractions showed that the weighted mean native SO4 content was five times higher in the PGJ than in the HER soil. Finally, native SO4 was strongly related to inorganic Fe, Al and Si (associated with allophane) at PGJ but only to inorganic Fe at HER. These results indicate that OM indirectly affects SO4 sorption through the influence organic substances exerts on the nature and distribution of pedogenic Fe, Al and Si compounds, such as allophane, in Podzolic profiles. Key words: Organic matter, sulfate, imogolite, allophane, silica, Podzol

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Quality of soil from the nickel mining area of Southeast Sulawesi, Indonesia, engineered using earthworms (Pheretima sp.)

Journal of Degraded and Mining Lands Management ◽

10.15243/jdmlm.2021.084.2995 ◽

2021 ◽

Vol 8 (4) ◽

pp. 2995-3005

Author(s):

Hasbullah Syaf ◽

Muhammad Albar Pattah ◽

Laode Muhammad Harjoni Kilowasid

Keyword(s):

Tap Water ◽

Soil Aggregates ◽

Aggregate Size ◽

Mining Area ◽

Size Class ◽

Soil Conditions ◽

Total N ◽

Organic C ◽

Size Classes ◽

Nickel Mining

Earthworms (Pheretima sp.) could survive under abiotic stress soil conditions. Furthermore, their activities as ecosystem engineers allow for the creation of soil biostructures with new characteristics. Therefore, this study aimed to investigate the effect of the abundance of Pheretima sp. on the aggregate size, physicochemistry, and biology of the topsoil from the nickel mining area of Southeast Sulawesi, Indonesia. It was carried out by first grouping their abundance into zero, two, four, six, and eight individuals per pot and then carrying out tests. The Pheretima sp. were then released onto the surface of the topsoil and mixed with biochar that was saturated with tap water in the pot overnight. The results showed that the abundance of the species had a significant effect on the size class distribution, and aggregate stability of the soil. Furthermore, the size of the soil aggregates formed was dominated by the size class 2.83 - 4.75 mm under both dry and wet conditions. Under dry conditions, three size classes were found, while under wet conditions, there were five size classes. The results also showed that the highest and lowest stability indexes occurred with zero and eight Pheretima sp., respectively. Furthermore, the abundance had a significant effect on pH, organic C, total N, CEC, and total nematodes. However, it had no significant effect on the total P, C/N ratio, total AMF spores, and flagellate. The highest soil pH occurred with zero Pheretima sp., while with six and two members of the species, the total nematode was at its highest and lowest populations, respectively. Therefore, it could be concluded that the species was able to create novel conditions in the topsoils at the nickel mining area that were suitable for various soil biota.

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Effects of Initial Water Content on Microstructure and Mechanical Properties of Lean Clay Soil Stabilized by Compound Calcium-Based Stabilizer

Materials ◽

10.3390/ma11101933 ◽

2018 ◽

Vol 11 (10) ◽

pp. 1933 ◽

Cited By ~ 6

Author(s):

Chenglong Yin ◽

Wei Zhang ◽

Xunli Jiang ◽

Zhiyi Huang

Keyword(s):

Water Content ◽

Soil Stabilization ◽

Clay Soil ◽

Soil Aggregates ◽

Optical Microscope ◽

Initial Water Content ◽

Reaction Products ◽

Unconfined Compression Test ◽

Initial Water ◽

X Ray

Initial water content significantly affects the efficiency of soil stabilization. In this study, the effects of initial water content on the compressibility, strength, microstructure, and composition of a lean clay soil stabilized by compound calcium-based stabilizer were investigated by static compaction test, unconfined compression test, optical microscope observations, environment scanning electron microscopy, energy dispersive X-ray spectroscopy, and X-ray diffraction. The results indicate that as the initial water content increases in the range studied, both the compaction energy and the maximum compaction force decrease linearly and there are less soil aggregates or agglomerations, and a smaller proportion of large pores in the compacted mixture structure. In addition, for specimens cured with or without external water supply and under different compaction degrees, the variation law of the unconfined compressive strength with initial water content is different and the highest strength value is obtained at various initial water contents. With the increase of initial water content, the percentage of the oxygen element tends to increase in the reaction products of the calcium-based stabilizer, whereas the primary mineral composition of the soil-stabilizer mixture did not change notably.

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Soil organic carbon and nitrogen sequestration and turnover in aggregates under subtropical leucaena–grass pastures

Soil Research ◽

10.1071/sr18016 ◽

2018 ◽

Vol 56 (6) ◽

pp. 632 ◽

Cited By ~ 4

Author(s):

Kathryn Conrad ◽

Ram C. Dalal ◽

Ryosuke Fujinuma ◽

Neal W. Menzies

Keyword(s):

Organic Matter ◽

Organic Carbon ◽

Soil Organic Carbon ◽

Soil Aggregates ◽

Soil Mass ◽

Δ13c And Δ15n ◽

Organic C ◽

Carbon And Nitrogen ◽

Nitrogen Sequestration ◽

C And N

Stabilisation and protection of soil organic carbon (SOC) in macroaggregates and microaggregates represents an important mechanism for the sequestration of SOC. Legume-based grass pastures have the potential to contribute to aggregate formation and stabilisation, thereby leading to SOC sequestration. However, there is limited research on the C and N dynamics of soil organic matter (SOM) fractions in deep-rooted legume leucaena (Leucaena leucocephala)–grass pastures. We assessed the potential of leucaena to sequester carbon (C) and nitrogen (N) in soil aggregates by estimating the origin, quantity and distribution in the soil profile. We utilised a chronosequence (0–40 years) of seasonally grazed leucaena stands (3–6 m rows), which were sampled to a depth of 0.3 m at 0.1-m intervals. The soil was wet-sieved for different aggregate sizes (large macroaggregates, >2000 µm; small macroaggregates, 250–2000 µm; microaggregates, 53–250 µm; and <53 µm), including occluded particulate organic matter (oPOM) within macroaggregates (>250 µm), and then analysed for organic C, N and δ13C and δ15N. Leucaena promoted aggregation, which increased with the age of the leucaena stands, and in particular the formation of large macroaggregates compared with grass in the upper 0.2 m. Macroaggregates contained a greater SOC stock than microaggregates, principally as a function of the soil mass distribution. The oPOM-C and -N concentrations were highest in macroaggregates at all depths. The acid nonhydrolysable C and N distribution (recalcitrant SOM) provided no clear distinction in stabilisation of SOM between pastures. Leucaena- and possibly other legume-based grass pastures have potential to sequester SOC through stabilisation and protection of oPOM within macroaggregates in soil.

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Localization of selenium in bacterial cells using TEM and energy dispersive X-ray analysis

Archives of Microbiology ◽

10.1007/bf00427860 ◽

1976 ◽

Vol 107 (1) ◽

pp. 1-6 ◽

Cited By ~ 25

Author(s):

B. A. Silverberg ◽

P. T. S. Wong ◽

Y. K. Chau

Keyword(s):

Energy Dispersive ◽

Bacterial Cells ◽

X Ray

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Comparison of Different Diagnostic Method for Mycobacteria Tuberculosis in Suspected Patients

Journal of Nepal Health Research Council ◽

10.3126/jnhrc.v7i2.3012 ◽

1970 ◽

Vol 7 (2) ◽

pp. 84-88

Author(s):

AR Khagi ◽

S Singh ◽

S Subba ◽

A Bajracharya ◽

R Tuladhar ◽

...

Keyword(s):

Comparative Study ◽

Sputum Smear ◽

Study Group ◽

Bacterial Cells ◽

X Ray ◽

Smear Examination ◽

Group A ◽

Chest X Ray ◽

Group B ◽

Sputum Smear Examination

Background: Microbial examination of smear of AFB by Z-N stain is currently the most rapid method for the detection of M. tuberculosis but its sensitivity is low i.e. required at least 10,000 bacterial cells per ml of sputum and also none specific, but auramine staining method has higher sensitivity than that of the Z-N stain but there are chances of false positive. Objective of this study was to find the correlation between chest X-ray, direct sputum smear examination by Ziehl-Neelsen stain, Auramine fluorochrome stain and sputum culture for M. tuberculosis. Methods: During that study period 250 x 3 samples were taken three each from 250 patients and divided into two groups A and B by performing Auramine fluorochrome stain in all samples . In group A, there were 150 fluorochrome stain positive samples. One each from 150 patient for comparative study of direct sputum smear examination by Ziehl-Neelsen stain, , culture on LJ medium and chest X-ray. Similarly in group B, next 100 fluorochrome stain negative specimens one each from 100 patients were taken for the comparative study of direct sputum smear examination by Ziehl-Neelsen stain, culture and chest X-ray. Results: In the study group A (n=150) all the specimens were positive in Auramine fluorochrome stain and all of them show positive in X-ray but only 134 showed positive in Ziehl-Neelsen stain and 136 showed positive in culture. In the study group B (n=100), all the specimens were negative in Auramine fluorochrome stain and all of them show negative in Ziehl-Neelsen stain but 14 of them were positive in culture and 24 were positive in chest X-ray. Conclusions: The diagnosis of PTB could be made by Auramine fluorochrome microscopy and culture. Key words: auramine fluorochrome stain; culture; mycobacterium tuberculosis; x-ray; ziehl-neelsen. DOI: 10.3126/jnhrc.v7i2.3012 Journal of Nepal Health Research Council Vol.7(2) Apr 2009 84-88

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Spatially Resolved Characterization of Biogenic Manganese Oxide Production within a Bacterial Biofilm

Applied and Environmental Microbiology ◽

10.1128/aem.71.3.1300-1310.2005 ◽

2005 ◽

Vol 71 (3) ◽

pp. 1300-1310 ◽

Cited By ~ 94

Author(s):

Brandy Toner ◽

Sirine Fakra ◽

Mario Villalobos ◽

Tony Warwick ◽

Garrison Sposito

Keyword(s):

Careful Consideration ◽

Bacterial Biofilm ◽

Bacterial Cells ◽

X Ray ◽

Spatially Resolved ◽

Nexafs Spectroscopy ◽

Promising Tool ◽

Scanning Transmission ◽

X Ray Absorption

ABSTRACT Pseudomonas putida strain MnB1, a biofilm-forming bacterial culture, was used as a model for the study of bacterial Mn oxidation in freshwater and soil environments. The oxidation of aqueous Mn+2 [Mn+2 (aq)] by P. putida was characterized by spatially and temporally resolving the oxidation state of Mn in the presence of a bacterial biofilm, using scanning transmission X-ray microscopy (STXM) combined with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at the Mn L2,3 absorption edges. Subsamples were collected from growth flasks containing 0.1 and 1 mM total Mn at 16, 24, 36, and 48 h after inoculation. Immediately after collection, the unprocessed hydrated subsamples were imaged at a 40-nm resolution. Manganese NEXAFS spectra were extracted from X-ray energy sequences of STXM images (stacks) and fit with linear combinations of well-characterized reference spectra to obtain quantitative relative abundances of Mn(II), Mn(III), and Mn(IV). Careful consideration was given to uncertainty in the normalization of the reference spectra, choice of reference compounds, and chemical changes due to radiation damage. The STXM results confirm that Mn+2 (aq) was removed from solution by P. putida and was concentrated as Mn(III) and Mn(IV) immediately adjacent to the bacterial cells. The Mn precipitates were completely enveloped by bacterial biofilm material. The distribution of Mn oxidation states was spatially heterogeneous within and between the clusters of bacterial cells. Scanning transmission X-ray microscopy is a promising tool for advancing the study of hydrated interfaces between minerals and bacteria, particularly in cases where the structure of bacterial biofilms needs to be maintained.

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