SOIL SAMPLING AND HANDLING, G.T. Patterson and M.R. Carter Soil Sampling Designs, D. Pennock, T. Yates, and J. Braidek Sampling Forest Soils, N. Belanger and K.C.J. Van Rees Measuring Change in Soil Organic Carbon Storage, B.H. Ellert, H.H. Janzen, A.J. VandenBygaart, and E. Bremer Soil Sample Handling and Storage, S.C. Sheppard and J.A. Addison Quality Control in Soil Chemical Analysis, C. Swyngedouw and R. Lessard DIAGNOSTIC METHODS for SOIL and ENVIRONMENTAL MANAGEMENT, J.J. Schoenau and I.P. O'Halloran Nitrate and Exchangeable Ammonium Nitrogen, D.G. Maynard, Y.P. Kalra, and J.A. Crumbaugh Mehlich 3 Extractable Elements, N. Ziadi and T. Sen Tran Sodium Bicarbonate Extractable Phosphorus, J.J. Schoenau and I. P. O'Halloran Boron, Molybdenum and Selenium, G. M. Hettiarachchi and U. C. Gupta Trace Element Assessment, W.H. Hendershot, H. Lalande, D. Reyes, and D. MacDonald Readily Soluble Aluminum and Manganese in Acid Soils, Y.K. Soon, N. Belanger, and W.H. Hendershot Lime Requirement, N. Ziadi and T. Sen Tran Ion Supply Rates Using Ion Exchange Resins, P. Qian, J.J. Schoenau, and N. Ziadi Environmental Soil Phosphorus Indices, A.N. Sharpley, P.J.A. Kleinman and J.L. Weld Electrical Conductivity and Soluble Ions, J.J. Miller and D. Curtin SOIL CHEMICAL ANALYSES, Y.K. Soon and W.H. Hendershot Soil Reaction and Exchangeable Acidity, W.H. Hendershot, H. Laland,e and M. Duquette Collection and Characterization of Soil Solutions, J.D. MacDonald, N. Belanger, S. Sauve, F. Courchesne, and W.H. Hendershot Ion Exchange and Exchangeable Cations, W.H. Hendershot, H. Lalande, and M. Duquette Non-Exchangeable Ammonium, Y.K. Soon and B.C. Liang Carbonates, T.B. Goh and A.R. Mermut Total and Organic Carbon, J.O. Skjemstad and J.A. Baldock Total Nitrogen, P.M. Rutherford, W.B. McGill, C.T. Figueiredo, and J.M. Arocena Chemical Characterization of Soil Sulphur, C.G. Kowalenko and M. Grimmett Total and Organic Phosphorus, I.P. O'Halloran and B.J. Cade-Menum Characterization of Available P by Sequential Extraction, H. Tiessen and J.O. Moir Extractable Al, Fe, Mn, and Si, F. Courchesne and M.C. Turmel Determining Nutrient Availability in Forest Soils, N. Belanger, David Pare, and W.H. Hendershot Chemical Properties of Organic Soils, A. Karam SOIL BIOLOGICAL ANALYSES, E. Topp and C.A. Fox Cultural Methods for Soil and Root Associated Microorganisms, J.J. Germida and J.R. de Freitas Arbuscular Mycorrhiza, Y. Dalpe and C. Hamel Root Nodule Bacteria and Symbiotic Nitrogen Fixation, D. Prevost and H. Antoun Microarthropods, J.P Winter and V.M. Behan-Pelletier Nematodes, T.A. Forge and J. Kimpinski Earthworms, M.J. Clapperton, G.H. Baker and C.A. Fox Enchytraeids, S.M. Adl Protozoa, S.M. Adl, D. Acosta-Mercado, and D.H. Lynn Denitrification Techniques for Soils, C.F. Drury, D.D. Myrold, E.G. Beauchamp, and W.D.Reynolds Nitrification Techniques in Soil Systems, C.F. Drury, S.C. Hart, and X.M. Yang Substrate-Induced Respiration and Selective Inhibition as Measures of Microbial Biomass in Soils, V.L. Bailey, J.L. Smith, and H. Bolton Jr. Assessment of Soil Biological Activity, R.P.Beyaert and C.A. Fox Soil ATP, R.P. Voroney, G. Wen, and R.P. Beyaert Lipid-Based Community Analysis, K.E. Dunfield Bacterial Community Analyses by Denaturing Gradient Gel Electrophoresis (DGGE), E. Topp, Y.-C. Tien, and A. Hartmann Indicators of Soil Food Web Properties, T.A. Forge and M. Tenuta SOIL ORGANIC MATTER ANALYSES, E.G. Gregorich and M.H. Beare Carbon Mineralization, D.W. Hopkins Mineralizable Nitrogen, Denis Curtin and C.A. Campbell Physically Uncomplexed Organic Matter, E.G. Gregorich and M.H. Beare Extraction and Characterization of Dissolved Organic Matter, M.H. Chantigny, D.A. Angers, K. Kaiser, and K. Kalbitz Soil Microbial Biomass C, N, P and S, R.P. Voroney, P.C. Brookes, and R.P. Beyaert Carbohydrates, M.H. Chantigny and D.A. Angers Organic Forms of Nitrogen, D.C. Olk Soil Humus Fractions, D.W. Anderson and J.J Schoenau Soil Organic Matter Analysis by Solid-State 13C Nuclear Magnetic Resonance Spectroscopy, M. J. Simpson and C. M. Preston Stable Isotopes in Soil and Environmental Research, B.H. Ellert and L. Rock SOIL PHYSICAL ANALYSES, D.A. Angers and F.J. Larney Particle Size Distribution, D. Kroetsch and C. Wang Soil Shrinkage, C.D. Grant Soil Density and Porosity, X. Hao, B.C. Ball, J.L.B. Culley, M.R. Carter, and G.W. Parkin Soil Consistency: Upper and Lower Plastic Limits, R.A. McBride Compaction and Compressibility, P. Defossez, T. Keller and G. Richard Field Soil Strength, G.C. Topp and D.R. Lapen Air Permeability, C.D. Grant and P.H. Groenevelt Aggregate Stability to Water, D.A. Angers, M.S. Bullock, and G.R. Mehuys Dry Aggregate Size Distribution, F.J. Larney Soil Air, R.E. Farrell and J.A. Elliott Soil-Surface Gas Emissions, P. Rochette and N. Bertrand Bulk Density Measurement in Forest Soils, D.G. Maynard and M.P. Curran Physical Properties of Organic Soils and Growing Media: Particle Size and Degree of Decomposition, L.E. Parent and J. Caron Physical Properties of Organic Soils and Growing Media: Water and Air Storage and Flow Dynamics, J. Caron, D.E. Elrick, J.C. Michel, and R. Naasz SOIL WATER ANALYSES, W.D. Reynolds and G.C. Topp Soil Water Analyses: Principles and Parameters, W.D. Reynolds and G.C. Topp Soil Water Content, G.C. Topp, G.W. Parkin, and Ty P.A Ferre Soil Water Potential, N.J. Livingston and G.C. Topp Soil Water Desorption and Imbibition: Tension and Pressure Techniques, W.D. Reynolds and G.C. Topp Soil Water Desorption and Imbibition: Long Column, W.D. Reynolds and G.C. Topp Soil Water Desorption and Imbibition: Psychrometry, W.D. Reynolds and G.C. Topp Saturated Hydraulic Properties: Laboratory Methods, W.D. Reynolds Saturated Hydraulic Properties: Well Permeameter, W.D. Reynolds Saturated Hydraulic Properties: Ring Infiltrometer, W.D. Reynolds Saturated Hydraulic Properties: Auger-Hole, G.C. Topp Saturated Hydraulic Properties: Piezometer, G.C. Topp Unsaturated Hydraulic Properties: Laboratory Tension Infiltrometer, F.J. Cook Unsaturated Hydraulic Properties: Laboratory Evaporation, O.O. B. Wendroth and N. Wypler Unsaturated Hydraulic Properties: Field Tension Infiltrometer, W.D. Reynolds Unsaturated Hydraulic Properties: Instantaneous Profile, W.D. Reynolds Estimation of Soil Hydraulic Properties, F.J. Cook and H.P. Cresswell Analysis of Soil Variability, B.C. Si, R.G. Kachanoski, and W.D. Reynolds APPENDIX Site Description, G.T. Patterson and J.A. Brierley General Safe Laboratory Operation Procedures, P. St-Georges INDEX

Soil Sampling and Methods of Analysis

Since the 1900s, the link between soil biotic activity, soil organic matter (SOM) decomposition and stabilization, and soil aggregate dynamics has been recognized and intensively been studied. By 1950, many studies had, mostly qualitatively, investigated the influence of the five major factors (i.e. soil fauna, microorganisms, roots, inorganics and physical processes) on this link. After 1950, four theoretical mile-stones related to this subject were realized. The first one was when Emerson [Nature 183 (1959) 538] proposed a model of a soil crumb consisting of domains of oriented clay and quartz particles. Next, Edwards and Bremner [J. Soil Sci. 18 (1967) 64] formulated a theory in which the solid-phase reaction between clay minerals, polyvalent cations and SOM is the main process leading to microaggregate formation. Based on this concept, Tisdall and Oades [J. Soil Sci. 62 (1982) 141] coined the aggregate hierarchy concept describing a spatial scale dependence of mechanisms involved in micro- and macroaggregate formation. Oades [Plant Soil 76 (1984) 319] suggested a small, but very important, modification to the aggregate hierarchy concept by theorizing the formation of microaggregates within macroaggregates. Recent research on aggregate formation and SOM stabilization extensively corroborate this modification and use it as the base for furthering the understanding of SOM dynamics. The major outcomes of adopting this modification are: (1) microaggregates, rather than macroaggregates protect SOM in the long term; and (2) macroaggregate turnover is a crucial process influencing the stabilization of SOM. Reviewing the progress made over the last 50 years in this area of research reveals that still very few studies are quantitative and/or consider interactive effects between the five factors. The quantification of these relationships is clearly needed to improve our ability to predict changes in soil ecosystems due to management and global change. This quantification can greatly benefit from viewing aggregates as dynamic rather than static entities and relating aggregate measurements with 2D and 3D quantitative spatial information.

A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics

Priming effects are strong short-term changes in the turnover of soil organic matter caused by comparatively moderate treatments of the soil. In the course of priming effects large amounts of C, N and other nutrients can be released or immobilized in soil in a very short time. These effects have been measured in many field and laboratory experiments; however, only a few of the studies were aimed at an extended investigation of the mechanisms of such phenomena. The aim of this overview is to reveal possible causes and processes leading to priming actions using the references on agricultural ecosystems and model experiments. Multiple mechanisms and sources of released C and N are presented and summarized in Tables for positive and negative real and apparent priming effects induced after the addition of different organic and mineral substances to the soil. Soil microbial biomass plays the key role in the processes leading to the real priming effects. The most important mechanisms for the real priming effects are the acceleration or retardation of soil organic matter turnover due to increased activity or amount of microbial biomass. Isotopic exchange, pool substitution, and different uncontrolled losses of mineralized N from the soil are responsible for the apparent N priming effects. Other multiple mechanisms (predation, competition for nutrients between roots and microorganisms, preferred uptake, inhibition, etc.) in response to addition of different substances are also discussed. These mechanisms can be distinguished from each other by the simultaneous monitoring of C and N release dynamics; its comparison with the course of microbial activity; and by the labelling of different pools with 14 C or 13 C and 15 N. Quantitative methods for describing priming effects and their dynamics using 14 C and 15 N isotopes, as well as for non-isotopic studies are proposed.

Review of mechanisms and quantification of priming effects.

The loss of carbon from roots (rhizodeposition) and the consequent proliferation of microorganisms in the surrounding soil, coupled with the physical presence of a root and processes associated with nutrient uptake, gives rise to a unique zone of soil called the rhizosphere. In this review, we bring together evidence to show that roots can directly regulate most aspects of rhizosphere C flow either by regulating the exudation process itself or by directly regulating the recapture of exudates from soil. Root exudates have been hypothesized to be involved in the enhanced mobilization and acquisition of many nutrients from soil or the external detoxification of metals. With few exceptions, there is little mechanistic evidence from soil-based systems to support these propositions. We conclude that much more integrated work in realistic systems is required to quantify the functional significance of these processes in the field. We need to further unravel the complexities of the rhizosphere in order to fully engage with key scientific ideas such as the development of sustainable agricultural systems and the response of ecosystems to climate change. Contents I. Introduction 460 II. What is rhizodeposition? 460 III. Regulation of rhizodeposition 460 IV. How large is the root exudation C flux? 463 V. How responsive is the root exudation C flux? 463 VI. How responsive is the microbial community to root exudation? 464 VII. The role of root exudates in nutrient acquisition 464 VIII. Mycorrhizal fungi and rhizodeposition 471 IX. Future thoughts 474 Acknowledgements 474 References 474.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-8137.2004.01130.x

Plant and mycorrhizal regulation of rhizodeposition

Tillage has been reported to reduce organic matter concentrations and increase organic matter turnover rates to a variable extent. The change of soil climate and the incorporation of aboveground C inputs within the soil lead to no unique effect on biodegradation rates, because of their strong interaction with the regional climate and the soil physical properties. The periodical perturbation of soil structure by tools and the subsequent drying‐rewetting cycles may be the major factor increasing organic matter decomposition rates by exposing the organic matter that is physically protected in microaggregates to biodegradation. This paper reviews the assessed effects of tillage on organic matter, the scale, extent and mechanisms of physical protection of organic matter in soils. # 2000 Elsevier Science B.V. All rights reserved.

/pdf/relationship-of-soil-organic-matter-dynamics-to-physical-1irgvi0hgq.pdf

Relationship of soil organic matter dynamics to physical protection and tillage

The predation by protozoa of bacteria was studied in relation to soil moisture regimes. In soil microcosms, maintained at three soil moisture levels, it was shown that the activity of protozoa was inhibited as soon as pores with pore necks > 3 μm were devoid of water. The activity of protozoa reduced the number of bacteria and increased the mineral N content in the soil under more favourable moisture conditions. In a series of experiments in which planted soil was subjected to soil moisture regimes with either continuous moist or fluctuating moist conditions, it was shown that protozoa generally stimulated the mineralization of N and the uptake of N by plants 5–10% compared to soils without protozoa. In addition the turnover of introduced 15N-labelled bacterial N was higher in soils with protozoa than in soils with only bacteria. Even though protozoa were forced to encyst upon drying of the soil, they reacted very rapidly to remoistening. Under conditions with modest fluctuating soil moisture conditions, protozoan activity resulted in an even higher plant 15N-N uptake than that in soils kept continuously moist. When fluctuations in the soil moisture content were more intense and applied more frequently, protozoa still stimulated the mineralization of N. Thus their more restricted activity tended to yield less N available for plant uptake than in continuously moist soils. Protozoa did not reduce bacterial numbers in all incubations and protozoan numbers were not affected by the soil moisture regimes. An important regulation by soil moisture fluctuations on the effect of food web interactions between bacteria and protozoa to mineralization of N is hypothesized.

15N-Nitrogen mineralization from bacteria by protozoan grazing at different soil moisture regimes

The effects of protozoan inoculum density and spatial separation of (prey) organisms on the turnover and transport of specific microbial populations in sterilized soil were studied in soil microcosms, applying a combination of techniques. The fate of introduced microbial biomass was followed by monitoring 14 C-CO 2 evolution. Dynamics of and genetic transfer between genetically marked bacteria were followed by selective plating using appropriate antibiotics. Three levels of protozoan densities, i.e. no protozoa, protozoa and a 1: 10 diluted protozoan inoculum were established. Two methods of soil inoculation, i.e. joint introduction and separate introduction of protozoa with a donor population and of a 14 C-labelled recipient population, respectively, were applied. The activity of protozoa, as judged from increased CO 2 evolution compared to soils not inoculated with protozoa, was larger when 100% of the soil was inoculated with protozoa (joint introduction) compared to inoculation of protozoa into only 33% of the soil which was mixed with 66% of a soil portion not inoculated with protozoa (separate introduction). The activity of protozoa accelerated the turnover of 14 C compared to soils without protozoa. The more protozoa added, the faster 14 C was respired both in soils with joint, and in soils with separate, introduction. The transfer of genetic material between introduced donor and recipient cells was not influenced by the presence of protozoa but was reduced when separate introduction was applied compared to joint introduction. Transfer of genetic material was only found during the first 2 days of the incubation. Substantial loss of genetic material (plasmid RP4) in the donor population was detected; the presence of protozoa enhanced both donor survival and plasmid maintenance. A stimulating effect of protozoa on cellular metabolism of substrate used by the donor population is hypothesized. These results picture soil as a system in which the distribution of microorganisms in the absence of fluctuations in climatic conditions is not changing in time: protozoa hardly moved through the soil and minimal translocation of bacteria was found.

Population dynamics and activity of bacteria and protozoa in relation to their spatial distribution in soil

The impact of protozoan grazing on the dynamics and mineralization of 14C- and 15N-labelled soil organic material was investigated in a microcosm experiment. Sterilized soil was planted with wheat and either inoculated with bacteria alone or with bacteria and protozoa or with bacteria and a 1:10 diluted protozoan inoculum. 14C−CO2 formation was continuously monitored. It served as an indicator of microbial activity and the respiration of soil organic C. The activity of protozoa increased the turnover of 14C-labelled substrates compared to soil without protozoa. The accumulated 14C−CO2 evolved from the soils with protozoa was 36% and 53% higher for a 1:10 and for a 1:1 protozoan inoculum, respectively. Protozoa reduced the number of bacteria by a factor of 2. In the presence of protozoa, N uptake by plants increased by 9% and 17% for a 1:10 and a 1:1 protozoan inoculum, respectively. Both plant dry matter production and shoot: root ratios were higher in the presence of protozoa. The constant ratio of 15N: 14+15N in the plants for all treatments indicated that in the presence of protozoa more soil organic matter was mineralized. Bacteria and protozoa responded very rapidly to the addition of water to the microcosms. The rewetting response in terms of the 14C−CO2 respiration rate was significantly higher for 1 day in the absence and for 2 days in the presence of protozoa after the microcosms had been watered. It was concluded that protozoa improved the mineralization of N from soil organic matter by stimulating the turnover of bacterial biomass. Pulsed events like the addition of water seem to have a significant impact on the dynamics of food-chain reactions in soil in terms of C and N mineralization.

Protozoan predation and the turnover of soil organic carbon and nitrogen in the presence of plants

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15N-Nitrogen mineralization from bacteria by protozoan grazing at different soil moisture regimes

Population dynamics and activity of bacteria and protozoa in relation to their spatial distribution in soil

Protozoan predation and the turnover of soil organic carbon and nitrogen in the presence of plants