Laboratory Methods for Soil Health Analysis, Volume 2

1 Cover

2 Series Page

3 Title Page

4 Copyright Page

5 Dedication Page

6 Foreword References

7 Preface References

8 1 Laboratory Methods for Soil Health Assessment: An Overview How Can a Farmer Assess Soil Health in the Field? What Do Researchers Need, and Can They Reach Consensus? What Do Commercial Analytical Laboratories Need? Summary and Conclusions References

9 2 Sampling Considerations and Field Evaluations for Soil Health Assessment Introduction Soil Variability Sampling Considerations Sample Collection, Processing, and Archival Field Evaluations Summary Acknowledgments References

10 3 Soil Organic Carbon Assessment Methods Summary Introduction References

11 4 Water‐Stable Soil Aggregate Assessment Introduction Soil sampling and preparation Water‐stable aggregation (WSA) Materials and Procedures Aggregate Sieving Apparatus Construction Supplies Water‐stable aggregate size distribution with the slaking method Sand‐Free Water‐Stable Soil Aggregates Supplies and procedure for sand content determination Aggregate mean weight diameter Summary References

12 5 Determination of Infiltration Rate and Bulk Density in Soils Soil Infiltration Soil Bulk Density Acknowledgments References

13 6 Chemical Reactivity: pH, Salinity and Sodicity Effects on Soil Health Introduction Natural Soil Salinization Processes Salt Accumulation and Solute Transport Mechanisms Anthropogenic Soil Salinization Processes Chemical Characterization of Salinity Sources Soil Chemistry, Biota and Ecosystem Services Chemistry Effects on Soil Biota Habitat Heterogeneity and Soil Microbial Diversity Agricultural Ecosystems: Degradation Prevention and Conservation Soil Health Indices Technological Advances in the Study of Soil Biogeochemical Interfaces Conclusions References

14 7 Nutrient Availability: Macro‐ and Micronutrients in Soil Quality and Health Introduction Conclusions References

15 8 Assessment and Interpretation of Soil‐Test Biological Activity Introduction Literature Review of Indicator and Method Method Interpretations References

16 9 Permanganate Oxidizable Carbon Soil Organic Carbon Pools Indicators of Biologically Active soil Carbon Permanganate‐Oxidizable Carbon Procedure to Quantify Poxc References

17 10 Is Autoclaved Citrate‐Extractable (ACE) Protein a Viable Indicator of Soil Nitrogen Availability? Introduction Nitrogen Availability Indices Autoclaved Citrate‐Extractable Protein Soil Sampling Considerations Methods and Materials for Protein Quantification Summary and Conclusions References

18 11 Metabolic Activity– Enzymes Introduction Enzymes as Soil Health Indicators Soil Sampling and Handling Method Interpretation– Putting Enzyme Measurements into Context References

19 12 PLFA and EL‐FAME Indicators of Microbial Community Composition Introduction PLFA Using the Buyer and Sasser (2012) High‐throughput Extraction Method Paired with the MIDI‐Sherlock System EL‐FAME Extraction Paired with the MIDI‐Sherlock System Tips and Tricks for FAME Extraction and Analysis Calculations and Interpretation of FAME Data Management Implications References

20 13 Microbial Community Composition, Diversity, and Function Introduction Methods for Identifying and Quantifying Microbial Communities Criteria for Method Selection Selected Method Protocol Analysis Section References

21 Epilogue References

22 End User License Agreement

1 Chapter 1 Table 1.1 Tier 1 Soil Health Indicators and Methods to be Assessed. Table 1.2 Tier 2 Soil Health Indicators and Methods to be Assessed

2 Chapter 2 Table 2.1 Synthesis of select resources addressing sampling considerations an... Table 2.2 Suggested minimum metadata for site characterization. Table 2.3 Definitions and attributes of different soil sampling designs.

3 Chapter 3 Table 3.1 Advantages and disadvantages of the most common methods for measuri...

4 Chapter 6Table 6.1 Guidelines for Interpretations of Water Quality for Irrigation.Table 6.2 USDA‐NRCS Soil pH Classifications (Soil Survey Manual, 1993).

5 Chapter 7Table 7.1 Average micronutrient concentrations in plants and the range of tot...Table 7.2 US state by state soil extractants used to determine soil micronutr...

6 Chapter 8Table 8.1 Compilation of studies reporting associations between the flush of ...Table 8.2 Compilation of studies reporting associations between the flush of ...

7 Chapter 9Table 9.1 Permanganate‐oxidizable C (POXC) coefficients of variation (CV) of ...

8 Chapter 10Table 10.1 Advantages and disadvantages of selected soil N methods and potent...

9 Chapter 11Table 11.1 Enzyme activities from selected studies across management and regi...Table 11.2 Description of the enzyme assay procedure and reagents needed for ...Table 11.3 Approaches for interpreting results from enzyme activities (EAs) a...

10 Chapter 12Table 12.1 Comparison of PLFA and EL‐FAME methods.Table 12.2 Key PLFA microbial group assignments used by the MIDI Sherlock Sys...

11 Chapter 13Table 13.1 Taxonomic and functional indicators of various soil functions that...

12 EpilogueTable E.1 Selected quotes advocating for recognition and better management of so...Table E.2 Selected Native American proverbs reflecting upon land and soil resour...

1 Chapter 2 Figure 2.1 Error components associated with soil property assessment. Figure 2.2 Generalized approaches to field evaluations of soil health. USDA‐...

2 Chapter 4 Figure 4.1 Soil sampling probes for aggregate size distribution. (A) Represe...Figure 4.2 Dimensional diagram of the modified Yoder (1936) wet‐sieving appa...Figure 4.3 The water level on the top sieve of the nest of sieves that conta...Figure 4.4 The placement of the submerged nest sieves containing soils and t...Figure 4.5 Soil macroaggregates on an individual sieve places in the aluminu...Figure 4.6 Dried soil macroaggregates and microaggregates at 105 oC for 24 h...

3 Chapter 5Figure 5.1 Clockwise steps for measuring soil infiltration rate using a sing...Figure 5.2 Constant‐head pressure infiltrometer in sugarbeet plots.Figure 5.3 Clockwise soil core sampling processes for measuring soil bulk de...

4 Chapter 6Figure 6.1 Salinity accumulation in the upper soil layer (0–90 cm) under the...Figure 6.2 Soil salinization around Kfar Baruch reservoir, Israel (Google Ea...Figure 6.3 Soil salinity (EC) distribution with depth around the Kfar Yehosh...Figure 6.4 Major ions profiles in the shallow unsaturated zone due to calcit...

5 Chapter 7Figure 7.1 Hypothetical function describing increasing soil‐extractable macr...

6 Chapter 8Figure 8.1 Cumulative C mineralization as a function of incubation time for ...Figure 8.2 Variations in lab protocol for short‐term C mineralization.Note: ...

7 Chapter 9Figure 9.1 Conceptual pools and potential methods to measure active soil org...Figure 9.2 A proposed soil health reporting framework using two recommended ...Figure 9.3 Overview of permanganate‐oxidizable C method.Figure 9.4 Declines in potassium permanganate (KMnO 4) stock solution pH that...

8 Chapter 10Figure 10.1 Flow chart of the ACE protein extraction, clarification and quan...Figure 10.2 A 96‐well reaction plate loaded with samples, blanks and standar...

9 Chapter 11Figure 11.1 Enzymatic activity in soil can be affected by management related...Figure 11.2 Enzyme activities commonly evaluated in agricultural soils inclu...Figure 11.3 General steps for an individual assay to measure activities of β...Figure 11.4 A conceptual overview of the methods used to determine: (a) micr...

10 Chapter 12Figure 12.1 The comparison of extraction procedures for phospholipid fatty a...Figure 12.2 Soil samples on end‐over‐end shaker.Figure 12.3 Capped samples in SpeedVac rotor using one half of the spaces.Figure 12.4 Aspirating aqueous layer from top of each sample.Figure 12.5 Washing wells with solvents using dedicated dispensette.Figure 12.6 Total phospholipid fatty acids and by microbial group for native...Figure 12.7 (a) Fungi to bacteria ratio; (b) Gram positive to Gram negative ...Figure 12.8 EL‐FAME profiles before and after grassland conversion tillage c...