Laboratory Methods for Soil Health Analysis, Volume 2

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Группа авторов. Laboratory Methods for Soil Health Analysis, Volume 2

Table of Contents

List of Tables

List of Illustrations

Guide

Pages

Soil Health Series: Volume 2 Laboratory Methods for Soil Health Analysis

Dedication

Foreword

References

Preface

References

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

2 Sampling Considerations and Field Evaluations for Soil Health Assessment

Introduction

Soil Variability

Sampling Considerations. Sources of Error

Site Characterization

Sampling Designs

Judgement Sampling

Simple Random Sampling

Stratified Random Sampling

Systematic Sampling

Composite Sampling

Sampling Depth

Timing and Frequency of Sampling

Sample Collection, Processing, and Archival

Field Evaluations

General Field Observations

Visual Soil Evaluations

Soil Health Test Kits

Sensor‐based Measurements

Summary

Acknowledgments

References

3 Soil Organic Carbon Assessment Methods

Summary

Introduction

Origin and Factors Affecting SOC

Functions of SOC

Biological Effects

Chemical Effects

Physical Effects

Crop Productivity

Measurement of SOC

Methods for SOC Analysis. Soil Sampling and Preparation

Dry Combustion. Apparatus

Reagents

Procedures

Pre‐treatment for soils with inorganic carbon content

Loss‐On‐Ignition (LOI) (Salehi et al., 2011; Schulte and Hopkins, 1996) Apparatus

Procedures

Calculation

Soil Inorganic C. Dry combustion Procedure

Other Analytical Methods and Issues Affecting Soil Carbon. Gravimetric method for loss of carbon dioxide (Loeppert and Suarez, 1996) Apparatus

Reagents

Procedure

Calculation

Biochar

SOC Stocks: Considerations on Sampling Depth and Mass Corrections

References

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

5 Determination of Infiltration Rate and Bulk Density in Soils

Soil Infiltration

Single‐Ring Infiltrometer (Bouwer, 1986; Reynolds, Elrick, Young, & Amoozegar, 2002)

Double‐Ring Infiltrometer (Bouwer, 1986; Jabro, Toth, & Jemison, 1996; Reynolds et al., 2002)

Constant‐Head Pressure Infiltrometer (Figure 5.2)

Soil Bulk Density

Soil Core Method

Acknowledgments

References

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

7 Nutrient Availability: Macro‐ and Micronutrients in Soil Quality and Health

Introduction. Macronutrients

Micronutrients

Soil Nutrient Availability Measurements

Acid to Neutral, Non‐Calcareous Soils

Neutral to Calcareous Soils

Conclusions

References

8 Assessment and Interpretation of Soil‐Test Biological Activity

Introduction. Importance of Soil Biological Activity to Soil Health and Functioning

Indicators of Soil Biological Activity

Laboratory‐Based Soil Respiration Methods

Chosen Method – Flush of CO2 During 3 d Following Rewetting of Dried Soil

Management Factors Influencing Soil‐Test Biological Activity

Literature Review of Indicator and Method. Consideration of Indicators for Determining Soil Biological Activity

Relationship of Soil Biological Activity to Important Soil Functions / Ecosystem Services

Issues of Concern With Various C Mineralization Indicators

Method

Materials

Reagents

Method

Calibration of the Flush of CO2 During 3 d With Other Methods

Interpretations

References

9 Permanganate Oxidizable Carbon: An Indicator of Biologically Active Soil Carbon

Soil Organic Carbon Pools

Indicators of Biologically Active soil Carbon

Particulate Organic Matter

Microbial Biomass Carbon

Extractable Organic Carbon

Permanganate‐Oxidizable Carbon. History of POXC

Functional Role of POXC

Methodological Standardization of POXC

Sensitivity of POXC to Management Practices

Relationship of POXC to Crop Yield and Productivity

Procedure to Quantify Poxc

Materials and Reagents

0.2 M KMnO4 Stock Solution Preparation (Makes 1 L)

Standard Preparation

Part 1. Standard Stock Solutions

Part 2. Dilution Step

Sample Reaction

Sample Dilution

Sample Quantification

Calculating Mass of POXC for Unknown Soil Samples

Example Calculation

Cleanup and Disposal

Procedural Notes. POXC Soil Mass

Repeatability of POXC with Time

Reductions in pH of KMnO4 Stock Solution

References

10 Is Autoclaved Citrate‐Extractable (ACE) Protein a Viable Indicator of Soil Nitrogen Availability?

Introduction

Nitrogen Availability Indices

Aerobic Incubation

Inorganic and Total Soil Nitrogen

Labile Soil Nitrogen Fractions

Autoclaved Citrate‐Extractable Protein

Soil Sampling Considerations

Methods and Materials for Protein Quantification. Materials and Reagents. Sodium Citrate Buffer and BCA Working Reagent Solutions

Sample Extraction and Clarification

Sample Quantification

Reagent Preparation

Procedure

Extraction

Clarification

Quantification

Calculations

Comments

Summary and Conclusions

References

11 Metabolic Activity– Enzymes

Introduction

Enzymes as Soil Health Indicators

Tillage and Crop Residues

Crop Diversity. Crop Rotations

Cover Crops

Perennial Systems

Biomass Removal– Perennial Systems

Inorganic Fertilizers, Organic Amendments and other Materials

Climate Change

Soil Sampling and Handling

Field Sampling

Sample Handling and Storage

Method

Bench Scale Individual Assays to Measure Activities of β‐Glucosidase, β‐Glucosaminidase, Phosphatases, and Arylsulfatase

Equipment, Materials, and Reagents

Combined Assay to Determine the Four EAs Simultaneously (CNPS Activity)

Equipment, Materials, and Reagents

Procedure

Calibration Curve for all Enzyme Assays

Interpretation– Putting Enzyme Measurements into Context. Use of EAs vs. Other Measurements

Calibration and Interpretation of EAs Independent of Soil Type and Region

Importance of Strict EA Protocols and Practical Modifications

Limitations of EAs as Soil Health Indicators

Future Research Directions

References

12 PLFA and EL‐FAME Indicators of Microbial Community Composition

Abbreviations

Introduction

Available Methods

Selected Methods: PLFA and EL‐FAME

Advantages and Disadvantages of PLFA and EL‐FAME Protocols

PLFA Using the Buyer and Sasser (2012) High‐throughput Extraction Method Paired with the MIDI‐Sherlock System. List of Supplies and Major Equipment for PLFA

Chemicals

Reagents. Internal Standard Solution

Phosphate Buffer (50 mM)

Bligh‐Dyer Extractant (enough for ~2 × 96 well plates)

Transesterification Reagent

5:5:1 methanol/chloroform/H2O

0.075 M acetic acid

Standard Operating Procedure for PLFA Extraction. Freeze dry soil

Extraction

Separation

Chromatography

Transesterification and Transfer to GC vials

EL‐FAME Extraction Paired with the MIDI‐Sherlock System. List of Supplies and Major equipment for EL‐FAME method

Reagents

Standard Operating Procedure for EL‐FAME Extraction. Methylation

Neutralization

Extraction

FAME Concentration in N Evaporation Chamber

Tips and Tricks for FAME Extraction and Analysis

Calculations and Interpretation of FAME Data

Management Implications

References

13 Microbial Community Composition, Diversity, and Function

Introduction

Methods for Identifying and Quantifying Microbial Communities. Traditional Techniques

Plate Counts

Community Level Physiological Profiles (CLPP)

Biochemical Techniques

Fatty Acids

Molecular‐Based Techniques

Partial Community Analysis. Quantitative Polymerase Chain Reaction (qPCR)

Amplicon Sequencing

Whole Community Analysis. Metagenomics

Transcriptomics

Criteria for Method Selection

Soil Health Indicator Effectiveness and Interpretation

Production Readiness

Measurement Repeatability

Other Considerations

Selected Method Protocol

List of Specialized Equipment

Soil Handling

Soil Moisture Determination

DNA Extraction

Reagents and Consumables

Procedure

Quality Check (optional, but Recommended)

Quantitative Polymerase Chain Reaction (qPCR)

Reagents and Consumables

Primer Selection

Procedure

Quality Check

Amplicon Bead Clean‐up

Reagents and Consumables

Procedure

Indexing PCR

Reagents and Consumables

Procedure

Indexed Amplicon Bead Clean‐up

Normalization and Pooling of Final Library

Materials and Consumables

Procedure

Library Amplicon Size Determination

Materials and Consumables

Procedure

Library Quantification and Dilution

Materials and Consumables

Procedure

MiSeq Library Denaturation and Dilution

Materials and Consumables

Procedure

MiSeq Loading, Sequencing, and Data Transfer

Procedure

Analysis Section. qPCR

Amplicon Sequence Processing and Analysis

References

Epilogue

References

Note

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Отрывок из книги

EDITORS Douglas L. Karlen, Diane E. Stott, and Maysoon M. Mikha

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Composite sampling can increase sampling accuracy and reduce analytical costs. Briefly, it involves collecting several homogenous samples in an area surrounding a sampling point and combining those samples into a single bulk (or composite) sample (Dick et al., 1996). For effective composite sampling, it is essential that each sub‐sample contributes equally and that there are no interactions among sub‐samples (Boone et al., 1999). Moreover, all sub‐samples must be collected from the same soil type and depth to be homogenous.

Composite sampling can be used with any of the above sampling designs, although it is less suited to systematic sampling because of the fixed sampling point constraints. Also, since multiple sub‐samples are combined and mixed, compositing samples in an area with a wide variation in physical disturbance should be avoided.

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