Revisiting the Standard Soil Test: the Potential of Macro- and Microbiological Measures to Improve Agricultural Health and Productivity
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University of South Carolina Scholar Commons Theses and Dissertations Fall 2019 Revisiting the Standard Soil Test: The Potential of Macro- and Microbiological Measures to Improve Agricultural Health and Productivity Gabriel Jacob Kenne Follow this and additional works at: https://scholarcommons.sc.edu/etd Part of the Environmental Health Commons Recommended Citation Kenne, G. J.(2019). Revisiting the Standard Soil Test: The Potential of Macro- and Microbiological Measures to Improve Agricultural Health and Productivity. (Doctoral dissertation). Retrieved from https://scholarcommons.sc.edu/etd/5547 This Open Access Dissertation is brought to you by Scholar Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. REVISITING THE STANDARD SOIL TEST: THE POTENTIAL OF MACRO- AND MICROBIOLOGICAL MEASURES TO IMPROVE AGRICULTURAL HEALTH AND PRODUCTIVITY by Gabriel Jacob Kenne Bachelor of Science University of Nebraska at Omaha, 2008 Master of Public Health Kansas State University, 2013 Submitted in Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy in Environmental Health Sciences The Norman J. Arnold School of Public Health University of South Carolina 2019 Accepted by: R. Sean Norman, Major Professor Anindya Chanda, Committee Member Robin “Buz” Kloot, Committee Member Geoff Zehnder, Committee Member Cheryl L. Addy, Vice Provost and Dean of the Graduate School © Copyright Gabriel Jacob Kenne, 2019 All Rights Reserved ii ABSTRACT The agricultural ecosystem has become the largest non-ice-covered terrestrial ecosystem on the planet and has significant direct and indirect impacts on the global health of both the environment and humanity. Recent shifts in modern agriculture are beginning to focus on the health of soil versus a focus traditionally on crop health and yield at any cost. By managing farmland regeneratively, systems are able to reverse many of the problems created by conventional land management such as erosion and unwanted nutrient runoff, and simultaneously create opportunities to move C from the atmosphere back into the soil. While the ways in which farmland is managed are beginning a necessary shift, the ways in which soil fertility is measured in the process of monitoring and understanding these management changes also need to be adjusted. This dissertation aims to begin that adjustment by evaluating data commonly overlooked in traditional soil tests and the effectiveness of both standard and new soil health tests at prescribing fertilizer recommendations in regeneratively managed soils, and exploring the potential of high-throughput metagenome analyses as a means to measure soil health. Organic Matter data collected from standard soils tests shows that statewide, SC has the potential to sequester 500,647 – 1,558,092 tons of atmospheric carbon per year with the adoption of no-till and cover cropping practices on its 1,967,288 acres of cropland. The yield-predictive capability of these same soil tests, as well as with Haney Soil Health tests, confirmed an expected yield-response to N fertilizer based on field trials, but both showed almost no soil test value that consistently correlated with actual iii crop yields through two full corn-wheat-soybean crop rotations in the coastal plains of SC, bringing into question the effectiveness of current soil testing methods. Finally, the examination of 6” soil metagenomes throughout a single winter wheat crop showed that traditional versus regenerative land management practices had some significant impacts on the soil microbiomes’ potential ability to cycle and recycle nitrogen. These data show the need for continued reexamination of both current agricultural systems as well as the tools by which these systems are measured, and their management decisions made. iv TABLE OF CONTENTS Abstract .............................................................................................................................. iii List of Tables .................................................................................................................... vii List of Figures .................................................................................................................. viii List of Abbreviations ...........................................................................................................x Chapter 1: Introduction ........................................................................................................1 Chapter 2: The Carbon Sequestration Potential of Regenerative Farming Practices in South Carolina, USA ...........................................................................................................4 2.1. Introduction .......................................................................................................4 2.2. Sample Collection & Analysis ..........................................................................7 2.3. Results .............................................................................................................10 2.4. Discussion .......................................................................................................11 2.5. Limitations ......................................................................................................16 2.6. Conclusion ......................................................................................................18 2.7. Figures and Tables ..........................................................................................20 Chapter 3: Comparing Predictive Capability of the Mehlich 1 and Haney Soil Health Tests on Regeneratively Managed Soil Fertility and Crop Productivity ...........................26 3.1. Introduction .....................................................................................................26 3.2. Methods...........................................................................................................35 3.3. Results .............................................................................................................43 3.4. Discussion .......................................................................................................47 3.5. Conclusions .....................................................................................................53 v 3.6. Figures and Tables ..........................................................................................55 Chapter 4: The Impact of Regenerative and Conventional Land Management Practices on the Functional Potential and Microbial Community Harboring Nitrogen-Cycling Genes Within the Soil ...................................................................................................................64 4.1. Introduction .....................................................................................................64 4.2. Methods...........................................................................................................75 4.3. Results .............................................................................................................82 4.4. Discussion .......................................................................................................89 4.5. Conclusions ...................................................................................................100 4.6. Figures and Tables ........................................................................................102 Chapter 5: Conclusions and Future Work ........................................................................134 References ........................................................................................................................137 Appendix A: Activation of Aflatoxin Biosynthesis Alleviates Total ROS in Aspergillus parasiticus ........................................................................................................................163 A.1. Introduction ..................................................................................................163 A.2. Results ..........................................................................................................165 A.3. Discussion ....................................................................................................170 A.4. Materials and Methods .................................................................................174 A.5. Figures and Tables .......................................................................................179 vi LIST OF TABLES Table 2.1 Description of individual projects and sampling methods used ........................24 Table 2.2 Mean increase in soil OM and C by sampling group ........................................24 Table 2.3 Mean annual rates of change in soil OM by soil texture ...................................25 Table 2.4 Compiled soil test organic matter values from single-event samples throughout SC by soil texture ...............................................................................................................25 Table 2.5 %OM at depth in a random sampling from the 3-year plots .............................25 Table 3.1 Fertilizer treatment applications (in kg/ha N-P2O5-K2O) by crop year for each treatment group ..................................................................................................................55 Table 3.2 Standard soil and Haney soil health test measures ............................................57