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Effects of Metam Sodium on Soil Microbial Communities: Numbers, Activity, and Diversity Effects of Metam Sodium on Soil Microbial Communities: Numbers, Activity, and Diversity Item Type text; Electronic Thesis Authors Sederholm, Maya Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 28/09/2021 02:23:37 Link to Item http://hdl.handle.net/10150/621893 EFFECTS OF METAM SODIUM ON SOIL MICROBIAL COMMUNITIES: NUMBERS, ACTIVITY, AND DIVERSITY By Maya Sederholm ____________________________ A Thesis SuBmitted to the Faculty of the DEPARTMENT OF SOIL, WATER AND ENVIRONMENTAL SCIENCE In Partial Fulfillment of the Requirements For the Degree of MASTER OF SCIENCE In the Graduate College THE UNIVERSITY OF ARIZONA 2016 STATEMENT BY AUTHOR The thesis titled Effects of Metam Sodium on Soil Microbial Communities: Numbers, Activity, and Diversity prepared by Maya Sederholm has Been suBmitted in partial fulfillment of requirements for a Master’s degree at the University of Arizona and is deposited in the University LiBrary to Be made availaBle to Borrowers under rules of the LiBrary. Brief quotations from this thesis are allowaBle without special permission, provided that an accurate acknowledgement of the source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may Be granted By the head of the major department or the Dean of the Graduate College when in his or her judgment the proposed use of the material is in the interests of scholarship. In all other instances, however, permission must Be oBtained from the author. SIGNED: Maya Sederholm APPROVAL BY THESIS DIRECTOR This thesis has been approved on the date shown below: Ian Pepper June 30, 2016 Professor, Soil, Water and Environmental Science 2 ACKNOWLEDGEMENTS This study was supported by the National Science Foundation (NSF) Water and Environmental Technology (WET) Center, The University of Arizona. I would like to thank Dr. Bradley Schmitz, Dr. Luisa Ikner, Alexander Wassimi, and Maria Campillo for their technical assistance in the laBoratory. I would like to thank Dr. Reina Maier for help with stoichiometry and Dr. Walter Betancourt and Dr. Aditi Sengupta for assistance on molecular analyses. I would like to thank Mr. Richard Wagner, Mr. Jeffrey Bliznick, Mr. Stephen Husman, Mr. Randy Norton, and Ms. Julia Rosen for helping with the construction, safety, and legal aspects of the project. We wish to acknowledge The University of Arizona Genetics Core for their sequencing services and Motzz Laboratory, Inc. for their soil analyses. Lastly, I would like to thank my academic advisor, Dr. Ian Pepper, for providing the opportunity to conduct this research project and for guiding me through my academic career. 3 TABLE OF CONTENTS LIST OF TABLES AND FIGURES ……………………………………………………………………………………………… 6 ABSTRACT ………………………………………………………………………………………………………………………...….. 7 CHAPTER 1: INTRODUCTION AND OBJECTIVES …………………………………………………….……………….. 8 CHAPTER 2: LITERATURE REVIEW ……………………………………..………………………………………………… 9 1. History of Fumigation ……………………………………..…………………………………………………………….…… 9 2. Metam Sodium ……………………………………..…………………………………………………………………..……… 10 3. Applications of MS ……………………………………..…………………………………………………………………..… 10 4. Epidemiological Studies ……………………………………..……………………………………………………..……… 11 5. Pesticide Regulation ……………………………………..……………………………………………………………..…… 13 6. Retention of MS and MITC …………………………………….……………………………………………………….…. 14 7. Combinations of Fumigants …………………………………………………………………………………………….... 15 8. Effects of MS on MicroBial Communities …………………………………………………………………………… 15 REFERENCES ……………………………………………………………………………………………………………….…..…. 17 APPENDIX A …………………………………………………………………………………………………………………..…… 20 1. INTRODUCTION ………………………………………………………………………………………………………….…… 22 2. METHODS ……………………………………………………………………………………………………………………….. 25 2.1. Safety Requirements for the Project ……………………………………………………………………...……….. 25 2.2. EstaBlishment of Field Plots …………………………………………………………………………………….…….. 25 2.3. Metam Sodium Application …………………………………………………………………………………..……….. 25 2.4. Field Sampling &Transport ………………………………………………………………………………………..….. 26 2.5. Soil Moisture Content ………………………………………………………………………………………………...….. 27 2.6. Heterotrophic Plate Counts ………………………………………………………………………………………….... 27 2.7. LuminUltra® ……………………………………………………………………………………………………………..….. 28 2.8. Dehydrogenase Activity Assay ……………………………………………………………………………………….. 28 2.9. DNA Extraction ………………………………………………………………………………………………………….….. 29 2.10. 16S Gene Amplification and Purification …………………………………………………………………….... 29 2.11. Sequencing and Analysis ……………………………………………………………………………………………... 29 2.12 Hazardous Waste Handling and Disposal …………………………………………………………………..….. 30 2.13. Statistical Analysis……………………………………………………………………………………………………….. 30 3. RESULTS ………………………………………………………………………………..……………………………………...… 31 3.1. Environmental Metadata ……………………………………………………………………………………………..… 31 3.2. CulturaBle Heterotrophic Numbers ……………………………………………………………………………...… 31 3.3. LuminUltra® Microbial Equivalents ……………………………………………………………………….……… 31 3.4. Dehydrogenase Activity Assay TPF Concentration ………………………………………………………..… 32 3.5. Molecular Results ………………………………………………………………………………………………………..… 32 3.6. MicroBial Diversity: Richness ………………………………………………………………………………………… 33 3.7. MicroBial Diversity: Community Composition …………………………………………………….………..… 33 4. DISCUSSION …………………………………………………………………………………………………………………….. 35 5. TABLES ………………………………………………………………………………………………………………………..….. 43 6. FIGURES ………………………………………………………………………………………………………………………….. 47 7. REFERENCES …………………………………………………………………………………………………………….…….. 54 APPENDIX B: SUPPLEMENTARY MATERIAL ………………………………………………………………………… 59 1. Motzz LaBoratory, Inc. Soil Analysis Report ………………………………………………………………………. 59 4 2. Total Activity: LuminUltra® ………………………………………………………………………………………...…… 59 3. Statistical Analyses ………………………………………………………………………………………………………..… 60 4. DNA Extraction Quality ………………………………………………………………………………………………….… 67 5. Number of Sequences per Sample …………………………………………………………………………………..… 68 6. Standard Operating Procedure …………………………………………………………………………………….…… 69 7. Chemical Hygiene Plan ………………………………………………………………………………………………..…… 72 8. Respirator Certification ………………………………………………………………………………………….………… 79 5 LIST OF TABLES AND FIGURES Chapter 1 TaBle 1. Occupational pesticide illnesses, California 1950-1988 Figure 1. MS decomposition in the environment Chapter 2 TaBle 1. Soil Sampling Schedule TaBle 2. Environmental Metadata TaBle 3. Numbers: HPCs and LuminUltra® TaBle 4. Total Activity: Dehydrogenase Activity Assay TaBle 5. OTU TaBle Summary Statistics TaBle 6. Relative Abundances of Top Phyla Figure 1. Schematic of Plot and Drip Irrigation System Figure 2. CarBoy, Irrigation System, and Tarp Set-Up Figure 3. Environmental Metadata Figure 4. Numbers: HPCs Figure 5. Numbers: LuminUltra® Figure 6. Total Activity: Dehydrogenase Activity Assay Figure 7. Number of OTUs per Sample Figure 8. Community Richness Figure 9. Community Composition- Phylum Figure 10. Community Composition- Order 6 ABSTRACT Metam sodium is a fumigant often used as a crop pretreatment in agriculture to control a wide array of pests that may inhiBit plant yields. Previously, there have only Been limited studies conducted on the effects of metam sodium on native soil microBial communities and plant pathogens, and results have been inconsistent. This present study utilized control and metam sodium-treated field plots to examine the effects of metam sodium on soil microBes in terms of numbers, activity, and diversity. Metam sodium did not cause significant changes in culturaBle heterotrophic numbers, as shown By heterotrophic plate counts, But may have adversely affected non-culturaBle microBes since metam sodium did affect microBial activity. Specifically, the LuminUltra® and dehydrogenase activity assays both showed a significant decrease in total activity in treated plots one day after soil treatment, with a return to pre- application conditions within seven days. Illumina Next-Generation Sequencing of the 16S rRNA gene showed slight changes in richness and community composition throughout the 28-day study, But initial and final communities were similar in Both control and treated soils. Overall, some soil microBes were adversely affected By metam sodium, But the resilience of the soil microBial community allowed for an apparent rapid recovery in terms of numbers, activity, and diversity. 7 CHAPTER 1: INTRODUCTION AND OBJECTIVES Fumigation is a method to control a wide range of pests in a variety of disciplines using various gaseous pesticides. Initially discovered to kill insects that diminish crop yields or destroy stored grains, fumigants are now used for other applications such as treating sewer roots in pipe systems or removing pathogens from Biosolids and manures. Soil fumigants are often applied to soil as a solution through drip irrigation systems or shanks, where the solution degrades into the gaseous component. Metam sodium (MS), one of the most widely used soil fumigants throughout the US, is a methyl dithiocarBamate salt that is often sold dissolved in water as a commercial product, such as Vapam®. Recently, MS was certified by the Environmental Protection Agency (EPA) as an approved method for converting Class B Biosolids to Class A due to its aBility to
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