University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2019 Microbial Degradation and Ecological Impacts of Biodegradable Plastic Mulch Films in Agricultural Soils Sreejata Bandopadhyay University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Bandopadhyay, Sreejata, "Microbial Degradation and Ecological Impacts of Biodegradable Plastic Mulch Films in Agricultural Soils. " PhD diss., University of Tennessee, 2019. https://trace.tennessee.edu/utk_graddiss/5682 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Sreejata Bandopadhyay entitled "Microbial Degradation and Ecological Impacts of Biodegradable Plastic Mulch Films in Agricultural Soils." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Environmental and Soil Sciences. Jennifer DeBruyn, Major Professor We have read this dissertation and recommend its acceptance: Sean Schaeffer, Douglas Hayes, Todd Reynolds Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Microbial Degradation and Ecological Impacts of Biodegradable Plastic Mulch Films in Agricultural Soils A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Sreejata Bandopadhyay December 2019 Copyright © 2019 by Sreejata Bandopadhyay. All rights reserved. ii DEDICATION I dedicate this work to my grandfather, Late Mr. Sudhindra Mohan Banerjee; my parents Mrs. Archita Bandopadhyay and Mr. Satyaban Bandopadhyay; and my sister Amrita. Intellectuals in their own right, my grandfather and my parents have had a profound influence on my educational journey. My grandfather was not only my mentor and science tutor all through my high school, but his influence has shaped me in many ways to be the person I am today. My path to graduate school in the US would not have been successful without the support and encouragement of my loving parents who have taught me that there is no substitute for hard work and those who are true to themselves will always succeed. This is for you. iii ACKNOWLEDGEMENTS First, I would like to thank my mentor, Dr. Jennifer DeBruyn, for giving me an opportunity to join her lab and pursue my doctoral studies. Her patience, encouragement, and guidance throughout this project has been instrumental in achieving this degree. Being an international student and living so far away from home, I have been fortunate to have had Dr. DeBruyn as an understanding and kind advisor. I would also like to thank my dissertation committee members - Dr. Douglas Hayes, Dr. Sean Schaeffer and Dr. Todd Reynolds - for their suggestions, constructive criticism and critical inputs that led to the successful completion of this project. I am much more confident and curious because of the influence of each one of you. My sincere gratitude to the Department of Biosystems Engineering and Soil Science at the University of Tennessee - its students, staff and faculty. This department has not only provided me with a platform for mentorship and exchange of scientific knowledge, but I have made life-long connections and friendships with people who have gone out of their way to help me when I needed them. Next, I would like to thank the Biodegradable Mulch Project Team at the University of Tennessee and Washington State University. I find myself fortunate to have worked with this team as it has given me a unique opportunity of transdisciplinary collaboration. Because of this project, I have worked with scientists and students from diverse disciplines and have learnt to see my own research in the context of and in relation to theirs. I thank my peers in this project, Marie English and Jose Liquet Gonzalez, for always being there for me; their friendship is something I will cherish beyond the realm of graduate school. My heartfelt gratitude to my friends in Knoxville who helped me through all the highs and lows by being my lifelines here and making Knoxville my second home. Rahul, Divyani, Avik, and Rani – I cannot thank you all enough for the support and love you gave me and for the amazing friendships I share with each one of you. Last, but not the least, I thank my parents and sister for their wisdom, inspiration and faith in me which motivates me to do better. And finally, to Tanmoy, for his unconditional support and unwavering belief in me. iv “Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less.” -Marie Curie (1867-1934) v ABSTRACT Agricultural plastic mulch films are used to improve crop yields by reducing weeds, moderating soil temperature and conserving soil moisture. Unfortunately, increased popularity of polyethylene (PE) mulch films have resulted in widespread pollution because they are non-biodegradable and have limited recycling options. Biodegradable plastic mulch films (BDMs) are emerging as a sustainable alternative to PE films. BDMs are meant to be tilled into the soil where they are expected to fully biodegrade. However, the biodegradation process is slow, and fragments can persist in soil for months. Limited research regarding the impacts of BDMs on soil microbial communities, and inadequate information on BDM-degrading microbes and factors that control biodegradation of BDMs have restricted their adoption. The objectives of this study were to 1) evaluate the effects of BDMs and PE on soil microbial community structure and function over two years (Spring 2015 - Spring 2017) in two geographical locations: Knoxville, TN, and Mount Vernon, WA, 2) identify potential BDM-degrading microbes using field and laboratory enrichment studies, and 3) evaluate the impacts of added nitrogen amendments on microbial decomposition of BDMs. Bacterial community structure and function were determined using 16S rRNA amplicon sequencing of soil DNA and extracellular enzyme assays. Microbial community structure and function differed between TN and WA (p < 0.05), and seasons of sampling within each location (p < 0.05); however, mulch treatment differences were not significant (p > 0.05). Microbial communities adhered to field-weathered BDMs (the plastic-ome) demonstrated enrichment of soil microbial taxa. Sequence data from BDMs in lab enrichments and isolates demonstrated that microbial colonization on the BDMs was driven by the composition of the mulch films. BDM decomposition was observed in soil microcosms with and without nitrogen amendments. However, nitrogen amendments to BDMs resulted in reduced mulch decomposition. Nevertheless, addition of mulch had minimal impacts on nitrification processes and enzyme activities in the microcosms, irrespective of nitrogen amendments. Limited effects of BDMs on soil microbial community structure and function suggest that BDMs may be a viable alternative to PE. The initial characterization of the “plastic-ome” lays a strong groundwork for future research on microbes degrading BDMs. vi TABLE OF CONTENTS INTRODUCTION ..................................................................................................... 1 Research questions .................................................................................................. 2 Organization of the dissertation .............................................................................. 2 CHAPTER I LITERATURE REVIEW .......................................................................................... 3 Plastic film mulching in agriculture ....................................................................... 3 Benefits of plastic mulch films ............................................................................... 4 Negative impacts of conventional polyethylene (PE) plastic ................................. 5 Alternatives to polyethylene (PE) mulches: The shift towards biodegradable mulches .................................................................................................................10 Paper based mulches ..........................................................................................10 Photodegradable mulches ..................................................................................11 Oxo-degradable mulches ...................................................................................12 Biodegradable plastic mulches (BDMs) ............................................................13 Microbial degradation of BDMs ...........................................................................16 Microbial colonization of BDM surface ............................................................17 Enzymatic degradation of BDM polymers ........................................................17 Microbial utilization of degradation products ...................................................31 Knowledge gap ..................................................................................................32 Characterizing