NON-FUMIGANT ALTERNATIVE SOIL MANAGEMENT PRACTICES FOR MITIGATING REPLANT DISEASE OF FRUIT TREES: MECHANISMS CONTRIBUTING TO PRATYLENCHUS PENETRANS SUPPRESSION by Tristan Tanner Watson B.Sc. (Honours), The University of British Columbia, 2013 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE COLLEGE OF GRADUATE STUDIES (Biology) THE UNIVERSITY OF BRITISH COLUMBIA (Okanagan) April 2018 © Tristan Tanner Watson, 2018 The following individuals certify that they have read, and recommend to the College of Graduate Studies for acceptance, a dissertation entitled: NON-FUMIGANT ALTERNATIVE SOIL MANAGEMENT PRACTICES FOR MITIGATING REPLANT DISEASE OF FRUIT TREES: MECHANISMS CONTRIBUTING TO PRATYLENCHUS PENETRANS SUPPRESSION submitted by Tristan Tanner Watson in partial fulfillment of the requirements of the degree of Doctor of Philosophy . Dr. Louise Nelson, Irving K. Barber School of Arts and Sciences Co-supervisor Dr. Thomas Forge, Agriculture and Agri-Food Canada Co-supervisor Dr. Melanie Jones, Irving K. Barber School of Arts and Sciences Supervisory Committee Member Dr. José Úrbez-Torres, Agriculture and Agri-Food Canada Supervisory Committee Member Dr. Paul Shipley, Irving K. Barber School of Arts and Sciences University Examiner Dr. Mario Tenuta, Faculty of Agricultural and Food Sciences, University of Manitoba External Examiner ii Abstract Replant disease presents a significant barrier to the reestablishment of orchards. In the Okanagan Valley, Canada, the root-lesion nematode, Pratylenchus penetrans, is widely distributed and implicated in poor growth of newly planted fruit trees. Restrictions on soil fumigants have generated interest in alternative management strategies for disease control. Using a combination of greenhouse and field experiments, this dissertation evaluated the effects of composts, bark chip mulch, biocontrol inoculation, and two different irrigation systems (drip emitter and microsprinkler) on the establishment of apple and sweet cherry trees in old orchard soil, P. penetrans population dynamics, as well as biotic and abiotic factors that may have contributed to enhanced plant growth and nematode suppression. In the first greenhouse experiment, compost amendments, but not biocontrol inoculation, improved growth of apple and sweet cherry seedlings in old orchard soil, suppressed P. penetrans, enhanced soil populations of total bacteria, 2,4- diacetylphloroglucinol-producing (DAPG+) bacteria, pyrrolnitrin-producing (PRN+) bacteria, and altered the composition of the soil microbial community. In the field experiment, compost amendment and surface application of bark chip mulch increased trunk diameters of sweet cherry trees planted at an old orchard site as well as suppressed P. penetrans populations. Compost enhanced rhizosphere populations of total bacteria, DAPG+ bacteria, and PRN+ bacteria, soil microbial activity, soil biological suppressiveness, and root colonization by arbuscular mycorrhizal fungi (AMF). Bark chip mulch enhanced rhizosphere populations of total fungi, soil microbial activity, and soil biological suppressiveness. Drip irrigation promoted greater trunk diameters and fruit yield, suppressed P. penetrans populations, and trees had greater root colonization by iii AMF relative to microsprinkler irrigation. In the second greenhouse experiment, compost amendments increased plant growth relative to that of untreated soil in six out of twelve of the orchard soil x compost type combinations evaluated, and suppressed P. penetrans in four out of twelve treatment combinations. Inoculation with antagonistic Pseudomonas isolates provided minor plant growth promotion and P. penetrans suppression in orchard soil. Overall, preplant incorporation of composts and surface application of bark chip mulch, alongside the use of drip irrigation resulted in the best establishment of sweet cherry trees in old orchard soil. iv Lay Summary Replant disease is responsible for the poor growth of fruit trees planted into soil previously used for tree-fruit production, and has been linked to elevated populations of plant-parasitic nematodes in soil, among other possible causes including fungal pathogens. Recent restrictions on use of soil fumigants are increasing the interest in alternative soil management strategies that can provide similar levels of disease control. Using a combination of greenhouse and field experiments, the goal of this research was to evaluate the effects of compost amendments, bark chip mulch, inoculation with potential biocontrol microbes, and choice of low-volume irrigation system (drip emitter versus microsprinkler) on the establishment of fruit trees planted into old orchard soil. This research demonstrated that preplant incorporation of composts and surface application of bark chip mulch, alongside the use of a drip irrigation system provided the best establishment of fruit trees replanted into old orchard soil. v Preface Chapter 2 is work that was conducted by myself under the guidance of Dr. Tom Forge and Dr. Louise Nelson. Segmented flow-injection analysis of soil mineral N content and combustion analysis of soil organic C and N contents were conducted by Dr. Denise Neilsen's research technician, Shawn Kuchta, at the Summerland Research and Development Centre. Optimization of the real-time polymerase chain reaction (PCR) assay for quantification of total fungi was performed in collaboration with Dr. Louise Nelson's Master of Science student, Paige Munro, at the University of British Columbia - Okanagan Campus. Optimization of the real-time PCR assay for quantification of total bacteria was performed by Dr. Tanja Vogel, at the University of British Columbia - Okanagan Campus. I designed and conducted the greenhouse experiment, collected the data, performed all other analyses, and conducted data analysis and interpretation. Chapter 3 is work that was conducted by myself, Dr. Tom Forge, Dr. Denise Neilsen, and Dr. Gerry Neilsen. Segmented flow-injection analysis of soil mineral N content, combustion analysis of soil organic C and N contents, and inductively coupled plasma-optical emission spectroscopy of leaf nutrient concentrations were performed by Dr. Gerry Neilsen's research technician, Lana Fukumoto. Set-up of time-domain reflectometry (TDR) equipment and subsequent monitoring of soil volumetric water contents in sub-plots were performed by Dr. Denise Neilsen's research technicians, Shawn Kutcha and Istvan Losso. From 2014 through 2016, nematodes were extracted from soil and root samples by Dr. Tom Forge's research technician, Paul Randall. Experimental design was decided upon by Dr. Tom Forge, Dr. Denise Neilsen, and Dr. Gerry Neilsen prior to my involvement in the project. I collected the samples, performed vi all other analyses, as well as conducted data analysis and interpretation. A portion of Chapters 2 and 3 has been published: Watson, T.T., Nelson, L.M., Neilsen, D., Neilsen, G.H., Forge, T.A. (2017) Organic soil amendments influence P. penetrans populations, beneficial rhizosphere microorganisms, and growth of newly planted sweet cherry. Applied Soil Ecology 117-118: 212-220. I wrote the manuscript with guidance and input from Dr. Tom Forge, Dr. Louise Nelson, Dr. Denise Neilsen, and Dr. Gerry Neilsen. I independently designed and conducted the greenhouse experiment. For the field experiment, I collected the soil samples, quantified nematodes from samples, quantified rhizosphere/soil microorganisms, and performed plant growth measurements. A portion of Chapter 3 has been published: Forge, T.A., Neilsen, D., Neilsen, G., Watson, T. (2016) Using compost amendments to enhance soil health and replant establishment of tree-fruit crops. Acta Horticulturae 1146: 103-108. I collected the soil samples, quantified nematodes from samples, and performed plant growth measurements. Chapter 4 is work that was conducted by myself under the guidance of Dr. Tom Forge and Dr. Louise Nelson. I designed and conducted the experiment, collected the data, performed all other analyses, and conducted data analysis and interpretation. A portion of Chapter 4 has been accepted for publication: Watson, T.T., Nelson, L.M., Neilsen, D, Neilsen, G.H., Forge, T.A. (XXXX) Evaluation of composts as a non- fumigant alternative to promote the establishment of fruit trees at old orchard sites. Acta Horticulturae (in press). I wrote the manuscript with guidance and input from Dr. Tom Forge and Dr. Louise Nelson. I independently designed and conducted the greenhouse experiments, as well as performed data analysis and interpretation. vii Table of Contents Abstract ............................................................................................................................. iii Lay Summary .................................................................................................................... v Preface ............................................................................................................................... vi Table of Contents ........................................................................................................... viii List of Tables .................................................................................................................. xiv List of Figures ................................................................................................................ xvii List of Abbreviations ..................................................................................................