CROPPING SYSTEM AND ALTITUDE AS DRIVERS OF SOIL MACROBIOTA AND NUTRIENT VARIABILITY FOR ARABICA COFFEE PRODUCTION IN MOUNT ELGON REGION BY SCOLA CHERUKUT B.Sc. AGRIC (MAK) REG. NO: 2015/HD02/496U A THESIS SUBMITTED TO THE DIRECTORATE OF RESEARCH AND GRADUATE TRAINING IN PARTIAL FULFILMENT OF THE REQUIREMENT FOR AWARD OF THE DEGREE OF MASTER OF SCIENCE IN CROP SCIENCE OF MAKERERE UNIVERSITY DECEMBER, 2018 i DEDICATION I dedicate this work to God, my parents Mr. Nelson Kusuro and Mrs. Jesca Kusuro, and to my brothers and sisters for their support in my career development. ii ACKNOWLEDGEMENTS I thank the Almighty God for giving me knowledge, wisdom and good health to conduct this study. I am highly grateful to RUFORUM that provided tuition, stipend and research funds and, the Africa initiative of the Volkswagen Foundation through the project on Productivity and biological diversity in the coffee-banana system in the Mt. Elgon Region of Uganda: Establishing Trends, Linkages and Opportunities, for additional research funds. In the same respect, I thank the farmers of the Mount Elgon region especially the districts of Kapchorwa and Sironko where the research was carried out. I am greatly indebted to Assoc. Prof. Jeninah Karungi and Dr. John Baptist Tumuhairwe for their professional guidance and mentorship. May God richly bless you! I thank my parents Mr. and Mrs. Nelson Kusuro, my brothers and sisters for their love and support, this has always kept me going. It cannot go without mention the support and constant prayers of my dear friends Orapa Nicholas Ijala Tony, Chemonges Martin, and Ayot Phoebe. There are many other people I may have not mentioned but I am grateful for all you have done for this project. May God richly bless you all! iii TABLE OF CONTENTS DECLARATION ............................................................................................................................. i DEDICATION ................................................................................................................................ ii ACKNOWLEDGEMENTS ........................................................................................................... iii TABLE OF CONTENTS ............................................................................................................... iv LIST OF TABLES ........................................................................................................................ vii LIST OF FIGURES ..................................................................................................................... viii LIST OF APPENDICES ................................................................................................................ ix ABSTRACT .................................................................................................................................... x CHAPTER ONE ............................................................................................................................. 1 Introduction ..................................................................................................................................... 1 1.1 Background ............................................................................................................................... 1 1.2 Problem statement ..................................................................................................................... 2 1.3 Justification of the study ........................................................................................................... 4 1.4 Study objectives ........................................................................................................................ 4 1.4.1 General objective ................................................................................................................... 4 1.4.2 Specific objectives ................................................................................................................. 5 1.5 Hypotheses ................................................................................................................................ 5 CHAPTER TWO ............................................................................................................................ 6 Literature Review............................................................................................................................ 6 2.1 Coffee agronomy and ecology .................................................................................................. 6 2.2 Overview of coffee production constraints ............................................................................... 6 2.3 Ecosystem services and their drivers in agro-ecosystems ........................................................ 7 2.4 Root mealybug (Hemiptera: Pseudococcidae) as a pest of coffee ............................................ 8 2.4.1 Description of root mealybug ................................................................................................ 8 2.4.2 Biology and ecology of the root mealybug ............................................................................ 8 2.4.3 Damage caused by the root mealybug ................................................................................... 9 2.4.4 Management of the root mealybug ........................................................................................ 9 2.5 Soil dwelling macrofauna in coffee systems .......................................................................... 10 2.5.1 Earthworms (Lumbricidae: Oligochaeta) ............................................................................ 10 2.5.2 Millipedes (Myriapoda: Diplopoda) .................................................................................... 12 iv 2.5.3 Ants (Hymnoptera: Formicidae) .......................................................................................... 12 2.6 Effect of cropping system on soil properties and coffee productivity .................................... 14 2.7 Effect of altitude on soil properties and coffee productivity .................................................. 15 CHAPTER THREE ...................................................................................................................... 16 Materials and Methods .................................................................................................................. 16 3.1 Description of study sites ........................................................................................................ 16 3.2 Study design ............................................................................................................................ 16 3.3 Data collection ........................................................................................................................ 17 3.3.1 Root mealybug ..................................................................................................................... 17 3.3.2 Soil properties and microclimate ......................................................................................... 17 3.3.3 Coffee yield .......................................................................................................................... 19 3.4 Data analysis ........................................................................................................................... 19 CHAPTER FOUR ......................................................................................................................... 20 Results ........................................................................................................................................... 20 4.1 Effect of cropping system and altitude on root mealybug severity ........................................ 20 4.2 Effect of cropping system and altitude on soil properties and microclimate .......................... 20 4.2.1 Abundance of earthworms ................................................................................................... 20 4.2.2 Abundance of millipedes ..................................................................................................... 21 4.2.3 Abundance of ants................................................................................................................ 22 4.2.4 Effect on soil moisture and temperature .............................................................................. 23 4.2.5 Effect on soil chemical properties ........................................................................................ 24 4.2.6 Effect of cropping system and altitude on microclimate ..................................................... 29 4.3 Effect of coffee cropping system and altitude on coffee yield indicators ............................... 30 4.3.1 Effect on number of fruiting nodes per branch .................................................................... 30 4.3.2 Effect on number of berries per branch ............................................................................... 31 CHAPTER FIVE .......................................................................................................................... 32 Discussion ..................................................................................................................................... 32 5.1 Effect of cropping system and altitude on the root mealybug ................................................ 32 5.2 Effect cropping system and altitude on soil properties