Institute of Plant Production and Agroecology in the Tropics and Subtropics University of Hohenheim Field: Global Food Security Prof. Dr. Georg Cadisch (Supervisor) Prediction of soil properties for agricultural and environmental applications from infrared and X-ray soil spectral properties Dissertation Submitted in fulfillment of the requirements for the degree "Doktor der Agrarwissenschaften" (Dr.sc.agr. / Ph.D. in Agricultural Sciences) to the Faculty of Agricultural Sciences presented by Towett, Erick Kibet Born on October 3 rd 1981 in Kericho, Kenya 2013 This thesis was accepted as a doctoral dissertation in fulfillment of the requirements for the degree "Doktor der Agrarwissenschaften” by the Faculty of Agricultural Sciences at University of Hohenheim on 31/10/2013 Date of oral examination: 09/12/2013 Examination Committee Supervisor and Review: Prof. Dr. Georg Cadisch Co-Reviewer: Prof. Dr. Torsten Müller Additional examiners: Prof. Dr. Karl Stahr Head of the Committee: Prof. Dr.-Ing. Stefan Böttinger. i Contents Abbreviations and acronyms .......................................................................................................v 1.0 Introduction to the thesis .......................................................................................................2 1.1 Background and rationale....................................................................................................2 1.2 Overview of soils in African context ...................................................................................3 1.3 Overview of the Africa Soil Information Service (AfSIS) project........................................6 1.4 Soil health and degradation .................................................................................................8 1.4.1 Major nutrient constraints............................................................................................9 1.4.2 Total versus plant-available nutrients.........................................................................10 1.5 Implications for food security............................................................................................11 1.6 Guidance approaches for agricultural and environmental management ..............................11 1.7 Promising methods for rapid soil assessment.....................................................................12 1.7.1 Infrared spectroscopy (IR).........................................................................................13 1.7.2 Total X-Ray Fluorescence Spectroscopy (TXRF) ......................................................14 1.7.3 X-Ray Diffraction (XRD)..........................................................................................15 1.8 The link between variability of soil properties and soil forming factors.............................16 1.9 Justification and opportunities...........................................................................................18 1.10 Hypotheses......................................................................................................................19 1.11 Objectives.......................................................................................................................19 1.12 Outline of the study.........................................................................................................20 1.13 References ......................................................................................................................21 2.0 Quantification of total element concentrations in soils using total X-ray fluorescence spectroscopy (TXRF) .........................................................................................................28 2.1 Abstract ............................................................................................................................28 2.2 Introduction ......................................................................................................................29 2.3 Materials and Methods......................................................................................................32 2.3.1 Sample selection and preparation...............................................................................33 2.3.2 Cleaning and preparation of TXRF sample carriers....................................................33 2.3.3 TXRF measurements.................................................................................................34 2.3.4 Pile-up peak correction..............................................................................................35 2.3.5 ICP-MS reference measurements...............................................................................38 2.3.6 Evaluation of TXRF method precision.......................................................................38 ii 2.3.7 TXRF method recalibration and determination of accuracy .......................................39 2.4 Results and Discussion......................................................................................................40 2.4.1 Comparisons of the analytical results after recalibration ............................................40 2.4.2 Evaluation of TXRF method precision.......................................................................49 2.4.3 Evaluation of TXRF method accuracy.......................................................................50 2.5 Conclusions ......................................................................................................................57 2.6 Acknowledgements...........................................................................................................62 2.7 References ........................................................................................................................62 3.0 Variability and patterns in total element composition of Sub-Saharan Africa soils using total X-ray fluorescence spectroscopy ........................................................................................67 3.1 Abstract ............................................................................................................................67 3.2 Introduction ......................................................................................................................68 3.3 Materials and methods ......................................................................................................71 3.3.1 Study area and sampling............................................................................................71 3.3.2 Sample preparation and analyses ...............................................................................75 3.3.3 Detection limits of the elements.................................................................................76 3.3.4. Data analysis ............................................................................................................77 3.4 Results and discussion.......................................................................................................79 3.4.1 TXRF Method repeatability.......................................................................................79 3.4.2 Total element concentration in soil samples...............................................................80 3.4.3 Principal component analysis of total element concentrations....................................83 3.4.4 Elemental variation between and within site ..............................................................87 3.4.5 Restricted maximum likelihood analysis of the proportion of variance.......................93 3.4.6 Relationship with Mehlich-3 soil tests .......................................................................95 3.4.7 Relationship with mineralogy and other site characteristics .......................................98 3.4.8 Element concentration versus mineralogy composition plus site and soil-forming factors .........................................................................................................................103 3.5 Conclusions ....................................................................................................................105 3.6 Acknowledgement ..........................................................................................................106 3.7 References ......................................................................................................................107 3.8 Annex .............................................................................................................................111 iii 4.0 Combined mid infrared and total X-ray fluorescence spectroscopy for predicting soil properties .........................................................................................................................119 4.1 Abstract ..........................................................................................................................119 4.2 Introduction ....................................................................................................................120 4.3 Material and Methods .....................................................................................................121 4.3.1 Study area, soil sampling and processing.................................................................121 4.3.2 Spectral analyses method.........................................................................................122 4.3.3 Reference soil analysis ............................................................................................123