Dairy Farm Effluents and Groundwater Contamination – Insights from the Vadose Zone Thesis submitted in partial fulfillment of the requirements for the degree of "DOCTOR OF PHILOSOPHY" by Shahar Baram Submitted to The Senate of Ben-Gurion University of the Negev 10 April 2013 Beer-Sheva Dairy Farm Effluents and Groundwater Contamination – Insights from the Vadose Zone Thesis submitted in partial fulfillment of the requirements for the degree of "DOCTOR OF PHILOSOPHY" by Shahar Baram Submitted to The Senate of Ben-Gurion University of the Negev Approved by the advisors: _________________________ _________________________ _________________________ Approved by the Dean of the Kreitman School of Advanced Graduate Studies: _________________________ 10 April 2013 Beer-Sheva This work was carried out under the supervision of Dr. Ofer Dahan and Prof. Zeev Ronen Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research (ZIWR) Faculty: Jacob Blaustein Institutes for Desert Research, and Dr. Daniel Kurtzman Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel. i Research-Student's Affidavit Research-Student's Affidavit when Submitting the Doctoral Thesis for Judgment I Shahar Baram, whose signature appears below, hereby declare that (Please mark the appropriate statements): _X_ I have written this Thesis by myself, except for the help and guidance offered by my Thesis Advisors. _X_ The scientific materials included in this Thesis are products of my own research, culled from the period during which I was a research student. ___ This Thesis incorporates research materials produced in cooperation with others, excluding the technical help commonly received during experimental work. Therefore, I am attaching another affidavit stating the contributions made by myself and the other participants in this research, which has been approved by them and submitted with their approval. Date:____________ Student's name:______________ Signature:____________ ii Acknowledgments Acknowledgements "Water is H2O, hydrogen two parts, oxygen one, but there is also a third thing, that makes water and nobody knows what that is": D.H. Lawrence (1885-1930), Pansies, 1929 First of all, I thank my wife and best friend, Ruth, for accompanying me in this adventure! Together, we found a little piece of heaven on earth where we formed our family and established our home. Many thanks to my supervisors, Ofer, Zeev and Dani, for being wonderful human beings and for their gracious guidance and kind help throughout the time of my studies and research at the Zuckerberg Institute for Water Research. In their unique way, they made this work an enjoyable quest for answers to questions. To all the students, researchers and staff of the Jacob Blaustein Institutes for Desert Studies – too many to name – who guided, assisted, and in innumerable ways, helped me throughout my research. Special thanks to Yuval Shani and Michael Kugel for their extensive help in all the technical aspects of my research. Special thanks to the dairy farm owner for allowing me to conduct my field research at his farm. This research was made possible through funding by The Israel Water Authority. iii Table of contents Table of Contents Research-Student's Affidavit ......................................................................................... ii Acknowledgements ...................................................................................................... iii Table of Contents .......................................................................................................... iv List of Figures ................................................................................................................ v List of Abbreviations .................................................................................................... vi Abstract ........................................................................................................................ vii 1. Introduction ................................................................................................................ 1 1.1 Scientific background .............................................................................................. 1 1.2 Objectives ................................................................................................................ 4 1.3 Significance of the research ..................................................................................... 5 1.4 Geohydrological background ................................................................................... 5 1.5 The degradation in the groundwater quality of Israel’s Coastal Aquifer ................. 7 1.6 Study site .................................................................................................................. 8 1.7 The dissertation structure ......................................................................................... 9 2. Published Papers ...................................................................................................... 11 3. Discussion and Summary ......................................................................................... 55 3.1 Key observations and findings ............................................................................... 55 3.2 Conclusions ............................................................................................................ 61 3.3 Future perspectives ................................................................................................ 62 4. Additional References (not included in published papers) ...................................... 63 5. Appendix A .............................................................................................................. 67 iv Figures List of Figures Figure 1. Map of Israel with its coastal aquifer............................................................6 Figure 2. Schematic cross section of the coastal aquifer in the study area...................6 - - Figure 3. Average nitrate (NO3 ) and chloride (Cl ) concentrations with time in operational cell No. 82 of Israel’s coastal aquifer........................................................8 v Abbreviations List of Abbreviations AMX Anammox-Bacteria AOA Ammonia-Oxidizing Archaea AOB Ammonia-Oxidizing Bacteria BLS Below Land Surface BOD Biological Oxygen Demand CAFO Concentrated Animal Feeding Operations CEC Cation Exchange Capacity CND Coupled Nitrification-Denitrification CWS Crack-Water Sampler DCIS Desiccation Crack Induced Salinization GIS Geographic Information System GWR Geographically Weighted Regression IDW Inverse Distance Weighted LPI Local Polynomial Interpolation N Nitrogen NOB Nitrite-Oxidizing Bacteria RBF Radial Basis Function TN Total Nitrogen VMS Vadose-zone Monitoring System WHO World Health Organization vi Abstract Abstract Earthen waste lagoons are commonly used to store liquid wastes from concentrated animal feeding operations (CAFOs), such as dairy farms. To reduce leakage from such lagoons, soil liners are normally constructed from heavy clay soils, which are regarded as less permeable due to their low saturated hydraulic conductivities. Unfortunately, it has repeatedly been shown that this practice fails to prevent substantial leaching of pollutants into the subsurface and leads to groundwater contamination. One of the main concerns with seepage from dairy earthen lagoons is the high concentrations of nitrogen-species [N-species: organic-nitrogen (organic-N), + ammonia (NH3) and ammonium (NH4 )] in the lagoon leachates. Studies on the fate of N-species in the vadose zone and groundwater underlying dairy earthen waste lagoon environments have shown that their fate can vary, both spatially and temporally between lagoons and within a single lagoon. In this study, water flow, contaminant transport and the fate of N-species in the vadose zone and groundwater underlying a dairy waste lagoon were studied using long-term in-situ measurements and supporting lab experiments. The study initially investigated the physical characteristics of the desiccation-crack networks that form naturally in the unsaturated clay sediments underlying the waste sources and their role in water infiltration and percolation mechanisms in the vadose zone. In-situ monitoring of temporal changes in the water content profile throughout the unsaturated zone indicated fast (m h-1) and deep (>12 m) propagation of water during intensive rain events and during fluctuations in wastewater level. The water percolation pattern indicated that a substantial amount of water crosses the clay soil and recharges the underlying calcareous sandstone. It was further suggested that desiccation cracks cross the entire clay layer, and subsist on land and in the subsurface year-round, even during the wet winter and at near saturation conditions. In addition to temporal preferential infiltration events, continuous slow (mm d-1) infiltration of wastewater was observed underlying the permanently flooded sections of the waste lagoon (away from its margins). Wastewater percolation from the lagoon bed was controlled by the hydraulic conductivity of fine organic material that settled on it and decreased the permeability of the clay matrix. As a result of low flux from the permanently flooded zones, unsaturated conditions prevailed immediately below the subsurface year round. vii Abstract Frequent sampling of the sediment pore water