ANIMAL WASTE AND THE ENVIRONMENT

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CHAPTER 2 – LITERATURE REVIEW

INTRODUCTION

All phases of dairy production leave an environmental (carbon) footprint. The magnitude of this footprint impacts on and is measurable in three main areas: (1) air quality and the atmosphere – affected by green-house gas emissions, (2) water quality and aquatic ecosystems – affected by run-off containing animal drugs and pathogens and, (3) soil and terrestrial ecosystems – altered because of water run-off, pesticides and fertilizer use (Bertrand and Barnett, 2010; FAO, 2010). The importance of early colostral Ig absorption by the neonatal calf for adequate transfer of passive immunity is well documented (Butler, 1983; Kruse, 1970). In spite of this knowledge, between 30% – 40% of dairy calves in the United States of America suffer from FPT (NAHMS, 2002). Past breeding strategies for dairy cattle have been aimed at achieving speedy genetic improvement, industry targets and raising profitability. However, whilst these strategies have been very successful they may very well impact negatively on the immunity of the animal (Lazarus et al., 2002; Zenger et al., 2007). The immune system is the body’s natural defense mechanism designed to protect the body against invasion by micro-organisms including bacteria, viruses and fungi (Zenger et al., 2007). A responsive immune system improves animal health and welfare and it is, hence,important for the producer to understand how to “build” a healthy immune system. Stress is known to influence and/or suppress the animal’s immune system which may lead to increased episodes of disease (Olson et al., 1980; Olson et al., 1981; Quigley, 2007). Environmental conditions such as periods of extreme heat, cold and ambient temperatures outside the thermoneutral range for calves may affect and internal absorption and transport of Ig from colostrum whose composition may show a reduced Ig content. These conditions are predisposing factors towards a compromised animal immune system (Olson et al., 1980; Olson et al., 1981; Quigley, 2007). During conditions of stress, glucocorticoids are released by the adrenal cortex. Cortisol is the primary glucocorticoid in cattle and has been shown to affect the immune system (Minton, 1994; Fulford and Harbuz, 2005). An impaired immune system may predispose a calf to developing diarrhea which is the foremost cause of mortality and morbidity in calves of less than 30 days old (Constable, 2004). The most common enteropathogens associated with calf diarrhea are Escherichia Coli, Rotavirus and Corona Virus, Clostridium perfringens, Salmonella spp. and Cryptosporidium spp. (Constable, 2004).

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ANIMAL WASTE AND THE ENVIRONMENT

The size of intensive livestock production systems in South Africa is ever-increasing and as most of these systems are associated with confined-housing livestock production systems, these systems increasingly serve as a source of surface-, groundwater- and soil-contamination.Methane gas – is a potent, short-lived (9-12 years in the atmosphere) greenhouse gas with a global warming potential of 25 times that of carbon dioxide (100+ years in the atmosphere). When ruminants produce protein from plants methane is produced.Atmospheric concentrations of methane are ever increasing and this has made scientist investigate and examine the sources. Cattle have been identified as source contributing to global warming. The multi-factorial influence of cattle includes feed intake, composition of the feed as well as the status of ruminal microflora (Johnson and Johnson, 1995). Livestock produce approximately 80 million metric tons (Tg) of methane gas worldwide per annum, about 73% of this can be attributed to the global population of 1.3 billion cattle (Gibbs and Johnson, 1994). A typical dairy cow is estimated to produce in the region of 400 g/day or 109 kg to 126 kg of methane gas per year. Methane production starts as early as 4 weeks of age when the first feed is retained in the reticulo-rumen for fermentation and digestion and gas production rises rapidly during the reticulo-rumen development stage. It causes a significant loss of feed energy subsequently increasing feed costs. Much can be done to reduce methane production if a farmer can manage to improve feed conversion efficiency (FCR) during this period (EPA, 1993), by improving diets to include more non-structural carbohydrates or more starchy feeds, increase dietary fat content and/or crude fat.
Manure management – At intensive enterprises, manure management is dependent on herd size, type of livestock and the stage of production at the farm. Historically, dairy operations have a large component of agronomic activity i.e. pasture-based production for which high levels of nitrogen (N) and phosphorus (P) are required. For this purpose and that of waste management, waste and effluent are recycled over fields and pastures for fertilizer use. Although surface application of N is considered to be “environmentally unfriendly” due to the loss of N (up to 50%) it is considered to have some positive spin-off in that it reduces the pathogen load due to ultra violet (UV) exposure and environmental conditions i.e. exposure to summer and winter conditions (Hutchinson, 2004). Liquid effluent and manure is expensive to transport and, therefore, is applied as close to the source as possible. It is clear that the amounts of manure and production wastage produced in a dairy operation are vast and so there is ample opportunity for exposure, contamination and re-contamination of the environment.

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ABSTRACT
PERSONAL DETAILS 
DEDICATION 
DECLARATION 
LIST OF FIGURES
LIST OF TABLES 
ABBREVIATIONS
ACKNOWLEDGEMENTS
TITLE 
1. CHAPTER 1 – BACKGROUND 
1.1 PROBLEM STATEMENT 
1.2 HYPOTHESES 
1.3 STUDY AIMS AND OBJECTIVES
2. CHAPTER 2 – LITERATURE REVIEW
2.1. INTRODUCTION 
2.2. ANIMAL WASTE AND THE ENVIRONMENT 
2.3. ENTRY OF ANTIBIOTICS INTO THE ENVIRONMENT
2.4. PERSISTENCE OF ANTIBIOTICS IN THE ENVIRONMENT 
2.5. OCCURANCE OF BACTERIA AND DEVELOPMENT OF RESISTANCE 
2.6. BACTERIAL SURVIVAL AND TRANSPORT IN THE ENVIRONMENT
2.7. IMMUNE SYSTEM
2.7.1. IMMUNITY
2.7.2. IMMUNOGLOBULINS
2.7.2.1. ONTOGENY OF THE BOVINE IMMUNE SYSTEM
2.7.3. COLOSTRUM
2.7.3.1. COLOSTROMETER
2.7.4. FAILURE OF PASSIVE TRANSFER (FPT) AND THE TIMING OF THE INITIAL COLOSTRUM FEEDING
2.8. NUCLEOTIDES
2.8.1. NUCLEOTIDE COMPOSITION
2.8.2 ROLE AND IMPORTANCE OF NUCLEOTIDES
2.8.3. EFFECT OF NUCLEOTIDES ON THE IMMUNE SYSTEM
2.8.4. DIGESTION, ABSORPTION AND METABOLISM OF NUCLEOTIDES
2.8.5. STORAGE OF NUCLEOTIDES
2.9. ANATOMY AND FUNCTION OF THE BOVINE DIGESTIVE TRACT
2.9.1. ESOPHAGEAL GROOVE (EG)
2.9.2. IMPORTANCE OF MINERALS TO RUMINANTS
2.9.3. METAL AMINO ACID CHELATED MINERALS
2.9.4. IMPORTANCE OF VITAMINS TO RUMINANTS
2.9.4.1 IMPORTANCE OF AMINO ACIDS TO RUMINANTS
2.9.5. IMPORTANCE OF PREBIOTICS TO RUMINANTS
2.10. GLUCOCORTICOIDS (I.E. CORTISOL) 
2.11. APPARENT EFFICIENCY OF ABSORPTION (AEA)
3.13. BLOOD ANALYSIS
4.13.1. BLOOD SAMPLE COLLECTION, HANDLING AND STORAGE
2.13. CONCLUSION 
3. CHAPTER 3 – RESEARCH METHODOLOGY 
3. INTRODUCTION 
3.1. STUDY AREA 
3.2. STUDY ANIMALS
3.2.1. ANIMAL SPECIES AND SAMPLE SIZE
3.2.2. GENERAL MANAGEMENT
3.2.3. DISEASES AND TREATMENTS
3.2.4. FEEDING OF THE STUDY ANIMALS
3.3. EXPERIMENTS
3.3.1. INVESTIGATIONAL VETERINARY PRODUCTS (IVP)
3.3.1.1. IVP1 – ORAL SUPPLEMENTATION
3.3.1.2. IVP2 – NUTRITIONAL NUCLEOTIDES
3.3.1.3. IVP3 – GLUCOCORTICOSTEROIDS
3.3.1.4. BLOOD COLLECTION
3.3.1.6. IgG TITRE
3.3.1.7. CORTISOL
3.3.1.8. FULL BLOOD COUNT (FBC)
3.3.1.9. HEALTH DATA
3.3.1.10. AVERAGE WEIGHT GAIN AND FEED CONVERSION RATIO
3.4. DATA STORAGE AND INTEGRITY 
3.5. STATISTICAL ANALYSIS AND INTERPRETATION
4. CHAPTER 4 – RESULTS 
5. CHAPTER 5 – DISCUSSION 
6. CHAPTER 6 – CONCLUSION 
7. CHAPTER 7 – RECOMMENDATIONS 
8. CONFLICT OF INTEREST 
9. AUTHORS CONTRIBUTION
10. REFERENCES 
ANNEXURE 1 – RAW DATA

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