Dissertationen zum Thema „Dairy environment“

For several decades, the practice of farming in mountain areas has played a key role to the proper management of the landscape, the conservation of the biodiversity as well as the soil protection. Moreover, it has significantly contributed to the protection of those areas from avalanches and fires, while at the same time it keeps reinforcing the local economy, thereby acting as a counterweight to abandonment. The mountain animal husbandry is by definition multifunctional and multidisciplinary. In fact, mountainous farming consists of a complex and dynamic system. The harmony and the balance between human activities and nature requires some of the most precious human skills, like patience, self-abnegation, endurance to handiwork and frugality, to name some, but above all, love for mother nature. These are characteristics that ensure continuity and vitality of the mountain for both humans and the surrounding nature. In Italy, almost half of the total land is classified as mountainous (47.5%). Nevertheless, farmers in mountainous regions (representing 30.9% of the national total) face several limitations. These limitations, linked to the existence of natural handicaps, cannot be easily overcome with investments. For example, in mountains the average temperatures are lower, resulting in shorter vegetative period. Moreover, the excessive fractionation, the major gradients and roughness of the lands and at the same time the lower fertility of soils, create the need for special machinery (often more expensive than those used in mainland farms) as well as increased labor and extra inputs for the farms. These factors can lead to a lower land (and consequently farm) productivity, which can be translated into a limited competitiveness of the mountain farms, compared to mainland. In addition, the difficulty of access and the distance of individual dairy farms from the lowland as well as the fewer processing facilities and their small size, create higher transportation costs and lower economies of scale. Thus, the overall objective of this thesis was to verify some parameters of sustainability that are of great importance for animal husbandry in the mountain areas. The province of Trento was selected as a model area for this type of research. More precisely, we have analyzed the relationship between dairy farms and management of the Alpine pastures, in the light of the environmental value of semi-natural grasslands. The first and second contributions are related to this goal. In the last part a survey was carried out to assess the environmental footprint of dairy farms of Trento province, focusing on innovative aspects of nutrition and management of the animals bred. More specifically, the goal of the first contribution was to analyze the role of the mountain livestock sector. At a first step, data were collected from the Veterinary Services of the province concerning the structures and the management of 395 Alpine summer pastures either with cattle (83 with only heifers and 262 including dairy cows) or sheep and goats (50 summer pastures). All the heifers and more than one third of dairy cows that kept on permanent farms of the province were brought to the temporary farms on the Alpine pastures during the summer season, with a frequency greater for cows of local and dual purpose breeds than specialized breeds (e.g. Holstein Friesian). Of the 610 permanent dairy farms associated with the Provincial Federation of Farmers, we have analyzed the differences between the dairy farms that move/do not move the lactating cows to Alpine summer pastures: i.e. the traditional dairy farms (small and medium size), with tied stall, local breeds and with low productivity, frequently using the summer pasture were compared to modern dairy farms of the same province. Results showed that the practice of transhumance to summer pasture has an important role for the dairy sector of Trento province, although the farmers changed the reasons why they choose to move the animals. In fact, the role of grazing as production support in the summer is relevant just for the traditional small and medium dairy farms, while in all cases it is important to access public subsidies that are undifferentiated between lactating cows, dry cows and replacement. The study displayed the fact that there is still the need to maintain the link between dairy farms and Alpine pastures, giving particular attention to the quality of the pasture management and the multi-functionality of services that can be provided by mountain farms. The second part aimed in evaluating the effect of pasturing of dairy cows on milk yield and quality. To this purpose, a many of traits was considered. Body Condition Score (BCS), milk production and quality, milk coagulation properties, different set of parameters and information relating to dairy processing were recorded and analyzed. In total, date regarding 799 lactating cows were collected and analyzed during 2012 from 15 temporary farms on Alpine summer pastures located in the region of Trentino. The cows were reared in 109 permanent dairy farms. Effects of the breed, parity and days in milk were taken into account. The effects of Alpine summer pasture, and in particular of the amount of compound feed given to cows, were also considered. Information was gathered not only during the period that the cows spent at the Alpine summer pasture, but also before and after the alpine season, with the objective to evaluate the changes due to the environmental changes. Results showed that the summer transhumance had an effect more or less relevant in determining a decrease in production, but also depending upon the breed. Specialized breeds, with higher production levels in permanent dairy farms, suffer a greater drop in production than the local and dual purpose breeds. This was somehow expected, since local breeds have a greater adaptability and lower nutrients requirements. Even the body condition score has been strongly influenced from the summer Alpine pasture. A decline in the first phase of the pastures and a subsequent recovery at the end of the pasture period was observed. Differences between breeds existed, with those specialized breeds showing a greater decrease in body condition. After the return from the Alpine pastures a decline in the percentage of fat content in milk (more evident in specialized breeds) was observed, while the protein content remained constant. Regarding the technological properties of milk, significant differences were found with the change of environment (after the reaching of temporary summer farms and after the return to permanent farms). The major differences for lactodynamographic properties as well as the individual cheese yields were observed between June and September. In summary, this work highlighted the better adaptation of local and dual purpose breeds in the Alpine environment and their good performance under environmental changes as well as the special conditions of the farming system in summer pasture. The last part of this thesis aimed to evaluate the environmental footprint of mountain dairy cattle farms. The study was conducted in a specific area of the Province of Trento. Data were collected from 38 dairy cattle farms of mixed breeds using different farming systems. Data on the general farm management, diet, the production performance, the agronomic management of the surfaces, the management of waste, and the energy consumption were collected. A specific questionnaire was developed and tested to this purpose. This specific questionnaire could also be used for further investigation in mountain region. The above mentioned data were used to calculate the carbon footprint of the herds using the Life Cycle Assessment (LCA) approach. The study included the entire product life, i.e. from production of raw materials and their processing till the final product (the functional unit was the kilogram of milk). All the inputs and outputs associated to the functional unit were taken into account. Three categories of environmental impact of the farms were considered: i) carbon footprint (contribution to the production of greenhouse gases), ii) acidification and iii) eutrophication. The values obtained for the three impact categories had large variability, with mean and standard deviation equal to 1.46 ± 0.58 kg for CO2 equivalent (eq), 27.18 ± 8.34 g for SO2 eq. and 7.91 ± 2.31 g for PO43- eq. per kg of milk (fat and protein corrected). The values obtained are comparable with previous studies carried out in mountain areas. The overall impact was divided between on-farm and off-farm components, and was shared according to mass allocation between milk and meat. Analysis of variance showed that the considered effects of housing (free vs fixed) and feed administration (traditional vs TMR), even if appeared statistically significant for some traits, slightly affected the high variability of the impact categories that can be observed among different dairy farms of the same group. This means that there are margins to mitigate the impact and increase the efficiency of farms with different structures and management. Overall, the results of the present thesis provided with some interesting insights on the sustainability assessment of dairy farming systems in mountainous areas, adopting innovative methodological approaches. Looking ahead, the results obtained from experimental approaches could be expanded on a large pool of dairy farms to identify the indicators of reference for the evaluation of the sustainability and multi-functionality of mountain farms.
La pratica dell’allevamento nel territorio montano ha avuto un ruolo fondamentale per la corretta gestione del paesaggio, la conservazione della biodiversità e la protezione del suolo. Inoltre svolge notevoli positività anche in termini di protezione dalle valanghe e dagli incendi, nel contrasto all'abbandono e soprattutto per lo sviluppo dell'economia locale. La zootecnia montana è per definizione multifunzionale e multidisciplinare. Infatti, spesso è artefice di uno sviluppo più complesso e dinamico, in grado di integrare altri comparti economici quali ad esempio il turismo o il sociale, assicurando continuità e vitalità alla montagna. In Italia quasi la metà del territorio è classificato come montano (47.5%) dove gli agricoltori presenti (30.9% sul totale nazionale) devono affrontare diverse limitazioni, legate all'esistenza di svantaggi naturali, che non sono facilmente affrontabili con investimenti. Le temperature medie inferiori, con conseguente periodo vegetativo più breve, l’eccessivo frazionamento, le maggiori pendenze e asperità dei suoli e allo stesso tempo la minore fertilità dei suoli stessi, la necessità di macchinari spesso più costosi come pure i tempi di lavoro più lunghi, hanno come conseguenze una minore produttività della terra, tradotto in una limitata competitività e produttività del lavoro. In aggiunta, la difficoltà di accesso e la lontananza delle singole aziende dal fondovalle, un minor numero di strutture di trasformazione e le loro ridotte dimensioni, sono la causa di maggiori costi di trasporto e minori economie di scala. L’obiettivo generale di questa tesi è di verificare alcuni parametri di sostenibilità di notevole rilievo per la zootecnia montana nella Provincia Autonoma di Trento. Nello specifico, sono state analizzate le relazioni tra bovinicoltura da latte e gestione degli alpeggi, alla luce della valenza ambientale delle praterie semi-naturali; il primo e il secondo contributo sono relativi a questo obiettivo. Nell'ultimo contributo è stata svolta un'indagine per calcolare l'impronta ambientale della bovinicoltura da latte trentina, con un innovativo focus sugli aspetti di nutrizione e gestione degli animali allevati. Nello specifico l’obiettivo del primo contributo è di analizzare il ruolo delle malghe nel comparto zootecnico montano. Sono stai raccolti dal servizio veterinario della Provincia i dati riguardanti le strutture e il management di 395 malghe dove erano presenti bovini da latte (83 solo manze e in 262 anche bovini adulti) e ovicaprini (50 strutture). Praticamente tutte le manze e più di un terzo delle vacche da latte allevate negli allevamenti di fondovalle della provincia sono portate al pascolo durante la stagione estiva, con una frequenza maggiore per le vacche di razze locali e a duplice attitudine rispetto a quelle specializzate. Delle 610 aziende di fondovalle associate alla Federazione allevatori, sono state analizzate le differenze tra le aziende che praticano/non praticano la monticazione delle vacche in lattazione: le aziende tradizionali di dimensioni medio-piccole, con stabulazione fissa, razze locali e con bassa produttività, usano più frequentemente la pratica dell’alpeggio rispetto alle aziende moderne. I risultati evidenziano come la pratica dell’alpeggio mantenga un ruolo importante per la zootecnia trentina, nonostante siano cambiate le motivazioni per cui gli allevatori scelgono di monticare gli animali. Il ruolo del pascolamento come supporto alla produzione nel periodo estivo rimane rilevante per le aziende tradizionali medio-piccole, mentre in tutti i casi riveste una particolare importanza, la possibilità di accedere a contributi indifferenziati tra bovini in lattazione, asciutta e rimonta. Si devono creare le condizioni perché il legame tra aziende e malghe possa essere mantenuto, con particolare attenzione alla qualità della gestione dei pascoli e alla multifunzionalità di servizi che possono essere forniti dalle aziende zootecniche montane. Il secondo contributo mira a valutare l'effetto della monticazione delle vacche da latte su caratteri produttivi e sulla condizione corporea, nello specifico: body condition score (BCS), produzione, qualità e proprietà di coagulazione del latte, e i parametri relativi alla trasformazione casearia. In totale sono stati raccolti e analizzati i dati di 799 vacche in lattazione, monticate nel 2012 su 15 malghe trentine che allevavano capi di diverse razze provenienti da 109 aziende permanenti. I parametri oggetto di studio sono stati messi in relazione alla razza, all’ordine di parto e ai giorni di lattazione, tenendo conto dell'effetto malga, e in particolar modo della quantità di mangime somministrato alle vacche. Il lavoro ha analizzato non solo il periodo di permanenza delle vacche in alpeggio ma anche prima e dopo la stagione di malga con l’obiettivo di valutare i cambiamenti dovuti al cambio di ambiente. I risultati evidenziano come la monticazione abbia un effetto più o meno rilevante nel determinare un calo di produzione a seconda delle razze. Le razze specializzate, con livelli produttivi più elevati nelle aziende permanenti, soffrono un maggior calo di produzione rispetto a quelle locali o a duplice attitudine, che si adattano meglio alle condizioni di alpeggio. Anche la condizione corporea degli animali è fortemente influenzata dall’alpeggio, con un calo nella prima fase della monticazione e un recupero successivo. Emergono delle differenze tra razze, con quelle specializzate che presentano un maggior calo di condizione corporea. Dopo la monticazione si è assistito ad un calo del contenuto percentuale di grasso nel latte (particolarmente evidente nelle razze specializzate), mentre il contenuto di proteine è rimasto costante. Per quanto riguarda le caratteristiche tecnologiche del latte, si sono riscontrate significative differenze sia dopo la monticazione, sia dopo il periodo estivo con il ritorno in azienda. Le maggiori differenze si sono però riscontrate tra giugno e settembre sia in termini di lattodinamografia sia in termini di rese. In conclusione, il lavoro evidenzia la migliore adattabilità delle razze locali e a duplice attitudine al cambiamento di ambiente e alle condizioni di allevamento in malga. Il terzo contributo ha l'obiettivo di valutare l’impronta ambientale di allevamenti montani di bovini da latte. È stato condotto un approfondito studio sul territorio della provincia di Trento, considerando un campione di 38 allevamenti di vacche da latte di razze miste con differenti sistemi di allevamento. Tramite visite aziendali sono stati raccolti dati relativi alla gestione e alimentazione dei bovini, alle prestazioni produttive, alla gestione agronomica delle superfici, alla gestione dei reflui e ai consumi energetici. A questo fine è stato sviluppato e testato un questionario specifico che potrà essere proposto per ulteriori indagini in ambito montano. La mole di dati raccolti è stata utilizzata per calcolare l’impronta ecologica degli allevamenti con approccio Life Cycle Assessment (LCA). Lo studio comprende l’intera vita del prodotto, dalla produzione delle materie prime, alla loro lavorazione e utilizzo finale considerando tutti gli input e gli output associati all’unità funzionale (il kg di latte). In questo studio sono state considerate tre categorie di impatto: carbon footprint (contributo alla produzione di gas serra), acidificazione ed eutrofizzazione, relative all’anno 2013. I valori ottenuti per le tre categorie di impatto presentano un’ampia variabilità, con medie e DS pari a: 1.46 ± 0.58 kg CO2 eq, 27.18 ± 8.34 g SO2 eq. e 7.91 ± 2.31 g PO43- eq. per kg FPCM. I valori ottenuti sono in linea con quanto riportato da altre ricerche condotte in ambito montano. L’impatto complessivo è stato diviso tra componenti on-farm e off-farm, e sono stati ripartiti gli impatti con allocazione di massa tra latte e carne. L’analisi della varianza ha messo in evidenza come gli effetti considerati (stabulazione, libera vs fissa, e modalità di somministrazione degli alimenti, tradizionale vs unifeed), pur significativi in alcuni casi, influiscano in maniera poco rilevante sulla variabilità delle categorie di impatto mentre esiste una rilevante variabilità dei risultati tra aziende diverse dello stesso gruppo. Ci sono quindi margini per mitigare l’impatto e aumentare l’efficienza degli allevamenti, anche con strutture e gestioni diverse. Nel complesso, i risultati della tesi offrono degli interessanti spunti sulla valutazione della sostenibilità della bovinicoltura da latte nelle aree montane, con approcci metodologici innovativi. In prospettiva, i risultati ottenuti dagli approcci sperimentali condotti potranno essere ampliati su un pool ampio di aziende al fine di identificare degli indicatori di riferimento per la valutazione della sostenibilità e multifunzionalità degli allevamenti montani.

All dairy cows in Europe wear unique identification tags in their ears. These eartags are standardized and contains the cows identification numbers, today only used for visual identification by the farmer. The cow also needs to be identified by an automatic identification system connected to milk machines and other robotics used at the farm. Currently this is solved with a non-standardized radio transmitter which can be placed on different places on the cow and different receivers needs to be used on different farms. Other drawbacks with the currently used identification system are that it is expensive and unreliable. This thesis explores the possibility to replace this non standardized radio frequency based identification system with a standardized computer vision based system. The method proposed in this thesis uses a color threshold approach for detection, a flood fill approach followed by Hough transform and a projection method for segmentation and evaluates template matching, k-nearest neighbour and support vector machines as optical character recognition methods. The result from the thesis shows that the quality of the data used as input to the system is vital. By using good data, k-nearest neighbour, which showed the best results of the three OCR approaches, handles 98 % of the digits.

ABSTRACT Aim of this thesis is to evaluate the genetic and racial structure of a dairy cattle breed reared in Tropics, joint to the investigation of the best selection methodology for productive traits adapted to low/medium input production system. The genetic and racial structure of the Carora Breed, a Venezuelan dairy cattle population, was studied through the analysis of the whole pedigree. The database included 4324 living animals (including culled bulls used for AI), born from 1983 to 2010. The racial composition of Carora breed was studied clustering the current population into 5 racial groups, identified on the basis of the individual racial proportion, in order to detect the breed composition in this synthetic breed. The Carora pedigree resulted quite complete, and the inbreeding level is below the level of 1%, even if the size of this breed is reduced. From this study an increase in the Brown Swiss genes proportion was detected, indicating the possibility of a reduction in adaptability linked to the features of this breed, typically suitable for temperate climates. Genetic parameters of weight at 18 months (W18) and milk yield (MY) of 1781 Venezuelan cows were estimated with a Multiple Trait Animal Model, including the direct breed effects and the epistatic loss. Results showed that direct breeds effects and epistatic loss affected milk trait, while they seemed not important for weight. An high percentage of European genes positively influenced milk production. Four random regression models were used on 95606 test day records to obtain genetic parameters for test day yield and persistency. Akaike’s information criterion (AIC) and minus twice log likelihood (-2logL), were used to compare the models and to choose the best one fitting the data. Estimated heritability for milk yield ranged from 0.21 to 0.30, while repeatability ranged from 0.50 to 0.56. Five persistency measures were calculated taking in account different point of the lactation. In general, heritability values for the five measures of persistency ranged from low to moderate (from 0.18 to 0.26), indicating the possibility of new selection opportunities. The use of persistency indexes accounting for milk yield, may allow the selection of individuals able to express their potential genetic values in tropical environment, without incurring in excessive heat stress losses.

This study, being part of a larger project - "Canadian/New Zealand GxE Interaction Trial" - is comparing Canadian and New Zealand sired heifers for growth traits within Canada, since differences for growth traits were found in the Polish strain comparison (Jasiorowski et al., 1987) and due to selection programs in the two countries. Twenty Canadian Holstein and twenty New Zealand Friesian progeny tested, A.I. bulls were randomly mated to over 1,000 cows in 10 Canadian herds. 3,539 records of weight and wither height from 475 heifers (i.e. 241 Canadian and 234 New Zealand sired) were generated. Subsets of the data for different stages of heifer maturity were analyzed separately. Herd and strain effects least squares means were estimated using analysis of variance. Genetic and phenotypic and correlations and heritability for weight and wither height were estimated by a Derivative-Free Restricted Maximum Likelihood (DFREML) algorithm and an animal model (AM). No differences were found between sire strains for weight except at 15 and 18 months where sib groups of Canadian (CN) sires were heavier than their New Zealand (NZ) contemporaries (393 vs 386 kg and 447 vs 445 kg, respectively). CN sired heifers were taller at all ages except at birth, 3 and 9 months of age. At 24 months CN heifers were 136 cm while NZ heifers were 133 cm. Heritability estimates for weight at birth was 0.62 for the CN strain and 0.59 for the NZ strain. CN estimates (3 to 6 months) and NZ estimates (3 to 9 months) were close to zero. Between 9 to 24 months CN strain estimates ranged from 0.44 to 0.69 while NZ estimates were 0.17 to 0.51. The joint estimates ranged from 0.10 to 0.66. Heritability estimates for wither height for CN strain at birth and between 9 to 21 months were between 0.34 to 0.66 and close to zero between 3 to 6 and at 24 months. The NZ estimates at birth, 18, 21 and 24 months were between 0.36 to 0.93 but close to zero between 3 to 15 months. The joint estimates ranged from 0.32 to 0.75 between 12 to 24 months. Genetic correlations between weight and wither height ranged from 0.62 to 1.0 for CN strain and from -0.04 to 0.91 for NZ strain between 4.5 to 21 months. At six months of age the genetic correlation for CN strain was -0.01 and NZ strain was 0.54. At birth, both sire groups had a genetic correlation of 1.0. At 24 months NZ strain had a genetic correlation of 0.84 while that of the CN strain was 0. Genetic correlations for the joint analysis ranged from 0.61 to 1.0 for all ages except at 6 months (0.18). Phenotypic correlations between weight and wither height were between 0.33 to 0.60 for CN group and 0.33 to 0.62 for NZ group. The joint estimates were 0.36 to 0.61. There were no differences in the phenotypic variances except at 9, 12 and 15 months. Genetic variances were different at all ages except at birth for weight.
Land and Food Systems, Faculty of
Graduate

Staphylococcus aureus is the major cause of bovine mastitis in European countries, a disease of major economic importance to the dairy industry. S. aureus isolates from intra-mammary infections were isolated from diverse clinical and geographical origins and were characterised by phenotypic and genotypic methods. S. aureus isolates were identified by their cultural and biochemical properties and were analysed by pulsed field gel electrophoresis (PFGE) after Smal digestion of DNA. A total of 382 S. aureus isolates from bovine intra-mammary infections, bovine skin lesions, milking personnel and non-farm-related human carriers were tested. Ten commercial dairy herds from NE Scotland were included in this study. S. aureus was not isolated from two of them. One herd showed the typical S. aureus infection (102 - 103 cfu ml-1) of low Total Bacterial Counts and low S. aureus numbers, while in the other seven herds S. aureus was isolated only in low numbers, indicating that elevated Bulk Tank Somatic Cell Counts were due to other organisms. S. aureus isolates were assigned by PFGE to 62 electrophoretic types (discriminatory index D = 0.91) and 17 antibiotypes (D = 0.68). The predominant electrophoretic type consisted of 81/382 isolates and its sub-type by 57/382 isolates. Clonal types of bovine intra-mammary infection S. aureus isolates were compared with isolates from other sites on the cows. In addition, epidemiologically unrelated S. aureus isolates from non-farm-related humans were also tested to compare the human and bovine reservoir of S. aureus. Certain clonal types prevailed in individual herds throughout the twelve-month sampling period, whereas the presence of other clonal types, were more sporadic. Certain clonal types were found in more than one herd suggesting that S. aureus isolates that belonged to these clonal types were particularly well-adapted to colonise and persist in the bovine mammary gland. Certain clonal types of S. aureus isolates recovered from cases of bovine mastitis had a broad geographical distribution, comprising isolates from N, NE, SW Scotland and Ireland. The findings of the present study confirm that certain clonal types have remained in circulation for the last 50 years. On the other hand, certain clonal types were found only in one particular geographical area. S. aureus was present in low numbers on bovine body sites from both beef and dairy cattle with the majority of isolates being recovered from the nasal cavity. S. aureus isolates recovered from cows' body sites belonged to different clonal types than those obtained from milk samples. S. aureus was not recovered from farm personnel. Furthermore, PFGE analysis of S. aureus bovine and non-farm-related human isolates suggested that there was no connection between these two sources. Sixty percent of S. aureus isolates tested in the present study were ?-lactamase positive. A high-level of tetracycline resistance was found among S. aureus isolates from a herd where the treatment used for eradication of the infection included tetracycline antibiotics. The induction of -S, aureus L-forms (cell wall-less forms) by antibiotics that inhibit cell wall synthesis was examined. Twelve isolates of S. aureus were treated with antibiotics. Ten were induced to L-forms, while two isolates produced no L-forms under the conditions used. Resistance to penicillin appeared to play no role in the induction of L-forms. S. aureus L-forms were not isolated from milk samples of dairy cattle infected with mastitis. The results of this study support the hypothesis that some S. aureus isolates are more persistent than others and widely distributed clonal types could be responsible for cases of bovine mastitis. Bovine skin lesions and the human reservoir probably are not able to serve as reservoirs of S. aureus isolates involved in bovine mastitis. Furthermore, the ability to induce L-forms in vitro suggests that these forms may have a role in the persistence of the disease.

Stocking density serves as a sub-clinical stressor impacting natural behavior and affective state of dairy cows. However, cows rarely experience stocking density as an isolated stressor. Understanding the effects of stocking density with additional management stressors such as low-fiber diets or feed restriction is the next step in alleviating stress and improving the well-being of lactating dairy cows housed in freestall barns. The overall goal of this dissertation was to evaluate the interaction of stocking density and the feeding environment on short-term production, behavioral, ruminal fermentation, and stress responses of lactating dairy cattle. The first two studies (Chapter 2 and 3) served as preliminary research for the main studies of this dissertation. The first study objective was to evaluate the effectiveness of using chopped wheat straw to reduce sub-acute ruminal acidosis (SARA) in order to formulate diets for the first main study. Treatments were low straw (0 kg dry matter (DM)/d; LS) and high straw (1.36 kg DM/d; HS). High straw appeared to effectively reduce SARA by lowering time below pH 5.8 with minimal impact on feed intake and rumination. The second study objective was to evaluate the effect of type of blood collection tube on haptoglobin concentration across two commercially-available haptoglobin assays and evaluate assay agreement in order to determine haptoglobin concentrations for the main studies. Lithium heparinized, sodium heparinized, and K2-EDTA plasma resulted in increased haptoglobin concentrations compared to serum using the Tri-Delta colorimetric assay, but no differences were observed using the Life Diagnostics ELISA assay. However, there was a lack of agreement between assays and further identification of a gold-standard assay is needed before analyzing haptoglobin for the main studies. The third study (Chapter 4) investigated the interaction of stocking density (100% and 142% of freestalls and headlocks) and source of forage fiber (no added straw and added straw at 3.5% ration DM). Treatments did not impact feed intake, but straw diets tended to reduce milk production. Increasing stocking density reduced lying time but increased efficiency of stall use. Though feeding and rumination times were unaffected, overstocking shifted the location of rumination away from the freestall. Increased stocking density tended to increase stress responses. Both greater stocking density and no straw diets increased SARA, and the combination of these stressors tended to exacerbate this pH response. Adding straw to the diet reduced the negative impacts of overstocking on ruminal pH. The fourth study (Chapter 5) evaluated the interaction of stocking density (100% and 142%) and feed access (5-h reduced feed access and no reduced feed access). Treatments had minimal impact on short-term feed intake and production. Overstocking affected behavior similar to responses observed in Chapter 4. Reducing feed access decreased feeding time, though cows altered feeding and rumination responses to maintain daily rumination. Both treatments shifted priorities for feeding and lying behavior, though increased stocking density had the larger impact. Though reduced feed access did not impact ruminal pH, an exacerbated response was observed when combined with increased stocking density. The combination of stocking density and feeding environment stressors exacerbate negative effects on biological function and should be avoided.

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Bactérias ácido lácticas (BAL) foram isoladas do ambiente de produção de leite e avaliadas quanto ao potencial benéfico. Testes preliminares e análise por PCR foram aplicados para selecionar e identificar através de sequenciamento de rRNA 16S 15 cepas de BAL: Lactobacillus (n = 11; Lb. casei MSI1, Lb. casei MSI5, Lb. casei MRUV1, Lb. casei MRUV6, Lb. acidophilus MVA3, Lb. nagelli MSIV4, Lb. harbinensis MSI3, Lb. harbinensis MSIV2, Lb. fermentum SIVGL1, Lb. plantarum MLE5 e Lb. plantarum MSI2), Pediococcus (n = 2; P. pentosaceus MLEV8 e P. acidilactici MSI7) e Weissella (n = 2; W. paramesenteroides MRUV3 e W. paramesenteroides MSAV5). Todas as linhagens selecionadas apresentaram resistência ao baixo pH e à presença de sais biliares. O teste API ZYM foi realizado para caracterizar a atividade enzimática entre as cepas e foi observada elevada atividade β-galactosidase em 13 delas. Todas as cepas apresentaram alta taxa de sobrevivência ao suco gástrico e as condições intestinais simulados, capacidade de auto-agregação e co- agregação com micro-organismos indicadores e alta hidrofobicidade da superfície celular. A maioria das cepas foi positiva para os genes de adesão map e EFTu. Os resultados de deconjugação de sais biliares mostraram forte desconjugação para todas as cepas. Todas as cepas mostraram bons resultados para assimilar lactose. Após esta etapa de caracterização do potencial benéfico, as 15 BAL foram avaliadas quanto ao potencial de virulência e de resistência antimicrobiana. A produção de fatores de virulência (hemólise, gelatinase, lipase, desoxirribonuclease e aminas biogênicas: lisina, tirosina, histidina e a ornitina) foi avaliada por métodos fenotípicos, a 25 °C e 37 °C, bem como a resistência a 17 antibióticos. Os isolados foram também submetidos à análise de PCR para identificar a presença de 49 genes associados a fatores de virulência. Nenhuma das cepas apresentou atividade hemolítica, produção de gelatinase, lipase, desoxirribonuclease e aminas biogênicas. Das 15 cepas selecionadas, para 12 tipos de antibióticos no método de difusão em disco, todas as amostras foram resistentes à oxacilina e sulfa/trimetoprim, 14 foram resistentes a gentamicina, 11 foram resistentes a clindamicina, nove cepas foram resistentes à vancomicina, oito cepas para rifampicina, cinco foram resistentes a eritromicina, quatro foram resistentes à tetraciclina, duas cepas foram resistentes à ampicilina, uma cepa foi resistente ao cloranfenicol e nenhuma apresentou resistência ao imipenem. Para um teste quantitativo do antibiograma, 5 antibióticos em fitas Etest® (bioMérieux) foram selecionados. Todas as 15 cepas foram resistentes à vancomicina, duas para rifampicina, uma para gentamicina e uma para o cloranfenicol. Em relação aos genes relacionados com virulência, 19 dos 49 genes testados estavam presentes em algumas cepas. Após a caracterização do potencial virulento das 15 BAL, estas foram avaliadas quanto ao potencial tecnológico para aplicação na indústria de laticínios. Todas as cepas apresentaram capacidade de acidificação, atingindo valores de pH entre 0.73 e 2.11 em 24 horas: Lb. casei MRUV6 apresentou maior capacidade de acidificação (pH 2.11 após 24 h). Dez cepas foram capazes de produzir diacetil a 37 °C, com exceção de Lb. casei MSI1, Lb. harbinensis MSI3, Lb. fermentum SIVGL1, Lb. plantarum MLE5 e W. paramesenteroides MRUV3. Todas as cepas foram capazes de produzir exopolissacarídeos, e apenas duas cepas apresentaram atividade proteolítica (Lb. casei MSI5 e W. paramesenteroides MSAV5). Com base nessa caracterização, Lb. casei MRUV6 foi selecionado para produzir o leite fermentado, armazenado a 4 °C e 10 °C e monitorado até 35 dias de vida útil. As amostras foram submetidas a métodos fenotípicos e moleculares para avaliar a presença de Lb. casei MRUV6 (plaqueamento convencional e RT-PCR, verificando a expressão de gapdh, um gene housekeeping) e verificar a expressão do gene bsh, relacionado à resistência à sais biliares (RT-PCR). A população de Lb. casei MRUV6 se apresentou estável durante todo o período de armazenamento a 4 °C e 10 °C a níveis em torno de 9.9 log UFC/g e também pelo monitoramento da expressão do controle endógeno GAPDH. No entanto, o gene bsh não foi expresso durante o período de armazenamento. O estudo demonstrou o potencial uso da cepa de Lb. casei MRUV6 isolada de um ambiente lácteo para a produção de um produto lácteo fermentado e sua estabilidade durante o armazenamento a 4 °C e 10 °C. Todos os isolados do estudo apresentaram características benéficas, segurança para utilização em alimentos e potencial tecnológico para utilização na indústria de laticínios. Além disso, os mesmos podem ainda ser submetidos a estudos adicionais para avaliações in vivo e realizar a caracterização como probióticos.
Lactic acid bacteria isolated from dairy environment were evaluated for beneficial potential. Preliminary screening and PCR analysis were applied to select and identified through 16s rRNA sequencing 15 LAB strains: Lactobacillus (n = 11; Lb. casei MSI1, Lb. casei MSI5, Lb. casei MRUV1, Lb. casei MRUV6, Lb. acidophilus MVA3, Lb. nagelli MSIV4, Lb. harbinensis MSI3, Lb. harbinensis MSIV2, Lb. fermentum SIVGL1, Lb. plantarum MLE5 and Lb. plantarum MSI2), Pediococcus (n = 2; P. pentosaceus MLEV8 and P. acidilactici MSI7) and Weissella (n = 2; W. paramesenteroides MRUV3 and W. paramesenteroides MSAV5). All selected strains showed resistance to acidic pH and to presence of bile salt. API ZYM test characterized enzymatic activity of the strains and high β-galactosidase activity was observed in 13 strains. All strains presented high values for survival rate to simulated gastric and intestinal conditions, ability to auto and co-aggregate with indicators microorganisms and high cell surface hydrophobicity. Most of the strains were positive for map and EFTu beneficial genes. Strong bile salts deconjugation was applied for all strains and all strains showed good results for assimilating lactose. After this first part of the study, the 15 BAL were evaluated for potential virulence and antimicrobial resistance. The production of virulence factors (hemolysis, gelatinase, lipase, deoxyribonuclease and biogenic amines: lysine, tyrosine, histidine and ornithine) was assessed by phenotypic methods at 25 °C and 37 °C, as well as the resistance to 17 antimicrobials. The isolates were also subjected to PCR to identify the presence of 49 genes associated with virulence factors. None of the strains presented hemolytic activity or the production of gelatinase, lipase, deoxyribonuclease and tested biogenic amines. Of the 15 selected cultures, for 12 types of antibiotics in the disc diffusion method, all strains were resistant for oxacillin and sulfa/trimethoprim, 14 were resistant to gentamicin, 11 were resistant to clindamycin, nine strains were resistant to vancomycin, eight strains to rifampicin, five were resistant to erythromycin, four were resistant to tetracycline, two strains were resistant to ampicillin, one strain was resistant to chloramphenicol and none was resistant for imipenem. For a quantitative test of the antibiogram, five antibiotics were selected in Etest ® strips (bioMérieux). All 15 strains were resistant to vancomycin, two for rifampicin, one for gentamicin and one for chloramphenicol. Regarding the virulence related genes, 19 genes from 49 tested were present in some strains. Results showed that five cultures showed the presence of the int gene, four cultures showed the presence of the ant(4')-Ia gene, three cultures were positive for vanC2, cpd and tdc, two cultures for vanA, tet(K), tet(S), ermA, bcrR, mur-2ed, asa1 and ccf, and one culture was positive for vanC1, ermB, aph(3')-IIIa, aac(6’)-le-aph(2”)-Ia, bcrB and hyl. After characterizing the virulent potential of the 15 BAL, these strains were evaluated for the technological potential for application in the dairy industry. All strains presented acidification capacity, reaching pH values between 0.73 and 2.11 in 24 hours: Lb. casei MRUV6 presented the highest acidification ability (pH 2.11 after 24 h). Ten strains were able to produce diacetyl at 37 °C, except by Lb. casei MSI1, Lb. harbinensis MSI3, Lb. fermentum SIVGL1, Lb. plantarum MLE5 and W. paramesenteroides MRUV3. All strains were able to produce exopolysaccharides, and only two strains presented proteolytic activity (Lb. casei MSI5 and W. paramesenteroides MSAV5). Based on this characterization, Lb. casei MRUV6 was selected for producing fermented milk, stored at 4 °C and 10 °C and monitored until 35 days of shelf life. Samples were subjected to phenotypical and molecular methods to quantify the presence of Lb. casei MRUV6 (conventional plating and RT-PCR, by checking the expression of gapdh, a housekeeping gene) and to verify the expression of bsh gene, related to resistance to bile salts (RT-PCR). Lb. casei MRUV6 population was stable during storage period at 4 and 10 °C at levels around 9.9 log CFU/g, and by monitoring the expression of gapdh gene. However, bsh gene was not expressed during storage period. The study demonstrated the potential use of the beneficial strain Lb. casei MRUV6 isolated from a dairy environment for the production of a fermented milk product, and its stability during storage at 4 and 10 °C. All isolates from the study presented beneficial characteristics, safety for use in food and technological potential for use in the dairy industry. In addition, they may further be subjected to further studies for in vivo evaluations and characterization as probiotics.

The pronounced responses of dairy calves to novel events such as weaning and mixing form an obvious welfare concern and represent an important challenge for the dairy industry. I hypothesized that providing calves a more natural social environment would reduce these responses. This thesis consists of 5 chapters, beginning with a general introduction (Chapter 1) and ending with a general discussion and conclusion (Chapter 5). Chapter 2 compares the effects of individual vs. pair housing on calf responses to weaning from milk as well as on the adjustment to a novel pen and novel social partners at mixing. This chapter shows that being housed with a social companion increases starter intake pre-weaning, has a buffering effect on vocal responses at weaning and improves the performance of calves after mixing when compared to calves housed individually. Chapter 3 describes the effects of housing dairy calves with an older companion on the development of feeding behavior before and after weaning from milk. This chapter shows that a weaned companion is an important social model during weaning, stimulating early intake of hay pre-weaning, starter intake post-weaning and improving growth relative to calves housed in groups of similar age. Chapter 4 describes the effects of the early social environment on the behavioral responses of dairy calves to environmental and social novelty. The results from this chapter show that individually housed calves are more reactive to both environmental and social novelty when compared to pair housed calves. Calves housed with an older companion are also more reactive to separation from group members but less reactive to the presence of an unfamiliar calf when compared to calves housed in groups of similar age. Chapter 5 discusses the results of this thesis and suggests that future research on the development of the affective and cognitive abilities of dairy calves in different social contexts can improve the welfare of commercially reared dairy calves. Providing calves access to conspecifics of similar age or an older companion can minimize calf responses to weaning from milk and reduce responsiveness to environmental and social novelty during mixing.

The study was designed to test the hypothesis that P excretion in manure of dairy cattle could be reduced by manipulating electrolyte balance of the diet. Feces was the main route of P excretion, but fecal P was not affected by dietary cation-anion (DCAB) (P > 0.05). Plasma concentration of P tended (P < 0.10) to be higher at lower DCAB levels, implying that DCAB may have influenced P homeostasis. The overall P balance was not affected by the different DCAB levels. The range of DCAB where both P excretion and animal performance could be optimised is very narrow (+250 to +350 mEq/kg DM), so using DCAB to control P excretion in dairy cattle requires caution. (Abstract shortened by UMI.)

Loss of native biological diversity is a world-wide problem of growing international concern. One of the main causes of native biodiversity loss is destruction and degradation of native habitat through land development for agriculture. The Waikato region is an example of the destruction and degradation of native habitat in association with the development and intensification of farming, including dairy farming. This thesis explores cultural reasons for the loss of native forest in the Waikato region, and reasons why fragments of native forest remain. The research involves a participant observation study of 'typical' dairy farm families for 9 months of the dairy year, in-depth interviews of dairy farmers who have protected a significant proportion of their land for conservation of native habitat, a questionnaire of dairy farmers, and an examination of dairy farm magazines and other literature to identify the values and attitudes that motivate dairy farmers in relation to land management and protection of native habitat. The title of the thesis suggests two elements that are important for understanding the loss and persistence of native forest in Waikato's farmed landscapes. Symbolic reason refers to the values, attitudes and perceptions of farmers that derive from socio-political and economic forces which encourage productivist practises that leave little opportunity for native forest to survive. Material agency refers to the local circumstances of particular farms and individual people which enable native forest to persist. The thesis argues that persistence of native forest depends on the idiosyncrasies of material circumstance in the face of relentless pressure to transform the production landscape for economic purposes. The thesis concludes with a suggestion that policies to assist survival of native habitat in farmed landscapes need to include ones that encourage the odds in favour of fortuitous circumstance. In the face of globalised economic pressures, policies for conservation of native biodiversity need to involve a 'portfolio' of measures that apply to individual landowners and the wider rural community by recognising, assisting and rewarding management for non-production values.

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CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Institutional voids are typically found in emerging economies. When governments lack in essential facilities, in order to ensure the well function of their supply chains, companies have to properly deal with this situation by themselves. An example is a situation happening in Rio Grande do Sul, Brazil, since 2013, where a sequence of investigations focused on the dairy industry. Due to a lack of regulation, milk was the target of adulterations throughout the supply chain processes of the companies. The frauds affected processes of companies from different sizes and nationalities. However, in this context, a local cooperative called Cooperativa Languiru, one of the leader dairy companies in the state, has different practices with its suppliers and was not affected by this contingency. Thus, the purpose of this research, through a case study, was to analyze the relationship between a dairy buying company and its suppliers in this environment of regulatory institutional voids. Aiming to have a wider perspective, this qualitative study explored how the lack of institutions affected the sector. As results, it was verified that political and economic interferences affect the chain as well as political lobby acts. Likewise, the lack of inspectors and infrastructure impact the well-functioning of it. Nevertheless, the close relation between the Cooperativa Languiru with its suppliers abled the company to have record results without having situations in terms of adulteration. Thus, this study proposed a research framework conceptualizing that firms must closely manage their relations with suppliers in order to deal with institutional voids.

Este trabalho foi realizado no verão de 2002 e teve como objetivo avaliar a influência de alguns recursos de climatização na produção de leite, na termorregulação dos animais e nos investimentos nas instalações. Foram utilizadas 10 primíparas e 17 vacas em lactação, distribuídas em instalação controle (ICO), instalação com nebulizador associado a ventiladores (ICL) e instalação com tela de sombreamento. A produção de leite e o consumo individual foram medidos diariamente para cada animal. A temperatura retal foi medida três vezes ao dia, em três animais de cada instalação; a temperatura de superfície da pele, três vezes ao dia em todos os animais; e a freqüência respiratória, duas vezes ao dia em todos os animais. Os dados climáticos de cada instalação foram registrados e posteriormente calculados os índices de temperatura e umidade (ITU), de globo negro e umidade (ITGU) e a entalpia. Foram selecionados e analisados 26 dias com entalpia elevada. O índice de globo negro e umidade foi menor no tratamento climatizado, porém a entalpia menor foi observada no tratamento com tela. O índice de temperatura e umidade não diferenciou o ambiente climático das instalações. Índice de temperatura e umidade entre 75 e 76, apesar de considerado estressante por diversas fontes da literatura, não foi associado à condição de estresse pelos animais. As vacas da instalação climatizada apresentaram freqüência respiratória e temperatura de pele significativamente menor em relação às vacas das demais instalações. As primíparas apresentaram freqüências respiratórias e temperaturas retais mais altas do que as vacas, em todos os horários. A maior produção de leite das vacas do tratamento tela foi associada à menor entalpia neste tratamento, em comparação aos demais. Os resultados econômicos demonstraram que foi viável a utilização de tela de sombreamento como recurso para minimizar o calor.
This work was carried out during the summer of 2002. The objective was to evaluate the influence of some cooling systems on the milk yield, animal thermoregulation and housing investments. Ten heifers and seventeen milking cows were distributed in the control housing (ICO), mist & fan housing (ICL) and screen shade (IT). The milk yield and the individual intake were daily measured for each animal. The rectal temperature was measured three times a day with three animals from each treatment. The skin surface temperature was collected three times a day for all the animals and the respiratory frequency two times a day for all the animals. The climatic data of each housing were registered to calculate the temperature humidity index (ITU), the black globe humidity index (ITGU) and enthalpy. Twenty six days of high enthalpy were selected and analyzed. The black globe humidity index was lower for the mist & fan treatment while the lowest enthalpy was observed for the screen shade treatment. The temperature humidity index was not able to differentiate the climatic environment of the houses. The study showed that temperature humidity index between 75 and 76 was not associated with stress conditions for the animals, although many researches propose this situation as stressing. The milking cows in the mist & fan treatment showed respiratory frequency and skin surface temperature significantly lower than the cows in the other treatments. The heifers presented respiratory frequency and rectal temperature higher than the cows in all the registration times. The higher milk yield of the cows in the screen shade treatment was associated with the lower enthalpy on this treatment in comparison with the others. Economic results demonstrated that screen shade was a feasible option to decrease the heat stress of the animals.

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The research was carried out at “Pedra Preta” farm, Itambé-PE, and aimed to analyze milk production, milk composition, fatty acid profile,physiological parameters, and behavior of Pitangueiras cows under grazing conditions and submitted to the presence or absence of shade in the paddock. The environment was monitored daily using a meteorological station at the research site. A complete randomized experimental design was used and 20 lactating cows were allocated inpaddocks with shade or without shade. Milk daily productivity did not differ for cow s submitted to the presence (9.02 kg/cow) or absence of shade (9.03 kg/cow). There was no difference also in the fatty acid profile and milk composition. Cows with shade available stayed under the shade during periods where thermal comfort index was greater. Physiological responses did not show significant differences, however, differences were observed between morning and afternoon periods, with greater values observed for the afternoon period. The use of artificial shade favoured animals’ weight gain.
O trabalho foi realizado na fazenda Pedra Preta, Itambé-PE, e foram avaliados: produção e composição do leite, perfil dos ácidos graxos, parâmetros fisiológicos e atividades comportamentais de vacas da raça Pitangueiras, submetidas à condição de pastejo com e sem acesso à sombra. O ambiente foi monitorado diariamente por intermédio de uma estação meteorológica no local do estudo. O delineamento experimental utilizado foi inteiramente casualizado, onde 20 vacas em lactação foram divididas em piquetes nos tratamentos com e sem acesso a sombra. Os valores da produção de leite não apresentaram diferenças significativas, para os tratamentos com e sem acesso a sombra (9,02 e 9,03 kg, respectivamente). Não houve diferença significativa no perfil dos ácidos graxos e composição do leite. Os animais com acesso a sombra buscaram o sombrite nos horários onde os índices de conforto térmico foram mais elevados. As variáveis fisiológicas não apresentaram diferenças significativas, houve variação com relação aos turnos, à tarde os valores obtidos foram mais elevados em comparação ao turno da manhã. O uso do sombrite foi favorável em relação ao ganho de peso dos animais.

Los resultados de esta tesis demostraron que es posible una evaluación y mejora ambiental constante de los sistemas lácteos mediante el uso de herramientas especializadas como CalcPEFDairy, auditorías energéticas e indicadores de economía circular; y que juntos son capaces de identificar y proponer medidas de mejora de alto impacto. Los resultados también demuestran la viabilidad de comunicar adecuadamente los resultados medioambientales obtenidos con CalcPEFDairy como una estrategia de marketing. La calidad y confiabilidad de los resultados obtenidos de las herramientas implementadas en esta tesis es tal que pueden usarse en un proceso de verificación externo para obtener una declaración ambiental y una Ecoetiqueta para un producto lácteo disponible en el mercado. Estas credenciales medioambientales verificadas brindan a los productores lácteos la posibilidad real de aumentar sus ganancias económicas sin afectar la sostenibilidad ambiental de su sistema productivo y productos.
Els resultats d'aquesta tesi van demostrar que és possible una avaluació i millora ambiental constant dels sistemes lactis mitjançant l'ús d'eines especialitzades com CalcPEFDairy, auditories energètiques i indicadors d'economia circular; i que junts són capaços d'identificar i proposar mesures de millora d'alt impacte. Els resultats també demostren la viabilitat de comunicar adequadament els resultats mediambientals obtinguts amb CalcPEFDairy com una estratègia de màrqueting. Ja que la qualitat i fiabilitat dels resultats obtinguts és tal que poden usar-se en un procés de verificació extern per obtenir una declaració ambiental i una Ecoetiqueta per a un producte lacti disponible al mercat. Aquestes credencials mediambientals verificades brinden als productors lactis la possibilitat real d'augmentar els seus guanys econòmics sense afectar la sostenibilitat ambiental del seu sistema productiu i productes.
This thesis results shows that a constant environmental assessment and improvement of dairy systems is possible through the use of specialised tools such as CalcPEFDairy, energy audits and circular economy indicators; which together are capable to identify and propose high impact improvement measures. The results demonstrate the feasibility of properly communicating the CalcPEFDairy environmental assessment outcomes as a marketing strategy since their quality and reliability is such that they can be used in an external verification process to obtain an environmental declaration and eco-label for a market available dairy product. This verified green credentials give dairy producers the real possibility of increasing their economic returns without affecting their system and products environmental sustainability.

Various bacterial products from BiOWiSHTM Technologies have been tested in dairy wastewater experiments to determine the bacterial mixes’ ability for enhanced degradation of biochemical oxygen demand (BOD), solids, and nitrate concentrations. The dairy wastewater was augmented with various bacterial composition obtained from BiOWiSHTM. The bacterial mixes experimented were US Aqua, Thai Aqua, BMT, Osprey, Fruit Wash, KLB, LCM1, and MDG. Method development was a crucial process to optimize and test the effects of the BiOWiSHTM Technologies bacterial mixes. After 5 experiments, the BOD tests showed that for some of the tests, the redosage of bacteria helped further drive the BOD concentrations to be lower than the control. With redose, the samples reduced BOD by 10 – 55% to samples that were not redosed. Although the redose adds supplemental BOD initially, the addition showed that in some cases, the bacterial sample BOD is lower than without any redose. For the solids testing, different solids tests showed either conclusive impacts of bioaugmentation or no effect. For the total solids (TS) and total suspended solids (TSS) tests, both showed about a 10% decrease or increase in solids throughout the experiments. The smaller solids components, volatile suspended solids (VSS), did demonstrate that the bacterial mixes reduced organic suspended solids more than the control. The bioaugmented samples reduced the VSS organic material by 5 – 15% compared to the control with BiOWiSHTM. Particle size distribution (PSD) tests provided a breakdown of which particle sizes were increasing and decreasing. Those samples bioaugmented with BiOWiSHTM showed that smaller particles (0.7 µm pore size) were getting assimilated by the bacteria which produced more bacteria (larger pore sizes of 5 µm). After the bacteria ran out of food, the sequentially smaller pore size (2.5 µm) increased while the smaller pore sizes (1.6 µm and 0.7 µm) remained low. The rate limiting step was determined to be 1.6 – 2.5 µm where the control’s zero rate constant was +1.4 mg/L-day whereas the USA and TA was -1.1 mg/L-day and -1.4 mg/L-day respectively. Thus, the BiOWiSHTM samples decreased TSS in smaller pore size filters by about 10 – 20% more than the control. Ion chromatography (IC) measured that nitrate levels were clearly reduced by 30 – 50% adding the BiOWiSHTM bacteria compared to the control. Therefore, the additional bacteria further denitrified the nitrate (NO3-) than if no BiOWiSHTM was added. Denitrification experiments were performed for pure Bacillus spores, KLB, that showed a 90% decrease of NO3- to the control. Keywords: bioaugmentation, BiOWiSHTM, BOD, dairy wastewater, dissolved solids, ion chromatography, nitrate, particle size distribution, redose, suspended solids, total solids, volatile suspended solids

For a small state such as New Zealand, trade and economic partnerships are extremely important for economic survival. However, the tyranny of distance complicates this somewhat. Historically, New Zealand has always been dependent on exporting agricultural products. There are examples in New Zealand’s history of innovative ideas being utilised to New Zealand’s economic advantage, such as the advent of refrigerated shipping to the United Kingdom. An important economic partner for New Zealand is the European Union. The European Union is the world’s largest trade power, a formidable partner for a small state, such as New Zealand, to contend with in trade related matters. The agricultural protectionist policies of the European Union are an issue for New Zealand to work around. However, the European Union is also a welcoming market for high quality products that New Zealand should supply. New Zealand’s small size means that the country has to focus on producing high quality products rather than mass production. This thesis proposes to make recommendations for the types of products New Zealand should export to the European Union, in what quantities, and by which methods. This is important for New Zealand producers and exporters to take into account if New Zealand is to expand its exports to the European Union.

This study explores issues arising from the adoption of the term 'clean and green' for marketing New Zealand dairy products. Three dimensions of environmental quality were investigated: that of sustainable dairying and best practice for the benefit of farmers and the industry; resource management legislation and being a 'good neighbour'; and export marketing opportunities and issues. The study was undertaken during a time of major structural upheaval in the dairy industry, including yearly company amalgamations in the study area, rapid conversion of farmland to dairying, as well as factory expansion to process the increasing supply of product. The focus of the study was on the individual farmer, how perceptions and preferences are formed, and how in turn, these influence farm practice. World views drawn from Cultural Theory were adopted as the basis for analysis. Farmers were classified according to particular world views and the symbolic and reflexive use of concepts such as 'clean and green' was analysed. A model of overlapping ecological, agricultural and social systems was used to develop a wider understanding of preference formation. Through a mixed methodology, focusing on a case study approach, farmer and stakeholder world views were compared on key themes, including the 'clean green' pastoral myth, 'cues for care' and environmental issues. Media discourse as well as consumer views were used to expand understanding of the context. The study found that both farmers (within their groups) and stakeholders held different objectives and opinions on environmental issues and options for change, based on their various world views and preferences. There was general agreement both among farmers and stakeholders on the New Zealand 'clean green' image and 'cues for care', or signs that indicate good farm management. The reason for this was demonstrated to be the way in which these two aspects are communicated; through symbolic images that each individual perceived in terms of their respective world view. A symbolic form of action, an environmental management system, was trialled with farmers. Analysis indicated that national aspirations created by the 'clean green' pastoral myth required farmers to respond to environmental expectations, but that an image that symbolized environment as care and quality, rather than as place was needed to provide a less ambiguous goal. The findings of the trial were integrated with theory to interpret context and develop policy, strategy and action proposals for a system for environmental quality for the industry. The study has implications for non-regulatory mechanisms relevant to sustainable dairy farming, communication within the rural community, and branding.

Environmental intolerance (EI) is a condition characterized by low tolerance to environmental stimuli at levels that would not affect most people. EI is an ill-defined condition from which sufferers experience highly individual multisystem symptoms following exposure from specific environmental sources. Subgroups of EI are typically distinguished by the source that cause negative effects. In this study, intolerance attributed to noise and odors was investigated. Most research on EI is conducted using cross sectional approaches and among the instruments used to quantify EI is the Noise Sensitivity Scale (NSS-11) and the Chemical Sensitivity Scale for Sensory Hyperreactivity (CSS-SHR). To fully understand EI, more longitudinal research is needed. The aim of this study was to establish how a recently developed smartphone app, intended for longitudinal research, compares to the NSS-11 and CSS-SHR with regards to its ability to detect EI. 12 participants (mean age 29 years, SD=10.7 years) filled out the NSS-11/CSS-SHR following a period of two weeks using the app. It was hypothesized that individuals scoring high/low on the NSS-11/CSS-SHR would also express high/low levels of EI as measured by reports in the app on the variables discomfort rating, number of unique symptoms reported and number of reports. Although analyses revealed effects in the direction of the hypothesis for all variables, Independent samples t-test analyses yielded no significant associations. Either there are in fact no differences, but speculatively, the lack of significant associations can also be attributed any the following: (1) the groups were to similar (2) the sample was too small (3) the participants used avoidance as coping strategies.

The dairy industry today is beginning to dedicate more focus on the growth of the calf from birth to first breeding to better improve the milk production as well as the overall performance of the individual cows. While the development of the rumen is one of the most vital contributors to the performance of the calf, it remains unknown what molecular mechanisms are responsible for the development of the rumen, and more specifically the proliferation of rumen epithelial cells. The objectives of this study were to investigate the existing data on rumen development through meta-analysis and to explore the effects of sodium butyrate and lipopolysaccharide (LPS) on rumen development in calves through experiment. In the first study a meta-analysis was performed to summarize the literature on calf performance and derive equations that relate rumen (e.g., rumen pH, reticulorumen weight, papillae area) and non-rumen factors (e.g., feed composition, form of feed, housing) to animal performance (e.g., intake of milk replacer (MR), starter, and forage; average daily gain (ADG); and feed efficiency). We looked at four different relationships to further investigate the connections between rumen, non-rumen, and performance factors. In the first and second relationships of interest, the effect of dietary and environmental variables on rumen variables and performance variables were examined, respectively. The third relationship of interest was how rumen variables influenced performance variables. The final relationship of interest was investigating the additive effects of the rumen, dietary, and environmental variables on the performance variables. Forward selection, multiple regression was used to derive equations to select variables that explained variation in the response variable in each model. Results showed that the variation in calf ADG was explained by daily forage intake, calves that were weaned, total starter intake, and total MR intake (concordance correlation coefficient (CCC) = 0.976). The variation in feed to gain ratio was explained by the weight of the ruminal contents, daily forage, MR, and starter intakes, percent of starter in the diet, and total starter intake (CCC = 0.992). The variation in daily forage intake was explained by the percent of the diet that was starter or MR (CCC = 0.998). The variation in daily starter intake was explained by the percent of acid detergent fiber in the starter, a pelleted starter (versus a texturized), diets including starter and forage (versus a milk replacer only diet), and the percent of the diet that was MR (CCC = 0.998). The variation in daily MR intake was explained by the percent of the diet that was starter, final body weight, ruminal propionate concentration, and daily starter intake (CCC = 0.918). Based on these analyses, although dietary and environmental factors are closely associated with calf performance, ruminal factors such as volatile fatty acid (VFA) concentration and ruminal contents appear to have additional, additive influences on calf performance. In the second study, 24 Holstein bull calves were challenged with oral doses of LPS and sodium butyrate. The hypothesis here was that LPS and sodium butyrate would instigate rumen cell proliferation independently and additively. Calves were assigned to one of four treatments: control (CON; n=5), butyrate (BUTY; n=5), LPS only (LPS-O) (n=6), or LPS plus butyrate (LPSB; n=6). All treatments were administered orally twice daily consisting of either: 0.9% saline (CON); 11 mM sodium butyrate (BUTY); LPS ranging from 2.5 to 40 µg/kg metabolic body weight (BW0.75, LPS), or both butyrate and LPS (LPSB). Calves were fed milk replacer (22% CP, 20% fat, as-fed) and starter (20% CP, 3% fat, as-fed) based on metabolic BW, or about 12% BW of MR and 3% BW of starter. Feed intake, fecal and respiratory scores, and rectal temperature were recorded daily. Calf BW, hip height, jugular blood samples, and rumen content samples (via oroesophageal tube) were collected weekly. Calves were weaned at 6 wk of age and euthanized at 8 wk of age, whereupon ruminal weights and ruminal samples for papillae area and epithelial thickness were collected. Blood and rumen samples were analyzed for concentrations of beta-hydroxybutyrate, glucose, LPS-binding protein, and VFA. Data were analyzed as a 2x2 factorial with the repeated effect of week. Three non-orthogonal contrasts (CON versus the average of all other treatments; LPS-O versus LPSB, and LPSB versus BUTY) were investigated. Feed intake, health measures, and blood metabolites did not differ by treatment. Calf BW increased by week (P < 0.0001). Irrespective of week, LPS calves weighed more and had higher ADG than BUTY calves (P = 0.020). Irrespective of week, withers height was greater in LPS compared to CON (P = 0.006). Rumen pH and rumen VFA concentrations did not differ by treatment but did decrease and increase, respectively, with week in conjunction with increased starter intake. Total empty forestomach (P = 0.014) and reticulorumen weights (P = 0.012) were greater in LPSB compared to BUTY. Overall, LPS and sodium butyrate appeared to have synergistically affected some, but not all rumen measurements without affecting calf growth, intake, or health. Results from the meta-analysis emphasize the importance of continuing to focus on the solid feed intake of the calf from birth through weaning. Implications from the LPS study are imperative to other dairy scientists who will attempt to further study the effects of LPS on the rumen.
Master of Science in Life Sciences
Dairy calves are born with an under-developed stomach. The stomach has four compartments: the rumen, reticulum, omasum, and abomasum. The rumen is the largest component where finger-like projections called papillae grow to absorb nutrients for the calf. It is vital to the calf that the rumen develops not only the papillae to absorb nutrients but also to foster a microbe-rich environment so the microbes can act as a defense mechanism for the calf to aid in fighting disease. While it is known that things like solid feed support the development of the rumen, the mechanism behind how that is happening still remains unclear in the literature. The objective of this study was first to better understand the relationships that exist in the literature between dietary, environmental, and ruminal factors, and second to investigate the claim that certain components of the bacteria in the rumen are stimulating rumen development independently and additively with sodium butyrate. In order to investigate the relationships amongst the dietary, environmental, and ruminal parameters, a computer program called R Studio was used to analyze over 30 different models that extracted data from a database that included a collection of 36 studies from the literature. This is also known as a meta-analysis. The associations of interest that we found were: average daily gain (ADG) of the calf was associated with daily forage intake, calves that were weaned, total starter intake, and total MR intake. Feed efficiency of the calf was associated with the weight of the ruminal contents, daily forage, milk replacer (MR), and starter intakes, percent of the diet composed of starter, and total starter intake. Daily forage intake was associated with the percent of the diet that was starter or MR. Daily starter intake was associated with acid detergent fiber in the starter, a pelleted starter (versus a texturized starter), diets including starter and forage (versus a MR only diet), and the percent of the diet that was MR. Daily MR intake was associated with the percentage of the diet that was starter, final body weight (BW), ruminal propionate concentration, and daily starter intake. These relationships emphasized that although dietary and environmental factors are more closely associated with calf performance, ruminal factors such as rumen contents and volatile fatty acid concentrations appear to have additional, additive influences on calf performance. The second part of the study objective was to explore an idea that, to our knowledge, has not been published in the literature. In the second study, 24 dairy calves were challenged with oral doses of a gram-negative bacteria lipopolysaccharide (LPS), and a short-chain fatty acid sodium butyrate. The hypothesis in this study was that the LPS and sodium butyrate would trigger metabolic pathways on the rumen cell membranes to a greater extent together, versus independently, to increase the amount of cells growing. Calves were assigned to one of four treatments: control (CON), butyrate (BUTY), LPS only (LPS-O), or LPS plus butyrate (LPSB). To study this effect, each treatment group was administered their respective treatment orally as a liquid twice daily. To measure the results, the following data was collected: feed intake, fecal and respiratory scores, rectal temperature BW, hip and withers height, blood samples, rumen content and pH samples, papillae area, epithelial thickness, and organ weights. Blood and rumen samples were analyzed for blood metabolites and volatile fatty acids concentrations respectively. Data were analyzed and results showed no difference amongst feed intake, health measures, rumen pH, rumen VFA concentration, and blood metabolites by treatment. Calves on the LPS treatment weighed more and had higher ADG than BUTY treatment calves. Withers height was higher in the LPS group when compared to CON. Stomach weights were higher in the LPSB group when compared to the BUTY group.

An integrated wastewater treatment facility at a dairy in Glendale, Arizona, consisting of an upper subsystem (solids separators, anaerobic lagoons, and aerobic ponds) and lower subsystem (wetland subsystems) has been proven to be successful in reducing indicator organisms and potential pathogens (bacteria, enteric viruses, and parasites). The collection sump of the new integrated system collects all dairy wastewater and pumps it to solid separators, which then flows by gravity to anaerobic lagoons and aerobic ponds. The upper subsystem achieved significant microbial reductions of >98 percent for total coliform, >91 percent for coliphage, >95 percent for enterococci, >91 percent for Listeria monocytogenes, and >99.9 percent for Cryptosporidium . Additional reductions although limited were observed in the outflow from the wetland cells.

Reciprocating biofilters known as ReCip is a viable technology to manage nutrients, mainly nitrogen, problems at livestock operations such as swine farms and dairies. Past studies have demonstrated that ReCip is more adept at total nitrogen (TN) removal than traditional subsurface flow wetland systems. The traditional substrate used to attach biomass was rock aggregate; this media may be hard to obtain for some agricultural projects, so alternate substrates are tested and compared with the rock aggregate. The purpose of the study was twofold: first, different biofilm media were tested and compared in terms of treatment performance and, second, the long-term performance of a ReCip in continuous operation for 3 years was characterized. Four, 2.67 square meter ReCip systems with different treatment media – rock aggregate, recycled concrete aggregate (RCA), vertical-flow plastic media, and walnut shells – were operated at a 2-day THRT over the course of a 16 week study. The TN removal efficiencies for rock aggregate, RCA, plastic media, and walnut shell media were 43%, 53%, 25%, and 69% respectively. Surface based mass TN removal rates for the same media were 103, 128, 172, and 276 kg/ha-d respectively. A 134.2 square meter ReCip with rock aggregate media was running concurrently with the smaller ReCip systems. This ReCip was constructed ant operated since January 2010. TN removal efficiency and mass removal rate were 44% and 105 kg/ha-day. These values were close to results from the smaller rock media system.

Identifying human activities is a key task for the development of advanced and effective ubiquitous applications in fields like Ambient Assisted Living. Depending on the availability of labeled data, recognition methods can be categorized as either supervised or unsupervised. Designing a comprehensive activity recognition system that works on a real-world setting is extremely challenging because of the difficulty for computers to process the complex nature of the human behaviors. In the first part of this thesis we present a novel supervised approach to improve the activity recognition performance based on sequential pattern mining. The method searches for patterns characterizing time segments during which the same activity is performed. A probabilistic model is learned to represent the distribution of pattern matches along sequences, trying to maximize the coverage of an activity segment by a pattern match. The model is integrated in a segmental labeling algorithm and applied to novel sequences. Experimental evaluations show that the pattern-based segmental labeling algorithm allows improving results over sequential and segmental labeling algorithms in most of the cases. An analysis of the discovered patterns highlights non-trivial interactions spanning over a signifcant time horizon. In addition, we show that pattern usage allows incorporating long-range dependencies between distant time instants without incurring in substantial increase in computational complexity of inference. In the second part of the thesis we propose an unsupervised activity discovery framework that aims at identifying activities within data streams in the absence of data annotation. The process starts with dividing the full sensor stream into segments by identifying differences in sensor activations characterizing potential activity changes. Then, extracted segments are clustered in order to find groups of similar segments each representing a candidate activity. Lastly, parameters of a sequential labeling algorithm are estimated using segment clusters found in the previous step and the learned model is used to smooth the initial segmentation. We present experimental evaluation for two real world datasets. The results obtained show that our segmentation approaches perform almost as good as the true segmentation and that activities are discovered with a high accuracy in most of the cases. We demonstrate the effectiveness of our model by comparing it with a technique using substantial domain knowledge. Our ongoing work is presented at the end of the section, in which we combine pattern-based method introduced in the first part of the thesis with the activity discovery framework. The results of the preliminary experiments indicate that the combined method is better in discovering similar activities than the base framework.

Identifying human activities is a key task for the development of advanced and effective ubiquitous applications in fields like Ambient Assisted Living. Depending on the availability of labeled data, recognition methods can be categorized as either supervised or unsupervised. Designing a comprehensive activity recognition system that works on a real-world setting is extremely challenging because of the difficulty for computers to process the complex nature of the human behaviors. In the first part of this thesis we present a novel supervised approach to improve the activity recognition performance based on sequential pattern mining. The method searches for patterns characterizing time segments during which the same activity is performed. A probabilistic model is learned to represent the distribution of pattern matches along sequences, trying to maximize the coverage of an activity segment by a pattern match. The model is integrated in a segmental labeling algorithm and applied to novel sequences. Experimental evaluations show that the pattern-based segmental labeling algorithm allows improving results over sequential and segmental labeling algorithms in most of the cases. An analysis of the discovered patterns highlights non-trivial interactions spanning over a signifcant time horizon. In addition, we show that pattern usage allows incorporating long-range dependencies between distant time instants without incurring in substantial increase in computational complexity of inference. In the second part of the thesis we propose an unsupervised activity discovery framework that aims at identifying activities within data streams in the absence of data annotation. The process starts with dividing the full sensor stream into segments by identifying differences in sensor activations characterizing potential activity changes. Then, extracted segments are clustered in order to find groups of similar segments each representing a candidate activity. Lastly, parameters of a sequential labeling algorithm are estimated using segment clusters found in the previous step and the learned model is used to smooth the initial segmentation. We present experimental evaluation for two real world datasets. The results obtained show that our segmentation approaches perform almost as good as the true segmentation and that activities are discovered with a high accuracy in most of the cases. We demonstrate the effectiveness of our model by comparing it with a technique using substantial domain knowledge. Our ongoing work is presented at the end of the section, in which we combine pattern-based method introduced in the first part of the thesis with the activity discovery framework. The results of the preliminary experiments indicate that the combined method is better in discovering similar activities than the base framework.

Thesis (M. Tech. (Environmental health: Food safety )) - Central university of Technology, Free State, 2013
Food processing plants and agricultural environments have a long-standing history of being known to provide a conducive environment for the prevalence and distribution of microorganisms which emanate as a consequence of activities undertaken in such premises. Microorganisms in the aforementioned environments may be found in the atmosphere (airborne), and/or on food contact surfaces. Airborne microorganisms from food handlers and in food products and raw materials (as part of bioaerosols) have in the past been implicated as having a potential to cause adverse health effects (especially in indoor environments) and therefore also to have economic implications. Recently their effect on food safety has received increased interest. The recent international interest in bioaerosols in the food industry has played a role in rapidly providing increased understanding of bioaerosols and their effects in different food processing environments. However, there is still a lack of research on the actual impact of bioaerosols over time in most of the food premises especially in Southern Africa and other developing countries. The overall purpose of this dissertation was to assess possible microbial contaminants and the role of selected environmental parameters on these microbes at a dairy farm plant in central South Africa. In relation to the purpose of the study, the objectives of this dissertation were to investigate and establish the food handler’s food safety knowledge, attitude, behaviour and practices. The sub-objective was to investigate the prevalence and distribution of microbial contaminants (both airborne and food contact surface populations), and concomitant environmental parameters. The microbe isolates from both investigations (i.e. air samples and food contact surfaces) were identified to strain level using matrix-assisted laser desorption ionization – time of flight mass spectrometry (MALDI-TOF MS). The findings of this study in relation to food handlers’ food safety knowledge, attitude, behaviour and practices indicated a dire need for training of employees as well as improved health and hygiene measures as emphasised by some of the identified strains. The environmental parameters (both indoor and outdoor) were similar, with no relationship established between airborne microbes’ prevalence and environmental parameters. The samples of the airborne microbial populations in both indoor and outdoor environments were similar. Airborne microbial counts at the dairy farm plant over the entire duration of the study ranged between 1.50 x 101cfu.m-3and 1.62 x 102cfu.m-3. Microbial counts on food contact surfaces ranged between 2.50 x 102 cfu.cm-2 and 1.10 x 105 cfu.cm-2 over the entire duration of the study. A wide variety of microorganisms (from air and food contact surfaces) such as the Gram-positive bacteria, Gram-negative bacteria, as well as fungi were present at the dairy farm plant. A number of the isolated genera have previously been associated with agricultural environments whilst others are associated with hospital environments. The positively identified strains were from genera such as Aeromonas, Arthrobacter, Candida, Pseudomonas, Pantoea, Citrobacter, Staphylococcus, Bacillus, Escherichia, Rhodococcus and Rhodotorula, amongst others. The isolation of microorganisms associated with food spoilage and foodborne disease outbreaks, which are known as indicator organisms such as Escherichia coli, Staphylococcus and Bacillus from both air and surface samples, signified possible faecal contamination and could be attributed to poor health and hygiene practices at the dairy farm plant. Despite the isolation of microorganisms associated with food spoilage and foodborne disease outbreaks, the isolation of microorganisms not usually associated with the food processing industry (usually associated with hospital environments) was an enormous and serious concern which suggested a need for further investigations at dairy farm plants as the implications of these pathogenic microorganisms in food is not known. The isolation of similar microorganisms from both the air samples and surface swabs suggests that airborne microbes have a potential of settling on food contact surfaces, therefore having a potential to contaminate dairy products which are known to be more prone to contamination and which, because of their nutritional status, serve as a good substrate for the growth of microorganisms.

Dairy processing waste (DPW) can cause many environmental problems if not treated well. Various wastewater treatment technologies have been applied to reduce the organics and inorganics in DPW. The overall objective of this research was to develop cost effective anaerobic digestion technology for hydrogen and methane production from DPW. This search included three phases of studies. In phase 1, we investigated continuous fermentations of algae, lawn grass clippings and DPW, commingled and digested in duplicate 60 L and 3,800 L Induced Bed Reactor (IBR) anaerobic digesters at mesophilic conditions in trials that went for about two years. The goal was to commingle municipal waste in such a way that no pH control chemicals would be required. The research also yielded information about solids loading rate (SLR), efficiency of chemical oxygen demand (COD) and solids removal and biogas production. Under the conditions of the study, commingling algae or grass with DPW made it possible to avoid the addition of pH control chemicals. In phase 2, we investigated the effects of pH, temperature, and hydraulic retention time (HRT) and organic loading rate (OLR) on hydrogen production from DPW in semicontinuous 60 L pilot IBR. Results show pH played a key role on hydrogen production and the optimal pH range was 4.8-5.5. Digestion under thermophilic temperatures (60 °C) had advantages of gaining higher hydrogen yield and suppressing the growth of methanogens. The optimal OLR was 32.9 g-COD/l-d at HRT of 3 days. Under optimal conditions, highest hydrogen yield was 160.7 ml/g-COD removed with 44.6% COD removal. In phase 3, a mathematic model was built and implemented in R based on Anaerobic Digestion Model No. 1 (ADM1) for predicting and describing the anaerobic hydrogen production process. The modified ADM1 was then validated by comparing the predictions with observations of anaerobic hydrogen production from dairy processing waste. The model successfully predicted hydrogen production, hydrogen content, methane content, VFA concentration, and digestion system stability. This study provides a useful mathematical model to investigate anaerobic hydrogen production process and stability.

Daily time series-based models are required to estimate the higher frequency fluctuations of nutrient loads and concentrations. Some mechanistic mathematical models can provide daily time series outputs of nutrient concentrations but it is difficult to incorporate non-numerical data, such as management scenarios, to mechanistic mathematical models. Bayesian networks (BNs) were designed to accept and process inputs of varied types of both numerical and non-numerical inputs. A Rank-Data distribution method (R-D method) was developed to provide large time series of daily predicted flows and Total Phosphorus (TP) loads to BNs driving daily time series estimates of T-P concentrations into Hyrum and Cutler Reservoirs, Cache County, Utah. Time series of water resources data may consist of data distributions and time series of the ranks of the data at the measurement times. The R-D method estimates the data distribution by interpolating cumulative failure probability (CFPs) plots of observations. This method also estimates cumulative failure probability of predictions on dates with no data by interpolating CFP time series of observations. The R-D method estimates time series of mean daily flows with less residual between predicted flows and observed flows than interpolation of observed flows using data sets sampled randomly at varying frequencies. Two Bayesian Networks, BN 1 (Bayesian Network above Hyrum Reservoir) and BN 2 (Bayesian Network below Hyrum Reservoir) were used to simulate the effect of the Little Bear River Conservation Project (LBRCP) and exogenous variables on water quality to explore the causes of an observed reduction in Total Phosphorus (TP) concentration since 1990 at the mouth of the Little Bear River. A BN provided the fine data distribution of flows and T-P loads under scenarios of conservation practices or exogenous variables using daily flows and TP loads estimated by R-D method. When these BN outputs were connected with the rank time series estimated by interpolation of the ranks of existing observations at measurement dates, time series estimation of TP concentrations into Cutler Reservoir under two different conservation practice options was obtained. This time series showed duration and starting time of water quality criterion violation. The TMDL processes were executed based on daily TP loads from R-D instead of mean or median values.