Escherichia coli (E. coli) are common and typically innocuous copiotrophic bacteria found in the mammalian gut microbiome. However, over the past 30 years, pathogenic E. coli have been responsible for several outbreaks of foodborne illness linked to contaminated produce. The introduction of Escherichia coli to an agricultural soil, via contaminated water, compost, or raw manure, exposes the bacterium to a medley of ecological forces not found in a mammalian gut environment. This study assesses a variety of abiotic and biotic soil factors that influence the ability of an "invasive" copiotrophic coliform bacterium to survive in compost-amended agricultural soil. The study included both field and laboratory components. In the lab experiment, a cocktail of rifampicin-resistant generic E.coli strains was added to sterile and non-sterile extracts of eight different composts and one soil sample from the field sites. E. coli abundance was monitored over a one-week period and composts were analyzed for their nutrient profile. In the field experiment, the same E. coli cocktail was sprayed on plots with the following treatments: 1) dairy windrow compost, 2) dairy vermicompost, 3) poultry windrow compost, or 4) no compost. E. coli abundance, soil water potential, soil temperature, extracellular enzyme activity, microbial respiration, phospholipid fatty acid biomarker abundance, and genetic sequencing of the microbial community were measured over a six-month field season. The lab experiment showed that E. coli were able to grow well in sterile compost extracts, without microbial competition for nutrients. Conversely, E. coli populations were only able to survive in non-sterile soil extracts. These results suggest that copiotrophic organisms adapted for high-nutrient environments may depend on the extracellular enzyme activity of native oligotrophic organisms to acquire sufficient nutrients to survive in soils. Results of the field experiment showed clear and interdependent effects of soil moisture and nutrient availability on microbial community dynamics and E. coli survival. Data suggest that saturated soils cause a decrease in microbial extracellular enzyme activity, and drying-rewetting cycles can cause respiration bursts, nutrient mineralization, and shifts in community composition. The saturation of soils, which mobilizes nutrients and may result in a decrease in competition from aerobic organisms, correlated directly with increased survival of E. coli. Additionally, amendment with ammonium-rich poultry compost resulted in the maintenance of high levels of E. coli throughout the field season. Despite an increase in microbial biomass from dairy vermicompost amendment, poultry compost was the only compost that had a significant effect on E. coli survival. The results suggest that nitrogen availability and water potential are strong drivers of E. coli's survival in soils. Correlations among abiotic factors, community composition, and E. coli survival reveal insights into the complex relationships that occur in disturbed agricultural soil environments. Further research on E. coli's response to targeted organisms, abiotic soil properties, and nutrient inputs could have implications for agricultural considerations in food safety and microbial ecology.

Submitted by (lucia.rodrigues@ufrpe.br) on 2017-02-21T12:45:37Z No. of bitstreams: 1 Arlinda Pereira Eloy.pdf: 539902 bytes, checksum: b58cec9ba237d600ff69b073b4bcf24c (MD5) / Made available in DSpace on 2017-02-21T12:45:37Z (GMT). No. of bitstreams: 1 Arlinda Pereira Eloy.pdf: 539902 bytes, checksum: b58cec9ba237d600ff69b073b4bcf24c (MD5) Previous issue date: 2003-03-14 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The Fusarium wilt, caused by Fusarium oxysporum f. sp. tracheiphilum, reduces cowpea yield in Northeastern Brazil. This work aimed to characterize the nature and ability to transfer cowpea Fusarium wilt suppressiveness of a soil; to analyze populational dynamic of F. oxysporum f. sp. tracheiphilum and others soilborne microorganisms in two soils with different levels of suppressiveness, as well as to determine the relation of disease severity and the reductions of yield in cowpea seeds, in two plant seasons. In the nature and transfer of suppressiveness analyses the two soils samples used were previously classified as suppressive (CAC) and conducive (GOI) to cowpea Fusarium wilt, and did not slown indigenous populations of Fusarium oxysporum. When the samples were infested with the pathogen and sown with BR 17 Gurguéia (highly susceptible) and IPA 206 (moderately susceptible) cowpea cultivars, total populations of both fungi and bacteria, and Bacillus spp. were higherin rhizosphere of the suppressive soil samples than in the conducive ones. The suppressiveness was not related to a suppressive effect on the pathogen population. Soil sterilization did not change the suppressive capability, pointing out its abiotic origin. The ability suppressiveness transfer to a conducive soil was demonstrated only. In the suppressive soil, a significant influence of pH levels on Fusarium wilt severity was verified, which decreased in increasing pH. The inoculum density alone did not determine the severity of Fusarium wilt on plants cultivated in both soils, due to the influence of the efficiency of the inoculum, which was significantly lower in the suppressive soil. Aiming to determine the linkage of disease severity to the reduction of cowpea seed yield, cultivated during two different period of time, an essay was carried out using plots artificially infested with the pathogen. The first planting was made in April 2002, while the second one in October, in thesame year. At the harvest, yield for each plot was determined through the total weight of seed per plant. After harvesting the severity of Fusarium wilt was evaluated in all plants. There was no significant correlation between inoculum densities of the pathogen that was present in the soil before planting and the disease severity. The yield in the first planting period was higher than in the second one, in non-infested plots, what may have been due to the water stress to which the plants were submitted right before the blossom.Differences between the severity average levels and yield losses were not verified for both essays. Fusarium wilt severity ranged between 3.2 and 93.3%, while the yield losses ranged between 2.2 and 98.1%. / A murcha-de-fusário, causada por Fusarium oxysporum f. sp. tracheiphilum, é responsável por grandes reduções de rendimento na cultura do caupi no Nordeste brasileiro. O trabalho teve como objetivos caracterizar a natureza e a capacidade de transferência de supressividade de um solo à murcha-de-fusário do caupi, analisar a dinâmica populacional de F. oxysporum f. sp tracheiphilum e outros microrganismos em dois solos com diferentes níveis de supressividade, bem como determinar a relação entre a severidade da doença e as reduções no rendimento de sementes de caupi em duas épocas de cultivo. Na análise da natureza e transferência da supressividade foram utilizadas amostras de dois solos, classificados previamente como supressivo (CAC) e conducivo (GOI) à murcha-de-fusário do caupi, nos quais não foram detectadas populações autóctones de F. oxysporum. Quando os solos foram infestados com o patógeno e semeados com as cultivares de caupi BR 17Gurguéia (altamente suscetível) e IPA 206 (moderadamente suscetível), as populações de fungos totais, bactérias totais e Bacillus spp. foram maiores na rizosfera no solo supressivo que no conducivo. A supressividade à doença não foi relacionada com um efeito supressivo sobre a população do patógeno. A esterilização não alterou a capacidade supressiva do solo, indicando sua natureza abiótica, bem como foi comprovada a capacidade de transferência da supressividade para o solo conducivo. Somente no solo supressivo foi constatada influência significativa dos níveis de pH na severidade da murcha-de-fusário, que decresceu proporcionalmente à elevação do pH. A eficiência do inóculo do patógeno foi significativamente inferior no solo supressivo. A análise da relação entre a severidade da doença e as reduções no rendimento de sementes de caupi cultivado em duas épocas, foiconduzida em parcelas artificialmente infestadas com o patógeno, em dois períodos de cultivo, sendo o primeiro plantio realizado em abril de 2002 e o segundo em outubro do mesmo ano. Na fase de colheita de cada época de plantio, foi determinado o rendimento por parcela, representado pelo peso total de sementes por planta. Após a colheita, a severidade da murcha-de-fusário foi avaliada em todas as plantas. Não foram constatadas correlações significativas entre as densidades de inóculo do patógeno detectadas nas parcelas antes do plantio e os níveis de severidade da doença. Nas parcelas não infestadas pelo patógeno, o rendimento no primeiro plantio foi superior ao do segundo plantio, o que pode ter sido conseqüência do estresse hídrico a que as plantas foram submetidas na fase de pré-floração. As reduções no rendimento de sementes foram influenciadas significativamente pelos níveis de severidade da doença. Não foram constatadas diferenças entre os níveis médios de severidade da doença e de perdas de rendimento nos dois períodos de cultivo. A severidade da murcha-de-fusário variou entre 3,2 e 93,3%, enquanto as perdas de rendimento entre 2,2 e 98,1%.

No description available.

No description available.

This dissertation examined recently issued regulatory standards using cheese and produce as model systems. FDA's 2015 Domestic and Imported Cheese and Cheese Products Compliance Program Guidelines (CPG) E. coli standards on cheese safety, and the extent to which these standards affect domestic and imported cheese commerce, was assessed. Results from FDA's Domestic and Imported Cheese Compliance Program for samples collected between January 1, 2004 and December 31, 2006 were analyzed. Of 3,007 cheese samples tested for non-toxigenic E. coli, 76% (2,300) of samples exceeded 10/g, FDA's target for regulatory activity. In cheese samples containing E. coli levels of 10/g and 100/g, there was no statistically significant association with presence of Listeria monocytogenes. However, associations between Staphylococcus aureus levels of 10,000 CFU/g and presence of Salmonella and L. monocytogenes were statistically significant, indicating that EU regulations targeting S. aureus as the pathogen of concern may be more appropriate than E. coli for cheese safety assessment. Compost amended soils in the Northeastern U.S. were assessed for the presence and survival of E. coli and Listeria spp. against FDA Food Safety Modernization Act (FSMA) requirements. Manure and poultry litter-based biological soil amendments of animal origin (BSAAO) must achieve pathogen reduction to reduce risk of pathogen contamination on the harvested produce. Two trials of replicated field plots of loamy (L) or sandy (S) soils were tilled and un-amended (NC) or amended with dairy compost (DC), poultry litter compost (PL), or poultry pellets (PP). Colony count and most probable number (MPN) methods were used to determine persistence of E. coli in these plots over 104 days post-inoculation. Detection of indigenous Listeria spp. were also examined in all plots. Higher E. coli populations were observed in PL and PP amended soils when compared to DC and NC plots. E. coli was detected at low levels on radish crops, where PL treatments encouraged greater levels of survival and growth than DC or NC. Study results verify that a 120 day interval following BSAAO application should be sufficient to ensure food safety of edible crops subsequently planted on these soils. The sensitivity of environmental monitoring methods and collection formats were evaluated to identify optimal procedures for detection of Listeria spp. on product contact surfaces within artisan cheese production environments. Four environmental surfaces (dairy brick, stainless steel, plastic, and wood; n=405/surface type) were inoculated with L. innocua, L.m. ATTC® 19115 and L.m. 1042, at high (106-107/cm2) and low (0.1-1/cm2) target concentrations. Inoculated surfaces were swabbed with World Bioproducts© EZ ReachTM and 3MTM environmental swabs (3MTM). Five enrichment and enumeration methods were used to compare sensitivity of recovery between environmental swabs. All swab formats performed equally on all environmental surfaces at high target concentrations. At low concentrations, PetrifilmTM and WBEZ swabs recovered Listeria spp. from 87.5% of plastic, stainless steel, and dairy brick surfaces, but only 62.7% of wooden surfaces; recovering 14.8%, 77%, and 96.3% of cells from initial inoculations of 0.01, 0.1, and 1/cm2, respectively . Our data demonstrate that results may be discrepant due to variation in the porosity of environmental surfaces and should be taken into consideration when implementing environmental sampling plans. Results from this thesis can be used to inform regulatory policy and help to achieve improved food safety.

"September 2001" Includes bibliographical references (leaves 206-230)

"September 2001" / Includes bibliographical references (leaves 206-230) / xviii, 230 leaves : ill., plates ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Agronomy and Farming Systems, 2002

The effect of land management including undisturbed native forest, native grassland, sugarcane (preharvest burnt or green cane harvested), exotic forest (gum, pine or wattle), orchard crops (banana, orange and avocado) and grazed kikuyu grass pastures on soil organic matter status, size of the microbial biomass and size and composition of the earthworm community was studied. The study locality was in the tropical, northern part of KwaZulu-Natal near the town of Eshowe and sites were on a number of sugar estates in the area. Concentrations of soil organic C were notably high under kikuyu pasture, native forest and banana and lowest under burnt cane. Among the land uses, values followed the order: kikuyu pasture ≥ native forest > banana > native grassland = orange ≥ trashed cane = gum ≥ pine ≥ avocado > wattle ≥ burnt cane. Soluble C was considerably higher under kikuyu pasture than other land uses. Soils under native forest and banana also had relatively high values while lowest values were recorded under burnt cane. Values for microbial biomass C showed broadly similar trends with land use to soluble C. Very high values for microbial biomass C (> 2000 mg kg⁻¹ ) and microbial quotient (> 4.5 %) were recorded under kikuyu pasture, native forest, banana and orange whilst lowest values for microbial biomass C ( 250 - 750 mg kg⁻¹ ) and microbial quotient (1- 2 %) were found for soils under avocado, trashed and burnt sugarcane. Earthworm numbers followed the order: kikuyu pasture > native forest > banana > orange > wattle = pine = gum = trashed sugarcane ≥ native grassland ⁻¹ avocado > burnt sugarcane. Values for earthworm numbers and biomass were closely correlated. Earthworm numbers, microbial biomass C and soluble C were closely correlated with each other but none were significantly correlated with soil organic C content. Earthworm numbers were also positively correlated with soil pH and exchangeable Ca content. A total of 11 species of earthworm were collected from the sample sites. Over 80 % of the individuals collected were accidentally-introduced exotic species which originated from India, South America and West Africa. Most land uses supported between 5 and 7 species. Wattle forest and sugarcane, however, had only 2 or 3 species. Juveniles dominated the community under all land uses except kikuyu pasture and avocado where the majority of earthworms were adults. Epigeic species dominated the community under native forest and native grassland and this was also the case under avocado and gum. For the other land uses endogeic species predominated. The most numerous earthworm species present was Pontoscolex coreththrurus which was present under all the land uses. It is a peregrine, endogeic species originating from South America and is thought to have been introduced via India. The most common epigeic species was the Indian species Amynthas rodericensis which made up a particularly notable portion of the community under native and gum forests, avocado and banana. The third most numerous species was A. minimus, also from India, which is a polyhumic, endogeic species. It was particularly numerous under kikuyu pasture. In 8 out of 11 land uses, P. corethrurus, A. rodericensis and A. minimus coexisted together. Another polyhumic, endogeic species, Dichogastersaliens, which originates from West Africa, was present particularly under oranges, wattle and sugarcane. The only land use that contained mainly native species was native grassland where Tritogenia douglasi and Acanthodrilidae sp predominated. It was concluded that organic matter content, microbial biomass C, soluble C and the size and composition of earthworm communities in soils of the study area are greatly affected by land management practice. As is the case in most other parts of the world, the earthworm community under agricultural land management is dominated by accidentally introduced exotic species and these have also emigrated into soils under native vegetation; The role of these species in influencing soil chemical, physical and microbial properties, and thus soil fertility, deserves further studying. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2002.

The effects of increasing periods under sugarcane monoculture (managed by preharvest burning) on soil organic matter content and related soil properties were investigated in the 0 to 10 cm layer of a sandy coastal Ochric Cambisol (Glenrosa soils) and a red Rhodic Ferralsol (Hutton soil) from the sugar belt of KwaZulu-Natal. The organic C content at both sites under undisturbed vegetation is about 48 g C kg-I. This declined exponentially with increasing years under sugarcane. For the Glenrosa site, organic C reached a new equilibrium level of about 20 g kg-I while at the Hutton soil the equivalent value was 41 g kg-I. The higher organic matter content maintained at the Hutton site was attributed mainly to clay protection of organic matter since the clay content of the Hutton soil was 61 % compared to the 18 % for the Glenrosa soil. The loss of soil organic matter under sugarcane resulted in a concomitant decline in soil microbial biomass C, microbial quotient, basal respiration, aggregate stability, arylsulphatase and acid phosphatase activity. The activities of arylsulphatase and acid phosphatase like those for concentrations of microbial biomass and organic C, were higher for the Hutton than Glenrosa soils. At the Glenrosa site, the natural OBC abundance in soils was used to calculate the loss offorest-derived, native soil C and the concomitant input of sugarcane-derived C. Sugarcane-derived C increased over time until it accounted for about 61 % of organic C in the surface 10 cm in soils that had been under sugarcane for greater than 50 years. The effects of agricultural land use (including burnt sugarcane) on organic matter content and related soil properties were compared with those under undisturbed native grassland in KwaZulu-Natal. Two separate farms situated on Oxisols were used and both contained fields with continuous long-term (>20 years) cropping histories. At site 1, soil organic C content in the surface 10 cm followed the order permanent kikuyu pasture> annual ryegrass pasture> native grassland> preharvest burnt sugarcane > maize under conventional tillage (CT). At site 2, organic C in the surface 20 cm decreased in the general order kikuyu pasture> native grassland > annual ryegrass pasture> maize under zero tillage (ZT) ~ maize (CT). Organic C, microbial biomass C, microbial quotient, basal respiration and aggregate stability were substantially greater in the surface 5 cm under maize ZT than maize CT. In the undisturbed sites (eg native grassland and kikuyu pasture) the metabolic quotient increased with depth. By contrast under maize CT and sugarcane there was no significant stratification of organic C, yet there was a sharp decrease in metabolic quotient with depth. Aggregate stability was high under both native grassland and kikuyu pasture and it remained high to 40 cm depth under the deep-rooted kikuyu pasture. Although soil organic C was similar under maize CT and sugarcane, values for microbial biomass C, microbial quotient, basal respiration and aggregate stability were lower, and those for metabolic quotient and bulk density were higher, under sugarcane. This was attributed to the fallow nature of the soil in the interrows of sugarcane fields. It was concluded that the loss of soil organic matter, microbial activity and aggregate stability is potentially problematic under maize CT and sugarcane and measures to improve organic matter status should be considered. For sugarcane, this could include green cane harvesting and the use of green manure crops in rotation. / Thesis (M.Sc.)- University of Natal, Pietermaritzburg, 2002.

Green roof design has proceeded without integration of arbuscular mycorrhizal fungi (AMF). A literature survey was therefore conducted in order to determine which aspects of green roof functioning might be enhanced by AMF, and subsequently levels of AMF and endophyte colonization were determined for seven plant species used in green roofs. Plants were sampled from an experimental green roof and from the field. A commercial growing medium was also tested for AMF inoculum potential. Colonization was poor in both field and rooftop samples of the commercially popular succulent, Sedum acre, but significantly higher in Solidago bicolor, a proposed green roof species. The commercial growing medium was found to contain extremely low levels of viable AMF propagules. Although the apparent lack of mycorrhizal dependency of S. acre helps to explain its popularity as a green roof plant, its overuse precludes the important ecosystem services potentially provided by AMF symbioses.