Agricultural soils in Nova Scotia are usually limed in order to raise soil pH to ensure optimum availability of soil nutrients. Wood ash, produced by burning wood-based fuels, is promoted as a substitute for agricultural lime. This study individually assessed two wood ash sources available to Nova Scotia producers through on-farm sampling as well as greenhouse bioassay and incubation experiments. The variables measured were soil pH, plant-available and total element concentrations in soil, total element concentrations in above ground plant tissue, botanical composition and pasture condition scores (PCS). Soil pH was significantly increased after the application of wood ashes, however the effect was short-lived for one ash (NewPage). Agricultural lime was the most effective at increasing pH. Total soil concentrations of Al, Cr, K and Na remained elevated one year after ash application to NewPage sites. Brooklyn Power ash contained excessive levels of Zn, Cd, Pb and As.

Manure is a commonly used soil fertilizer, but there are concerns that this practice could affect the spread of antibiotic resistance genes (ARGs) from farm to fork. A microcosm-scale study evaluated the effect of prior antibiotic use (manure-based soil amendments generated from dairy and beef cattle with or without antibiotic administration), composting, and soil type on the quantity of ARGs and the microbial community composition of dairy and beef manure applied soil. ARGs were analyzed through novel metagenomic techniques and quantitative polymerase chain reaction of sul1, tet(W), and 16S rRNA gene, while the microbial community composition was determined via 16S rRNA amplicon sequencing. The results indicated that while prior antibiotic administration elevated the relative abundance of ARGs and changed the microbial community of raw manure applied soils, composting reduced this effect. However, compost applied soils still had a higher relative abundance of ARGs than the unamended soils and occasionally soil applied with raw manure of untreated cattle. Soil type may be a mediating factor as there were differences observed between the three soil types (sandy loam, silty clay loam, and silty loam) with sandy loam amended soils often having the least attenuation of ARGs. As the relative abundance of ARGs was still elevated and the microbial community composition still significantly different from the unamended soils after 120 days, these results suggest that 120 days is not a long enough waiting period between biological soil amendments and crop harvest for ARG dissipation. / Master of Science / Antibiotics are lifesaving drugs that kill infection-causing bacteria. However, bacteria are living organisms and can adapt to stresses, such as antibiotics. When antibiotics are used, not all of the targeted bacteria are necessarily killed, and populations of resistant bacteria can survive. Resistant bacteria can not only continue to grow, but can also share their resistance capabilities with other unrelated bacteria through the transfer of antibiotic resistance genes (ARGs). ARGs are segments of DNA encoding mechanisms for the bacteria to survive antibiotic attack, such as pumping antibiotics outside of the cell or strengthening the cell wall so antibiotics cannot enter. The transfer of ARGs to human pathogens is of utmost concern, as it can cause once treatable diseases to turn deadly. Antibiotics are thus a double-edged sword because they can save lives on one hand, while their overuse or misuse can undermine their effectiveness by increasing antibiotic resistance. In the U.S. and many other countries, the biggest user of antibiotics is the livestock industry. Thus, there is growing interest in possible routes by which antibiotic resistance can spread from agriculture to humans. While some previous work has been done on direct contact with animals and meat products, less attention has been paid to the potential role raw produce grown in soils fertilized with manure-based amendments. This study thus sought to determine which factors impact ARG levels in soil. Questions of interest included: What is the effect of composting raw manure prior to soil application? Does prior treatment of cattle with antibiotics matter? Does the soil type influence the levels of ARGs? Do the ARG composition and microbial community composition respond similarly to such factors? These and other questions were evaluated in a controlled environment by simulating amended field conditions in small glass jars (microcosms) containing mixtures of different soils and manure-based amendments. Three different soils were amended with one of the following manure-based amendments: raw manure from antibiotic administered cattle, composted manure of antibiotic administered cattle, raw manure from cattle not given antibiotics, composted manure of untreated cattle, and no amendment. This experimental setup was done in duplicate, one for treatments from dairy cows and one for the beef steer treatments. The experiment lasted 120 days, as that is a current standard for how long organic farmers must wait between manure application and crop harvest. Samples were taken throughout the 120-day experiment, and the quantity of targeted ARGs was determined by analyzing the DNA through qPCR, while the overall ARG profile was studied using a new tool, called metagenomics. To identify the kinds of bacteria present in the samples (microbial community composition), the 16S rRNA gene, which is a universal gene in organisms, was targeted and sequenced via amplicon sequencing. The results of these analyses indicated that administering antibiotics to cattle and then subsequently amending soil with their manure was associated with the highest levels of ARGs compared to the other treatments, but composting reduced the effect of prior antibiotic use. Depending on the ARG, composting decreased ARG levels relative to the other treatments, but in some instances, it increased ARGs compared to soils with raw manure of untreated cattle. Even after composting, there were still higher levels of ARGs in the soil than unamended soils. Different soil types did react differently to the amendments, but more research is needed. All of the treatments resulted in different changes to the microbial community composition and did not return to the unamended soil’s community structure even after 120 days. Overall, based on these results, ARGs and the microbial community do not return to the initial condition within 120 days, which is a recommended wait time between amendment and harvest, while composting and soil type appear to be mediating factors. Additional research is needed to further advance understanding of potential mitigation options and to benchmark them to defined and measureable risk endpoints.

For sustained production, organic agriculture depends on plant needs being synchronized with the release of nutrients from organic amendments during decomposition within the soil. Because decomposition is strongly dependent on soil moisture and temperature, nutrient needs may not always be met as planned or synchronous with plant need. Unlike conventional agriculture, fast acting amendments are not readily available. Much of the evidence that vermicompost benefits crop production comes from studies on seed germination and production of starts in greenhouses. Yet, there is a dearth of information derived from field studies. Soil, soil and water nitrogen, plant development, and marketable yield were investigated by implementing field plot trials with both starts grown in greenhouses (Experiment 1) and directly seeded (Experiment 2) crops to test hypotheses on fertility, economics and environmental impacts. Results from Experiment 1 showed that plant production was dramatically increased both in the greenhouse as well as subsequently in the field for vermicompost treatments and directly correlates to economic differences. Results from Experiment 2 show that plant production differences between compost treatments vary by site. There was no significant difference in soil and soil water NO3-N, NH4-N and Total Inorganic Nitrogen (TIN) among treatments, site or experiment. The timely rate of plant development in greenhouse started VC treatments shows great potential to be the first to market with fresh produce when other treatments are still waiting to transplant.

Adsorption kinetics and adsorption-desorption of atrazine on organoclay composites prepared with the surfactant 6-piperazin-1-yl-N,N'-bis-(1,1,3,3-tetramethyl-butyl)-(1,3,5)triazine-2,4-diamine and Houston Black clay were studied using the indirect batch equilibration procedure. The organoclay composites sorbed significantly more atrazine than the Houston Black clay. Adsorption equilibrium was reached after 72 h for the organoclay composites. Atrazine adsorption isotherms were described by linear partitioning. The Koc values ranged from 605 to 5271 L kg-1 for the organoclay composites compared to a value of 41 L kg-1 for the Houston Black clay. The organoclay composite containing 20% surfactant on a total weight basis provided the most efficient adsorption of atrazine, although organoclay composites containing much lower amounts of surfactant also adsorbed significant amounts of atrazine. An average of 11% of sorbed atrazine was released during desorption. Characterization of desorption products showed only atrazine molecules being released from the organoclay composites.

Adsorption kinetics and adsorption-desorption of atrazine on organoclay composites prepared with the surfactant 6-piperazin-1-yl-N,N'-bis-(1,1,3,3-tetramethyl-butyl)-(1,3,5)triazine-2,4-diamine and Houston Black clay were studied using the indirect batch equilibration procedure. The organoclay composites sorbed significantly more atrazine than the Houston Black clay. Adsorption equilibrium was reached after 72 h for the organoclay composites. Atrazine adsorption isotherms were described by linear partitioning. The Koc values ranged from 605 to 5271 L kg-1 for the organoclay composites compared to a value of 41 L kg-1 for the Houston Black clay. The organoclay composite containing 20% surfactant on a total weight basis provided the most efficient adsorption of atrazine, although organoclay composites containing much lower amounts of surfactant also adsorbed significant amounts of atrazine. An average of 11% of sorbed atrazine was released during desorption. Characterization of desorption products showed only atrazine molecules being released from the organoclay composites.

Salmonella has been shown to survive in soils for extended periods. Anaerobic soil disinfestation (ASD) represents a promising alternative to fumigation used to manage soilborne diseases and pests; however, little is known about ASD's impact on Salmonella. The study aimed to compare Salmonella die-off following inoculation in ASD and non-ASD processed soil and compare Salmonella die-off in amended and non-amended soils following ASD. Two independent experiments were arranged in randomized complete block designs (four replications per treatment). Sandy-loam soil was inoculated with a Salmonella cocktail (5.5±0.2 log CFU/g) and amended with field-applicable rates of rye (R), rapeseed (RS), hairy vetch (HV), or pelletized poultry litter (PPL). Non-amended, anaerobic (ANC) and non-amended, aerobic controls (AC) were performed in parallel. Soils were irrigated to saturation and covered with plastic mulch. ASD was terminated by removal of plastic (3-weeks). Triplicate soil samples were collected pre-ASD and 0, 1, 2, 3, 7, 10, 14, 21, 28, 31, 35, 38 and 42d post-ASD. Post-ASD soil was irrigated weekly. Salmonella was quantified using standard methods and a modified MPN enrichment protocol. Concentrations between treatments and time-points were analyzed for significance (P≤0.05). Separate log-linear models were used to examine effect of amendment and irrigation on Salmonella die-off during ASD and post-ASD. Salmonella concentrations decreased in all treatments during ASD with the greatest decrease being observed in ASD and non-ASD controls. Among ASD-processed, amended soil, the rye and rapeseed amendments had the greatest decrease in Salmonella concentrations. Salmonella concentrations decreased by ~1 log between pre-ASD and post-soil saturation (95% Confidence Interval (CI) =-1.31, -0.99), and by approximately 2 logs between pre-ASD and termination of ASD (CI=-2.14, -1.83). Salmonella concentrations were ~1 log higher in ASD-processed, pelletized poultry litter-amended soil, compared to the ASD control (CI=0.81, 1.26). The average daily die-off rate of Salmonella post-ASD was -0.05 log per g (CI=-0.05, -0.04). Following irrigation, Salmonella concentrations were 0.14 log greater, compared to no irrigation within 7 d (CI=0.05, 0.23). Salmonella serovar distribution differed by treatment, with >70% survival of Newport in pelletized poultry litter. ASD does not eliminate Salmonella concentrations in soil; instead some amendments may enhance Salmonella survival. / Master of Science in Life Sciences / Anaerobic soil disinfestation (ASD) is the process of removing soilborne weeds, soilborne diseases and insect by creating an anaerobic environment in the soil by incorporating easily decomposable soil amendments, covering with plastic mulch, and irrigating to saturation. The anaerobic soil environment persists for two- to six-weeks. ASD represents a promising alternative to fumigation used to manage soil-borne diseases and pests. However, little is known about ASD's impact on Salmonella, which has been shown to survive in soils for extended periods of time and can contaminate the edible part of produce. This study aimed to determine if ASD is an effective strategy to reduce or eliminate Salmonella from soils that contain typical amendments added to promote soil health, determine the distribution of Salmonella serovars in ASD treated soils, and examine the impact of irrigation. Two independent experiments were conducted in growth chambers. A common soil type in produce growing regions of the Eastern Shore of VA, sandy-loam soil was inoculated with a five-serovar Salmonella cocktail (~5.5±0.2 log CFU/g) and mixed with field-applicable rates of rye, rapeseed, hairy vetch, or pelletized poultry litter. ASD processed soils were irrigated to field saturation, covered with plastic mulch, and left for 3 weeks. Post-ASD, soils were irrigated weekly. Salmonella was quantified at least once per week for up to 6 weeks in soil samples collected in triplicate pre-ASD, post-field saturation, and post-ASD. The three-week anaerobic soil environment, created during ASD, allowed for greater Salmonella survival, compared to the aerobic soil environment. Salmonella survival in ASD processed soil was dependent on amendment. Salmonella concentrations decreased in all treatments during ASD with the greatest decrease being observed in ASD and non-ASD controls. Among ASD-processed, amended soil, the rye and rapeseed amendments had the greatest decrease in Salmonella concentrations. Pelletized poultry litter amended soil, in combination with ASD, had the highest Salmonella concentration, while rye had the lowest at each time-point post-ASD. Salmonella serovar distribution differed by treatment with greater survival of S. Poona in rye, S. Braenderup in hairy vetch and S. Newport in pelletized poultry litter. , Salmonella concentrations were 0.14 log greater, compared to no irrigation within 7 d. Overall, ASD did not eliminate Salmonella in soils. Compared to non-ASD processed soil, ASD processed soil had greater survival of Salmonella and the soil amendment used influenced the survival ability. While more research is needed on ASD and different soil amendments, the findings of this research would suggest pelletized poultry litter not be used as an amendment (i.e., carbon source in ASD) for fields used to grow produce eaten raw, especially when soils are potentially contaminated with Salmonella.

Thesis (MScEng)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: According to recent studies, biochar has the potential to improve soil fertility, mitigate climate change, reduce off-site pollution and assist in managing wastes. The application of biochar to soil is not a new concept; Amazonian dark earths are carbon-rich soils with high soil fertility that were created before 1541. Vacuum pyrolysis is a thermo-chemical conversion technique in which biomass is transformed into bio-oil, biochar and non-condensable gas. The objective of this work was to investigate the chemical and physical properties of biochar produced from vacuum pyrolysis of black wattle, vineyard annual prunings and sugar cane bagasse for their potential as soil amendment and adsorbent. The vacuum pyrolysis of black wattle, vineyard prunings and sugar cane bagasse (pyrolysis temperature: 460°C, pressure: 8kPaabs, heating rate: 17°C/min) resulted in biochar yields of 23.5%, 31.0% and 19.7% on a weight basis, respectively. The nature of the biomass had a substantial effect on yields of the products. High ash content combined with high lignin composition led to higher biochar yields for vineyard prunings. The highest surface acidity was observed for sugar cane bagasse (2.3 mmol/g), whereas the lowest surface acidity was observed for vineyard biochar (1.67 mmol/g). Consequently, the pH of the biochars was in the order: vineyard (10.43)> black wattle (9.74)> sugar cane bagasse (6.56). The cation exchange capacities (CEC) of biochars were 122 cmol/kg, 101 cmol/kg and 65 cmol/kg for sugar cane bagasse, black wattle and vineyard, respectively. The electrical conductivities (EC) were highly correlated with feedstock nature. The Ca and K rich vineyard biochar resulted in the highest EC (0.83 dS/m), whilst EC values of black wattle and sugar cane bagasse were 0.67 dS/m and 0.17 dS/m, respectively. Biochars contained substantial amounts of plant-available nutrients, while being low in toxic inorganic content (Pb, As, Cd). The BET surface areas of sugar cane bagasse, black wattle and vineyard were 259 mª/g, 241 mª/g and 91 mª/g, respectively. The adsorption capacity was found to increase with increased contact time and initial solution concentration. The experimental equilibrium time were found to be 3505 min, 1350 min and 150 min for adsorption of 20 mg/L methylene blue solution for vineyard, black wattle and sugar cane bagasse, respectively. Equilibrium data were well fitted to Langmuir and Freundlich isotherms. The maximum adsorption capacities were found to be 15.15 mg/g, 14.49 mg/g and 19.23 mg/g for vineyard, black wattle and sugar cane bagasse when modelled with Langmuir isotherms. The adsorption kinetics was found to follow the pseudo-second order kinetic model. In summary, biochar from sugar cane bagasse is a promising adsorbent for the removal of basic dyes due to its high surface area and microporous structure. This biochar can be applied to slightly acidic soils for nutrient retention and the exchange of nutrients. On the other hand, possessing high amounts of nutrients, biochars from black wattle and vineyard are potential soil amendentment agents. Biochar from black wattle is more beneficial compared to biochar from vineyard due to its higher surface area, microporosity and cation exchange capacity. / AFRIKAANSE OPSOMMING: Volgens onlangse studies, het houtskool die potensiaal om grond vrugbaarheid te verbeter, klimaat verandering te versag, besoedeling te verlaag en ondersteuning te verleen in die bestuur van afval. Die toevoeging van houtskool in grond is nie ‘n nuwe konsep nie; Amazone donker gronde is koolstof ryk gronde met hoë vrugbaarheid wat voor 1541 geskep is. Vakuum pirolise is ‘n termo-chemiese omskakelings tegniek waarin biomassa afgebreek word na bio-olie, houtskool en nie-kondenseerbare gasse. Die doelwit van hierdie werk was om die chemiese en fisiese eienskappe van houtskool, wat geproduseer is deur die vakuum pirolise van swart wattel, jaarlikse wingerd snoeisels, en suikerriet bagasse, vir hulle potensiaal vir grond verbetering en adsorpsie toepassings te ondersoek. Die vakuum pirolise van swart wattel, jaarlikse wingerd snoeisels, en suikerriet bagasse (pirolise temperatuur: 460°C, druk: 8kPaabs, verhittingstempo: 17°C/min) het houtskool opbrengste van 23.5%, 31.0% en 19.7% op massa basis, respektiewelik tot gevolg. Die tipe biomassa het ‘n beduidende effek op die opbrengs van die produkte. Hoë as-inhoud, gekombineer met hoë lignien inhoud, lei tot hoër houtskool opbrengste vir wingerd snoeisels. Die hoogste oppervlak suurheid is gevind vir suikerriet bagasse (2.3 mmol/g), terwyl die laagste waarde gevind is vir die wingerd snoeisels (1.67 mmol/g). Gevolglik, is die pH van die houtskole in die volgorde van: wingerd (10.43) > swart wattle (9.74) > suikerriet bagasse (6.56). Die katioon uitruiling vermoë (CEC) van die houtskole was 122 cmol/kg, 101 cmol/kg and 65 cmol/kg vir suikerriet bagasse, swart wattel en wingerd snoeisels respektiewelik. Die elektriese konduktiwiteite (EC) is gekorreleer met die eienskappe van die biomassas. Die Ca en K ryke wingerd snoeisel houtskool het die hoogste EC waarde (0.83 dS/m) tot gevolg, terwyl die EC waardes vir swart wattel en suikerriet bagasse bepaal is as 0.67 dS/ 0.16 dS/m respektiewelik. Die houtskole het groot hoeveelhede plant-beskikbare voedingstowwe bevat, terwyl dit laag was in toksiese anorganiese stowwe (Pb, As, Cd). Die BET oppervlak areas van suikerriet bagasse, swart wattel en wingerd snoeisels was 259 mª/g, 241 mª/g en 91 mª/g respektiewelik. Daar is gevind dat die adsorpsie kapasiteit toeneem met toenemende kontak tyd met die aanvanklike oplossing. Die eksperimentele ewewigs tye is gevind as 350 min, 1350 min en 150 min vir die adsorpsie van ‘n 20 mg/L metileen blou oplossing vir wingerd snoeisels, swart wattel en suikerriet bagasse, respektiewelik. Die ewewigs data het die Langmuir en Freundlich isoterme goed gepas. Die maksimum adsorpsie kapasiteite is gevind as 15.15 mg/g, 14.9 mg/g en 19.23 mg/g vir wingerd snoeisels, swart wattel en suikerriet bagasse wanneer dit gemodeleer is met Langmuir isoterme. Daar is bevind dat die adsorpsie kinetika ‘n pseudo-tweede orde kintika model volg. In opsomming, houtskool van suikerriet bagasse is ‘n veelbelowende adsorpsie middel vir die verwydering van basiese kleurstowwe, as gevolg van die hoë oppervlak area en mikroporie-struktuur van hierdie houtskool. Dié houtskool kan gebruik word op effense suur gronde vir voedingstof behoud en uitruiling. Aan die ander kant, houtskole van swart wattel en wingerd snoeisels wat hoë hoeveelhede voedingsstowwe bevat, is potensiële grond verbeterings middels. Houtskool afkomstig van swart wattel is meer voordelig as die van wingerd snoeisels, as gevolg van die hoër oppervlak area, mikroporositeit en katioon uitruilings vermoë van die swart wattel houtskool.

The effects of sulfur-containing amendments (H₂SO₄,Al₂(SO₄)₃ and gypsum) or crust formation, soil chemical properties, seedling emergence and yields of onions (Allium cepa), tomatoes (Lycopersicum esculentum) and chili peppers (Capsicum sp.) were studied on a Pima clay loam soil. Treatments were surface applied on a strip above the seeds. The chemicals influenced the penetrometer index, soil-pH, electrical conductivity, DPTA-extractable soil Fe, Cu, Zn, Mu and seedling emergence in two greenhouse experiments. Gypsum and H₂SO₄ increased seedling emergence while Al₂(SO₄)₃ reduced the soil-pH and EC more than H₂SO₄ and gypsum. Based upon penetrometer readings, H₂SO₄ was the best anti-crusting agent tested followed by gypsum and Al₂(SO₄)₃. At the end of the study, all soil samples were very low in KCl extractable Al, showing that Al toxicity was not responsible for seedling damage. Gypsum decreased levels of Mn and Zn but did not affect Fe and Cu. Al₂(SO₄)₃ increased Fe and Zn, decreased Cu but did not affect Mn. H₂SO₄ did not affect extractable Mn, Cu, Zn and Fe levels. In a field study using two water qualities at Safford, gypsum produced the most tomato seedlings whereas Al₂(SO₄)₃ and H₂SO₄ produced the least. Onion stand counts were not affected by the chemicals with either water. Gypsum, H₂SO₄ and Al₂(SO₄)₃ polymer produced the highest pepper stand counts with the saltier water but there were no differences with lower salt water. Tomatoes produced the highest yield with gypsum and lowest with H₂SO₄ and Al₂(SO₄)₃ with saltier water. With lower salt water, gypsum produced highest yield, followed by the H₂SO₄. Both H₂SO₄ treatments produce low yields. Onions showed no treatment response under lower salt water, while with saltier water, gypsum and H₂SO₄ produced the highest yields. Pepper yields were not affected by amendments with the lower salt water. Al₂(SO₄)₃ polymer, H₂SO₄ and gypsum increased yields with the saltier water. Varieties of peppers and tomatoes produced different yields in response to water quality in a supplementary field study.

Tree transplanting practices influence plant survival, establishment, and subsequent landscape value. The inability to adequately quantify effects of inappropriate tree planting and transplanting practices threatens long-term viability and productivity (sustainability) of trees within terrestrial ecosystems. Tree planting depth, i.e. location of the root collar relative to soil grade, is of particular concern for tree growth, development, and performance in the landscape. A series of model studies was conducted to investigate effects of planting depth, container production methods, and transplanting practices on landscape establishment of container-grown trees. Studies included determining the effect of planting depth and soil amendments on live oak (Quercus virginiana Mill.) and baldcypress (Taxodium distichum (L.) L. Rich.), the effect of planting depth during container production and subsequent landscape establishment of lacebark elm (Ulmus parvifolia Jacq.), the effect of planting depth and irrigation practices on landscape establishment of sycamore (Platanus occidentalis L.), and the effect of planting depth and transplant season on landscape establishment of baldcypress. Optimum planting depth varied among species and was dependent on cultural practices and/or environmental conditions. Overall, live oak and baldcypress growth was better when planted with root collars at grade in sand in raised beds compared to planting below grade in control soils. Lacebark elm growth was greater when planted at grade during the initial container production phase and below grade in the second container production phase. Subsequent landscape establishment was variable, but planting at grade to 5 cm above grade produced greater growth. Sycamore trees planted below grade had increased mortality and decreased growth compared to trees planted at grade or above grade, while irrigation had no effect. Baldcypress planted above grade had reduced growth compared to those planted at or below grade, while transplant season had no effect. Species and cultivars within species may differ markedly in their response to environmental/cultural stresses, including planting depth. Each tree species originating from a specific environment may represent an ecotype adapted to that particular environment. Therefore, tree survival and performance may depend on the difference between the environment from which the tree was grown and the experimental system into which it is introduced.

Vermicompost transforms agricultural waste into a high quality soil amendment, though market acceptance remains in its infancy. This study examines how growers’ willingness to pay for vermicompost is affected by grower’s crop, region, income per acre, knowledge level of vermicompost and compost, previous use of compost, and the willingness to pay for compost. The survey results pulled together 223 responses from California growers. It was discovered growers’ had less knowledge of vermicompost than compost but were willing to pay more for vermicompost. There was statistical difference amongst the responses. It was shown the market value per ton of vermicompost lies between $20 and $30; and feasibility of a potential vermicompost facility depends on transportation costs of the finished product. A vermicompost company should focus on North Coast grape growers.