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The soilborne diseases of potato (Solanum tuberosum) caused by Rhizoctonia solani (stem canker and tuber black scurf) are important factors limiting yields and quality of intensively managed potato crops in New Zealand. International studies have shown that biofumigation using Brassica plants is a promising component of integrated disease management with potential to reduce agrichemical usage for disease control. To date, there is limited evidence on the efficacy of biofumigation for controlling soil-borne diseases of potato in New Zealand. The goal of this research was to investigate the biofumigation potential of selected plants for suppression of R. solani AG3-PT and AG2-1, which cause potato diseases. In vitro studies showed that of the 10 plant types tested, three, including ‘Caliente’ mustard, brown mustard and ‘Nemat’ arugula, gave the greatest inhibition of the mycelium growth of R. solani AG3-PT and AG2-1 isolates, at 5-10 g of macerated plant tissues per Petri dish, or 5-10% (w:w) when incorporated into soil. Shoot or shoot plus root tissues of selected biofumigants, harvested at the mid-flowering growth stage, were the most effective for reducing mycelium growth of R. solani isolates. Increased conversion of R. solani mycelium into sclerotia was observed at 1% or 5% (w:w) soil incorporation for ‘Caliente’ mustard and 1% (w:w) for brown mustard or ‘Nemat’ arugula. The subsequent germination of retrieved R. solani sclerotia was reduced at 10% (w:w) soil incorporation of ‘Nemat’ arugula. The subsequent mycelium growth from retrieved R. solani colonised barley grains was completely inhibited at 10% (w:w) soil incorporation of ‘Caliente’ mustard, brown mustard or ‘Nemat’ arugula. Biofumigation potential against R. solani AG3-PT was assessed in different soil edaphic conditions, using qPCR and measurements of soil microbial activity (dehydrogenase activity, DHA). Biofumigant treatments at soil pH of 6.6, 20°C and 40% water holding capacity (WHC), or at 15°C and 40% WHC, gave the greatest reductions of R. solani AG3-PT inoculum levels in soil. In addition, biofumigant treatments at pH 6.6, 15°C, and 40 or 70% WHC, or in the combination of 15°C and 40% WHC, resulted in the greatest DHA levels. The soils amended with macerated ‘Caliente’ mustard tissue (5% w:w) and after incubation at 15°C, reduced the stem canker severity on potato ‘Jersey Benne’ plants, and increased plant height and dry biomass compared with the pathogen inoculated controls. The effects of the selected biofumigant treatments for reducing R. solani AG3-PT inoculum, and suppressing infection of ‘Russet Burbank’ potato plants, were assessed in a shadehouse experiment, using qPCR and DHA assessments. The results showed that the biofumigant treatments reduced and maintained R. solani AG3-PT inoculum (and potentially other AGs) at low levels during the experiment, in soil, and stems, stolons and tubers of potato plants. However, there was no differential effect of biofumigant treatments on soil microbial activity (DHA). The biofumigant treatments also reduced severity of tuber powdery scab caused by Spongospora subterranea, and incidence of dead stems caused by Colletotrichum coccodes. Potato plant yield parameters were increased by the biofumigant treatments. Effects of cover crops, including ‘Caliente’ mustard, oat or ‘Graza’ radish, on soil microbial communities were assessed by DHA measurements, soil carbon utilisation profiles (CUP), and PCR-DGGE in soil samples taken from three potato field trials near Timaru (2015/16, 2016/17) and Ashburton (2015/16), Canterbury. DHA increased after cover crop treatments. The events of crop incorporation and plant growth over the sampling period and the oat treatment affected the CUPs of the soil microbial communities. Results from PCR-DGGE showed that different cover/potato crops or growth stages strongly affected the structure (species composition), richness, and diversity indices for communities of total fungi, arbuscular mycorrhizal fungi (AMF), Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. In addition, cover crop treatments affected the soil microbial communities. ‘Caliente’ mustard altered the community structures of total fungi in the three field trials, and reduced the richness and diversity indices for total fungi communities in the two Timaru field trials. ‘Caliente’ mustard also affected the Proteobacteria community structures in soil samples from the two Timaru field trials, but increased richness and reduced the diversity of Betaproteobacteria in soil from the Timaru trial (2015/16). This biofumigant treatment also reduced the diversity of Alphaproteobacteria in soil samples from the Ashburton field trial (2015/16). ‘Graza’ radish treatment only affected AMF community structure in samples from one field trial (Timaru, 2016/17), but had no effects on the community structures, richness or diversity of AMF or the other microbial groups in samples from the other fields. Oat treatment reduced the richness of the total fungi and Gammaproteobacteria communities in soil from the Timaru field trial (2016/17). This study has provided supportive information that biofumigant plants and crops could be incorporated as a management strategy to control economically important diseases of potato.

New Zealand’s 5.3 million strong dairy herd returns approximately 106 million litres of urine to pasture soils daily. The urea in that urine is rapidly hydrolysed to ammonium (NH₄⁺), which is then nitrified, with denitrification of nitrate (NO₃⁻) ensuing. Nitrous oxide (N₂O), a potent greenhouse gas (GHG), is produced via nitrification and denitrification, which are enzyme-catalysed processes mediated by soil microbes. Thus microbes are linked intrinsically to urine patch chemistry. However, few previous studies have investigated microbial dynamics in urine patches. Therefore the objective of these four experiments was to investigate the effects on soil microbial communities of cow urine deposition. Methods used included phospholipid fatty acid (PLFA) analyses of microbial community structure and microbial stress, dehydrogenase activity (DHA) assays measuring microbial activity, and headspace gas sampling of N₂O, ammonia (NH₃) and carbon dioxide (CO₂) fluxes. Experiment 1, a laboratory study, examined the influence of soil moisture and urinary salt content on the microbial community. Both urine application and high soil moisture increased microbial stress, as evidenced by significant changes in PLFA trans/cis and iso/anteiso ratios. Total PLFAs and DHA showed a short-term (< 1 week) stimulatory effect on microbes after urine application. Mean cumulative N₂O-N fluxes were 2.75% and 0.05% of the nitrogen (N) applied, from the wet (70% WFPS) and dry (35% WFPS) soils, respectively. Experiment 2, a field trial, investigated nutrient dynamics and microbial stress with plants present. Concentrations of the micronutrients, copper, iron and molybdenum, increased up to 20-fold after urine application, while soil phosphorus (P) concentrations decreased from 0.87 mg kg ⁻¹ to 0.48 mg kg⁻¹. Plant P was also lower in urine patches, but total PLFAs were higher, suggesting that microbes had utilised the available nutrients. Microbial stress again resulted from urine application but, in contrast to experiment 1, the fungal biomass recovered after its initial inhibition. Studies published during the course of this thesis reported that hippuric acid (HA) and its hydrolysis product benzoic acid (BA) significantly reduced N₂O-N emissions from synthetic cow urine, thus experiment 3 investigated this effect using real cow urine. Cumulative N₂O-N fluxes were 16.8, 5.9 and 4.7% of N applied for urine (U) alone, U+HA and U+BA, respectively. Since NH₃-N volatilisation remained unchanged, net gaseous N emissions were reduced. Trends in total PLFAs and microbial stress were comparable to experiment 1 results. Experiment 4 studied HA effects at different temperatures and found no inhibition of N₂O-N fluxes from HA-amended urine. However, mean cumulative N₂O-N fluxes were reduced from 7.6% of N applied at 15–20°C to 0.2% at 5–10°C. Total cumulative N emissions (N₂O-N + NH₃-N) were highest at 20°C (17.5% of N applied) and lowest at 10°C (9.8% of N applied). Microbial activity, measured as potential DHA, increased with increasing temperature. This work has clearly shown that the stimulation and inhibition of the soil microbial community by urine application are closely linked to soil chemistry and have significant impacts not only on soil nutrient dynamics but also on N₂O-N emissions and their possible mitigation.