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Optomechanics studies the interaction between the optical force and mechanical objects, and has led to intensive developments in ultra-sensitive measurements, coherent quantum control, optical tweezers, etc. Silicon photonics is a material platform from which Photonics Integrated Circuits can be made, and provide a perfect solution for minimising optical systems. This thesis studies the integration of optomechanics and silicon photonics-integrated silicon optomechanics, and explores its applications in distributed fibre optical sensing (DFOS) and optical trapping. A novel 1.5 µm thick Silicon on Insulator (SOI) platform is also demonstrated, which is advantageous to the two applications compared to the widely-used thin SOI platform. Firstly, this thesis proposes to use the integrated cavity optomechanical system to generate optical probe signals for DFOS. The proposed application is based on optomechanical oscillation (OMO), through which optical pulse trains (OPT) and sweepingwavelength optical signals (SWOS) for the DFOS application can be generated. Comprehensive analyses on the OMO threshold and oscillation characteristics are conducted, and the extinction ratio (ER), duty cycle (DC) of the OPT and the sweeping range of the SWOS are derived. Examples of utilising OMO-based OPT and SWOS for DFOS applications are then demonstrated. The proposed OMO-based OPT generator and OMO-Based SWOS generator do not rely on external RF sources and optical modulators and can be fully integrated with silicon photonics platform. They thus provide unconventional methods to reshape the optical source generation in DFOS. Secondly, this thesis presents the design, optimisation and scaling effect of a dualwaveguide optical trap on a SOI platform by comprehensive numerical simulations in Lumerical FDTD Solutions. The simulations demonstrate that the waveguide thickness is a crucial parameter in designing a dual waveguide optical trap. It was found the optimal waveguide thickness generally increases with the gap distance, accompanied by a periodic feature. The optimal waveguide thickness and gap distance display clear scaling effects over the optical wavelength. This thesis also proposes to use the OMO process to load micro/nano-particles. The OMO process can break the adhesive connection between the micro/nano-particles and the container's surface. The works above not only pave the way for the design and optimisation of dual-waveguide optical trappings for various applications, but also lays the foundation of a fully on-chip optical trapping system working on vacuum or air. Lastly, this thesis experimentally demonstrated a novel 1.5 µm thick SOI platform for integrated optomechanics, rather than the widely-used thin SOI with a top silicon layer less than 300 nm. For both the above two applications, thick SOI shows its advantages. Thick SOI is suitable for fabricating low-frequency mechanical resonators, which are necessary for long-distance DFOS applications. Thick SOI is also essential for dualwaveguide optical trapping with a larger gap distance. In addition, the 1.5 µm thick SOI has high power handling capability, low propagation loss, large mode size, and comparatively small bend radius. Individual integrated silicon optomechanical components based on 1.5 µm SOI platform are designed, fabricated, and measured, including waveguides, grating couplers, MMIs, Bragg gratings, optical microresonators and mechanical resonators. The measurement results show that all the individual photonics components function well. These works lay a solid foundation for the full integration of a silicon optomechanical system in the future.

Apple Replant Disease (ARD), caused by an accumulation of soil-borne fungal and oomycete pathogens in the soil, is an economically important disease of apples. Current management relies on the use of broad-spectrum chemical fumigation. Banning of chemical products has seen increased research into biological management strategies for ARD. This study aimed to test the efficacy of a number of commercially available biological soil amendments to improve the establishment of young apple trees in an attempt to minimise the detrimental effects of ARD. It also looked at changes in planting position and rootstock selection at planting to manage ARD and how climate change abiotic factors affect bulk apple soil microbiome communities. The efficacy of single species amendments was variety specific in the field. There was a increased rate of tree girth expansion in Gala trees amended pre-planting with Pseudomonas fluorescens but the same effect was not observed with Braeburn trees. The single species amendments did not increase the establishment of young apple trees either individually or in a consortium of amendments in semi-field conditions. In both field and semi-field conditions pre-plant amendment significantly altered the abundance of individual operational taxonomic units (OTUs) associated with both beneficial and pathogenic taxa of plants. The planting position in the inter-row alleyways and the genetic relationship of the new rootstock to the previously planted rootstock on the site were both identified to minimise ARD severity. In addition, a significant effect of CO₂ concentration and temperature increase on bulk soil microbiome communities was observed but this was not as significant as site management (organic vs conventional) effect. This research will aid with the development of management strategies for ARD by integrating single species biological amendments and cultural approaches with other management practices.

The diversity of arbuscular mycorrhizal fungi (AMF) and relative abundance among species may affect their ecological impact. Species-specific primers for qPCR quantification of Funneliformis geosporus and F.mosseae DNA were developed to quantify their relative abundance for use in studying mixed inocula in roots of strawberry under different conditions of water stress. Co-occupation of the same root by both species was shown to commonly occur but the relative abundance of the two species varied with water stress. Greater root colonisation was observed microscopically under water stress but this increased colonisation was often accompanied with decreased amounts of fungal DNA in the root. Funneliformis mosseae tended to become more abundant under water stress relative to F. geosporus. There was significant correlation in the fungal colonisation measurements from the microscopic and qPCR methods under some conditions, but the nature of this relationship varied greatly with AMF inoculum and abiotic conditions. Water stress experiments, undertaken with strawberry (Fragaria x ananassa) show a reduction of plant development when subjected to regulated deficit irrigation (RDI) conditions. The effect on growth of AMF colonisation and relative abundance of two co-occurring species of AMF, F. geosporus and F. mosseae, were determined in cultivated strawberry under conditions of water stress. Three AMF inoculation treatments (a single treatment either of F. mosseae BEG25, F. geosporus BEG11 or a 50:50 mixed inoculation treatment of both species) were compared to un-inoculated plants. This study demonstrated that in strawberry plants, under these experimental conditions, single species inoculation treatments gave similar benefits to the host as the mixed inoculation treatment regardless of irrigation regime, suggesting colonisation was of greater importance than mycorrhizal fungal species. The addition of AMF inocula to plants, subjected to reduced irrigation of up to 40%, restored plant growth to the same or higher values as the non-mycorrhizal, fully-watered plants. The water use efficiency of plants was greater under the RDI regime and in AMF-inoculated plants, but there were no significant differences between plants inoculated with the single or combined inoculum. The occurrence of multiple variant sequences within the rRNA genes of the AMF is now widely accepted; however the mechanisms for this are not currently clear. This work investigated the effect of different culture conditions (in vitro and in planta culture) on sequence diversity and relative abundance of a culture of Rhizophagus clarus. Next generation sequencing, using the Illumina platform, generated three major sequence variants that were the most common sequence variants in all conditions. All other sequences grouped phylogenetically about these three major sequence types along with an outgroup of less common sequence types. This study demonstrated that changes in the frequency of dominant sequence variants had occurred when AMF are maintained for two years under different culture conditions.