The role of indigenous people in environmental management is subject to the legal framework imposed by a dominant ‘Western’ culture (McGregor, 2009, Kahn, 2013). Provision for indigenous participation in environmental decision making often allows for only a single voice, assuming homogeneity within a framework that seeks biophysical sustainability (Coombes, 2005). Indigenous people are disenfranchised from making a meaningful contribution from their perspective (Jackson, 2006). This has been the case for Maori in New Zealand who have been alienated from their lands and are reliant on statutory participatory processes to engage with environmental management. The methods of participation, their operation and failures are well documented. Yet there has been little analysis of the ways in which indigenous participation occurs that explores the political context critically (Coombes et al, 2012). In particular there is little in-depth research that examines the ways in which indigenous people might try and find a place within the legal framework and the impact this has within their own tribe, with other Maori and on their culture and identity. This ethnographic, participant observation aims to find out whether the New Zealand environmental management framework has space for distinctive Maori participation. The tribe have to create identities that fit into the non-Maori legislative structure. The iwi identity is highly contested with other Maori tribal groups. There are often negative personal consequences of engaging in environmental management leading to considerable institutional fragility. As a result strategic relationships develop between Maori themselves and with non-Maori. The implementation of the resource management framework assumes Maori issues are ‘cultural’, fixed and historic. When tribes engage in the processes they find their potential limited by this implementation. This classification is reinforced both through participation in the system and broader environmental management practices.

Leishmaniasis has been described by the World Health Organisation as a ‘neglected disease’ and not well understood, which reflects the variations in transmission cycle, reservoirs, vectors, clinical manifestations, and its associations with many human factors. One country where Cutaneous Leishmaniasis (CL) is a major health issue is Saudi Arabia. This thesis investigates factors influencing the prevalence of CL in Al-Dawadmi Governorate, Saudi Arabia in the period between January 2006 and April 2011 from a multidisciplinary perspective. Meteorological data were used to investigate the influence of climatic variables on the seasonality of CL in the study area. The research also involved surveys of land use / cover around six communities in the protectorate and a case-control study of 125 CL cases and 125 controls to assess the role of socio-economic factors. Additionally, an assessment was made of CL cases that were not officially reported to the health authority. Four main factors were found to influence the prevalence of CL cases in the governorate. There was a very strong, temporally-lagged, relationship between monthly temperature and rainfall and reporting of CL cases. Within individual communities, the case-control results indicated there was a strong association between the presence of certain land cover types or land uses within 300 metre and the probability of contracting CL. A number of socio-economic and demographic factors were also found to be correlated with a higher risk of contracting CL. In addition, socio-economic factors and contrasts in accessibility to health services influenced the reporting of CL cases to the authorities. Overall, the results suggest that a multi-faceted approach to reducing the prevalence of CL is required. Public authorities need to be aware of the meteorological trigger conditions, undertake reservoir eradication activities in certain circumstances, improve access to key diagnostic health services and, most cost-effectively, undertake initiatives to improve public awareness of the key risk factors, relevant mitigation measures and the advantages of seeking prompt treatment.

There is a growing interest in understanding how the built food environment influences health behaviours. Whilst policy interest in the influence of food environments on diet and body weight is growing, the evidence base is limited, particularly for environments beyond the home neighbourhood. Research in children is of particular importance, as it is known that dietary behaviours and weight tend to track into adulthood. This thesis addresses the gap in knowledge surrounding the influence of exposure to the food environment on weight and diet in children. It also takes into consideration the interactions with socio-economic status. Existing research exploring the environmental influences on diet and weight in children is reviewed, and a conceptual framework of key determinants identified is presented. Three studies are presented which investigate associations between different measures of exposure to the food environment and diet and weight. A systematic review investigating the use of GPS in studies of the food environment is also conducted. Additionally, a novel method for assessing environmental exposure is presented. The results from this research suggest that unhealthy food environments measured at an area level are generally conducive to weight gain and poorer diet, while the opposite is true for healthier food environments. Furthermore, this thesis supports the hypothesis that diet, weight and access to food are patterned by social class, and that the food environment partially mediates the well-known association between socio-economic status and weight status. However, findings were equivocal when using measuring exposure to the food environment at an individual level. This suggests that correctly measuring the characteristics of the food environment is important in order to disentangle their effects on health outcomes, and calls for efforts to attempt to reduce the heterogeneity in measures of the food environment employed.

Short-chain alkanes are gaseous hydrocarbons that contribute to photochemical pollution and ozone production in the atmosphere. A number of studies have shown that Rhodococcus species possess the ability to metabolite a wide range of hydrocarbons since they contain multiple hydrocarbon-degrading enzymes such as soluble diiron monooxygenases (SDIMOs) and alkB-type alkane monooxygenases. This study aimed to investigate the role of multiple alkane-degrading enzymes in the metabolism of gaseous alkanes in Rhodococcus jostii strain 8. R. jostii strain 8 was isolated from a propane enrichment culture using petroleum-contaminated soil as an inoculum. R. jostii strain 8 could grow on ethane, propane, butane, octane, naphthalene and some potential intermediates in alkane metabolism. Oxidation studies showed that R. jostii strain 8 is likely to oxidise propane via both terminal and sub-terminal oxidation of propane and that these activities are induced in propane-grown cells. Alcohol dehydrogenase assays were carried out in order to determine cofactor and substrate ranges of these enzymes. Results showed that alcohol dehydrogenases involved in the metabolism of gaseous alkanes are NDMA-dependent. The size of the genome sequence of R. jostii strain 8 is 8.5 Mbp with a G+C content of 67%. The closest relative of R. jostii strain 8, based on 16S rRNA sequence, is Rhodococcus jostii RHA1 with 99% identity. However, growth profiles and a number of catabolic genes in the genome of R. jostii strain 8 clearly indicated that this bacterium is different from R. jostii RHA1. R. jostii strain 8 contains two alkane-degrading enzyme systems – a propane monooxygenase and an alkB-type alkane monooxygenase. Polypeptide analysis on cell-free extracts from cells grown on gaseous alkanes using SDS-PAGE indicated that propane monooxygenase is inducible during growth on propane. Expression studies using RT-qPCR of prmA and alkB showed that prmA was highly expressed during growth on propane. The exact involvement of alkB-type alkane monooxygenase in the degradation of alkanes was still unclear. A gene transfer system for R. jostii strain 8 was established. Marker-exchanged mutagenesis of prmA and alkB was attempted. Construction of mutated-prmA and mutated-alkB plasmids was achieved. Electroporation conditions were successfully optimised in order to transfer linear DNA into R. jostii strain 8. However, mutants lacking active prmA or alkB are still needed to further study their phenotypes and to provide more evidence supporting the role of these two enzymes.

Laboratory experiments on the physiological response of picophytoplankton to light, temperature and nutrient limitations were conducted. The impact of climate change in a RCP8.5 model scenario simulation was investigated. An acclimated and a dynamic photosynthesis response model reproduce the physiological response to light. Long-term damage (accumulated over days) through photoinhibition is underestimated by the dynamic model. The maximum rate of photosynthesis is significantly lower for picoprokaryotes (0.81 − 1.44 d-1) than for picoeukaryotes (1.93 − 4.93 d-1). Also, their affinity for light is higher (7.15 − 12.42 g C m2 (mol photons g Chl)-1 compared to 3.42 − 9.81 g C m2 (mol photons g Chl)-1). Optimum growth rates differ significantly between the groups (0.47 ± 0.17 d-1 for picoprokaryotes and 1.05 ± 0.47 d-1 for picoeukaryotes). The temperature tolerance range is higher for picoeukaryotes (2.8°C − 32.4°C compared to 13.7°C − 27°C). The maximum picophytoplankton community growth has a Q10 value of 2.3. For picoprokaryotes the Q10 value is even higher (4.9). The cell composition in both groups deviates significantly from the Redfield ratio under nutrient saturated conditions with a lower phosphorus demand in picoprokaryotes. Under nutrient limitation nitrogen: carbon is reduced by 15 − 42%, and phosphorus: carbon by 37 − 65%. Chlorophyll a: carbon is significantly lower under both nitrogen (-50 − -82% ) and phosphorus (-62 − -91 %) limitations. The half-saturation constants are in the range between 0.01 ± 0.02 and 0.19 ± 0.23 μmol NH4+ L-1 for individual picoeukaryotes. These findings agree with theoretical assumptions related to size with an advantage in subtropical oligotrophic light limited environments and highlight the requirement of data on picoeukaryotes. Climate change leads to enhanced stratification of the water column, reduced availability of nutrients and an increased contribution of picophytoplankton to total phytoplankton biomass weakening the biological pump.

Observations suggest that the properties of Antarctic Bottom Water (AABW) are changing, causing significant steric sea level rise. Understanding the causes of these changes is critical for projections of future sea level, yet previous generations of climate models failed to represent AABW accurately. Present-day biases in AABW potential temperature, salinity and density are assessed for models from the Coupled Model Intercomparison Project phase 5 (CMIP5). CMIP5 models either have inaccurate bottom water properties in the present-day Southern Ocean or form AABW via the wrong process, open ocean deep convection in the subpolar gyres. Under climate change scenarios, open ocean deep convection is responsible for bringing the warming signal to the Southern Ocean abyss. It is then advected equatorwards by AABW transport. In turn, the decrease in density associated with the warming results in a weakened density-driven AABW transport. The mean of 24 CMIP5 models projects a mean global steric sea level rise of 3.8 mm by 2100 for the abyssal 500 m, albeit with a large uncertainty due to the cross-model disagreement on bottom salinity changes. The parameterisation of overflows does not show an improvement in AABW properties. Sensitivity experiments are performed on the model HadGEM3. The trigger for deep convection in the Weddell Sea, a positive sea ice anomaly leading to anomalies in the mixed layer depth, is identified. Varying three vertical mixing parameters modifies the original mixed layer anomaly, leading to a range of responses from arrested deep convection to deep convection over the entire Weddell Sea. In the arrested convection simulations, the Antarctic Circumpolar Current strength is improved and the AABW properties and North Atlantic Deep Water formation are unchanged. These experiments indicate a possible way to stop Weddell Sea deep convection in models, to improve their Southern Ocean representation.

This thesis considers the northwest-southeast, diagonal, orientation of the South Pacific and South Atlantic Convergence Zones (SPCZ and SACZ, respectively) which provide vital precipitation locally and influence mean climate globally. Their basic formation mechanism is not fully understood. A conceptual framework is developed to explain the mechanism responsible for the SPCZ diagonal orientation. Wind shear and Rossby wave refraction cause vorticity centres in the subtropical jet to develop a diagonal orientation and propagate equatorward towards the eastern Pacific upper-tropospheric westerlies. Ascent ahead of cyclonic vorticity anomalies in the wave then triggers deep convection parallel to the vorticity centre. Latent heat from condensation forces additional ascent and upper-tropospheric divergence; through vortex stretching this leads to an anticyclonic vorticity tendency. The calculation of a vorticity budget shows this tendency is strong enough to dissipate the wave. A similar sequence of events triggers diagonal bands of convection in the SACZ, though the vortex stretching feedback is not strong enough to dissipate the Rossby wave. An atmospheric general circulation model is used to investigate this mechanism. In an experiment the parametrisation of convection is modified: dynamic Rossby wave forcing is decoupled from the usual thermodynamic response. Consequently, Rossby waves over the SPCZ region are not dissipated, confirming the feedback in the framework. Furthermore, it is shown that SPCZ convective events decrease the strength of the eastern Pacific upper-tropospheric westerlies. Further experiments show which surface boundary conditions support the SPCZ diagonal orientation. Continental configuration, orography and absolute Sea Surface Temperatures (SST) do not have a significant influence. The key boundary condition is the zonally asymmetric component of the SST distribution. This leads to a strong subtropical anticyclone over the southeast Pacific that transports and supplies moisture to the SPCZ. Convection is triggered when the dynamical forcing from Rossby waves is present.

Three experiments were conducted to explore the effects of gasified biochar on contrasting temperate soil types in East Anglia, an agricultural area in eastern England, with a focus on the influence of soil properties. In a laboratory experiment comparing eight dissimilar soil types, adding up to 2.5% biochar improved field capacity by up to 42% (15% on average) and available water capacity by up to 48% (22% on average), but silty soils were less responsive. BD was reduced by up to 19% (10% on average). In a three-season outdoor pot trial with spring wheat (Triticum aestivum), four soil types were treated with biochar (at 0%, 0.1%, 0.5% & 2.5%). Biochar affected crop yield and soil properties, mainly positively, especially pH, CEC, base cations, field capacity, saturated hydraulic conductivity and some micronutrients. Positive yield responses appeared to be predominantly due to the influence of biochar on soil hydrology, increasing water-holding capacity on sandy soils in dry weather, while improving infiltration during excessively wet weather on a silty clay loam. In a trial on three contrasting soils in one field, cropped with winter barley (Hordeum vulgare), biochar (at 0, 50 t ha–1 & 100 t ha–1) had a range of predominantly positive effects. There were no significant increases in crop yield in this well managed agroecosystem, but variables which responded significantly included pH, some nutrients in the soil and in the crop, and grain moisture content. There was also evidence that biochar improved grain quality by reducing grain protein content on sandy soils, and increasing it on loam, keeping it within the tolerable limits of the malting barley industry in both cases. Potentially toxic elements (PTEs) within the barley grain (Zn, Cu, As, Ni, Cd and Cr) were not raised to levels critical to food safety. The overarching conclusion is that soil type, as defined by its physical, chemical and biological characteristics, is highly influential with respect to a range of effects that BC has on soil properties and crop responses, and that such characteristics need not only to be factored into future BC research, but should be the focus of studies aimed at identifying critical threshold values.

Winter annual Arabidopsis thaliana plants require a prolonged period of cold, known as vernalization, to ensure prompt floral transition occurs in spring. This thesis addresses the question of whether partial saturation of cold requirements might delay flowering under future climate scenarios. Laboratory experiments set up to parameterize a predictive model revealed a surprising optimal vernalizing temperature for the Swedish accession Lov-1. Field experiments in Northern Sweden support the theory that this optimum likely reflects adaptation to autumn, rather than winter temperatures. A chilling unit model incorporating empirically derived parameters forecast an overall increase in effective vernalizing days for A. thaliana in northern Sweden. This increase is the result of an overall reduction in sub-zero temperatures that are predicted for northerly latitudes by the end of the century. Reductions in the number of effective vernalizing days were predicted for England and Spain, however these are unlikely to counteract the forcing effects of increased spring temperatures at these locations. This thesis also presents a novel method that enables single RNA molecules to be visualized for the first time in plants. This method was used to determine cell-to-cell variation and subcellular distribution of key vernalization gene transcripts before, during and after cold exposure. These results provide a unique insight into how plants perceive and integrate longterm temperature cues at the cellular level In summary, this thesis predicts the potential impact of climate change on A. thaliana vernalization across its species’ range. It also dissects transcriptional mechanisms that underlie long-term temperature integration. Modulation of these mechanisms is likely to be key for survival of some wild species and for maximizing crop yields under future climate scenarios.

Isoprene is a climate active gas emitted from natural and anthropogenic sources in quantities equivalent to the global methane flux to the atmosphere. 90 % of the emitted isoprene is produced enzymatically in the chloroplast of terrestrial plants from dimethylallyl pyrophosphate via the methylerythritol pathway. The main role of isoprene emission by plants is to reduce the damage caused by heat stress through stabilizing cellular membranes. Isoprene emission from microbes, animals, and humans has also been reported, albeit less understood than isoprene emission from plants. Despite large emissions, isoprene is present at low concentrations in the atmosphere due to its rapid reactions with other atmospheric components, such as hydroxyl radicals. Isoprene can extend the lifetime of potent greenhouse gases, influence the tropospheric concentrations of ozone, and induce the formation of secondary organic aerosols. While substantial knowledge exists about isoprene production and atmospheric chemistry, our knowledge of isoprene sinks is limited. Soils consume isoprene at a high rate and contain numerous isoprene-utilizing bacteria. However, Rhodococcus sp. AD45 is the only terrestrial isoprene-degrading bacterium characterized in any detail. A pathway for isoprene degradation involving a putative soluble monooxygenase has been proposed. In this study, we report the isolation of two novel isoprene-degrading bacteria and characterization of the isoprene gene clusters in their draft genomes. Using marker exchange mutagenesis, transcription assays and proteomics analyses, we provide conclusive evidence that isoprene is metabolized in Rhodococcus sp. AD45 through the induced activity of soluble isoprene monooxygenase, a close relative to well known soluble diiron center monooxygenase enzymes. Metabolic gene PCR assays based on a key component of isoprene monooxygenase were also developed to detect isoprene degraders in the environment. The diversity of active isoprene degraders in the terrestrial environment was investigated using DNA-stable isotope probing experiments combined with 454 pyrosequencing.