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Microorganisms are the most abundant life forms on Earth. It is estimated that there are around 10 thousand, billion, billion, billion individual organisms belonging to two main microbial groups (the bacteria and archaea). This is 1 million times more than the estimated number of stars in the known Universe. It is believed that most of this vast population is found in deep sediments far below the ground and the sea floor. It is easy to think that this huge repository of buried biological (microbial) diversity is irrelevant to mankind, but nothing could be further from the truth. This intra-terrestrial microbiota has been coined the 'deep biosphere' and it is central to the cycling of matter over geological timescales. Of more immediate concern is the role that certain deep biosphere organisms have played in modifying oil in situ in petroleum reservoirs. Most of the world's oil (e.g. the giant tar sand deposits in Western Canada) has been degraded by microbes in situ long before humans recovered the first drop of crude oil. Research from our group has uncovered the microbial processes responsible for crude oil biodegradation in petroleum reservoirs and identified biological and geological factors that promote biodegradation. One of these factors is temperature. The temperature of the Earth's crust increases with depth by approximately 2-3 C every 100 meters and petroleum reservoirs at temperatures above 90 C are not subject to biodegradation. However cooler, shallower reservoirs are not always biodegraded. These non-degraded, cool shallow reservoirs once resided at greater depths but have been moved by geological uplift to shallower depths. It appears that they are not re-colonized by oil-degrading bacteria and the oil in these reservoirs remains intact. This process of transient heating of a petroleum reservoir which kills the resident oil-degrading microbiota has been termed palaeopasteurization. Research in the Arctic has provided a window into the petroleum reservoir deep biosphere. Cold Arctic sediments harbour bacteria that have optimal activity at around 50 C and may have come from leaky warm petroleum reservoirs because their closest relatives were previously identified in hot oil wells. These organisms form spores which are highly resistant to environmental extremes and act as survival capsules that protect the bacteria on their journey from deep within the Earth. These bacteria thrive without oxygen (anaerobes) and the spores resist exposure to oxygen. Sediments in the UK harbour spore-forming bacteria that degrade crude oil without oxygen, providing another link between bacteria and petroleum reservoirs. This project aims to determine if spore-forming oil-degrading and Arctic bacteria ultimately derive from petroleum reservoirs and if the process of palaeopasteurization kills them and prevents them seeding surface sediments. The project focuses on fundamental science at the interface between biology and geology and has practical implications. A supply of hydrocarbon degrading anaerobes from the deep biosphere has implications for microbial diversity in surface sediments where these bacteria may play a role in oil clean up in oxygen depleted sediments (i.e., in coastal sediments but also the deep Gulf of Mexico seafloor near the Macondo wellhead). Related bacteria also cause problems in the oil industry by producing the toxic gas hydrogen sulphide in a process known as reservoir souring. This reduces the value of oil and poses a hazard to workers. The UK hosts a major offshore oil industry that contributes significantly to employment and economic prosperity. During the transition between a fossil carbon energy economy and a renewable energy economy, the need remains for innovative operational practices to reduce the environmental impact of oil production and exploration; much of this is underpinned by an understanding of microorganisms associated with oil production and oil degradation in the environment.

The Gangetic Plain is a large fertile area at the foot of the Himalayas, covering most of northern India. Home to around 400 million inhabitants, it is one of the most densely inhabited regions in South-East Asia. With its fertile soils, monsoon precipitation and vast groundwater aquifers, the plains have been at the heart of the Indian agricultural revolution. Over the last 4 decades, the introduction of new fertilisers and crops, and the construction of large-scale irrigation systems have been major drivers of socio-economic development in the region. These practices have, however, also led to severe groundwater decline and strains on other water resources. Changing feedbacks of water and energy between the land-surface and atmosphere may have even altered the local climate system. A strong economic development is expected to continue these trends in the near future and future climate change is also expected to increase the pressure on local water resources systems. Identifying the major causes of observed historical changes in water availability and predicting the future impact of local water management strategies under climate change are particularly challenging, yet indispensable for the sustainable management of water resources. For example: assessing the sustainability of groundwater aquifers requires knowledge of global climate influences, but also of the influence of land-use, abstractions and soil moisture dynamics; furthermore, the unprecedented scale of land-use changes and increased irrigation are expected to have influenced local climate through feedbacks of water and energy. In order to unravel and quantify the impact of different drivers of change, a fully integrated analysis of the major water fluxes in the Gangetic Plain is needed. This study would be the first to analyse changes in the main water fluxes and feedbacks of the Gangetic Plain in a fully integrated modelling set-up. The approach will enable the separation of the impact of local and regional land use change from that of global climate drivers. We will develop a custom-built coupled hydrological model for the region using available groundwater and surface water modelling toolboxes. This model will be calibrated and tested using a variety of different sources of information, from local measurements, satellite observations and global climate (reanalysis) datasets. Subsequently, we will run the model with different land-use and water extraction scenarios. This will allow us to quantify the impact of land-use change and extraction on the main hydrological fluxes and water resources. At the same time, the hydrological model will generate high-resolution data about soil moisture changes resulting from historical land-use, as well as different hypothetical scenarios. By feeding these scenarios into a global climate model, we will study the potential feedbacks of large-scale changes in soil moisture on the Indian monsoon system. A pair of state-of-the-art global climate models will be used: the UK MetOffice Unified Model (MetUM) and the NCAR Community Atmosphere Model (CAM4). In a final step, the superimposed impact of climate change will be assessed and future predictions of water availability will be generated. For this purpose, we will use the new CMIP5 ensemble of climate models. Using a statistical approach, these models will be downscaled to a level useful for application over the Gangetic Plains. The integrated hydrological model can then be run with these future climate projections to assess the impact of future climate change on regional and local water availability. Two local case studies will address the usefulness of such projections and their uncertainties in a local ecosystem-oriented management setting.

The studies of ecology and evolution are closely related. Ecologists seek to understand the environmental factors that explain the distribution and abundance of species, while evolutionary biologists investigate the process of natural selection and the evolution that results, by examination of adaptation in phenotypes and genotypes. It is curious in these times of environmental change that one of the biggest gaps in our understanding of the natural world falls exactly at the intersection between ecology and evolution: we know less than we should about how the environment shapes the evolution of biodiversity. Although it is generally understood that the environment is the cause of adaptation, the links between them have seldom been explicitly explored. Many ecological studies do not consider how the environmental variation that they measure affects evolution, while many studies of evolution measure selection or adaptation without considering their environmental causes, concentrating instead on the consequences for evolution of what is genetically possible. Explicit study of the involvement of the environment in evolution has the potential to fuel a paradigm shift in our comprehension of fundamental evolutionary patterns. For example: (i) Divergence. Evolution has resulted in abundant diversity in the natural world, but the extent of this divergence within related groups of organisms is often circumscribed. Are these limits, on the kind of organisms that evolve, a consequence of what is genetically possible, or do they result from similarities in the environments to which the organisms are exposed? (ii) Convergence. Within the greater divergence, organisms have often apparently converged on similar evolutionary solutions, suggesting that evolutionary outcomes are to some extent repeatable. Is the repeated evolution of similar organisms in different places the result of genetic biases or environmental determinants? If the latter, do similar organisms always evolve in similar environments, or can different environments favour the same outcome of organismal form? Vice versa, do similar environmental combinations always result in essentially the same organism, or are there different evolutionary solutions to similar environmental problems? (iii) Novelty. Although similar organisms in different places often converge on repeated evolutionary solutions, evolution also occasionally comes up with solutions that are different from the general pattern, by dint of developing, or having lost, some distinguishing feature or combination of features. Is such evolutionary novelty the result of particularly unusual environments? Most previous studies of how the environment affects evolution have measured only a single, or small number of aspects of both the organism and the environment, but thorough answers to the questions we pose require a more comprehensive understanding of multiple different aspects of organism and environment, and of how they interact and affect other. Our approach requires the use of recently developed multivariate statistical methods that allow the simultaneous analysis of many organismal traits and many environmental variables. Adaptive radiation is the differentiation of an ancestral species into divergent new populations or species. The abundance of variation in both environment and biodiversity make adaptive radiations the perfect natural laboratories to address our questions. We will use data from replicated adaptive radiations of three-spined stickleback fish in Scotland, Iceland, western Canada and Alaska in order to answer our questions and achieve a comprehensive understanding of how the environment affects evolution. Three-spined stickleback are originally marine fish that have invaded freshwater throughout the northern hemisphere since the last ice age. Freshwater stickleback can occupy contrasting environments and exhibit great phenotypic variation, providing a perfect system for our study.

Our understanding of the biogeochemical cycling of carbon in the oceans has been revolutionised through our ability to analyse several of the parameters that describe the carbonate system via gas exchange and the aqueous acid-base thermodynamic equilibria. Thus, the individual, or more commonly, combined measurement of dissolved inorganic carbon (DIC), hydrogen ion concentration (pH), total alkalinity (TA) and the partial pressure of carbon dioxide (pCO2) has provided us with the ability to determine the influence that primary production, respiration, and calcium carbonate precipitation and dissolution have on the chemistry of the oceans. Although the geographical and temporal data coverage of the CO2 system has increased since the inception of techniques to measure all its directly observable parameters, large gaps still exist in the oceanic data base. Particular black spots are the polar oceans and especially under sea ice cover. This is an important consideration, especially as the polar oceans are experiencing environmental change as a result of ocean acidification, which is particularly rapid in the land-locked Arctic Ocean. In addition, the presence of sea ice adds complexity to the polar environment as it consists of a dynamic environment of numerous inter-connected or isolated micro-habitats that expand and contract during the seasonal cycle of formation and decay of sea ice. The study of the complex, sea ice environment is important as it in now recognized as an active interface in the interaction between the ocean and the atmosphere, through which carbon species, transform and migrate. The biogeochemical information about the polar oceans is limited in part due to its relative inaccessibility, especially when there is ice cover, the complexity of the environment and the difficulty in working in harsh conditions, but also due to a lack of appropriate methods to work at these temperatures and knowledge of the change in the value of equilibrium constants used in determining parameters of the CO2 system under these conditions. Thus, our knowledge of the CO2 system at near-zero polar waters and the sub-zero temperatures in the brine enriched micro-habitats of sea ice is currently rudimentary compared with that in oceanic waters where the temperature is above-zero.As not all of the parameters that can describe the CO2 system fully (TA, DIC, pH, pCO2) can be reliably measured in some of the polar environments, this has meant that the value of the unmeasured or unmeasurable parameters must be calculated, a process that requires extrapolation of physical-chemical equations that really should only be used with above-zero temperatures and salinity less than 50. This type of extrapolation of can lead to large differences in the calculated pCO2 and pH. Thus, the aim of our research is to provide the necessary analytical tools and experimental data so that the CO2 system in polar environments can be investigated with the same degree of sophistication as that currently afforded in temperate and tropical temperature and salinity conditions. To be able to achieve this, we have chosen existing methods of measuring pH and pCO2 in ocean waters, which we can reliable modify to measure the same parameters in brine enriched solutions at sub-zero temperatures. Using our high quality measurements, we will determine the coefficients that are essential for the determination of CO2 system and subsequently test the validity of this approach by measuring any 2 (out of 4) directly observable physical-chemical parameters of the CO2 system to predict the remaining two. In the marine community, the use of these constants, tools, and analytical methodology will aid investigation of ongoing and future changes in the CO2 chemistry, carbon-based fluxes, and saturation with respect to calcium carbonate minerals in high latitude oceans, setting important constraints on model predictions of past, present, and future climate excursions.

Health is a critical aspect of human wellbeing, interacting with material and social relations to contribute to people's freedoms and choices. Especially in Africa, clusters of health and disease problems disproportionately affect poor people. Healthy ecosystems and healthy people go together, yet the precise relationships between these remain poorly understood. The Dynamic Drivers of Disease in Africa Consortium will provide a new theoretical conceptualisation, integrated systems analysis and evidence base around ecosystem-health-wellbeing interactions, linked to predictive models and scenarios, tools and methods, pathways to impact and capacity-building activities geared to operationalising a 'One Health' agenda in African settings. Ecosystems may improve human wellbeing through provisioning and disease regulating services; yet they can also generate ecosystem 'disservices' such as acting as a reservoir for new 'emerging' infectious disease from wildlife. Indeed 60% of emerging infectious diseases affecting humans originate from animals, both domestic and wild. These zoonoses have a huge potential impact on human societies across the world, affecting both current and future generations. Understanding the ecological, social and economic conditions for disease emergence and transmission represents one of the major challenges for humankind today. We hypothesise that disease regulation as an ecosystem service is affected by changes in biodiversity, climate and land use, with differential impacts on people's health and wellbeing. The Consortium will investigate this hypothesis in relation to four diseases, each affected in different ways by ecosystem change, different dependencies on wildlife and livestock hosts, with diverse impacts on people, their health and their livelihoods. The cases are Lassa fever in Sierra Leone, henipaviruses in Ghana, Rift Valley Fever in Kenya and trypanosomiasis in Zambia and Zimbabwe. Through the cases we will examine comparatively the processes of disease regulation through ecosystem services in diverse settings across Africa. The cases are located in a range of different Africa ecosystem types, from humid forest in Ghana through forest-savanna transition in Sierra Leone to wooded miombo savanna in Zambia and Zimbabwe and semi-arid savanna in Kenya. These cases enable a comparative exploration of a range of environmental change processes, due to contrasting ecosystem structure, function and dynamics, representative of some of the major ecosystem types in Africa. They also allow for a comparative investigation of key political-economic and social drivers of ecosystem change from agricultural expansion and commercialisation, wildlife conservation and use, settlement and urbanisation, mining and conflict, among others. Understanding the interactions between ecosystem change, disease regulation and human wellbeing is necessarily an interdisciplinary challenge. The Consortium brings together leading natural and social scientific experts in the study of environmental change and ecosystem services; socio-economic, poverty and wellbeing issues, and health and disease. It will work through new partnerships between research and policy/implementing agencies, to build new kinds of capacity and ensure sustained pathways to impact. In all five African countries, the teams involve environmental, social and health scientists, forged as a partnership between university-based researchers and government implementing/policy agencies. Supporting a series of cross-cutting themes, linked to integrated case study work, the Consortium also brings together the University of Edinburgh, the Cambridge Infectious Diseases Consortium and Institute of Zoology (supporting work on disease dynamics and drivers of change); ILRI (ecosystem, health and wellbeing contexts); the STEPS Centre, University of Sussex (politics and values), and the Stockholm Resilience Centre (institutions, policy and future scenarios).