2 bourses de thèse ouvertes à candidature :
• EASTBIO Impact of Biological Nitrification Inhibition on enhanced and sustainable crop production. Deadline le 6 janvier 2021.
One of the current greatest societal challenge is to deliver more productive and sustainable agriculture to feed the World’s growing population. Such challenge requires maximising the efficiency and sustainability of agricultural practices and resources. In this project, the student will work with groups specialised in soil microbial ecology, in natural product chemistry and plant genetics to tackle this challenge.
Nitrification is a crucial step of the nitrogen cycle as it oxidises ammonia into nitrate1. This has important economic and environmental consequences, with important loss of nitrogen fertiliser, nitrate leaching into groundwater soil and nitrous oxide production2. Synthetic nitrification inhibitors are available to farmers, but their application incur additional financial costs, which farmers with less resources afford with difficulty. Another approach to solve this nitrogen use efficiency dilemma is to use the natural nitrification inhibition compounds produced by plants, such as Brachiolactone3. This biological nitrification inhibition (BNI) process has large consequences for delivering a more productive and sustainable agriculture.
Such BNI approach has particular interest for tropical countries with large amount of degraded land requiring application of nitrogen fertilisers to agri-ecosystems, such as Indonesia. In addition to massive soil degradation due to deforestation and land-use changes, these agricultural soils are also subject to impact of climate change with large flooding events, increasing the demand for improved sustainable agricultural productivity. This project will therefore focus on understanding the BNI mechanisms in a variety of cultivated plants across Indonesia and it will benefit from an established collaborative network between UK and Indonesian researchers.
This project will focus on analysis of microbial activity and diversity upon growth of a range of crops, used for human food, animal fodder and biofuel production, including Sorghum and corn, which are important crops worldwide. Their genetic diversity will include well-studied varieties in research centres and other varieties used by local farmers across the Indonesia. Therefore, providing a sustainable alternative to their agricultural production would have important local economic and environmental advantages, with opportunities for worldwide implementation. In addition to plant varieties, the nature and amount of nitrogen fertilisers applied to agricultural soils are also likely to influence the BNI efficiency. Therefore, such effect will be analysed through a series of field-based and greenhouse experiments. Finally, since the first discovery of BNI molecule3, there has been limited chemical characterisation of these factors. This project therefore aims to fill this gap of knowledge by extracting and spectroscopically characterising these molecules.
Therefore, the key aims of this project are:
1) Determine the efficiency of BNI across a large variety of cultivated plants
2) Evaluate the effect of nitrogen fertilisation on the BNI efficiency
3) Identify the BNI using mass spectrometry molecular networking
4) Isolate the molecules responsible for the BNI
This PhD studentship will provide training in microbial activity and diversity characterisation (via ecosystem function and high-throughput sequencing), field and greenhouse plant growth, spectroscopic chemical characterisation and statistical analysis. The student will join dynamic research groups with international reputations and will gain experience of work in the tropics.
Lien d’information pour en savoir plus.
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• QUADRAT DTP: Ecological and evolutionary processes associated with environmental change in microbial populations. Deadline le 18 janvier 2021.
Understanding how biological diversity is created and maintained has been a key challenge for biologists for more than a century. Diversity is greatest in bacteria and archaea and its description has been dramatically improved by high-throughput sequencing which has been applied to a large range of land-use ecosystems. Large public genomic repositories now provide a fantastic opportunity to move beyond description and to solve some of the mysteries concerning the physiological and evolutionary mechanisms involved in biological diversification. Lateral gene transfer has been proposed as a key mechanism driving prokaryotic adaptation and this mechanism occurs within microbial population, including both closely related or more distant organisms. This project aims to analyse the microevolutionary mechanisms responsible for the creation and maintenance of diversity across several terrestrial ecosystems.
Microevolutionary mechanisms within microbial populations have been largely ignored by microbiologists partly due to the species concept debate and to the previously poor genetic diversity recovered from highly diverse natural microbial populations. However, the release of ultra-deep sequencing technology (such as Illumina NovaSeq) now opens new opportunities for microbial population analyses, such as population metagenomics, which allows exploration and interpretation of the myriad of individual haplotypes that provide the population-level diversity of natural microbiomes.
The proposed research will therefore use available deep metagenomics sequencing from a range of soils to establish a population metagenomics bioinformatics pipeline. Once established, the student will generate some novel deep metagenomics sequencing across a range of soil ecosystems to test specific hypotheses relating to the physiological and evolutionary microbial adaptation required in different land-use soils and across several environmental gradients. This project will also involve some in vivo experimental environmental perturbations (1) to determine the effect of several environmental changes on the existing standing variation in the native and perturbed populations as well as their consequences for ecosystem services, processes, function and resilience.
The PhD student will join a dynamic team of researchers headed by Dr Gubry-Rangin (University of Aberdeen). This well-established group with a world-wide reputation in microbial ecology and a high-impact track record focuses on ecology and evolution of microbial populations in various ecosystems (2,3). The student will also strongly interact with the research group of Prof. Creevey (Queen’s University Belfast), widely renowned for ecological theory and bioinformatics approaches and with the one of Prof. Hallett (University of Aberdeen), expert in soil science. All required training (including on bioinformatics) will be provided.
The PhD student will be part of a cohort of PhD students interested in environmental management, biodiversity and earth systems science, and will collaborate with a broad network of end-users and stakeholders. An excellent scientific environment will be provided to the student, with training on several state-of-the-art technological facilities, including genomic platforms and cutting-edge molecular and environmental facilities. The PhD student will therefore benefit from excellence in environmental science research with specific knowledge on research impact and policies critical for achieving Sustainable Development Goals, while gaining a diverse range of transferable and generic skills to ensure their competitive future career paths.