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Several competitive PhD positions are currently open, so please visit findAPhD website or follow me on twitter!

Please check this advert if interested in microbial cultivation and genomics: 

 https://www.findaphd.com/phds/project/super-dtp-the-impact-of-environmental-change-on-the-ecological-and-evolutionary-dynamics-of-symbiotic-sponge-communities/?p168822 

(sorry, only open to UK students)

Technological expertise

Our technical expertise is quite varied, from lab-based to dry-based approaches. The questions investigated are driving the use of approaches and tools, and if we don’t have specific expertise, we collaborate with experts. Below is a non-exhaustive list of tools and facilities we have access to. Genomics tools can complement environment-based studies to understand microbes' physiological or environmental adaptation, which can be tested using cultivation-based approaches, controlled microcosm experiments, or by investigating complex gene functions. The group brings multi-technical expertise ranging from hands-on experimentation using culturing of nitrifiers, soil and environmental analysis techniques, molecular investigative techniques and growth of plants to bioinformatics and data analysis development. 

Archaeal and bacterial nitrifier culture collection

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Pure or enriched nitrifier strains are essential to confirm the physiology of different ammonia-oxidising phylotypes. Previous and current cultivated strains have allowed to understand the microbial environmental adaptations to pH, temperature or oligotrophic conditions, advancing insights into detailed metabolic information regarding substrate affinities or greenhouse gas production. Archaeal and bacterial nitrifiers are challenging to enrich, isolate and maintain due to these organisms' sensitivity and slow growth. Despite limitations, our lab has a history of isolation of several key archaeal and bacterial strains from soils. We host a comprehensive culture collection of several nitrifier strains from ammonia-oxidising archaea, ammonia-oxidising bacteria and nitrite-oxidising bacteria. 

Stable-Isotope Probing

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Stable isotope probing (SIP) is a powerful technique used to identify and study the metabolic active microbial groups in diverse environments. By introducing isotopically labelled compounds (such as 13CO2 or H218O) into soil, we can track the uptake and assimilation of these labelled substrates by specific microbes. This allows for the identification of active microbial populations involved in specific metabolic processes, such as carbon and nitrogen cycling.

Molecular approaches (DNA, RNA, proteomics)        

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Genome sequences are among the more powerful tools available for studying new organisms as they allow detailed metabolic prediction, as well as being a gateway to more detailed phylogenomic reconstruction of evolutionary history. The expression of genes encompasses their transcription into mRNA followed by translation into protein. An omics approach of genomic, transcriptomic and proteomic methods can provide an integrated measure of gene expression allowing for identification of genes and pathways involved in metabolic processes.

Soil ecosystem processes

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Organisms may be defined as specialists or generalists by the range of environments in which they thrive (their niche). Conventional wisdom in ecology of higher organisms predicts a strong trade-off between niche breadth and fitness. Our group studies the niche breadth trait and its effects on fitness in numerous contexts, including environmental change. How niche breadth affects community assembly and diversity in the context of environmental change in natural environments is of particular interest

Bioinformatics

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We use bioinformatics to explore diverse aspects of ecology and evolution. At the community level, we use high throughput amplicon and shotgun metagenomic analyses to investigate niche breadth and specificity, phylosymbiosis and functional metagenomics. We also combine this with long read and Sanger sequencing for individual genome construction and phylogenomic analyses. See our github page for some of our pipelines and analyses. For all these analyses, we have access to a High-performance Computer (Maxwell).

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