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Size matters! - Bacterial genome size and its implications in ecological traits and niche distribution.

  • Full or part time
  • Application Deadline
    Wednesday, January 16, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

"""What if all animals can be divided into just two groups - the large and the small? This certainly is not true with animals, but when it comes to bacteria we are less certain.""

Body size in animals has significant correlations with ecological traits, such as metabolism, population size, ecological range and niche breadth. However much less is known whether these observations hold true in the bacterial kingdom. Studies indicate that the interaction between an organism and its ecological niche, for example, resource availability and environmental stability, selects the genome size of the species.

The exact mechanisms driving the genome sizes are still not well understood. It has, however, been speculated that species living in invariant niches tend to have small genomes, as stability acts to reduce genome size due the metabolic burden of replicating DNA with no adaptive value such as in obligatory and intracellular pathogens or mutualists. Due to their metabolic diversity, species with large genomes are potentially able to tackle a wider range of environmental conditions and tend to be more ecologically successful where resources are scarce but diverse, and where there is little penalty for slow growth. As a result of these two competing “forces”, bacterial genome sizes have previously been shown to exhibit a bimodal distribution.

However, a recent study by the supervisory team revealed that there is a significant bias in the genome sequencing efforts towards a certain group of species, and that correcting the bias using species nomenclature and clustering of the 16S rRNA gene, results in a unimodal rather than the previously published bimodal distribution (Gweon et al., 2017). We however did not reject the possibility of a bimodal distribution in bacterial genome size, and there are still a number of observations which point to the possibility of a bimodal distribution including the bimodality in flow cytometric analysis of bacterial DNA content (Schattenhofer et al., 2011; Morán et al., 2015), and discovery of a whole new array of species with small genomes from environmental metagenomes (Giovannoni et al., 2014; Morán et al., 2015).

In this project, we will combine both wetlab work and bioinformatics to attempt to solve these unanswered questions by using (i) existing and new computational methods, including predictive modelling and machine learning approaches for assessing publicly available databases; and (ii) extensive lab techniques including flow cytometry and Next Generation Sequencing to examine distribution of genome sizes in various environmental niches.

The project will be ideal for a graduate student (biological science or non-biological background) with existing computational or mathematical skills, and who has an interest in collating theories and methods. When applying for this position please provide evidence of the following: Interest in the aims of the QMEE CDT, Research experience/potential, Academic training (degree class obtained or expected in BSc/MSc; at least two academic references).

The supervisory team for the project will include Dr Soon Gweon at the University of Reading and Dr Daniel Read at the Centre for Ecology and Hydrology.

To apply please send your CV, cover letter and academic references to Dr Soon Gweon by 5pm on 16 January 2019. The cover letter should explain your interest in and suitability for the project and the QMEE College of Doctoral Training. Informal enquiries are welcome.

- Gweon HS, Bailey MJ, Read DS. Assessment of the bimodality in the distribution of bacterial genome sizes. ISME J. 2017;11(3):821-824
- Schattenhofer M, Wulf J, Kostadinov I et al. Phylogenetic characterisation of picoplanktonic populations with high and low nucleic acid content in the North Atlantic Ocean. Syst Appl Microbiol 2011 34(6):470-5
- Giovannoni SJ, Cameron Thrash J, Temperton B, Implications of streamlining theory for microbial ecology. ISME J. 2014;8(8):1553-65
- Morán XAG, Alonso-Sáez L, Nogueira E et al. More, smaller bacteria in response to ocean’s warming? 2015 Proc R Soc B 282:20150371
"

Funding Notes

This project is in competition for funding from the NERC QMEE CDT View Website. Commencing autumn 2019 if successful. Full studentships (fees and stipend) are available to UK and other EU nationals who have resided in the UK for three years prior to commencing the studentship. Citizens of an EU member state are eligible for a fees-only award, and must be able to support themselves for the duration of the studentship at the RCUK level.



References

References: https://www.reading.ac.uk/biologicalsciences/about/staff/h-s-gweon.aspx

Eligibility requirements: Applicants should hold a minimum of a UK Honours Degree at 2:1 level or equivalent or a Masters degree in a relevant subject, such as Computer Science, Biological Sciences, Biochemistry, Molecular Biology, Biomedical Sciences, Genetics or Bioinformatics. Programming skills are essential.


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