Using Reverse Metagenomics to characterise nematode communities and soil health

This project will extend a novel metagenomic approach to characterise nematode communities living in soil.

The studentship is part of the ARIES doctoral training partnership, funded by NERC and starts October 2019.

Apply for this course

Read the eligibility criteria and application guidance below, then apply though the University of East Anglia's online application system.

Application deadline: 8 January 2019

Overview

Free-living nematodes are present in huge numbers in the soil. A few species are estimated to cause tens of billions ($USD) of damage to crops globally each year. Other soil nematode species are predators of pests, with some used as biocontrol agents.

Currently identification is reliant on morphology, which is slow, costly, and fails to identify to species. Thus farmers use preventative spraying with toxic and indiscriminate chemicals to protect crops. If it were possible to classify nematode communities, farmers could match crop to suitable fields. This would reduce costs and pesticide use, improve soil health, and potentially protect biodiversity.

The supervisors have developed a method called Reverse Metagenomics to identify eukaryotic species in mixed samples. Briefly, each species of interest is ‘genome skimmed’:  low-coverage sequencing. These constitute the reference database. Then an environmental ‘query’ sample is sequenced with long-read technology. Each of the long reads is classified to a reference skim. We have used this method to characterise pollen collected by bees.

Supervision and training

We will extend Reverse Metagenomics to nematodes by skimming individual nematodes, followed by kmer-matching (Ondov et al. 2016) to cluster species.

We will use a low-cost library-prep method developed by co-supervisor Matt Clark (Mascher et al. 2017). From each skim, we can also assemble high-copy-number genes for assignment against databases.

We expect many nematodes not to have names, but higher level assignment can be achieved with phylogenetic placement. This way, we can take mixed samples of nematodes and generate both skims and quantify their compositions.

The student will develop this pipeline and work with a commercial company to apply the method to UK agricultural soils.

Methodology

The student will be trained in a full suite of genomics methods: Illumina (short-) and long-read (Min/GridION/PromethION) sequencing, kmer analysis, and statistical analysis. The student will also learn bioinformatic scripting and project management. We plan an internship at Prof Yu’s lab at the Kunming Institute of Zoology.

Person specification

Any science background is suitable, although some previous laboratory experience will be helpful for you to know whether you like that side of things. Programming will be a large part of the PhD.

Eligibility

ARIES studentships are available to UK and EU applicants only.

Residency rules apply. In general, UK and EU nationals who will have been resident in the UK for three years or more at the time when their PhD begins will be eligible for a full ARIES studentship. UK and EU nationals who have been resident outside the UK but within the EU during the qualifying period will usually be eligible for a ‘fees only’ studentship, which pays research costs and tuition fees but gives no help with living expenses.

In case of uncertainty, the planned university of registration should be contacted for eligibility advice; or the ARIES administrators.

All applicants need to comply with the registered university's English-language requirements.

Applicants should have obtained or be about to obtain a First or Upper Second Class UK Honours degree, or equivalent qualifications gained outside the UK. Applicants with a Lower Second Class degree will be considered if they also have a master's degree. Applicants with a minimum Upper Second Class degree and significant relevant non-academic experience are encouraged to apply.

How to apply

Applications for the PhD are processed through the University's of East Anglia's online application service.

Applications will need to be supported by:

  • A full CV
  • A statement that gives (for example) details of the candidate’s interest in the studentship project, and any skills etc they can bring to it
  • Electronic copies of certificate(s) and transcript(s) for all relevant qualifications (degrees etc)
  • Two references, of which at least one must be an academic reference.

The application deadline is 23:59 on 8 January 2019.

Any questions?

If you have any questions about the project please contact

Main supervisor: Prof Douglas Yu

Supervisors

University of East Anglia

Main supervisor: Prof Douglas Yu

Co-supervisor: Prof Matt Hutchings

The Natural History Museum

Co-supervisor: Dr Matt Clark

References

Tang, M., Hardman, C.J., Ji, Y.Q., Meng, G.L., Liu, S.L., Tan, M.H., Yang, S.Z., Moss, E.D., Yang, C.X., Bruce, C., Nevard, T., Potts, S.G., Zhou, X., and D.W. Yu. (2015) High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Meth Ecol & Evol. 6:1034–1043

Leggett, R.M., Clark, M.D. 2017. A world of opportunities with nanopore sequencing. Journal of Experimental Botany. 68:20

Mascher, M., H. Gundlach, A. Himmelbach, S. Beier, S. O. Twardziok, T. Wicker, V. Radchuk, …, Clark, M.D., et al. 2017. A chromosome conformation capture ordered sequence of the barley genome. Nature 544:427

Ondov, B. D., T. J. Treangen, P. Melsted, A. B. Mallonee, N. H. Bergman, S. Koren, and A. M. Phillippy. 2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology 17:132.

Stirling, G.R. 2000. Nematode Monitoring Strategies for vegetable crops. A report for the Rural Industries Research and Development Corporation. RIRDC Publication No 00/25.

ARIES Doctoral Training Partnership

The ARIES (Advanced Research and Innovation in the Environmental Sciences) doctoral training partnership draws together expertise from five universities and nine research centres, as well as over forty other research-users.

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