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Metagenomics of bacteria and bacteriophages of ants and their nests

Principal Supervisor: Dr Rob Hammond - Department of Genetics

Co-supervisor: Professor Martha Clokie

PhD project title: Metagenomics of bacteria and bacteriophages of ants and their nests

University of Registration: University of Leicester

Project outline:

Humans are faced with continual attack from microorganisms that lead to disease. However, treatment of such diseases is threatened by antibiotic resistance. Given this, it is timely to investigate new ways that microorganisms are controlled. A potentially productive avenue is to investigate 1) how species with high disease threats have evolved to deal with the potential dangers of microorganism associated disease, and 2) alternatives to antibiotics.

We propose an innovative PhD project investigating the bacteria and their bacteriophages that inhabit ants and their nests. Our rationale is that ants have both a lifestyle and evolutionary history that means that have evolved to cope with a high threat of disease by microorganisms and potentially bacteriophages might be important in this. This high threat level is supported by ants self-medicating and possessing symbiotic bacteria that help control pathogenic bacteria [1].

All 14,000+ species of ants live in integrated social groups of varying complexity. Colony size varies from tens to millions of individuals but in all species individuals live in close proximity to one another, often at very high densities. Such social living makes disease transmission likely, especially as colony members forage in the wider environment, returning with resources and disease. Trophollaxis – mouth to mouth feeding – increases disease transmission, while homeostatically regulated nests encourage microorganisms to flourish. Importantly, sociality in ants is longstanding, having evolved >150 million years ago. This high threat environment has therefore shaped ant evolution for many tens of millions of years. Given ants are ecologically dominant in many environments ants have evolved effective mechanisms to cope with this disease onslaught.

Bacteriophages are viruses that infect bacteria. They are beginning to be viewed as important drivers of bacterial population dynamics and evolution [2] but also as novel therapeutic agents [3]. However, the study of phages in the natural environment is in its infancy [3] and little is known about the bacteriophages that infect ants and their nests. Teaming up these two areas of research – ant biology and phage biology – is exciting and timely and certainly rewarding.

Proposed work. We will use next generation sequencing to identify the metagenome of ants and their nests. Total bacteriophage metagenomes will be analysed by sampling nest material and ants and suspending it in a stabilising phage buffer. Viral fractions can be filtered out (0.22 micrometre filter) and precipitated using iron chloride. The DNA is then retrieved from these samples using techniques previously established the Clokie lab. Full viral metagenomes will be sequenced on Illumina. In addition, we will also identify bacteria and fungi using multiplex PCR amplification Illumina sequencing of 16sRNA (bacteria) and the ITS region of rRNA (fungi).

We will investigate a number of ant species that share the same habitat (e.g. pine woodland) but that differ in colony size. For example, Formica rufa (100-400 thousand individuals) and Leptothorax acervorum (100-200 individuals).

Questions to be answered: 

  • What bacteria / bacteriophages are found?
  • To what extent does bacteria and bacteriophage diversity vary between nests /populations/species?
  • Does bacteriophage diversity correlate with bacterial diversity?
  • Does bacteriophage diversity correlate with colony size?
  • To what extent does bacteria and bacteriophage diversity vary between castes in the same nest? Ant castes have quite different roles (queen reproduce, workers forage, defend and tend larvae) and show spectacular differences in longevity (some queens can live for >30 years, workers ~1 year).

References:

  1. Bos N., Sundström L., Fuchs S., Freitak D. 2015 Ants medicate to fight disease. Evolution 69(11), 2979-2984. (doi:10.1111/evo.12752).
  2. McFall-Ngai M., Hadfield M.G., Bosch T.C.G., Carey H.V., Domazet-Lošo T., Douglas A.E., Dubilier N., Eberl G., Fukami T., Gilbert S.F., et al. 2013 Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A 110(9), 3229-3236. (doi:10.1073/pnas.1218525110).
  3. Clokie M.R.J., Millard A.D., Letarov A.V., Heaphy S. 2011 Phages in nature. Bacteriophage 1(1), 31-45. (doi:10.4161/bact.1.1.14942).

BBSRC Strategic Research Priority: Molecules, cells and systems

Techniques that will be undertaken during the project:

  • Sampling in the field
  • DNA extraction from bacteria and bacteriophages
  • PCR amplification
  • Illumina library construction
  • Next generation sequence data handing
  • Bioinformatics (e.g. genome assembly)
  • Molecular taxonomy

Contact: Dr Rob Hammond, University of Leicester