Earthworm microbiomics


Earthworms are the single largest contributors to the soil invertebrate biomass in many ecosystems and have long been recognized for the benefits they bring to the environment. Important functions of earthworms include processes such as soil aeration, bioturbation and organic matter fragmentation that are vital for promoting soil structural development and nutrient cycling . As soil organisms, earthworms are in intimate contact with changing soil chemistries and bio-available pollutants. It is essential to understand how these soil organisms adapt, in terms of both physiology and evolution, to these highly variable environments. The earthworm plays host to a number of discrete bacterial communities acquired either horizontally from the surrounding soil, as with the gut fauna, or through vertical parental transmission, as observed for the nephridial symbiotes. The earthworm gut microfauna exists within a discrete anaerobic environment and plays host to organisms containing unique suites of nitrogen fixing bacteria transforming the chemistry of the soil as it traverses the gut. We will test the overarching hypothesis that “Earthworm microbiomes contribute directly to the host’s phenotypic plasticity” by use metagenomic analyses to determine the role played by these bacterial microbiomes in the ability of the earthworm to adapt to the extreme ranges of soil chemistry, both natural and anthroprogenic.


The overall aim of the project will be to determine the mechanistic contribution played by the earthworm microbiome to the host ecology and plasticity by achieving the following objectives:

  • To informatically profile the phylogenetic composition and transcriptional activity of the microbiomes (gut and nephridial) in genetically homogeneous populations of earthworms resident on soil of contrasting chemistry (heavy metals and pH).
  • To derive the relationship between host genotype and microbiome phylogeny overlaid with function metagenomic analysis.
  • To determine the fitness of earthworms hosting microbiomes transplanted from hosts resident on contrasting soil chemistry (heavy metals and pH).
  • To describe and evaluate the changes in the earthworm microbiomes occurring when hosts are transplanted into soils with chemistries contrasting with their resident habitat.
  • To determine whether mobile genetic elements (mobilome) within the earthworm microbiome facilitate viability within host resident to extreme soil environments.