Environmental Microbiology

Module code: BS3013

Module co-ordinator: Professor Martha Clokie 

In this module you will explore current views of microbial evolution, evaluate the continuing roles played by microbes in the environment, and consider the non-pathogenic roles of microbes in the human body. We will critically assess current views on the origins of life and the evolution of the major microbial taxa, drawing on evidence from the fossil record, abiogenic syntheses experiments, and molecular evidence in gene sequence. We will investigate the key roles played by microbes in the aquatic and terrestrial environment, including soil structure, element cycles, metal extraction and human health, and evaluate important plant-microbe interactions such as the rhizobium-legume symbiosis and the possibilities for manipulating such systems to agronomic advantage.

Topics covered

  • The early Earth as an environment: prebiotic evolution; abiogenic synthesis of organic components; the Precambrian fossil record; evolution of cell types; microbial diversity; the species concept; origins of eukaryotes
  • Metagenomics and other techniques used in microbial ecology
  • Plant-microbe interactions: manipulation of the rhizosphere by microbial inoculation; the uses of microbes in biological control of plant disease; the molecular biology of the interaction between Rhizobium spp. and the roots of legumes 
  • Microbes and metals: the molecular biology of metal transformations and metal resistance in selected bacteria; the use of microbes in leaching low-grade ores (biohydrometallurgy) 
  • The carbon cycle: global considerations; carbon cycling; methanogenesis, and methane oxidation – organisms and biochemistry
  • The aquatic environment: microbiology of fresh-water environments – organisms and geochemistry; the marine environment as a microbial habitat; extreme environments
  • The sulphur cycle: global considerations; the organisms and their contribution; biochemistry of sulphur reduction and sulphur oxidation; geochemical effects of sulphur transformation – ore deposition and evidence for microbiological involvement in economically significant ore deposits; detrimental effects of sulphur bacteria, corrosion of metals
  • The nitrogen cycle: global considerations; organisms and their contribution; biochemistry of dinitrogen fixation, nitrification and agronomic significance of plant-microbe interactions, e.g. Rhizobium and Frankia
  • Environmentally important microbial fungi: the diversity and implications of fungi associated with human environments
  • Bacteriophages: their diversity and roles in microbial communities
  • The human microbiome: the diversity and roles of non-pathogenic microbes associated with the human body


  • 30 one-hour lectures
  • 10 one-hour seminars
  • 2 one-hour tutorials


  • Presentation, 15 minutes (15%)
  • Essay, 2,000 words (15%)
  • Exam (70%)