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Microbial Ecology

Module titleMicrobial Ecology
Module codeBIO3099
Academic year2018/9
Module staff

Dr Dan Bebber (Convenor)

Duration: Term123
Duration: Weeks


Number students taking module (anticipated)


Description - summary of the module content

Module description

To a first approximation, life on Earth is microbial, and the transformation of Earth from a barren ball of rock to the oxygen-rich environment that supports us is a direct result of microbial metabolism. Even the human body contains more microbial than human cells. From global biogeochemical cycles to the interactions between individual organisms and their retinue of beneficial and detrimental microorganisms, understanding microbial ecology – the interactions between microbes and their environment – is key to understanding the functioning of Planet Earth. We will study carbon and nutrient cycling in the oceans, how terrestrial ecosystems are formed and controlled by microbes, the impact of plant-microbe interactions on forests and food production, and the applications of microbial biotechnology.

Pre-lecture content will be delivered online and followed with interactive student-staff sessions, where we will improve your core academic skills: how to analyse and present data; how write an excellent essay; how to deal with Big Data; how to make science accessible for a general audience; and how to give an interesting talk – all while learning about the roles that microbes play in ecosystems and biotechnology.

Module aims - intentions of the module

You will learn about the important roles of microbes in three biomes: the oceans, natural terrestrial ecosystems (primarily forests), and managed terrestrial ecosystems (crop production). You will uncover the role of microbes in major global challenges such as climate change and food security. The growth of nucleotide sequencing and other technologies has led to an explosion of data and knowledge on microbes. Understanding these technologies will be an important outcome of the module, linking to lectures on applications in biotechnology and sustainable agriculture. Module content is updated every year to explore topical research areas, including those carried out by the lecturers, and are of global relevance.

The classes will be structured around training in the core skills of: data analysis and visualisation and science communication (verbal and written). For example, you will learn about methods of exploring very large datasets using statistical methods that reveal the structures within Big Data. Rather than listening passively to lectures, you will work in class to produce the kinds of outputs (e.g. blog articles, posters, short talks, publishable figures) that are key tools in research.

Through the practicals and assessments, you will develop skills relevant to future employment:

  • How to critically assess the content and quality of information sources (e.g. articles) and summarise this content concisely and accurately for different audiences (e.g. via short talks, posters or blogs)
  • How to give oral presentations that excite and interest the audience
  • How to write essays that present information in a readable and engaging manner
  • How to discuss ideas and information in small groups and work with colleagues to develop analyses and synthesise information
  • How to present data informatively and beautifully.

Intended Learning Outcomes (ILOs)

ILO: Module-specific skills

On successfully completing the module you will be able to...

  • 1. Describe in detail carbon and nutrient cycles in the oceans, and discuss controls on primary production rates
  • 2. Summarise microbial control of terrestrial ecosystems and nutrient cycles, and discuss the effects of global change on these cycles
  • 3. Discuss the applications of microbes in biotechnology and sustainable agriculture
  • 4. Describe how microbial activity on ancient Earth and other planets can be reconstructed

ILO: Discipline-specific skills

On successfully completing the module you will be able to...

  • 5. Discuss microbial diversity and its determinants, and understand phylogenetic relationships among microbes
  • 6. Elucidate the role of microbes in biogeochemical cycles and biosphere-climate feedback mechanisms
  • 7. Explain biotic interactions among microbes and between microbes and plants

ILO: Personal and key skills

On successfully completing the module you will be able to...

  • 8. Analyse data and make elegant figures
  • 9. Make science accessible to a general audience
  • 10. Write an excellent essay
  • 11. Give an interesting and informative presentation

Syllabus plan

Syllabus plan

Classes will be divided into four sections: The transformation of the Earth from an inert rock to a living planet; the biogeochemistry of the oceans; the microbial ecology of soils; and the applications of microbes in biotechnology. In each class you will work on particular core skill, producing a piece of work that will be assessed formatively. A second class will reinforce that skill, and your outputs will be assessed summatively as a portfolio of work.

An important component of the module will be your contributions to examples of microbial ecosystem function and biotechnology. You will write a summative essay on the role of microbes in ecosystem function, biogeochemistry, and/or biotechnology, expanding on the different groups of organisms active in these processes and the importance of these processes globally. You will also give a short presentation on your essay subject to the class.

Learning and teaching

Learning activities and teaching methods (given in hours of study time)

Scheduled Learning and Teaching ActivitiesGuided independent studyPlacement / study abroad

Details of learning activities and teaching methods

CategoryHours of study timeDescription
Scheduled learning and teaching18Classes working on core skills
Scheduled learning and teaching4Student talks
Guided Independent study58Online lectures and associated reading
Guided Independent study40Practising core skills
Guided Independent study30Preparation for class presentations


Formative assessment

Form of assessmentSize of the assessment (eg length / duration)ILOs assessedFeedback method
Quiz10 minutes1-7Oral
Graphical and statistical data analysis1 hour1-8Written
Blog article and podcast1 hour1-7, 9Written
Poster1 hour1-9 Written

Summative assessment (% of credit)

CourseworkWritten examsPractical exams

Details of summative assessment

Form of assessment% of creditSize of the assessment (eg length / duration)ILOs assessedFeedback method
Scientific essay502000 words1-7, 10Written
Assessed coursework (poster, blog, presentation, data analysis)50Variable, depending on class1-9, 11Written, oral


Details of re-assessment (where required by referral or deferral)

Original form of assessmentForm of re-assessmentILOs re-assessedTimescale for re-assessment
Scientific essayEssay1-7, 10August Ref/Def
Assessed courseworkPoster1-9, 11August Ref/Def

Re-assessment notes

Deferral – if you miss an assessment for certificated reasons judged acceptable by the Mitigation Committee, you will normally be either deferred in the assessment or an extension may be granted. On deferral, the assessed coursework will be re-assessed by poster. The mark given for a re-assessment taken as a result of deferral will not be capped and will be treated as it would be if it were your first attempt at the assessment.

Referral – if you have failed the module overall (i.e. a final overall module mark of less than 40%) you will be required to re-submit the essay or a poster as necessary. The mark given for a re-assessment taken as a result of referral will be capped at 40%.


Indicative learning resources - Basic reading

Overview of the module aims:

Some introductory reading (you can read each of these in a few hours):

  • Astrobiology: A Very Short Introduction by David C. Catling, OUP (2013)
  • Agriculture: A Very Short Introduction by Paul Brassley and Richard Soffe, OUP (2016)
  • Bacteria: A Very Short Introduction by Sebastian G.B. Amyes, OUP (2013)
  • Earth System Science: A Very Short Introduction by Tim Lenton, OUP (2016)
  • Fungi: A Very Short Introduction by Nicholas P. Money, OUP (2016)
  • Microbiology: A Very Short Introduction by Nicholas P. Money, OUP (2014)

Longer popular science books:

  • Coral Reefs in the Microbial Seas by Forest Rohwer, Plaid Press (2010)
  • Life on a Young Planet by Andrew H. Knoll, Princeton University Press (2013)

Main textbooks:

  • Brock Biology of Microorganisms 14th Edition, by Madigan et al., Pearson
  • Agrios'Plant Pathology by Agrios GN and Beckerman J, Academic press

Indicative learning resources - Web based and electronic resources

Module has an active ELE page

Indicative learning resources - Other resources

  • Primary research publications and review articles covering various topics will made available.

Key words search

Food security, plant pathogen, fungi, plant disease, host-pathogen interactions, epidemiology, climate change, biofilms, bioremediation, biotechnology, soil microbiome

Credit value15
Module ECTS


Module pre-requisites

BIO2095 Plants and People and BIO2078 Medical and General Microbiology

Module co-requisites


NQF level (module)


Available as distance learning?


Origin date


Last revision date