BSc Microbiology with a Modern Language

Year of entry: 2024

Course unit details:
Environmental Microbiology

Course unit fact file
Unit code EART21102
Credit rating 10
Unit level Level 5
Teaching period(s) Semester 2
Available as a free choice unit? No


The unit will be delivered by SEES environmental microbiologists, augmented with invited guest lectures as appropriate covering emerging “hot topics” in the area. Initial lectures will focus on the “microbiological basics” to make sure that all of the students on the course have the required foundations, followed by lectures (and group activities) covering microbial diversity on Earth, microbial habitats and community dynamics, and finally microbial processes that control the elemental cycles on our planet (linking molecular-scale processes to global impacts). Techniques that underpin this rapidly advancing field will also be described and demonstrated via visits to SEES research laboratories. Lectures and group activities on the “fundamentals” of environmental microbiology will also be complemented by more applied content, showing how these natural processes can be utilised in diverse areas of science of

technology. These will include environmental biotechnology, bioremediation, geodisposal of waste materials, food security and climate mitigation.


The lecture course will include the following topics

-Introduction to environmental microbiology (background to course, basic biology primer).

-Techniques for microbiology (including sampling, DNA/RNA/Cell cultivation).

-The origin of life, and microbial diversity from 3.5 billion years of microbial evolution.

-Microbial habitats (soil water, the atmosphere).

-Microbial controls on the carbon, nitrogen and sulfur cycles.

-Trace element and metal cycling (Fe/Mn, trace/toxic metals and radionuclides).

-Effects of climate change on microbial processes including effects on carbon cycling.

-Environmental applications; environmental biotechnology and bioremediation, microbial controls on geodisposal, plant-soil-microbial interactions and food security



 1st year Earth & Planetary Science or Environmental Science


The aim of this course is to provide insight into the role that microbes play on a wide range of environmental processes, describing the molecular-scale mechanisms that underpin globally important bioprocesses. The fundamental principles of environmental microbiology will be described (including microbial habitats, evolution, community dynamics and elemental cycling) alongside applied content that will show how microbial processes can be harnessed for a wide range of environmental and biotechnological applications.


Learning outcomes


On the successful completion of the course, students will be able to:


Describe and apply a range of techniques important for environmental microbiology research, including techniques from both the biosciences (including genomic approaches) and the physical sciences. 



Evaluate how microorganisms control the chemistry of Earth, controlling a wide range of elemental cycles.



Critically analyse seminal environmental microbiology papers from the peer review literature.



Assess how natural microbiological processes can be used for applications including environmental biotechnology, bioremediation, geodisposal and food security.




Week 1: Introduction to environmental microbiology (background to course, basic biology primer).

Week 2: Techniques for geomicrobiology (DNA/RNA/Cell cultivation)

Week 3: Sampling for extremophiles; breakout session. Oral presentations

Week 4: The origin of life, and microbial diversity from 3.5 billion years of microbial evolution

Week 5: Microbial habitats on modern earth (soil Antarctic/Arctic/Peat, water, the atmosphere).

Week 6: Microbial controls on the carbon cycle (+ bioremediation organics)

Week 7: Microbial controls on the nitrogen and sulfur cycles (+ bioremediation topics).

Week 8: Trace element and metal cycling (Fe/Mn, trace/toxic metals and radionuclides)

Week 9: Effects of climate change on microbial processes

Week 10: Plant-soil-microbial interactions and food security.

Week 11: Seminal papers poster session

Week 12: Past papers and revision


Teaching and learning methods

The unit will be based around 20 x 1 hour lectures, with time included for discussions with the students. The lectures will be posted as Powerpoint presentations on Blackboard, and podcasts will be enabled. Lecture content will be augmented by further reading, including seminal reviews and research papers, which will be cited in the lectures. Students will be expected to attend each lecture as an introduction to the topic being discussed, and then learn the material from the Blackboard content and further reading via independent study.

Group work will further augment the lecture content via directed learning targeting (1) microbial characterisation methodologies, and (2) seminal advances from the peer reviewed literature. This will give the students experience in team-work and presentation skills (oral and poster), while improving the understanding of the wide range of techniques underpinning environmental microbiology. It will also encourage a critical appraisal of the scientific literature. For the latter, seminal papers will be cited throughout the lectures, with clear instructions showing why the papers are important. The students can choose one of these papers to present to their colleagues as a seminal piece of work in a final “miniconference” poster session, or they can choose alternative papers from their independent reading. Examples of what would be required in the group presentations will be provided in advance, and formative feedback given to the groups immediately after the classes.


Short online multiple-choice tests will help the students strengthen their understanding of environmental microbiology techniques and concepts described in the lectures and demonstrated during laboratory tours. A revision session will be held in the last week of teaching, to help prepare the students for the final exam.

Assessment methods

Method Weight
Written exam 70%
Oral assessment/presentation 30%

Feedback methods


Assessment type

% Weighting within unit

Hand out and hand in dates



How, when and what feedback is provided

    ILO tested




    2 hours

Written after exam



(poster) on

seminal papers from the literature


    Week 12

1 hr mini      conference

Written after poster presentations





Recommended reading


Selected chapters from:  Pepper Environmental Microbiology, Brock Microbiology, Ehrlich Geomicrobiology (various editions)

Research papers and key reviews cited in the lectures. Direct links provided in lectures.


For Information and advice on Link2Lists reading list software, see:


Study hours

Scheduled activity hours
Lectures 18
Seminars 4
Independent study hours
Independent study 78

Teaching staff

Staff member Role
David Johnson Unit coordinator
Clare Robinson Unit coordinator
Jonathan Lloyd Unit coordinator

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