BI3B67-Microbiology Field Course

Module Provider: School of Biological Sciences
Number of credits: 20 [10 ECTS credits]
Level:6
Terms in which taught: Summer term module
Pre-requisites: BI1S1 Introductory Microbiology
Non-modular pre-requisites: Takes place in Summer after the Part 2 Exams, registration takes place in the Spring Term. Numbers restricted
Co-requisites:
Modules excluded:
Current from: 2019/0

Module Convenor: Prof Robert Jackson

Email: r.w.jackson@reading.ac.uk

Type of module:

Summary module description:

This module will be part-field and part-lab based in either Northern Iceland or Colombia (rotating every year) to gain skills in microbiology and specifically to examine the unusual microbes that inhabit extreme environments, such as glacial rivers and volcanic geothermal areas (Iceland) or mid-altitude Andean forest and low altitude Carribean jungle and banana plantation (Colombia). The base for this module will be the University of Akureyri (UnAk), Iceland or EAFIT University, Medellin, Colombia. Akureyri is in the Arctic region and is in close proximity to glacial rivers and volcanic geothermal zones, which will be visited for sampling. N.B. Access to geothermal sites will be dependent on current safety recommendations. Medellin is in the tropical region and with excellent access to sites for sampling.


Aims:

The aim of this module is to provide students with an opportunity to learn field-based sampling techniques and to learn about the microbial biodiversity in the Arctic and tropics and how it is changing. This will be done by teaching the students sampling and analysis techniques. The practical aspect will facilitate a better understanding of science outside the laboratory, but it will also improve students’ learning of theory on microbial evolution and function, particularly those of extremophiles. Therefore, the project will be a novel and exciting addition to teaching and learning. Moreover, we aim to make the field trip a joint module with Icelandic students, Colombian and American students, so that our hosts at UnAk or EAFIT will partner us in teaching.


Assessable learning outcomes:

By the end of the module it is expected that the student will be able to:




  • Design an appropriate approach for sampling from different environments

  • Implement a range of culturing techniques to isolate different microorganisms

  • Identify different characteristics of extremophiles

  • Identify and implement analytical techniques including genomics for characterisation of extremophiles

  • Understand the roles of microbes in various environments and how the environment shapes bacterial evolution

  • Understand the microbial characteristics that enable survival in extreme conditions and potential biotechnological applications


Additional outcomes:

Interaction with other EU/South American/North American students and life in an Icelandic/Colombian university, including innovative teaching methods such as distance learning.


Outline content:

The field trip will be preceded by seminars to discuss the outline of the trip and to aid the students in designing the approaches they will take for sampling and analyses. In Iceland/Colombia, the students will spend 3-4 days sampling, with examples described below.




  1. Extremophile analysis: sampling from geothermal pools and volcano slopes.

  2. Glacial microbial biodiversity: water, glacier and lichen sampling.

  3. Tropical microbial biodiversity: jungle and banana plantation.

  4. River/mountain/cave/desert sampling to analyze microbial biodiversity from different extreme habitats.



Once the samples have been acquired, the students will then use the laboratory facilities at UnAk/EAFIT to culture the microbes and carry out different techniques to characterise the diversity and the microbes, these are detailed below.




  • Culturing bacteria and extremophiles.

  • Plating bacteria for most probable number analysis using indicator dyes.

  • Use tests to analyse for SRB and NRBs.

  • Multiplex PCR for group-specific analysis.

  • Microscopy to analyse extremophile cells.

  • Examination of biocontrol properties.



Concerning the 5-6 day period in the laboratory, we are aiming to give a lecture at the beginning of the day and a seminar at the end of the day, with practical work in the middle. In Iceland, we aim to obtain lectures from members of the Arctic council in Iceland and Canada at other institutions, by a distance learning link, as well as lectures from people at UnAk and other institutions in Iceland. In Colombia, we aim to obtain lectures from members of EAFIT, Universidad de Antioquia, Reading, Akureyri and University of Massachusetts.


Brief description of teaching and learning methods:

There will be pre-trip discussion sessions, field trips to take samples and record environmental data, plus several sessions in the laboratory to identify and analyse microbes. Informal advice from the supervisors will be available throughout the data collection. The data from the field trip will be compiled and the data analysed. A symposium day will be held whereby students are grouped into teams and make a presentation of their results (a free day will be provided the day before this to allow them to do this). The results from their field and lab work will be recorded in a lab book, which will be assessed daily. A lay blog will be written and submitted for the first day of Autumn term. The lab book and a dissertation, including background introduction, materials and methods, results and discussion, will be written and submitted by the middle of Autumn term.


Contact hours:
  Autumn Spring Summer
Lectures 9
Seminars 5
Tutorials 5
Fieldwork 27
Guided independent study: 100
       
Total hours by term 146
       
Total hours for module 200

Summative Assessment Methods:
Method Percentage
Dissertation 65
Project output other than dissertation 5
Oral assessment and presentation 15
Practical skills assessment 15

Summative assessment- Examinations:

Summative assessment- Coursework and in-class tests:

15% - symposium presentation

15% - lab book

5% - blog

65% - dissertation (6,000 words max)


Formative assessment methods:

Penalties for late submission:
The Module Convener will apply the following penalties for work submitted late:

  • where the piece of work is submitted after the original deadline (or any formally agreed extension to the deadline): 10% of the total marks available for that piece of work will be deducted from the mark for each working day[1] (or part thereof) following the deadline up to a total of five working days;
  • where the piece of work is submitted more than five working days after the original deadline (or any formally agreed extension to the deadline): a mark of zero will be recorded.

  • The University policy statement on penalties for late submission can be found at: http://www.reading.ac.uk/web/FILES/qualitysupport/penaltiesforlatesubmission.pdf
    You are strongly advised to ensure that coursework is submitted by the relevant deadline. You should note that it is advisable to submit work in an unfinished state rather than to fail to submit any work.

    Assessment requirements for a pass:
    A mark of 40% overall

    Reassessment arrangements:

    Re-assessment is by 2-hour written examination in August.


    Additional Costs (specified where applicable):
    1) Required text books:
    2) Specialist equipment or materials:
    3) Specialist clothing, footwear or headgear:
    4) Printing and binding:
    5) Computers and devices with a particular specification:
    6) Travel, accommodation and subsistence: Estimated costs for field trip:

    Flights to Iceland - £350
    Internal transportation in Iceland (to Akureyri and for field trips - £150
    Accommodation (2 weeks) - £150
    Subsistence - £250
    Project costs - £100

    Last updated: 8 April 2019

    THE INFORMATION CONTAINED IN THIS MODULE DESCRIPTION DOES NOT FORM ANY PART OF A STUDENT'S CONTRACT.

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