Site Navigation

BIOM7009 - Microbial Ecosystems

Title:Microbial Ecosystems
Long Title:Microbial Ecosystems
Module Code:BIOM7009
Duration:1 Semester
Credits: 5
NFQ Level:Intermediate
Field of Study: Microbiology
Valid From: Semester 1 - 2020/21 ( September 2020 )
Module Delivered in 2 programme(s)
Module Coordinator: Brigid Lucey
Module Author: Deirdre Purfield
Module Description: This module provides an introduction to the characterization of agricultural microbial ecosystems with emphasis on the soil, water and animal microbiomes. The diagnostic tools to analyse such microbiomes and the role of microbes in food fermentation will also be evaluated.
Learning Outcomes
On successful completion of this module the learner will be able to:
LO1 Outline diagnostic approaches used to analyse the microbial diversity and function in ecosystems
LO2 Elucidate the role of microbes in soil and water environments
LO3 Understand how microbiomes contribute to animal metabolism and health
LO4 Describe the role of microbial fermentation and evaluate the importance of microorganisms in the agri-food sector
LO5 Perform relevant practicals, interpret results and write scientific reports
Pre-requisite learning
Module Recommendations

This is prior learning (or a practical skill) that is strongly recommended before enrolment in this module. You may enrol in this module if you have not acquired the recommended learning but you will have considerable difficulty in passing (i.e. achieving the learning outcomes of) the module. While the prior learning is expressed as named MTU module(s) it also allows for learning (in another module or modules) which is equivalent to the learning specified in the named module(s).

Incompatible Modules
These are modules which have learning outcomes that are too similar to the learning outcomes of this module. You may not earn additional credit for the same learning and therefore you may not enrol in this module if you have successfully completed any modules in the incompatible list.
No incompatible modules listed
Co-requisite Modules
No Co-requisite modules listed

This is prior learning (or a practical skill) that is mandatory before enrolment in this module is allowed. You may not enrol on this module if you have not acquired the learning specified in this section.

No requirements listed

Module Content & Assessment

Indicative Content
Diagnostic tools
Sampling the environment, microbial culture, 16S and shotgun metagenomic analyses, microbial evolution, and phylogenetic analysis. Database interrogation and local alignment. Introduction to operational taxonomic unit assignment and ecological diversity measures.
Soil and water microbial ecosystems
Soil and water microbial ecosystems. Describe the diversity, ecology, and functions of the main groups of soil microorganisms. Identification of microbial agents associated with waterborne diseases and evaluate methods used for the microbiological testing of water.
Microbial populations in animals
The role of the animal microbiome in animal health, nutrition, and methane production. Ruminant, gut, uterine, and mammary microbiome classification. Factors affecting microbiome content, dysbiosis and the microbiota gut-brain axis.
Microbes in food production
Microbial Fermentation and microbiome characterisation within dairy, meat, animal and health products. Properties of starter cultures, bioreactor/fermenter design and different types of fermentation.
Assessment Breakdown%
Course Work50.00%
End of Module Formal Examination50.00%
Course Work
Assessment Type Assessment Description Outcome addressed % of total Assessment Date
Multiple Choice Questions Theory assessment on lecture material 1,2 30.0 Week 6
Practical/Skills Evaluation Students will be required to demonstrate their practical skills during weekly practicals and submit detailed written reports on their findings. 1,2,5 20.0 Every Second Week
End of Module Formal Examination
Assessment Type Assessment Description Outcome addressed % of total Assessment Date
Formal Exam Written exam 1,2,3,4 50.0 End-of-Semester
Reassessment Requirement
Repeat examination
Reassessment of this module will consist of a repeat examination. It is possible that there will also be a requirement to be reassessed in a coursework element.

The institute reserves the right to alter the nature and timings of assessment


Module Workload

Workload: Full Time
Workload Type Workload Description Hours Frequency Average Weekly Learner Workload
Lecture Theory and concepts 2.0 Every Week 2.00
Lab Practical sessions 2.0 Every Second Week 1.00
Independent & Directed Learning (Non-contact) Self-directed learning/practical reports 4.0 Every Week 4.00
Total Hours 8.00
Total Weekly Learner Workload 7.00
Total Weekly Contact Hours 3.00
This module has no Part Time workload.

Module Resources

Recommended Book Resources
  • Larry L. Barton, Diana E. Northup 2011, Microbial Ecology, Wiley-Blackwell [ISBN: 0470048174]
Supplementary Book Resources
  • Frans J. de Bruijn 2011, Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats, Wiley?Blackwell [ISBN: 978047064719]
  • Rachael E. Antwis, Xavier A. Harrison, Michael J Cox 2020, Microbiomes of Soils, Plants and Animals: An Integrated Approach (Ecological Reviews), Cambridge University Press [ISBN: 1108462480]
Recommended Article/Paper Resources
  • F. De Filippis, E. Parente and D Ercolini 2017, Metagenomics insights into food fermentations, Microbial Biotechnology, 10(1)
  • Finkel et al. 2017, Understanding and exploiting plant beneficial microbes, Current Opinion in Plant Biology, 38
  • Fierer N 2017, Embracing the unknown: disentangling the complexities of the soil microbiome, Nature Reviews Microbiology, 15, 579
  • Huws, SA et al. 2018, Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future, Frontiers in Microbiology, 9, 2161
Other Resources

Module Delivered in

Programme Code Programme Semester Delivery
CR_SAGBI_8 Bachelor of Science (Honours) in Agri-Biosciences 5 Elective
CR_SAGBI_7 Bachelor of Science in Agri-Biosciences 5 Elective

Cork Institute of Technology
Rossa Avenue, Bishopstown, Cork

Tel: 021-4326100     Fax: 021-4545343
Email: help@cit.edu.ie