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Advanced Environmental Microbiology

Code: 42937 ECTS Credits: 9
Degree Type Year Semester
4313775 Applied Microbiology OB 0 2


Olga Sanchez Martinez

Teaching groups languages

You can check it through this link. To consult the language you will need to enter the CODE of the subject. Please note that this information is provisional until 30 November 2023.


Nuria Gaju Ricart
Jordi Mas Gordi
Maria Ramos Martinez Alonso
Antonio Sole Cornella


Students are advised to carry out a review of basic microbiology concepts as well as aspects related to microbial ecology, environmental microbiology, and the use of molecular techniques in these disciplines.

Objectives and Contextualisation

In this module the student will be provided of theoretical and practical knowledge on advanced methodologies for the study of microorganisms in natural and artificial environments. The learning and understanding of these methodologies will allow him/her to acquire the necessary baggage for the use of microorganisms in the resolution of environmental problems.


  • Apply the appropriate methodologies for sample collection, characterisation and analysis of microbial populations and communities.
  • Design tools and strategies based on microorganisms to optimise industrial processes, assess the environmental impact of human activity and recover polluted environments.
  • Solve problems in new or little-known situations within broader (or multidisciplinary) contexts related to the field of study.
  • Use acquired knowledge as a basis for originality in the application of ideas, often in a research context.
  • Use and manage bibliographic information and computer resources related to microbiology and related sciences.
  • Use scientific terminology to account for research results and present these orally and in writing.

Learning Outcomes

  1. Apply appropriate sampling strategies and techniques for microbial communities in natural and artificial ecosystems.
  2. Characterise microorganism populations and communities from environmental samples.
  3. Design bioremediation and biorecovery strategies based on microorganisms.
  4. Know procedures and strategies based on microorganisms for pest and disease control.
  5. Know the different bioindicators and bioassays based on microorganisms that help to assess environmental impacts.
  6. Recognise microorganisms' role as causal agents of decay.
  7. Solve problems in new or little-known situations within broader (or multidisciplinary) contexts related to the field of study.
  8. Use acquired knowledge as a basis for originality in the application of ideas, often in a research context.
  9. Use and manage bibliographic information and computer resources related to microbiology and related sciences.
  10. Use scientific terminology to account for research results and present these orally and in writing.


1. Basic concepts of experimental design for the study of microbial communities

2. Analysis of biotope and biocenosis

3. Experimental laboratory models for the study of microbial communities

4. Optical and electron microscopy applied to environmental microbiology

5. Molecular microbial ecology

6. Analysis of the impact of human activity on natural environments

7. Environmental pollution and bioremediation


The teaching methodology includes three types of activities, which have been programmed in an integrated way so that at the end the student acquires the skills indicated in this guide.

Theory block

Expositive theoretical lectures will be given where the basic contents of the module will be explained.

Specialized Seminars

There will also be seminars, given by experts in the different fields of environmental microbiology.

Block of practical classes

It includes:

Experimental laboratory practices: different sessions will be held on high resolution microscopy techniques, both optical and electronic, to determine changes in biodiversity and the uptake of metals by microorganisms in bioreparation processes of contaminated environments.

Classroom practices:There will be several sessions on experimental design for environmental sampling and characterization of microbial diversity in environmental samples, as well as various classes in which different real or hypothetical environmental problems will be solved. An ABP (problem-based learning) methodology will be used, in which students will address the cases raised by working in small groups in the classroom.

Finally, there will be different oral presentations in class to solve the problems posed.

Computer practices: several sessions will be held in the computer room to introduce the student in the treatment and computer analysis of molecular data to study the diversity of microbial communities and the changes they experience in response to different environmental factors or human performances. The following aspects will be addressed:

1. Selection of primers by an in silico study to carry out a study ofmicrobial diversity of a given environment.

2. Statistical analysis of genetic profiles obtained through fingerprinting techniques.

3. Detection of diversity indexes based on the genetic profile of the microbial community.

4. Edition of sequences and determination of their phylogenetic affiliation.


Annotation: Within the schedule set by the centre or degree programme, 15 minutes of one class will be reserved for students to evaluate their lecturers and their courses or modules through questionnaires.


Title Hours ECTS Learning Outcomes
Type: Directed      
Experimental laboratory and computer practices 16 0.64 1, 7, 8, 9, 10
Expert seminars 10 0.4 5, 8
Practical classes 21 0.84 5, 7, 9, 10
Theoretical lectures 8 0.32 5, 8
Type: Supervised      
Tutorials of the practical classes 12 0.48 1, 4, 7, 9, 10
Type: Autonomous      
Preparation of case studies 30 1.2 1, 2, 5, 4, 3, 6, 9
Preparation of experimental and computer practices lab exercices 15 0.6 7, 8, 9, 10
Preparation of oral presentations 25 1 7, 9, 10
Search and management of information 30 1.2 9, 10
Study 25 1 1, 5, 4, 7, 6, 10
Text reading 30 1.2 5, 4, 8, 9, 10


Continuous evaluation

The specific and transversal skills will be evaluated through different activities:

1. Written test (40%): There will be a written examination of the theoretical-practical contents. This exam will include short questions and / or test questions.

2. Assessment of the block of practical classes (60%). Laboratory  and classroom work, as well as the resolution of the exercises raised during practices accomplishment, will be assessed.

 Final considerations:

Practical classes are not eligible for the retake process. Students who do not pass the theoretical-practical assessment will be able to retake it on the date scheduled for that purpose. To be eligible for the retake process, the student should have been previously evaluated in a set of activities equaling at least two thirds of the final score of the course or module. Thus, the student will be graded as "No Avaluable" if the weighthin of all conducted evaluation activities is less than 67% of the final score.

In order to pass the module it is mandatory to attend all theoretical and practical classes, as well as oral defense sessions of case studies.

Single evaluation

The single evaluation consists of a single synthesis test in which the theoretical and practical contents of the subject will be evaluated. The test will consist of short-answer questions aimed at assessing whether the conceptual objectives of the subject have been achieved,  as well as multiple-choice and/or true/false test-type questions. The grade obtained in this summary test will account for 40% of the final grade for the subject. The single assessment will be done on the same day as the written exam of the subject.

The evaluation of the module of practical classes (classroom and laboratory) will follow the same process as the continuous evaluation. The obtained grade will account for 60% of the final mark of the subject. The practical module attendance is compulsory at all sessions.

Assessment Activities

Title Weighting Hours ECTS Learning Outcomes
Assessment of computer practices 15 0 0 9, 10
Assessment of experimental laboratory practices 10 0 0 2, 10
Assessment of practical classes in the classroom 35 0 0 1, 5, 4, 3, 7, 6, 8, 9, 10
Theoretical-practical assessment 40 3 0.12 5, 4, 7, 6, 9, 10


It will be the student's responsibility to search and consult the bibliography necessary for the follow-up and completion of the module. In these links, it can be found an infographic prepared by the Library Service to facilitate the location of electronic books: https://ddd.uab.cat and https://ddd.uab.cat/pub/guibib/224929/bibrecdigitals.pdf

The teachers will give adequate advice to the students in this regard.


The usual Microsoft environment programs will be used. It is possible to use some more specific free access software that the students will look for according to their needs to solve the exercises in the computer room.