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2022/2023

Prokaryote Diversity

Code: 101027 ECTS Credits: 3
Degree Type Year Semester
2500502 Microbiology OB 2 2

Contact

Name:
Maria Ramos Martinez Alonso
Email:
maira.martinez@uab.cat

Use of Languages

Principal working language:
catalan (cat)
Some groups entirely in English:
No
Some groups entirely in Catalan:
No
Some groups entirely in Spanish:
No

Other comments on languages

Classes are held in catalan or spanish

Prerequisites

There are no official prerequisites; However, it is advisable for the student to review the concepts that refer to the microbial world, studied previously.

Objectives and Contextualisation

This is a compulsory course of the second year of the Degree in Microbiology, which introduces students to the basic knowledge of prokaryotic diversity, with special emphasis on the structural and ecophysiological characteristics of the large prokaryotic groups we know, and their importance .

The main objective of the course is to provide basic training for the study of the microbial diversity, physiology and metabolism of the main prokaryotic groups.

The specific objectives of the cours are the following:

  •     Recognize the diversity of prokaryotic microorganisms
  •     Understand the principles ofclassical and molecular taxonomy.
  •     Know how to distinguish the characteristics that define the different taxonomic groups, their structural particularities, their ecophysiological characteristics and their importance.
  •     Learn how to apply the knowledge studied to carry out the identification and characterization of the main prokaryotic groups.

Competences

  • Apply knowledge of theory to practice
  • Communicate orally and in writing.
  • Develop critical reasoning skills in the field of study and in relation to the social context.
  • Know and interpret microbial diversity, the physiology and metabolism of microorganisms and the genetic bases that govern their vital functions.
  • Obtain, select and manage information.
  • Use bibliography or internet tools, specific to microbiology or other related disciplines, both in English and in the first language.
  • Work individually or in groups, in multidisciplinary teams and in an international context.

Learning Outcomes

  1. Apply knowledge of theory to practice
  2. Communicate orally and in writing.
  3. Develop critical reasoning skills in the field of study and in relation to the social context.
  4. Evaluate the role of microorganisms in important industrial processes and as producers of key compounds for the development of our societies and the improvement of quality of life
  5. Identify metabolic diversity in microbes and relate it to the different groups of microorganisms.
  6. Identify the role of the different microbial groups in the environment and in the cycles of the elements, and their environmental implications
  7. Obtain, select and manage information.
  8. Recognise and consult microbial collections of model cultures.
  9. Recognise the diversity of the microbial world and identify the different groups it is composed of.
  10. Recognise the role of microorganisms as agents of disease or toxicological problems in human beings, animals and plants.
  11. Use bibliography or internet tools, specific to microbiology or other related disciplines, both in English and in the first language.
  12. Work individually or in groups, in multidisciplinary teams and in an international context.

Content

THEORY

Unit 1. Introduction to prokaryotic diversity

What do we mean by prokayotic diversity? Phylogeny and implications in taxonomy.

Unit 2. Microbial systematics

Classification, nomenclature and identification. Classification systems. Polyphasic taxonomy: phenotypic, genotypic and phylogenetic methods. Classification units. The species concept for prokaryotes. Bergey´s Manual of Systematic Bacteriology. Culture collections.

Unit 3. Archaea domain

Structural particularities of archaea. Phylogeny and metabolism. Euyarcahaeota. Crenarchaeota. New archaeal phyla.

Unit 4. The deep-branching bacterial groups

Adaptations to life at high temperatures, and high radiation. Ecophysiological characteristics of the different groups and key genera.

Unit 5. Gram-Negative Bacteria I

Characteristics of the main groups of green phototrophic bacteria. General characteristics, ecological relevance and key genera. Main chemotrophic groups: Structure, classification and ecophysiology.

Unit 6. Gram-negative bacteria II

Proteobacteria. Morphological, physiological and metabolic diversity. Phylogenetic divisions. Main members of the group and their significance.

Unit 7. Gram-positive bacteria and mycoplasma

Morphological and ecophysiological characteristics, main phylogenetic groups and applied importance.

Unit 8. Extension of prokaryotic diversity

What do we know about the diversity of prokaryotes? Current tools available to assess the hidden diversity of bacteria and archaea. Phylogenetic groups dominated by sequences of uncultivated microorganisms. Distribution and characterization.

SEMINARS

Introduction to identification techniques through the resolutionof6 practical cases:

  •  Methods of isolation of microorganisms
  •  Techniques of microscopic observation
  •   Methods for identification and characterization of microorganisms

 

Methodology

The Diversity of Procariotes course consists of two modules, which have been programmed in an integrated way so that the student will have to relate throughout the course the content and activities programmed in order to achieve the indicated skills in the section of the same name of this guide.

Several learning strategies will be combined:

Theory classes. These master or expository classes represent the main activity to be performed in the classroom, and allow the acquisition of basic concepts by a large number of students, in relatively little time, attending these classes, which will have to be complemented with the study of the topics explained. For the teaching of each subject, presentations like Power Point and diverse teaching material will be used and delivered to the students.

Case-resolution Seminars. These are sessions of work for groups with a small number of students, based on working methodological aspects, through the study of practical cases. For the resolution of the practical cases, groups of 5 students will work on a specific case, which will be presented orally and, later, will be discussed in the classroom collectively. In this methodology, the teacher has a conductive role, through questions that encourage reflection and debate among students.

Tutorials. Tutorials can be done in groups or individually. The first ones will be programmed at the request of the students. The objective of these sessions is to resolve doubts, clarify concepts, establish the knowledge acquired and facilitate the study of the students. They can also be used to solve doubts that students have about the preparation of practical cases. The sessions of tutorials will not be master classes. Likewise, the students will be able to perform individual tutorials in the office of the professor (C3-329).
 
Additional information: The student will have at the Moodle space all the documentation delivered by the teacher for the good monitoring of the course. He / she will also be able to consult the teaching space of the Degree Coordination to obtain updated information.

 

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.

Activities

Title Hours ECTS Learning Outcomes
Type: Directed      
Theory lectures 18 0.72 6, 5, 10, 8, 9, 4
case-resolution seminars 6 0.24 1, 3, 6, 7, 10, 8, 2, 12, 11, 4
Type: Supervised      
Individual/group tutorials 2 0.08 1, 3, 6, 5, 7, 10, 8, 9, 2, 12, 11, 4
Type: Autonomous      
Bibliography search 5 0.2 1, 3, 7, 11
Learning consolidation: study 20 0.8 3, 6, 5, 7, 10, 8, 9, 12, 11, 4
Preparation of oral presentation 9 0.36 3, 7, 2, 12, 11
Text reading 10 0.4 3, 7, 11

Assessment

The evaluation of the course will be individual and continued through the following tests:

Assessment of the theory lectures module (70% of the overall grade). Throughout the course two written tests will be scheduled, which will be cumulative; That is to say, the second test will include all the theoretical contents of the subject. The first test will have a weight of 40% and the second of 60%. If the student obtains in the second test a note superior to the first one, the final note of this module will be the one of the second test. Each test will include short answer questions and multiple-choice and / or true / false test questions.

Assessment of cas-resolution seminars module (30% of the overall grade). The evaluation of this activity will consist of the following tests: a) Oral presentation of the practical case, in class of seminars, for each group of work, and b) Written tests consisting of multiple choice questions that will include the different aspects treated in the classes of seminars. These tests will have a weight of 6 and 4 points, over 10, respectively. Only the average will be considered if the score of  a) and b) is equal or superior to 4.

Final Considerations:

  • To pass the subject, you must obtain a qualification of 5 or higher in each module. Students who do not pass any of the modules will be able to retake them on the scheduled date for the final evaluation of the subject. The re-assessment of the theory module will consist on an overall examinarion of the subject matter that will include short answer questions and multiple-choice and / or true / false test questions. The re-assessment examination of the seminar module will involve a multiple-choice question test on the presentations of all practical cases worked in the seminar sessions.
  • 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. Thus, the student will be graded as Non-evaluable if the weighing of all conducted evaluation activities is less than 67% of the final score.
  • Students who can not attend an individual assessment test for a justified cause and provide the corresponding documentation, will be entitled to take the test in question on another date.
  • Students wishing to improve the final grade of the course will waive the qualification previously obtained, and all the written tests, corresponding to the different modules of the subject, will have to be examined, the day set for the final evaluation.
  • From the second enrolment, the repeating students will not have to carry out the activities, nor the evaluations of those skills tha have been passed, corresponding to the cas-resolution seminars modul. That is, the mark obtained in this module will be saved, as long as they have been passed.

 

Assessment Activities

Title Weighting Hours ECTS Learning Outcomes
Cas-resolution seminars assessment 30 1.5 0.06 1, 3, 7, 2, 12, 11
Final exam 42 2 0.08 6, 5, 10, 8, 9, 2, 4
Midterm exam 28 1.5 0.06 6, 5, 10, 8, 9, 2, 4

Bibliography

Recommended books:

- Brown JW. 2015. Principles of microbial diversity. 1st ed. ASM Press.

- Madigan MT, Martinko JM, Bender KS, Buckley DH, Stahl DA. 2015. Brock Biología de los Microorganismos. 14ª ed. Pearson Education.

- Madigan MT, Bender KS, Buckley DH, Sattley WM, Stahl DA. 2021. Brock Biology of Microorganisms. 16th ed. Pearson SA.

- Martín A, Béjar V, Gutiérrez JC, Llagostera M, Quesada E. 2019. Microbiología Esencial. 1ª ed. Editorial Médica Panamericana.

- Ogunseitan O. 2008. Microbial diversity. Form and function in Prokaryotes. Blackwell Publishing.

- Staley JT, Reysenbach AL. 2002. Biodiversity of microbial life: foundation of earth's biosphere. Willey-Liss, Inc, New York.

- Willey J, Sherwood LM, Woolverton CJ. 2008. Microbiología de Prescott, Harley y Klein. 7ª ed. MacGraw-Hill.

- Willey JM, Sandman KM, Wood DH. 2020. Prescott's Microbiology. 11th ed. MacGraw-Hill.

 

Oher useful reference books:

- The Prokaryotes.

   Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (Editors). 2013-14.The Prokaryotes. Fourth Edition. 11 vol. Springer, New York.

  • Volume  1: The Prokaryotes: Prokaryotic Biology and Symbiotic Associations
  • Volume  2: The Prokaryotes: Applied Bacteriology and Biotechnology
  • Volume  3: The Prokaryotes: Prokaryotic Physiology and Biochemistry
  • Volume  4: The Prokaryotes: Prokaryotic Communities and Ecophysiology
  • Volume  5: The Prokaryotes: Human Microbiology
  • Volume  6: The Prokaryotes: Alphaproteobacteria and Betaproteobacteria
  • Volume  7: The Prokaryotes: Firmicutes and Tenericutes
  • Volume  8: The Prokaryotes:Actinobacteria
  • Volume  9: The Prokaryotes: Gammaproteobacteria
  • Volume 10: The Prokaryotes: Deltaproteobacteria and Epsilonproteobacteria
  • Volume 11: The Prokaryotes: Other Major Lineages of Bacteria and the Archaea

 

- The Prokaryotes: a handbook on the biology of bacteria

   DworkinM, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (Editors). 2006. Third Edition. 7 vol. Springer, New York.

  • Volume 1: Symbiotic Associations, Biotechnology, AppliedMicrobiology
  • Volume 2: Ecophysiology and Biochemistry
  • Volume 3: Archaea. Bacteria: Firmicutes,Actinomycetes
  • Volume 4: Bacteria: Firmicutes, Cianobacteria
  • Volume 5: Proteobacteria: Alpha and Beta Subclasses
  • Volume 6: Proteobacteria: Gamma Subclase
  • Volume 7: Proteobacteria: Delta and Epsilon Subclasses. Deeply Rooting  Bacteria

 

- Bergey's Manual® of Systematic Bacteriology

   Garrity G (Ed.) 2001-2012. Bergey's Manual of Systematic Bacteriology. Second Edition. 5 vol. Springer,

   Volume package:

  • Volume 1: Boone DR, Castenholz RW (Eds.). 2001. Bergey's Manual of Systematic Bacteriology, Second Edition. Volume One : The Archaea and the Deeply Branching and Phototrophic Bacteria. Springer, New York.
  • Volume 2: Brenner DJ, Krieg NR, Staley JT (Eds.). 2005. Bergey's Manual of Systematic Bacteriology, Second Edition, Volume Two: Tthe Proteobacteria. Springer, New York.
  • Volume 3: De Vos P, Garrity G,Jones D, Krieg NR, Ludwig W,Rainey FA, Schleifer K-H, Whitman WB (Eds.). 2009. Bergey's Manual of Systematic Bacteriology: Volume 3: The Firmicutes. Springer, New York.
  • Volume 4: Krieg NR, Ludwig W, Whitman WB, Hedlund BP, Paster BJ, Staley JT, Ward N, Brown D (Eds.). 2010. Bergey's Manual of Systematic Bacteriology, Second Edition. Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes),Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Springer, New York.
  • Volume 5: GoodfellowM, Kämpfer P,Busse H-J, Trujillo M, Suzuki K-I, Ludwig W, WhitmanWB (Eds.). 2012. Volume 5: The Actinobacteria. Springer, New York.

 

- Bergey's Manual® of Systematics of Archaea and Bacteria

  Whitman WB (Ed.). 2015. Bergey's Manual of Systematics of Archaea and Bacteria (digital Ed.). First Edition. John Wiley & Sons, Inc.  http://wileyonlinelibrary.com/ref/bergeysmanual

 

In this link it can be found an infographic prepared by the Library Service to facilitate the location of electronic books: https://bibcercador.uab.cat/discovery/search?search_scope=CourseReserves&vid=34CSUC_UAB:VU1&query=course_code,contains,101027

 

Webs of interes:

http://www.microbelibrary.org

http://microbewiki.kenyon.edu

Software

No specific software is needed in this subject.