Environmental Microbiology

Code:

BIOL3017

Acronym:

BIOL3017

Level:

300

Keywords
Classification	Keyword
OFICIAL	Biology

Instance: 2022/2023 - 1S

Active?	Yes
Responsible unit:	Department of Biology
Course/CS Responsible:	Bachelor in Biology

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
L:B	72	Official Study Plan	3	-	6	48	162

Teaching language

Suitable for English-speaking students

Objectives

I – Acquisition of essential knowledge in Environmental Microbiology, considering the current scientific developments in the field.

II – Understand the importance of environmental microbiology in the context of emerging societal challenges, namely in terms of agricultural production; pollution and bioremediation; emergence of infectious diseases; biological safety; biotechnology; ecosystem sustainability; etc.

 

Learning outcomes and competences

I – Be capable to understand and critically comment on works and methodologies used in Environmental Microbiology.

II – To develop basic laboratory skills related to the different Environmental Microbiology subjects addressed in the lab classes.

III – Develop individual and team work skills, namely concerning bibliographic research and explaining and summarizing Environmental Microbiology subjects.

Working method

Presencial

Pre-requirements (prior knowledge) and co-requirements (common knowledge)

Basic concepts in microbiology.

Program

Syllabus

Introduction to Environmental Microbiology.

I - Soil microbiology. The microbiology of the biogeochemical cycles of carbon and nitrogen. Importance of microorganisms in the decomposition of organic matter in the soil. Rhizosphere and rhizoplane microbiology (e.g. mycorrhizae, endophytic fungi). The actinomycetes.

II – Water microbiology. The different aquatic environments and associated microbial communities.
Waterborne bacterial diseases: cholera, salmonellosis, and legionnaires' disease. Examples of important epidemics and pandemics. Gastrointestinal infections caused by Enterobacteriaceae (E. coli, Shigela sp., among others). Indicator microorganisms of water quality. Limitations. Legislation.
Gastrointestinal poisoning caused by cyanobacteria.
Viral diseases spread by water.

III - Aeromicrobiology.
Airborne bacterial diseases: pneumonic plague, anthrax, and legionellosis. The life cycles and ecology of the etiological agents. Brief description of clinical signs and symptoms. Prophylaxis and therapy.
Fungal respiratory diseases, e.g. aspergillosis.
Viral respiratory infections. Influenza and coronavirus.
Importance of epidemiology to understand respiratory diseases. The epidemiologic triangle. Concepts in epidemiology (outbreak/epidemic/pandemic/incidence/morbidity and mortality rates/etc).
Methods in aeromicrobiology.
Aeromicrobiology and bioterrorism.

IV - Microbiology of extreme environments. Halophilic and xerophilic microorganisms. Psychrophilic and thermophilic microorganisms. Habitats and physiological and structural adaptations.
The microbiology of extreme environments and the foundations of astrobiology. Analysis of the soils of the Moon and Mars. Panspermia Theory? Aerospace microbiology: microbiological experiments in space.

V - Microbiology of polluted environments. Petroleum microbiology. Microbes as depollution agents. Major ecological disasters. Microbiology of organochlorines. Dioxins and DDT. Rubber microbiology. Microbiology of plastics.

VI - Microbiology of metals. The relative toxicity of metals. Molecular mechanisms of toxicity. Microbiology of arsenic and mercury. Mechanisms of toxicity and resistance. Environmental contamination, ecological disasters and their consequences.

LAB CLASSES

WATER MICROBIOLOGY. Analysis of water samples collected at various points of the Douro River estuary. Bacteria indicators of water quality: levels of fecal coliforms and enterococci. Determination of the total viable bacteria and antibiotic resistant bacteria.

MICROBIOLOGY OF POLLUTED ENVIRONMENTS. Experience on petroleum biodegradation . Practice of the Most Likely Number of Degrading Microorganisms. Isolation of degrading bacteria.

MICROBIOLOGY OF EXTREME ENVIRONMENTS: Assessing the communities of prokaryotic microorganisms of extreme hypersaline environments in order to distinguish obligate halophilic microorganisms from halotolerant and non-salt tolerant microorganisms, as well as to analyze the diversity and taxonomic structure of the halophilic microbiome of salt salterns.

AIR MICROBIOLOGY: Isolation and quantification of bacteria and fungi in outdoor and indoor air samples. Evaluation of microbiological parameters of air quality.

 Bibliografia

Environmental microbiology. 3rd edition, 2015. Pepper, I.L., Gerba, C.P., & Gentry, T.J. Eds. Amsterdam : Elsevier/AP, cop. 2015. ISBN 978-0-12-394626-3

Standard methods for the examination of water and wastewater. 18th edition, 1992. Greenberg, A.E., Clesceri, L.S. & Eaton, A.D. Eds. Washington: American Public Health Association. ISBN 978-0-87553-207-3

Manual of environmental microbiology. 2nd edition, 2002. Hurst, C. J., Crawford, R.L., Knudsen, G. R., McInerney, M. J., & Stetzenbach, L. D. Eds. Washington: ASM Press, ISBN 978-1-55581-199-0

Brock biology of microorganisms. 12th edition, 2009. San Francisco: Pearson/Benjamin Cummings, cop. 2009. Rev. ed. of: Brock biology of microorganisms / Michael T. Madigan. 11th ed. 2006. ISBN 978-0-321-53615-0

Prescott's principles of microbiology. 2009. Willey, J. M., Sherwood, L.M.& Woolverton, C.J. - Boston: McGraw-Hill Higher Education. ISBN 978-0-07-337523-6

Other references on specific topics will be made available to students.

Mandatory literature

Ian L. Pepper; Environmental microbiology. ISBN: 978-0-12-394626-3
Christon J. Hurst; Manual of environmental microbiology. ISBN: 978-1-55581-199-0
Arnold E. Greenberg; Standard methods for the examination of water and wastewater. ISBN: 978-0-87553-207-3

Complementary Bibliography

Joanne M. Willey; Prescott.s principles of microbiology. ISBN: 978-0-07-337523-6
Michael T. Madigan; Brock biology of microorganisms. ISBN: 978-0-321-53615-0

Teaching methods and learning activities

Lectures are essentially expository, but favoring and encouraging student’s participation.

Practical classes will involve the preparation, execution, interpretation and discussion of the laboratory results concerning the different lab subjects. The laboratory activities will preferably be carried out in groups of four students in order to develop teamwork skills.

A lab manual will be made available so that the laboratory practices can be carried out by the student’s working groups autonomously.

The results obtained must be analyzed within the group to be presented by the different groups to the class for discussion.

SIGARRA, MOODLE and/or TEAMS platforms will be used to support theoretical and practical classes.

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation	Weight (%)
Exame	70,00
Apresentação/discussão de um trabalho científico	30,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Frequência das aulas	48,00
Estudo autónomo	114,00
Total:	162,00

Eligibility for exams

According the regulations, for this course the students are required to attend at least 25% of the lab classes.

Calculation formula of final grade

EX - Exam - 70% (14 out of 20) (Observations: assessment of the syllabus (55%) and labs (15%) contents).

VP - Presentation/discussion of a scientific work - 30% (6 out of 20) (Observations: prepared by each lab group with the participation of all students, addressing the lab experiments and following guidelines which will be made avalable to the students).

Final Grade = EX + VP

Examinations or Special Assignments

None.

Internship work/project

None.

Special assessment (TE, DA, ...)

None.

Classification improvement

Only the assessment component related to the Exam (70%) might be repeated to improve the final grade.