PLANT SC 2520WT - Microbiology and Biotechnology II

Waite Campus - Semester 1 - 2015

An introduction to the biology of microorganisms of importance in agriculture, food, wine and natural ecosystems and the application of biotechnology to increase the nutritional composition, yield and safety of food and beverages, for developed and developing nations. Microbiology topics to be considered include: microbial growth, energy sources and nutritional categories; form and function of major groups of microorganisms; classification and identification; features of saprophytic, pathogenic, symbiotic and commensal lifestyles; interactions of microorganisms with their environment, including plants and animals; case studies of natural and managed microbial ecosystems. Biotechnology examples include DNA marker-assisted selection in plant breeding, genetic modification (GM) approaches and enzyme engineering for efficient food processing and production, non-alcoholic and alcoholic fermentations, food additives. The role of the community, media and government in delivering safe, ethical and sustainable biotechnology solutions is investigated through current examples.

  • General Course Information
    Course Details
    Course Code PLANT SC 2520WT
    Course Microbiology and Biotechnology II
    Coordinating Unit School of Agriculture, Food and Wine
    Term Semester 1
    Level Undergraduate
    Location/s Waite Campus
    Units 3
    Contact Up to 6 hours per week
    Available for Study Abroad and Exchange Y
    Incompatible PLANT SC 2500WT and OENOLOGY 2501WT and PLANT SC 3500WT
    Assumed Knowledge BIOLOGY 1101 and BIOLOGY 1201 or equivalent
    Course Description An introduction to the biology of microorganisms of importance in agriculture, food, wine and natural ecosystems and the application of biotechnology to increase the nutritional composition, yield and safety of food and beverages, for developed and developing nations. Microbiology topics to be considered include: microbial growth, energy sources and nutritional categories; form and function of major groups of microorganisms; classification and identification; features of saprophytic, pathogenic, symbiotic and commensal lifestyles; interactions of microorganisms with their environment, including plants and animals; case studies of natural and managed microbial ecosystems. Biotechnology examples include DNA marker-assisted selection in plant breeding, genetic modification (GM) approaches and enzyme engineering for efficient food processing and production, non-alcoholic and alcoholic fermentations, food additives. The role of the community, media and government in delivering safe, ethical and sustainable biotechnology solutions is investigated through current examples.
    Course Staff

    Course Coordinator: Dr Carolyn Schultz

    Course Timetable

    The full timetable of all activities for this course can be accessed from Course Planner.

  • Learning Outcomes
    Course Learning Outcomes
    1 Explain the role and importance of microorganisms
    2 Describe the form and function of bacteria, fungi, viruses and protozoa
    3 Understand the principles of identifying and classifying organisms
    4 Understand the principles of growth and reproduction of bacteria, fungi and viruses
    5 Discuss beneficial and deleterious activities of microorganisms in agriculture, food and wine
    6 Demonstrate an understanding of the processes involved in the recognition and manipulation of key groups of microorganisms
    7 Use terminology, appropriate to the field of biotechnology, correctly and contextually
    8 Apply a range of biotechnological solutions to improve the nutrition of food and/or the sustainability of food production for future generations
    9 Conduct, analyse and interpret results of experiments, and effectively communicate these in written reports.
    10 Demonstrate the ability to work in a team
    University Graduate Attributes

    This course will provide students with an opportunity to develop the Graduate Attribute(s) specified below:

    University Graduate Attribute Course Learning Outcome(s)
    Knowledge and understanding of the content and techniques of a chosen discipline at advanced levels that are internationally recognised. 1-10
    The ability to locate, analyse, evaluate and synthesise information from a wide variety of sources in a planned and timely manner. 1-10
    An ability to apply effective, creative and innovative solutions, both independently and cooperatively, to current and future problems. 1-10
    Skills of a high order in interpersonal understanding, teamwork and communication. 9,10
    A proficiency in the appropriate use of contemporary technologies. 6,7,9,10
    A commitment to continuous learning and the capacity to maintain intellectual curiosity throughout life. 1-9
    A commitment to the highest standards of professional endeavour and the ability to take a leadership role in the community. 1-10
    An awareness of ethical, social and cultural issues within a global context and their importance in the exercise of professional skills and responsibilities. 1-10
  • Learning & Teaching Activities
    Learning & Teaching Modes

    Lectures are used to deliver content relevant to the specified course objectives. Lectures include the opportunity for open discussion, questions and problem solving activities. Selected biotechnology lectures are supported by formative pre-lecture online (LAMS) activities to support in class activities and discussions.

     

    Tutorials aim to develop and support the material covered in the lectures as well as provide a forum for acquiring skills and knowledge necessary to complete the assessment tasks. The tutorials take the form of class discussions, demonstrations and problem-solving activities.

     

    Practicals aim to apply the knowledge and skills covered in the lectures and tutorials linking theory to practice. They provide students with.

    Workload

    The information below is provided as a guide to assist students in engaging appropriately with the course requirements.

    A student enrolled in a 3 unit course, such as this, should expect to spend, on average 12 hours per week on the studies required. This includes both the formal contact time required to the course (e.g., lectures and practicals), as well as non-contact time (e.g., reading and revision).
    Learning Activities Summary

    Lecture 1 Introduction: overview of course, teaching staff. Definition of microbiology. Role and importance of microbiology in agriculture and related areas. Interactions of microorganisms with invertebrates. Brief history, principles of microbiological methods and culture media.

    Lecture 2 Microbial growth. Definition of growth (binary fission, budding, extension), energy and nutritional requirements of bacteria and fungi. Environment and microbial growth: temperature, atmosphere, pH, moisture, osmotic pressure, light. Growth curve for unicellular organisms. Sterilisation: principles and practice (heat, irradiation, chemical sterilants, filtration).

     Lecture 3 Bacteria. Membranes, walls, glycocalyx, flagella, pili, endospores. Variation in morphological and biochemical characteristics of bacteria; use in routine identification.  Examples from groups of agricultural and oenological importance.

     Lecture 4 Fungi. Vegetative structures: yeasts, hyphae, hyphal growth, modified hyphae, hyphal aggregations, importance of these structures. Reproductive structures: asexual and sexual spores, their formation and importance. Mechanisms of spore dispersal.

     Lecture 5 Viruses. Structure, function, classification and importance as pathogens of humans, animals and plants. Host responses to virus infection.

     Lecture 6 Techniques for identification and classification. Microbial systematics: concepts, nomenclature.  Criteria used in classification and identification of bacteria and fungi: morphology, physiology, biochemistry, nucleic acids, genetic methods.

     Lecture 7 Introduction to microbial ecosystems. Colonisation of substrates, biofilms, recognition and cell-cell signalling. Lifestyles; free-living, saprophytic, commensal, symbiotic, parasitic lifestyles.

     Lecture 8 Microbial activities: microorganisms in food. Effects of composition of food on microbial growth and spoilage. The role of bacteria, yeasts and filamentous fungi in the preparation of fermented food. Food spoilage and food preservation.

     Lectures 9 and 10 Microbial activities: microbes as pathogens. Definition and importance of disease, Koch's postulates, necrotrophs and biotrophs. The disease triangle and disease cycle. Toxins (including mycotoxins). Disease management.

     Lectures 11 and 12 Microbial activities: microorganisms as beneficial organisms. The nitrogen cycle, with emphasis on the role of microorganisms. Nitrogen fixation and nitrogenase. Free-living and symbiotic nitrogen fixation. Rhizobium, formation of nodules, economic and environmental benefits of symbiotic nitrogen fixation. Bioremediation, compost and silage.

     Lectures 13 and 14 Fermentation in wine and food: Pure cultures, their selection, generation and maintenance. Role of microorganisms. Potential for manipulation to improve fermentation efficiency and control of by-products. Designing organisms to suit specific processes and processors.  [Dr Paul Chambers]

     Lectures 15 and 16 What is biotechnology? Introduction to history and current practice of plant improvement, with examples including mutation breeding and embryo rescue. Application of genetic maps and molecular markers in plant improvement. Examples provided highlight the large number of traits (characteristics) that are selected for in modern breeding programs (for grains, tomato, apples and berries). [Dr Carolyn Schultz]

     Lectures 17 and 18 The emerging technologies and their potential applications. Genetically modified (transgenic) plants: What, why and how? Strategies and targets for genetic manipulations of cereals, grapevines and other food crops. Examples used cover broad spectrum of application from improved ecological sustainability, human health, novel functions and protection of plant varieties. [Dr Carolyn Schultz]

     Lectures 19 and 20 Role of OGTR and FSANZ in biosafety and risk assessment. Examples of released transgenic crops. Substantial equivalence. Biotechnology in food safety, quality control and nutrition: Use of human cell lines to compare bioavailability of nutrients. [Dr Carolyn Schultz]

     Lectures 21 and 24 The commercial use of enzymes in industries such as cheese manufacture, the production of sweeteners and wine production, will be discussed in the context of enzymic properties that are required for large scale processes. In addition, the role of plant cell wall components and carbohydrate-modifying enzymes will be related to burgeoning interest in human health and nutrition, and in renewable biofuel production. [Assoc Prof Rachel Burton]

     Practicals and tutorials (tutorials are held in first hour of designated sessions)

    Practical 1

    Tutorial: Introduction, assessment procedures (Venue: Charles Hawker Centre auditorium (= LT 107)

    Culture techniques: aseptic technique, methods for culture of bacteria - streak plating, spread plating, antibiotic sensitivity testing; sub-culture of bacteria to slopes; sub-culture of fungi by point inoculation.

    Use of dissecting and compound microscopes (revision). Calibration of ocular micrometers.

     Practical 2

    Assess cultures from week 1 and re-streak single colony from mixed bacterial culture towards establishing a pure culture.

    Single-celled microorganisms: colony morphology – what to look for and how useful is it?

    Microscopic features: morphology of living and stained cells (methylene blue, Gram stain), demonstration of staining for endospores.

    Identification of bacteria by morphology and biochemical tests.

    Counting bacteria using the Standard Plate Count procedure.

     Practical 3

    Tutorial (small groups): complete assessment of “pure” cultures of bacteria from weeks 1 and 2; count colonies in Standard Plant Count from week 2; bacteria and fungi – structure and function.

    Multi-celled microorganisms: examine structures of fungi in non-stained and stained preparations, with emphasis on types of hyphae, spores and spore-bearing structures.

    Inoculate chickpea and faba bean plants with Uromyces viciae-fabae and Botrytis cinerea, for studies of biotrophic and necrotrophic pathogens in practical 5.

     Practical 4

    Tutorial: Introduction to project work (Venue: Charles Hawker Centre auditorium (= LT 107)

    Project work on beneficial and deleterious activities of microorganisms: examination of various foodstuffs and other materials for microbial colonisation and spoilage.

    Practical 5

    Project: assess initial cultures, sub-culture to establish pure cultures (1 hour).

    Microbes as pathogens:  characteristics of biotrophic and necrotrophic plant pathogens - examine symptoms on chickpea and faba bean plants inoculated with Uromyces viciae-fabae and Botrytis cinerea in practical 3.

    Koch’s postulates: demonstration.

    Viruses: examine symptoms produced in host plants and their use in identifying the pathogen. Classification of viruses by size and shape.

     Practical 6

    Tutorial (small groups): review progress in project and discuss expectations for poster presentation and assessment.

    Project: examine cultures, assess substrate breakdown (plate assays), collect final results.

     Week 7 Practical time slot

    Optional redeemable mid-semester exam.

     Practical 7 (over two weeks, in week 8 & 9)

    Techniques for the identification and comparison of genetically modified organisms.

     Practical 8 (over two weeks, in week 10 & 11)

    Purification and use of a recombinant enzyme to reduce flour viscosity in food processing. Gluten testing of consumer products.

    Specific Course Requirements

    Lab coat

    Reading lists to be provided (no required textbook)

    Small Group Discovery Experience
    Incorporate Academic Mentors & other SGDE requirements into the existing Microbiology project Students will work in groups of 4 and will be assigned an academic mentor.
  • Assessment

    The University's policy on Assessment for Coursework Programs is based on the following four principles:

    1. Assessment must encourage and reinforce learning.
    2. Assessment must enable robust and fair judgements about student performance.
    3. Assessment practices must be fair and equitable to students and give them the opportunity to demonstrate what they have learned.
    4. Assessment must maintain academic standards.

    Assessment Summary
    Assessment Task Type of assessment Percentage of total assessment for grading purposes Hurdle (Yes or No) Learning Outcome
    Quizzes on practical exercises and underlying theory Formative

    0%

    No 2,3,4,6
    Practical/tutorial report on form and function of microorganisms Formative (week 1-2)
    Summative (week 2-3)
    0%
    5%
    No 2,3,4,6
    Practical report on microorganisms as pathogens Summative 5% No 1,5,6,9,10
    Project reporting  Summative 15% No 1-5,6,9,10
    Practical report on identifying GMOs Summative 10% No 7,9
    Practical report on purification and use of recombinant proteins Summative 10% No 7,9
    Written exam(s) Summative 55% Yes 1-9
    Assessment Related Requirements

    To pass the course, a student must obtain 40% for the written exam(s) (i.e. 24 out of 60). Students who miss assessed practicals because of illness, bereavement (or other compassionate grounds) or unavoidable commitments are given an assignment in lieu of the assessment piece (replacement assessment). No other additional assessment is available for Practical Components.

    Assessment Detail

    The written exam(s) account for 55% of the final mark (50% is for microbiology and 50% for biotechnology). The exams will assess the students’ knowledge, their ability to apply knowledge and their critical analysis skills. There is an optional redeemable written exam in week 7 (worth 50%). Questions will be set by each lecturer, with marks according to the number of lectures given.

    Practical and tutorials reports account for 45% of the final mark, as follows:

    Form and function of microorganisms, practical/tutorial report due at end of tutorial 2 or practical 3 (5% of final mark)

    Plant disease, practical report due at end of practical session (5% of final mark)

    Project on microbial activities, group poster and individual journal, due 2-3 weeks after lab work completed (15% of final mark)

    Practical report on identifying GMOs. Is a full practical report write up (Aims, Introduction, Results, Discussion, Conclusion).  (10% of final mark)

    Practical report on purification and use of recombinant proteins. The assessment task for this prac gets students to focus on data presentation and summarising key points from four different, but related experiments. A formative assessment component is included to provide students with feedback before submission of the final assessment task. (10% of final mark).

    Practical reports will be promptly assessed to provide continual feedback to students and a sense of progressive accomplishment in the course. Students will receive written feedback on each of practical reports submitted for assessment.

    Submission

    If an extension is not applied for, or not granted then a penalty for late submission will apply.  A penalty of 10% of the value of the assignment for each calendar day that the assignment is late (i.e. weekends count as 2 days), up to a maximum of 50% of the available marks will be applied. This means that an assignment that is 5 days late or more without an approved extension can only receive a maximum of 50% of the marks available for that assignment.

    Course Grading

    Grades for your performance in this course will be awarded in accordance with the following scheme:

    M10 (Coursework Mark Scheme)
    Grade Mark Description
    FNS   Fail No Submission
    F 1-49 Fail
    P 50-64 Pass
    C 65-74 Credit
    D 75-84 Distinction
    HD 85-100 High Distinction
    CN   Continuing
    NFE   No Formal Examination
    RP   Result Pending

    Further details of the grades/results can be obtained from Examinations.

    Grade Descriptors are available which provide a general guide to the standard of work that is expected at each grade level. More information at Assessment for Coursework Programs.

    Final results for this course will be made available through Access Adelaide.

  • Student Feedback

    The University places a high priority on approaches to learning and teaching that enhance the student experience. Feedback is sought from students in a variety of ways including on-going engagement with staff, the use of online discussion boards and the use of Student Experience of Learning and Teaching (SELT) surveys as well as GOS surveys and Program reviews.

    SELTs are an important source of information to inform individual teaching practice, decisions about teaching duties, and course and program curriculum design. They enable the University to assess how effectively its learning environments and teaching practices facilitate student engagement and learning outcomes. Under the current SELT Policy (http://www.adelaide.edu.au/policies/101/) course SELTs are mandated and must be conducted at the conclusion of each term/semester/trimester for every course offering. Feedback on issues raised through course SELT surveys is made available to enrolled students through various resources (e.g. MyUni). In addition aggregated course SELT data is available.

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