LIFE IN THE SOIL ENVIRONMENT LAB


Course Objectives | Grading Scale | Weekly Course Schedule

 

Printer Friendly Version

 

Instructor: Nhu Nguyen

Office: _________
Office Hours: Both are also available by appointment.
Email: _______________
Telephone: ____________________

 

Lab: TBA
Location: TBA
Prerequisites: BIOL 171L and 172L, or MICR 351L, or consent
Corequisite: The lab must be taken concurrently with 480 or after passing the 480 course.

 

Course description:The soil is arguably one of the most important resources available to humanity.  It is the foundation in which most of the plants (including food crop) on the planet can be found and a cradle of an incredible diversity of life on this planet.  In this class, we will use a multidisciplinary and integrative approach to understanding of the continuum of life in the soil: viruses, bacteria, archaea, fungi, protists, and invertebrates.  We will learn through hands on experience how they function alone, in the context of each other, and together how they cause huge changes in both natural and human-influenced environments.

 

Course structure: This lab course consists of one 3 hours/week lab with topics that would reflect lecture materials.  A mid-term and a final account for 45% of your grade.  You will be assessed through a combination of practical skills and written reasoning.  These types of question depend on the practical skill, but may include short answers, as well as simple calculations.  You will be responsible for keeping a lab notebook (either physical or electronic) for observations as well as keeping notes.  For each lab, you will be responsible for writing a lab report in scientific format (to be provided in details).  These lab reports will assess your ability to write scientifically while making connections between experimental data and current knowledge.  Weekly written quizzes accounts for 20% of your grade and you may be assessed through various types of questions such as multiple choice, short answers, true/false, fill in the blanks, matching, and short essays.  The term project oral presentation accounts for 10% of your grade.  Term projects are independent and team-based projects that you will conduct throughout the semester with guidance from the instructor to investigate various aspects of soil biology.  You will record and analyze your data and prepare an oral presentation that is given to the class at the end of the semester.  The details of the projects will be provided at the beginning of the semester in details.

 

Course objectives:

  1. Acquire practical skills used to study the soil organismal diversity, the roles that they play in manipulation of essential ecosystem processes, and how they contribute to overall soil health.
  2. Apply experimental results to explain effects of various organisms on soil processes and connect these processes to the natural environments, effects on human society, and the overall future health of the planet.
  3. Demonstrate skills in writing, speaking, listening, questioning, and leadership.

 

Based on TAE student learning outcomes, students will be able to:

  1. Demonstrate practical skills of soil biology from genes to ecosystems and how it is fundamental to the health of soils and agriculture.
  2. Demonstrate the ability to critically evaluate scientific evidence from laboratory experiments and provide sufficient reasoning to apply these findings to modern agriculture and the environment.
  3. Demonstrate the ability to apply available tools and fundamental principles of soil biology to develop solutions to solve agricultural and environmental issues.
  4. Demonstrate proficiency in oral and written communication and leadership through lab group experiments, term project, presentation, and written lab reports.

Textbook: Not required.  Material will be distributed by instructor.

 

Grading components:

Exams (2)
45%
Lab reports (12)
 30%
Quizzes (12)
 15%
Project presentation
 10%
  
 Total 100%
Letter Grade Assignment:

 

A+ = 97-100, A = 93-96, A- = 90-92
B+ = 87-89, B = 84-86, B- = 80-83
C+ = 77-79, C = 74-76, C- = 70-73
D+ = 67-69, D = 64-66, D- = 60-63
F = <60


Makeups: Exams and quizzes may be made up but only with university accepted documents.  It is at the discretion of the instructor to determine acceptable reasons for makeups outside of accepted documents.  You must make prior arrangements if you know you will miss a class.  It is up to the students to arrange a makeup with the instructor.  Makeups must be taken prior to the next exam or quiz.

 

Academic Integrity:
Cheating will result in a 0 score for exams and quizzes, and may result in disciplinary action.  Please review UH Manoa's policies on academic integrity.

 

Lab
Lab topic
 		Topics and Skills to acquire
Lab 1
 Intro to labs & term projects;
Winogradsky columns I
 Introduction to labs, end of semester term projects/presentations, Winogradsky columns to understanding soil microbiology.
Lab 2 Microscopy techniques
 Learn microscopy basics, making personal microscopes.  Apply skills to observing soil organisms.  Skills: using the microscope, making slides for observation.
Lab 3
 Isolation of soil microbes
 Isolating microbes from the environment.  Learn serial dilution techniques for enumeration of fungi, bacteria, and unicellular photosynthetic soil organisms.  Calculate and compare the abundance of microbes from different environment.  Assess their importance in these environments.  Skills: Usage of pipets, serial dilution techniques, sterile culturing techniques, working with soil microbes. 
Lab 4 Soil bacteria
 Using staining techniques to observe and enumerate soil bacteria.  Compare the abundance of soil bacteria between rhizosphere and bulk soils.  Identify and evaluate the advantages and weaknesses of these techniques.  Skills: Staining techniques for soil bacteria, working with plant roots.
Lab 5
 Mycorrhizal fungi
 Using staining techniques to observe and enumerate mycorrhizal fungi.  Compare the abundance of these fungi in organic and conventional agriculture conditions.  Analyze these data using statistical methods, and evaluate the effects of organic agriculture on mycorrhizal fungi.  Skills: staining techniques for mycorrhizal fungi, working with roots, estimation of % root colonized, basic statistical methods.
Lab 6
 Faunal diversity I - arthropods
 Isolation and identification of arthropods from soils using the burlese funnel technique.  Identify the arthropods through pictorial and dichotomous keys.  Predict the diversity of arthropods in different soil environments and assess how these different environments affect soil faunal diversity.  Skills: arthropod extractions from soils, usage of keys for identification, micromanipulation of arthropods, basic statistical methods.
Lab 7
 Faunal diversity II - nematodes & other worms
 Isolation and identification of nematodes from soils using the wet sieving technique.  Predict the abundance of arthropods in different soil environments and assess how these different environments affect nematode abundance.  Skills: Wet sieving, extraction of nematodes from soils, mounting tiny specimens.

LAB MIDTERM
  
 Lab 10
 Decomposition of organic matter
 Perform a decomposition experiment using various leafy materials.  Measure the CO2 loss to the atmosphere and calculate the biomass loss.  Evaluate the decomposition rates differences between larger and smaller leafy particles.  Skills: experimental manipulations of dead plant material, using microbalance, using measuring CO2 through classical chemistry, estimate rate processes.
Lab 8
 Soil crusts and photosynthetic organisms
 Observe and isolate the organisms in soil crusts.  Be able to identify the specialized structures of photosynthetic cyanobacteria.  Compare the diversity in soil crusts to the diversity beneath the crust.  Reason whether differences may exist.  Skills: Wet mounting of various types of soil organisms.
Lab 9
 Nitrogen fixing organisms
 Examination of nitrogen fixing organisms and their relationships to plants and general soils environment.  Count the number of nitrogen fixing bacteria from different types of legume nodules and assess how their abundance may contribute to their overall nitrogen requirements.  Skills: extraction of nitrogen fixers from plant tissue, enumeration of N fixers, microdisection and mounting of plant tissue to observe N fixers.
Lab 11
 Nutrients in soil
 Extract and quantify of soil nutrients (nitrate, ammonium, phosphorus, and potassium) from plants that have been treated with a "probiotic" product.  Use statistical tests to show differences, and evaluate the positive or negative potentials of using this product in agriculture.  Skills: chemical extraction of nutrient sources in soils, using reflectochemistry, basic statistical measurements.
Lab 12
 Enzymatic reactions in microbes
 Use enzyme assays to measure the ability of microbes to break down soil organic matter.  Use statistical tests to compare the differences between the ability of microbes to break down soil organic matter.  Use statistical tests to compare the differences between the ability of bacteria and fungi to break down organic matter.  Evaluate which group of organisms perform best in decomposition.  Skills: use
Lab 13
 Winogradksy columns II: Lab period to work on presentation
 Complete observation of Winogradksy columns.  Connect your observations to literature to predict the type of organism as well as the biochemistry that is occurring in the columns.  Use class period to complete on lab presentation material.  Skills: long-term observations and analysis of an experiment, literature research.
Lab 14
 Oral presentation of term project
 Improve your public speaking skills by presenting your data in a logical and precise manner.  Skill: oral presentation
Lab 15
 Oral presentation of term project
 Improve your public speaking skills by presenting your data in a logical and precise manner.  Skill: oral presentation

LAB FINAL