We're going on a microbe safari
To "see" what we can't see.
Under toilets, in corners, and in my tea,
Who knows where they might be?
They might even be on me!

Oh, in the environment there are microbes galore,
Bacilli and cocci and so much more.
Look for them clinging to your teeth or your toes,
There's probably a million just in your nose.
Those microbes really know where to goes.

• CSung to the tune of "Going on a Jungle Adventure" from Barney Videotape "Let's Pretend".

PURPOSE

• To give you experience designing a research project of interest to you
• To give you experience in grantsmanship and the scientific peer review process
• To give you experience gathering, organizing, and reporting scientific data using the standard scientific format

INTRODUCTION

Your mother always told you to wash your hands before dinner, and she was right to do so. Everything you touch in the environment, including your body and other organisms, could be home to microorganisms. But how many microbes are there? What are they doing? What do they look like? Who are they related to? How can their activities be controlled? These are some of the questions microbiologists ask in order to understand ecosystems, disease transmission, and the interactions of microbes with other organisms.

In this exercise, you will work in a group of four to five students to develop a research project that answers a microbiological question of interest to you. You will be given great flexibility in choosing a research topic. The only limits will be time, supplies available to you, your skills in microbiology, and two stipulations that I make. The first stipulation is that your study must include measurements of microbial abundance. The second is that you characterize at least one microbe isolated in your study using the techniques you have learned in this course. Your attempts to measure microbial abundance and to characterize one or more microbes must be relevant and meaningful to the goals of your research project. Before beginning the research, your team will submit a research proposal to a review panel. After responding to the reviewers' comments, experimentation will begin. Upon completion of the project, your research team will prepare a scientific paper detailing the project. This paper will be submitted for peer review before publication in the Class Journal of Experimental Microbiology. In writing the journal article, your team will demonstrate that it:

• formulated one or more testable hypotheses.
• designed a good research project.
• controlled important variables.
• defined key terms operationally.
• interpreted the data appropriately, including unexpected results.
• understands the scope and sequence of the scientific report format.
• understands the importance of quantification to scientific writing.

THE EXERCISE

PREPARATION

1. Begin thinking and talking to your teammates about a possible research project.

2. Each group will purchase a notebook to use as a lab notebook. The notebook will be used by the group to record all aspects of the research project.

3. Read the handout "Writing from the Moment of Observation". This handout describes the best procedures for recording the information about a research project.

WRITE THE RESEARCH PROPOSAL

1. Along with other members of your team, determine a microbiological question of interest to all team members.

2. Devise a research plan to answer that question. Below is a list of materials you will have available to complete your research project.

As you develop your plan, consider the following:

• How is knowing the abundance of microbes related to your research question?
• How is knowing the characteristics of one or more isolates related to your research question?
• Do you have any preconceived notions regarding the abundance and diversity of microbes relevant to your research problem?
• How will you measure abundance? How will you characterize the microbes? How will you ensure that you measure what you think you are measuring?

3. Write a research proposal for submission to the review panel. The research proposal is due to your lab instructor by the date indicated in the syllabus. Use the following format when writing your proposal. If you do not follow this format, the research proposal will be returned without being reviewed, delaying the completion of your project.

• Title
• Statement of Goals: In this section, briefly describe the overall experiment(s) and the goals of the project.
• Introduction: In this section, develop the ideas, experiences and other factors that led to the development of the proposed research. Also clearly state the question(s) being addressed by the project and the significance of the project.
• Experimental Procedures: In this section, outline the experimental procedures you will use to answer the question(s) posed by your project. Include a detailed time line showing the projected dates when experimental procedures will be started and completed. When preparing the time line keep in mind that although some lab time will be allotted to the Microbe Safari, some procedures may need to be done at other times. Note: The time line dates are not written in stone, but they will show the review panel that your team has carefully thought through the experiments and knows that they can be completed within the time allotted for the Microbe Safari exercise.
• Materials required for the project, including control organisms.

4. Revise and resubmit your research proposal, if needed. If resubmitted, your team must respond to the reviewers' comments in the revised proposal. The revised proposal is due to your lab instructor by the date indicated in the syllabus.

IMPLEMENT THE RESEARCH PROPOSAL

Each team will work together to complete the experimental procedures and gather relevant data. The team's activities will be recorded in the team's lab notebook.

PREPARE A JOURNAL ARTICLE TO BE SUBMITTED TO THE CLASS JOURNAL OF EXPERIMENTAL MICROBIOLOGY

1. Each group will submit one article. Each team will begin writing the article in lab on the date indicated in the syllabus.

2. The article will be submitted for peer review in lab on the date indicated in the syllabus. NOTE: Attach the team's lab notebook to the submitted article.

3. The final article, ready for publication, will be submitted in lab on the date indicated in the syllabus.

4. Use the following guidelines for writing the article:

• GENERAL COMMENTS: Writing and communicating information is an essential part of the scientific process. When scientists carry out experiments that yield new and important information, they report the results in scientific journals. This allows others to use the information in their own research projects or teaching. Although these papers are technical papers, they still serve the purpose of telling a story. In this case the story relates what experiments were done, how they were done, why they were done, what results were observed, and the interpretation and significance of the results. Since the story is written after the research is completed, the article is written in the past tense. Writing a scientific report in the form of a journal article is a skill that requires a great deal of practice. Be prepared to make many revisions before the final article is submitted for publication.
• FORMAT: The information reported in the journal article should be organized into the following sections.

TITLE: The title is brief, but should include important descriptors of the project so that the experimental approach used can be anticipated. For instance: "The Isolation, Enumeration, and Morphological and Metabolic Characterization of Bacteria from Martian Soil."

ABSTRACT: This is a brief summary that outlines the major results reported in the article and their significance.

INTRODUCTION: In this section, introduce the reader to the research problem. This section includes a clear statement of any hypotheses being tested. Before stating the hypotheses, describe the observations and experiences that led to their formulation. For instance, if a scientist hypothesizes that Martian microbes are different than Earth microbes, an explanation or description of earlier observations or other factors that lead to its formulation should accompany the hypothesis.

EXPERIMENTAL METHODS: In this section, describe how the experiments were done and what tools, media, and reagents were used. This section should be organized to reflect the order in which results will be presented in the Results section. Standard microbiological procedures need not be described; instead, cite the lab manual or other sources. For instance, if a Gram stain was done, refer the reader to the lab manual in the text and include a complete citation for the lab manual in the reference section of the article. A common method is to number each reference, and then to insert the number for a reference in appropriate locations throughout the article.

RESULTS: Many kinds of data are presented in this section. Always try to organize data into figures or tables whenever appropriate, while still remembering that the story of the results is being told in this section. Therefore, in this section, the results are described in general terms in the text (i.e. point out major results) and the details are illustrated in the accompanying tables and figures. The construction of informative tables and figures takes practice. Consult your instructor if you have any questions.

DISCUSSION: This is often the hardest section to write so be prepared to think about, write, and rewrite this section many times before initial submission. In the discussion section, the data are interpreted and evaluated. Below is a list of the kinds of information included in this section:

• a brief summary of the major results;
• a discussion about whether the results support the hypotheses stated in the introduction;
• arguments regarding why the results did or did not support the hypotheses;
• descriptions of possible sources of error in the results;
• a discussion of alternate explanations of the results, both expected and unexpected;
• a discussion of additional experiments that could be done.

REFERENCES: List any books, articles or other materials used as a resource for your paper. Many methods for citing these resources can be used. A commonly used format is illustrated in the box to the right.

EVALUATION This project is worth a total of 50 points. The score for the project will be determined using the attached score sheet. Submit the score sheet with the ready-for-publication draft of the article. Your individual grade will be determined after evaluating each team member's contribution, as described in the Assessment handout.

GRADING This assignment will be graded using the attached score sheet.

___ Submission of Required Drafts of Research Proposal and Journal Article (3 points) ^a

All Required Drafts Are Submitted	Deadlines Are Met
Yes (1) ___ No (0)___	Always (3)b___ Usually (2, e.g., one draft is late)___ Rarely (1, e.g., 2-3 drafts are late)___ Never (0)

a Number of possible points.
b The numbers in parentheses indicate the mastery level.

To Score:

• If all required drafts are submitted, then record the mastery level for the "Deadlines are Met" criterion as the points earned.
• Score 0 points if one or more of the required drafts is not submitted.

___Maintenance Of Lab Notebook (9 points)

Procedures Used in the Project Are Recorded	Results Obtained by the Project Are Recorded	Entries Contain Sufficient Detail for Reader to Evaluate How Competently the Experiments Were Executed and the Results Interpreted
All (3)___ Most (2)___ Many are missing (1)___ None are recorded (0)___	All (3)___ Most (2)___ Many are missing (1)___ None are recorded (0)___	Always (3)___ Usually (2)___ Rarely (1)___ Never (0)___

^{To Score:}

• If all three mastery levels are at least 1, then sum the mastery levels and record that total as the points earned.
• Score 0 points if one or more of the mastery levels is 0.

___Title of Article (2 points)

Title Serves to Attract Attention of Interested Audience	Title Allows Reader to Anticipate Experimental Design
Yes (1) ___ No (0)____	Yes (3)___ No (0) ___

To Score:

• Sum the mastery levels and record that total as the points earned.
• Score 0 points, if the article is not titled

___Abstract (4 points)

Outlines Major Results	Indicates Significance of Results
All (2) ___ Some (1)___ None (0)___	Clearly stated (2)___ Poorly stated (1)___ Not done (0) ___

To Score:

• Sum the mastery levels and record that total as the points earned.
• Score 0 points, if there is no abstract.

___Introduction (6 points)

Indicates Purpose of Research	Indicates Significance of Research
Clearly stated (2)___ Poorly stated (1)___ Not done (0) ___	Clearly stated (2)___ Poorly stated (1)___ Not done (0) ___

To Score:

• Sum the mastery levels and record that total as the points earned.

___Description Of Procedures (13 points)

Descriptions Are Detailed Enough to Allow Precise Replication of Experiments	When Appropriate, Description Also Includes Information on Variables Expected to Impact Outcome or Interpretation of Experiments; These Variables Could Not be Manipulated	Each Procedure or Sets of Related Procedures Are Reported in Concise Paragraphs	Descriptive Paragraphs Are Organized to Reflect Relatedness of Procedures and/or Chronology	All Procedures Are Described in Experimental Methods
Yes (4) ___ Minor omissions (3)___ Major omissions (2)___ Experiment cannot be replicated (1)___	Yes or not applicable (2)___ Some (1)___ No (0)__	Yes (3)___ Some unnecessary information (2)___ Wordy descriptions (2)___ Written as a series of steps (1)___	Yes (3)___ Somewhat (2)___ Poorly organized (1)___	Yes (1)___ No (0)___

To Score:

• If there are no major omissions, then sum the mastery levels and record that total as the points earned.
• If there are major omissions or the experiments are not replicable, then use that mastery level (e.g., 2 or 1, respectively) as the points earned.

  ---

___Experimental Design (13 points)

Includes Measures of Microbial Abundance	Includes Procedures That Characterize One or More Isolates	Operational Definitions Are Clearly Stated	Uses Experimental Procedures That Are Appropriate to the Purpose of the Research	Clearly Demonstrates the Use of Appropriate Controls	Completes Procedures in a Competent Manner
Yes (1) ___ No (0) ___	Many (2)___ Some (1)___ None (0)__	Yes (2) ___ Implied (1) Not stated (0)	All are (3)___ Most are (2)___ Many are not (1)___ None are (0)___	Consistently (3)___ Infrequently (2)___ Never (1)___	Consistently (3)___ Infrequently (2)___ Never (1)___

To Score:

• If the experimental design includes measures of microbial abundance and characterization of one or more microbes, then sum the mastery levels and use that number as the points earned.
• If there are no measures of microbial abundance or no microbes are characterized, then the sum the mastery levels of all other criteria and divide that total by 2. Record the result as the points earned.

  ---

___Communication of Results (12 points)

Results Are Presented in Paragraphs	Order of Presentation Parallels Order of Experiments	Results Are Presented in Enough Detail for Reader to Interpret Their Meaning	When Appropriate, Well-Constructed, Properly Titled and Labeled Tables and Figures Are Used to Visually Display Results	All Results Are Reported in Results
Yes (2) ___ No (1) ___	Consistently (3)___ Infrequently (2)___ Never (1)___	Consistently (3)___ Infrequently (2)___ Never (1)___	Yes (or not needed) (3)___ Yes, but not labeled (2)___ Yes, but not well constructed (1)___ No visuals were used even though they should have been (0)___	Yes (1) ___ No (0) ___

To Score:

• If the results are presented in paragraph form, then sum the mastery levels and record that total as the points earned.
• If the results are not presented in paragraph form, then the add 1 to the sum of the mastery levels for the last 3 criteria. Record that total as the points earned.

  ---

___Interpretation Of Data (11 points)

The Inferences Drawn Are Consistent with the Data and with Information Regarding Any Uncontrolled Variables	Expected Results Are Explained	Unexpected Results Are Noted and Possible Explanations and/or Suggestions for Further Research Are Made	Each Hypothesis Made Is Either Accepted or Rejected	A Clear Distinction Is Made Between Fact and Implication
Consistently (3)___ Infrequently (2)___ Never (1)___	Consistently (2)___ Infrequently (1)___ Never (0)___	Consistently (2)___ Infrequently (1)___ Never (0)___	Consistently (2)___ Infrequently (1)___ Never (0)___	Consistently (2)___ Infrequently (1)___ Never (0)___

To Score:

• Sum the mastery levels and record that number as the points earned

  ---

___Discussion (7 points)

Purpose and Major Findings Are Summarized	Implications of Results Are Related to Interested Audiences	Order of Discussion of the Results Parallels the Order of Experiments Described in Experiments & Methods	All Interpretations of the Data Are Reported in the Discussion
Most are (2)___ Many are not (1)___ No summary (0)___	Yes (2)___ No (1)___	Consistently (2)___ Sometimes (1)___ Never (0)___	Yes (1)___ No (0)___

To Score:

• Sum the mastery levels and record that number as the points earned

  ---

___Citation of Resources for Paper (6 points)

Bibliography Is Attached	Reader Can Locate Cited Documents, Articles, Books, and Web Sites in Library and on WWW	Sources of Factual Information Are Documented in the Text
Yes___ No___	Always (3)___ Usually (2) ___ Rarely (1) ___ Not at all (0) ___	Always (3)___ Usually (2) ___ Rarely (1) ___ Not at all (0) ___

To Score:

• If bibliography is attached and at least one of the resources can be located in the library of on the WWW, sum the mastery levels, and record that number as the points earned.
• If the bibliography is attached, but none of the resources can be located in the library or WWW, 0 points are earned.
• If bibliography is not attached, 0 points are earned

___Quality of Writing (14 points)

Overall Organization	Paragraph Structure	Sentence Structure		Proofreading & Editing	Scientific Names Are Written Properly
Overall presentation is logical and the main theses of the paper are easily understood (3) ___ Some organization problems, but the main theses of the paper are easily understood (2)___ Organization is so poor that the main theses of the paper are difficult to understand (1)___	Consistently good paragraph structure is observed (2)___ Poorly constructed paragraphs are frequently observed (1)___	Grammatical errors are rare (3)___ Grammatical errors are relatively common, but do not significantly impact readers ability to understand meaning of sentence (2)___ Grammatical errors are so serious and/or frequent that understanding sentences is difficult (1)___		No typos and spelling errors (3)___ Some typos and spelling errors (2)___ Many typos and spelling errors (1)___	Always (3)___ Usually (2)___ Rarely (1)___ Never (0)___

To Score: Sum the mastery levels and record the total as the points earned