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Lab methods Assignments

Supplemental pdfs

Characterization write-up

As part of our project we seek to produce a compendium of species inhabiting local waters. Each entry, which will be limited to two pages in two-column format including figures, tables, and references, will include detailed observations by the author (you, that is), a key to how you identified the species, and a literature-based summary of the species including its occurrence, natural history, and economic and/or medical importance.

Reference materials

In order to characterize an isolate you will need to consult Bergey's Manual of Determinative Bacteriology (1994 or 2000 edition) for identification and Bergey's Manual of Systematic Bacteriology (second edition, on line) to confirm your identification. A document on how to use Bergey's manuals has been posted in Files.

Submission guidelines for Compendium entries

When you have characterized your selected isolate to the species level you should be ready to write up your work. If you wish, you may submit a first draft of the paper, consisting of the first three sections (Source, Description of isolate, and Identification). The Identification section should include what taxa remain to be considered and a general scheme for completing the identification. Instructors will provide advice and feedback, including whether or not you appear to be on the right track.

Please submit the first draft and/or the final assignment in electronic format as a Microsoft Word or portable document (.pdf) file in the form of full column double spaced 8 1/2" x 11" printed pages with 1" margins, 12 pt. type. Use Times New Roman, aligned left (not justified) for all text including title and subheadings. Your paper, including any illustrations, should not exceed 8 pages (equivalent to two single spaced two column pages in publishable form). Do not submit the document in the final two column single spaced format.

Required content and format

  • Title (Family: Genus species), 16 pt. bold type
  • Author and affiliation, plain 12 pt. italics
  • Employ subheadings as described below, using 12 pt bold type.

Source of isolate

Include the location from which the sample was taken, media from which it was recovered, and date recovered. [location: Oak Ridge North, Montgomery County, Texas]

Description of isolate

In the first paragraph describe your isolate in the manner of species descriptions in Bergey's Manual. Include only observations that you made yourself, including Gram stain result, cell shape and arrangement (e.g., rods, cocci, singly, in pairs, chains, tetrads, clusters), and size range. Report the relationship to oxygen, motile or motility not observed, colony characteristics, growth habits, optimum growth temperature (if observed), and any other relevant characteristics such as odor or production of water soluble or fluorescent pigment.

In a second paragraph describe all physiological characteristics that you yourself observed, such as oxidase and/or catalase activity, gas or acid production on specific substrates, indole, methyl red, Voges-Proskauer results, etc.

In a third paragraph address any discrepancies between the published characteristics of the species and observations that you made on your isolate. Give full consideration to occurrence of the species, namely where it is reported to be found. Reconsider your identification if the species is not reported to be isolated from water and/or soil samples. Using a footnote, provide a full citation with page number for the description. You must explain why such the discrepancies may be discounted. This section is especially important.


Report how you used your observations to characterize your isolate. Start with the Gram stain results and describe how you systematically narrowed the possible taxa from broader to narrower categories and eventually to a single species. When appropriate, include reasons for eliminating alternative taxa. You must make a convincing case for your identification. If you do not have the means to narrow the choices to a single species then you may suggest how you would proceed to complete the characterization.

Natural history and importance

Based on a literature search, describe the natural history of the species. If possible, report when it was first described and by whom. Describe any alternative names and/or past misclassifications that made it into the literature. Describe any known relationships with other species (e.g., parasitic, pathogenic, saphrophytic, commensal, etc.). Has the species any economic or medical importance? If applicable, report historical or recent events in which the species played or may have played a role. Is the species or are strains of the species of any research value? If the species itself is not well studied, you may include similar information on the genus.


Include a glossary of terms that may be unfamiliar to an individual with biology background but not necessarily with a strong background in microbiology.

Literature cited

Use single spacing for full citations with a break between entries. Use the author/date method of citing articles and books in text (e.g., Caprette, 2011). Minimize the use of websites, as they are not necessarily permanent or reliable. Websites should be cited in text by author if possible (Smith), or by organization if no author is available (National Institutes of Health). Use the examples below as a guide to listing sources in the Literature Cited section.

Figures should be provided when they provide valuable information toward identification of the species, such as pigmentation, growth patterns, or unusual cell types. Useful figures might include a portion of an agar plate with typical colonies, a micrograph (spores in phase contrast, Gram stain characteristics), or an important assay result. Attach figures to the end of the document identified by number, and provide a list of legends, also identified by figure number.

Formats for literature cited

Journal article
Patterson KL, Porter JW, Ritchie KB, Polson SW, Mueller E, Peters EC, Santavy DL, Smith GW. The etiology of white pox, a lethal disease of the Caribbean elkhorn coral, Acropora palmata. Proc Natl Acad Sci USA 99: 8725–30, 2002

Cole, Leonard A. (1988). Clouds of Secrecy: The Army's Germ-Warfare Tests Over Populated Areas. Totowa, New Jersey: Rowman & Littlefield.

Book chapter or article
Bartol, C. R., & Bartol, A. M. (2005). History of Forensic Psychology. In I. B. Weiner & A. K. Hess (Eds.), The Handbook of Forensic Psychology (pp.1-27). Hoboken, NJ: Wiley.

Web page (if no other source is available)
Anía BJ. Serratia: overview. Retrieved 24-Apr 09

Web page with no author indicated
Food and Drug Administration. AM2 PAT, Inc. Issues Nationwide Recall of Pre-Filled Heparin Lock Flush Solution USP (5 mL in 12 mL Syringes). Retrieved 24-Apr 09.

Created by David R. Caprette, Teaching Professor, Rice University ( 20 Feb 2017] for the course BIOC 318, Laboratory Studies in Microbiology. Please feel free to copy and/or modify these materials for use in your own academic or other nonprofit program. If you don't mind letting me know of such intentions I'll be happy to hear from you.
Last updated [20 Feb 2017