
Welcome page Timetable Background Local info Water issues Projects Characterization Sample article (pdf) How to use Bergey's Manuals Methods Rules Media/culture Aseptic technique Staining/interpretation Isolation strategies Assays/characterization Microscopy Cultural characteristics Media preparation and training Training sessions Media preparation Laboratory safety and conduct Experimental Biosciences Resources	Survey of Bacterial Species Our department has been contracted to conduct a qualitative analysis of bacterial populations in the Lakes region. The information will be used to determine the area's potential for rehabilitation of habitat and repopulation with native species. A complete characterization of each species that we identify as indigenous to the area will be published in a Compendium of Local Flora. 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, a key to the identification of 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 Bacterilology (1994 or 2000 edition, hard copy) for identification and Bergey's Manual of Systematic Bacteriology (second edition, on line) to confirm your identification. A link to "How to use Bergey's Manuals) is posted in the left menu. Submissions guidelines for Compendium entries Following the initial characterization, consisting of Gram stain and wet mount observations, relationship to oxygen, and additional observations and assays that are used to narrow down possible taxa, students should be prepared to select a single isolate to characterize to the species level. At this time students will be asked to 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 identificaiton. Instructors will provide advice and feedback, including whether or not you appear to be on the right track. Please see the Timetable for exact due dates and where to submit the work. Please submit the first draft and 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. Four such pages correspond approximately to a single two column printed page, single spaced. Do not submit the document in the final two column single spaced format. Use Times New Roman, aligned left (not justified) for all text including title and subheadings. Required content and format (see the posted Sample Article) Title (Family: Genus species), 16 pt. bold type Author and affiliation, plain 12 pt. italics Use subheadings as described below and illustrated in the sample article, 12 pt bold type. Source of isolate – Include the specific pond from which the sample was taken, media from which it was recovered, and date recovered. 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. Identification – 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. Glossary – 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, as in the sample article. 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 following examples 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 on separate pages. 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 Book 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. http://emedicine.medscape.com/article/228495-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). http://www.fda.gov/oc/po/firmrecalls/am2pat12_07.html. Retrieved 24-Apr 09. Sample article (characterization_example.pdf) The information in this article is provided for illustration purposes only. The example is double spaced in a format suitable for submitted articles
	Created by David R. Caprette (caprette@rice.edu), Rice University 20 Jul 07 Updated 18 May 15 Copyright and Intended Use

Background

Media preparation
and training

Survey of Bacterial Species

Our department has been contracted to conduct a qualitative analysis of bacterial populations in the Lakes region. The information will be used to determine the area's potential for rehabilitation of habitat and repopulation with native species. A complete characterization of each species that we identify as indigenous to the area will be published in a Compendium of Local Flora. 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, a key to the identification of 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 Bacterilology (1994 or 2000 edition, hard copy) for identification and Bergey's Manual of Systematic Bacteriology (second edition, on line) to confirm your identification. A link to "How to use Bergey's Manuals) is posted in the left menu.

Submissions guidelines for Compendium entries

Following the initial characterization, consisting of Gram stain and wet mount observations, relationship to oxygen, and additional observations and assays that are used to narrow down possible taxa, students should be prepared to select a single isolate to characterize to the species level. At this time students will be asked to 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 identificaiton. Instructors will provide advice and feedback, including whether or not you appear to be on the right track. Please see the Timetable for exact due dates and where to submit the work.

Please submit the first draft and 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. Four such pages correspond approximately to a single two column printed page, single spaced. Do not submit the document in the final two column single spaced format. Use Times New Roman, aligned left (not justified) for all text including title and subheadings.

Required content and format (see the posted Sample Article)

Title (Family: Genus species), 16 pt. bold type
Author and affiliation, plain 12 pt. italics
Use subheadings as described below and illustrated in the sample article, 12 pt bold type.
Source of isolate – Include the specific pond from which the sample was taken, media from which it was recovered, and date recovered.
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.
Identification – 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.
Glossary – 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, as in the sample article. 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 following examples 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 on separate pages.

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

Book
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. http://emedicine.medscape.com/article/228495-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). http://www.fda.gov/oc/po/firmrecalls/am2pat12_07.html. Retrieved 24-Apr 09.

Sample article (characterization_example.pdf)

The information in this article is provided for illustration purposes only. The example is double spaced in a format suitable for submitted articles

Created by David R. Caprette (caprette@rice.edu), Rice University 20 Jul 07
Updated 18 May 15
Copyright and Intended Use

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