{"id":1227,"date":"2018-02-09T00:21:06","date_gmt":"2018-02-09T00:21:06","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/?post_type=chapter&#038;p=1227"},"modified":"2025-03-05T04:49:38","modified_gmt":"2025-03-05T04:49:38","slug":"prokaryotic-species-identification","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/chapter\/prokaryotic-species-identification\/","title":{"raw":"Prokaryotic Species Identification","rendered":"Prokaryotic Species Identification"},"content":{"raw":"<div class=\"textbox learning-objectives\">\r\n<h3>Learning Outcomes<\/h3>\r\n<ul>\r\n \t<li>Explain how prokaryotic species are identified<\/li>\r\n<\/ul>\r\n<\/div>\r\nTo this point we have talked about the two broad domains of prokaryotes: Archaea and Bacteria. Before continuing our study of these organisms, it is important to address a basic question: <em>how does one define a prokaryotic species<\/em>?\u00a0This may seem like a basic question, but it's a complex and even controversial one if you're a microbiologist.\r\n\r\nFor <strong>eukaryotes<\/strong>, most scientists <strong>define a species<\/strong> as a group of organisms that can <strong>interbreed<\/strong> and have fertile offspring. This definition makes sense for species that reproduce sexually, but it doesn't work so well for organisms like bacteria. Bacteria reproduce asexually to make clones of themselves\u2014they don't interbreed.\r\n\r\nScientists instead classify bacteria and archaea into taxonomic groups based on similarities in appearance, physiology, and genes.[footnote]Purves, W. K., Sadava, D., Orians, G. H., and Heller, H. C. (2003). Bacteria and archaea: The prokaryotic domains. In <em>Life: The science of biology<\/em> (7th ed., pp. 533). Sunderland, MA: Sinauer Associates, Inc.[\/footnote] Many are given names using traditional Linnean taxonomy, wiith a genus and species. Still, the question of how and whether prokaryotes should be grouped into species remains a topic of debate among scientists. The right \u201cspecies concept\u201d for these organisms is still a work in progress.[footnote]Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F. L., and Swings, J. (2005). Re-evaluating prokaryotic species. <em>Nat. Rev. Microbiol., 3<\/em>, 733-739. <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16138101\" target=\"_blank\" rel=\"noopener\">http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16138101<\/a>.[\/footnote]\r\n<h2>Metagenomics: A new window on microbes<\/h2>\r\nScientists estimate there may be millions of prokaryotic species (or species-like groups), but we know very little about most of them. This is starting to change thanks to large-scale DNA sequencing.\r\n\r\nDNA sequencing makes it possible for scientists to study entire prokaryotic communities in their natural habitat\u2014including the many prokaryotes that are unculturable, and would previously have been \"invisible\" to researchers.\r\n\r\nThe collective genome of such a community is called its metagenome, and the analysis of metagenome sequences is known as metagenomics.\u00a0For example, a DNA sample can be taken from a hot spring microbial mat, such as the beautiful, multicolored mats found in Yellowstone National Park. Even a tiny sample from this rich community includes many, many individuals of different species.[footnote]Klatt, C. G., Wood, J. M., Rusch, D. B., Bateson, M. M., Hamamura, N., Heidelberg, J. F., Grossman, A. R., Bhaya, D., Cohan, F. M., K\u00fchl, M., and Bryant, D. A. (2011). Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. <em>ISME J, 5<\/em>, 1262-1278. Retrieved from <a href=\"https:\/\/dpb.carnegiescience.edu\/sites\/dpb.carnegiescience.edu\/files\/Klatt_2011.pdf\" target=\"_blank\" rel=\"noopener\">https:\/\/dpb.carnegiescience.edu\/sites\/dpb.carnegiescience.edu\/files\/Klatt_2011.pdf<\/a>.[\/footnote]\r\n\r\n<img class=\"aligncenter size-full wp-image-1228\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/2840\/2018\/02\/09001919\/05ba0647b5dbee09ccaa32433bb04b9ba805f63e.jpg\" alt=\"Photograph of a hot spring; the bacterial mat is orange, red, brown, yellow, and blue.\" width=\"416\" height=\"601\" \/>\r\n\r\nBy sequencing and analyzing metagenome DNA samples, scientists can sometimes piece together entire genomes of previously unknown species. In other cases, they use sequence information from specific genes to figure out what types of prokaryotes are present (and how they are related to each other or to known species). The genes found in the DNA samples can also provide clues about the metabolic strategies of the organisms in the community.[footnote]Sharpton, Thomas J. (2014). An introduction to the analysis of shotgun metagenomic data. <em>Front. Plant Sci<\/em>. <a href=\"http:\/\/dx.doi.org\/10.3389\/fpls.2014.00209\" target=\"_blank\" rel=\"noopener\">http:\/\/dx.doi.org\/10.3389\/fpls.2014.00209<\/a>.[\/footnote]\r\n<div class=\"textbox tryit\">\r\n<h3>Try It<\/h3>\r\nhttps:\/\/assess.lumenlearning.com\/practice\/77666d1d-7660-423b-925f-f9cab5966d0c\r\n\r\n<\/div>","rendered":"<div class=\"textbox learning-objectives\">\n<h3>Learning Outcomes<\/h3>\n<ul>\n<li>Explain how prokaryotic species are identified<\/li>\n<\/ul>\n<\/div>\n<p>To this point we have talked about the two broad domains of prokaryotes: Archaea and Bacteria. Before continuing our study of these organisms, it is important to address a basic question: <em>how does one define a prokaryotic species<\/em>?\u00a0This may seem like a basic question, but it&#8217;s a complex and even controversial one if you&#8217;re a microbiologist.<\/p>\n<p>For <strong>eukaryotes<\/strong>, most scientists <strong>define a species<\/strong> as a group of organisms that can <strong>interbreed<\/strong> and have fertile offspring. This definition makes sense for species that reproduce sexually, but it doesn&#8217;t work so well for organisms like bacteria. Bacteria reproduce asexually to make clones of themselves\u2014they don&#8217;t interbreed.<\/p>\n<p>Scientists instead classify bacteria and archaea into taxonomic groups based on similarities in appearance, physiology, and genes.<a class=\"footnote\" title=\"Purves, W. K., Sadava, D., Orians, G. H., and Heller, H. C. (2003). Bacteria and archaea: The prokaryotic domains. In Life: The science of biology (7th ed., pp. 533). Sunderland, MA: Sinauer Associates, Inc.\" id=\"return-footnote-1227-1\" href=\"#footnote-1227-1\" aria-label=\"Footnote 1\"><sup class=\"footnote\">[1]<\/sup><\/a> Many are given names using traditional Linnean taxonomy, wiith a genus and species. Still, the question of how and whether prokaryotes should be grouped into species remains a topic of debate among scientists. The right \u201cspecies concept\u201d for these organisms is still a work in progress.<a class=\"footnote\" title=\"Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F. L., and Swings, J. (2005). Re-evaluating prokaryotic species. Nat. Rev. Microbiol., 3, 733-739. http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16138101.\" id=\"return-footnote-1227-2\" href=\"#footnote-1227-2\" aria-label=\"Footnote 2\"><sup class=\"footnote\">[2]<\/sup><\/a><\/p>\n<h2>Metagenomics: A new window on microbes<\/h2>\n<p>Scientists estimate there may be millions of prokaryotic species (or species-like groups), but we know very little about most of them. This is starting to change thanks to large-scale DNA sequencing.<\/p>\n<p>DNA sequencing makes it possible for scientists to study entire prokaryotic communities in their natural habitat\u2014including the many prokaryotes that are unculturable, and would previously have been &#8220;invisible&#8221; to researchers.<\/p>\n<p>The collective genome of such a community is called its metagenome, and the analysis of metagenome sequences is known as metagenomics.\u00a0For example, a DNA sample can be taken from a hot spring microbial mat, such as the beautiful, multicolored mats found in Yellowstone National Park. Even a tiny sample from this rich community includes many, many individuals of different species.<a class=\"footnote\" title=\"Klatt, C. G., Wood, J. M., Rusch, D. B., Bateson, M. M., Hamamura, N., Heidelberg, J. F., Grossman, A. R., Bhaya, D., Cohan, F. M., K\u00fchl, M., and Bryant, D. A. (2011). Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J, 5, 1262-1278. Retrieved from https:\/\/dpb.carnegiescience.edu\/sites\/dpb.carnegiescience.edu\/files\/Klatt_2011.pdf.\" id=\"return-footnote-1227-3\" href=\"#footnote-1227-3\" aria-label=\"Footnote 3\"><sup class=\"footnote\">[3]<\/sup><\/a><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-1228\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/2840\/2018\/02\/09001919\/05ba0647b5dbee09ccaa32433bb04b9ba805f63e.jpg\" alt=\"Photograph of a hot spring; the bacterial mat is orange, red, brown, yellow, and blue.\" width=\"416\" height=\"601\" \/><\/p>\n<p>By sequencing and analyzing metagenome DNA samples, scientists can sometimes piece together entire genomes of previously unknown species. In other cases, they use sequence information from specific genes to figure out what types of prokaryotes are present (and how they are related to each other or to known species). The genes found in the DNA samples can also provide clues about the metabolic strategies of the organisms in the community.<a class=\"footnote\" title=\"Sharpton, Thomas J. (2014). An introduction to the analysis of shotgun metagenomic data. Front. Plant Sci. http:\/\/dx.doi.org\/10.3389\/fpls.2014.00209.\" id=\"return-footnote-1227-4\" href=\"#footnote-1227-4\" aria-label=\"Footnote 4\"><sup class=\"footnote\">[4]<\/sup><\/a><\/p>\n<div class=\"textbox tryit\">\n<h3>Try It<\/h3>\n<p>\t<iframe id=\"assessment_practice_77666d1d-7660-423b-925f-f9cab5966d0c\" class=\"resizable\" src=\"https:\/\/assess.lumenlearning.com\/practice\/77666d1d-7660-423b-925f-f9cab5966d0c?iframe_resize_id=assessment_practice_id_77666d1d-7660-423b-925f-f9cab5966d0c\" frameborder=\"0\" style=\"border:none;width:100%;height:100%;min-height:300px;\"><br \/>\n\t<\/iframe><\/p>\n<\/div>\n\n\t\t\t <section class=\"citations-section\" role=\"contentinfo\">\n\t\t\t <h3>Candela Citations<\/h3>\n\t\t\t\t\t <div>\n\t\t\t\t\t\t <div id=\"citation-list-1227\">\n\t\t\t\t\t\t\t <div class=\"licensing\"><div class=\"license-attribution-dropdown-subheading\">CC licensed content, Shared previously<\/div><ul class=\"citation-list\"><li>Prokaryote classification and diversity. <strong>Provided by<\/strong>: Khan Academy. <strong>Located at<\/strong>: <a target=\"_blank\" href=\"https:\/\/www.khanacademy.org\/science\/biology\/bacteria-archaea\/prokaryote-metabolism-ecology\/a\/prokaryote-classification-and-diversity\">https:\/\/www.khanacademy.org\/science\/biology\/bacteria-archaea\/prokaryote-metabolism-ecology\/a\/prokaryote-classification-and-diversity<\/a>. <strong>License<\/strong>: <em><a target=\"_blank\" rel=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\">CC BY-NC-SA: Attribution-NonCommercial-ShareAlike<\/a><\/em><\/li><\/ul><\/div>\n\t\t\t\t\t\t <\/div>\n\t\t\t\t\t <\/div>\n\t\t\t <\/section><hr class=\"before-footnotes clear\" \/><div class=\"footnotes\"><ol><li id=\"footnote-1227-1\">Purves, W. K., Sadava, D., Orians, G. H., and Heller, H. C. (2003). Bacteria and archaea: The prokaryotic domains. In <em>Life: The science of biology<\/em> (7th ed., pp. 533). Sunderland, MA: Sinauer Associates, Inc. <a href=\"#return-footnote-1227-1\" class=\"return-footnote\" aria-label=\"Return to footnote 1\">&crarr;<\/a><\/li><li id=\"footnote-1227-2\">Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F. L., and Swings, J. (2005). Re-evaluating prokaryotic species. <em>Nat. Rev. Microbiol., 3<\/em>, 733-739. <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16138101\" target=\"_blank\" rel=\"noopener\">http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16138101<\/a>. <a href=\"#return-footnote-1227-2\" class=\"return-footnote\" aria-label=\"Return to footnote 2\">&crarr;<\/a><\/li><li id=\"footnote-1227-3\">Klatt, C. G., Wood, J. M., Rusch, D. B., Bateson, M. M., Hamamura, N., Heidelberg, J. F., Grossman, A. R., Bhaya, D., Cohan, F. M., K\u00fchl, M., and Bryant, D. A. (2011). Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. <em>ISME J, 5<\/em>, 1262-1278. Retrieved from <a href=\"https:\/\/dpb.carnegiescience.edu\/sites\/dpb.carnegiescience.edu\/files\/Klatt_2011.pdf\" target=\"_blank\" rel=\"noopener\">https:\/\/dpb.carnegiescience.edu\/sites\/dpb.carnegiescience.edu\/files\/Klatt_2011.pdf<\/a>. <a href=\"#return-footnote-1227-3\" class=\"return-footnote\" aria-label=\"Return to footnote 3\">&crarr;<\/a><\/li><li id=\"footnote-1227-4\">Sharpton, Thomas J. (2014). An introduction to the analysis of shotgun metagenomic data. <em>Front. Plant Sci<\/em>. <a href=\"http:\/\/dx.doi.org\/10.3389\/fpls.2014.00209\" target=\"_blank\" rel=\"noopener\">http:\/\/dx.doi.org\/10.3389\/fpls.2014.00209<\/a>. <a href=\"#return-footnote-1227-4\" class=\"return-footnote\" aria-label=\"Return to footnote 4\">&crarr;<\/a><\/li><\/ol><\/div>","protected":false},"author":17,"menu_order":8,"template":"","meta":{"_candela_citation":"[{\"type\":\"cc\",\"description\":\"Prokaryote classification and diversity\",\"author\":\"\",\"organization\":\"Khan Academy\",\"url\":\"https:\/\/www.khanacademy.org\/science\/biology\/bacteria-archaea\/prokaryote-metabolism-ecology\/a\/prokaryote-classification-and-diversity\",\"project\":\"\",\"license\":\"cc-by-nc-sa\",\"license_terms\":\"\"}]","CANDELA_OUTCOMES_GUID":"fcb1270c-9128-4d35-8dae-7e0c67f0a656, 49347fef-d0ac-42a7-a660-e1e5cc1c626e","pb_show_title":"on","pb_short_title":"","pb_subtitle":"","pb_authors":[],"pb_section_license":""},"chapter-type":[],"contributor":[],"license":[],"class_list":["post-1227","chapter","type-chapter","status-publish","hentry"],"part":216,"_links":{"self":[{"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/pressbooks\/v2\/chapters\/1227","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/pressbooks\/v2\/chapters"}],"about":[{"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/wp\/v2\/types\/chapter"}],"author":[{"embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/wp\/v2\/users\/17"}],"version-history":[{"count":10,"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/pressbooks\/v2\/chapters\/1227\/revisions"}],"predecessor-version":[{"id":3136,"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/pressbooks\/v2\/chapters\/1227\/revisions\/3136"}],"part":[{"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/pressbooks\/v2\/parts\/216"}],"metadata":[{"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/pressbooks\/v2\/chapters\/1227\/metadata\/"}],"wp:attachment":[{"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/wp\/v2\/media?parent=1227"}],"wp:term":[{"taxonomy":"chapter-type","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/pressbooks\/v2\/chapter-type?post=1227"},{"taxonomy":"contributor","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/wp\/v2\/contributor?post=1227"},{"taxonomy":"license","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/wm-nmbiology2\/wp-json\/wp\/v2\/license?post=1227"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}