{"id":1210,"date":"2017-01-18T19:25:36","date_gmt":"2017-01-18T19:25:36","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/wm-biology2\/?post_type=chapter&#038;p=1210"},"modified":"2017-07-05T16:50:20","modified_gmt":"2017-07-05T16:50:20","slug":"prokaryotic-diversity","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/chapter\/prokaryotic-diversity\/","title":{"raw":"Prokaryotic Diversity","rendered":"Prokaryotic Diversity"},"content":{"raw":"<h2>Discuss the diversity of prokaryotic cells<\/h2>\r\n[caption id=\"attachment_1238\" align=\"alignright\" width=\"399\"]<img class=\" wp-image-1238\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193416\/Figure_22_00_01-1024x572.jpg\" alt=\"The photo shows a hot spring with a vivid blue color in the middle and a golden color around the edge.\" width=\"399\" height=\"223\" \/> Figure\u00a01.\u00a0Certain prokaryotes can live in extreme environments such as the Morning Glory pool, a hot spring in Yellowstone National Park. The spring\u2019s vivid blue color is from the prokaryotes that thrive in its very hot waters. (credit: modification of work by Jon Sullivan)[\/caption]\r\n\r\nIn the recent past, scientists grouped living things into five kingdoms\u2014animals, plants, fungi, protists, and prokaryotes\u2014based on several criteria, such as the absence or presence of a nucleus and other membrane-bound organelles, the absence or presence of cell walls, multicellularity, and so on. In the late 20th\u00a0century, the pioneering work of Carl Woese and others compared sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a more fundamental way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes\u2014including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.\r\n\r\nTwo of the three domains\u2014Bacteria and Archaea\u2014are prokaryotic. Prokaryotes were the first inhabitants on Earth, appearing 3.5 to 3.8 billion years ago. These organisms are abundant and ubiquitous; that is, they are present everywhere. In addition to inhabiting moderate environments, they are found in extreme conditions: from boiling springs to permanently frozen environments in Antarctica; from salty environments like the Dead Sea to environments under tremendous pressure, such as the depths of the ocean; and from areas without oxygen, such as a waste management plant, to radioactively contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, are responsible for certain illnesses, and serve an important role in the preparation of many foods.\r\n<div class=\"textbox learning-objectives\">\r\n<h3>Learning Objectives<\/h3>\r\n<ul>\r\n \t<li>Describe the evolutionary history of prokaryotes<\/li>\r\n \t<li>Discuss the distinguishing features of extremophiles<\/li>\r\n \t<li>Understand why it is difficult to culture prokaryotes<\/li>\r\n \t<li>Discuss why prokaryotes often form biofilms<\/li>\r\n<\/ul>\r\n<\/div>\r\n<h2>Evolutionary History of Prokaryotes<\/h2>\r\nProkaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things. Prokaryotes recycle <b>nutrients<\/b>\u2014essential substances (such as carbon and nitrogen)\u2014and they drive the evolution of new ecosystems, some of which are natural and others man-made. Prokaryotes have been on Earth since long before multicellular life appeared.\r\n\r\nWhen and where did life begin? What were the conditions on Earth when life began? Prokaryotes were the first forms of life on Earth, and they existed for billions of years before plants and animals appeared. The Earth and its moon are thought to be about 4.54\u00a0billion years old. This estimate is based on evidence from radiometric dating of meteorite material together with other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of the Earth. At this time too, strong volcanic activity was common on Earth, so it is likely that these first organisms\u2014the first prokaryotes\u2014were adapted to very high temperatures. Early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.\r\n<h3>Microbial Mats<\/h3>\r\nMicrobial mats or large biofilms may represent the earliest forms of life on Earth; there is fossil evidence of their presence starting about 3.5 billion years ago. A <b>microbial mat<\/b> is a multi-layered sheet of prokaryotes (Figure\u00a02) that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically grow where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise them carry out different metabolic pathways, and that is the reason for their various colors. Prokaryotes in a microbial mat are held together by a glue-like sticky substance that they secrete called extracellular matrix.\r\n\r\nThe first microbial mats likely obtained their energy from chemicals found near hydrothermal vents. A <b>hydrothermal vent<\/b> is a breakage or fissure in the Earth\u2019s surface that releases geothermally heated water. With the evolution of photosynthesis about 3 billion years ago, some prokaryotes in microbial mats came to use a more widely available energy source\u2014sunlight\u2014whereas others were still dependent on chemicals from hydrothermal vents for energy and food.\r\n\r\n[caption id=\"attachment_1239\" align=\"aligncenter\" width=\"1024\"]<img class=\"size-large wp-image-1239\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193521\/Figure_22_01_01-1024x411.jpg\" alt=\"The part a photo shows a reddish-yellow mound with small chimneys growing out of it. Part b micrograph shows rod-shaped bacteria about two microns long swimming over a thicker mat of bacteria.\" width=\"1024\" height=\"411\" \/> Figure\u00a02. This (a) microbial mat, about one meter in diameter, grows over a hydrothermal vent in the Pacific Ocean in a region known as the \u201cPacific Ring of Fire.\u201d The mat helps retain microbial nutrients. Chimneys such as the one indicated by the arrow allow gases to escape. (b) In this micrograph, bacteria are visualized using fluorescence microscopy. (credit a: modification of work by Dr. Bob Embley, NOAA PMEL, Chief Scientist; credit b: modification of work by Ricardo Murga, Rodney Donlan, CDC; scale-bar data from Matt Russell)[\/caption]\r\n<figure><\/figure>\r\n<h3>Stromatolites<\/h3>\r\nFossilized microbial mats represent the earliest record of life on Earth. A <b>stromatolite<\/b> is a sedimentary structure formed when minerals are precipitated out of water by prokaryotes in a microbial mat (Figure\u00a03). Stromatolites form layered rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on Earth where stromatolites are still forming. For example, growing stromatolites have been found in the Anza-Borrego Desert State Park in San Diego County, California.\r\n\r\n[caption id=\"attachment_1240\" align=\"aligncenter\" width=\"1024\"]<img class=\"size-large wp-image-1240\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193631\/Figure_22_01_02ab-1024x372.jpg\" alt=\"Photo A shows a mass of gray mounds in shallow water. Photo B shows a swirl patter in white and gray marbled rock.\" width=\"1024\" height=\"372\" \/> Figure\u00a03. (a) These living stromatolites are located in Shark Bay, Australia. (b) These fossilized stromatolites, found in Glacier National Park, Montana, are nearly 1.5 billion years old. (credit a: Robert Young; credit b: P. Carrara, NPS)[\/caption]\r\n<figure><\/figure>\r\n<h3>The Ancient Atmosphere<\/h3>\r\n<figure><\/figure>\r\n[caption id=\"attachment_1241\" align=\"alignright\" width=\"400\"]<img class=\" wp-image-1241\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193702\/Figure_22_01_03-e1484768251762.jpg\" alt=\"This photo shows a woman squatting next to a stream of green-colored water.\" width=\"400\" height=\"231\" \/> Figure\u00a04. This hot spring in Yellowstone National Park flows toward the foreground. Cyanobacteria in the spring are green, and as water flows down the gradient, the intensity of the color increases as cell density increases. The water is cooler at the edges of the stream than in the center, causing the edges to appear greener. (credit: Graciela Brelles-Mari\u00f1o)[\/caption]\r\n\r\nEvidence indicates that during the first two billion years of Earth\u2019s existence, the atmosphere was <b>anoxic<\/b>, meaning that there was no molecular oxygen. Therefore, only those organisms that can grow without oxygen\u2014<b>anaerobic<\/b> organisms\u2014were able to live. Autotrophic organisms that convert solar energy into chemical energy are called <b>phototrophs<\/b>, and they appeared within one billion years of the formation of Earth. Then, <b>cyanobacteria<\/b>, also known as blue-green algae, evolved from these simple phototrophs one billion years later. Cyanobacteria (Figure\u00a04) began the oxygenation of the atmosphere. Increased atmospheric oxygen allowed the development of more efficient O<sub>2<\/sub>-utilizing catabolic pathways. It also opened up the land to increased colonization, because some O<sub>2\u00a0<\/sub>is converted into O<sub>3<\/sub> (ozone) and ozone effectively absorbs the ultraviolet light that would otherwise cause lethal mutations in DNA. Ultimately, the increase in O<sub>2<\/sub> concentrations allowed the evolution of other life forms.\r\n<div class=\"textbox exercises\">\r\n<h3>Practice\u00a0Questions<\/h3>\r\nMicrobial mats __________.\r\n<ol>\r\n \t<li>are the earliest forms of life on Earth<\/li>\r\n \t<li>obtained their energy and food from hydrothermal vents<\/li>\r\n \t<li>are multi-layered sheet of prokaryotes including mostly bacteria but also archaea<\/li>\r\n \t<li>are all of the above<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"125455\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"125455\"]Answer d. Microbial mats <strong>are all of the above<\/strong>.\r\n\r\n[\/hidden-answer]\r\n\r\nThe first organisms that oxygenated the atmosphere were\r\n<ol>\r\n \t<li>cyanobacteria<\/li>\r\n \t<li>phototrophic organisms<\/li>\r\n \t<li>anaerobic organisms<\/li>\r\n \t<li>all of the above<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"566688\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"566688\"]Answer a. The first organisms that oxygenated the atmosphere were\u00a0<strong>cyanobacteria<\/strong>.[\/hidden-answer]\r\n\r\n<\/div>\r\n<h2>Life in Moderate and Extreme Environments<\/h2>\r\nSome organisms have developed strategies that allow them to survive harsh conditions. Prokaryotes thrive in a vast array of environments: some grow in conditions that would seem very normal to us, whereas others are able to thrive and grow under conditions that would kill a plant or animal. Almost all prokaryotes have a cell wall, a protective structure that allows them to survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are able to form endospores that resist heat and drought, thereby allowing the organism to survive until favorable conditions recur. These adaptations, along with others, allow bacteria to be the most abundant life form in all terrestrial and aquatic ecosystems.\r\n\r\nOther bacteria and archaea are adapted to grow under extreme conditions and are called <b>extremophiles<\/b>, meaning \u201clovers of extremes.\u201d Extremophiles have been found in all kinds of environments: the depth of the oceans, hot springs, the Arctic and the Antarctic, in very dry places, deep inside Earth, in harsh chemical environments, and in high radiation environments, just to mention a few.\r\n\r\n[caption id=\"attachment_1244\" align=\"alignright\" width=\"300\"]<img class=\" wp-image-1244\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193928\/Figure_22_01_04.jpg\" alt=\"This micrograph shows an oval Deinococcus about 2.5 microns in diameter cell dividing.\" width=\"300\" height=\"345\" \/> Figure\u00a05. <em>Deinococcus radiodurans<\/em>, visualized in a\u00a0false color transmission electron micrograph (credit: modification of work by Michael Daly; scale-bar data from Matt Russell)[\/caption]\r\n\r\nOther extremophiles, like <b>radioresistant<\/b> organisms, do not prefer an extreme environment (in this case, one with high levels of radiation), but have adapted to survive in it. For example,\u00a0<em>Deinococcus radiodurans<\/em>, shown in Figure\u00a05, is a prokaryote that can tolerate very high doses of ionizing radiation. It has developed DNA repair mechanisms that allow it to reconstruct its chromosome even if it has been broken into hundreds of pieces by radiation or heat.\r\n\r\nThese organisms give us a better understanding of prokaryotic diversity and open up the possibility of finding new prokaryotic species that may lead to the discovery of new therapeutic drugs or have industrial applications. Because they have specialized adaptations that allow them to live in extreme conditions, many extremophiles cannot survive in moderate environments.\r\n\r\nThere are many different groups of extremophiles: they are identified based on the conditions in which they grow best, and several habitats are extreme in multiple ways. For example, a soda lake is both salty and alkaline, so organisms that live in a soda lake must be both alkaliphiles and halophiles (Table\u00a01).\r\n<table id=\"tab-ch22-01-01\" summary=\"\">\r\n<thead>\r\n<tr>\r\n<th colspan=\"2\">Table\u00a01. Extremophiles and Their Preferred Conditions<\/th>\r\n<\/tr>\r\n<tr>\r\n<th>Extremophile Type<\/th>\r\n<th>Conditions for Optimal Growth<\/th>\r\n<\/tr>\r\n<\/thead>\r\n<tbody>\r\n<tr>\r\n<td>Acidophiles<\/td>\r\n<td>pH 3 or below<\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Alkaliphiles<\/td>\r\n<td>pH 9 or above<\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Thermophiles<\/td>\r\n<td>Temperature 60\u201380 \u00b0C (140\u2013176 \u00b0F)<\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Hyperthermophiles<\/td>\r\n<td>Temperature 80\u2013122 \u00b0C (176\u2013250 \u00b0F)<\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Psychrophiles<\/td>\r\n<td>Temperature of \u221215\u201310 \u00b0C (5\u201350 \u00b0F) or lower<\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Halophiles<\/td>\r\n<td>Salt concentration of at least 0.2 M<\/td>\r\n<\/tr>\r\n<tr>\r\n<td>Osmophiles<\/td>\r\n<td>High sugar concentration<\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n<h3>Prokaryotes in the Dead Sea<\/h3>\r\nOne example of a very harsh environment is the Dead Sea, a hypersaline basin that is located between Jordan and Israel. Hypersaline environments are essentially concentrated seawater. In the Dead Sea, the sodium concentration is 10 times higher than that of seawater, and the water contains high levels of magnesium (about 40 times higher than in seawater) that would be toxic to most living things. Iron, calcium, and magnesium, elements that form divalent ions (Fe<sup>2+<\/sup>, Ca<sup>2+<\/sup>, and Mg<sup>2+<\/sup>), produce what is commonly referred to as \u201chard\u201d water. Taken together, the high concentration of divalent cations, the acidic pH (6.0), and the intense solar radiation flux make the Dead Sea a unique, and uniquely hostile, ecosystem[footnote]Bodaker, I, Itai, S, Suzuki, MT, Feingersch, R, Rosenberg, M, Maguire, ME, Shimshon, B, and others. Comparative community genomics in the Dead Sea: An increasingly extreme environment. <em>The ISME Journal<\/em> 4 (2010): 399\u2013407, doi:10.1038\/ismej.2009.141. published online 24 December 2009.[\/footnote] (Figure\u00a06).\r\n\r\n[caption id=\"attachment_1245\" align=\"aligncenter\" width=\"1024\"]<img class=\"size-large wp-image-1245\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18194015\/Figure_22_01_05-1024x419.jpg\" alt=\"Photo A shows the Dead Sea and its accompanying brown shoreline. Micrograph B shows rod-shaped halobacteria.\" width=\"1024\" height=\"419\" \/> Figure\u00a06. (a) The Dead Sea is hypersaline. Nevertheless, salt-tolerant bacteria thrive in this sea. (b) These halobacteria cells can form salt-tolerant bacterial mats. (credit a: Julien Menichini; credit b: NASA; scale-bar data from Matt Russell)[\/caption]\r\n\r\nWhat sort of prokaryotes do we find in the Dead Sea? The extremely salt-tolerant bacterial mats include <em>Halobacterium<\/em>, <em>Haloferax volcanii <\/em>(which is found in other locations, not only the Dead Sea), <em>Halorubrum sodomense<\/em>, and <em>Halobaculum gomorrense<\/em>, and the archaea <em>Haloarcula marismortui<\/em>, among others.\r\n<h2>Culturing Prokaryotes<\/h2>\r\n[caption id=\"attachment_1246\" align=\"alignright\" width=\"400\"]<img class=\" wp-image-1246\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18194126\/Figure_22_01_06.jpg\" alt=\"Two bacterial plates with red agar are shown. Both plates are covered with bacterial colonies. On the right plate, which contains hemolytic bacteria, the red agar has turned clear where bacteria are growing. On the left plate, which contains non-hemolytic bacteria, the agar is not clear.\" width=\"400\" height=\"267\" \/> Figure\u00a07. In these agar plates, the growth medium is supplemented with red blood cells. Blood agar becomes transparent in the presence of hemolytic <em>Streptococcus<\/em>, which destroys red blood cells and is used to diagnose <em>Streptococcus<\/em> infections. The plate on the left is inoculated with non-hemolytic <em>Staphylococcus<\/em> (large white colonies), and the plate on the right is inoculated with hemolytic <em>Streptococcus<\/em> (tiny clear colonies). If you look closely at the right plate, you can see that the agar surrounding the bacteria has turned clear. (credit: Bill Branson, NCI)[\/caption]\r\n\r\nMicrobiologists typically grow prokaryotes in the laboratory using an appropriate culture medium containing all the nutrients needed by the target organism. The medium can be liquid, broth, or solid. After an incubation time at the right temperature, there should be evidence of microbial growth (Figure\u00a07).\r\n\r\nThe process of culturing bacteria is complex and is one of the greatest discoveries of modern science. German physician Robert Koch is credited with discovering the techniques for pure culture, including staining and using growth media. His assistant Julius Petri invented the Petri dish whose use persists in today\u2019s laboratories. Koch worked primarily with the <em>Mycobacterium tuberculosis <\/em>bacterium that causes tuberculosis and developed postulates to identify disease-causing organisms that continue to be widely used in the medical community. Koch\u2019s postulates include that an organism can be identified as the cause of disease when it is present in all infected samples and absent in all healthy samples, and it is able to reproduce the infection after being cultured multiple times. Today, cultures remain a primary diagnostic tool in medicine and other areas of molecular biology.\r\n\r\nSome prokaryotes, however, cannot grow in a laboratory setting. In fact, over 99 percent of bacteria and archaea are unculturable. For the most part, this is due to a lack of knowledge as to what to feed these organisms and how to grow them; they have special requirements for growth that remain unknown to scientists, such as needing specific micronutrients, pH, temperature, pressure, co-factors, or co-metabolites. Some bacteria cannot be cultured because they are obligate intracellular parasites and cannot be grown outside a host cell.\r\n\r\nIn other cases, culturable organisms become unculturable under stressful conditions, even though the same organism could be cultured previously. Those organisms that cannot be cultured but are not dead are in a <b>viable-but-non-culturable<\/b> (VBNC) state. The VBNC state occurs when prokaryotes respond to environmental stressors by entering a dormant state that allows their survival. The criteria for entering into the VBNC state are not completely understood. In a process called <b>resuscitation<\/b>, the prokaryote can go back to \u201cnormal\u201d life when environmental conditions improve.\r\n\r\nIs the VBNC state an unusual way of living for prokaryotes? In fact, most of the prokaryotes living in the soil or in oceanic waters are non-culturable. It has been said that only a small fraction, perhaps one percent, of prokaryotes can be cultured under laboratory conditions. If these organisms are non-culturable, then how is it known whether they are present and alive? Microbiologists use molecular techniques, such as the polymerase chain reaction (PCR), to amplify selected portions of DNA of prokaryotes, demonstrating their existence. Recall that PCR can make billions of copies of a DNA segment in a process called amplification.\r\n<h2>Prokaryotic Biofilms<\/h2>\r\n[caption id=\"attachment_1247\" align=\"alignright\" width=\"399\"]<img class=\" wp-image-1247\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18194543\/800px-Biofilm_sur_eauPortAuray.jpg\" alt=\"photograph of a river with a filmy grey layer on its surface\" width=\"399\" height=\"219\" \/> Figure\u00a08. A biofilm on the surface of the water in the on the edge of the Port of Saint-Goustan in Auray[\/caption]\r\n\r\nUntil a couple of decades ago, microbiologists used to think of prokaryotes as isolated entities living apart. This model, however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. A <span data-type=\"term\">biofilm<\/span> is a microbial community (Figure\u00a08) held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described as well as some composed of a mixture of fungi and bacteria.\r\n\r\nBiofilms are present almost everywhere: they can cause the clogging of pipes and readily colonize surfaces in industrial settings. In recent, large-scale outbreaks of bacterial contamination of food, biofilms have played a major role. They also colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets, as well as places on the human body, such as the surfaces of our teeth.\r\n\r\nInteractions among the organisms that populate a biofilm, together with their protective exopolysaccharidic (EPS) environment, make these communities more robust than free-living, or planktonic, prokaryotes. The sticky substance that holds bacteria together also excludes most antibiotics and disinfectants, making biofilm bacteria hardier than their planktonic counterparts. Overall, biofilms are very difficult to destroy because they are resistant to many common forms of sterilization.\r\n<div class=\"textbox exercises\">\r\n<h3>Practice Question<\/h3>\r\nThere are five stage of biofilm development:\r\n\r\n[caption id=\"attachment_1248\" align=\"aligncenter\" width=\"725\"]<img class=\"wp-image-1248 size-full\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18194728\/Figure_22_01_07.png\" alt=\"During the first stage of biofilm development, a few bacteria adhere to a surface. During stage 2, the bacteria grow hairy appendages called pili. During stage 3, the microfilm grows into lumpy colonies. In stage 4, the microfilm grows into a more ball-like shape that is anchored to the surface by a smaller clump of bacteria. In stage 5, the ball of bacteria is larger, and bacteria with flagella swim away.\" width=\"725\" height=\"450\" \/> Figure\u00a09. Five stages of biofilm development are shown. Micrographs of a <em>Pseudomonas aeruginosabiofilm<\/em> in each of the stages of development are shown. (credit: D. Davis, Don Monroe, PLoS)[\/caption]\r\n\r\n&nbsp;\r\n<ul>\r\n \t<li>During stage 1, initial attachment, bacteria adhere to a solid surface via weak van der Waals interactions.<\/li>\r\n \t<li>During stage 2, irreversible attachment, hairlike appendages called pili permanently anchor the bacteria to the surface.<\/li>\r\n \t<li>During stage 3, maturation I, the biofilm grows through cell division and recruitment of other bacteria. An extracellular matrix composed primarily of polysaccharides holds the biofilm together.<\/li>\r\n \t<li>During stage 4, maturation II, the biofilm continues to grow and takes on a more complex shape.<\/li>\r\n \t<li>During stage 5, dispersal, the biofilm matrix is partly broken down, allowing some bacteria to escape and colonize another surface.<\/li>\r\n<\/ul>\r\nCompared to free-floating bacteria, bacteria in biofilms often show increased resistance to antibiotics and detergents. Why do you think this might be the case?\r\n\r\n[practice-area rows=\"4\"][\/practice-area]\r\n[reveal-answer q=\"805834\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"805834\"]The extracellular matrix and outer layer of cells protects the inner bacteria. The close proximity of cells also facilitates lateral gene transfer, a process by which genes such as antibiotic resistance genes are transferred from one bacterium to another. And even if lateral gene transfer does not occur, one bacterium that produces an exo-enzyme that destroys antibiotic may save neighboring bacteria.[\/hidden-answer]\r\n\r\n<\/div>\r\n<h2><strong>Check Your Understanding<\/strong><\/h2>\r\nAnswer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does\u00a0<strong>not<\/strong>\u00a0count toward your grade in the class, and you can retake it an unlimited number of times.\r\n\r\nUse this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section.\r\n\r\nhttps:\/\/assessments.lumenlearning.com\/assessments\/4934","rendered":"<h2>Discuss the diversity of prokaryotic cells<\/h2>\n<div id=\"attachment_1238\" style=\"width: 409px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1238\" class=\"wp-image-1238\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193416\/Figure_22_00_01-1024x572.jpg\" alt=\"The photo shows a hot spring with a vivid blue color in the middle and a golden color around the edge.\" width=\"399\" height=\"223\" \/><\/p>\n<p id=\"caption-attachment-1238\" class=\"wp-caption-text\">Figure\u00a01.\u00a0Certain prokaryotes can live in extreme environments such as the Morning Glory pool, a hot spring in Yellowstone National Park. The spring\u2019s vivid blue color is from the prokaryotes that thrive in its very hot waters. (credit: modification of work by Jon Sullivan)<\/p>\n<\/div>\n<p>In the recent past, scientists grouped living things into five kingdoms\u2014animals, plants, fungi, protists, and prokaryotes\u2014based on several criteria, such as the absence or presence of a nucleus and other membrane-bound organelles, the absence or presence of cell walls, multicellularity, and so on. In the late 20th\u00a0century, the pioneering work of Carl Woese and others compared sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a more fundamental way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The domain Bacteria comprises all organisms in the kingdom Bacteria, the domain Archaea comprises the rest of the prokaryotes, and the domain Eukarya comprises all eukaryotes\u2014including organisms in the kingdoms Animalia, Plantae, Fungi, and Protista.<\/p>\n<p>Two of the three domains\u2014Bacteria and Archaea\u2014are prokaryotic. Prokaryotes were the first inhabitants on Earth, appearing 3.5 to 3.8 billion years ago. These organisms are abundant and ubiquitous; that is, they are present everywhere. In addition to inhabiting moderate environments, they are found in extreme conditions: from boiling springs to permanently frozen environments in Antarctica; from salty environments like the Dead Sea to environments under tremendous pressure, such as the depths of the ocean; and from areas without oxygen, such as a waste management plant, to radioactively contaminated regions, such as Chernobyl. Prokaryotes reside in the human digestive system and on the skin, are responsible for certain illnesses, and serve an important role in the preparation of many foods.<\/p>\n<div class=\"textbox learning-objectives\">\n<h3>Learning Objectives<\/h3>\n<ul>\n<li>Describe the evolutionary history of prokaryotes<\/li>\n<li>Discuss the distinguishing features of extremophiles<\/li>\n<li>Understand why it is difficult to culture prokaryotes<\/li>\n<li>Discuss why prokaryotes often form biofilms<\/li>\n<\/ul>\n<\/div>\n<h2>Evolutionary History of Prokaryotes<\/h2>\n<p>Prokaryotes are ubiquitous. They cover every imaginable surface where there is sufficient moisture, and they live on and inside of other living things. In the typical human body, prokaryotic cells outnumber human body cells by about ten to one. They comprise the majority of living things in all ecosystems. Some prokaryotes thrive in environments that are inhospitable for most living things. Prokaryotes recycle <b>nutrients<\/b>\u2014essential substances (such as carbon and nitrogen)\u2014and they drive the evolution of new ecosystems, some of which are natural and others man-made. Prokaryotes have been on Earth since long before multicellular life appeared.<\/p>\n<p>When and where did life begin? What were the conditions on Earth when life began? Prokaryotes were the first forms of life on Earth, and they existed for billions of years before plants and animals appeared. The Earth and its moon are thought to be about 4.54\u00a0billion years old. This estimate is based on evidence from radiometric dating of meteorite material together with other substrate material from Earth and the moon. Early Earth had a very different atmosphere (contained less molecular oxygen) than it does today and was subjected to strong radiation; thus, the first organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of the Earth. At this time too, strong volcanic activity was common on Earth, so it is likely that these first organisms\u2014the first prokaryotes\u2014were adapted to very high temperatures. Early Earth was prone to geological upheaval and volcanic eruption, and was subject to bombardment by mutagenic radiation from the sun. The first organisms were prokaryotes that could withstand these harsh conditions.<\/p>\n<h3>Microbial Mats<\/h3>\n<p>Microbial mats or large biofilms may represent the earliest forms of life on Earth; there is fossil evidence of their presence starting about 3.5 billion years ago. A <b>microbial mat<\/b> is a multi-layered sheet of prokaryotes (Figure\u00a02) that includes mostly bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically grow where different types of materials interface, mostly on moist surfaces. The various types of prokaryotes that comprise them carry out different metabolic pathways, and that is the reason for their various colors. Prokaryotes in a microbial mat are held together by a glue-like sticky substance that they secrete called extracellular matrix.<\/p>\n<p>The first microbial mats likely obtained their energy from chemicals found near hydrothermal vents. A <b>hydrothermal vent<\/b> is a breakage or fissure in the Earth\u2019s surface that releases geothermally heated water. With the evolution of photosynthesis about 3 billion years ago, some prokaryotes in microbial mats came to use a more widely available energy source\u2014sunlight\u2014whereas others were still dependent on chemicals from hydrothermal vents for energy and food.<\/p>\n<div id=\"attachment_1239\" style=\"width: 1034px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1239\" class=\"size-large wp-image-1239\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193521\/Figure_22_01_01-1024x411.jpg\" alt=\"The part a photo shows a reddish-yellow mound with small chimneys growing out of it. Part b micrograph shows rod-shaped bacteria about two microns long swimming over a thicker mat of bacteria.\" width=\"1024\" height=\"411\" \/><\/p>\n<p id=\"caption-attachment-1239\" class=\"wp-caption-text\">Figure\u00a02. This (a) microbial mat, about one meter in diameter, grows over a hydrothermal vent in the Pacific Ocean in a region known as the \u201cPacific Ring of Fire.\u201d The mat helps retain microbial nutrients. Chimneys such as the one indicated by the arrow allow gases to escape. (b) In this micrograph, bacteria are visualized using fluorescence microscopy. (credit a: modification of work by Dr. Bob Embley, NOAA PMEL, Chief Scientist; credit b: modification of work by Ricardo Murga, Rodney Donlan, CDC; scale-bar data from Matt Russell)<\/p>\n<\/div>\n<figure><\/figure>\n<h3>Stromatolites<\/h3>\n<p>Fossilized microbial mats represent the earliest record of life on Earth. A <b>stromatolite<\/b> is a sedimentary structure formed when minerals are precipitated out of water by prokaryotes in a microbial mat (Figure\u00a03). Stromatolites form layered rocks made of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on Earth where stromatolites are still forming. For example, growing stromatolites have been found in the Anza-Borrego Desert State Park in San Diego County, California.<\/p>\n<div id=\"attachment_1240\" style=\"width: 1034px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1240\" class=\"size-large wp-image-1240\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193631\/Figure_22_01_02ab-1024x372.jpg\" alt=\"Photo A shows a mass of gray mounds in shallow water. Photo B shows a swirl patter in white and gray marbled rock.\" width=\"1024\" height=\"372\" \/><\/p>\n<p id=\"caption-attachment-1240\" class=\"wp-caption-text\">Figure\u00a03. (a) These living stromatolites are located in Shark Bay, Australia. (b) These fossilized stromatolites, found in Glacier National Park, Montana, are nearly 1.5 billion years old. (credit a: Robert Young; credit b: P. Carrara, NPS)<\/p>\n<\/div>\n<figure><\/figure>\n<h3>The Ancient Atmosphere<\/h3>\n<figure><\/figure>\n<div id=\"attachment_1241\" style=\"width: 410px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1241\" class=\"wp-image-1241\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193702\/Figure_22_01_03-e1484768251762.jpg\" alt=\"This photo shows a woman squatting next to a stream of green-colored water.\" width=\"400\" height=\"231\" \/><\/p>\n<p id=\"caption-attachment-1241\" class=\"wp-caption-text\">Figure\u00a04. This hot spring in Yellowstone National Park flows toward the foreground. Cyanobacteria in the spring are green, and as water flows down the gradient, the intensity of the color increases as cell density increases. The water is cooler at the edges of the stream than in the center, causing the edges to appear greener. (credit: Graciela Brelles-Mari\u00f1o)<\/p>\n<\/div>\n<p>Evidence indicates that during the first two billion years of Earth\u2019s existence, the atmosphere was <b>anoxic<\/b>, meaning that there was no molecular oxygen. Therefore, only those organisms that can grow without oxygen\u2014<b>anaerobic<\/b> organisms\u2014were able to live. Autotrophic organisms that convert solar energy into chemical energy are called <b>phototrophs<\/b>, and they appeared within one billion years of the formation of Earth. Then, <b>cyanobacteria<\/b>, also known as blue-green algae, evolved from these simple phototrophs one billion years later. Cyanobacteria (Figure\u00a04) began the oxygenation of the atmosphere. Increased atmospheric oxygen allowed the development of more efficient O<sub>2<\/sub>-utilizing catabolic pathways. It also opened up the land to increased colonization, because some O<sub>2\u00a0<\/sub>is converted into O<sub>3<\/sub> (ozone) and ozone effectively absorbs the ultraviolet light that would otherwise cause lethal mutations in DNA. Ultimately, the increase in O<sub>2<\/sub> concentrations allowed the evolution of other life forms.<\/p>\n<div class=\"textbox exercises\">\n<h3>Practice\u00a0Questions<\/h3>\n<p>Microbial mats __________.<\/p>\n<ol>\n<li>are the earliest forms of life on Earth<\/li>\n<li>obtained their energy and food from hydrothermal vents<\/li>\n<li>are multi-layered sheet of prokaryotes including mostly bacteria but also archaea<\/li>\n<li>are all of the above<\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q125455\">Show Answer<\/span><\/p>\n<div id=\"q125455\" class=\"hidden-answer\" style=\"display: none\">Answer d. Microbial mats <strong>are all of the above<\/strong>.<\/p>\n<\/div>\n<\/div>\n<p>The first organisms that oxygenated the atmosphere were<\/p>\n<ol>\n<li>cyanobacteria<\/li>\n<li>phototrophic organisms<\/li>\n<li>anaerobic organisms<\/li>\n<li>all of the above<\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q566688\">Show Answer<\/span><\/p>\n<div id=\"q566688\" class=\"hidden-answer\" style=\"display: none\">Answer a. The first organisms that oxygenated the atmosphere were\u00a0<strong>cyanobacteria<\/strong>.<\/div>\n<\/div>\n<\/div>\n<h2>Life in Moderate and Extreme Environments<\/h2>\n<p>Some organisms have developed strategies that allow them to survive harsh conditions. Prokaryotes thrive in a vast array of environments: some grow in conditions that would seem very normal to us, whereas others are able to thrive and grow under conditions that would kill a plant or animal. Almost all prokaryotes have a cell wall, a protective structure that allows them to survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are able to form endospores that resist heat and drought, thereby allowing the organism to survive until favorable conditions recur. These adaptations, along with others, allow bacteria to be the most abundant life form in all terrestrial and aquatic ecosystems.<\/p>\n<p>Other bacteria and archaea are adapted to grow under extreme conditions and are called <b>extremophiles<\/b>, meaning \u201clovers of extremes.\u201d Extremophiles have been found in all kinds of environments: the depth of the oceans, hot springs, the Arctic and the Antarctic, in very dry places, deep inside Earth, in harsh chemical environments, and in high radiation environments, just to mention a few.<\/p>\n<div id=\"attachment_1244\" style=\"width: 310px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1244\" class=\"wp-image-1244\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18193928\/Figure_22_01_04.jpg\" alt=\"This micrograph shows an oval Deinococcus about 2.5 microns in diameter cell dividing.\" width=\"300\" height=\"345\" \/><\/p>\n<p id=\"caption-attachment-1244\" class=\"wp-caption-text\">Figure\u00a05. <em>Deinococcus radiodurans<\/em>, visualized in a\u00a0false color transmission electron micrograph (credit: modification of work by Michael Daly; scale-bar data from Matt Russell)<\/p>\n<\/div>\n<p>Other extremophiles, like <b>radioresistant<\/b> organisms, do not prefer an extreme environment (in this case, one with high levels of radiation), but have adapted to survive in it. For example,\u00a0<em>Deinococcus radiodurans<\/em>, shown in Figure\u00a05, is a prokaryote that can tolerate very high doses of ionizing radiation. It has developed DNA repair mechanisms that allow it to reconstruct its chromosome even if it has been broken into hundreds of pieces by radiation or heat.<\/p>\n<p>These organisms give us a better understanding of prokaryotic diversity and open up the possibility of finding new prokaryotic species that may lead to the discovery of new therapeutic drugs or have industrial applications. Because they have specialized adaptations that allow them to live in extreme conditions, many extremophiles cannot survive in moderate environments.<\/p>\n<p>There are many different groups of extremophiles: they are identified based on the conditions in which they grow best, and several habitats are extreme in multiple ways. For example, a soda lake is both salty and alkaline, so organisms that live in a soda lake must be both alkaliphiles and halophiles (Table\u00a01).<\/p>\n<table id=\"tab-ch22-01-01\" summary=\"\">\n<thead>\n<tr>\n<th colspan=\"2\">Table\u00a01. Extremophiles and Their Preferred Conditions<\/th>\n<\/tr>\n<tr>\n<th>Extremophile Type<\/th>\n<th>Conditions for Optimal Growth<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>Acidophiles<\/td>\n<td>pH 3 or below<\/td>\n<\/tr>\n<tr>\n<td>Alkaliphiles<\/td>\n<td>pH 9 or above<\/td>\n<\/tr>\n<tr>\n<td>Thermophiles<\/td>\n<td>Temperature 60\u201380 \u00b0C (140\u2013176 \u00b0F)<\/td>\n<\/tr>\n<tr>\n<td>Hyperthermophiles<\/td>\n<td>Temperature 80\u2013122 \u00b0C (176\u2013250 \u00b0F)<\/td>\n<\/tr>\n<tr>\n<td>Psychrophiles<\/td>\n<td>Temperature of \u221215\u201310 \u00b0C (5\u201350 \u00b0F) or lower<\/td>\n<\/tr>\n<tr>\n<td>Halophiles<\/td>\n<td>Salt concentration of at least 0.2 M<\/td>\n<\/tr>\n<tr>\n<td>Osmophiles<\/td>\n<td>High sugar concentration<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>Prokaryotes in the Dead Sea<\/h3>\n<p>One example of a very harsh environment is the Dead Sea, a hypersaline basin that is located between Jordan and Israel. Hypersaline environments are essentially concentrated seawater. In the Dead Sea, the sodium concentration is 10 times higher than that of seawater, and the water contains high levels of magnesium (about 40 times higher than in seawater) that would be toxic to most living things. Iron, calcium, and magnesium, elements that form divalent ions (Fe<sup>2+<\/sup>, Ca<sup>2+<\/sup>, and Mg<sup>2+<\/sup>), produce what is commonly referred to as \u201chard\u201d water. Taken together, the high concentration of divalent cations, the acidic pH (6.0), and the intense solar radiation flux make the Dead Sea a unique, and uniquely hostile, ecosystem<a class=\"footnote\" title=\"Bodaker, I, Itai, S, Suzuki, MT, Feingersch, R, Rosenberg, M, Maguire, ME, Shimshon, B, and others. Comparative community genomics in the Dead Sea: An increasingly extreme environment. The ISME Journal 4 (2010): 399\u2013407, doi:10.1038\/ismej.2009.141. published online 24 December 2009.\" id=\"return-footnote-1210-1\" href=\"#footnote-1210-1\" aria-label=\"Footnote 1\"><sup class=\"footnote\">[1]<\/sup><\/a> (Figure\u00a06).<\/p>\n<div id=\"attachment_1245\" style=\"width: 1034px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1245\" class=\"size-large wp-image-1245\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18194015\/Figure_22_01_05-1024x419.jpg\" alt=\"Photo A shows the Dead Sea and its accompanying brown shoreline. Micrograph B shows rod-shaped halobacteria.\" width=\"1024\" height=\"419\" \/><\/p>\n<p id=\"caption-attachment-1245\" class=\"wp-caption-text\">Figure\u00a06. (a) The Dead Sea is hypersaline. Nevertheless, salt-tolerant bacteria thrive in this sea. (b) These halobacteria cells can form salt-tolerant bacterial mats. (credit a: Julien Menichini; credit b: NASA; scale-bar data from Matt Russell)<\/p>\n<\/div>\n<p>What sort of prokaryotes do we find in the Dead Sea? The extremely salt-tolerant bacterial mats include <em>Halobacterium<\/em>, <em>Haloferax volcanii <\/em>(which is found in other locations, not only the Dead Sea), <em>Halorubrum sodomense<\/em>, and <em>Halobaculum gomorrense<\/em>, and the archaea <em>Haloarcula marismortui<\/em>, among others.<\/p>\n<h2>Culturing Prokaryotes<\/h2>\n<div id=\"attachment_1246\" style=\"width: 410px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1246\" class=\"wp-image-1246\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18194126\/Figure_22_01_06.jpg\" alt=\"Two bacterial plates with red agar are shown. Both plates are covered with bacterial colonies. On the right plate, which contains hemolytic bacteria, the red agar has turned clear where bacteria are growing. On the left plate, which contains non-hemolytic bacteria, the agar is not clear.\" width=\"400\" height=\"267\" \/><\/p>\n<p id=\"caption-attachment-1246\" class=\"wp-caption-text\">Figure\u00a07. In these agar plates, the growth medium is supplemented with red blood cells. Blood agar becomes transparent in the presence of hemolytic <em>Streptococcus<\/em>, which destroys red blood cells and is used to diagnose <em>Streptococcus<\/em> infections. The plate on the left is inoculated with non-hemolytic <em>Staphylococcus<\/em> (large white colonies), and the plate on the right is inoculated with hemolytic <em>Streptococcus<\/em> (tiny clear colonies). If you look closely at the right plate, you can see that the agar surrounding the bacteria has turned clear. (credit: Bill Branson, NCI)<\/p>\n<\/div>\n<p>Microbiologists typically grow prokaryotes in the laboratory using an appropriate culture medium containing all the nutrients needed by the target organism. The medium can be liquid, broth, or solid. After an incubation time at the right temperature, there should be evidence of microbial growth (Figure\u00a07).<\/p>\n<p>The process of culturing bacteria is complex and is one of the greatest discoveries of modern science. German physician Robert Koch is credited with discovering the techniques for pure culture, including staining and using growth media. His assistant Julius Petri invented the Petri dish whose use persists in today\u2019s laboratories. Koch worked primarily with the <em>Mycobacterium tuberculosis <\/em>bacterium that causes tuberculosis and developed postulates to identify disease-causing organisms that continue to be widely used in the medical community. Koch\u2019s postulates include that an organism can be identified as the cause of disease when it is present in all infected samples and absent in all healthy samples, and it is able to reproduce the infection after being cultured multiple times. Today, cultures remain a primary diagnostic tool in medicine and other areas of molecular biology.<\/p>\n<p>Some prokaryotes, however, cannot grow in a laboratory setting. In fact, over 99 percent of bacteria and archaea are unculturable. For the most part, this is due to a lack of knowledge as to what to feed these organisms and how to grow them; they have special requirements for growth that remain unknown to scientists, such as needing specific micronutrients, pH, temperature, pressure, co-factors, or co-metabolites. Some bacteria cannot be cultured because they are obligate intracellular parasites and cannot be grown outside a host cell.<\/p>\n<p>In other cases, culturable organisms become unculturable under stressful conditions, even though the same organism could be cultured previously. Those organisms that cannot be cultured but are not dead are in a <b>viable-but-non-culturable<\/b> (VBNC) state. The VBNC state occurs when prokaryotes respond to environmental stressors by entering a dormant state that allows their survival. The criteria for entering into the VBNC state are not completely understood. In a process called <b>resuscitation<\/b>, the prokaryote can go back to \u201cnormal\u201d life when environmental conditions improve.<\/p>\n<p>Is the VBNC state an unusual way of living for prokaryotes? In fact, most of the prokaryotes living in the soil or in oceanic waters are non-culturable. It has been said that only a small fraction, perhaps one percent, of prokaryotes can be cultured under laboratory conditions. If these organisms are non-culturable, then how is it known whether they are present and alive? Microbiologists use molecular techniques, such as the polymerase chain reaction (PCR), to amplify selected portions of DNA of prokaryotes, demonstrating their existence. Recall that PCR can make billions of copies of a DNA segment in a process called amplification.<\/p>\n<h2>Prokaryotic Biofilms<\/h2>\n<div id=\"attachment_1247\" style=\"width: 409px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1247\" class=\"wp-image-1247\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18194543\/800px-Biofilm_sur_eauPortAuray.jpg\" alt=\"photograph of a river with a filmy grey layer on its surface\" width=\"399\" height=\"219\" \/><\/p>\n<p id=\"caption-attachment-1247\" class=\"wp-caption-text\">Figure\u00a08. A biofilm on the surface of the water in the on the edge of the Port of Saint-Goustan in Auray<\/p>\n<\/div>\n<p>Until a couple of decades ago, microbiologists used to think of prokaryotes as isolated entities living apart. This model, however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. A <span data-type=\"term\">biofilm<\/span> is a microbial community (Figure\u00a08) held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described as well as some composed of a mixture of fungi and bacteria.<\/p>\n<p>Biofilms are present almost everywhere: they can cause the clogging of pipes and readily colonize surfaces in industrial settings. In recent, large-scale outbreaks of bacterial contamination of food, biofilms have played a major role. They also colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets, as well as places on the human body, such as the surfaces of our teeth.<\/p>\n<p>Interactions among the organisms that populate a biofilm, together with their protective exopolysaccharidic (EPS) environment, make these communities more robust than free-living, or planktonic, prokaryotes. The sticky substance that holds bacteria together also excludes most antibiotics and disinfectants, making biofilm bacteria hardier than their planktonic counterparts. Overall, biofilms are very difficult to destroy because they are resistant to many common forms of sterilization.<\/p>\n<div class=\"textbox exercises\">\n<h3>Practice Question<\/h3>\n<p>There are five stage of biofilm development:<\/p>\n<div id=\"attachment_1248\" style=\"width: 735px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1248\" class=\"wp-image-1248 size-full\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1223\/2017\/01\/18194728\/Figure_22_01_07.png\" alt=\"During the first stage of biofilm development, a few bacteria adhere to a surface. During stage 2, the bacteria grow hairy appendages called pili. During stage 3, the microfilm grows into lumpy colonies. In stage 4, the microfilm grows into a more ball-like shape that is anchored to the surface by a smaller clump of bacteria. In stage 5, the ball of bacteria is larger, and bacteria with flagella swim away.\" width=\"725\" height=\"450\" \/><\/p>\n<p id=\"caption-attachment-1248\" class=\"wp-caption-text\">Figure\u00a09. Five stages of biofilm development are shown. Micrographs of a <em>Pseudomonas aeruginosabiofilm<\/em> in each of the stages of development are shown. (credit: D. Davis, Don Monroe, PLoS)<\/p>\n<\/div>\n<p>&nbsp;<\/p>\n<ul>\n<li>During stage 1, initial attachment, bacteria adhere to a solid surface via weak van der Waals interactions.<\/li>\n<li>During stage 2, irreversible attachment, hairlike appendages called pili permanently anchor the bacteria to the surface.<\/li>\n<li>During stage 3, maturation I, the biofilm grows through cell division and recruitment of other bacteria. An extracellular matrix composed primarily of polysaccharides holds the biofilm together.<\/li>\n<li>During stage 4, maturation II, the biofilm continues to grow and takes on a more complex shape.<\/li>\n<li>During stage 5, dispersal, the biofilm matrix is partly broken down, allowing some bacteria to escape and colonize another surface.<\/li>\n<\/ul>\n<p>Compared to free-floating bacteria, bacteria in biofilms often show increased resistance to antibiotics and detergents. Why do you think this might be the case?<\/p>\n<p><textarea aria-label=\"Your Answer\" rows=\"4\"><\/textarea><\/p>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q805834\">Show Answer<\/span><\/p>\n<div id=\"q805834\" class=\"hidden-answer\" style=\"display: none\">The extracellular matrix and outer layer of cells protects the inner bacteria. The close proximity of cells also facilitates lateral gene transfer, a process by which genes such as antibiotic resistance genes are transferred from one bacterium to another. And even if lateral gene transfer does not occur, one bacterium that produces an exo-enzyme that destroys antibiotic may save neighboring bacteria.<\/div>\n<\/div>\n<\/div>\n<h2><strong>Check Your Understanding<\/strong><\/h2>\n<p>Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does\u00a0<strong>not<\/strong>\u00a0count toward your grade in the class, and you can retake it an unlimited number of times.<\/p>\n<p>Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section.<\/p>\n<p>\t<iframe id=\"lumen_assessment_4934\" class=\"resizable\" src=\"https:\/\/assessments.lumenlearning.com\/assessments\/load?assessment_id=4934&#38;embed=1&#38;external_user_id=&#38;external_context_id=&#38;iframe_resize_id=lumen_assessment_4934\" frameborder=\"0\" style=\"border:none;width:100%;height:100%;min-height:400px;\"><br \/>\n\t<\/iframe><\/p>\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-1210\">\n\t\t\t\t\t\t\t <div class=\"licensing\"><div class=\"license-attribution-dropdown-subheading\">CC licensed content, Original<\/div><ul class=\"citation-list\"><li>Introduction to Prokaryotic Diversity. <strong>Authored by<\/strong>: Shelli Carter and Lumen Learning. <strong>Provided by<\/strong>: Lumen Learning. <strong>License<\/strong>: <em><a target=\"_blank\" rel=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\">CC BY: Attribution<\/a><\/em><\/li><\/ul><div class=\"license-attribution-dropdown-subheading\">CC licensed content, Shared previously<\/div><ul class=\"citation-list\"><li>Biology. <strong>Provided by<\/strong>: OpenStax CNX. <strong>Located at<\/strong>: <a target=\"_blank\" href=\"http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8\">http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8<\/a>. <strong>License<\/strong>: <em><a target=\"_blank\" rel=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\">CC BY: Attribution<\/a><\/em>. <strong>License Terms<\/strong>: Download for free at http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8<\/li><li>Biofilm sur eauPortAuray. <strong>Authored by<\/strong>: F.Lamiot. <strong>Located at<\/strong>: <a target=\"_blank\" href=\"https:\/\/commons.wikimedia.org\/wiki\/File:Biofilm_sur_eauPortAuray.jpg\">https:\/\/commons.wikimedia.org\/wiki\/File:Biofilm_sur_eauPortAuray.jpg<\/a>. <strong>License<\/strong>: <em><a target=\"_blank\" rel=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by-sa\/4.0\/\">CC BY-SA: Attribution-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-1210-1\">Bodaker, I, Itai, S, Suzuki, MT, Feingersch, R, Rosenberg, M, Maguire, ME, Shimshon, B, and others. Comparative community genomics in the Dead Sea: An increasingly extreme environment. <em>The ISME Journal<\/em> 4 (2010): 399\u2013407, doi:10.1038\/ismej.2009.141. published online 24 December 2009. <a href=\"#return-footnote-1210-1\" class=\"return-footnote\" aria-label=\"Return to footnote 1\">&crarr;<\/a><\/li><\/ol><\/div>","protected":false},"author":17,"menu_order":2,"template":"","meta":{"_candela_citation":"[{\"type\":\"cc\",\"description\":\"Biology\",\"author\":\"\",\"organization\":\"OpenStax CNX\",\"url\":\"http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8\",\"project\":\"\",\"license\":\"cc-by\",\"license_terms\":\"Download for free at http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8\"},{\"type\":\"original\",\"description\":\"Introduction to Prokaryotic Diversity\",\"author\":\"Shelli Carter and Lumen Learning\",\"organization\":\"Lumen Learning\",\"url\":\"\",\"project\":\"\",\"license\":\"cc-by\",\"license_terms\":\"\"},{\"type\":\"cc\",\"description\":\"Biofilm sur eauPortAuray\",\"author\":\"F.Lamiot\",\"organization\":\"\",\"url\":\"https:\/\/commons.wikimedia.org\/wiki\/File:Biofilm_sur_eauPortAuray.jpg\",\"project\":\"\",\"license\":\"cc-by-sa\",\"license_terms\":\"\"}]","CANDELA_OUTCOMES_GUID":"51ab1c86-f92a-425c-8706-93d1cdedba4e, 042b6db5-3b7d-4db8-bc37-ad7f725eb02f, dc8468e0-de2c-45ab-8490-ef71cde8cb95, 754d6d8f-9419-4636-8ddc-40d396f1271a, 7a3b9528-3771-43c9-831b-40327f13885d","pb_show_title":"on","pb_short_title":"","pb_subtitle":"","pb_authors":[],"pb_section_license":""},"chapter-type":[],"contributor":[],"license":[],"class_list":["post-1210","chapter","type-chapter","status-publish","hentry"],"part":1195,"_links":{"self":[{"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/pressbooks\/v2\/chapters\/1210","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/pressbooks\/v2\/chapters"}],"about":[{"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/wp\/v2\/types\/chapter"}],"author":[{"embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/wp\/v2\/users\/17"}],"version-history":[{"count":9,"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/pressbooks\/v2\/chapters\/1210\/revisions"}],"predecessor-version":[{"id":5878,"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/pressbooks\/v2\/chapters\/1210\/revisions\/5878"}],"part":[{"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/pressbooks\/v2\/parts\/1195"}],"metadata":[{"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/pressbooks\/v2\/chapters\/1210\/metadata\/"}],"wp:attachment":[{"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/wp\/v2\/media?parent=1210"}],"wp:term":[{"taxonomy":"chapter-type","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/pressbooks\/v2\/chapter-type?post=1210"},{"taxonomy":"contributor","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/wp\/v2\/contributor?post=1210"},{"taxonomy":"license","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/suny-wmopen-biology2\/wp-json\/wp\/v2\/license?post=1210"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}