Chapter 13 Notes

Until the late 20th century, scientists most grouped living things into 5 kingdoms – animals, plants, fungi, protists, & bacteria – based on several criteria, such as the absence or presence of a nucleus & other membrane-bound organelles, absence or presence of cell walls, multicellularity, & mode of nutrition. In the late 20th century, the pioneering work of Carl Woese & others compared nucleotide sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a dramatically different way to group organisms on Earth. Based on differences in the structure of cell membranes & in rRNA, Woese & his colleagues proposed that all life on Earth evolved along three lineages, called domains. The 3 domains are called Bacteria, Archaea, & Eukarya. Two of the 3 domains – Bacteria & Archaea – are prokaryotic, meaning that they lack both a nucleus & true membrane-bound organelles. Based on membrane structure & rRNA, they are now considered to be as different from each other as they are from the 3rd domain, Eukarya. Prokaryotes were the 1st inhabitants on Earth, perhaps appearing approximately 3.9 billion years ago. The Eukarya includes the familiar kingdoms of animals, plants, & fungi. They also include a diverse group of kingdoms formerly grouped as protists. 13.1 Prokaryotic Diversity Prokaryotes are present everywhere. There are more prokaryotes inside & on the exterior of the human body than there are human cells in the body. Prokaryotes recycle nutrients – essential substances (such as carbon & nitrogen) - & they drive the evolution of new ecosystems, some of which are natural while others are man-made. Prokaryotic Diversity The recognition of prokaryotic diversity forced a new understanding of the classification of all life & brought us closer to understanding the fundamental relationships of all living things, including ourselves. Early Life on Earth Prokaryotes were the 1st forms of life on Earth, & they existed for billions of years before plants & animals appeared. Evidence indicates that during the 1st 2 billion years of Earth’s existence, the atmosphere was anoxic, meaning that there was no oxygen. Only those organisms that can grow without oxygen – anaerobic organisms – were able to live. Organisms that convert solar energy into chemical energy are called phototrophs. Phototrophic organisms that required an organic source of carbon appeared within 1 billion years of the formation of Earth. Then, cyanobacteria, also known as blue-green algae, evolved from these simple phototrophs 1 billion years later. Cyanobacteria can use carbon dioxide as a source of carbon. Cyanobacteria began the oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of other life forms. Before the atmosphere became oxygenated, the planet was subjected to strong radiation; thus the 1st organisms would have flourished where they were more protected, such as in ocean depths or beneath the surface of Earth. At this time, too, strong volcanic activity was common on Earth, so it is likely that these 1st organisms – the 1st prokaryotes – were adapted to very high temperatures. We can conclude that the 1st organisms that appeared on Earth likely were able to withstand harsh conditions. Microbial mats may represent the earliest forms of life on Earth, & there is fossil evidence of their presence, starting about 3.5 billion years ago. A microbial mat is a large biofilm, a multi-layered sheet of prokaryotes, including mostly bacteria and archaea. Microbial mats are a few centimeters thick, & they typically grow on moist surfaces. Their various types of prokaryotes carry out different metabolic pathways, & for this reason, they reflect various colors. Prokaryotes in a microbial mat are held together by a gummy-like substance that they secrete. The 1st microbial mats likely obtained their energy from hydrothermal vents. A hydrothermal vent is a fissure in Earth’s 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 – sunlight – whereas others were still dependent on chemicals from hydrothermal vents for food. Fossilized microbial mats represent the earliest record of life on Earth. A stromatolite is a sedimentary structure formed when minerals are precipitated from water by prokaryotes in a microbial mat. Stromatolites form layered rocks made of carbonate or silicate. Bacteria & archaea that grow under extreme conditions are called extremophiles, meaning “lovers of extremes.” Extremophiles have been found in extreme environments of all kinds, including the depths of the oceans, hot springs, the Artic, & the Antarctic, very dry places, deep inside Earth, harsh chemical environments, & high radiation environments. Many of these extremophiles cannot survive in moderate environments. Biofilm A biofilm is a microbial community held together in a gummy-textures matrix, consisting primarily of polysaccharides secreted by the organisms, together with some proteins & nucleic acids. Biofilms from attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described. Biofilms are present almost everywhere. They cause the clogging of pipes & readily colonize surfaces in industrial settings. They have played roles in recent, large-scale outbreaks of bacterial contamination of food. Biofilms also colonize household surfaces, such as kitchen counters, cutting boards, sinks, & toilets. Interactions among the organisms that populate a biofilm and their protective environment make these communities more robust than free-living, or planktonic, prokaryotes. Biofilms are difficult to destroy because they are resistant to many common sterilization forms. Characteristics of Prokaryotes All cells have 4 common structures: a plasma membrane that functions as a barrier for the cell & separate the cell from its environment; cytoplasm, a jelly-like substance inside the cell; genetic material (DNA & RNA); & ribosomes, where protein synthesis takes place. Prokaryotes come in various shapes, but many fall into 3 categories: cocci (spherical), bacilli (rod-shaped), & spirilla (spiral-shaped). The Prokaryotic Cell 3638550457909200Prokaryotes are unicellular organisms that lack organelles surrounded by membranes. They do not have a nucleus but instead have a single chromosome – a piece of circular DNA located in an area of the cell called the nucleoid. Most prokaryotes have a cell wall lying outside the plasma membrane. The cell wall functions as a protective layer & are responsible for the organism’s shape. The capsule found in some species enables the organisms to attach to surfaces & protects them from dehydration. Some species may also have flagella (singular, flagellum) used for locomotion, & pili (singular, pilus) used for attachment to surfaces & other bacteria for conjugation. Plasmids, which consist of small, circular pieces of DNA outside of the main chromosome, are also present in many species of bacteria. Both Bacteria & Archaea are types of prokaryotic cells. They differ in the lipid composition of their cell membranes & in the characteristics of their cell walls. Both types of prokaryotes have the same basic structures, but these are built from different chemical components that are evidence of an ancient separation of their lineages. The archaeal plasma membrane is chemically different from the bacterial membrane; some archaeal membranes are lipid monolayers instead of phospholipid bilayers. The Cell Wall The cell wall is a protective layer that surrounds some prokaryotic cells & gives them shape & rigidity. It is located outside the cell membrane & prevents osmotic lysis. Bacterial cell walls contain peptidoglycan, composed of polysaccharide chains cross-linked to peptides. Bacteria are divided into 2 major groups: Gram-positive & Gram-negative, based on their reactions to a procedure called Gram staining. 2996854270623800The different responses to the staining procedure are caused by cell wall structure. Gram-positive organisms have a thick wall consisting of many layers of peptidoglycan. Gram-negative bacteria have a thinner cell wall composed of a few layers of peptidoglycan & additional structures, surrounded by an outer membrane. Archaeal cell walls do not contain peptidoglycan. There are 4 different types of archaeal cell walls. One type is composed of pseudopeptidoglycan. The other 3 cell walls contain polysaccharides, glycoproteins, & surface-layer proteins known as S-layers. Reproduction Prokaryotes do not undergo mitosis. The chromosome loop is replicated, & the 2 resulting copies attached to the plasma membrane move apart as the cell grows in a process called binary fission. The prokaryote, now enlarged, is pinched inward at its equator, & the 2 resulting cells, which are clones, separate. Binary fission does not provide an opportunity for genetic recombination, but prokaryotes can alter their genetic makeup in 3 ways. In a process called transformation, the cell takes in DNA found in its environment that is shed by other prokaryotes, alive or dead. A pathogen is an organism that causes a disease. If a nonpathogenic bacterium takes up DNA from a pathogen & incorporates the new DNA in its chromosome, it too may become pathogenic. In transduction, bacteriophages, the viruses that infect bacteria, move DNA from one bacterium to another. Archaea have a different set of viruses that infect them & translocate genetic material from one individual to another. During conjugation, DNA is transferred from one prokaryote to another using pilus which brings the organisms into contact with one another. The DNA transferred is usually a plasmid, but parts of the chromosome can also be moved. Cycles of binary fission can be very rapid, on the order of minutes from some species. This short generation time coupled with mechanisms of genetic recombination results in the rapid evolution of prokaryotes, allowing them to respond to environmental changes (such as the introduction of an antibiotic) very quickly. How Prokaryotes Obtain Energy & Carbon Prokaryotes fill many niches on Earth, including being involved in nutrient cycles such as the nitrogen & carbon cycles, decomposing dead organisms, & growing & multiplying inside living organisms, including humans. Different prokaryotes can use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight. Chemotrophs obtain their energy from chemical compounds. Bacterial Diseases in Humans Devasting pathogen-borne diseases & plagues, both viral & bacterial in nature, have affected & continue to affect humans. All pathogenic prokaryotes are Bacteria There are no known pathogenic Archaea in humans or any other organism. Pathogenic organisms evolved alongside humans. Historical Perspective There are records of infectious diseases as far back as 3,000 B.C. Several significant pandemics caused by Bacteria have been documented over several hundred years. Some of the largest pandemics led to the decline of cities & cultures. Many were zoonoses that appeared with the domestication of animals. Zoonosis is a disease that infects animals but can be transmitted from animals to humans. Infectious diseases remain among the leading causes of death worldwide. The development of antibiotics did much to lessen the mortality rates from bacterial infections, but access to antibiotics is not universal, & the overuse of antibiotics had led to the development of resistant strains of bacteria. In 430 B.C. the plague of Athens killed ¼ of the Athenian troops that were fighting in the Great Peloponnesian War. The source of the plague may have been identified recently when researchers from the University of Athens were able to analyze DNA from teeth recovered from a mass grave. The scientists identified nucleotide sequences from a pathogenic bacterium that causes typhoid fever. From 541 to 750 A.D., an outbreak called the plague of Justinian (likely bubonic plague) eliminated, by some estimates, ¼ to ½ of the human population. One of the most devastating pandemics was the Black Death (1346-1361), which is believed to have been another outbreak of bubonic plague by the bacterium Yersinia pestis. This bacterium is carried by fleas living on black rats. Bubonic plague struck London hard again in the mid-1600s Although contracting bubonic plague before antibiotics meant almost certain death, the bacterium responds to several types of modern antibiotics, & mortality rates from plague are now very low. Over the centuries, Europeans developed resistance to many infectious diseases. European conquerors brought disease-causing bacteria & viruses with them when they reached the Western hemisphere, triggering epidemics that completely devastated populations of Native Americans. The Antibiotic Crisis The word antibiotic comes from the Greek anti, meaning “against,” & bios, meaning “life.” An antibiotic is an organism-produced chemical that is hostile to the growth of other organisms. One of the main reasons for resistant bacteria is the overuse & incorrect use of antibiotics, such as not completing a full course of prescribed antibiotics. The incorrect use of antibiotics results in the natural selection of resistant forms of bacteria. The antibiotic kills most of the infecting bacteria, & therefore only the resistant forms remain. These resistant forms reproduce, increasing the proportion of resistant forms over non-resistant ones. Another problem is the excessive use of antibiotics in livestock. The routine use of antibiotics in animal feed promotes bacterial resistance as well. In the US, 70% of the antibiotics produced are fed to animals. These antibiotics are not used to prevent disease, but to enhance the production of their products. Staphylococcus aureus, often called “staph,” is a common bacterium that can live in & on the human body, which usually is easily treatable with antibiotics. A very dangerous strain has made the news over the past few years. This strain, methicillin-resistant Staphylococcus aureus (MRSA), is resistant to many commonly used antibiotics, including methicillin, amoxicillin, penicillin, & oxacillin. While MRSA infections have been common among people in healthcare facilities, it is appearing more commonly in healthy people who live or work in dense groups. The Journal of the American Medical Association reported that, among MRSA-afflicted persons in healthcare facilities, the average age is 68 years, while people with “community-associated MRSA” (CA-MRSA) have an average age of 23 years. Society is facing an antibiotic crisis. Some scientists believe that after years of being protected from bacterial infections by antibiotics, we may be returning to a time in which a simple bacterial infection could again devastate the human population. Foodborne Diseases Prokaryotes are everywhere: They readily colonize the surface of any type of material, & food is not an exception. Outbreaks of bacterial infection related to food consumption are common. Foodborne disease is an illness resulting from the consumption of food contaminated with pathogenic bacteria, viruses, or other parasites. The Center for Disease Control & Prevention (CDC) has reported that “76 million people get sick, more than 300,000 are hospitalized, & 5,000 Americans die each year from foodborne illness.” The characteristics of foodborne illnesses have changed over time. In the past, it was relatively common to hear about sporadic cases of botulism, the potentially fatal disease produced by a toxin from the anaerobic bacterium Clostridium botulinum. Proper sterilization & canning procedures have reduced the incidence of this disease. Most cases of foodborne illnesses are now linked to produce contaminated by animal waste. All types of food can potentially be contaminated with harmful bacteria of different species. Recent outbreaks of Salmonella reported by the CDC occurred in foods as diverse as peanut butter, alfalfa sprouts, & eggs. Beneficial Prokaryotes Not all prokaryotes are pathogenic. Pathogens represent only a very small percentage of the diversity of the microbial world. Life on this planet would not be possible without prokaryotes. Prokaryotes, & Food & Beverages According to the United Nations Convention on Biological Diversity, biotechnology is “any technological applications that use biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use.” The concept of “specific use” involves some sort of commercial application. Genetic engineering, artificial selection, antibiotic production, & cell culture are current topics of study in biotechnology. Humans used prokaryotes to create products before the term biotechnology was even coined. Some of the goods & services are as simple as cheese, yogurt, sour cream, vinegar, sauerkraut, & fermented seafood that contains both bacteria & archaea. Cheese production began around 4,000 years ago when humans started to breed animals & process their milk. Evidence suggests that cultured milk products, like yogurt, have existed for at least 4,000 years. Using Prokaryotes to Clean up Our Planet: Bioremediation Microbial bioremediation is the use of prokaryotes to remove pollutants. Bioremediation has been used to remove agricultural chemicals that leach soil into groundwater. Certain toxic metals, such as selenium & arsenic compounds, can also be removed from water by bioremediation. The reduction of SeO2-4 to SeO2-3 & Se0 is a method used to remove selenium ions from water. Mercury is an example of a toxic metal that can be removed from an environment by bioremediation. Several species of bacteria can carry out the biotransformation of toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas aeruginosa, can convert Hg2+ to Hg0, which is non-toxic to humans. Probably one of the most useful & interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills. To clean up these spills, bioremediation is promoted by adding inorganic nutrients that help bacteria already present in the environment to grow. Hydrocarbon-degrading bacteria feed on the hydrocarbons in the oil droplet, breaking them into inorganic compounds. Some species, such as Alcanivorax borkumensis, produce surfactants that solubilize the oil, while other bacteria degrade the oil into carbon dioxide. Researchers have genetically engineered other bacteria to consume petroleum products; indeed, the 1st patent application for a bioremediation application in the U.S. was for a genetically modified oil-eating bacterium. Prokaryotes in & on the Body There are 10 – 100x as many bacterial & archaeal cells inhabiting our bodies as we have cells in our bodies. Some of these are in mutually beneficial relationships with us, in which both the human host & the bacterium benefit, while some of the relationships are classified as commensalism, a type of relationship in which the bacterium benefits & the human host is neither benefitted nor harmed. Human gut flora lives in the large intestine & consists of hundreds of species of bacteria & archaea, with different individuals containing different species mixes. The primary functions of these prokaryotes for humans appear to be the metabolism of food molecules that we cannot break down, assistance with the absorption of ions by the colon, synthesis of vitamin K, training of the infant immune system, maintenance of the adult immune system, maintenance of the epithelium of the large intestine, & formation of a protective barrier against pathogens. The different surfaces of the skin, such as the underarms, the head, & the hands, provide different habitats for different communities of prokaryotes. The few studies conducted so far have identified bacteria that produce antimicrobial compounds as probably responsible for preventing infections by pathogenic bacteria. Researchers are actively studying the relationships between various diseases & alterations to the composition of human microbial flora. Some of this work is being carried out by the Human Microbiome Project, funded in the United States by the National Institutes of Health. 13.2 Eukaryotic Origins The fossil record & genetic evidence suggest that prokaryotic cells were the 1st organisms on Earth. These cells originated approximately 3.5 billion years ago, which was about 1 billion years after Earth’s formation, & were the only life forms on the planet until eukaryotic cells emerged approximately 2.1 billion years ago. During the prokaryotic reign, photosynthetic prokaryotes evolved that were capable of applying the energy from sunlight o synthesize organic materials from carbon dioxide & an electron source. Photosynthesis using water as an electron donor consumes carbon dioxide & releases molecular oxygen (O2) as a byproduct. The functioning of photosynthetic bacteria over millions of years progressively saturated Earth’s water with oxygen & then oxygenated the atmosphere, which previously contained a much greater concentration of carbon dioxide & much lower concentrations of oxygen. Other early prokaryotes evolved mechanisms, such as aerobic respiration, to exploit the oxygenated atmosphere by using oxygen to store energy contained within organic molecules. Aerobic respiration is a more efficient way of obtaining energy from organic molecules, contributing to these species' success. The evolution of aerobic prokaryotes was an important step toward the evolution of the 1st eukaryote, but several other distinguishing features had to evolve as well. Endosymbiosis The origin of eukaryotic cells was largely a mystery until a revolutionary hypothesis was comprehensively examined in the 1960s by Lynn Margulis. The endosymbiotic theory states that eukaryotes are a product of one prokaryotic cell engulfing another, one living within another, & evolving together over time until the separate cells were no longer recognizable as such. It has become clear that many nuclear eukaryotic genes & the molecular machinery responsible for replicating & expressing those genes appear closely related to the Archaea. The metabolic organelles & the genes responsible for many energy-harvesting processes had their origins in bacteria. Several endosymbiotic events likely contributed to the origin of the eukaryotic cell Mitochondria Eukaryotic cells may contain anywhere from 1 to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1- 10 micrometers in length & exists in the cell as a moving, fusing, & dividing oblong spheroid. As the atmosphere was oxygenated by photosynthesis, & as successful aerobic prokaryotes evolved, evidence suggests that an ancestral cell engulfed & kept alive a free-living, aerobic prokaryote. This gave the host cell the ability to use oxygen to release energy stored in nutrients. Several lines of evidence support that mitochondria are derived from this endosymbiotic event. Mitochondria are shaped like a specific group of bacteria & are surrounded by 2 membranes, which would result when one membrane-bound organism was engulfed by another membrane-bound organism. The mitochondrial inner membrane involves substantial infoldings or cristae resembling certain bacteria's textured outer surface. Mitochondria divide on their own by a process that resembles binary fission in prokaryotes. Mitochondria have their own circular DNA chromosomes that carry genes like those expressed by bacteria. Mitochondria also have special ribosomes & transfer RNAs that resemble these components in prokaryotes. These features all support that mitochondria were once free-living prokaryotes. Chloroplasts Chloroplasts are one type of plastid, a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, & pigments. Chloroplasts contain the green pigment chlorophyll & play a role in photosynthesis. Genetic & morphological studies suggest that plastids evolved from endosymbiosis of an ancestral cell that engulfed a photosynthetic cyanobacterium. Plastids are similar in size & shape to cyanobacteria & are enveloped by 2 or more membranes, corresponding to the inner & outer membranes of cyanobacteria. Plastids also contain circular genomes & divide by a process reminiscent of prokaryotic cell division. Mitochondria likely evolved before plastids because all eukaryotes have either functional mitochondria or mitochondria-like organelles Plastids are only found in a subset of eukaryotes, such as terrestrial plants & algae. The exact steps leading to the 1st eukaryotic cell can only be hypothesized, & some controversy exists regarding which events took place & in what order. Other scientists suggest that membrane proliferation & compartmentalization, not endosymbiotic events, lead to the development of mitochondria & plastids. Most studies support the endosymbiotic hypothesis of eukaryotic evolution. The early eukaryotes were unicellular like most protists are today, but as eukaryotes became more complex, the evolution of multicellularity allowed cells to remain small while still exhibiting specialized functions. 225425202755500The ancestors of today’s multicellular eukaryotes are thought to have evolved about 1.5 billion years ago. 13.3 Protists Eukaryotic organisms that did not fit the criteria for the kingdoms Animalia, Fungi, or Plantae historically were called protists & were classified into the kingdom Protista. Protists include the single-celled eukaryotes living in pond water, although protist species live in a variety of other aquatic & terrestrial environments & occupy many different niches. Not all protists are microscopic & single-celled; there exist some very large multicellular species, such as the kelps. During the past 2 decades, the field of molecular genetics has demonstrated that some protists are more related to animals, plants, & fungi than they are to other protists. Protist lineages originally classified into the kingdom Protista have been reassigned into new kingdoms or other existing kingdoms. The term “protist” is still used informally to describe this tremendously diverse group of eukaryotes. As a collective group, protists display an astounding diversity of morphologies, physiologies, & ecologies. Characteristics of Protists There are over 100,000 described living species of protists, & it is unclear how many undescribed species may exist. Since many protists live in symbiotic relationships with other organisms & these relationships are often species-specific there is a huge potential for undescribed protist diversity that matches the diversity of the hosts. Nearly all protists exist in some type of aquatic environment, including freshwater & marine environments, damp soil, & even snow. Several protist species are parasites that infect animals or plants. A parasite is an organism that lives on or in another organism & feeds on it, often without killing it. A few protist species live on dead organisms or their wastes & contribute to their decay. Protist Structure The cells of protists are among the most elaborate of all cells. Most protists are microscopic & unicellular, but some true multicellular forms exist. A few protists live in colonies that behave in some ways as a group of free-living cells & in other ways as multicellular organisms. Protists are composed of enormous, multinucleate, single cells that look like amorphous blobs of slime or, in other cases, like ferns. Many protist cells are multinucleated; in some species, the nuclei are different sizes & have distinct roles in protist cell function. Single protist cells range from less than a micrometer to the 3-meter lengths of the multinucleate cells of the seaweed Caulerpa. Protist cells may be enveloped by animal-like cell membranes or plant-like cell walls. Others are encased in glassy silica-based shells or wound with pellicles of interlocking protein strips. The pellicle functions like a flexible coat of armor, preventing the protist from being torn or pierced without compromising its range of motion. Most protists are motile, but different types of protists have evolved varied modes of movement. Some protists have one or more flagella, which they rotate or whip. Others are covered in rows or tufts of tiny cilia that they beat in coordination to swim. Others send out lobe-like pseudopodia from anywhere on the cell, anchor the pseudopodium to a substrate, & pull the rest of the cell toward the anchor point. Some protists can move toward the light by coupling their locomotion strategy with a light-sensing organ. How Protists Obtain Energy Protists exhibit many forms of nutrition & may be aerobic or anaerobic. Photosynthetic protists (photoautotrophs) are characterized by the presence of chloroplasts. Other protists are heterotrophs & consume organic materials (such as other organisms) to obtain nutrition. Amoebas & some other heterotrophic protist species ingest particles by a process called phagocytosis, in which the cell membrane engulfs a food particle & brings it inward, pinching off an intracellular membranous sac, or vesicle, called a food vacuole. 3313430-7302500This vesicle then fuses with a lysosome, & the food particle is broken down into small molecules that can diffuse into the cytoplasm & be used in cellular metabolism. Undigested remains ultimately are expelled from the cell through exocytosis. Some heterotrophs absorb nutrients from dead organisms, or their organic wastes, & others can use photosynthesis or feed on organic matter, depending on conditions. Reproduction Protists reproduce by a variety of mechanisms. Most are capable of some form of asexual reproduction, such as binary fission to produce 2 daughter cells, or multiple fission to divide simultaneously into many daughter cells. Others produce tiny buds that go on to divide & grow to the size of the parental protist. Sexual reproduction, involving meiosis & fertilization, is common among protists, & many protist species can switch from asexual to sexual reproduction when necessary. Sexual reproduction may allow the protist to recombine genes & produce new variations of progeny that may be better suited to surviving in the new environment. Sexual reproduction is often associated with cysts that are at a protective, resting stage. The cysts may be particularly resistant to temperature extremes, desiccation, or low pH. This strategy allows certain protists to “wait out” stressors until their environment becomes more favorable for survival or until they are carried to a different environment because cysts exhibit virtually o cellular metabolism. Protist Diversity Protists that exhibit similar morphological features may have evolved analogous structures because of similar selective pressures – rather than because of recent common ancestry. This phenomenon is called convergent evolution. The emerging classification scheme groups the entire domain of Eukaryota into 6 “supergroups” that contain all the protists as well as animals, plants, & fungi. These include the Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, & Opisthokonta. The supergroups are believed to be monophyletic All organisms within each supergroup are believed to have evolved from a single common ancestor, & thus all members are most closely related to each other than to organisms outside that group. Human Pathogens Many protists are pathogenic parasites that must infect other organisms to survive & propagate. Protists parasites include the causative agents of malaria, African sleeping sickness, & waterborne gastroenteritis in humans. Other protist pathogens prey on plants, affecting the massive destruction of food crops. Plasmodium Species Members of the genus Plasmodium must infect a mosquito & a vertebrate to complete their life cycle. In vertebrates, the parasite develops in liver cells & goes on to infect red blood cells, bursting from & destroying the blood cells with each asexual replication cycle. Of the 4 Plasmodium species known to infect humans, P. falciparum accounts for 50% of all malaria cases & is the primary cause of disease-related fatalities in tropical regions of the world. During the course of malaria, P. falciparum can infect & destroy more than ½ of a human’s circulating blood cells, leading to severe anemia. In response to waste products released as the parasites burst from infected blood cells, the host immune system mounts a massive inflammatory response with delirium-inducing fever episodes, as parasites destroy red blood cells, spilling parasite waste into the bloodstream. P. falciparum is transmitted to humans by the African malaria mosquito, Anopheles gambiae. Techniques to kill, sterilize, or avoid exposure to this highly aggressive mosquito species are crucial to malaria control. Trypanosomes T. brucei, the parasite that is responsible for African sleeping sickness, confounds the human immune system by changing its thick layer of surface glycoproteins with each infectious cycle. The glycoproteins are identified by the immune system as foreign matter, & a specific antibody defense is mounted against the parasite. T. brucei has thousands of possible antigens, & with each subsequent generation, the protist switches to a glycoprotein coating with a different molecular structure. T. brucei can replicate continuously without the immune system ever succeeding in clearing the parasite. Without treatment, African sleeping sickness leads invariably to death because of the damage it does to the nervous system. In Latin America, another species in the genus, T. cruzi, is responsible for Chagas disease. T. cruzi infections are mainly caused by a blood-sucking bug. The parasite inhabits heart & digestive system tissues in the chronic phase of infection, leading to malnutrition & heart failure caused by abnormal heart rhythms Plant Parasites Protist parasites of terrestrial plants include agents that destroy food crops. The oomycete Plasmopara viticola parasitizes grape plants, causing a disease called downy mildew. Grape plants infected with P. viticola appear stunted & have discolored withered leaves. Phytophthora infestans is an oomycete responsible for potato late blight, which causes potato stalks & stems to decay into black slime. Widespread potato blight caused by P. infestans precipitated the well-known Irish potato famine in the 19th century that claimed the lives of approximately 1 million people & led to the emigration from Ireland of at least 1 million more. Beneficial Protists Protists play critically important ecological roles as producers, particularly in the world’s oceans. They are equally important on the other end of food webs as decomposers. Protists as Food Sources Protists are essential sources of nutrition for many other organisms. In some cases, as in plankton, protists are consumed directly. Photosynthetic protists serve as producers of nutrition for other organisms by carbon fixation. Photosynthetic dinoflagellates called zooxanthellae pass on most of their energy to the oral polyps that house them. The polyps provide a protective environment & nutrients for the zooxanthellae. The polyps secrete the calcium carbonate that builds coral reefs. Without dinoflagellate symbionts, corals lose algal pigments in a process called coral bleaching, & they eventually die. Protists themselves & their products of photosynthesis are essential – directly or indirectly – to the survival of organisms ranging from bacteria to mammals. As primary producers, protists feed a large proportion of the world’s aquatic species. Approximately ¼ of the world’s photosynthesis is conducted by protists, particularly dinoflagellates, diatoms, & multicellular algae. Protists do not create food sources only for sea-dwelling organisms. Certain anaerobic species exist in the digestive tracts of termite & wood-eating cockroaches, where they contribute to digesting cellulose ingested by these insects as they bore through wood. The actual enzyme used to digest the cellulose is produced by bacteria living within the protist cells. Agents of Decomposition Many fungus-like protists are saprobes, organisms that feed on dead organisms or the waste matter produced by organisms (saprophyte is an equivalent term) & are specialized to absorb nutrients from nonliving organic matter. Many types of oomycetes grow on dead animals or algae. Saprobic protists have the essential function of returning inorganic nutrients to the soil & water. This process allows for new plant growth, which in turn generates sustenance for other organisms along the food chain. Without saprobic species, such as protists, fungi, & bacteria, life would cease to exist as all organic carbon became “tied up” in dead organisms. 13.4 Fungi The word fungus comes from the Latin word for mushroom The kingdom of Fungi includes an enormous variety of living organisms collectively referred to as Eumycota, or true fungi. Edible mushrooms, yeasts, black mold, & Penicillium notatum are all members of the kingdom Fungi, which belongs to the domain Eukarya As eukaryotes, a typical fungal cell contains a true nucleus & many membrane-bound organelles Fungi were once considered plant-like organisms; however, DNA comparisons have shown that fungi are more closely related to animals than plants. Fungi are not capable of photosynthesis. They use complex organic compounds as sources of energy & carbon. Some fungal organisms multiply only asexually, whereas others undergo both asexual reproduction & sexual reproduction Most fungi produce many spores that are disseminated by the wind. Fungi play an essential role in ecosystems because they are decomposers & participate in the cycling of nutrients by breaking down organic materials into simple molecules. Fungi often interact with other organisms, forming mutually beneficial or mutualistic associations. Fungi also cause serious infections in plants & animals. In humans, fungal infections are generally considered challenging to treat because, unlike bacteria, they do not respond to traditional antibiotic therapy since they are also eukaryotes. These infections may prove deadly for individuals with a compromised immune system. Fungi have many commercial applications. The food industry uses yeasts in baking, brewing, & winemaking. Many industrial compounds are byproducts of fungal fermentation Fungi are the source of many commercial enzymes & antibiotics Cell Structure & Function Fungi are eukaryotes & as such have a complex cellular organization. Fungal cells contain a membrane-bound nucleus. A few types of fungi have structures comparable to the plasmid (loops of DNA) seen in bacteria. Fungal cells also contain mitochondria & a complex system of internal membranes, including the endoplasmic reticulum & Golgi apparatus. Fungal cells do not have chloroplasts. Although the photosynthetic pigment chlorophyll is absent, many fungi display bright colors, ranging from red to green to black. The poisonous Amanita muscaria (fly agaric) is recognizable by its bright red cap with white patches. Pigments in fungi are associated with the cell wall & play a protective role against ultraviolet radiation. Some pigments are toxic. Fungal cells are surrounded by a thick cell wall The rigid layers contain the complex polysaccharides chitin & glucan & not cellulose which is used by plants. Chitin, also found in the exoskeleton of insects, gives structural strength to the cell walls of fungi. The cell wall protects the cell from desiccation & predators. Fungi have plasma membranes like other eukaryotes, except the structure is stabilized by ergosterol, a steroid molecule that functions like the cholesterol found in animal cell membranes. Most members of the kingdom Fungi are nonmotile. Flagella are produced only by the gametes in the primitive division of Chytridiomycota. Growth & Reproduction The vegetative body of a fungus is called a thallus and can be unicellular or multicellular. Some fungi are dimorphic because they can go from being unicellular to multicellular depending on environmental conditions. Unicellular fungi are generally referred to as yeasts. Saccharomyces cerevisiae (baker’s yeast) & Candida species (the agents of thrush) are examples of unicellular fungi. Most fungi are multicellular organisms. They display 2 distinct morphological stages: vegetative & reproductive. The vegetative stage is characterized by a tangle of slender thread-like structures called hyphae (singular, hypha), whereas the reproductive stage can be more conspicuous. A mass of hyphae is called mycelium. It can grow on a surface, in soil or decaying material, in liquid, or even in or living tissue. Although individual hypha must be observed under a microscope, the mycelium of a fungus can be very large with some speices truly being “the fungus humongous.” The giant Armillaria ostoyae (honey mushroom) is considered the largest organism on Earth, spreading across over 2,000 acres of underground soil in eastern Oregon. It is estimated to be at least 2,400 years old. Most fungal hyphae are divided into separate cells by end walls called septa (singular, septum). In most divisions of fungi, tiny holes in the septa allow for the rapid flow of nutrients & small molecules from cell to cell along the hyphae. They are described as perforated septa. The hyphae in bread molds (which belong to the division Zygomycota) are not separated by septa. They are formed of large cells containing many nuclei, an arrangement described as coenocytic hyphae. Fungi thrive in environments that are moist & slightly acidic & can grow with or without light. They vary in their oxygen requirements. Most fungi are obligate aerobes, requiring oxygen to survive. Other species, such as the Chytridiomycota that reside in the rumen of cattle, are obligate anaerobes, meaning that they cannot grow & reproduce in an environment with oxygen. Yeasts are intermediate. They grow best in the presence of oxygen but can use fermentation in the absence of oxygen. The alcohol produced from yeast fermentations is used in wine & beer production, & the carbon dioxide they produce carbonates beer & sparkling wine & makes bread rise. Fungi can reproduce sexually or asexually In both sexual & asexual reproduction, fungi produce spores that disperse from the parent organism by wither floating in the win of hitching a ride on an animal. Fungal spores are smaller & lighter than plant seeds, but they are not usually released as high in the air. The giant puffball mushroom bursts open & releases trillions of spores The huge number of spores released increases the likelihood of spores landing in an environment that will support growth. How Fungi Obtain Nutrition Fungi are heterotrophs They use complex organic compounds as a source of carbon rather than fixing carbon dioxide from the atmosphere Fungi do not fix nitrogen from the atmosphere They must obtain it from their diet Unlike animals that ingest food & then digest it internally in specialized organs, fungi perform these steps in the reverse order. Digestion precedes ingestion First, exoenzymes, enzymes that catalyze reactions on compounds outside of the cell, are transported out of the hyphae where they break down nutrients in the environment. Then, the smaller molecules produced by the external digestion are absorbed through the large surface areas of the mycelium. The fungal storage polysaccharide is glycogen rather than starch, as found in plants. Fungi are mostly saprobes, organisms that derive nutrients from decaying organic matter. They obtain their nutrients from dead or decomposing organic material, mainly plant material. Fungal exoenzymes can break down insoluble polysaccharides, such as the cellulose & lignin of dead wood, into readily absorbable glucose molecules. Because of their varied metabolic pathways, fungi fulfill an important ecological role & are being investigated as potential tools in bioremediation. Some species of fungi can be used to break down diesel oil & polycyclic aromatic hydrocarbons. Other species take up heavy metals such as cadmium & lead. Fungal Diversity The kingdom Fungi contains 4 major divisions that were established according to their mode of sexual reproduction. Polyphyletic, unrelated fungi that reproduce without a sexual cycle, are placed for convenience in a 5th division, & a 6th major fungal group that does not fit well with any of the previous 5 has recently been described. Rapid advances in molecular biology and the sequencing of 18S rRNA continue to reveal new & different relationships between the various categories of fungi The traditional divisions of Fungi are the Chytridiomycota (chytrids), the Zygomycota (conjugated fungi), the Ascomycota (sac fungi), & the Basidiomycota (club fungi). An older classification scheme grouped fungi that strictly use asexual reproduction into Deuteromycota, a group that is no longer in use. The Glomeromycota belongs to a newly described group. Pathogenic Fungi Many fungi have negative impacts on other species, including humans & the organisms they depend on for food. Fungi may be parasites, pathogens, &, in very few cases, predators. Plant Parasites & Pathogens Most plant pathogens are fungi that cause tissue decay & eventual death of the host. In addition to destroying plant tissue directly, some plant pathogens spoil crops by producing potent toxins Fungi are also responsible for food spoilage & the rotting of stored crops The fungus Claviceps purpurea causes ergot, a disease of cereal crops (especially of rye). Although the fungus reduces the yield of cereals, the effects of the ergot’s alkaloid toxins on humans & animals are of much greater significance In animals, the disease is referred to as ergotism The most common signs & symptoms are convulsions, hallucination, gangrene, & loss of milk in cattle. The active ingredient of ergot is lysergic acid, which is a precursor of the drug LSD Smuts, rusts, & powdery or downy mildew are other examples of common fungal pathogens that affect crops. Aflatoxins are toxic & carcinogenic compounds released by fungi of the genus Aspergillus. Periodically, harvests of nuts & grains are tainted by aflatoxins, leading to the massive recall of products, sometimes ruining producers, & causing food shortages in developing countries. Animal & Human Parasites & Pathogens Fungi attack animals directly by colonizing & destroying tissues. Humans & other animals can be poisoned by eating toxic mushrooms or foods contaminated by fungi. Individuals who display hypersensitivity to molds & spores develop strong & dangerous allergic reactions. Fungal infections are generally very difficult to treat because, unlike bacteria, fungi are eukaryotes. Antibiotics only target prokaryotic cells, whereas compounds that kill fungi also adversely affect the eukaryotic animal host. Many fungal infections (mycoses) are superficial & termed cutaneous mycoses. They are usually visible on the skin of the animal. Fungi that cause the superficial mycoses of the epidermis, hair, & nails rarely spread to the underlying tissue. These fungi are often misnamed “dermatophytes” from the Greek dermis skin & phyte plant, but they are not plants. Dermatophytes are also called “ringworms” because of the red ring that they cause on the skin. These fungi secrete extracellular enzymes that break down keratin causing several conditions such as athletes’ foot, jock itch, & other cutaneous fungal infections. These conditions are usually treated with over-the-counter topical creams & powders & are easily cleared. More persistent, superficial mycoses may require prescription oral medications. Systemic mycoses spread to internal organs, most commonly entering the body through the respiratory system. Coccidioidomycosis (valley fever) is commonly found in the southwestern U.S., where the fungus resides in the dust. Once inhaled, the spores develop in the lungs & cause signs & symptoms like those of tuberculosis. Histoplasmosis is caused by the dimorphic fungus Histoplasma capsulatum It causes pulmonary infections &, in rare cases, swelling of the membranes of the brain & spinal cord. Treatment of many fungal diseases requires the use of antifungal medications that have serious side effects. Opportunistic mycoses are fungal infections that are either common in all environments or part of the normal biota. They affect mainly individuals who have a compromised immune system. Patients in the late stages of AIDS suffer from opportunistic mycoses, such as Pneumocystis, which can be life-threatening. The yeast Candida spp., which is a common member of the natural biota, can grow unchecked if the pH, the immune defenses, or the normal population of bacteria is altered, causing yeast infections of the vagina or mouth. Fungi may even take on a predatory lifestyle. In soil environments that are poor in nitrogen, some fungi resort to predation of nematodes. Species of Arthrobotrys fungi have several mechanisms to trap nematodes. These have constricting rings within their network of hyphae. The rings swell when the nematode touches it & closes around the body of the nematode, thus trapping it. The fungus extends specialized hyphae that can penetrate the body of the worm & slowly digest the hapless prey. Beneficial Fungi Fungi play a crucial role in the balance of ecosystems. They colonize most habitats on Earth, preferring dark, moist conditions. They can thrive in seemingly hostile environments, such as the tundra, thanks to a successful symbiosis with photosynthetic organisms They are major decomposers of nature. With their versatile metabolism, fungi break down organic matter that is insoluble & would not be recycled otherwise. Importance to Ecosystems Food webs would be incomplete without organisms that decompose organic matter & fungi are key participants in this process. Decomposition allows for the cycling of nutrients such as carbon, nitrogen, & phosphorus back into the environment so they are available to living things, rather than being trapped in dead organisms. Fungi are particularly important because they have evolved enzymes to break down cellulose & lignin, components of plant cell walls that few other organisms are able to digest, releasing their carbon content. Fungi are also involved in ecologically important coevolved symbioses, both mutually beneficial & pathogenic with organisms from the other kingdoms. Mycorrhiza, a term combining the Greek roots myco meaning fungus & rhizo meaning root refers to the association between vascular plant roots & their symbiotic fungi. Somewhere between 80-90% of all plant species have mycorrhizal partners. The fungal mycelia use their extensive network of hyphae & large surface area in contact with the coil to channel water & minerals from the soil into the plant The plant supplies the products of photosynthesis to fuel the metabolism of the fungus. Ectomycorrhizae depend on fungi enveloping the roots in a sheath (called a mantle) & a net of hyphae that extends into the roots between the cells. In a 2nd type, the Glomeromycota fungi form arbuscular mycorrhiza. In this mycorrhiza, the fungi form arbuscle, a specialized highly branched hypha, which penetrates root cells & is the site of the metabolic exchanges between the fungus & the host plant. Orchids rely on the 3rd type of mycorrhiza. Orchids form small seeds without much storage to sustain germination & growth. Their seeds will not germinate without a mycorrhizal partner (usually Basidiomycota) After nutrients in the seed are depleted, fungal symbionts support the growth of the orchid by providing necessary carbohydrates & minerals Some orchids continue to be mycorrhizal throughout their lifecycle. Lichens blanket many rocks & tree barks, displaying a range of colors & textures. Lichens are important pioneer organisms that colonize rock surfaces in otherwise lifeless environments such as are created by the glacial recession. The lichen can leach nutrients from the rocks & break them down in the 1st step to creating soil. Lichens are also present in mature habitats on rock surfaces or the trunks of trees. They are an important food source for caribou. Lichens are not a single organism, but rather a fungus (usually an Ascomycota or Basidiomycota species) living in close contact with a photosynthetic organism The body of a lichen, referred to as a thallus, is formed of hyphae wrapped around the green partner. The photosynthetic organism provides carbon & energy in the form of carbohydrates & receives protection from the elements by the thallus of the fungal partner Some cyanobacteria fix nitrogen from the atmosphere, contributing nitrogenous compounds to the association The fungus supplies minerals & protection from dryness & excessive light by encasing the algae in its mycelium The fungus also attaches the symbiotic organism to the substrate. Fungi have evolved mutualistic associations with numerous arthropods The association between species of Basidiomycota & scale insects is one example The fungal mycelium covers & protects the insect colonies The scale insects foster a flow of nutrients from the parasitized plant to the fungus Leaf-cutting ants of Central & South America literally farm fungi. They cut disks of leaves from plants & pile them up in gardens Fungi are cultivated in these gardens, digesting the cellulose that the ants cannot break down Once smaller sugar molecules are produced & consumed by the fungi, they in turn become a meal for the ants. The ants also patrol their garden, preying on competing fungi Both ants & fungi benefit from the association The fungus receives a steady supply of leaves & freedom from competition, while the ants feed on the fungi they cultivate. Importance to Humans Fungi are important to human life on many levels They influence the well-being of human populations on a large scale because they help nutrients cycle in ecosystems As animal pathogens, fungi help to control the populations of damaging pests These fungi are very specific to the insects they attack & do not infect other animals or plants. The fungus Beauveria bassiana is a pesticide that is currently being tested as a possible biological control for the recent spread of emerald ash borer. The mycorrhizal relationship between fungi & plant roots is essential for the productivity of farmland. Without the fungal partner in the root systems, 80-90% of trees & grasses would not survive Mycorrhizal fungal inoculants are available as soil amendments from gardening supply stores & promoted by supporters of organic agriculture. We also eat some types of fungi Mushrooms figure prominently in the human diet. Morels, shitake mushrooms, chanterelles, & truffles are considered delicacies The humble meadow mushroom, Agaricus campestris, appears in many dishes. Molds of the genus Penicillium ripen many kinds of cheese They originate in the natural environment such as the caves of Roquefort, France, where wheels of sheep milk cheese are stacked to capture the molds responsible for the blue veins & pungent taste of the cheese. Fermentation – of grains to produce beer, & of fruits to produce wine – Is an ancient art that humans in most cultures have practiced for millennia. Wild yeasts are acquired from the environment & used to ferment sugars into CO2 & ethyl alcohol under anaerobic conditions. Pasteur was instrumental in developing a reliable stain of brewer’s yeast, Saccharomyces cerevisiae, for the French brewing industry in the late 1850s. It was one of the 1st examples of biotechnology patenting Yeast is also used to make bread that rises The carbon dioxide they produce is responsible for the bubbles produced in the dough that become the air pockets of the baked bread Many secondary metabolites of fungi are of great commercial importance. Antibiotics are naturally produced by fungi to kill or inhibit the growth of bacteria, & limit competition in the environment Valuable drugs isolated from fungi include the immunosuppressant drug cyclosporine, the precursors of steroid hormones, & ergot alkaloids used to stop bleeding Some fungi are important model research organisms including the red bread mold Neurospora crassa & the yeast, S. cerevisiae