Ch 28 Introduction

1. Ch 28 Introduction • Bacteria and Archaea form two of the three largest branches on the tree of life. The third major branch or domain is Eukarya, the eukaryotes. • Virtually all members of the bacteria and archaea are unicellular and all are prokaryotic (lacking a membrane-bound nucleus). • Bacteria and archaea are distinguished by the types of molecules that make up their plasma membranes and cell walls, and by the machinery they use to transcribe DNA and translate mRNA into proteins.

2. The Biological Impact of Bacteria and Archaea • The oldest fossils found thus far are of 3.5-billion-year-old bacteria. Eukaryotes do not appear in the fossil record until 1.7 billion years later. • Only 5000 species of bacteria and archaea have been named and described, but biologists are virtually certain that millions exist. • Over 400 species live in the human digestive tract. • About 128 species live in the lining of the human stomach. • Approximately 500 species live in the human mouth.

3. The Abundance of Prokaryotes • About 1013 cells make up your body, but living on it are about 1012 bacterial cells on your skin, and about 1014 bacterial and archaeal cells in your digestive tract. • A teaspoon of soil contains billions of microbes. • Current estimates place the number of living prokaryotes at over 5 x 1030—lined end-to-end they would stretch longer than the Milky Way!

4. The Habitat Diversity of Prokaryotes • Bacteria and archaea live almost everywhere, from below the Earth’s surface to on Antarctic sea ice. • 10 percent of the world’s biomass may be comprised of prokaryotes living under the ocean. • Bacteria and archaea have been found at depths of 10,000 m, and in temperatures ranging from 0° to 121°C. • Entirely new phyla of bacteria and archaea have been recently discovered.

5. Medical Importance • The first human disease-causing archaean, associated with the dental condition called periodontitis, was just discovered in 2004. • Bacteria that cause disease are said to be pathogenic. • Only a tiny fraction of the bacterial species living on and in the human body is pathogenic. • Pathogenic bacteria tend to affect tissues at the body’s entry points, such as wounds or pores in the skin, the respiratory and gastrointestinal tracts, and the urogenital canal.

6. Some Bacteria Cause Disease • An infectious disease is one spread by being passed from an infected individual to an uninfected individual. • The experiments of Robert Koch in the late 1800s became the basis for the germ theory of disease, which holds that infectious diseases are caused by bacteria and viruses (acellular particles that parasitize cells). • Koch’s postulates confirm a causative link between a specific infectious disease and a specific microbe:

7. Koch’s Postulates • The microbe must be present in individuals suffering from the disease and absent from healthy individuals. • The organism must be isolated and grown in a pure culture away from the host organism. • If organisms from the pure culture are injected into a healthy experimental animal, the disease symptoms should appear. • The organism should be isolated from the diseased experimental animal, again grown in pure culture, and demonstrated to be the same as the original organism.

8. Some Bacteria Cause Disease • In industrialized countries, improvements in sanitation and nutrition have dramatically reduced mortality rates due to infectious diseases since 1900. • Most of the decline in deaths due to infectious diseases occurred before the introduction of antibiotics.

9. What Makes Some Bacterial Cells Pathogenic? • Virulence, or the ability to cause disease, is heritable • Some species have both pathogenic virulent strains and harmless strains. • In Escherichia coli, for example, the virulence of the strain depends upon the length of the genome and the toxicity of the resulting proteins.

10. The Past, Present, and Future of Antibiotics • The discovery of antibiotics (molecules that kill bacteria) in 1928 and their widespread use starting in the 1940s allowed physicians to effectively combat most bacterial infections. • (NOT viral infections) • However, overuse of antibiotics since the late twentieth century has lead to antibiotic-resistant strains of bacteria.

11. Bacteria’s Role in Bioremediation • Some of the most serious pollutants in soils, rivers, and ponds consist of organic solvents or fuels that leaked or were spilled into the environment. • These pollutants are toxic, do not dissolve in water, and accumulate in sediments. • Bioremediation is the use of bacteria and archaea to degrade pollutants.

12. Bacteria’s Role in Bioremediation • Bioremediation uses two complementary strategies: • Fertilizing contaminated sites to encourage the growth of existing bacteria and archaea that degrade toxic compounds. • “Seeding,” or adding, specific species of bacteria and archaea to contaminated sites.

13. Extremophiles • Bacteria or archaea that live in high-salt, high-temperature, low-temperature, or high-pressure habitats are called extremophiles. • Extremophiles have become a hot area of research for several reasons: • Understanding extremophiles may help explain how life on Earth began. • Astrobiologists use extremophiles as model organisms in the search for extraterrestrial life. • Enzymes that function at extreme temperatures and pressures are useful in industrial processes, such as the use of Taq polymerase in PCR.

14. Using Enrichment Cultures • One classical technique for isolating new types of bacteria and archaea is the use of enrichment cultures. • In this process, cells are sampled from the environment and grown under specific conditions. These enrichment cultures are based on establishing a specific set of growing conditions―temperature, lighting, substrate, types of available food, etc. • Cells that thrive under the specified conditions will increase in numbers enough to be isolated and studied in detail. • Enrichment cultures led to the discovery of new bacterial species, including the heat-loving thermophiles that live more than a mile beneath the Earth’s surface.

19. Using Direct Sequencing • Direct sequencing is a new technique for documenting the presence of bacteria and archaea that have never been seen because they cannot be grown in pure culture. • It is based on identifying phylogenetic species—populations that have enough distinctive characteristics to represent an independent species.

20. The Process of Direct Sequencing • Specific genes from the sample are isolated using PCR. • These genes are sequenced and compared with sequences in existing databases. • If the sequences are markedly different, then the sample probably contains previously undiscovered organisms.

21. Results of Direct Sequencing • Prior to direct sequencing, archaea were traditionally placed into one of four groups: • Extreme halophiles • Sulfate reducers • Methanogens • Extreme thermophiles • However, direct sequencing revealed that archaea have a much wider range and variability than previously believed.

22. Evaluating Molecular Phylogenies • Some of the most useful phylogenetic trees for domains Bacteria and Archaea have been based on studies of the RNA molecule found in the small subunit of ribosomes, 16S and 18S RNA. • In the late 1960s Carl Woese and colleagues determined and compared the 16S and 18S RNA molecules from a wide array of species. • The results of their comparison comprise the universal tree or tree of life.

23. Evaluating Molecular Phylogenies • The universal tree illustrates that earlier phylogenetic trees based on morphology, which showed the major division as between prokaryotes and eukaryotes, were incorrect. • The tree of life based on ribosomal RNA sequences shows the three domains—Archaea, Bacteria, and Eukarya—that are now accepted as correct.

25. Morphological Diversity • Bacteria and archaea show extensive morphological diversity in terms of size, shape, and motility. • The volume of bacterial species ranges from 0.15 m3 to 200 x 106m3. • Bacteria range in shape from filaments, spheres, rods, and chains to spirals. • Bacteria have a range of modes of motility.

27. Cell Wall Composition • Within bacteria, two general types of cell wall exist that can be distinguished by treatment with a dye called the Gram stain. • Gram-positive cells (which look purple under a microscope) retain Gram stain better than Gram-negative cells (which look pink). • Gram+: cell wall contains lots of a carbohydrate called peptidoglycan • Gram-: 2 layers in cell wall, thin layer of peptidoglycan, outer layer of phospholipid bilayer

28. Metabolic Diversity: Bacteria/Archaea can eat ANYTHING! • Bacteria and archaea may use one of three sources of energy for ATP production: light, organic molecules, or inorganic molecules. • Phototrophs use light energy to promote electrons to the top of electron transport chains. ATP is then produced by photophosphorylation. • Chemoorganotrophs oxidize organic molecules with high potential energy. ATP may be produced by cellular respiration using sugars as electron donors or by fermentation pathways. • Chemolithotrophs oxidize inorganic molecules with high potential energy. ATP is produced by cellular respiration with inorganic compounds serving as the electron donor.

29. Metabolic Diversity • Bacteria and archaea may obtain building-block compounds in one of two ways, by synthesizing them from simple starting materials or by absorbing them from their environment. • Autotrophs manufacture their own carbon-containing compounds. • Heterotrophs live by consuming them. • Of the six possible ways of producing ATP and obtaining carbon, just two are observed among eukaryotes. But bacteria and archaea do them all.

30. Prokaryotic Metabolism • The basic chemistry required for photosynthesis, cellular respiration, and fermentation originated in these lineages. Then the evolution of variations on each of these processes allowed prokaryotes to diversify into millions of species that occupy diverse habitats.

31. Producing ATP via Cellular Respiration • Bacteria and archaea can exploit a wide variety of electron donors and acceptors to accomplish cellular respiration. • When electron donors other than sugars and electron acceptors other than oxygen are used, by-products other than water and carbon dioxide are produced. • The metabolic diversity of bacteria and archaea explains: • their ecological diversity. • their key role in cleaning up some types of pollution. • their role in global change, including nutrient cycling.

32. Producing ATP via Fermentation • Fermentation is a strategy for making ATP without using electron transport chains. However, fermentation is much less efficient than cellular respiration. • The diversity of enzymatic pathways in bacterial and archaeal fermentations extends the metabolic repertoire of these organisms.

33. Producing ATP via Photosynthesis • Photosynthetic species use the energy in light to raise electrons to high-energy states. • As these electrons are stepped down in energy through electron transport chains, the energy released is used to generate ATP. • Species that use water as a source of electrons carry out oxygenic photosynthesis. Many phototrophic bacteria use molecules other than water as the electron donor in anoxygenic photosynthesis.

34. Photosynthetic Prokaryotes • Bacteria and archaea can photosynthesize in one of three ways: • Light activates the pigment bacteriorhodopsin, which uses the absorbed energy to create a proton gradient, followed by ATP synthesis via chemiosmosis. • A recently discovered bacterium that lives near hydrothermal vents on the ocean floor absorbs geothermal radiation rather than light for photosynthesis. • Pigments that absorb light raise electrons to high-energy states. The energy released as these electrons move through electron transport chains is used to generate ATP.

35. Obtaining Building-Block Compounds • Compared to eukaryotes, the metabolic capabilities of bacteria and archaea are remarkably sophisticated and complex. • Like eukaryotes, some bacteria and archaea use the Calvin cycle to transform carbon dioxide to organic molecules, and other bacteria and archaea obtain carbon by absorbing organic compounds released in dead tissues.

36. Obtaining Building-Block Compounds • Many prokaryotes obtain building-block compounds in ways that are quite different from eukaryotes: • Several groups of bacteria fix CO2 using pathways other than the Calvin cycle. • Methanotrophs use methane (CH4) rather than CO2 as their carbon source. Other bacteria can use carbon monoxide (CO) or methanol (CH3OH) as a starting material. • Compared to eukaryotes, the metabolic capabilities of bacteria and archaea are remarkably sophisticated and complex.

37. Ecological Diversity and Global Change • Bacteria and archaea can live in extreme environments and use toxic compounds as foodbecause they produce extremely sophisticated enzymes. • The complex chemistry and abundance of bacteria and archaea make them potent forces for global change.

38. The Oxygen Revolution • No free molecular oxygen existed for the first 2.3 billion years of Earth's history. • Cyanobacteria, a lineage of photosynthetic bacteria, were the first organisms to perform oxygenic (oxygen-producing) photosynthesis. • Cyanobacteria were responsible for changing the Earth’s atmosphere to one with a high concentration of oxygen.

39. The Oxygen Revolution • Once oxygen was common in the oceans, cells could carry out aerobicrespiration. • Prior to this, only anaerobicrespiration was possible; cells had to use compounds other than oxygen as the final electron acceptor in the electron transport chain during cellular respiration. • Oxygen is highly electronegative and so is an efficient electron acceptor. Much more energy is released as electrons move through ETCs with oxygen as the ultimate acceptor than is released with other acceptor substances.

41. Nitrogen Fixation and the Nitrogen Cycle • All organisms require nitrogen (N) to synthesize proteins and nucleic acids. • Although molecular nitrogen (N2) is abundant in the atmosphere, most organisms cannot use it directly. • Therefore, all eukaryotes and many bacteria and archaea must obtain their N in a form such as ammonia (NH3) or nitrate (NO3).

42. The Nitrogen Cycle • The only organisms capable of converting molecular nitrogen to ammonia, a process called nitrogen fixation, are specific bacteria. • Certain species of aquatic cyanobacteria can fix nitrogen. • On land, nitrogen-fixing bacteria live in close association with plants—often taking up residence in root structures called nodules.

43. Nitrogen Cycling • The nitrite (NO2) that some bacteria produce as a by-product of respiration does not build up in the environment but rather is used as an electron acceptor by other species and converted to molecular nitrate (NO3), which in turn is converted to molecular nitrogen (N2) by yet another suite of bacterial and archaeal species. • In this way, bacteria and archaea are responsible for driving the movement of nitrogen atoms through ecosystems around the globe.

44. Nitrate Pollution • The widespread use of ammonia fertilizers is causing serious pollution. • When ammonia is added to the soil, much of it is used by bacteria as food, which then release nitrite (NO2–) or nitrate (NO3–). • Nitrates cause pollution in aquatic environments. • In an aquatic ecosystem, nitrates can decrease the oxygen content, causing anaerobic “dead zones” to develop.

45. Summary of Prokaryotic Diversity • Bacteria and Archaea may be small in size, but because of their abundance, ubiquity, and ability to do sophisticated chemistry, they have an enormous influence on the global environment. Gulf of Mexico dead zone

46. Key Lineages of Bacteria and Archaea • The relationships among the major lineages within Bacteria and Archaea are still uncertain in some cases. • However, most of the lineages themselves are well studied.

47. Bacteria • Bacteria are a monophyletic group. Within this group there are at least 16 major lineages. • Some were recognized by distinctive morphological characteristics, others by phylogenetic analyses of gene sequence data.

48. Bacteria • Firmicutes are Gram positives and most are rod shaped or spherical. • They are metabolically diverse. • Species in this group are important components of soil. • Some species in this group cause diseases, yet we use some to ferment milk into yogurt. • Spirochaeles (spirochetes) are distinguished by their corkscrew shape and unusual flagella. • Most spirochetes produce ATP via fermentation. • These bacteria are very common in aquatic habitats. • Spirochetes cause the diseases syphilis and Lyme disease.

49. Bacteria • Actinobacteria are Gram positive, and shape varies from rods to filaments. • Many of the soil-dwelling species are found as chains of cells that form extensive branching filaments called mycelia. • Many species are heterotrophs. Some species live as decomposers in soil; some live in association with plant roots and fix nitrogen. • Tuberculosis and leprosy are caused by members of this group. • Species from the genus Streptomyces produce over 500 distinct antibiotics. Mycobacterium leprae Mycelia

50. Bacteria • Chlamydiae are spherical and very tiny. • They are endosymbionts—they live as parasites inside animal cells and get almost all of their nutrition from their hosts. • These bacteria can cause blindness and urogenital tract infections in humans.