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Bacterial Diversity Prokaryotes represent a broad group of organisms that for many years were classified by R.H. Whittaker in a five kingdoms system as Monerans. The five-kingdom system, proposed in 1968, has become a popular standard and with some refinement is still used in many works, or forms the basis for newer multi-kingdom systems. The Monerans include all of the prokaryotic cells and reflects collectively close to 4 billion years of evolution. Until recently (the last 10 – 20 years) scientist (biologists) were restricted in the means by which they could organize or relate these organisms in a meaningful context. And yet it is fair to say that they have been for practical purposes fairly successful. The classical approach to prokaryote identification relied on three criteria. 1 – shape of cell, and colony morphology 2 – nutritional capabilities 3 – staining properties Without much more to go on these properties were used with a fair amount of sophistication in order to identify an organism. More recently, Carl Woese, at the University of Illinois, embraced a comprehensive molecular study that has shed a tremendous amount of light upon our understanding of bacterial diversity and evolutionary relatedness. The term molecular systematics uses molecular analysis in order to organize and arrange different organisms in an evolutionary context. Molecular systematic approaches have resulted in a new paradigm that employs a new and more inclusive level in the hierarchical scheme used by biologist for purposes of classification. This higher order level is the domain. Summer 2008 Workshop in Biology and Multimedia for High School Teachers Harvard University Life Sciences – HHMI Outreach Program Interestingly, all of the eukaryotic organisms that were once organized within the four kingdoms (protists, plants, animals and fungi) are now represented by a single domain, the Eukarya. The prokaryotes, which originally were organized into a single kingdom, monara, have now been expanded to include two separate domains. These two domains are identified the Eubacteria and the Archaea. Part Ahttp://www.uphs.upenn.edu/bugdrug/antibiotic_manual/Gram1.h tm The web page cited discusses the culture and identification of infectious agents. Read through these pages and try to answer some of these basic questions. Who first developed the Gram stain? What are the two major groups identified by this method of staining? What does Gram staining rely on? What are some organisms that do not readily stain with the gram stain? Summer 2008 Workshop in Biology and Multimedia for High School Teachers Harvard University Life Sciences – HHMI Outreach Program http://www.uphs.upenn.edu/bugdrug/antibiotic_manual/Gram3.h tm Identify some of major gram-positive organisms. Identify some of the major gram-negative organisms. Now go to http://pathmicro.med.sc.edu/fox/culture.htm and consider the molecular analysis described? Part B. Each group of organisms has signature sequences, regions of its SSU-rRNA (this is RNA associated with the small subunit of the ribosome) that have unique nucleotide sequences acquired by an accumulation of mutations in the ancestor of that taxonomic group. These can be domain-specific sequences at comparable locations in ribosomal RNA or other nucleic acids. They can even be species specific. Analysis of what important molecule is used for as the “gold standard” for species classification. ___________________________________________________________ ________ How is one able to get this information from organisms that are not easily cultured in the laboratory? ___________________________________________________________ ________ http://euarch.blogspot.com/2007/11/archaea.html In this unit you will explore the some of the major clades of each of these groups. Summer 2008 Workshop in Biology and Multimedia for High School Teachers Harvard University Life Sciences – HHMI Outreach Program The two major prokaryotic domains resulting from the work of Carl Woese are the Eubacteria and the Archeabacteria. Although both are prokaryotes they show some major distinctions. Try to answer the following questions using the following link. Click here for an excellent overview of the Archaea and the Bacteria. Sometimes the Archaea are referred to as the “extremophiles” or lover of the extremes. These are further divided into major phyla. What are some of the major groupings or phyla represented in the Archea? How is the cell wall of the Archaea different from the true bacteria? For example, what does it lack? What contributes to its capacity to withstand extreme conditions? The Eubacteria or true bacteria are divided into a number of major clades: Proteobacteria This large and diverse clade of gram-negative bacteria includes photoautotrophs, chemoautotrophs, and heterotrophs. Proteobacteria include both anaerobic and aerobic species. Molecular systematists recognize three to five major subgroups of proteobacterial species depending on whose system you are reading. I. The purple bacteria include photo-autotrophic and photoheterotrophic bacteria. Many of which contain bacteriochlorophylls located in membrane invaginations. Many species are obligate anaerobes and are found in mud, ponds, lakes and sediment. The ancestral bacterium that evolved into mitochondria through endosymbiosis is thought to be a relative of the purple non sulfur bacteria. This conclusion is based on similar metabolic features of mitochondria and purple non Summer 2008 Workshop in Biology and Multimedia for High School Teachers Harvard University Life Sciences – HHMI Outreach Program sulfur bacteria and on comparisons of the base sequences in their 16S rRNAs. II. Next, there are the chemoautotrophic proteobacteria. Many of these organisms play key ecological roles in nitrogen metabolism . They can be free living or symbionts. Rhizobium which is found in the root nodules of leguminous plants such as alfalfa, pea and clover and Agrobacterium tumerfacians, which is an important organism adapted by researchers as a tool for gene transfer in dicots. III. The chemoheterotrophic bacteria include the enterics, which are important residents of the intestinal flora of animals. They include E. coli, Shigella dysenteriae and Salmonella. Other organisms included in the proteobactera include the myxobacxteria and bdellovibrios The Myxobacteria form the most elaborate colonies of all prokaryotes. The cells secrete a slimy ooze which permits them to glide through soil. Under certain conditions of stress they can form a "fruiting" body, which may be brightly colored and as large as a millimeter in diameter. The fruiting body releases spores that will become active in favorable environments. Another proteobacterim includes bdellovibrios. These are predators that attack other bacteria. A bdellovibrio canl drill boring into its prey by spinning at relatively very high speeds. Major clades of Eubacteria other than the proteobacteria include: Clamidyas - These parasites can survive only within the cells of animals, depending on their hosts for resources as basic as ATP. The gram-negative walls of chlamydias are unusual among bacteria in that they lack peptidoglycan. One species, Chlamydia trachomatis , is the most common cause of blindness in the world and also causes nongonococcal urethritis, the most common sexually transmitted disease (STD) in the United States. Summer 2008 Workshop in Biology and Multimedia for High School Teachers Harvard University Life Sciences – HHMI Outreach Program Spirochetes - Rotation of internal flagellum-like filaments produces a corkscrewlike movement. Many spirochetes are free- living, but the group also includes some notorious pathogens: Treponema pallidum causes the STD syphilis, and Borrelia burgdorferi is the pathogen of Lyme disease. Gram positive bacteria Many mycoplasmas are soil bacteria, one species of mycoplasma causes "walking pneumonia" in humans. Which species is responsible for "walking pneumonia" in humans? ____________________________________________________ ____________________________________________________ How many genes are found in the mycoplasma? ____________________________________________________ How dos this compare with the genome of Escherchia coli? ____________________________________________________ ____________________________________________________ ____________________________________________________ Actinomycetes – These are a large group of gram positive bacteria that take on a filimentous phenotype. Some are branched forms and superficially resemble molds. The resemblance of fungi and the filamentous forms of actinomycetes is an example of __________________ evolution between the prokaryotes and the eukaryotes in the soil environment. Actinomycetes and streptomycetes are associated with insects and provide a rich source of antibiotics. This fact has not escaped the attention of the pharmaceutical companies. Actinomycetes are the primary source of which antibiotic? _____________________________________________________ Actinomycetes such as Streptomyces have a world-wide distribution in soils. They are important in aerobic decomposition of organic compounds and have an important role in biodegradation and the carbon cycle. Also included Summer 2008 Workshop in Biology and Multimedia for High School Teachers Harvard University Life Sciences – HHMI Outreach Program with the gram positive bacteria are Bacillus and Clostridium; anthrax is caused by Bacillus anthracis,; Clostridium botulinum produces the toxin that causes the potentially fatal disease botulism. Staphylococcus associated with skin infections, Streptococcus, is the agent of strep throat, and the mycoplamas which are the smallest of all known cells. The pyogenic cocci (pyogenic refers to bacterial infections that make pus or form abscesses.) Which organisms are responsible for producing 1/3 of all human infections? ____________________________________________________ ____________________________________________________ ____________________________________________________ ____________________________________________________ ____________________________________________________ ____________________________________________________ Cyanobacteria - These photoautotrophs are the only prokaryotes with plantlike, oxygenic photosynthesis. Chloroplasts evolved from a cyanobacterium. They provide enormous amounts of food for freshwater and marine ecosystems and play important ecological roles in global nitrogen, carbon and oxygen cycles. Some filamentous colonies like Anabanea have cells specialized for nitrogen fixation. What is the name of the specialized cells that are able to fix nitrogen? ____________________________________________________ What is the name of the cyanobacterium that is the leading candidate for the type of bacterium that might have undergone endosymbiotic events that led to the development of the plant chloroplast. ____________________________________________________ These structures are layered chalk deposits, which exhibit a continuous geologic record covering 2.7 billion years. ____________________________________________________ How do cyanobacteria maintain buoyancy in the aquatic environments? Summer 2008 Workshop in Biology and Multimedia for High School Teachers Harvard University Life Sciences – HHMI Outreach Program ____________________________________________________ Summer 2008 Workshop in Biology and Multimedia for High School Teachers Harvard University Life Sciences – HHMI Outreach Program