Lecture 241. Define ecosystem, ecology, community, population and guild.a. Ecosystem- Microbial communities that interact with communities of macroorganisms and the physiocochemical environment b. Ecology- Study of microorganisms in their natural or managed environmentsc. Community- Mixtures of different guilds conducting complementary physiological processes in a habitat interact to form microbial communitiesd. Population- Individual cells of the same type multiply to form populationse. Guilds- Populations of organisms doing similar metabolism constitute groups2. Explain the difference between richness and abundance a. Richnessi. How many different species in one locationii. Phylotypes are used to express the richness in a community using the 16S rRNA geneb. Abundancei. How many of each species 3. Study the freshwater lake microbial ecosystem – understand energy inputs; define allochthonous a. Energy inputsi. Sunlightii. Organic Carbon1. Made within the ecosystem; photosynthesis; decomposition of dead organisms and feces2. Made outside the ecosystem; terrestrial plant matter, animal waste, decomposing dead animalsb. Allochthonous carbon- Carbon from outside the ecosystem4. Explain how microscopy can be used with different types of stains; what is a viability stain a. Use microscopy and fluorescent dyes that stain DNA, or discriminate deadform live cells- these are used directly on environmental samplesb. These stains are used in fluorescent microscopy of environmental samples to visualize both live and dead cellsc. Viability stains- Dead/Live stains5. Be able to describe in general terms what FISH is and how it works a. FISH- Fluorescence in situ hybridization b. Utilizes sequence-specific oligonucleotides that have an attached fluorescent molecule to detect specific organism within populationsc. Stepsi. Synthesize oligonucleotide (celled the probe) specific for the organism you are looking for probes can be synthesized to be general or specificii. Chemically attach a fluorescent dye molecule to the oligonucleotideiii. Treat sample containing cells to make membranes permeable to the oligonucleotide + dye moleculeiv. Examine sample using fluorescence microscopy; only cells in whichthe oligonucleotide has correctly base paired (hybridized) will be fluorescent6. Compare and contrast the community sampling and environmental genomics approaches a. Community Sampling- PCR amplify 16S rRNA gene and do DNA sequencing, then compare with other sequencesb. Environmental genomics- Use high- throughout sequencing methods to obtain DNA sequence of genomes of all community membersc. LOOK AT SLIDE7. Describe how single gene PCR products are generated and analyzed for community sampling a. Amplify single gene, for example gene encoding 16S rRNAb. Sequence and generate tree8. Know the basics of what phylochips are and how they work a. Phylochips Definition- DNA microarrays can be designed using oligonucleotides with seqyebces useful for phylogenetic analysisb.9. Interpret the different graphical ways community analysis data is presented10. Define the human microbiomea. All of the microbes living in and on the human body11. Know what human microbiome studies hope to discover a. Human Microbiome is all of the microbes living in and on the human bodyb. Many studies have been undertaken to discoveri. What microbes are normally found at any one site in a healthy humanii. How the microbial community at ant site changes as a result of nutrition, disease states and medical treatmentsc. Most of these studies use the 16S rRNA sequencing and then constructionphylogenetic
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