05 measurement classification

05 measurement classification - CEE 266 ENVIRONMENTAL...

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Unformatted text preview: CEE 266 ENVIRONMENTAL BIOTECHNOLOGY Lecture 5 (Microbial Enumeration and Classification) Measurement of Growth   Direct microscopic counts   Plating and serial dilution   Particle counters   Optical density   Dry cell weight   Chemical constituents, e.g., protein, ATP, enzymes, antibodies, lipids   DNA/RNA measurements, analyses   Genomics, metagenomics Direct Microscopic Counts Figure 6.14 Dilution Plating/ Viable Counts Fig 6.15 Serial Dilution and Plating Fig 6.16 Spectrophotometric Measurement Fig 6.17 Microbial Activity Measurements Fig 22.17 ATP Measurement http://www.luminultra.com/images/stories/Training/QG21-I-dATP-Assay.gif Single Gene Analysis Quantification of DNA and RNA www.bioresearchonline.com www.gene-quantifiation.com Whole-genome Microarray Cell lysis RNA isolation DNA removal Cells Reverse transcription Purified RNA Labeling and hybridization ss-cDNA Scanning 102 101 Data Analysis 100 10-1 10-2 102 103 104 105 106 107 Microbiological Nomenclature   Binomial Nomenclature: Genus name + species name (+ strain)   Italicized or underlined   Genus name is capitalized and may be abbreviated   Species name is never abbreviated   E.g. Escherichia coli or E. coli   Hierarchy of taxonomic units Domain Phylum Class Order Family Genus Species Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia coli Microbial Classification   Phenotype: The functional characteristics.   Observations by microscopy (eg. morphology, structure) or biochemical analysis (metabolic diversity) or habitat (ecological diversity).   Genotype: The genetic characteristics.   Using DNA markers to trace evolutionary relationships. Microbial Classification   Morphology   Prokaryotes/eukaryotes, Gram +/-, shape, motility   Physiology   Carbon source, energy source, habitat, adaptation   Chemotaxonomy   Cell wall lipids, fatty acids, quinones   Phylogenetics   Genes, %G+C content Morphological Diversity Gram Stain – Cell Wall Classification http://www.biologie.uni-hamburg.de/b-online/library/micro229/terry/229sp00/lectures/cells2.html Optimum Temperatures for Growth Figure 6.19 Pressure Tolerance Figure 23.20 Adaptation to pH http://textbookofbacteriology.net/themicrobialworld/nutgro.html Salt Tolerance Figure 6.25 Oxygen and Microbial Growth   Aerobes: require oxygen to live   Anaerobes: do not require oxygen and may even be killed by exposure •  Facultative organisms: can live with or without oxygen •  Aerotolerant anaerobes: can tolerate oxygen and grow in its presence even though they cannot use it   Microaerophiles: can use oxygen only when it is present at levels reduced from that in air Oxygen Adaptation Brock, Fig 6.27 Four-Electron Reduction of O2 to H2O Figure 6.29 Enzymes that Destroy Toxic Oxygen Species Figure 6.30 Metabolic Diversity Trophic Levels Energy Source Carbon Source Metabolic Class Light CO2 Phototroph/photoautotroph Light organics Photoheterotroph Inorganic compounds CO2 Lithoautotroph/chemolithotroph Inorganic compounds organics Chemoorganotrophs Organic compounds organics chemoorganoheterotrophs Phylogenetic Tree of Life www.astro.yale.edu Pseudonocardia dioxanivorans Gram-positive actinomycete Cell size 1-3 µm White aerial and yellow substrate mycelia fragment into rod-shaped, non-motile units (Mahendra & Alvarez-Cohen, IJSEM, 2005) Mycolateless cell wall; A1γ type peptidoglycan Major PLFAs 16:0 iso, 16:0 10 me & 17:0 10 me 74 % G+C Optimal growth at 30°C (15-34°C), pH 6 (5-8), up to 4% salt tolerance C & N Sources Utilized •  Ethers - 1,4-Dioxane, tetrahydrofuran, tetrahydropyran, 1,3-dioxane, 2-methyl-1,3-dioxolane, diethyl ether, butyl methyl ether •  Benzene, toluene •  Alcohols •  Carbohydrates •  Carboxylic acids •  Amino acids •  Vitamins •  TSB, R2A, casamino acids •  Aerobic autotrophic growth on H2 and CO2 (Mahendra & Alvarez-Cohen, IJSEM, 2005) •  •  •  •  •  •  •  •  •  •  •  •  •  •  Dinitrogen Ammonia Nitrite Nitrate Urea Amino acids Methylamine Ethylamine Uric acid Ethylenediamine Putrescine Xanthine Xanthosine Alloxan Phylogenetic Position (Mahendra & Alvarez-Cohen, IJSEM, 2005) ...
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This note was uploaded on 02/02/2012 for the course CEE 266 taught by Professor Shailymahendra during the Fall '11 term at UCLA.

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