Microbial Ecology - Microbial Ecology Study of biodiversity...

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Microbial Ecology Study of biodiversity of microbes in nature Measure activities, effects of microbes Organizational levels Populations Guilds Communities Ecosystems Biogeochemical cycles
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Methods in Microbial Ecology Enrichment & Isolation Enrichment culture Highly selective medium Appropriate inoculum Winogradsky column Glass cylinder Fill ~ 1/3 with modified soil, sediment Overlay with water Expose to moderate light Obtain pure culture (?)
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The Winogradsky Column
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Viability & Quantification Fluorescent Staining DNA-binding stains Acridine Orange (3,6-bis-[dimethylamino]-acridium chloride) Orange or green DAPI (4’,6-diamido-2-phenylindiole) Stains blue Used for enumeration
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DAPI Staining Escherichia coli
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Viability Staining Bacillus cereus & Micrococcus luteus
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Fluorescent Antibody Staining Sulfolobolus acidocaldarius
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Tagging with Green Fluorescent Protein Pseudomonas aeruginosa
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Genetic Stains Fluorescent in situ hybridization (FISH) phylogenetic probes Species-specific signature sequences Highly specific Simple to perform Multiple probing of single sample FISH Community analysis Study “unculturable” organisms Determine morphology, abundance, microbial associations
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Morphology & Genetic Diversity
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Multiple FISH Probes Nitrifying bacteria Ammonium-oxidizing bacteria
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Multiple FISH Probes
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Genetic Stains FISH Chromosomal painting Identify specific genes Locate, count specific metabolic populations In situ reverse transcriptase FISH Locates specific genes Detects expression specific genes
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Chromosomal Painting & ISRT FISH E. coli Oceanospirillium linum Chromosomal Painting ISRT Microbulbifer hydrolyticus Sagittula stellata
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PCR & Microbial Community Analysis
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