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Biological Problems in Water Microbiology

Biological Problems in Water Microbiology. Exploring differences/changes in water-based microbial communities due to a given variable or set of variables. Strengths of project: Inquiry-based Modular and Flexible Interdisciplinary Learning Outcomes – Students will demonstrate:

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Biological Problems in Water Microbiology

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  1. Biological Problems in Water Microbiology • Exploring differences/changes in water-based microbial communities due to a given variable or set of variables. • Strengths of project: • Inquiry-based • Modular and Flexible • Interdisciplinary • Learning Outcomes – Students will demonstrate: • the appropriate utilization of bioinformatic tools and sequence databases to address biological problems. • an understanding of microbial diversity. • an understanding of how the environment shapes microbial communities and their function.

  2. Phylogenetic Trees – Structure of Microbial Communities Contaminated vs. Non-Contaminated Watershed Sites Project Workflow • RDP • Tree Builder • Phylogen.fr • PhyML • TreeDyn Sample Collection Total DNA Extraction Sequence Data Sequence 16S rRNA Genes (Out sourced) • RDP • Libcompare • Cluster (Goodner) Comparative Metagenomic Analysis Enrichment Cultures DNA Extraction Sequence 16S rRNA Gene (In Lab) Sequence Data Bacterial Identification • RDP • Seqmatch • NCBI • Blast Select Isolates Sequence Data Phylogenetic Trees – Diversity of Microbes • RDP • Tree Builder • Phylogen.fr • PhyML • TreeDyn Phenotypic Characterization

  3. Project Workflow - Environmental Microbiology Module Wet-lab Computer based Sample Collection 16S rDNA sequence analysis Winogradsky columns? Isolate based Analysis DNA Extraction 16S rDNA PCR Sequencing (Lecture) RDP NCBI BLAST Enrichment Cultures MUSCLE Classifier SeqMatch Tree Builder Select Isolates Phylogeny Phenotypic Characterization Diversity

  4. Project Workflow – Integrative Biology Projects(UIO) Computer based-only project Select Sample Sources for Comparison (2) Characterization of sites (Literature Based) Relationship with metabolism and environment? A. Genome (isolate) approach Pick two related microorganisms from each site IMG Phylogenetic Profiler: find unique genes ? 2 Metagenomes IMG-M Compare Metagenomes B. Metagenome approach Function

  5. ALUM CREEK WATER PROJECT The quality of our water: How do we know? Spring 2011 - Chemical characterization of water (Env. Sci.) - Coliform analysis (Princ. of Bio.) - Winogradsky columns Fall 2011 - Hypothesis building (Genetics, Biochem., Env. Sci.) - Metagenomic analysis (Genetics, Biochem.)

  6. E. Wiley Accelerated Integrated Science Sequence (AISS) (combined intro biology, chemistry & physics) -one year- Statistical differences in water microbial populations Information used to understand and model relationships in natural world Probability -BLAST, phylogenetic trees Structure Protein domains, transmembrane predictions, enzyme structure/function - conservation of catalytic site residues -Pfam, PDB, TMHMM, etc. Metabolic pathways – do selection of microbes from each sample have full complement of glycolytic enzymes? If not, why not? Specialization according to ‘energy niches’ Energy -IMG BLAST Dynamics Population dynamics, rates of change in communities -in response to ??????

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