David Biesboer, TR Muth, Wendy Trzyna, Mike Larkin, Joanna Klein, Stephanie Lammelin - PowerPoint PPT Presentation

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David Biesboer, TR Muth, Wendy Trzyna, Mike Larkin, Joanna Klein, Stephanie Lammelin

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  1. Environmental Metagenomics Consortium David Biesboer, TR Muth, Wendy Trzyna, Mike Larkin, Joanna Klein, Stephanie Lammelin

  2. Introduction • What’s important about water? • Students must be informed about this issue. • What can microbiologists bring to this? • Microbial diversity and relative community size • Relationship between geographic location/environment and microbial community composition • Contamination by pathogens

  3. Metagenomics to address issue • Current Research • Testing the water: marine metagenomics. Langridge G., Nat Rev Microbiol. 2009 Aug;7(8):552. • Bacterial diversity of metagenomic and PCR libraries from the Delaware River. Cottrell, Matthew T.; Waidner, Lisa A.; Yu, Liying1; Kirchman, David L. Environmental Microbiology, Volume 7, Number 12, December 2005 , pp. 1883-1895(13) • Using metagenomics, we can involve students in relevant cutting edge research in which they learn a variety of techniques

  4. Advantage of Consortium • Multi-institution collaboration • Combination of resources • Reduced cost • Varied expertise • Varied locations • Intentionally Student Driven

  5. Ohio River Huntington, WV

  6. East River Brooklyn, NY

  7. Breakneck Creek, Rootstown, OH

  8. Lake Johanna St. Paul, MN

  9. Lake Itasca, MN

  10. Spelga Lough, Northern Ireland

  11. Target Audience • High school through advanced undergraduate • Courses • General biology, environmental science, general microbiology, applied microbiology, genetics

  12. Student procedures • Collect water sample • Other data to collect and record • Water Temperature, pH, chemistry (O2, P, N) • Local Environment • Residential, industrial, agricultural, etc. • Remote sensing • Optional – flow rate, macroinvertebrates, microintertebrates, vertebrates, etc.

  13. Student procedures, cont. • Growth • Plate sample to enumerate culturable microbes present • DNA isolation • Kit: Qiagen, power soil max? • Archive • PCR • 16s rRNA primers • Tagged • Bioinformatics

  14. Our Job… • Develop training modules for each of these steps • Currently working on bioinformatics module

  15. Bioinformatics Training Module • Assemble collection of partial 16s rRNA sequences from Genbank for students to practice with. • Create handout for using BLAST at NCBI and/or JGI • Instruct students to search with practice sequences • Guided questions about results

  16. Practice Sequences 1: gi|255683807|gb|FJ999942.1| Agrobacterium tumefaciens strain EQH13 16S ribosomal RNA gene, partial sequence 2: gi|148466380|gb|EF590316.1| Agrobacterium vitis 16S ribosomal RNA gene, partial sequence 3: gi|155382358|gb|EF634040.1| Azotobacter chroococcum strain ISSDS-867 16S ribosomal RNA gene, partial sequence 4: gi|290784594|dbj|AB548822.1| Klebsiella sp. NCCP-142 gene for 16S rRNA, partial sequence 5: gi|241995056|gb|GQ214020.1| Rhodococcus opacus strain HCCS 16S ribosomal RNA gene, partial sequence 6:gi|258489543|gb|FJ662467.1| Pseudomonas sp. IR35 16S ribosomal RNA gene, partial sequence 7: gi|125489359|gb|EF215796.1| Uncultured gamma proteobacterium clone PM1-24 16S ribosomal RNA gene, partial sequence 8: gi|257412298|gb|EU862080.2| Pseudomonas fluorescens strain H41 16S ribosomal RNA gene, partial sequence 9: gi|60100258|gb|AY780013.1| Vibrio fischeri isolate VFISC1 16S ribosomal RNA gene, partial sequence

  17. Summary • See you at ASM-CUE!!!