Environmental Metagenomics Consortium David Biesboer, TR Muth, Wendy Trzyna, Mike Larkin, Joanna Klein, Stephanie Lammelin
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
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
Advantage of Consortium • Multi-institution collaboration • Combination of resources • Reduced cost • Varied expertise • Varied locations • Intentionally Student Driven
Ohio River Huntington, WV
East River Brooklyn, NY
Breakneck Creek, Rootstown, OH
Lake Johanna St. Paul, MN
Target Audience • High school through advanced undergraduate • Courses • General biology, environmental science, general microbiology, applied microbiology, genetics
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.
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
Our Job… • Develop training modules for each of these steps • Currently working on bioinformatics module
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
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
Summary • See you at ASM-CUE!!!