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CAN variation in SOIL microbial communities help us understand invasiveness of plants?

CAN variation in SOIL microbial communities help us understand invasiveness of plants?. TR Muth, Norris Muth, & Gabrielle Cannon. Background: Invasive species present an applied problem as well as an opportunity to address basic research questions.

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CAN variation in SOIL microbial communities help us understand invasiveness of plants?

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  1. CAN variation in SOIL microbial communities help us understand invasiveness of plants? TR Muth, Norris Muth, & Gabrielle Cannon

  2. Background: Invasive species present an applied problem as well as an opportunity to address basic research questions. • Why are native species often outcompeted by introduced species? introduced purple loosestrife native cattails

  3. Acer as a Model System Invasive Status non-invasive invasive alien Introduction Status native

  4. Research Goals • Characterize the differences in root microbial communities between introduced invasive species and native species (congeners). • Investigate possible role of root microbial community members in facilitating growth of introduced invasive species or constraining the growth of native species. • In turn, investigate the role of introduced invasive species on soil microbial communities.

  5. Hypotheses • To the extent that invasive plants (introduced or native) are generalists, we expect to see them associated with common widespread fungal taxa, while rare fungal taxa are more often associated with non-invasives. • Furthermore, we expect greater diversity of soil fungi to be associated with native species, while introduced species should have fewer co-adapted associates.

  6. Learning Goals • After participation in this module students should be able to – • determine native and introduced ranges of a species • develop or critically evaluate sample collection and sample processing protocols relevant to metagenomic study • use QIIME to process and analyze metagenomic data sets

  7. V&C Core Concepts • Evolution • Evolutionary history and biogeography • Local adaptation (or lack thereof) • OTUs and evolutionary distance (e.g. UniFrac data) • Systems • Positive and negative interactions between plants and soil microbial communities (e.g. mycorrhizae, pathogens, plant growth promoting bacteria, allelopathy).

  8. V&C Core Competencies • Ability to Apply the Process of Science • Study design, sample collection, DNA (RNA) purification, barcoding and relevant preparation steps specific for intended NGS platform • Ability to Use Quantitative Reasoning • Statistical analysis • Ability to Tap Into the Interdisciplinary Nature of Science • Overlaps between conservation, community ecology, microbiology, bioinformatics • Ability to Understand the Relationship Between Science and Society • Intentionally introduced species and globalization • Community composition and ecosystem service

  9. DNA Sequence Requirements • IlluminaMiSeqsequencing of the 18S rRNA ITS region • Could be expanded to bacteria through 16S rRNA gene sequencing • Could be expanded to whole genome shot-gun sequencing and/or RNA-Seq

  10. Earth Microbiome Project, J. Gilbert Laboratory

  11. Computational Requirements • Ability to support QIIME and R. Need for cluster access will depend on the size of the data sets.

  12. Assessment • Pre and post tests to include coverage of: • content • plant-soil microbial interactions • local adaptation • biogeography and invasive species • metagenomictechniques and applications • attitudes/awareness • scientific inquiry • centrality of evolution to biology / utility of evolution as applied science • invasive species

  13. Lecture Topics • Plant-soil Communities – specifically, plant-plant (competition, inhibition) and plant-soil microbial interactions (mutualisms, pathogenicity, etc.) • Community diversity • Adaptation and co-evolution (as relating to species interactions) • Biogeography and dispersal (patterns, mechanisms, consequences) • Principles of metagenomics (sequencing and sequence variation, taxa and target regions, OTUs, community analysis)

  14. Discussion Topics • To what extent do plant communities determine the niches of soil microbial communities, or vice versa? • If native species are adapted to their local conditions, why do introduced invasive species out compete them? • If dispersal of organisms is a normal process, can we meaningfully distinguish native and introduced species?

  15. Time Line Variable depending on whether only computational work will be performed (on pre-existing data) or whether both sample collection/processing and computational work will be included in a more comprehensive manner. • Unit 1: Identify systems and/or study sites • Unit 2a: Collect and process samples • Unit 2b. Troubleshooting sample processing • -sequence samples or send samples for sequencing- • Unit 3: Revisit background context – the relevance of biogeography, community interactions, & evolution • Unit 4: Computation and analysis

  16. References • Bell E. Using research to teach an "introduction to biological thinking". Biochemistry and Molecular Biology Education. 2011;39(1):10-6. • Buchwitz BJ, Beyer CH, Peterson JE, Pitre E, Lalic N, Sampson PD, Wakimoto BT. Facilitating long-term changes in student approaches to learning science. CBE Life Sciences Education. 2012;11(3):273-82. • Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., . . . Knight, R. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America, 108(SUPPL. 1), 4516-4522. • Dolan EL. Next steps for vision and change: Moving from setting the vision to change. CBE Life Sciences Education. Volume 11, Issue 3, 4 September 2012, Pages 201-202 • Handelsman J, Ebert-May D, Beichner R, Bruns P, Chang A, DeHaan R, Gentile J, Lauffer S, Stewart J, Tilghham SM, Wood WB. Scientific teaching. Science. 2004;304(5670):521-2. • Lopatto D. Undergraduate research experiences support science career decisions and active learning. CBE Life Sciences Education. 2007;6(4):297-306. • Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J., & Knight, R. (2011). UniFrac: An effective distance metric for microbial community comparison. ISME Journal, 5(2), 169-172. • Shaffer, C.D., Alvarez, C., Bailey, C., Barnard, D., Bhalla, S., Chandrasekaran, C., Chandrasekaran, V., Chung, H.-M., Dorer, D.R., Du, C., Eckdahl, T.T., Poet, J.L., Frohlich, D., Goodman, A.L., Gosser, Y., Hauser, C., Hoopes, L.L.M., Johnson, D., Jones, C.J.Kaehler, M., Kokan, N., Kopp, O.R., Kuleck, G.A., McNeil, G., Moss, R., Myka, J.L., Nagengast, A., Morris, R., Overvoorde, P.J., Shoop, E., Parrish, S., Reed, K., Regisford, E.G., Revie, D., Rosenwald, A.G., Saville, K., Schroeder, S., Shaw, M., Skuse, G., Smith, C., Smith, M., Spana, E.P., Spratt, M., Stamm, J., Thompson, J.S., Wawersik, M., Wilson, B.A., Youngblom, J., Leung, W., Buhler, J., Mardis, E.R., Lopatto, D., Elgin, S.C.R. The genomics education partnership: Successful integration of research into laboratory classes at a diverse group of undergraduate institutions. CBE Life Sciences Education. 2010;9(1):55-69. • Udovic D, Morris D, Dickman A, Postlethwait J, Wetherwax P. Workshop biology: Demonstrating the effectiveness of active learning in an introductory biology course. Bioscience. 2002;52(3):272-81. • Wei CA, Woodin T. Undergraduate research experiences in biology: Alternatives to the apprenticeship model. CBE Life Sciences Education. 2011;10(2):123-31. • Woodin T, Celeste Carter V, Fletcher L. Vision and change in biology undergraduate education, a call for action-initial responses. CBE Life Sciences Education. 2010;9(2):71-3.

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