What controls long-term changes in freshwater microbial community composition? (NSF-DEB 0639790)

Project Leads: Byron C. Crump and George W. Kling
Technicians: Johanne Albrigtsen, Michelle Stuart, Jennifer Nannen, Joanna Green, Jennifer Kostrzewski, Amanda Field, Alex Mettler
Graduate Students: Heather Adams, Sarah Barbrow, Jason Dobkowski
Undergraduate REUs: Amy Markstein, Tracy Coolidge, Jeff Boyer, Ashley Larsen, Sarah Hay
Educators: DJ Kast (PolarTREC), Robert Warrilow (RET), Sally Cresidio (RET), Lauren Watel (PolarTREC)
Collaborators: Rose M. Cory, Linda Amaral-Zettler, John E. Hobbie, Craig T. Nelson, Julia Larouche, W. Breck Bowden, Anne Giblin

Overview: Microbial ecology came to the forefront of biological and ecological science in the 1990s with the development of high-throughput DNA sequencing and other molecular techniques.  Recently this field entered a second age of understanding that microbial diversity was organized into patterns at various scales, consistent with ecological concepts that were once thought applicable only to macro-organisms.  Evidence of these patterns in diversity contradicts the traditional microbial hypothesis from Bass-Becking (1934) that “Everything is everywhere, but the environment selects,” and indicates that, as with larger organisms, dispersal processes influence microbial diversity even at regional and local scales.  It is clear that both dispersal and environmental conditions are related to patterns of diversity, but to date the mechanistic controls and the relative importance of these factors have not been determined.  The goal of this research project is to resolve these controls with field and lab experiments that monitor the phylogenetic composition and ecosystem function (metabolism) of microbial communities. 

Intellectual Merit: This work builds on a six-year record showing consistent spatial and temporal patterns of microbial growth and community composition in ~25 lakes and streams of the Toolik Lake Research Area in Arctic Alaska.  Using experiments coupled with established sampling protocols and routines (leveraging the Arctic Long Term Ecological Research monitoring program), this research will answer 3 basic questions, and focus on the long-term aspects of dispersal events and climate change:
1.  How does environment influence microbial community composition and rate of function?
2.  How are distribution patterns of microbial communities in lakes, streams, and soils influenced by dispersal via down-slope water flow? 
3.  How are seasonal, inter-annual, and long-term shifts in microbial community composition related to temporal shifts in environmental conditions such as those caused by climate change?

Long-term investigations of microbial communities are critical for understanding patterns of diversity and their controls, especially because the most enduring dispersal events are also most rare.  Moreover, because this work is located in the Arctic it will capture the earliest biological effects of global climate change. The Toolik Research Area (http://www.uaf.edu/toolik/) is ideal for this because climate change has yet to affect environmental conditions critical for microbe dispersal and function (e.g., hydrology), and thus the current 6-year dataset establishes a baseline condition.

Also, and perhaps most important, molecular technology for analyzing microbial communities is advancing rapidly, and a cohesive, long-term archive of DNA samples and associated environmental information will be extremely valuable in the future for application of these new analyses.

Publications

Nalven, S. G., Ward, C. P., Payet, J. P., Cory, R. M., Kling, G. W., Sharpton, T. J., Sullivan, C. M., and B. C. Crump. 2020. Experimental metatranscriptomics reveals the costs and benefits of dissolved organic matter photo‐alteration for freshwater microbes. Environmental Microbiology 8:3505-3521. doi: 10.1111/1462-2920.15121

Thompson, L.R., Sanders, J.G., McDonald, D., Amir, A., Ladau, J., Locey, K.J., et al. 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551:457. doi:10.1038/nature24621

Ward, C. P., S. G. Nalven, B. C. Crump, G. W. Kling, and R. M. Cory. 2017. Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration. Nature Communications 8:8.

Hosen, J. D., C. M. Febria, B. C. Crump, and M. A. Palmer. 2017. Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition. Frontiers in Microbiology 8:1452, DOI: 10.3389/fmicb.2017.01452.

Adams, H. E., B. C. Crump, and G. W. Kling. 2015. Isolating the effects of storm events on arctic aquatic bacteria: temperature, nutrients, and community composition as controls on bacterial productivity. Frontiers in Microbiology 6:250, DOI: 10.3389/fmicb.2015.00250

Febria, C. M., Hosen, J. D., Crump, B. C., Palmer, M. A., and D. D. Williams. 2015. Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison. Frontiers in Microbiology 6:522, DOI 10.3389/fmicb.2015.00522

Cameron, K. A., B. Hagedorn, M. Dieser, B. C. Christner, K. Choquette, R. Sletten, B. Crump, C. Kellogg, and K. Junge. 2015. Diversity and potential sources of microbiota associated with snow on western portions of the Greenland Ice Sheet. Environmental Microbiology 3:594-609.

Cory, R. M., C. P. Ward, B. C. Crump, and G. W. Kling. 2014. Sunlight controls water column processing of carbon in arctic fresh waters. Science 345:925-928

Kling, G. W., H. E. Adams, N. D. Bettez, W. B. Bowden, B. C. Crump, A. E. Giblin, K. E. Judd, K. Keller, G. W. Kipphut, and E. R. Rastetter. 2014. Land–Water Interactions. Alaska’s Changing Arctic: Ecological Consequences for Tundra, Streams, and Lakes:143.

Luecke, C., A. E. Giblin, N. D. Bettez, G. A. Burkart, B. C. Crump, M. A. Evans, G. Gettel, S. MacIntyre, W. J. O’Brien, and P. A. Rublee. 2014. The Response of Lakes Near the Arctic LTER to Environmental Change. Alaska’s Changing Arctic: Ecological Consequences for Tundra, Streams, and Lakes:238.

Adams, H. E., B. C. Crump, and G. W. Kling. 2014. Metacommunity dynamics of bacteria in a freshwater lake; the role of species sorting and mass effects.  Frontiers in Aquatic Microbiology 5:82, doi: 10.3389/fmicb.2014.00082

Cory R. M., Crump B. C., Dobkowski J. A, and G. W. Kling. 2013. Surface exposure to sunlight stimulates CO2 release from permafrost soil carbon in the Arctic. Proc. Natl. Acad. Sci. U. S. A. DOI 10.1073/pnas.1214104110.

Larouche, J. R., Bowden, W. B., Giordano, R., Flinn, M. B., and B. C. Crump.  2012. Microbial biogeography of arctic streams: exploring influences of lithology and habitat. Frontiers in Microbiology DOI:10.3389/fmicb.2012.00309.

Crump, B. C., L. A. Amaral-Zettler, G. W. Kling. 2012. Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils.ISME Journal doi:10.1038/ismej.2012.9. 

Adams, H. E., B. C. Crump, and G. W. Kling. 2010. Temperature controls on aquatic bacterial production and community dynamics in arctic lakes and streams. Environmental Microbiology 12:1319-1333. 

Crump, B. C., B. J. Peterson, P. A. Raymond, R. M. W. Amon, A. Rinehart, J. W. McClelland, and R. M. Holmes. 2009. Circumpolar Synchrony in Big River Bacterioplankton. Proceedings of the National Academy of Sciences, USA 106(50): 21208–21212.

Crump, B. C., H. E. Adams, J. E. Hobbie, and G. W. Kling. 2007. Biogeography of freshwater bacterioplankton in lakes and streams of an Arctic tundra catchment. Ecology 88:1365-1378. 

Judd, K. E., B. C. Crump, and G. W. Kling. 2007. Bacterial responses in activity and community composition to photo-oxidation of dissolved organic matter from soil and surface waters.  Aquatic Sciences 69:96-107