River Organic Matter and Environmental ‘Omics
(NSF-DEB 1457794, 1457494, 1457494) 

Title: Linking microbial diversity, gene expression, and the transformation of terrestrial organic matter in major U.S. rivers
P.I.s: Byron C. Crump, Peter Raymond, Aron Stubbins, George Aiken, Brett Poulin
Postdoctoral Scientists: Jérôme Payet, Jacob Hosen, Leanne Powers
Graduate Students: Christina Codden
Undergraduate Students: Kacia Montiel, Bryna Rackerby, Abigail Stover, Kimberlee Ott, Bailey Burk, Shawn Doran, Jennifer Doran, Charles Leal, Zach Levin, Philip Meyer, Sally Albright, Ben Krieske, Marilee Hoyle
Technicians: Sara Breitmeyer, Kenna Butler, Marnie Jo Zirbel

Overview: Rivers are the principle conduits between the major global organic carbon stores on land and those in the ocean. Dissolved organic matter (DOM) is a master variable in rivers, impacting light attenuation, metal transport, and metabolism. Riverine bacteria rely on DOM for sustenance and, in using DOM, respire a fraction and alter the composition of the remaining DOM. The relationship between microbes and DOM is a crucial but poorly understood shaper of river ecosystem function. One major gap is our understanding of specific metabolic capabilities of bacteria and how they interact with organic matter quality to carry out the key ecosystem function of transforming and metabolizing riverborne DOM. Integrating new and cutting-edge tools in genetics and DOM geochemistry, this project will describe in molecular detail the ecological and genetic mechanisms by which terrestrial DOM is modified and mineralized to carbon dioxide during transport from land to sea by determining the interactions and feedbacks between microbial functional diversity, gene expression, and DOM metabolism in U.S. rivers. 

Intellectual Merit : Continental and seasonal gradients in climate influence the amount and composition of DOM, water residence time, and important micronutrients in rivers, yet we lack detailed knowledge of how variation in these attributes interacts with microbial populations and genetic pathways to determine DOM transformations and shape microbial ecology. This research will address the hypothesis that microbial genetic mechanisms in river ecosystems are closely linked to climate and landscape features that control river environmental conditions, particularly DOM quality. It argues that microbial functioning is shaped by DOM composition, climate, and river chemistry. These shaping forces alter the functional genetic capabilities required for competitive success within riverine microbial communities, and, thus, drive shifts in functional gene expression and phylogenetic composition, that, in turn, increase the efficiency of DOM metabolism and biogeochemical processes. It hypothesizes that: (1) The functional genetic composition and gene expression patterns of riverine microbial communities are correlated with the composition of riverine DOM; (2) Community gene expression patterns vary predictably in response to shifts in the available forms of DOM; and, (3) The composition of riverine bacterial communities correlates with the composition of riverine DOM over space and time, and varies with watershed-specific climatic factors. 

Hypothesis 1 will be addressed with an empirical study of microbial community gene content (metagenomics), gene expression (metatranscriptomics), and DOM diversity (FT-ICR MS) during four seasons in five rivers that encompass a broad range of DOM composition. Hypotheses 2 will be addressed with an experimental study to identify active organisms and genes expressed by freshwater microbial communities in response to DOM amendments, and to analyze in detail subsequent changes in DOM chemistry caused by microbial metabolism. Hypothesis 3 will be addressed with an empirical study of microbes, DOM, and river chemistry in 36 major U.S. rivers sampled through a collaboration with the U.S. Geological Survey. Statistical approaches being developed through the Microsoft-sponsored international working group (BioGeoChemistry Data System) will be applied to link microbial and DOM data. This research will be the first systematic study to link the molecular diversity of microbes with the molecular diversity of DOM in drainage networks at any scale. 

Broader Impacts: PIs will collaborate with the Yale Peabody Museum Evolution program for inner-city New Haven high-school students to train interns and develop an interactive museum display on NASQAN rivers and large river ecosystems for display at science museums in New Haven, CT and Portland, OR. This project will also train graduate and postdoctoral researchers at OSU, UGA and Yale, and will involve underrepresented students from Savannah St. Univ., an HBCU with strong ties to UGA. Findings will be incorporated into courses taught by the PIs. All data will be archived appropriately following metadata standards. This research will expand collaborations among the PIs, and with the USGS, the DOE Joint Genome Institute, the Max Planck Group for Marine Geochemistry, the DOM-omics working group, and the Earth Microbiome Project.

Publications

Ishikawa, N. F., Butman, D., and Raymond, P. A. 2019. Radiocarbon age of different photoreactive fractions of freshwater dissolved organic matter.Organic Geochemistry 135: 11–15.

Good, S. P., D. R. URycki, and B. C. Crump. 2018. Predicting Hydrologic Function With Aquatic Gene Fragments. Water Resour. Res. 54: 2424–2435. 

Wagner, S., J. Brandes, A. I. Goranov, T. W. Drake, R. G. M. Spencer, and A. Stubbins. 2017. Online quantification and compound-specific stable isotopic analysis of black carbon in environmental matrices via liquid chromatography-isotope ratio mass spectrometry. Limnol. Oceanogr. Methods 15: 995–1006. 

Moran, M. A., Kujawinski, E. B., Stubbins, A., Fatland, R., Aluwihare, L. I., Buchan, A., Crump, B. C., Dorrestein, P. C., Dyhrman, S. T., Hess, N. J., Howe, B., Longnecker, K., Medeiros, P. M., Niggemann, J., Obernosterer, I., Repeta, D. J., Waldbauer, J. R. 2017. Deciphering Ocean Carbon in a Changing World. Proceedings of the National Academy of Sciences, USA

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